@unpublished {1260, title = {Functional organization of the neural circuitry for male courtship behavior in Drosophila.}, year = {Submitted}, month = {08/2014}, author = {Baker, Bruce S} } @article {4931, title = {Recent progress in membrane protein structures and investigation methods.}, journal = {Current Opinion in Structural Biology}, volume = {22}, year = {In Press}, month = {2012 Aug}, pages = {467-8}, issn = {1879-033X}, doi = {10.1016/j.sbi.2012.07.002}, author = {Gonen, T and Waksman, G.} } @article {70359, title = {Adapting upright light sheet fluorescence microscopy for imaging at air-liquid interface}, journal = {bioRxiv}, year = {2026}, month = {2026 Apr 09}, abstract = {

Light sheet fluorescence microscopy (LSFM) is increasingly appreciated as the gold standard for gentle, volumetric imaging with fast acquisition speeds and/or long imaging durations. However, the often-constrained sample space of these microscopes has precluded a specific class of biological specimens from being studied with these tools: those requiring an air-liquid interface (ALI). Here, we present a device for robust imaging at ALI on an upright light sheet microscope with dipping objectives. We demonstrate the system using three relevant use-cases: ex vivo embryonic mouse salivary glands, human epidermal equivalent cultures, and in vivo adult Drosophila melanogaster brains. While the device presented is engineered for one specific light sheet microscope design, it provides a blueprint for easy adaptation to other systems. In doing so, it can potentially spur the use of LSFM for model systems that have so far been unable to take advantage of this powerful technology.

}, doi = {10.64898/2026.04.07.716945}, url = {https://www.biorxiv.org/content/early/2026/04/09/2026.04.07.716945}, author = {Hobson, Chad M. and Izumi, Kenji and Aaron, Jesse S. and Bharathan, Navaneetha Krishnan and Ceriani, M. Fernanda and Giang, William and Ispizua, Juan I. and Kowalczyk, Andrew P. and Lee, Rachel M. and Morales, E. Angelo and Puls, Owen F. and Quarles, Ellen and Rodriguez-Caron, Micaela and Stahley, Sara N. and Tassara, Francisco and Wang, Shaohe and Yao, Shunze and Tsuchiya, Takanori and Chew, Teng-Leong} } @article {70284, title = {Astrocyte-induced internal state transitions reshape brainwide sensory, integrative, and motor computations}, journal = {bioRxiv}, year = {2026}, month = {2026 Feb 05}, abstract = {

Animals rapidly adapt to changing circumstances by shifting how they perceive, integrate, and act. Such flexibility is often attributed to transitions between internal states that exert widespread influence across the brain. Yet the mechanisms that drive state transitions and how they reconfigure brainwide computation remain unclear. Larval zebrafish, when actions are rendered futile by decoupling visual flow feedback from swimming in virtual reality, enter a temporary passive, energy-preserving state. In this state, astrocyte calcium levels are elevated, and swim reinitiation requires greater accumulated visual motion. Using whole-brain, cellular-resolution activity imaging, we observed widespread circuit alterations underlying this disengaged state: neuronal visual responses weakened, visual motion integration over time became dramatically leakier, motor inhibition increased, and motor preparation slowed, together suppressing conversion of sensory evidence into action. Astrocyte calcium rose during futile swimming, tracked the emergence and resolution of these brainwide changes, and was both necessary and sufficient to drive them. Thus, astrocytes orchestrate internal states that profoundly reshape neural computations, most powerfully at intermediate integrative processing stages, to meet changing demands.

}, doi = {10.64898/2026.02.05.704034}, url = {https://www.biorxiv.org/content/early/2026/02/05/2026.02.05.704034}, author = {Lim, Jing-Xuan and Wei, Ziqiang and Narayan, Sujatha and Zhang, Yan and Hasseman, Jeremy P. and Kolb, Ilya and Zheng, Jihong and Sheikhattar, Alireza and Mi, Xuelong and Zheng, Wei and Yang, Xueying and Beriashvili, Mariam and Fleishman, Greg and Wee, Caroline L. and de Zeeuw, Chris and Yu, Guoqiang and Babadi, Behtash and Rubinov, Mikail and Looger, Loren L. and Bergles, Dwight E. and Fitzgerald, James E. and Ahrens, Misha B.} } @article {70003, title = {BPS2026 {\textendash} De novo-designed rhodamine binders for advanced fluorescence microscopy}, journal = {bioRxiv}, year = {2026}, month = {2026 Feb 19}, abstract = {

Fluorescence microscopy is a powerful tool for studying biomolecules in their native environments, offering high spatio-temporal resolution but requiring fluorescent labels. Current live-cell compatible labeling strategies repurpose natural systems, such as fluorescent proteins or proteins that bind fluorescent ligands. While advances have been made to engineer natural proteins into labels with minimal size, high brightness, as well as enhanced thermo- and photostability, these approaches often require trade-offs among desirable properties due to the inherent limitations of re-engineering natural proteins. In this work, we present rhodamine binder (Rhobin) tags{\textemdash}de novo-designed proteins that bind rhodamine-derived fluorophores. Unlike traditional approaches, Rhobin tags were developed by directly incorporating desirable features during the computational design process, which resulted in compact binders with outstanding thermostability. Their nanomolar substrate affinity, rapid labeling kinetics, and orthogonality to established labeling systems such as HaloTag and SNAP-tag facilitate versatile live and fixed-cell imaging of diverse subcellular targets in mammalian cells. Transient fluorophore binding further enables advanced imaging techniques, including live-cell super-resolution STED microscopy with reduced photobleaching and single-molecule localization microscopy in live and fixed cells. To the stability of Rhobin tags under extreme environmental conditions, we demonstrate showcase protein tagging and timelapse imaging in the extremophile\ Sulfolobus acidocaldarius\ living at 75{\textdegree}C, an application previously inaccessible with existing tags. We anticipate that Rhobin tags will become a central component in the toolbox of fluorescent labels and will pave the way for a new generation of modular protein tags and biosensors with tailor-made properties.

}, doi = {10.1016/j.bpj.2025.11.2270}, url = {https://doi.org/10.1016/j.bpj.2025.11.2270}, author = {Yserentant, Klaus and Chen, Yuda and Hong, Kibeom and Kuang, Yiming and Bhowmick, Arghya and Charles-Orszag, Arthur and Lord, Samuel J. and Lu, Lei and Hou, Kaipeng and Mann, Samuel I and Grimm, Jonathan B and Lavis, Luke D and Mullins, R. Dyche and DeGrado, William F and Huang, Bo} } @article {70312, title = {BPS2026 {\textendash} Molecular architecture of the fungal-specific potassium channel TOK1}, journal = {Biophysical Journal}, volume = {125}, year = {2026}, month = {2026 Feb 19}, pages = {20a}, abstract = {

Potassium (K+) channels play a vital role in helping fungal pathogens like\ Candida albicans\ adapt to hostile environments within the human body, including during infection. Among these, two-pore domain, outwardly rectifying K+\ (TOK) channels, unique to fungi, have remained insufficiently characterized, despite evidence that they support processes in fungi, such as ion homeostasis, growth, and virulence, highlighting their potential as antifungal targets. Here, we present the cryo-EM structure of\ C. albicans\ TOK1 (CaTOK), the first resolved structure of a TOK channel and of any fungal K+\ channel. CaTOK reveals an eight-transmembrane helical fold unlike any other K+\ channel structure determined to date, including a domain formed by helices S1-S4 with unexpected structural homology to channel auxiliary subunits critical for human neuronal signaling. Additionally, a unique cytosolic C-terminal domain interfaces with pore-lining helices, suggesting a role in channel regulation. These findings uncover previously unrecognized structural elements that broaden our understanding of K+channel diversity and regulation and provide initial clues into the structural basis for the unique functional attributes of the TOK family.

}, issn = {00063495}, doi = {10.1016/j.bpj.2025.11.316}, url = {https://doi.org/10.1016/j.bpj.2025.11.316}, author = {Durocher, Brice and Manville, R{\'\i}an W. and Yan, Rui and Yu, Zhiheng and Abbott, Geoffrey W. and Miller, Alexandria N.} } @article {70313, title = {BPS2026 {\textendash} Real-time visualization and analysis of fibrin polymerization}, journal = {Biophysical Journal}, volume = {125}, year = {2026}, month = {Jan-02-2026}, pages = {227a - 228a}, abstract = {

To form a blood clot, fibrinogen is converted into fibrin through the action of the enzyme thrombin. Fibrin then polymerizes longitudinally and laterally as it matures into a fiber. Polymerization results in a dense, 3-dimensional branched network. Previous research has shown the relevance of these fibrin gel structures in hemostatic conditions; however, the mechanism by which they form has not been fully resolved. Using light sheet microscopy, 3-dimensional volumes of the fibrin polymerization process were captured. Manual annotation of these microscopy videos revealed that fiber branch points occur through the collision and the binding of diffusing fibers rather than through the splitting of growing fiber termini. However, the density of fibers and amount of data greatly slows manual annotation-based analysis and limits the ability to capture important data, such as growth rates and fiber stiffness. To more quickly process these data, a computational approach was utilized. A custom tracking pipeline, suited to the networks formed by cylindrical fibrin fibers, was developed, beginning with an AI-based classifier. This custom pipeline allowed for the tracking of uniquely labeled fibers over time. Automated merge detection between linking phases further improved accuracy. Additionally, network formation was analyzed through skeletonization techniques to measure the number of branches per junction over time. Combining the skeletonization and tracking methods, single fibers were identified by their lack of branch points and tracked. The addition of branch points to previously tracked objects served as a signal for merge detection. This approach yielded measurements of single fibrin fiber diffusion rates, as well as the first volumetric and length growth rates of fibers throughout polymerization. In addition, the gel point was quantified by analyzing the span of connected objects to characterize the network consolidation over time at the level of single fibers.

}, issn = {00063495}, doi = {10.1016/j.bpj.2025.11.1510}, url = {https://doi.org/10.1016/j.bpj.2025.11.1510}, author = {Miller, Dylan M. and Elangovan, Aravind and Belcher, Heather A. and Lee, Rachel M. and Hobson, Chad M. and Crosley, Key and Hart, David M. and Laverty, Brittany Bannish E. and Guthold, Martin and Hudson, Nathan E.} } @article {70300, title = {BPS2026 - Structural basis of the TOK1 potassium channel from Candida albicans}, journal = {Biophysical Journal}, volume = {125}, year = {2026}, month = {2026 Feb 19}, pages = {194a}, abstract = {

Many fungi utilize high turgor pressure for morphogenesis, requiring tight regulation of ionic gradients. Ion regulation is important for pathogenesis, reproduction, and general homeostasis across the fungal kingdom. In the major human fungal pathogen\ Candida albicans, potassium (K+) channels fine-tune ionic balance under stressful environmental conditions, contributing to colonization of the human host. Two-pore domain, outwardly rectifying potassium (TOK) channels, uniquely found in fungi, remain insufficiently characterized despite early evidence implicating them in diverse intracellular processes essential for cellular growth and viability, and their potential as antifungal targets. Here, we describe the first atomic resolution structure of a fungal potassium channel{\textemdash}TOK1 from\ C. albicans\ (CaTOK){\textemdash}revealing a membrane topology distinct from all other known K+\ channel classes. We propose that CaTOK1 utilizes two unique regions{\textemdash}TOK auxiliary subunit-like channel (TALC) domain and a structured c-terminal bundle{\textemdash}to regulate TOK1 gating. Conformational analysis of TOK1 pore features an inner helical gating mechanism with {\textquotedblleft}up{\textquotedblright} and {\textquotedblleft}down{\textquotedblright} conformations similar to mammalian dimeric K+\ channels. These findings provide a structural framework for understanding TOK channel activity and lay the groundwork for future studies on fungal ion homeostasis, pathogenicity, and therapeutic development.

}, issn = {0006-3495}, doi = {https://doi.org/10.1016/j.bpj.2025.11.1313}, url = {https://www.sciencedirect.com/science/article/pii/S0006349525020636}, author = {Durocher, Brice and Manville, R{\'\i}an and Yan, Rui and Yu, Zhiheng and Abbott, Geoffrey and Miller. Alexandria N.} } @article {70309, title = {Brain-wide hierarchical and sexually dimorphic tuning for social vocalizations}, journal = {bioRxiv}, year = {2026}, month = {2026 Mar 04}, abstract = {

Acoustic communication is widespread among vertebrates and central to social behavior. Yet how brain-wide circuits identify conspecific signals and distinguish acoustic elements with different, often sex-specific social valence remains poorly understood. Here we present the first whole-brain analysis of neuronal responses to conspecific vocalisations in vertebrates, using the transparent fish Danionella cerebrum. Combining volumetric calcium imaging with playbacks probing the stimulus space of the natural sound repertoire, we uncover an unexpectedly early and specialized processing hierarchy: hindbrain nuclei already segregate vocalization-like pulse trains from tones, midbrain regions sharpen these representations and extract temporal features that define vocalization type, and the central posterior thalamic nucleus responds selectively to conspecific vocalization rates and thus acts as a gate for social sounds. Male and female brains share this early feature code but diverge in diencephalic and telencephalic regions, where identical acoustic features evoke sex-specific population activity patterns that parallel dimorphic behavior. Together, our results provide the first cellular-resolution, brain-wide account of social sound processing in a vertebrate, from early categorical segregation to thalamic gating and sex-specific population responses in social circuits.

}, doi = {10.64898/2026.03.04.709502}, url = {https://www.biorxiv.org/content/early/2026/03/04/2026.03.04.709502}, author = {Henninger, Jorg and Hoffmann, Maximilian and Kadobianskyi, Mykola and Veith, Johannes and Berlage, Caroline and Groneberg, Antonia and Markov, Daniil and Schulze, Lisanne and Svanidze, Ana and Maler, Leonard and Judkewitz, Benjamin} } @article {70335, title = {Compartmentalized cytoplasmic tradewinds direct soluble proteins.}, journal = {Nat Commun}, volume = {17}, year = {2026}, month = {2026 Mar 30}, abstract = {

Proteins essential for signaling, morphogenesis, and migration traverse the complex intracellular landscape via vesicular trafficking, microtubule-based transport, and diffusion. However, the precise mechanisms guiding soluble proteins toward their functional destinations have remained elusive. Here, we demonstrate that soluble proteins are directed toward the cell{\textquoteright}s advancing edge through advection-diffusion enhanced by intracellular fluid flow. We reveal that advective transport occurs within a specialized compartment at the cell{\textquoteright}s leading edge, separated from the rest of the cytoplasm by an actin-myosin condensate barrier. The barrier limits protein mixing between the compartment and the rest of the cytoplasm, maintaining localized protein concentrations. Contraction at the barrier generates a molecularly non-specific fluid flow that drives the forward movement of treadmilling actin monomers, actin-binding proteins, adhesion molecules, and even inert proteins. Dynamic changes in the local curvature of the barrier steer the fluid flow to direct proteins toward protrusive regions of the leading edge. This advective mechanism synchronizes protein distribution with local changes in cell morphology. Outside this compartment, diffusion dominates as the principal mode of soluble protein transport. Our findings uncover previously unrecognized compartmentalization strategies that regulate soluble protein concentrations and coordinate their efficient distribution for homeostasis, protrusion, and adhesion.

}, keywords = {Actins, Animals, Cell Compartmentation, Cytoplasm, Diffusion, Humans, Myosins, Protein Transport, Solubility}, issn = {2041-1723}, doi = {10.1038/s41467-026-70688-6}, url = {https://doi.org/10.1038/s41467-026-70688-6}, author = {Galbraith, Catherine G and English, Brian P and Boehm, Ulrike and Galbraith, James A} } @article {70248, title = {Connectivity underlying motor cortex activity during goal-directed behaviour.}, journal = {Nature}, volume = {649}, year = {2026}, month = {2026 Jan 01}, pages = {416-422}, abstract = {

Neural representations of information are shaped by long-range input and local network interactions. Previous studies linking neural coding and cortical connectivity have focused on input-driven activity in the sensory cortex. Here we studied neural activity in the motor cortex while mice gathered rewards with multidirectional tongue reaching. This behaviour does not require training, allowing us to probe neural coding and connectivity before activity is shaped by extended learning. Motor cortex neurons were tuned to target location and reward outcome, and typically responded during and after movements. We studied the underlying network interactions in vivo by estimating causal neural connections using an all-optical method. Mapping connectivity between more than 20,000,000 excitatory neuron pairs showed a multi-scale columnar architecture in layer 2/3 of the motor cortex. Neurons displayed local (less than 100 {\textmu}m) like-to-like excitatory connectivity according to target-location tuning, and inhibition over longer spatial scales. Connectivity patterns comprised a continuum, with abundant sparsely connected neurons and rare densely connected neurons that function as network hubs. Hub neurons were weakly tuned to target location and reward outcome but influenced more neighbouring neurons. This network of neurons, encoding location and outcome of movements to different motor goals, may be a general substrate for rapid learning of complex, goal-directed behaviours.

}, keywords = {Animals, Female, Goals, Learning, Male, Mice, Mice, Inbred C57BL, Motor Cortex, Movement, Neural Pathways, Neurons, Reward, Tongue}, issn = {1476-4687}, doi = {10.1038/s41586-025-09758-6}, url = {https://doi.org/10.1038/s41586-025-09758-6}, author = {Finkelstein, Arseny and Daie, Kayvon and Rozsa, Marton and Darshan, Ran and Svoboda, Karel} } @article {70292, title = {Correlates of head-fixed directional forelimb movements in mouse superior colliculus and substantia nigra pars reticulata.}, journal = {Neuroscience}, year = {2026}, month = {2026 Feb 12}, abstract = {

Coordinated lateralized movements are critical for natural orienting behaviors, but their neural bases remain poorly understood. The deep superior colliculus (dSC) integrates a wide range of inputs to select targets for orienting movements and coordinates downstream activity to initiate and execute movement. The substantia nigra pars reticulata (SNr) is thought to disinhibit dSC to facilitate movement, but much remains unknown about the relationship between SNr activity, dSC activity, and movement. We recorded from both regions using high-density probes in head-fixed mice performing directional orienting tasks. We found that dSC and SNr activity reflected task variables preceding and throughout movement. However, the direction-dependence of dSC activity was weaker than in other orienting behaviors, and the relationship between movement-related dSC and SNr activity was inconsistent with disinhibition of dSC determining the initiation or direction of movement. Analyses of similar data curated by the International Brain Laboratory yielded consistent results. These findings suggest diverse roles for modulatory input from SNr to dSC in shaping motor behavior.

}, issn = {1873-7544}, doi = {10.1016/j.neuroscience.2026.02.010}, url = {https://doi.org/10.1016/j.neuroscience.2026.02.010}, author = {Doykos, Ted K and Yamauchi, Taylor and Buteau, Anna and Hanson, Spencer and Dudman, Joshua T and Felsen, Gidon and Stubblefield, Elizabeth A} } @article {70298, title = {Deciphering hippocampal place codes in weak theta rhythms.}, journal = {Nat Commun}, year = {2026}, month = {2026 Feb 13}, abstract = {

Local field potentials (LFPs) reflect coordination among neural populations, yet their exact relationship to neural computation remains unknown. One exception is the theta rhythm of the rodent hippocampus, which organizes sequential firing among place cells, enabling spike timing to track the animal{\textquoteright}s path through its environment. But when the animal stops, the theta rhythm becomes irregular, which is assumed to disrupt its ability to carry spatial information. Here we challenge this assumption by developing an artificial neural network that discovers position-tuned theta rhythms (pThetas) from LFPs even in the absence of strong theta oscillations. Using recordings from male rats, we provide evidence that pTheta is distinct from the dominant theta rhythm, while reflecting rhythmic coordination among place cell populations. Our work suggests that weak and intermittent oscillations, as seen in many brain regions and species, can convey information commensurate with population spike codes when decoded using information-based rather than variance-based principles.

}, issn = {2041-1723}, doi = {10.1038/s41467-026-69438-5}, url = {10.1038/s41467-026-69438-5}, author = {Agarwal, Gautam and Akera, Seiji and Lustig, Brian and Pastalkova, Eva and Lee, Albert K and Sommer, Friedrich T} } @article {70268, title = {A dendrite-resolved, in vivo transfer function from spike patterns to dendritic Ca2+}, journal = {bioRxiv}, year = {2026}, month = {2026 Jan 21}, abstract = {

Dendrites transform local electrical activity into intracellular Ca2+ signals that drive plasticity1,2, yet the voltage{\textrightarrow}Ca2+ mapping during natural behavior remains poorly defined. Here, we measure this transfer function via simultaneous voltage and Ca2+ imaging throughout the dendritic arbors of hippocampal CA2 pyramidal neurons in behaving mice. Dendritic Ca2+ exhibited a hierarchical activation pattern dominated by back-propagating action potentials: simple spikes primarily drove somatic and proximal Ca2+, whereas complex spikes produced larger somatic Ca2+ signals and propagated farther into distal dendrites, sometimes in a branch-selective manner. Dendrite-restricted co-activation of voltage and Ca2+ without concurrent somatic events was rare. A biophysics-inspired model accurately predicted local Ca2+ transients from local voltage waveforms. Our data and model provide a quantitative understanding of when {\textendash} and why {\textendash} dendritic Ca2+ signals in CA2 pyramidal cells arise during behavior.

}, doi = {10.64898/2026.01.18.700189}, url = {https://www.biorxiv.org/content/early/2026/01/21/2026.01.18.700189}, author = {Wu, Xiang and Lee, Byung Hun and Park, Pojeong and Wong-Campos, J. David and Xu, Junjie and Plutkis, Sarah E. and Lavis, Luke D. and Cohen, Adam E.} } @article {70303, title = {A dual-color miniature endoscope for calcium imaging in behaving mice}, journal = {iScience}, year = {2026}, month = {2026 Mar 28}, abstract = {

Calcium imaging with miniature endoscopes has become an essential tool in neuroscience, but conventional miniscopes typically record signals from only a single calcium indicator. Here, we present a dual-color miniature endoscope (miniscope) that enables simultaneous calcium imaging from two neuronal populations using spectrally distinct genetically encoded indicators. In freely moving mice, we used this system to record activity from striatal neurons of the direct (dSPN) and indirect (iSPN) pathways. We showed that dSPNs were activated earlier than iSPNs during contraversive movements, with dSPNs preferentially active during acceleration and iSPNs during deceleration. During ipsiversive turns, however, this temporal relationship was reversed. These findings indicate that dSPNs and iSPNs are not concurrently active, but instead exhibit complementary, direction-dependent dynamics that govern movement velocity. Our dual-color miniscope provides a compact, cost-effective platform for simultaneous two-population imaging, offering new opportunities to dissect coordinated activity across neural circuits in freely behaving animals.

}, doi = {10.1016/j.isci.2026.115514}, url = {https://doi.org/10.1016/j.isci.2026.115514}, author = {Zhang, Jinyong and Hong, Feiyang and Kim, Jiwon and Bakhurin, Konstantin and Kim, Namsoo and Yin, Henry H.} } @article {70323, title = {Endocytome profiling uncovers cell-surface protein dynamics underlying neuronal connectivity.}, journal = {Neuron}, year = {2026}, month = {2026 Mar 12}, abstract = {

Endocytosis actively remodels the neuronal surface proteome to drive diverse cellular processes, yet its global extent and effects on neural circuit development have defied comprehensive interrogation. Here, we introduce endocytome profiling: a systematic, cell-type-specific approach for mapping cell-surface protein (CSP) dynamics in situ. Quantitative proteomic analysis of developing Drosophila olfactory receptor neuron (ORN) axons generated an endocytic atlas comprising over 1,000 proteins and revealed the extent to which the cell-surface proteome is remodeled to meet developmental demands. Targeted interrogation of a junctional CSP showed that its endosome-to-surface ratio is precisely balanced to enable developmental axon pruning while preserving mature axon integrity. Multi-omic integration uncovered widespread transcellular signaling and identified a growth factor secreted by neighboring neurons to direct ORN axon targeting via endocytic regulation of its receptor. Endocytome profiling provides unprecedented access to cell-surface proteome dynamics and offers a platform to dissect proteome-scale remodeling across diverse cell types and contexts.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2026.01.027}, url = {https://doi.org/10.1016/j.neuron.2026.01.027}, author = {McLaughlin, Colleen N and Ji, Hui and Dong, Katherine X and Xu, Chuanyun and Wong, Kenneth Kin Lam and Li, Zhuoran and Luginbuhl, David J and Xu, Charles and Lyu, Cheng and Qin, Wei and Li, Jiefu and Udeshi, Namrata D and Carr, Steven A and Ting, Alice Y and Luo, Liqun} } @article {70315, title = {Evolutionarily conserved neural dynamics across mice, monkeys, and humans}, journal = {bioRxiv}, year = {2026}, month = {2026 Mar 07}, abstract = {

On evolutionary timescales, brain circuits adapt to support survival in each species{\textquoteright} ecological niche. While some anatomical aspects of neural circuitry are conserved across species with distant evolutionary origins, each species also exhibits specific circuit adaptations that enable its behavioral repertoire. It remains unclear whether homologous brain regions leverage analogous neural computations as different species perform common behaviors such as reaching and manipulating objects. Here, we directly assessed conservation of neural computations using intracortical recordings from mouse, monkey, and human motor cortex{\textemdash}a homologous region across many mammals{\textemdash}during motor behaviors crucial for survival. We hypothesized that, despite their phylogenetic distance, rodents and primates produce movements through conserved neural computations implemented by motor cortical population dynamics. Remarkably, we found that movement-related neural dynamics were highly conserved across species, while variations in behavioral output were uniquely captured in neural trajectory geometries. Strikingly, neural dynamics during movement across species were more conserved than those across brain regions in the same human and between motor preparation and execution in the same monkeys. Lastly, through manipulation of neural network models trained to perform reaching movements, we reinforce that conservation of neural dynamics across species likely stems from shared circuit constraints. We thus assert that evolution maintains neural computations across phylogeny even as behavioral repertoires expand.

}, doi = {10.64898/2026.03.06.709637}, url = {https://www.biorxiv.org/content/early/2026/03/07/2026.03.06.709637}, author = {Codol, Olivier and Asclipe, Margaux and Sobinov, Anton R. and Chen, Zihao and Park, Junchol and Hatsopoulos, Nicholas G. and Dudman, Joshua T. and Gallego, Juan A. and Lajoie, Guillaume and Perich, Matthew G.} } @article {70330, title = {Evolutionary basis of male same-sex sexual behavior by multiple pheromone switches in Drosophila.}, journal = {Curr Biol}, year = {2026}, month = {2026 Mar 20}, abstract = {

Male same-sex sexual behavior (SSB) is widespread among animal species, but its proximate (mechanistic) and ultimate (evolutionary) explanations remain unclear. A prevailing view is that SSB reflects impaired sex recognition, especially in insects. By unbiased behavioral screening, we identified a Drosophila species, D. santomea, in which males seldom attack and spontaneously court males vigorously, in addition to females. Behavioral, chemical, and optogenetic neuronal manipulations indicate that D. santomea males can distinguish conspecific sex and retain functional aggression circuitry. Instead, male SSB reflects three evolved pheromonal changes affecting two separate signaling systems, resulting in both reduced pheromone production and behavioral valence reversal. One of these occurs unexpectedly in females and may have evolved to prevent hybridization with an interfertile, geographically overlapping sibling species. Remarkably, male SSB and similar pheromonal changes also selectively co-occur in D. persimilis, a geographically and phylogenetically distant species and member of another sympatric sibling pair, implying evolutionary convergence in the two young taxa. The results identify a pheromonal mechanism for rapid social evolution in Drosophila and suggest a plausible evolutionary origin for male SSB as arising in concert with female adaptations that ensure reproductive isolation during speciation.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2026.02.046}, url = {https://doi.org/10.1016/j.cub.2026.02.046}, author = {Ouadah, Youcef and Naragon, Thomas H and Smihula, Hayley and Behrman, Emily L and Khallaf, Mohammed A and Ding, Yun and Stern, David L and Parker, Joseph and Anderson, David J} } @article {70286, title = {Extracting large-scale neural activity with Suite2p}, journal = {bioRxiv}, year = {2026}, month = {2026 Feb 06}, abstract = {

Neural recordings using optical methods have improved dramatically. For example, we demonstrate here recordings of over 100,000 neurons from the mouse cortex obtained with a standard commercial microscope. To process such large datasets, we developed Suite2p, a collection of efficient algorithms for motion correction, cell detection, activity extraction and quality control. We also developed new approaches to benchmark performance on these tasks. Our GPU-accelerated non-rigid motion correction substantially outperforms alternative methods, while running over five times faster. For cell detection, Suite2p outperforms the CNMF algorithm in Caiman and Fiola, finding more cells and producing fewer false positives, while running in a fraction of the time. We also introduce quality control steps for users to evaluate performance on their own data, while offering alternative algorithms for specialized types of recordings such as those from one-photon and voltage imaging.

}, doi = {10.64898/2026.02.04.703741}, url = {https://www.biorxiv.org/content/early/2026/02/06/2026.02.04.703741}, author = {Stringer, Carsen and Ki, Chris and DelGrosso, Nicholas and LaFosse, Paul and Zhang, Qingqing and Pachitariu, Marius} } @article {70244, title = {Fast dendritic excitations primarily mediate back-propagation in CA1 pyramidal neurons during behavior}, journal = {bioRxiv}, year = {2026}, month = {2026 Jan 03}, abstract = {

Dendrites integrate synaptic inputs to trigger action potentials, and dendrites carry back-propagating action potentials (bAPs) to synapses where these signals contribute to plasticity. Despite strong evidence for a rich repertoire of nonlinear dendritic excitations, the in vivo roles of these excitations in dendritic integration and back-propagation remain uncertain. Here, we used high-speed voltage imaging through a chronically implanted microprism to map membrane potential dynamics from basal to apical dendrites of CA1 neurons in mice navigating in a virtual reality environment. Despite complex dendritic branch morphology, the dynamics were largely captured by 2 or 3 electrical compartments: basal, soma, and apical. Fast dendritic spikes almost always started from bAPs, indicating that dendritic spikes are primarily a consequence rather than a cause of somatic spiking. These fast spikes sometimes triggered slower apical dendritic plateau depolarizations, which drove complex spikes at the soma. We found that the biophysics of dendritic excitability determined the distribution of simple and complex spikes across a place field. Our results show how CA1 pyramidal neurons convert synaptic inputs to spiking outputs and suggest a primary role of dendritic nonlinearities in mediating activity-dependent plasticity.

}, doi = {10.64898/2026.01.03.696606}, url = {https://www.biorxiv.org/content/early/2026/01/03/2026.01.03.696606}, author = {Lee, Byung Hun and Park, Pojeong and Wu, Xiang and Wong-Campos, J. David and Xu, Junjie and Xiong, Marley and Qi, Yitong and Huang, Yi-Chieh and Itkis, Daniel G. and Plutkis, Sarah E. and Lavis, Luke D. and Cohen, Adam E.} } @article {70337, title = {Fatty acid regulation of feeding in Caenorhabditis elegans reveals the potential ancestral origin of a GLP-1-like multiagonist signaling system.}, journal = {Proc Natl Acad Sci U S A}, volume = {123}, year = {2026}, month = {2026 Apr 07}, pages = {e2530979123}, abstract = {

Regulation of food intake in mammals is complex and controlled by an interplay between hedonic and homeostatic signals, including hormones like leptin, which senses fat storage and suppresses food intake. lack leptin and leptin receptors but still exhibit controlled eating. Here, we show that in eating can be regulated by a balance between saturated and monounsaturated fatty acids interacting with transcriptional pathways regulating lipid synthesis, c-AMP response element binding protein and AMP kinase. This effect is mediated at the endoplasmic reticulum through formation of phospholipids and activation of the IRE-1 sensor in the nervous system, which controls behavior through neuronal serotonin and the G-protein-coupled ligand/receptor pair PDF-1/PDFR-1. We show that this peptide/receptor pair may be an ancestral precursor of the whole family of GLP-1/GIP-related peptides and their receptors. Indeed, administration of a 37 amino acid peptide derived from PDF-1 resulted in a reduction in body weight and improved insulin sensitivity in mice. In worms, signaling through this pathway induced food-leaving behavior on concentrated food and roaming behavior on dispersed food, a state we have termed "food-apathy," paralleling pharmacologic effects of GLP-1/GIP-related peptides in humans. These findings highlight the potential evolutionary origin of this family of hormones and their receptors, and its link to metabolic and neuronal responses in control of feeding behavior.

}, keywords = {Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Eating, Fatty Acids, Feeding Behavior, Glucagon-Like Peptide 1, Mice, Signal Transduction}, issn = {1091-6490}, doi = {10.1073/pnas.2530979123}, url = {https://doi.org/10.1073/pnas.2530979123}, author = {Zhu, Feimei and Castillo-Quan, Jorge Iv{\'a}n and Ogawa, Takafumi and Wu, Ziyun and Ding, Lang and Sura, Mansi and Watanabe, Yoshiyuki and Lentschat, Hannah and Fern{\'a}ndez-C{\'a}rdenas, L Paulette and Dag, Ugur and Beck-Sickinger, Annette and Wang, Meng C and Kahn, C Ronald and Blackwell, T Keith} } @article {70246, title = {High performance sorting of motor unit action potentials with EMUsort}, journal = {bioRxiv}, year = {2026}, month = {2026 Jan 07}, abstract = {

Understanding how neural signals control muscle activity during behavior is a key challenge in motor neuroscience. To this end, recent advances in intramuscular multielectrode arrays have enabled high-quality multichannel recordings of many motor unit action potentials (MUAPs) in freely moving subjects. However, identifying individual MUAP events within multichannel recordings is a significant challenge for existing spike sorting methods, which are typically optimized for identifying action potentials from neurons in the brain. To overcome this challenge, we developed the Enhanced Motor Unit sorter (EMUsort), an extension of Kilosort4 (KS4) that achieves high-performance MUAP spike sorting. We applied EMUsort to high-resolution intramuscular recordings from rat forelimb during locomotion and monkey forelimb during a reaching task. EMUsort improves upon prior methods by addressing key challenges encountered with MUAP datasets, including: 1) long time delays across electrodes due to propagation along muscle fibers, 2) more complex waveform shapes compared to neuronal action potentials, and 3) a high degree of MUAP overlap due to cumulative motor unit recruitment. We compared EMUsort to existing spike sorting methods quantitatively using simulated datasets that closely emulated the rat and monkey datasets we recorded. EMUsort provided median error rate reductions of 67.5\% and 49.9\% during periods of high motor unit activation for the rat and monkey datasets, respectively. In sum, EMUsort provides a substantial improvement to MUAP spike sorter accuracy, especially during regions of high MUAP overlap, in an easy-to-use software package.

}, doi = {10.64898/2026.01.06.697952}, url = {https://www.biorxiv.org/content/early/2026/01/07/2026.01.06.697952}, author = {O{\textquoteright}Connell, Sean and Michaels, Jonathan A. and Wang, Runming and Mamidipaka, Sahit and Venkatesh, Manikandan and Aresh, Nevin and Pachitariu, Marius and Pruszynski, J. Andrew and Sober, Samuel J. and Pandarinath, Chethan} } @article {70321, title = {High performance sorting of motor unit action potentials with EMUsort}, journal = {eLife}, year = {2026}, month = {2026 Mar 16}, abstract = {

Understanding how neural signals control muscle activity during behavior is a key challenge in motor neuroscience. To this end, recent advances in intramuscular multielectrode arrays have enabled high-quality multichannel recordings of many motor unit action potentials (MUAPs) in freely moving subjects. However, identifying individual MUAP events within multichannel recordings is a significant challenge for existing spike sorting methods, which are typically optimized for identifying action potentials from neurons in the brain. To overcome this challenge, we developed the Enhanced Motor Unit sorter (EMUsort), an extension of Kilosort4 (KS4) that achieves high-performance MUAP spike sorting. We applied EMUsort to high-resolution intramuscular recordings from rat forelimb during locomotion and monkey forelimb during a reaching task. EMUsort improves upon prior methods by addressing key challenges encountered with MUAP datasets, including: 1) long time delays across electrodes due to propagation along muscle fibers, 2) more complex waveform shapes compared to neuronal action potentials, and 3) a high degree of MUAP overlap due to cumulative motor unit recruitment. We compared EMUsort to existing spike sorting methods quantitatively using simulated datasets that closely emulated the rat and monkey datasets we recorded. EMUsort provided median error rate reductions of 67.5\% and 49.9\% during periods of high motor unit activation for the rat and monkey datasets, respectively. In sum, EMUsort provides a substantial improvement to MUAP spike sorter accuracy, especially during regions of high MUAP overlap, in an easy-to-use software package.

}, doi = {10.7554/elife.110417.1}, url = {http://dx.doi.org/10.7554/eLife.110417.1}, author = {O{\textquoteright}Connell, Sean and Michaels, Jonathan A and Wang, Runming and Mamidipaka, Sahit and Venkatesh, Manikandan and Aresh, Nevin and Pachitariu, Marius and Pruszynski, J Andrew and Sober, Samuel J and Pandarinath, Chethan} } @article {70093, title = {iGABASnFR2 is an improved genetically encoded protein sensor of GABA}, journal = {eLife}, year = {2026}, month = {2026 Mar 18}, abstract = {

Monitoring GABAergic inhibition in the nervous system has been enabled by development of an intensiometric molecular sensor that directly detects GABA. However, the first generation iGABASnFR exhibits low signal-to-noise and suboptimal kinetics, making in vivo experiments challenging. To improve sensor performance, we targeted several sites in the protein for near-saturation mutagenesis and evaluated the resulting sensor variants in a high throughput screening system using evoked synaptic release in primary cultured neurons. This identified a sensor variant, iGABASnFR2, with 4.2-fold improved sensitivity and 20\% faster kinetics, and binding affinity that remained in a range sensitive to changes in GABA concentration at synapses. We also identified sensors with an inverted response, decreasing fluorescence intensity upon GABA binding. We termed the best such negative-going sensor iGABASnFR2n, which can be used to corroborate observations with the positive-going sensor. These improvements yielded a qualitative enhancement of in vivo performance when compared directly to the original sensor. iGABASnFR2 enabled the first measurements of direction-selective GABA release in the retina. In vivo imaging in somatosensory cortex revealed that iGABASnFR2 can report volume-transmitted GABA release following whisker stimulation. Overall, the improved sensitivity and kinetics of iGABASnFR2 make it a more effective tool for imaging GABAergic transmission in intact neural circuits.

}, doi = {10.7554/eLife.108319.3}, url = {https://doi.org/10.7554/eLife.108319.3}, author = {Kolb, Ilya and Hasseman, Jeremy P and Matsumoto, Akihiro and Jensen, Thomas P and Kopach, Olga and Arthur, Benjamin J and Zhang, Yan and Tsang, Arthur and Reep, Daniel and Tsegaye, Getahun and Zheng, Jihong and Patel, Ronak H and Looger, Loren L and Marvin, Jonathan S and Korff, Wyatt L and Rusakov, Dmitri A and Yonehara, Keisuke and Turner, Glenn C} } @article {70322, title = {Image analysis tools for Electron Microscopy}, journal = {bioRxiv}, year = {2026}, month = {2026-03-14}, abstract = {

Electron Microscopy (EM) is widely used in many scientific fields, particularly in life sciences, offering high-resolution information on the ultrastructure of biological organisms. Accurate characterization of EM image quality is important for assessing the EM tool performance, in addition to sample preparation protocol, imaging conditions, etc.This paper provides an overview of tools we developed as plugins for the popular image processing package Fiji (ImageJ) (1). These tools include signal-to-noise ratio analysis, contrast evaluation, and resolution analysis, as well as the capability to import images acquired on custom FIB-SEM instruments (2). We have also made these tools available in Python, with both versions available on GitHub.

}, doi = {10.64898/2026.03.11.711125}, url = {https://www.biorxiv.org/content/early/2026/03/14/2026.03.11.711125}, author = {Shtengel, David H. and Shtengel, Gleb and Xu, C. Shan and Hess, Harald F.} } @article {70355, title = {Imaging around the globe: Tailoring microscopy outreach to local research demands.}, journal = {J Microsc}, year = {2026}, month = {2026 Apr 10}, abstract = {

The global microscopy community has made wide efforts in imaging technology dissemination, especially to lower- and middle-income countries. Yet, many efforts have not fully realised their aim of increased, sustained microscopy utilisation. To guide future outreach initiatives towards more positive results, we analysed over 2300 unique applications across seven recent international microscopy workshops. We found significant differences in research priorities, as well as in microscopy experience and applications between lower- and higher-income regions. We discuss the importance of tailoring technology dissemination, training curricula, and capacity-building to these regional variations.

}, issn = {1365-2818}, doi = {10.1111/jmi.70087}, url = {https://doi.org/10.1111/jmi.70087}, author = {Schmidt, Anja and Balasubramanian, Harikrushnan and Komoto, Shinya and Malacrida, Leonel and Prats, Clara and Reiche, Michael and Aaron, Jesse and Chew, Teng-Leong} } @article {70283, title = {Imp1 acts as a dosage- and stage-dependent temporal rheostat orchestrating radial glial fate transitions and cortical morphogenesis}, journal = {eLife}, year = {2026}, month = {2026 Feb 06}, abstract = {

Cortical neurogenesis proceeds through a precise temporal program in which radial glia sequentially generate distinct neuronal subtypes and later glia, yet how post-transcriptional regulators coordinate these transitions remain poorly understood. We previously identified that a decreasing temporal gradient of the RNA-binding protein Imp encodes neural stem cell age in\ Drosophila. In this work, we extend our investigation to Imp1, a mammalian homologue of Imp, and its role in murine neocortical development. Using TEMPO to track birth-order dynamics, we demonstrate that sustained Imp1 overexpression during early neurogenesis arrests temporal fate progression, shifting neuronal populations toward deeper cortical layers V-VI. Immunostaining with layer-specific transcription factors Cux1 and Ctip2 confirmed that laminar repositioning results from genuine changes in neuronal identity rather than migratory defects, with neurons adopting molecular identities matching their final positions. Temporal window-specific manipulations reveal distinct stage-specific effects where early-stage Imp1 induction produces cascading effects on fate specification and moderately delays the neuronal-to-gliogenic transition, while mid-stage induction induces neuronal accumulation in the subplate region. Live imaging of organotypic cultures reveals continuous neuronal recruitment within intermediate and ventricular zones, with mid-stage-born neurons accumulating at significantly faster rates than earlier cohorts. Strikingly, mid-stage Imp1 overexpression also induces ectopic glial-like foci distributed throughout the cortical plate, featuring dramatic cellular expansion and morphological heterogeneity. These findings establish Imp1 as a dosage- and stage-dependent temporal rheostat orchestrating developmental transitions in radial glial progenitors, controlling neuronal fate decisions and spatial organization. This work advances our understanding of molecular timing mechanisms governing neuronal diversity in the mammalian cortex.

}, doi = {10.7554/elife.109847.1}, url = {http://dx.doi.org/10.7554/eLife.109847.1}, author = {Azur, Romie Angelo G and Feliciano, Daniel and Espinosa-Medina, Isabel and Adhikari, Raghabendra and Lilao-Garz{\'o}n, Joaquin and Jansen, Ella and Yang, Ching-Po and Lee, Tzumin} } @conference {70247, title = {LDDMEm: Large Deformation Diffeomorphic Metric Embedding}, booktitle = {Medical Image Computing and Computer Assisted Intervention {\textendash} MICCAI 2025}, year = {2026}, month = {2026 JAN 01}, abstract = {

We present a method, open-source software, and experiments which embed arbitrary deformation vector fields produced by any method (e.g., ANTs or VoxelMorph) in the Large Deformation Diffeomorphic Metric Mapping (LDDMM) framework. This decouples formal diffeomorphic shape analysis from image registration, which has many practical benefits. Shape analysis can be added to study designs without modification to already chosen image registration methods and existing databases of deformation fields can be reanalyzed within the LDDMM framework without repeating image registrations. Pairwise time series studies can be extended to full time series regression with minimal added computing. The diffeomorphic rigor of image registration methods can be compared by embedding deformation fields and comparing projection distances. Finally, the added value of formal diffeomorphic shape analysis can be more fairly evaluated when it is derived from and compared to a baseline set of deformation fields. In brief, the method is a straightforward use of geodesic shooting in diffeomorphisms with a deformation field as the target, rather than an image. This is simpler than the image registration case which leads to a faster implementation that requires fewer user derived parameters.

}, doi = {10.1007/978-3-032-04947-6_31}, url = {https://www.doi.org/10.1007/978-3-032-04947-6_31}, author = {Fleishman, Greg M. and Fletcher, P. Thomas} } @article {70281, title = {Live dynamics of induced cell-cell fusion between mitotic and interphasic cells}, journal = {bioRxiv}, year = {2026}, month = {2026 Jan 27}, abstract = {

The cell cycle is tightly regulated by checkpoint mechanisms that ensure faithful duplication and segregation of the genome. Here, we induced cell-cell fusion between mitotic and interphase cells to study how nuclei from different cell cycle stages behave in a shared cytoplasm. We found that mitosis is a dominant cell cycle state: the mitotic cytoplasm can drive interphase nuclei into mitosis, whereas, in high ratios of interphase versus mitotic nuclei, fusion forced mitotic nuclei to exit mitosis. Both outcomes represent checkpoint override events with impactful consequences. Interphase nuclei forced into mitosis form aberrant mitotic spindles, show partially condensed DNA and ultimately undergo mitotic catastrophe. Conversely, forced mitotic exit resulted in reformation of nuclear envelope membranes around condensed chromosomes, forming nuclei with a defective nuclear import machinery. Altogether, cell-cell fusion revealed an unexpected plasticity in cell cycle control and highlight cell-cell fusion experiments as a powerful experimental system to study how competing cytoplasmic states are integrated in a shared cytoplasm.

}, doi = {10.64898/2026.01.27.700572}, url = {https://www.biorxiv.org/content/early/2026/01/27/2026.01.27.700572}, author = {Afonso, Olga and Feliciano, Daniel and Lippincott-Schwartz, Jennifer} } @article {70264, title = {Live dynamics of induced cell-cell fusion between mitotic and interphasic cells}, journal = {bioRxiv}, year = {2026}, month = {2026 Jan 27}, abstract = {

The cell cycle is tightly regulated by checkpoint mechanisms that ensure faithful duplication and segregation of the genome. Here, we induced cell-cell fusion between mitotic and interphase cells to study how nuclei from different cell cycle stages behave in a shared cytoplasm. We found that mitosis is a dominant cell cycle state: the mitotic cytoplasm can drive interphase nuclei into mitosis, whereas, in high ratios of interphase versus mitotic nuclei, fusion forced mitotic nuclei to exit mitosis. Both outcomes represent checkpoint override events with impactful consequences. Interphase nuclei forced into mitosis form aberrant mitotic spindles, show partially condensed DNA and ultimately undergo mitotic catastrophe. Conversely, forced mitotic exit resulted in reformation of nuclear envelope membranes around condensed chromosomes, forming nuclei with a defective nuclear import machinery. Altogether, cell-cell fusion revealed an unexpected plasticity in cell cycle control and highlight cell-cell fusion experiments as a powerful experimental system to study how competing cytoplasmic states are integrated in a shared cytoplasm.

}, doi = {10.64898/2026.01.27.700572}, url = {https://www.biorxiv.org/content/early/2026/01/27/2026.01.27.700572}, author = {Afonso, Olga and Feliciano, Daniel and Lippincott-Schwartz, Jennifer} } @article {70282, title = {Live dynamics of induced cell-cell fusion between mitotic and interphasic cells}, journal = {bioRxiv}, year = {2026}, month = {2026 Jan 27}, abstract = {

The cell cycle is tightly regulated by checkpoint mechanisms that ensure faithful duplication and segregation of the genome. Here, we induced cell-cell fusion between mitotic and interphase cells to study how nuclei from different cell cycle stages behave in a shared cytoplasm. We found that mitosis is a dominant cell cycle state: the mitotic cytoplasm can drive interphase nuclei into mitosis, whereas, in high ratios of interphase versus mitotic nuclei, fusion forced mitotic nuclei to exit mitosis. Both outcomes represent checkpoint override events with impactful consequences. Interphase nuclei forced into mitosis form aberrant mitotic spindles, show partially condensed DNA and ultimately undergo mitotic catastrophe. Conversely, forced mitotic exit resulted in reformation of nuclear envelope membranes around condensed chromosomes, forming nuclei with a defective nuclear import machinery. Altogether, cell-cell fusion revealed an unexpected plasticity in cell cycle control and highlight cell-cell fusion experiments as a powerful experimental system to study how competing cytoplasmic states are integrated in a shared cytoplasm.

}, doi = {10.64898/2026.01.27.700572}, url = {https://www.biorxiv.org/content/early/2026/01/27/2026.01.27.700572}, author = {Afonso, Olga and Feliciano, Daniel and Lippincott-Schwartz, Jennifer} } @article {70354, title = {Luminal surface proteome of the brain vasculature uncovers blood-brain barrier regulators.}, journal = {Science}, volume = {392}, year = {2026}, month = {2026 Apr 09}, pages = {eaea2100}, abstract = {

At the blood-tissue interface, vasculature luminal surface is critical for molecular transport, signaling transduction, and cell extravasation. Here, we present a method for proteomic profiling of the vasculature luminal surface in vivo, broadly applicable to any vertebrate. Quantitative mass spectrometry revealed the luminal surface proteome of the mouse brain vasculature and its temporal evolution from development to aging. In vivo genetic perturbation found that the arginine transporter SLC7A1 and the nitric oxide synthase NOS3 are needed for blood-brain barrier integrity in neonatal but not adult mice, whereas the hyaluronan degradation enzyme HYAL2 safeguards the barrier throughout the lifespan. By characterizing the proteomic dynamics of the vasculature luminal surface, the study links the metabolism of nitric oxide and hyaluronan to blood-brain barrier integrity.

}, keywords = {Aging, Animals, Blood-Brain Barrier, Brain, Cell Adhesion Molecules, Hyaluronic Acid, Mice, Nitric Oxide, Nitric Oxide Synthase Type III, Proteome, Proteomics}, issn = {1095-9203}, doi = {10.1126/science.aea2100}, url = {https://doi.org/10.1126/science.aea2100}, author = {Zhu, Zijian and Jiang, Zuzhi and Wang, Yupu and Nguyen, Khanh and Zhang, Yuxiang and Lian, Cameron Genxuan and Mani, D R and Zheng, Jun and Ding, Lang and Gao, Shihong Max and Xia, Ruyue Alps and Kuszpit, Anne and Lindo, Sarah and Lopez, Crystall and Lindsey, Catherine and Groff, Brooke and Chen, Xinhong and Wu, Jiahui and Xia, Weiliang and Li, Wei and Liu, Xiaorong and Gradinaru, Viviana and Carr, Steven A and Udeshi, Namrata D and Li, Jiefu} } @article {70241, title = {Machine learning prediction of analyte-induced fluorescence perturbations in DNA-functionalized carbon nanotubes}, journal = {Nano Letters}, year = {2026}, month = {2026 Jan 07}, abstract = {

Single-walled carbon nanotubes (SWCNTs) functionalized with single-stranded DNAs can function as near-infrared nanosensors for molecular analytes. However, predicting which analytes elicit strong optical responses for specific nanosensors remains challenging. We developed machine learning (ML) models to predict analyte-induced fluorescence changes in a DNA{\textendash}SWCNT dopamine nanosensor. Using a data set of 63 small molecules sampling chemical space around dopamine, we encoded analytes with RDKit fingerprints, with or without HOMO and LUMO energies, and applied principal component analysis to identify structural motifs associated with optical response strength. We trained support vector regression and classification models using two strategies: ensembles of 200 models and cross-validation. Regression models achieved mean\ R2\ values of 0.2{\textendash}0.4, with cross-validation outperforming ensembles, while classifiers reached mean F1 scores of \~{}0.8. Cross-validation performed best for predictions on a blind set of 21 molecules. These findings show that ML can capture structure{\textendash}response patterns in modest data sets and guide in silico DNA{\textendash}SWCNT nanosensor design.

}, doi = {10.1021/acs.nanolett.5c05206}, url = {https://doi.org/10.1021/acs.nanolett.5c05206}, author = {Chakraborty, Sayantani and Krasley, Andrew T. and Smith, Colby H. and Beyene, Abraham G. and Vukovi{\'c}, Lela} } @article {70293, title = {Machine learning-guided spatial omics for tissue-scale discovery of cell-type-specific architectures}, journal = {bioRxiv}, year = {2026}, month = {2026 Feb 13}, abstract = {

Multiplexed protein imaging enables spatially resolved analysis of molecular organization in tissues, but existing spatial proteomics platforms remain constrained in scalability, throughput, and integration with RNA measurements and interpretable computational analysis. Here, we present an integrated spatial omics framework that combines highly multiplexed protein and RNA imaging with explainable machine learning to map cell-type-specific molecular and structural architectures at tissue scale. Using this platform, we simultaneously profiled up to 46 proteins and 79 RNA species across \~370,000 cells in intact mouse brain tissue at diffraction-limited subcellular resolution (\~260 nm). We developed a scalable, open-source computational pipeline for large-scale image processing and analysis, and show that nuclear protein and chromatin features alone are sufficient to accurately classify brain cell types and their spatial organization. Incorporation of explainable deep learning further enabled identification of human-interpretable, cell-type-specific subnuclear structural features directly from imaging data, with independent quantitative validation. Together, this integrated experimental and computational framework enables tissue-scale spatial proteomics-based cell-type classification and structural feature discovery, providing a broadly applicable platform for mechanistic studies, high-content screening, and translational applications.

}, doi = {10.64898/2026.02.12.705598}, url = {https://www.biorxiv.org/content/early/2026/02/13/2026.02.12.705598}, author = {Lian, Yumin and Adjavon, Diane-Yayra and Kawase, Takashi and Kim, Jun and Fleishman, Greg and Preibisch, Stephan and Funke, Jan and Liu, Zhe J.} } @article {70336, title = {Many cells make light work: Self-generated gradients organize Dictyostelium aggregates and neutrophil swarms.}, journal = {Cold Spring Harb Perspect Biol}, year = {2026}, month = {2026 Mar 30}, abstract = {

Cells work together to accomplish complex tasks. For example, both neutrophils and Dictyostelid collectives use self-generated multicellular signaling gradients to coordinate aggregation over large areas through local interactions. However, these aggregation programs occur for different reasons that necessitate different implementations. Dictyostelids are soil-dwelling amoeba that aggregate when starving to facilitate dispersal to new locations. These aggregates do not require specific locations or group sizes. In contrast, neutrophils are innate immune cells that collectively migrate to sites of injury and infection. These swarms need to occur in specific locations and must be constrained in size to avoid collateral damage to the host. Here, we review how these evolutionarily divergent systems sculpt long-range gradients at the molecular and cellular levels, discussing their similarities and differences in light of their distinctive goals. Convergence on self-generated gradients for aggregation despite different goals suggests that it is an optimal strategy to bring individuals together in complex environments.

}, issn = {1943-0264}, doi = {10.1101/cshperspect.a041739}, url = {https://doi.org/10.1101/cshperspect.a041739}, author = {Strickland, Evelyn and Durel, John F and Sgro, Allyson E and Weiner, Orion D} } @article {70316, title = {Measuring Amorphous Motion: Application of Optical Flow to Three-Dimensional Fluorescence Microscopy Images}, journal = {bioRxiv}, year = {2026}, month = {2026 Mar 10}, abstract = {

Motion is an essential component of any living system. It is rich with information, but it is often challenging to quantitatively extract biologically informative results from the motion apparent in microscopy images. This challenge is exacerbated by the wide variety in biological movement, which often takes the form of difficult-to-segment amorphous structures undergoing complex motion. An image processing technique known as optical flow can capture motion at each pixel in an image, thus bypassing the need for object segmentation or a priori definition of motion types. This makes it a powerful tool for quantitative assessment of biological systems from the protein to organism scale. However, despite its flexibility and strengths for analyzing fluorescence microscopy images, its adoption in the bioimaging community has been limited by the availability of easy-to-use tools and guidance in results interpretation. Here we describe an optical flow tool, OpticalFlow3D, that can be run in Python or MATLAB and is compatible with three-dimensional microscopy images. Using biological examples across length scales, we illustrate how OpticalFlow3D can enable new biological insight.

}, doi = {10.64898/2026.03.06.710169}, url = {https://www.biorxiv.org/content/early/2026/03/10/2026.03.06.710169}, author = {Lee, Rachel M and Eisenman, Leanna R. and Hobson, Chad and Aaron, Jesse S. and Chew, Teng-Leong} } @article {70266, title = {Mechanically-induced Septin Networks protect nuclear integrity}, journal = {bioRxiv}, year = {2026}, month = {2026 Jan 21}, abstract = {

The cytoskeleton is a key mediator of mechanical interactions in cells, but specific contributions of septins remains unclear. Septins preferentially localize with a subset of actin stress fibers positioned under the nucleus, where they are situated between the membrane and stress fibers. Removing the nucleus from the cell results in the loss of these subnuclear septin-decorated stress fibers. Surprisingly, however, their formation can be rescued using a large glass bead in place of the nucleus. Similarly, applying a compressive force to the cell via confinement, whether externally or through internally generated actomyosin forces, results in increased septin accumulation in regions where the nucleus engages the cell cortex. Finally, loss of septin filaments via knockdown of SEPT7 increases the likelihood of nuclear membrane rupture during confinement. Together these data suggest that septins act as a dynamic mechanosensitive protective mechanism to buffer mechanical forces on the nucleus.

}, doi = {10.64898/2026.01.20.700414}, url = {https://www.biorxiv.org/content/early/2026/01/21/2026.01.20.700414}, author = {Utgaard, Margaret E. and Caillier, Alexia and Chandrasekar, Shreya and Tidei, Joseph J. and Balasubramanian, Harikrushnan and Lee, Rachel M. and Puls, Owen and Khuon, Satya and Aaron, Jesse and Chew, Teng-Leong and Beach, Jordan R. and Oakes, Patrick W.} } @article {70240, title = {Memory from variability: Heritable short-term cellular memory emerges from stochastic biochemical reaction networks}, journal = {bioRxiv}, year = {2026}, month = {2026 Jan 01}, abstract = {

Cells exhibit a mysterious form of selective heritable short-term memory, influencing outcomes as diverse as cell fate decisions in embryos and environmental responses in cancer cells and bacteria. Here, we present a simple theoretical framework explaining how this selective memory can arise from the reactions regulating molecular levels in cells. Our key insight is that related cells retain more similar molecular concentrations relative to random cells when a greater variance of possible concentration states is created during a single cell generation than is created by cell division across a population. This persistence of molecular similarity down a lineage constitutes a form of heritable short-term memory. We identify the biochemical networks that produce, modify, and degrade molecules as an underexplored source of these additional molecular concentration states. Using experimentally informed simulations, we find that the strength and duration of molecular similarity down a lineage depend on tunable network properties, explaining why some cellular traits persist only briefly while others last generations. These contributions to molecular concentration variance from biochemical reaction networks act in concert with gene expression and other regulatory processes to shape the protein composition of cells. Our framework yields clear, testable predictions for determining how biochemical network architectures drive non-genetic cellular inheritance.

}, doi = {10.64898/2025.12.31.694479}, url = {https://www.biorxiv.org/content/early/2026/01/01/2025.12.31.694479}, author = {Aronson, Mark S. and Zhou, Brian Y. and Fitzgerald, James E. and Sgro, Allyson E.} } @article {70333, title = {Midgestation metabolic constraint in purine metabolism drives distinct strategies for placenta and fetal growth}, journal = {bioRxiv}, year = {2026}, month = {2026 Mar 18}, abstract = {

Purine nucleotides are essential for mammalian development1,2. Purine monophosphates support cell signaling and proliferation and are synthesized by cells through either de novo synthesis or a salvage pathway3. We previously identified a midgestational metabolic transition in mice (gestational days gd10.5{\textendash}11.5) characterized by changes in purine metabolism4. Midgestation is a period of rapid growth for placenta and embryo, yet it remains unclear how the placental tissues expand without directly competing with the embryo for biosynthetic resources. Here, we show that this midgestational metabolic transition is associated with a marked reduction in embryonic expression of purine salvage enzymes, which constrains embryonic metabolism and leads to different strategies for purine synthesis between the placenta and embryo. Midgestation embryos are unable to engage the purine salvage pathway even when de novo purine synthesis is blocked either in vivo or in ex utero embryo culture, whereas placental tissue and trophoblasts retain the capacity to use either pathway. Disruption of de novo purine synthesis in mice causes reduced embryonic growth, impaired axial elongation, and abnormal brain and placental development, which are only partially rescued by supplementation with purine salvage precursors. In human placenta, trophoblast stem cells readily switch between the de novo and salvage pathways based on nutrient availability, and syncytiotrophoblasts (STB) preferentially rely on the salvage pathway. We identified guanosine monophosphate (GMP) as a metabolic checkpoint regulating STB differentiation, with insufficient GMP levels causing degradation of the small GTPase Rheb and failure of mTOR activation. Supplementation of purine salvage substrates restored GMP synthesis and STB differentiation in humans, but not mice. Further, in vivo measurements in humans revealed that maternal circulating hypoxanthine decreases during pregnancy and is further reduced in women with clinically small placentas, highlighting the role of hypoxanthine in supporting placental growth. These results uncover compartmentalized purine salvage between the embryo and placenta as a mechanism that limits competition for biosynthetic resources and enables coordinated growth during mammalian development.

}, doi = {10.64898/2026.03.18.712680}, url = {https://www.biorxiv.org/content/early/2026/03/18/2026.03.18.712680}, author = {Xu, Weizhi and De La Cruz, Nancy and Woods, Andrea and Lokshtanov, Dmitry and Gao, Shihong and Khan, Nawal and Wright, Sylvia and Florian-Rodriguez, Maria E. and McIntire, Donald D. and Duryea, Elaine L and Nelson, David B. and Spong, Catherine Y. and Herrera, Christina L. and Hanna, Jacob H. and Srivatsan, Sanjay and Aguilera-Castrejon, Alejandro and Solmonson, Ashley} } @article {70288, title = {Mitochondrial Ca efflux controls neuronal metabolism and long-term memory across species.}, journal = {Nat Metab}, year = {2026}, month = {2026 Feb 11}, abstract = {

From insects to mammals, essential brain functions, such as forming long-term memories (LTMs), increase metabolic activity in stimulated neurons to meet the energetic demand associated with brain activation. However, while impairing neuronal metabolism limits brain performance, whether expanding the metabolic capacity of neurons boosts brain function remains poorly understood. Here, we show that LTM formation of flies and mice can be enhanced by increasing mitochondrial metabolism in central memory circuits. By knocking down the mitochondrial Ca exporter Letm1, we favour Ca retention in the mitochondrial matrix of neurons due to reduction of mitochondrial H/Ca exchange. The resulting increase in mitochondrial Ca over-activates mitochondrial metabolism in neurons of central memory circuits, leading to improved LTM storage in training paradigms in which wild-type counterparts of both species fail to remember. Our findings unveil an evolutionarily conserved mechanism that controls mitochondrial metabolism in neurons and indicate its involvement in shaping higher brain functions, such as LTM.

}, issn = {2522-5812}, doi = {10.1038/s42255-026-01451-w}, url = {https://doi.org/10.1038/s42255-026-01451-w}, author = {Amrapali Vishwanath, Anjali and Comyn, Typhaine and Mira, Rodrigo G and Brossier, Claire and Pascual-Caro, Carlos and Faour, Maya and Boumendil, Kahina and Chintaluri, Chaitanya and Ramon-Duaso, Carla and Fan, Ruolin and Ghosh, Kishalay and Farrants, Helen and Berwick, Jean-Paul and Sivakumar, Riya and Lopez-Manzaneda, Mario and Schreiter, Eric R and Preat, Thomas and Vogels, Tim P and Rangaraju, Vidhya and Busquets-Garcia, Arnau and Placais, Pierre-Yves and Pavlowsky, Alice and de Juan-Sanz, Jaime} } @article {70256, title = {Model-agnostic linear-memory online learning in spiking neural networks.}, journal = {Nat Commun}, year = {2026}, month = {2026 Jan 19}, abstract = {

Spiking neural networks (SNNs) offer a promising paradigm for modeling brain dynamics and developing neuromorphic intelligence, yet an online learning system capable of training rich spiking dynamics over long horizons with low memory footprints has been missing. Existing online approaches either incur quadratic memory growth, sacrifice biological fidelity through oversimplified models, or lack end-to-end automated tooling. Here, we introduce BrainTrace, a model-agnostic, linear-memory, and automated online learning system for spiking neural networks. BrainTrace standardizes model specification to encompass diverse neuronal and synaptic dynamics; implements a linear-memory online learning rule by exploiting intrinsic properties of spiking dynamics; and provides a compiler that automatically generates optimized online-learning code for arbitrary user-defined models. Across diverse dynamics and tasks, BrainTrace achieves strong learning performance with a low memory footprint and high computational throughput. Critically, these properties enable online fitting of a whole-brain-scale Drosophila SNN that recapitulates region-level functional activity. By reconciling generality, efficiency, and usability, BrainTrace establishes a foundation for spiking network modeling at scale.

}, issn = {2041-1723}, doi = {10.1038/s41467-026-68453-w}, url = { https://doi.org/10.1038/s41467-026-68453-w}, author = {Wang, Chaoming and Dong, Xingsi and Ji, Zilong and Xiao, Mingqing and Jiang, Jiedong and Liu, Xiao and Huan, Yuxiang and Wu, Si} } @article {70242, title = {mRNAbow: A versatile gene expression system for multiplexed fluorescent imaging using optimized in vitro transcribed mRNA}, journal = {bioRxiv}, year = {2026}, month = {2026 Jan 02}, abstract = {

Messenger RNA (mRNA) transfection enables rapid, transient protein expression without nuclear entry, providing a powerful alternative to DNA or viral delivery in post-mitotic and otherwise difficult-to-transfect cells. Although in vitro transcribed (IVT) mRNAs have revolutionized therapeutic applications, their adoption in experimental biology remains limited by challenges in synthesis, variability across cell types, and concerns about cytotoxicity. Here, we define design principles that maximize IVT mRNA performance across diverse cellular and organismal systems. Through systematic comparison of capping strategies and base modifications, including N1-methyl-pseudouridine, 5-methylcytidine, and 5-methoxyuridine, we identify modifications that enhance translation while minimizing activation of cellular stress responses. Optimized transcripts drive robust protein expression within four hours, persist for up to one week, and support multiplexed expression of structurally and functionally distinct proteins in mammalian cells, including cancer cell lines, iPSC-derived systems, primary cells, and organoids, as well as in vivo in zebrafish embryos and in less genetically tractable models such as Danionella cerebrum and sea urchin embryos. To further expand accessibility for community use, we developed mRNAbow, a platform for generating low-toxicity mRNAs encoding organelle-targeted fluorescent proteins and biosensors for multiplex imaging, with corresponding plasmids made publicly available. Together, these advances establish a generalizable framework for IVT mRNA design and expand experimental access to synthetic mRNA technologies for dissecting cellular architecture and dynamics.

}, doi = {10.64898/2026.01.02.697412}, url = {https://www.biorxiv.org/content/early/2026/01/02/2026.01.02.697412}, author = {Choi, Heejun and Halanych, Coral and Kasberg, William and Testa, Michael D. and Rubin-Elgressy, Sarah and Nguyen, Phuong and Walpita, Deepika and Tsang, Arthur and Cortes, Dan and Song, Erin Yue and Wu, Haodi and Weissman, Irving L and Espinosa-Medina, Isabel and Satou, Chie and Song, Jia L. and Matus, David Q. and Lippincott-Schwartz, Jennifer} } @article {70348, title = {A multi-resolution imaging and analysis pipeline for comparative circuit reconstruction in insects}, journal = {eLife}, year = {2026}, month = {2026 Apr 7}, abstract = {

Connectomics has become essential for the study of brain function, yet for most research groups it remains prohibitively costly in imaging time, data storage, and analysis. Here, we present an imaging, processing, and analysis pipeline for multi-resolution image acquisition and circuit reconstruction. Applied to the central complex of six insect species, we were able to obtain global projectomes at cellular resolution (40-50 nm) with embedded local connectomes describing key computational compartments at synaptic resolution (8-12 nm). We provide standardized protocols for volume EM sample preparation, image acquisition and image alignment, combined with existing methods for {\textmu}CT block trimming, automatic segmentation, synapse detection, collaborative skeleton tracing with CATMAID, and segmentation proofreading via CAVE. We validated our workflow by reconstructing head direction cells across all six insect species, which revealed deep conservation at the level of cell types, cell numbers and projection patterns, while also revealing circuit level specializations. Overall, our pipeline democratizes comparative connectomics by making this method accessible for small research groups with modest resources.

}, doi = {10.7554/elife.110789.1}, url = {http://dx.doi.org/10.7554/eLife.110789.1}, author = {Gillet, Valentin and Sayre, Marcel E and Badalamente, Griffin S and Schieber, Nicole L and Tedore, Kevin and Funke, Jan and Heinze, Stanley} } @article {70311, title = {A multi-resolution imaging and analysis pipeline for comparative circuit reconstruction in insects}, journal = {bioRxiv}, year = {2026}, month = {2026 Feb 28}, abstract = {

Connectomics has become essential for the study of brain function, yet for most research groups it remains prohibitively costly in imaging time, data storage, and analysis. Here, we present an imaging, processing, and analysis pipeline for multi-resolution image acquisition and circuit reconstruction. Applied to the central complex of six insect species, we were able to obtain global projectomes at cellular resolution (40-50 nm) with embedded local connectomes describing key computational compartments at synaptic resolution (8-12 nm). We provide standardized protocols for volume EM sample preparation, image acquisition and image alignment, combined with existing methods for {\textmu}CT block trimming, automatic segmentation, synapse detection, collaborative skeleton tracing with CATMAID, and segmentation proofreading via CAVE. We validated our workflow by reconstructing head direction cells across all six insect species, which revealed deep conservation at the level of cell types, cell numbers and projection patterns, while also revealing circuit level specializations. Overall, our pipeline democratizes comparative connectomics by making this method accessible for small research groups with modest resources.

}, doi = {10.64898/2026.02.25.708065}, url = {https://www.biorxiv.org/content/early/2026/02/28/2026.02.25.708065}, author = {Gillet, Valentin and Sayre, Marcel E. and Badalamente, Griffin S. and Schieber, Nicole L. and Tedore, Kevin and Funke, Jan and Heinze, Stanley} } @article {70297, title = {Nanoscale imaging of expanded cells and proteins with spontaneously blinking dyes}, journal = {bioRxiv}, year = {2026}, month = {2026 Feb 23}, abstract = {

Expansion microscopy (ExM) enables nanoscale imaging on standard microscopes, but combining ExM with single-molecule localization microscopy (SMLM) remains difficult, owing to the incompatibility of expanded hydrogels with photoswitching buffers. Here, we introduce a single-step expansion microscopy method that allows SMLM with spontaneously blinking dyes in 6-14{\texttimes} expanded samples, without re-embedding. We demonstrate nanometer-resolution imaging by resolving the organization of the nuclear pore complex (NPC) and the molecular structure of recombinant homotrimeric proliferating cell nuclear antigen (PCNA).

}, doi = {10.64898/2026.02.23.707413}, url = {https://www.biorxiv.org/content/early/2026/02/23/2026.02.23.707413}, author = {Taban, Danush and Jungblut, Marvin and Budiarta, Made and Helmerich, Dominic A. and Kiesel, Cerridwen and Plutkis, Sarah E. and Lavis, Luke D. and Krah, Donatus and Shaib, Ali H. and Doose, S{\"o}ren and Kollmannsberger, Philip and Rizzoli, Silvio O. and Beliu, Gerti and Sauer, Markus} } @article {70304, title = {Nanoscale imaging of expanded cells and proteins with spontaneously blinking dyes}, journal = {bioRxiv}, year = {2026}, month = {2026 Feb 23}, abstract = {

Expansion microscopy (ExM) enables nanoscale imaging on standard microscopes, but combining ExM with single-molecule localization microscopy (SMLM) remains difficult, owing to the incompatibility of expanded hydrogels with photoswitching buffers. Here, we introduce a single-step expansion microscopy method that allows SMLM with spontaneously blinking dyes in 6-14{\texttimes} expanded samples, without re-embedding. We demonstrate nanometer-resolution imaging by resolving the organization of the nuclear pore complex (NPC) and the molecular structure of recombinant homotrimeric proliferating cell nuclear antigen (PCNA).

}, doi = {10.64898/2026.02.23.707413}, url = {https://www.biorxiv.org/content/early/2026/02/23/2026.02.23.707413}, author = {Taban, Danush and Jungblut, Marvin and Budiarta, Made and Helmerich, Dominic A. and Kiesel, Cerridwen and Plutkis, Sarah E. and Lavis, Luke D. and Krah, Donatus and Shaib, Ali H. and Doose, S{\"o}ren and Kollmannsberger, Philip and Rizzoli, Silvio O. and Beliu, Gerti and Sauer, Markus} } @article {70338, title = {Neurobiology of foraging: An integrative approach.}, journal = {Annu Rev Neurosci}, year = {2026}, month = {2026 Mar 30}, abstract = {

Foraging, defined as the search for food to sustain one{\textquoteright}s energetic needs, is a fundamental behavior performed by almost all animals to survive in their environment. Foraging involves a variety of physiological processes, including metabolic and cognitive computations. In this review, we provide a brief historical overview of foraging and foraging theory, highlight recent insights into the neural mechanisms of foraging, and contextualize them within the broader neuroscience literature. We present an integrative approach to foraging that combines neural mechanisms of foraging with ecological, behavioral, and physiological mechanisms.

}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-091724-040841}, url = {https://doi.org/10.1146/annurev-neuro-091724-040841}, author = {Dennis, Emily Jane and El Hady, Ahmed} } @article {70331, title = {NPAS4 refines spatial and temporal firing in CA1 pyramidal neurons}, journal = {bioRxiv}, year = {2026}, month = {2026 Mar 22}, abstract = {

NPAS4 is an activity-dependent transcription factor that, in CA1 of the hippocampus, regulates inhibitory synapses made onto the active pyramidal neuron. In principle, NPAS4 thereby allows the past activity of a neuron to influence how it encodes information, although this has not yet been demonstrated. Here, we generated a sparse, CA1-specific knockout (KO) of NPAS4 in the mouse hippocampus and used optogenetic tagging to identify KO neurons in vivo. Recordings from intermingled wild-type (WT) and KO neurons in awake behaving animals revealed that NPAS4 deletion degrades spatial representations and temporal precision of spiking: KO neurons exhibited larger place fields with reduced in-field firing and increased out-of-field firing, less stable place fields, reduced coupling to local field potential theta oscillations, and diminished phase precession. These findings demonstrate that NPAS4 plays a crucial role in refining the spatial and temporal properties of CA1 pyramidal neuron spikes, which themselves are thought to be fundamental building blocks of more complex processes such as learning and memory.

}, doi = {10.64898/2026.03.22.713468}, url = {https://www.biorxiv.org/content/early/2026/03/22/2026.03.22.713468}, author = {Payne, Anja and Heinz, Daniel A. and Santiago, Chiaki and Hagopian, Lara L. and Ganasi, Rolando Sceptre and Quirk, Clare and Hartzell, Andrea L. and Leutgeb, Jill K. and Leutgeb, Stefan and Bloodgood, Brenda L.} } @article {70287, title = {Orofacial behaviors, not eye movements, govern neural activity in mouse visual cortex}, journal = {bioRxiv}, year = {2026}, month = {2026 Feb 05}, abstract = {

Neural activity in mouse primary visual cortex (V1) correlates strongly with orofacial movements. Such strong modulation has not been found in the primate visual cortex during eye fixation [1], which led to the suggestion that the modulation may primarily depend on eye movements in both species [2]. Here we examined the influence of eye movements on neural activity in mouse visual cortex both in complete darkness and in the presence of different types of visual input. In all cases, we found that eye movements explain a smaller fraction of neural activity variance compared to orofacial behaviors. Additionally, we found that eye movements were correlated to orofacial movements, such as whisking and sniffing, and thus may be indirectly correlated to neural activity. These results further emphasize the impact of movement signals on mouse visual cortex during free viewing behavior.

}, doi = {10.64898/2026.02.04.703800}, url = {https://www.biorxiv.org/content/early/2026/02/05/2026.02.04.703800}, author = {Syeda, Atika and N{\'u}{\~n}ez-Ochoa, Miguel Angel and Zhong, Lin and Pachitariu, Marius and Stringer, Carsen} } @article {70250, title = {Oxytocin modulation of spinal circuits drives therapeutic benefits of massage}, journal = {bioRxiv}, year = {2026}, month = {2026 Jan 12}, abstract = {

Across social species, social touch enhances well-being and reduces pain {\textemdash} two seemingly distinct benefits that enhance survival. Yet where and how the nervous system integrates these functions, and whether a single mechanism could serve both, remains unknown. Here we show that massage triggers oxytocin release, which shapes both pain and touch reward at the earliest stage of central processing {\textemdash} the spinal cord {\textemdash} through a single, state-dependent circuit mechanism. We report that in humans, massage enhances well-being, effects that correlate with endogenous oxytocin release. In mice, gentle touch activates hypothalamic oxytocin neurons that project directly to the spinal dorsal horn. Genetic manipulation of spinal oxytocin circuits alters behavioral responses to both gentle touch and noxious stimuli. Spinal calcium imaging and slice electrophysiology reveal that oxytocin acts on both excitatory and inhibitory spinal neurons to sculpt the relative activity of spinal ascending systems that convey both social touch and pain to the brain. Extending these findings to humans, we show that oxytocin receptors are also expressed on spinal excitatory and inhibitory neurons, and that endogenous oxytocin during massage correlates with altered spinal touch processing. Thus, spinal oxytocin signaling provides an evolutionarily conserved mechanism for the therapeutic benefits of massage.

}, doi = {10.64898/2026.01.11.698886}, url = {https://www.biorxiv.org/content/early/2026/01/12/2026.01.11.698886}, author = {Bohic, Manon and Salamone, Paula Celeste and Zuo, Wanhong and Negm, Ahmed and Fulton, Sasha Leilani and Du, Shibin and Jayakumar, Swathi and Keating, Jessica and Soubeyre, Vanessa and Gradwell, Mark Andrew and Upadhyay, Aman and Shorter, Lucero and Kim, Joel and Inoue, Yukiko Ueno and Inoue, Takayoshi and Mensch, Brett and Ye, Jiang-Hong and Peirs, Cedric and Poulen, Gaetan and Lonjon, Nicolas and Vachiery-Lahaye, Florence and Bauchet, Luc and Bourinet, Emmanuel and Olausson, Hakan and Abdus-Saboor, Ishmail and Tao, Yuan-Xiang and Boehme, Rebecca and Abraira, Victoria E.} } @article {70177, title = {A pair of interneurons that assign positive valence to sweet sensation in Drosophila}, journal = {Curr Bill}, year = {2026}, month = {2026 Jan 29}, abstract = {

Assigning valence-appeal or aversion-to gustatory stimuli and relaying it to higher-order brain regions to guide flexible behaviors is crucial to survival. Yet the neural circuits that transform taste into motivationally relevant signals remain poorly defined in any model system. In Drosophila melanogaster, substantial progress has been made in mapping the sensorimotor pathways encoding intrinsic valence for feeding and the architecture of the dopaminergic reinforcement system. However, where and how "effective" (i.e., real-time) valence is first imposed on a taste has long been a mystery. Here, we identified a pair of subesophageal zone interneurons in Drosophila, termed Fox, that impart reinforcing positive valence to sweet taste and convey this signal to the mushroom body, the fly{\textquoteright}s associative learning center. We show that Fox neuron activity is necessary and sufficient to drive appetitive behaviors and can override a tastant{\textquoteright}s intrinsic neutral or aversive valence without impairing taste quality discrimination. Furthermore, Fox neurons relay the positive valence to specific dopaminergic neurons that mediate appetitive memory formation. Our findings reveal a circuit mechanism through which effective valence is bestowed upon sweet sensation and transformed into a reinforcing signal that supports learned sugar responses. The Fox neurons form a convergent-divergent "hourglass" circuit motif, acting as a bottleneck for valence assignment and distributing motivational signals to higher-order centers. This architecture confers both robustness and flexibility in reward processing-an organizational principle that may generalize across species.

}, doi = {10.1016/j.cub.2025.12.058}, url = {https://doi.org/10.1016/j.cub.2025.12.058}, author = {Christie, Kevin William and Dadyala, Tarandeep Singh and Sinakevitch, Irina Troufakina and Chung, Phuong and Ito, Masayoshi and Shao, Lisha} } @article {70346, title = {Pearling drives mitochondrial DNA nucleoid distribution.}, journal = {Science}, volume = {392}, year = {2026}, month = {2026 Apr 02}, pages = {102-109}, abstract = {

The distribution of mitochondrial DNA-containing nucleoids is essential for mitochondrial function and genome inheritance; however, no known mechanisms can explain nucleoid segregation or their regular positioning. In this work, we found that mitochondria frequently undergo a reversible biophysical instability termed "pearling," transforming from a tubular into a regularly spaced beads morphology. Physiological pearling imposed a characteristic length scale and simultaneously mediated nucleoid disaggregation and established internucleoid distancing with high precision. Pearling onset was triggered by calcium influx, whereas the density of lamellar cristae invaginations modulated pearling prevalence and preserved nucleoid spacing following recovery. The dysregulation of mitochondrial calcium influx or inner membrane cristae integrity caused aberrant nucleoid clustering. Our results identify pearling as a mechanism governing nucleoid distribution and inheritance and offer insights into its regulation.

}, keywords = {Animals, Calcium, Cell Line, Tumor, DNA, Mitochondrial, Humans, Mitochondria, Mitochondrial Dynamics, Mitochondrial Membranes, Saccharomyces cerevisiae}, issn = {1095-9203}, doi = {10.1126/science.adu5646}, url = {https://doi.org/10.1126/science.adu5646}, author = {Landoni, Juan C and Lycas, Matthew D and Macuada, Josefa and Stepp, Willi and Jaccard, Romeo and Obara, Christopher J and Moore, Andrew S and Hoffman, David and Lippincott-Schwartz, Jennifer and Marshall, Wallace and Sturm, Gabriel and Manley, Suliana} } @article {70294, title = {Phasor analysis of RGB camera data enables fluorescence microscopy unmixing and brightfield segmentation in a commercial microscope}, journal = {bioRxiv}, year = {2026}, month = {2026 Feb 16}, abstract = {

Spectral information plays a crucial role in biological imaging, yet conventional epifluorescence and histological techniques often rely on RGB image acquisition, limiting the resolution of spectrally overlapping components. Here, we present a phasor-based spectral analysis framework adapted for RGB images, enabling unsupervised segmentation and unmixing without the need for hyperspectral systems or sequential acquisition. By applying a discrete Fourier transform to the red, green, and blue intensities at each pixel, we generate a two-dimensional phasor plot where spectral relationships are encoded in modulation and phase. We demonstrate the utility of this approach across three distinct applications: segmentation of lung histology images stained with hematoxylin and eosin to quantify alveolar collapse, analysis of autofluorescence in skin lesions (nevi and melanoma) to highlight pathological spectral signatures, and spectral unmixing in multicolor-labeled U2OS cells to resolve overlapping fluorophores. Our method improves signal separation, reduces noise, and enhances biological interpretability using standard RGB acquisition. These findings establish RGB phasor analysis as a practical and powerful tool for spectral decomposition and segmentation in microscopy, bridging the gap between conventional imaging and advanced spectral analysis.

}, doi = {10.64898/2026.02.13.705652}, url = {https://www.biorxiv.org/content/early/2026/02/16/2026.02.13.705652}, author = {Schuty, Bruno and Garcia, Maria Jose and Khuon, Satya and Malacrida, Leonel S} } @article {70302, title = {Phenotypic CRISPR screens identify NLRX1 as an essential activator of the human mitochondrial permeability transition}, journal = {Proceedings of the National Academy of Sciences}, volume = {123}, year = {2026}, month = {2026 Feb 25}, pages = {e2535298123}, abstract = {

Mitochondria utilize calcium to increase ATP synthesis. However, excessive matrix calcium activates the mitochondrial permeability transition (mPT), a process that permeabilizes the mitochondrial inner membrane and leads to cell death. While initially characterized 50 y ago, the proteins underlying the process are unclear, although integral membrane proteins were expected to be the porous entities during calcium overload. Here, we designed two assays to study the mPT using high-throughput methodologies. By surveying 19,113 proteins in human cells, we identified four proteins that sensitize the human mPT, but only one that was essential for mPT activation, mitochondrial-localized NRLX1. Surprisingly, NLRX1 is not an integral membrane protein, and our work did not identify any essential integral membrane proteins for the human mPT. The mitochondrial permeability transition (mPT) is an evolutionarily conserved destructive process that permeabilizes the inner mitochondrial membrane in response to calcium overload. The molecular mechanism underlying the mPT is not established. To unambiguously identify essential proteins, we designed two phenotypic assays for mitochondrial calcium overload and applied them to FACS-based CRISPR screening in human cells, ultimately evaluating 19,113 genes. The first screen studied mitochondrial membrane potential (MMP) collapse in response to calcium overload. Top-ranked genes were the essential proteins of the mitochondrial calcium uniporter complex, MCU and EMRE, reflecting that the calcium-induced MMP collapse results from mitochondrial calcium entry and not the mPT. The second screen measured the permeability of the inner mitochondrial membrane. Here, the fluorescent interaction of a membrane impermeant 600 Da dye and a mitochondrial-targeted HaloTag protein was studied under mPT activating conditions; calcium overload and the thiol-reactive molecule phenylarsine oxide. With secondary validation, we identified four protein-encoding genes that delayed or prevented the mPT under knockout: NF2, REST, BPTF, and NRLX1. Knockout of the nonmitochondrial proteins BPTF, NF2, or REST increased mitochondrial calcium retention capacity (CRC). However, calcium release or sensitivity to cyclosporin A (CsA) persisted, indicative of mPT sensitizers. Only knockout of the mitochondrial matrix protein, NLRX1, increased CRC, abolished calcium release, and was CsA-insensitive. This top-ranked hit of the mitochondrial permeability screen meets the definition of an essential mPT activator. Integral membrane proteins, including all previously proposed mPT candidates, were not essential activators.

}, doi = {10.1073/pnas.2535298123}, url = {https://www.pnas.org/doi/abs/10.1073/pnas.2535298123}, author = {William C. Valinsky and Robert P. Ray and Kathy S. Schaefer and Jonathan B. Grimm and Carla Nicolini and Luke D. Lavis and David E. Clapham} } @article {69949, title = {Proprioceptive limit detectors mediate sensorimotor control of the Drosophila leg}, journal = {Nat Commun}, year = {2026}, month = {2026 Feb 12}, abstract = {

Many animals possess mechanosensory neurons that fire when a limb nears the limit of its physical range, but the function of these proprioceptive limit detectors remains poorly understood. Here, we investigate a class of proprioceptors on the Drosophila leg called hair plates. Using calcium imaging in behaving flies, we find that a hair plate on the fly coxa (CxHP8) detects the limits of anterior leg movement. By reconstructing CxHP8 axons in an electron microscopy dataset, we found that they are wired to excite posterior leg movement and inhibit anterior leg movement. Consistent with this connectivity, optogenetic activation of CxHP8 neurons elicited posterior postural reflexes, while silencing altered the swing-to-stance transition during walking. Finally, we use comprehensive reconstruction of peripheral morphology and downstream connectivity to predict the function of other hair plates distributed across the fly leg. Our results suggest that each hair plate is specialized to control specific sensorimotor reflexes that are matched to the joint limit it detects. They also illustrate the feasibility of predicting sensorimotor reflexes from a connectome with identified proprioceptive inputs and motor outputs.

}, doi = {10.1038/s41467-026-69333-z}, url = {https://doi.org/10.1038/s41467-026-69333-z}, author = {Pratt, Brandon G. and Dallmann, Chris J. and Chou, Grant M. and Siwanowicz, Igor and Walling-Bell, Sarah and Cook, Andrew and Sustar, Anne and Azevedo, Anthony and Tuthill, John C.} } @article {70340, title = {Rapidly evolving aphid gall effector proteins exhibit saposin-like folds}, journal = {bioRxiv}, year = {2026}, month = {2026 Mar 28}, abstract = {

Many insects manipulate plants by injecting effector proteins. In one extreme example of this molecular {\textquotedblleft}hijacking{\textquotedblright}, Hormaphis cornu aphids inject bicycle proteins into Hamamelis virginiana (Witch Hazel), contributing to the development of novel organs called galls. Bicycle proteins share no amino acid sequence similarity with proteins of known function. Here, we report the crystal structures of two divergent bicycle proteins. Both proteins contain saposin-like folds: one with multiple disulfide bonds exhibits a helix swap; the other has no disulfide bonds and possesses two tandem domains. To explore the structural evolution of bicycle proteins, we predicted bicycle protein structures with Alphafold2 (AF2). While AF2 did not recover the two experimental structures using existing databases, it succeeded after we provided multiple sequence alignments (MSAs) containing protein sequences encoded in new genome sequences from closely related aphid species. Using this customized approach at scale, we generated 2400 high-confidence predictions for bicycle proteins from seven aphid species. This dataset revealed that bicycle proteins without cysteines are outliers in fold space and appear to have evolved from ancestral proteins with disulfide-bonded saposin-like folds. While all bicycle proteins contain predicted saposin-like folds, they display a vast diversity of structural and physicochemical properties. While this diversity thwarts prediction of conserved functions encoded in structure, it suggests that bicycle proteins have evolved to target diverse plant processes and/or to evade plant immune surveillance.Significance statement Parasites introduce specialized {\textquotedblleft}effector{\textquotedblright} proteins into hosts, both to suppress host immunity and to release nutrients. The molecular functions and structures of most effector proteins are unknown. Effector proteins often evolve rapidly and share no similarity with proteins of known function. Here, we demonstrate that machine learning algorithms can accurately predict the structures of aphid {\textquotedblleft}bicycle{\textquotedblright} effector proteins when supplemented with data from closely related species. We exploit this finding to generate predictions of 2400 bicycle protein structures. These proteins exploit a common motif, yet exhibit diverse structures that form distinct structural clusters. Despite the clustering of these proteins in structure space, they occupy a nearly uniformly physicochemical space, suggesting that they encode a large diversity of molecular functions.

}, doi = {10.64898/2026.03.27.712717}, url = {https://www.biorxiv.org/content/early/2026/03/28/2026.03.27.712717}, author = {Bhinderwala, Fatema and Korgaonkar, Aishwarya and Gopalakrishna, Kota and Mathers, Thomas C. and Shigenobu, Shuji and Bazan, J. Fernando and Hogenhout, Saskia A. and Calero, Guillermo and Gronenborn, Angela M. and Stern, David L.} } @article {69515, title = {Recent experience and internal state shape local search strategies in flies}, journal = {Curr Biol}, year = {2026}, month = {2026 Mar 18}, abstract = {

After finding food, a foraging animal must decide whether to continue feeding or to explore the environment for potentially better options. One strategy to negotiate this tradeoff is to perform local searches around the food while repeatedly returning to feed. We studied this behavior in flies and used genetic tools to uncover the underlying behavioral strategies. Over time, flies gradually expand their search, shifting from primarily exploiting food sources to exploring the environment, a change likely driven by increased satiety. We found that flies{\textquoteright} search patterns preserve these dynamics even as the overall range of the search is modulated by starvation. In contrast, search induced by optogenetic activation of sugar-sensing neurons does not show these dynamics. We asked what navigational strategies underlie local search. Using a generative model, we found that a change in locomotor pattern after food consumption could account for repeated returns to the food, but not the relatively direct return trajectories that flies make even from far away. Such trajectories likely rely on alternative strategies, such as path integration or sensory taxis. We tested this by individually silencing their likely neural components, the compass system, olfaction, and hygrosensation. The only substantial effect was from perturbing hygrosensation, which reduced the number of long exploratory trips with subsequent return to the food. Our study illustrates that local search comprises multiple behavioral features that evolve over time based on both internal and external factors, providing a path toward uncovering the underlying neural mechanisms.

}, doi = {10.1016/j.cub.2026.02.037}, url = {https://https://doi.org/10.1016/j.cub.2026.02.037/content/early/2024/06/28/2024.06.26.600764}, author = {Goldschmidt, Dennis and Guo, Yipei and Chitnis, Shivam S and Christoforou, Christina and Turner-Evans, Dan and Ribeiro, Carlos and Hermundstad, Ann M and Jayaraman, Vivek and Haberkern, Hannah} } @article {70339, title = {Reconstituting mouse embryogenesis Ex utero from Gastrulation to fetal development reveals maternally independent metabolic programs}, journal = {bioRxiv}, year = {2026}, month = {2026 Mar 17}, abstract = {

Mammalian development takes place inside the maternal uterus, creating technological constraints that make difficult the study of embryogenesis in live developing embryos. A central challenge for understanding the role of metabolism in mammalian development is discriminating placental and uterine-regulated signals from embryo-intrinsic processes independent of maternal influence, a process that until now has remained inseparable during gastrulation and organogenesis1{\textendash}3. Ex utero culture systems allowing continuous growth of embryos during pre-gastrulation to organogenesis4,5 offer a promising solution to this challenge. Here, we present optimized ex utero culture platforms that support faithful development of mouse embryos from gastrulation (embryonic day 6.5/7.5) through the fetal period (embryonic day \~12.5) and harnessed these platforms for dissecting metabolic transitions in vivo during embryogenesis independently of uterus and placenta. We characterized the metabolome of in utero and ex utero whole embryos, fetal organs and culture medium between embryonic days E6.5 and E12.5 by liquid chromatography mass-spectrometry (LC-MS) metabolomics, isotope tracing, and single cell transcriptomics. These datasets present a comprehensive overview of the dynamic embryonic metabolism during gastrulation and organogenesis in utero and ex utero. This analysis revealed that the midgestational metabolic switch occurring at E10.5-E11.5 is faithfully recapitulated ex utero, indicating that this transition is intrinsically programmed in embryonic tissues and does not require direct maternal or placental cues. Notably, oxygen availability modulated the extent of this transition, but elevated oxygen was insufficient to induce it prematurely, demonstrating that the switch is developmentally timed and only partially environmental-responsive. We further harnessed the ex utero platform for identifying and perturbing a mitochondrial redox shift at E7.5-E8.5 that is critical for developmental progress after gastrulation. These findings uncover the remarkable metabolic plasticity of the mammalian embryo, demonstrating its capacity to sustain growth independently of maternal inputs from the establishment of the body plan through the onset of the fetal period. Moreover, they highlight the use of long-term ex utero culture as a unique framework for dissecting the mechanisms that shape embryogenesis under physiological and experimentally perturbed conditions, while functionally uncoupling embryonic programs from maternal and placental influences.

}, doi = {10.64898/2026.03.17.710314}, url = {https://www.biorxiv.org/content/early/2026/03/18/2026.03.17.710314}, author = {Lokshtanov, Dmitry and Gao, Shihong Max and Xu, Weizhi and Kosman, Avraham and Roncato, Francesco and De La Cruz, Nancy and Khan, Nawal A. and Woods, Andrea and Campbell, Ian and Woehler, Andrew and Christoforou, Christina and Ding, Lang and Hu, Amy and Copeland, Monique and Wang, Lihua and Yang, Xiushuai and Raley, Castle and Delventhal, Kym M. and Herrera, Antonio and Valente, Alessandro and Wright, Sylvia and Gomez-Cesar, Elidet and Shlomo, Raanan and Golenchenko, Sergey and Oldak, Bernardo and Yilmaz, Alperen and Gurhan-Sebinc, Gulben and Comar, Mehmet-Yunus and Viukov, Sergey and Novershtern, Noa and Zhang, Hua and Duong, Thao and Li, Lingjun and Khatib, Nizar and Kakun, Reli Rachel and Espinosa-Medina, Isabel and Florian-Rodriguez, Maria E. and LaManno, Gioele and Tillberg, Paul W. and Wang, Meng C. and Maza, Itay and Srivatsan, Sanjay and Solmonson, Ashley and Hanna, Jacob H. and Aguilera-Castrejon, Alejandro} } @article {70257, title = {Redefining colocalization analysis with a novel phasor mixing coefficient}, journal = {Journal of Cell Science}, volume = {139}, year = {2026}, month = {2026 Jan 19}, pages = {jcs264388}, abstract = {

The first step to probing any potential interaction between two biomolecules is to determine their spatial association. In other words, if two biomolecules localize similarly within a cell, then it is plausible they could interact. Traditionally, this is quantified through various colocalization metrics. These measures infer this association by estimating the degree to which fluorescent signals from each biomolecule overlap or correlate. However, these metrics are, at best, proxies, and they depend strongly on various experimental choices. Here, we define a new strategy that leverages multispectral imaging and phasor analysis, termed the phasor mixing coefficient (PMC). The PMC measures the precise mixing of fluorescent signals in each pixel. We demonstrate how the PMC captures complex biological subtlety by offering two distinct values, a global measure of overall color mixing and the homogeneity thereof. We additionally show that the PMC exhibits less sensitivity to signal-to-noise ratio, intensity threshold and background signal compared to canonical methods. Moreover, this method provides a means to visualize color mixing at each pixel. We show that the PMC offers users a nuanced and robust metric to quantify biological association.

}, issn = {0021-9533}, doi = {10.1242/jcs.264388}, url = {https://doi.org/10.1242/jcs.264388}, author = {Puls, Owen F. and Aaron, Jesse S. and Quarles, Ellen K. and Khuon, Satya and Eisenman, Leanna R. and Kamaid, Andres and Malacrida, Leonel and Chew, Teng-Leong} } @article {70275, title = {Rethinking insecticide toxicology for the 21st century.}, journal = {Insect Biochem Mol Biol}, year = {2026}, month = {2026 Jan 29}, pages = {104502}, abstract = {

Insecticides remain indispensable for crop protection and food security, yet their widespread use may contribute to the global decline of beneficial insect populations. Efforts to mitigate these impacts are hampered by a fragmented understanding of how insects metabolise insecticides and how sublethal exposures affect physiology, behaviour, and fitness. Here, we synthesise current understanding of metabolic detoxification and highlight critical gaps: the tissue- and time-dependent dynamics of insecticide entry and processing, the triggers and architecture of xenobiotic transcriptional responses, the role of rapid non-transcriptional regulation, and the population-level consequences of sublethal effects. We also outline emerging experimental strategies for addressing these questions and propose a next-generation research pipeline centred on multi-endpoint phenomics across life stages and sentinel species, integrated with AI-driven predictive toxicology, as a framework for identifying safer chemicals. We propose an integrated framework unifying molecular, physiological, and ecological responses to sublethal exposure to guide the design of insecticides that maintain effective pest control while safeguarding insect biodiversity and the ecosystems it underpins.

}, issn = {1879-0240}, doi = {10.1016/j.ibmb.2026.104502}, url = {https://doi.org/10.1016/j.ibmb.2026.104502}, author = {G{\'a}ndara, Lautaro and Martelli, Felipe and Ravenscroft, Thomas and Crocker, Justin and Batterham, Philip} } @article {70251, title = {SCREWx: A Screwless, Chronic, Recoverable, and Lightweight Neuropixels fixture for freely-moving rodents}, journal = {bioRxiv}, year = {2026}, month = {2026 Jan 06}, abstract = {

High-density Neuropixels probes enable the study of large neural populations with single-cell and sub-millisecond resolution. While single-probe and acute head-fixed experiments have yielded critical scientific insights, understanding the neural mechanisms underlying many complex behaviors requires simultaneous multi-region recordings in freely moving, chronically implanted animals. Various probe fixtures have been developed to enable high-density recording, but existing designs impose critical limitations: their substantial weight restricts the maximum probe count that smaller animals can support, their bulky dimensions constrain the proximity of targeted brain regions, and their complex assembly risks damaging the probe during insertion and recovery. In this paper, we present a lightweight, fully 3D-printable, compact, and screwless fixture for chronic Neuropixels implants in freely moving rodents that features simple mechanisms for stable implantation and safe extraction. Our fixture design enables stable, high-yield single-unit recordings for months-long experiments, along with an 83\% successful probe extraction rate. This fixture design provides a robust and accessible solution for long-term, multi-probe chronic Neuropixels recordings, increasing experimental throughput and enabling more complex experimental designs to investigate brain-wide neural dynamics.

}, doi = {10.64898/2026.01.06.697790}, url = {https://www.biorxiv.org/content/early/2026/01/06/2026.01.06.697790}, author = {Cheng, Alexandra and DeWeese, Tate and Zhou, Yueqing and Sueoka, Yotaro and Koukuntla, Sai and Green, Merrill and Cullen, Kathleen and Knierim, James and Graves, Austin and Harris, Timothy} } @article {70179, title = {Secretome translation shaped by lysosomes and lunapark-marked ER junctions.}, journal = {Nature}, year = {2026}, month = {2026 Jan 01}, pages = {227{\textendash}236 }, abstract = {

The endoplasmic reticulum (ER) is a highly interconnected membrane network that serves as a central site for protein synthesis and maturation. A crucial subset of ER-associated transcripts, termed secretome mRNAs, encode secretory, lumenal and integral membrane proteins, representing nearly one-third of human protein-coding genes. Unlike cytosolic mRNAs, secretome mRNAs undergo co-translational translocation, and thus require precise coordination between translation and protein insertion. Disruption of this process, such as through altered elongation rates, activates stress response pathways that impede cellular growth, raising the question of whether secretome translation is spatially organized to ensure fidelity. Here, using live-cell single-molecule imaging, we demonstrate that secretome mRNA translation is preferentially localized to ER junctions that are enriched with the structural protein lunapark and in close proximity to lysosomes. Lunapark depletion reduced ribosome density and translation efficiency of secretome mRNAs near lysosomes, an effect that was dependent on eIF2-mediated initiation and was reversed by the integrated stress response inhibitor ISRIB. Lysosome-associated translation was further modulated by nutrient status: amino acid deprivation enhanced lysosome-proximal\ translation, whereas lysosomal pH neutralization suppressed it. These findings identify a mechanism by which ER junctional proteins and lysosomal activity cooperatively pattern secretome mRNA translation, linking ER architecture and nutrient sensing to the production of secretory and membrane proteins.

}, issn = {1476-4687}, doi = {10.1038/s41586-025-09718-0}, url = {https://doi.org/10.1038/s41586-025-09718-0}, author = {Choi, Heejun and Liao, Ya-Cheng and Yoon, Young J and Grimm, Jonathan and Wang, Nan and Lavis, Luke D and Singer, Robert H and Lippincott-Schwartz, Jennifer} } @article {70332, title = {Seeing lipids where they live}, journal = {Nat Cell Biol}, year = {2026}, month = {2026 Mar 20}, abstract = {

A study establishes a correlative light and electron microscopy workflow that reveals how individual lipid species distribute across nanoscale membrane domains, uncovering sphingomyelin sorting within the early endosome.

}, issn = {1476-4679}, doi = {10.1038/s41556-026-01919-7}, url = {https://doi.org/10.1038/s41556-026-01919-7}, author = {Weigel, Aubrey} } @article {70358, title = {Sex-specific plasticity mechanisms mediating fear extinction}, journal = {bioRxiv}, year = {2026}, month = {2026 Apr 10}, abstract = {

There is strong evidence that synaptic plasticity is a critical cellular mechanism underlying learning and memory. Although the forms of synaptic plasticity used by different circuits and cell types vary, a widespread presumption is that the male and female brain has evolved to use the same form of plasticity within the same circuits during performance on the same task. Here, we used complimentary approaches to determine how activity in the mouse frontal cortex supports the extinction of associative memories in a context-dependent manner. While in vivo recordings show that both male and female mice have similar cue-relevant activity patterns and ensemble dynamics in excitatory neurons from the infralimbic cortex (IL) during learning, activity in amygdala-projecting IL neurons was indispensable for extinction memories only in male mice. Likewise, male but not female mice showed evidence for the recruitment of IL by structural remodeling and clustering of dendritic spines on these neurons, and extinction memory impairments were evident only in male mice after projection-specific IL deletion of the glutamate receptor subunit GRIN2B. This work provides strong evidence that synaptic plasticity mechanisms employed during learning and critical for memory retrieval differ between males and females, which undercuts the utility of one-size-fits all therapeutic approaches for mental health conditions in which memory is disrupted.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.64898/2026.04.10.717763}, url = {https://www.biorxiv.org/content/early/2026/04/10/2026.04.10.717763}, author = {Graham, Kourtney and Pomeroy-Tuck, Justice and O{\textquoteright}Brien, Grace K. and Kent-Webber, Lacey and Drillen, Anna L. and Coddington, Luke and Zhao, Xinyu and Bloss, Erik B.} } @article {70277, title = {Stem cell control and cancer initiation by an autocrine, injury-activated Igf complex}, journal = {bioRxiv}, year = {2026}, month = {2026 Feb 04}, abstract = {

Stem cells rapidly proliferate after injury to repair damaged tissue, and chronic injury predisposes to cancer. However, injury-activated mitogens, the mechanisms that keep them inactive until injury, and their role in cancer are not understood. Here we identify Igf2 as the injury-activated mitogen for neuroendocrine stem cells, a facultative airway stem cell and origin of small cell lung cancer. Igf2 is constitutively produced by the stem cells but sequestered in inactive form by co-expressed Igf binding proteins. Injury releases Igf2 and induces proliferation by activating its receptors and repressing Rb tumor suppressor, which normally enforces stem cell quiescence. Persistent pathway activation initiates oncogenesis. Thus, in addition to its classical hormonal roles in physiology, growth, and aging, Igf operates locally with Igf binding proteins and Rb to control injury-induced stem cell activation and cancer. This pathway may also control related stem cells and cancers of the body and brain.

}, doi = {10.64898/2026.02.02.703150}, url = {https://www.biorxiv.org/content/early/2026/02/04/2026.02.02.703150}, author = {Zhang, Yue and Ouadah, Youcef and Liu, Yin and Kumar, Maya and Morck, Makenna and Krasnow, Mark A} } @article {70310, title = {Structural Basis for C8 methylation of 23S ribosomal RNA by Cfr}, journal = {bioRxiv}, year = {2026}, month = {2026 Mar 02}, abstract = {

Cfr methylates C8\ of adenosine 2503 (A2503) in 23S\ ribosomal RNA (rRNA) and will also methylate C2\ of A2503 after methylating C8. C8methylation confers resistance to more than five classes of clinically used antibiotics, highlighting it as a worrisome mechanism of antibiotic resistance. Here, we report the structure of Cfr, determined by cryogenic electron microscopy (Cryo-EM). Despite its small size (\~{}36 kDa), we exploit a transient protein{\textendash}RNA crosslink that forms during catalysis, which requires Cys105 to resolve. Using a Cfr Cys105Ala variant and an 87-nucleotide strand of rRNA, we isolate the crosslinked species and determine its structure to 3.0 {\r A} resolution. Notably, the 87-mer rRNA adopts an L-shaped conformation characteristic of tRNAs, rather than the conformation it assumes in the ribosome.

}, doi = {10.64898/2026.02.27.707579}, url = {https://www.biorxiv.org/content/early/2026/03/02/2026.02.27.707579}, author = {Esakova, Olga A. and Jung, James and Lee, Hyunwook and Cho, Sung Hyun and Alumasa, John and Schwalm, Erica L. and Grove, Tyler L. and Bauerle, Matthew R. and Hafenstein, Susan L. and Yu, Zhiheng and Booker, Squire J.} } @article {70276, title = {Synchronization of behavioral and cardiac dynamics in larval zebrafish.}, journal = {Cell Rep}, volume = {45}, year = {2026}, month = {2026 Feb 03}, pages = {116947}, abstract = {

Animals reprioritize behavioral goals in response to internal physiological states. Using larval zebrafish, we investigated whether engagement with a visuomotor task, the optomotor response (OMR), is coupled to cardiac dynamics. We discovered that threats lead to tachycardia that is synchronized with behavioral suppression. The change in heart rate is represented in the activity of specific neuronal populations. Severing the input to the sympathetic ganglia or ablating the vagus nerve revealed that the threat-related changes to behavioral state do not require interoceptive pathways. Direct tachycardic optopacing of the heart similarly suppressed the OMR response, but by reducing cardiac filling during diastole, thereby impacting oxygen delivery to the CNS. Optopacing also changed the activity of specific brain regions but in neurons distinct from those associated with threat-induced tachycardia. These cardiac function-associated central changes may have relevance to autonomic imbalances in anxiety, stress, and orthostatic disorders.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2026.116947}, url = {https://doi.org/10.1016/j.celrep.2026.116947}, author = {Herrera, Kristian J and Zarghani-Shiraz, Arman and Ahrens, Misha B and Engert, Florian and Fishman, Mark C} } @article {70245, title = {A System for live sorting of neuronal spiking activity from large-scale recordings}, journal = {bioRxiv}, year = {2026}, month = {2026 Jan 02}, abstract = {

Online monitoring and quantification of neural signals has tremendous value both for neurofeedback experiments and for brain-computer interfaces. Unfortunately, established methods of online monitoring primarily involve the use of thresholded neural activity rather than sorted single-neuron spikes. The recent introduction of large-scale, high-density electrophysiology has enabled the recording of activity from hundreds of neurons simultaneously in both model organisms and human participants. This development highlights the need for a robust and easily implementable system for sorting spikes during data collection for {\textquoteleft}live{\textquoteright} analyses of neuronal signals. Here, we describe a system for live sorting of neuronal activity (LSS) based on the widely used Kilosort platform. The LSS workflow utilizes an initial period of recorded neural data to identify waveform templates using Kilosort 4. LSS then interfaces with the SpikeGLX API to retrieve small batches (e.g. 50 ms) of data and for processing online. We measured the similarity of single-neuron activity sorted live by LSS to that sorted offline in neurophysiological recordings from macaque visual cortex using Neuropixels probes. We show that LSS closely replicates the post-stimulus time histograms and visual response tuning curves of single-neurons obtained using offline sorting. Furthermore, we show that decoding neural signals online with LSS consistently outperforms online decoding of thresholded activity, and that LSS can achieve the same performance as that obtained with offline sorting.

}, doi = {10.64898/2025.12.29.696938}, url = {https://www.biorxiv.org/content/early/2026/01/02/2025.12.29.696938}, author = {Muralidharan, Shreyas and Leng, Calvin and Orts, Lucas and Trepka, Ethan and Zhu, Shude and Panichello, Matthew and Jonikaitis, Donatas and Pennington, Jacob and Pachitariu, Marius and Moore, Tirin} } @article {70357, title = {Time-resolved cryo-EM reveals conformational trajectory of allosteric activation in isocitrate lyase}, journal = {bioRxiv}, year = {2026}, month = {2026 Apr 09}, abstract = {

Isocitrate lyase 2 (ICL2) from Mycobacterium tuberculosis undergoes dramatic conformational rearrangements upon binding to the allosteric effector acetyl-CoA. Time-resolved cryo-EM captured conformational states along the ICL2 activation trajectory, revealing how acetyl-CoA binding at the allosteric sites leads to asymmetric, half-of-site activity at the catalytic centres. These findings support a conformational selection model of allostery, whereby acetyl-CoA binding shifts the pre-existing equilibrium towards an active state of the enzyme.

}, doi = {10.64898/2026.04.08.716820}, url = {https://www.biorxiv.org/content/early/2026/04/09/2026.04.08.716820}, author = {Taka, Jamie and Jung, James and Guo, Shuning and Jiao, Wanting and Kwai, Brooke X. C. and de Carvalho, Luiz Pedro S and McNeil, Matthew and Huang, Evelyn Yu-Wen and Yu, Zhiheng and Leung, Ivanhoe K. H. and Bashiri, Ghader} } @article {70356, title = {Transformation-tolerant object recognition in tree shrews despite lacking a fovea}, journal = {bioRxiv}, year = {2026}, month = {2026 Apr 14}, abstract = {

Object recognition depends on the ability to extract stable representations across changes in how they are viewed, yet it remains unclear how this capacity depends on visual acuity and cortical hierarchy. We combined behavioral testing and computational modeling to determine whether tree shrews, close relatives of primates with lower spatial acuity, can perform transformation-tolerant object recognition. Front-end modeling incorporating species-specific optics and photoreceptor sampling showed that, when scaled for acuity, tree shrew retinal filtering preserves the similarity structure of natural image categories relevant for object recognition. Behaviorally, tree shrews reliably discriminated complex objects across variations in position, scale, and viewpoint, including when embedded within natural scenes, and generalized to novel exemplars. Their recognition behavior was best explained by visual features emphasizing differences in global shape and size between objects and by representations from intermediate and deep layers of hierarchical neural network models. These results demonstrate that visual processing supporting object-level generalization can arise within visual systems lacking high-acuity front-end optics and establish the tree shrew as a key model for understanding the computational and evolutionary origins of high-level vision.

}, doi = {10.64898/2026.04.10.717715}, url = {https://www.biorxiv.org/content/early/2026/04/14/2026.04.10.717715}, author = {Meyer, Emily E and Ong, Wei Song and Song, Chenjie and Cottaris, Nicolas P and Zhang, Ling-Qi and Collina, Jared and Brainard, David H and Arcaro, Michael J} } @article {70329, title = {Unstructured transcription factor interactions enable emergent specificity.}, journal = {Science}, year = {2026}, month = {2026 Mar 19}, pages = {eaeb6487}, abstract = {

How intrinsically disordered regions (IDRs) influence chromatin binding and nuclear organization of transcription factors (TFs) remains unclear. We employed proximity-assisted photoactivation (PAPA), a single-molecule protein-protein interaction sensor, to investigate how IDRs might influence TF interactions with each other and with chromatin in live cells. We found that the Sp1 DNA binding domain (DBD) interacted poorly with chromatin and did not colocalize with Sp1. Weak interaction of the isolated IDR with full-length Sp1 was enhanced by fusion to various unrelated DBDs. Live imaging of polytene chromosomes confirmed that an IDR could confer sharp locus specificity on an otherwise nonspecific DBD. These findings suggest that TF specificity emerges on chromatin when ensembles of diverse, unstructured interactions are scaffolded by transient DNA contacts.

}, issn = {1095-9203}, doi = {10.1126/science.aeb6487}, url = {https://doi.org/10.1126/science.aeb6487}, author = {Abidi, Abrar A and Cattoglio, Claudia and Tang, Natalie N and Fan, Vinson B and Dailey, Gina M and Hay, Amir D and Kunamaneni, Prasanthi and Milkie, Daniel E and Darzacq, Xavier and Betzig, Eric and Tjian, Robert and Graham, Thomas G W} } @article {70285, title = {Whole-brain co-mapping of gene expression and neuronal activity at cellular resolution in behaving zebrafish}, journal = {bioRxiv}, year = {2026}, month = {2026 Feb 10}, abstract = {

The brain{\textquoteright}s capabilities rely on both the molecular properties of individual cells and their interactions across brain-wide networks. However, relating gene expression to activity in individual neurons across the entire brain remains elusive. Here we developed an experimental-computational platform, WARP, for whole-brain imaging of neuronal activity during behavior, expansion-assisted spatial transcriptomics, and cellular-level registration of these two modalities. Through joint analysis of whole-brain neuronal activity during multiple behaviors, cellular gene expression, and anatomy, we identified functions of molecularly defined populations {\textemdash} including luminance coding in a cckb-pou4f2 midbrain population and task-structured activity in pvalb7-eomesa hippocampal-like neurons {\textemdash} and defined over 2,000 other function-gene-anatomy subpopulations. Analysis of this unprecedented multimodal dataset also revealed that most gene-matched neurons showed stronger activity correlations, highlighting a brain-wide role for gene expression in functional organization. WARP establishes a foundational platform and open-access dataset for cross-experiment discovery, high-throughput function-to-gene mapping, unification of cell biology and systems neuroscience, and scalable circuit modeling at the whole-brain scale.

}, doi = {10.64898/2026.02.07.704095}, url = {https://www.biorxiv.org/content/early/2026/02/10/2026.02.07.704095}, author = {Marquez Legorreta, Emmanuel and Fleishman, Greg M. and Hesselink, Luuk W. and Eddison, Mark and Smeets, Kasper and Stringer, Carsen and Keller, Philipp J. and Narayan, Sujatha and Chen, Alex B. and Mensh, Brett D. and Sternson, Scott M. and Englitz, Bernhard and Tillberg, Paul W. and Ahrens, Misha B.} } @article {69864, title = {Abstract 2420: Deep learning enables automated detection of circulating tumor cell-immune cell interactions with prognostic insights in cancer}, journal = {Cancer Research}, volume = {85}, year = {2025}, month = {2025 Apr 21}, pages = {2420-2420}, abstract = {

Circulating tumor cells (CTCs) are critical biomarkers for predicting therapy response and survival in breast cancer patients. Multicellular CTC clusters exhibit enhanced metastatic potential, yet their detection and characterization are constrained by low frequency in blood samples and reliance on labor-intensive manual analysis. Advancing these methods could significantly improve prognostic evaluation and therapeutic strategies.Leveraging FDA-approved CellSearch technology and single-cell sequencing, we analyzed 2, 853 blood specimens, longitudinally collected from 1358 patients with advanced cancer (breast, prostate, etc) and other diseases. Integrating machine learning and deep learning tools, we developed a novel CTCpose platform to automate detection and analysis of CTCs, immune cells, and their interactions. Using artificial intelligence (AI)-driven image analysis, we extracted over 270 cellular and nuclear features including intensity, morphometry, fourier shape, gradient/edge, and haralick of cytokeratin, CD45, and DAPI expression patterns, enabling precise characterization of CTCs, white blood cells (WBCs), CTC clusters, and their interactions with immune cells (WBCs).The CTCpose platform enabled automated identification of CTCs, WBCs, homotypic CTC clusters, heterogenous CTC-WBC clusters, and immune cell clusters, providing comprehensive insights into cell morphology, biomarker expression, and spatial organization. These features correlated with patient survival, disease progression, and treatment response. Our findings highlight the clinical significance of CTC-immune cell interactions and dynamic alterations of CTCs (singles and clusters) and underscore their potential in stratifying patients into distinct risk categories.This study demonstrates the transformative potential of deep learning in overcoming limitations of traditional CTC detection methods and integrating imaging data with large cohorts of patient data. By automating and enhancing the analysis of CTC-immune cell interactions, we present a robust framework for developing predictive models with direct clinical relevance. This work opens avenues for personalized treatment strategies, underscoring the impact of AI in advancing precision oncology.Yuanfei Sun, Joshua R. Squires, Andrew Hoffmann, Youbin Zhang, Allegra Minor, Anmol Singh, David Scholten, Chengsheng Mao, Yuan Luo, Deyu Fang, William J. Gradishar, Massimo Cristofanilli, Carsen Stringer, Huiping Liu. Deep learning enables automated detection of circulating tumor cell-immune cell interactions with prognostic insights in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2420.

}, issn = {0008-5472}, doi = {10.1158/1538-7445.AM2025-2420}, url = {https://doi.org/10.1158/1538-7445.AM2025-2420}, author = {Sun, Yuanfei and Squires, Joshua R. and Hoffmann, Andrew and Zhang, Youbin and Minor, Allegra and Singh, Anmol and Scholten, David and Mao, Chengsheng and Luo, Yuan and Fang, Deyu and Gradishar, William J. and Cristofanilli, Massimo and Stringer, Carsen and Liu, Huiping} } @article {70023, title = {Abstract B049: Deep learning enables identification of cell types and clusters (iCTC) in immune tumor ecosystems for prognostic assessment in cancer}, journal = {Clinical Cancer Research}, volume = {31}, year = {2025}, month = {2025 Jul 10}, pages = {B049-B049}, abstract = {

Spatial multiomic profiling has been transforming the understanding of local tumor ecosystems. Yet, the spatial analyses of tumor-immune interactions at systemic levels, such as in liquid biopsies, are challenging. Within the last 10 years, we have longitudinally collected nearly 3,000 patient blood samples for multiplexing imaging of circulating tumor cells (CTCs) and their interactions with white blood cells (WBCs). Multicellular CTC clusters exhibit enhanced metastatic potential. The detection of CTCs and characterization of tumor immune ecosystems are constrained by (1) low frequency of CTCs in blood samples; (2) specific lineages of immune cells are not recognized by limited channels of current imaging methods, (3) reliance on labor-intensive manual analysis slows down the discovery of biomarkers for predicting therapy response and survival in cancer patients. We hypothesize that an AI-powered platform will accelerate the lineage and spatial characterization of tumor immune ecosystems for prognostic evaluations.

}, issn = {1078-0432}, doi = {10.1158/1557-3265.AIMACHINE-B049}, url = {https://doi.org/10.1158/1557-3265.AIMACHINE-B049}, author = {Squires, Joshua R. and Sun, Yuanfei and Hoffmann, Andrew D. and Zhang, Youbin and Minor, Allegra C. and Singh, Anmol and Scholten, David and Ding, Hannah and Mao, Chengsheng and Platanias, Leonidas C. and Luo, Yuan and Fang, Deyu and Gradishar, William J. and Cristofanilli, Massimo and Stringer, Carsen and Liu, Huiping} } @article {69948, title = {Accelerating neuron reconstruction with PATHFINDER}, journal = {bioRxiv}, year = {2025}, month = {2025 May 21}, abstract = {

Comprehensive mapping of neural connections is essential for understanding brain function. Existing automated methods for connectome reconstruction from high-resolution images of brain tissue introduce errors that require extensive and time-consuming manual correction, a critical bottleneck in the field. To address this, we developed PATHFINDER, an AI system that segments volumetric image data, identifies potential ways to assemble neuron fragments, and evaluates the plausibility of resulting shapes to reconstruct complete neurons. Using a dataset of all axons in an IBEAM-mSEM volume of mouse cortex, we show that PATHFINDER reduces the error rate in axon reconstruction by an order of magnitude over previous state of the art, leading to an improvement in proofreading throughput of up to 84{\texttimes} relative to prior estimates in the context of a whole mouse brain. By drastically reducing the manual effort required for analysis, this advance unlocks the potential for both large-scale connectome mapping and routine investigation of smaller volumes.

}, doi = {10.1101/2025.05.16.654254}, url = {https://www.biorxiv.org/content/early/2025/05/21/2025.05.16.654254}, author = {Januszewski, Micha{\l} and Templier, Thomas and Hayworth, Kenneth Jeffrey and Peale, David and Hess, Harald} } @article {69560, title = {Activity-dependent synapse elimination requires caspase-3 activation}, journal = {eLife}, year = {2025}, month = {2025 Jul 10}, abstract = {

During brain development, synapses are initially formed in excess and are later eliminated in an activity-dependent manner, with weak synapses being preferentially removed. Previous studies identified glia as mediators of synapse removal, but it is unclear how glia specifically target weak synapses. Here we show that, in the developing mouse visual pathway, inhibiting synaptic transmission induces postsynaptic activation of caspase-3. Caspase-3 is essential for synapse elimination driven by both spontaneous and experience-dependent neural activity. Synapse weakening-induced caspase-3 activation determines the specificity of synapse elimination mediated by microglia but not astrocytes. Furthermore, in a mouse model of Alzheimer{\textquoteright}s disease, caspase-3 deficiency protects against synapse loss induced by amyloid-β deposition. Our results reveal caspase-3 activation as a key step in activity-dependent synapse elimination during development and synapse loss in neurodegeneration.

bioRxiv preprint:\ https://doi.org/10.1101/2024.08.02.606316

}, doi = {10.7554/eLife.101779.2}, url = {https://doi.org/10.7554/eLife.101779.2}, author = {Yu, Zhou and Gutu, Andrian and Kim, Namsoo and O{\textquoteright}Shea, Erin K.} } @article {70014, title = {Aggression across sexes from a contextual- and circuit-based perspective.}, journal = {Curr Opin Neurobiol}, volume = {93}, year = {2025}, month = {2025 Jun 26}, pages = {103071}, abstract = {

Often referred to as a {\textquoteright}fight,{\textquoteright} survival involves intense competition over resources. Threat displays and high-intensity attacks are just a few of the aggressive actions exhibited during these contests. Certain motor programs are species-specific, like the vibration of a rattlesnake tail. However, conserved behavioral features are found across species, which appear to be mirrored within the brain. Further parallels have been found across sexes between aggression-promoting contexts and the underlying neuronal circuits. Unraveling the complex web of conserved and variable circuit mechanisms has been considerably advanced by the generation of brain-wiring diagrams in adult female and male Drosophila melanogaster. Here, I will summarize current research, primarily in Drosophila, on how contexts, sensory cues, and internal states regulate aggression across sexes.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2025.103071}, url = {https://doi.org/10.1016/j.conb.2025.103071}, author = {Schretter, Catherine E} } @article {70129, title = {Alternating angle milling suppresses streaking artifacts in FIB-SEM imaging}, journal = {bioRxiv}, year = {2025}, month = {2025 Sep 26}, abstract = {

Focused ion beam scanning electron microscopy (FIB-SEM) (1{\textendash}3) has been used in life sciences to produce large volumetric datasets with high resolution information on ultrastructure of biological organisms. 3D image acquisition is accomplished by serial removal of thin layers of material using focused ion beam (FIB) milling followed by scanning electron microscopy (SEM) imaging.One of the challenges in the standard FIB-SEM imaging protocol is that FIB milling results in characteristic artifacts, known as {\textquotedblleft}streaks{\textquotedblright} or {\textquotedblleft}curtains{\textquotedblright}. These streaks are caused by non-uniform material removal forming long straight trenches parallel to the FIB milling direction. These artifacts get worse along the milling direction and ultimately limit size of the SEM field of view.Various methods have been proposed to mitigate the streaks in acquired images. While these techniques often provide noticeable visual improvement, the underlying problem remains. The structural information in the {\textquotedblleft}streaked{\textquotedblright} areas is lost due to non-uniform material removal during milling and cannot be fully recovered.We propose a simple modification allowing for a significant reduction of milling non-uniformities of streaks. We demonstrate the effectiveness of this approach on various samples.

}, doi = {10.1101/2025.09.25.678572}, url = {https://www.biorxiv.org/content/early/2025/09/26/2025.09.25.678572}, author = {Shtengel, Gleb and Qiu, Wei and Aaron, Jesse and Crowe, Arthur S. and Polilov, Alexey A. and Karkali, Katerina and Bleck, Christopher K.E. and Hess, Harald H.} } @article {69974, title = {Analysis of deep learning for automated recognition of immune cells interacting with CTCs for prognostic assessment in cancer.}, journal = {Journal of Clinical Oncology}, volume = {43}, year = {2025}, month = {2025 May 28}, pages = {e13028-e13028}, abstract = {

e13028Background: Liquid biopsy has emerged as a powerful, minimally invasive tool for predicting treatment response and survival in breast and other advanced cancers. However, the detection and characterization of circulating tumor cells (CTCs) {\textemdash} a key factor in metastatic progression{\textemdash}remain challenging due to their low frequency and reliance on manual, time-intensive validation using only a couple of established methods for immunofluorescence staining, such as CellSearch. Harnessing deep learning for automated CTC detection and characterization of the blood cells interacting with CTCs holds the potential to advance prognostic evaluations and guide more effective therapies significantly. Methods: Leveraging FDA-approved CellSearch technology and sequencing approaches, we analyzed 2,853 blood specimens, longitudinally collected from 1358 patients with advanced cancer (breast, prostate, etc) and additional diseases. We built a novel deep learning platform, CTCpose, which integrates machine learning and AI-driven image analysis to automate the detection and categorization of CTCs, white blood cells (WBCs), and their clustering interactions. We extracted cellular and nuclear features to enable precise evaluation of individual CTCs, WBCs, homotypic CTC clusters, heterotypic CTC{\textendash}WBC clusters, and immune cell aggregates. Results: By employing the CTCpose platform, we achieved fully automated identification of CTCs and immune cells, unraveling the spatial organization and functional characteristics of both homotypic and heterotypic clusters. These highly granular assessments revealed clinically significant correlations with patient survival, disease progression, and therapeutic outcomes. Our data underscore the critical role of CTC{\textendash}immune cell interactions and the dynamic shifts in CTC phenotypes{\textemdash}both as single cells and clusters{\textemdash}in stratifying patients by risk and informing treatment strategies. Conclusions: This work illustrates the transformative power of deep learning in the analysis of liquid biopsy samples. By overcoming the limitations of traditional CTC detection, we have established a robust framework that integrates imaging data with large-scale patient cohorts to deliver predictive models of high clinical relevance. The CTCpose platform not only refines our understanding of CTC{\textendash}immune cell biology but also paves the way for personalized oncology approaches, highlighting the impactful convergence of artificial intelligence and precision medicine.

}, doi = {10.1200/JCO.2025.43.16_suppl.e13028}, url = {https://ascopubs.org/doi/abs/10.1200/JCO.2025.43.16_suppl.e13028}, author = {Liu, Huiping and Squires, Joshua and Sun, Yuanfei and Hoffmann, Andrew Daniel and Zhang, Youbin and Platanias, Leonidas C. and Gradishar, William John and Cristofanilli, Massimo and Stringer, Carsen} } @article {70052, title = {Aurora 2.0: A fluorogenic dye library for expanding the capability of protein-adaptive Differential Scanning Fluorimetry (paDSF).}, journal = {SLAS Discov}, year = {2025}, month = {2025 Aug 8}, pages = {100259}, abstract = {

Differential Scanning Fluorimetry (DSF) is a biophysical assay that is used to estimate protein stability in vitro. In a DSF experiment, the increased fluorescence of a solvatochromatic dye, such as Sypro Orange, is used to detect the unfolding of a protein during heating. However, Sypro Orange is only compatible with a minority of proteins (\< 30\%), limiting the scope of this method. We recently reported that protein-adaptive DSF (paDSF) can partially solve this problem, wherein the protein is initially pre-screened against \~{}300 chemically diverse dyes, termed the Aurora collection. While this approach significantly improves the number of targets amenable to DSF, it still fails to produce protein-dye pairs for some proteins. Here, we report the expansion of the dye collection to Aurora 2.0, which includes a total of 517 structurally diverse molecules and multiple new chemotypes. To assess performance, these dyes were screened against a panel of \~{}100 proteins, which were selected, in part, to represent the most challenging targets (e.g. small size). From this effort, Aurora 2.0 achieved an impressive success rate of 94\%, including producing dyes for some targets that were not matched in the original collection. These findings support the idea that larger, more chemically diverse libraries improve the likelihood of detecting melting transitions across a wider range of proteins. We propose that Aurora 2.0 makes paDSF an increasingly powerful method for studying protein stability, ligand binding and other biophysical properties in high throughput.

}, issn = {2472-5560}, doi = {10.1016/j.slasd.2025.100259}, url = {https://doi.org/10.1016/j.slasd.2025.100259}, author = {Charvat, Annemarie F and Mason-Chalmers, Kayleigh and Grabinska-Rogala, Aneta and Shivakumar, Shloka and Gale-Day, Zachary and Wu, Taiasean and Millbern, Zoe and Grimm, Jonathan and Carroll, Emma C and Nilsson, Peter and Lavis, Luke and Vinueza, Nelson R and Gestwicki, Jason E} } @article {69848, title = {A Bayesian model to count the number of two-state emitters in a diffraction limited spot.}, journal = {Nano Lett}, year = {2025}, month = {2025 Apr 04}, abstract = {

We address the problem of inferring the number of independently blinking fluorescent light emitters, when only their combined intensity contributions can be observed. This problem occurs regularly in light microscopy of objects smaller than the diffraction limit, where one wishes to count the number of fluorescently labeled subunits. Our proposed solution directly models the photophysics of the system, as well as the blinking kinetics of the fluorescent emitters as a fully differentiable hidden Markov model, estimating a posterior distribution of the total number of emitters. We show that our model is more accurate and increases the range of countable subunits by a factor of 2 compared to current state-of-the-art methods. Furthermore, we demonstrate that our model can be used to investigate the effect of blinking kinetics on counting ability and therefore can inform optimal experimental conditions.

}, issn = {1530-6992}, doi = {10.1021/acs.nanolett.4c06304}, url = {https://doi.org/10.1021/acs.nanolett.4c06304}, author = {Hillsley, Alexander and Stein, Johannes and Tillberg, Paul W and Stern, David L and Funke, Jan} } @article {69992, title = {Bioimaging Brasil: democratizing in vivo optical microscopy to drive scientific progress across a vast nation.}, journal = {Nat Methods}, year = {2025}, month = {2025 Jun 16}, issn = {1548-7105}, doi = {10.1038/s41592-025-02686-3}, url = {https://doi.org/10.1038/s41592-025-02686-3}, author = {Antunes, Ma{\'\i}sa Mota and Oliveira, Andr{\'e} Gustavo and de Paula, Cristina Maria and Chew, Teng-Leong and Paula-Neto, Heitor A and Menezes, Gustavo B} } @article {69744, title = {Bio-inspired 3D-printed phantom: Encoding cellular heterogeneity for characterization of quantitative phase imaging}, journal = {Measurement}, volume = {247}, year = {2025}, month = {2025 Apr 15}, pages = {116765}, abstract = {

Quantitative phase imaging (QPI) has proven to be a valuable tool for advanced biological and pharmacological research, providing phase information for the study of cell features and physiology in label-free conditions. The next step for QPI to become a gold standard is the quantitative assessment of the phase gradients over the different microscopy setups. Given the large variety of QPI systems, a systematic comparison is a challenging task, and requires a calibration target representative of the living samples. In this paper, we introduce a tailor-made 3D-printed phantom derived from phase images of eukaryotic cells. It comprises typical morphologies and optical thicknesses found in biological cultures and is characterized with digital holographic microscopy (reference measurements). The performance of three different full field QPI optical systems, in terms of optical path difference and dry mass accuracy, were evaluated. This phantom opens up other possibilities for the validation of reconstruction algorithms and post-processing routines, and paves the way for calibration targets designed ad hoc for specific biological questions.

}, keywords = {Cell phantom, Inter-laboratory comparison, Metrology, Phase calibration target, Quantitative phase imaging, Two-photon polymerization lithography}, issn = {0263-2241}, doi = {10.1016/j.measurement.2025.116765}, url = {https://www.sciencedirect.com/science/article/pii/S0263224125001241}, author = {Sylvia Desissaire and Micha{\l} Ziemczonok and Tigrane Cantat-Moltrecht and Arkadiusz Ku{\'s} and Guillaume Godefroy and Lionel Herv{\'e} and Chiara Paviolo and Wojciech Krauze and C{\'e}dric Allier and Ondrej Mandula and Ma{\l}gorzata Kujawi{\'n}ska} } @article {69796, title = {BPS2025 - Local cytoplasmic tradewinds direct soluble proteins to their targets}, journal = {Biophysical Journal}, volume = {124}, year = {2025}, month = {2025 Feb 13}, pages = {375a - 376a}, abstract = {

Inside the cell, proteins essential for signaling, morphogenesis, and migration navigate the complex, ever-changing environment through vesicular trafficking or microtubule-driven mechanisms. However, the mechanisms by which soluble proteins reach their target destinations remain unknown. Here, we show that soluble proteins are directed toward the cell{\textquoteright}s advancing edge by advection, diffusion facilitated by fluid flow. The advective transport mechanism operates in a compartment at the front of the cell isolated from the rest of the cytoplasm by a semi-permeable actin-myosin barrier that restricts protein mixing between the compartment and the rest of the cytoplasm. Contraction at the barrier generates a molecularly non-specific fluid flow that propels treadmilling actin monomer, actin-binding, adhesion, and even inert proteins forward. Changes in the dynamic local curvature of the barrier direct the flow, targeting proteins toward the protruding regions of the leading edge, effectively coordinating the distribution of proteins needed for local changes in cellular dynamics. Outside the compartment, diffusion is the primary mode of soluble protein transport. Our findings suggest that cells possess previously unrecognized organizational strategies for managing soluble protein concentration and distributing them efficiently for activities such as protrusion and adhesion.

}, issn = {00063495}, doi = {10.1016/j.bpj.2024.11.2032}, url = {https://doi.org/10.1016/j.bpj.2024.11.2032}, author = {Galbraith, Catherine G. and English, Brian P. and Boehm, Ulrike and Galbraith, James} } @article {68829, title = {Brain-wide analysis reveals movement encoding structured across and within brain areas}, journal = {Nat Neurosci}, year = {2025}, month = {2025 Nov 18}, abstract = {

Movement-related activity has been detected across much of the brain, including sensory and motor regions. However, much remains unknown regarding the distribution of movement-related activity across brain regions, and how this activity relates to neural computation. Here we analyzed movement-related activity in brain-wide recordings of more than 50,000 neurons in mice performing a decision-making task. We used multiple machine learning methods to predict neural activity from videography and found that movement-related signals differed across areas, with stronger movement signals close to the motor periphery and in motor-associated subregions. Delineating activity that predicts or follows movement revealed fine-scale structure of sensory and motor encoding across and within brain areas. Through single-trial video-based predictions of behavior, we identified activity modulation by uninstructed movements and their impact on choice-related activity analysis. Our work provides a map of movement encoding across the brain and approaches for linking neural activity, uninstructed movements and decision-making.

}, doi = {10.1038/s41593-025-02114-x}, url = {https://doi.org/10.1038/s41593-025-02114-x}, author = {Ziyue Aiden Wang and Susu Chen and Yi Liu and Dave Liu and Karel Svoboda and Nuo Li and Shaul Druckmann} } @article {70121, title = {Brainwide hemodynamics predict EEG neural rhythms across sleep and wakefulness in humans.}, journal = {PLoS Comput Biol}, volume = {21}, year = {2025}, month = {2025 Sep 19}, pages = {e1013497}, abstract = {

The brain exhibits rich oscillatory dynamics that play critical roles in vigilance and cognition, such as the neural rhythms that define sleep. These rhythms continuously fluctuate, signaling major changes in vigilance, but the widespread brain dynamics underlying these oscillations are difficult to investigate. Using simultaneous EEG and fast fMRI in humans who fell asleep inside the scanner, we developed a machine learning approach to investigate which fMRI regions and networks predict fluctuations in neural rhythms. We demonstrated that the rise and fall of alpha (8-12 Hz) and delta (1-4 Hz) power-two canonical EEG bands critically involved with cognition and vigilance-can be predicted from fMRI data in subjects that were not present in the training set. This approach also identified predictive information in individual brain regions across the cortex and subcortex. Finally, we developed an approach to identify shared and unique predictive information, and found that information about alpha rhythms was highly separable in two networks linked to arousal and visual systems. Conversely, delta rhythms were diffusely represented on a large spatial scale primarily across the cortex. These results demonstrate that EEG rhythms can be predicted from fMRI data, identify large-scale network patterns that underlie alpha and delta rhythms, and establish a novel framework for investigating multimodal brain dynamics.

}, keywords = {Adult, Brain, Brain Mapping, Computational Biology, Electroencephalography, Female, Hemodynamics, Humans, Machine Learning, Magnetic Resonance Imaging, Male, Sleep, Wakefulness, Young Adult}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1013497}, url = {https://doi.org/10.1371/journal.pcbi.1013497}, author = {Jacob, Leandro P L and Bailes, Sydney M and Williams, Stephanie D and Stringer, Carsen and Lewis, Laura D} } @article {69987, title = {CalciumInsights: An Open-Source, Tissue-Agnostic Graphical Interface for High-Quality Analysis of Calcium Signals}, journal = {bioRxiv}, year = {2025}, month = {2025 Jun 04}, abstract = {

Fluctuations and propagation of cytosolic calcium levels at both the cellular and tissue levels show complex patterns, referred to as calcium signatures, that regulate growth, organ development, damage responses, and survival. The quantitative analysis of calcium signatures at the cellular level is essential for identifying unique patterns that coordinate biological processes. However, a versatile framework applicable to multiple tissue types, allowing researchers to compare, measure, and validate diverse responses and recognize conserved patterns across model organisms, is missing. Here, we present a post-processing tool, CalciumInsights, which leverages the R packages Shiny and Golem. This tool has a graphical user interface and does not require software programming experience to perform calcium signal analysis. The open-source software has a modular framework with standardized functionalities that can be tailored for various research approaches. CalciumInsights provides descriptive statistical analysis through various metrics extracted from dynamic calcium transients and oscillations, such as peak amplitude, area under the curve, frequency, among others. The tool was evaluated with fluorescence imaging data from three model organisms: Danio rerio, Arabidopsis thaliana, and Drosophila melanogaster, demonstrating its ability to analyze diverse biological responses and models. Finally, the open-source nature of CalciumInsights enables community-driven improvements and developments for enabling new applications.

Author Summary: This manuscript introduces CalciumInsights, an open-source tool for calcium signature analysis. Designed to be a versatile tool that works with various tissue types and biological systems, CalciumInsights has an easy-to-use graphical user interface. Our program simplifies metrics extraction while maintaining the quality of the analysis by integrating several algorithms. CalciumInsights stands out for its user-friendliness, ease of use, and robust data exploration features, such as tunable filters for improved accuracy. These features promote inclusivity and lower barriers to scientific research by making calcium signature analysis accessible to users of all programming skill levels.

}, doi = {10.1101/2025.06.04.657923}, url = {https://www.biorxiv.org/content/early/2025/06/09/2025.06.04.657923}, author = {Suarez-Gomez, Deiver and Perez-Rosas, Norma C and Miranda-Contreras, Gabriel I and Colom-Bra{\~n}a, Santiago R and Zhang, Weiwei and Mim, Mayesha Sahir and Tan, Shelly and Gazzo, David and Tepole, Adrian Buganza and Deng, Qing and Reeves, Gregory T and Isaza-Brando, Clara E and Staiger, Christopher J. and Umulis, David and Zartman, Jeremiah and Cabrera-R{\'\i}os, Mauricio} } @article {70045, title = {Cdc42 regulates apical membrane fusion via the Rab11a{\textendash}VAMP2 pathway in salivary gland acinar cells}, journal = {bioRxiv}, year = {2025}, month = {2025 Jul 31}, abstract = {

Epithelial polarity is essential for proper tissue organization and function, yet the molecular mechanisms governing apical membrane formation during secretory epithelial development remain incompletely understood. Here, we investigate the role of the small GTPase Cdc42 in salivary gland acinar cell development using a mouse model designed to knock out Cdc42 specifically at the onset of acinar cell formation. Loss of Cdc42 resulted in defective apical membrane formation accompanied by accumulation of vesicles around the apical lumen. These vesicles contained the apical water channel AQP5 and the apical recycling endosome (ARE) marker Rab11a, while the basolateral transporter NKCC1 retained normal localization, indicating an apical-selective trafficking defect. Importantly, Cdc42 deficiency caused a selective 40\% reduction in the expression of the SNARE protein VAMP2, while other vesicle trafficking proteins including VAMP8, SNAP23, and EEA1 remained unchanged. Our findings reveal that Cdc42 controls apical membrane formation by maintaining VAMP2 expression, which is essential for the fusion of Rab11a-positive recycling endosomes. The accumulation of fusion-incompetent AREs near the apical surface demonstrates the critical role of the Cdc42-VAMP2 pathway in epithelial development. These results provide new insights into how polarity regulators integrate vesicle trafficking and fusion machinery, and may have implications for understanding glandular diseases involving epithelial polarity defects.

}, doi = {10.1101/2025.07.31.667845}, url = {https://www.biorxiv.org/content/early/2025/08/01/2025.07.31.667845}, author = {Shitara, Akiko and Nagase, Haruna and Bleck, Christopher K. E. and Ohno, Yuta and Kataoka, Hideo and Satoh, Keitaro and Kashimata, Masanori} } @article {70035, title = {Cell type-specific contributions to a persistent aggressive internal state in female Drosophila}, journal = {Elife}, volume = {12}, year = {2025}, month = {2025 Jul 25}, abstract = {

Persistent internal states are important for maintaining survival-promoting behaviors, such as aggression. In female\ Drosophila melanogaster, we have previously shown that individually activating either aIPg or pC1d cell types can induce aggression. Here we investigate further the individual roles of these cholinergic, sexually dimorphic cell types, and the reciprocal connections between them, in generating a persistent aggressive internal state. We find that a brief 30-second optogenetic stimulation of aIPg neurons was sufficient to promote an aggressive internal state lasting at least 10 minutes, whereas similar stimulation of pC1d neurons did not. While we previously showed that stimulation of pC1e alone does not evoke aggression, persistent behavior could be promoted through simultaneous stimulation of pC1d and pC1e, suggesting an unexpected synergy of these cell types in establishing a persistent aggressive state. Neither aIPg nor pC1d show persistent neuronal activity themselves, implying that the persistent internal state is maintained by other mechanisms. Moreover, inactivation of pC1d did not significantly reduce aIPg-evoked persistent aggression, arguing that the aggressive state did not depend on pC1d-aIPg recurrent connectivity. Our results suggest the need for alternative models to explain persistent female aggression.

Preprint:\ https://www.biorxiv.org/content/10.1101/2023.06.07.543722v2

}, keywords = {Aggression, Animals, Behavior, Animal, Drosophila melanogaster, Female, Neurons, Optogenetics}, issn = {2050-084X}, doi = {10.7554/eLife.88598}, url = {https://doi.org/10.7554/elife.88598}, author = {Chiu, Hui and Robie, Alice A and Branson, Kristin and Vippa, Tanvi and Epstein, Samantha and Rubin, Gerald M and Anderson, David J and Schretter, Catherine E} } @article {69749, title = {Cell type-specific driver lines targeting the Drosophila central complex and their use to investigate neuropeptide expression and sleep regulation}, journal = {elife}, year = {2025}, month = {2025 Jan 21}, abstract = {

The central complex (CX) plays a key role in many higher-order functions of the insect brain including navigation and activity regulation. Genetic tools for manipulating individual cell types, and knowledge of what neurotransmitters and neuromodulators they express, will be required to gain mechanistic understanding of how these functions are implemented. We generated and characterized split-GAL4 driver lines that express in individual or small subsets of about half of CX cell types. We surveyed neuropeptide and neuropeptide receptor expression in the central brain using fluorescent\ in situ\ hybridization. About half of the neuropeptides we examined were expressed in only a few cells, while the rest were expressed in dozens to hundreds of cells. Neuropeptide receptors were expressed more broadly and at lower levels. Using our GAL4 drivers to mark individual cell types, we found that 51 of the 85 CX cell types we examined expressed at least one neuropeptide and 21 expressed multiple neuropeptides. Surprisingly, all co-expressed a small neurotransmitter. Finally, we used our driver lines to identify CX cell types whose activation affects sleep, and identified other central brain cell types that link the circadian clock to the CX. The well-characterized genetic tools and information on neuropeptide and neurotransmitter expression we provide should enhance studies of the CX.

}, doi = {10.7554/elife.104764.2}, url = {http://dx.doi.org/10.7554/eLife.104764.2}, author = {Wolff, Tanya and Eddison, Mark and Chen, Nan and Nern, Aljoscha and Sundaramurthi, Preeti and Sitaraman, Divya and Rubin, Gerald M} } @article {69207, title = {Cellpose3: One-click image restoration for improved cellular segmentation.}, journal = {Nat Methods}, year = {2025}, month = {2025 Feb 12}, abstract = {

Generalist methods for cellular segmentation have good out-of-the-box performance on a variety of image types; however, existing methods struggle for images that are degraded by noise, blurring or undersampling, all of which are common in microscopy. We focused the development of Cellpose3 on addressing these cases and here we demonstrate substantial out-of-the-box gains in segmentation and image quality for noisy, blurry and undersampled images. Unlike previous approaches that train models to restore pixel values, we trained Cellpose3 to output images that are well segmented by a generalist segmentation model, while maintaining perceptual similarity to the target images. Furthermore, we trained the restoration models on a large, varied collection of datasets, thus ensuring good generalization to user images. We provide these tools as {\textquoteright}one-click{\textquoteright} buttons inside the graphical interface of Cellpose as well as in the Cellpose API.

}, doi = {10.1038/s41592-025-02595-5}, url = {https://doi.org/10.1038/s41592-025-02595-5}, author = {Stringer, Carsen and Pachitariu, Marius} } @article {69901, title = {Cellpose-SAM: Superhuman generalization for cellular segmentation}, journal = {bioRxiv}, year = {2025}, month = {2025 May 1}, abstract = {

Modern algorithms for biological segmentation can match inter-human agreement in annotation quality. This however is not a performance bound: a hypothetical human-consensus segmentation could reduce error rates in half. To obtain a model that generalizes better we adapted the pretrained transformer backbone of a foundation model (SAM) to the Cellpose framework. The resulting Cellpose-SAM model substantially outperforms inter-human agreement and approaches the human-consensus bound. We increase generalization performance further by making the model robust to channel shuffling, cell size, shot noise, downsampling, isotropic and anisotropic blur. The new model can be readily adopted into the Cellpose ecosystem which includes finetuning, human-in-the-loop training, image restoration and 3D segmentation approaches. These properties establish Cellpose-SAM as a foundation model for biological segmentation.

}, doi = {10.1101/2025.04.28.651001}, url = {https://www.biorxiv.org/content/early/2025/05/01/2025.04.28.651001}, author = {Pachitariu, Marius and Rariden, Michael and Stringer, Carsen} } @article {70185, title = {The CENP-A chaperone complex spatially organizes centromeres}, journal = {bioRxiv}, year = {2025}, month = {2026 Nov 09}, abstract = {

Centromeres, defined by CENP-A-containing nucleosomes, direct the assembly of kinetochores for spindle attachment. In mitosis, CENP-A and the constitutive centromere-associated network (CCAN) of the inner kinetochore are arranged into bipartite subdomains within clearings of chromatin. However, it remains unclear whether any of these features exist before mitosis. We show that in interphase, CENP-A and the CCAN assemble \~200-300 nm shell-like structures that enclose a chromatin-poor central cavity. Strikingly, this cavity is occupied by the interphase-specific CENP-A chaperone complex, which promotes CENP-A assembly once per cell cycle. However, chaperone presence, but not CENP-A incorporation, is required to generate both the shell architecture and the chromatin clearing. The CCAN scaffold CENP-C, which links CENP-A nucleosomes to the chaperone complex, exhibits radial organization spanning the entire structure and is essential for its formation. These data uncover a previously unrecognized structural role for the CENP-A chaperone machinery in establishing interphase centromere architecture and suggest a mechanism by which this machinery configures centromeres for faithful kinetochore assembly and genome stability.

}, doi = {10.1101/2025.11.07.687291}, url = {https://www.biorxiv.org/content/early/2025/11/09/2025.11.07.687291}, author = {Gupta, Hindol and Haase, Julian and Wu, Yicong and Chen, Jiji and Karadimov, George and Shroff, Hari and Kelly, Alexander E.} } @article {69903, title = {Challenges of microscopy technology dissemination to resource-constrained communities.}, journal = {Nat Methods}, year = {2025}, month = {2025 May 06}, abstract = {

No abstract available.

}, issn = {1548-7105}, doi = {10.1038/s41592-025-02690-7}, url = {https://doi.org/10.1038/s41592-025-02690-7}, author = {Aaron, Jesse S and Jacobs, Caron A and Malacrida, Leonel and Keppler, Antje and French, Paul and Fletcher, Daniel A and Wood, Christopher and Brown, Claire M and Wright, Graham D and Ogawa, Satoshi and Maina, Mahmoud and Chew, Teng-Leong} } @article {70184, title = {Chemical modulation of gut bacterial metabolism induces colanic acid and extends the lifespan of nematode and mammalian hosts.}, journal = {PLoS Biol}, volume = {23}, year = {2025}, month = {2025 Nov 11}, pages = {e3002749}, abstract = {

Microbiota-derived metabolites have emerged as key regulators of longevity. The metabolic activity of the gut microbiota, influenced by dietary components and ingested chemical compounds, profoundly impacts host fitness. While the benefits of dietary prebiotics are well-known, chemically targeting the gut microbiota to enhance host fitness remains largely unexplored. Here, we report a novel chemical approach to induce a pro-longevity bacterial metabolite in the host gut. We discovered that wild-type Escherichia coli strains overproduce colanic acids (CAs) when exposed to a low dose of cephaloridine, leading to an increased life span in the host organism Caenorhabditis elegans. In the mouse gut, oral administration of low-dose cephaloridine induced transcription of the capsular polysaccharide synthesis (cps) operon responsible for CA biosynthesis in commensal E. coli at 37 {\textdegree}C, and attenuated age-related metabolic changes. We also found that low-dose cephaloridine overcomes the temperature-dependent inhibition of CA biosynthesis and promotes its induction through a mechanism mediated by the membrane-bound histidine kinase ZraS, independently of cephaloridine{\textquoteright}s known antibiotic properties. Our work lays a foundation for microbiota-based therapeutics through chemical modulation of bacterial metabolism and highlights the promising potential of leveraging bacteria-targeting drugs in promoting host longevity.

}, keywords = {Animals, Caenorhabditis elegans, Escherichia coli, Gastrointestinal Microbiome, Longevity, Mice, Polysaccharides}, issn = {1545-7885}, doi = {10.1371/journal.pbio.3002749}, url = {https://doi.org/10.1371/journal.pbio.3002749}, author = {Hu, Guo and Savini, Marzia and Cooke, Matthew Brandon and Wei, Xin and Deng, Dinghuan and Gao, Shihong M and Xia, Ruyue Alps and Guan, Youchen and Wen, Alice X and Yu, Xin and Wang, Jin and Jiang, Chao and Herman, Christophe and Li, Jiefu and Wang, Meng C} } @article {70221, title = {A chemically switchable synthetic condensate platform for reversible protein sequestration and release}, journal = {ACS Chem Biol}, year = {2025}, month = {2025 Dec 14}, abstract = {

Creating artificial organelles that sequester and release specific proteins in response to a small molecule in mammalian cells is an attractive approach for regulating protein function. In this work, by combining phase-separated condensates formed by the tandem fusion of two oligomeric proteins with a trimethoprim (TMP)-responsive nanobody switch for GFP (LAMA; ligand-modulated antibody fragment), we developed a synthetic condensate system that initially sequesters GFP-tagged proteins within condensates and rapidly releases them into the cytoplasm upon TMP treatment. The released proteins can then be resequestered by washing out the TMP. This system enabled user-defined, temporal, rapid, and reversible control of cellular processes, including membrane ruffling mediated by exogenously expressed GFP-Vav2 and modulation of the cellular localization of endogenous ERK2-GFP generated by genome knock-in. Our results highlight the utility of the LAMA-based synthetic condensate platform as a novel, chemically switchable tool for regulating protein function through controlled protein sequestration and release in mammalian cells.

}, issn = {1554-8937}, doi = {10.1021/acschembio.5c00719}, url = {https://doi.org/10.1021/acschembio.5c00719}, author = {Fukaya, Yoko and Yoshikawa, Masaru and Aoki, Kazuhiro and Farrants, Helen and Johnsson, Kai and Tsukiji, Shinya} } @article {70026, title = {CHLOK: a chemigenetic multicolor labeling system to visualize neuronal birthdate and circuit integration}, journal = {Research Square}, year = {2025}, month = {2025 Jul 08}, abstract = {

Understanding how neurons integrate into developing circuits and contribute to functional activity is essential for decoding brain development and plasticity. However, current methods to study neuronal integration often suffer from low throughput, limited spatiotemporal resolution, or invasive procedures that hinder in vivo functional analysis. To overcome these challenges, we present a birthdate-labeling strategy, named CHLOK, based on HaloTag technology and a broad palette of fluorescent synthetic dyes. This approach enables precise multicolor labeling of neurons according to their maturation stage and allows flexible integration into functional assays through compatibility with calcium imaging and optogenetics. We validated CHLOK by mapping birthdate-resolved neuronal activity in the developing visual and motor systems of zebrafish larvae. Our results reveal distinct functional contributions of early- versus late-born neurons, providing new insights into the temporal dynamics of circuit formation. Furthermore, we demonstrate the versatility of this approach, showcasing age-specific multicolor calcium and voltage imaging as well as optogenetic manipulation. By overcoming key limitations of existing techniques, CHLOK offers a powerful, versatile and non-invasive tool for studying neural integration, circuit development and function in vivo.

}, doi = {10.21203/rs.3.rs-7039578/v1}, url = {https://doi.org/10.21203/rs.3.rs-7039578/v1}, author = {Faini, Giulia and Tuffery, Matthieu and Saleem, Amna and Zhang, Lixia and Du, Felix and Le Bourdelles, Guillaume and Duroure, Karine and Schreiter, Eric R and Tanese, Dimitrii and Emiliani, Valentina and Del Bene, Filippo and Koyama, Minoru} } @article {69902, title = {Chromatix: A differentiable, GPU-accelerated wave-optics library}, journal = {bioRxiv}, year = {2025}, month = {2025 May 2}, abstract = {

Modern microscopy methods incorporate computational modeling of optical systems as an integral part of the imaging process, either to solve inverse problems or enable optimization of the optical system design. These methods often depend on differentiable simulations of optical systems, yet no standardized framework exists{\textemdash}forcing computational optics researchers to repeatedly and independently implement simulations that are prone to errors, difficult to reuse in other applications, and often computationally suboptimal. These common problems limit the potential impact of computational optics as a field. We present Chromatix: an open-source, GPU-accelerated differentiable wave optics library. Chromatix builds on JAX to enable fast simulation of diverse optical systems and inverse problem solving, scaling these simulations from single-CPU laptops to multi-GPU servers. The library implements various optical elements (e.g., lenses, polarizers and spatial light modulators) and multiple light propagation models (e.g., Fresnel approximation, angular spectrum and off-axis propagation) that can be flexibly combined to model various computational optics applications such as snapshot microscopy, holography, and phase retrieval of multiple scattering samples. These simulations can be automatically parallelized to scale across multiple GPUs with a single-line change to the modeling code, enabling simulation and optimization of previously impractical optical system designs. We demonstrate Chromatix{\textquoteright}s capacity to substantially accelerate optics simulation and optimization on existing methods in computational optics, speeding up optical simulation and optimization from 2-6{\texttimes} on a single GPU to up to 22{\texttimes} on 8 GPUs (depending on the particular system being modeled) compared to the original implementations. Chromatix establishes a standard for wave optics simulations, democratizing access to and expanding the design space of computational optics.i

}, doi = {10.1101/2025.04.29.651152}, url = {https://www.biorxiv.org/content/early/2025/05/02/2025.04.29.651152}, author = {Deb, Diptodip and Both, Gert-Jan and Bezzam, Eric and Kohli, Amit and Yang, Siqi and Chaware, Amey and Allier, C{\'e}dric and Cai, Changjia and Anderberg, Geneva and Eybposh, M. Hossein and Schneider, Magdalena C. and Heintzmann, Rainer and Rivera-Sanchez, Fabrizio A. and Simmerer, Corey and Meng, Guanghan and Tormes-Vaquerano, Jovan and Han, SeungYun and Shanmugavel, Sibi Chakravarthy and Maruvada, Teja and Yang, Xi and Kim, Yewon and Diederich, Benedict and Joo, Chulmin and Waller, Laura and Durr, Nicholas J. and P{\'e}gard, Nicolas C. and La Rivi{\`e}re, Patrick J. and Horstmeyer, Roarke and Chowdhury, Shwetadwip and Turaga, Srinivas C.} } @article {70146, title = {Chromosome scale genomes of two invasive Adelges species enable virtual screening for selective adelgicides.}, journal = {G3 (Bethesda)}, volume = {16}, year = {2025}, month = {2026 Jan 01}, abstract = {

Two invasive adelgids are associated with widespread damage to several North American conifer species. Adelges tsugae, hemlock woolly adelgid, was introduced from Japan and reproduces parthenogenetically in North America, where it has rapidly decimated Tsuga canadensis and Tsuga caroliniana (eastern and Carolina hemlocks, respectively). Adelges abietis, eastern spruce gall adelgid, introduced from Europe, forms distinctive pineapple-shaped galls on several native spruce species. While not considered a major forest pest, it weakens trees and increases susceptibility to additional stressors. Broad-spectrum insecticides that are often used to control adelgid populations can have off-target impacts on beneficial insects. Whole genome sequencing was performed on both species to aid in development of targeted solutions that may minimize ecological impact. Adelges abietis was sequenced using barcoded linked-reads from 30 pooled individuals, with Hi-C scaffolding performed using data from a single individual collected from the same host plant. Adelges tsugae used long-read sequencing from pooled nymphs. The assembled A. tsugae and A. abietis genomes, pooled from several parthenogenetic females, are 220.75 Mbp and 253.16 Mbp, respectively. Each consists of eight autosomal chromosomes, as well as two sex chromosomes (X1/X2), supporting the XX-XO sex determination system. The genomes are over 96\% complete based on BUSCO assessment. Genome annotation identified 11,424 and 12,060 protein-coding genes in A. tsugae and A. abietis, respectively. Comparative analysis of proteins across 29 hemipteran species and 14 arthropod outgroups identified 31,666 putative gene families. Gene family evolution analysis with CAFE revealed lineage-specific expansions in immune-related aminopeptidases (ERAP1) and juvenile hormone binding proteins (JHBP), contractions in juvenile hormone acid methyltransferases (JHAMT), and conservation of nicotinic acetylcholine receptors (nAChR). These genes were explored as candidate families towards a long-term objective of developing adelgid-selective insecticides. Structural comparisons of proteins across seven focal species (Adelges tsugae, Adelges abietis, Adelges cooleyi, Rhopalosiphum maidis, Apis mellifera, Danaus plexippus, and Drosophila melanogaster) revealed high conservation of nAChR and ERAP1, while JHAMT exhibited species-specific structural divergence. The potential of JHAMT as a lineage-specific target for pest control was explored through virtual screening of drugs and pesticides.

bioRxiv preprint:\ https://doi.org/10.1101/2024.11.21.624573

}, issn = {2160-1836}, doi = {10.1093/g3journal/jkaf232}, url = {https://doi.org/10.1093/g3journal/jkaf232}, author = {Glendening, Adam M and Stephens, Cole and Vuruputoor, Vidya S and Chaganti, Tesko and Myles, Meghan N and Stern, David L and Abdelalim, Muhammad and Juang, Yu-Pu and Hogenhout, Saskia A and Mathers, Thomas C and Pauloski, Nicole and Cernak, Tim A and Wegrzyn, Jill L and Fetter, Karl C} } @article {70165, title = {A Class of Markovian self-reinforcing processes with power-law distributions}, journal = {arXiv}, year = {2025}, month = {2025 Oct 21}, abstract = {

Solar flares, email exchanges, and many natural or social systems exhibit bursty dynamics, with periods of intense activity separated by long inactivity. These patterns often follow power- law distributions in inter-event intervals or event rates. Existing models typically capture only one of these features and rely on non-local memory, which complicates analysis and mechanistic interpretation. We introduce a novel self-reinforcing point process whose event rates are governed by local, Markovian nonlinear dynamics and post-event resets. The model generates power-law tails for both inter-event intervals and event rates over a broad range of exponents observed empirically across natural and human phenomena. Compared to non-local models such as Hawkes processes, our approach is mechanistically simpler, highly analytically tractable, and also easier to simulate. We provide methods for model fitting and validation, establishing this framework as a versatile foundation for the study of bursty phenomena.

}, doi = {10.48550/arXiv.2510.19034}, url = {https://arxiv.org/abs/2510.19034}, author = {Pavlo Bulanchuk and Sue Ann Koay and Sandro Romani} } @article {69729, title = {Collateral connectomes of Esr1-positive hypothalamic neurons modulate defensive behavior plasticity}, journal = {bioRxiv}, year = {2025}, month = {01/2025}, abstract = {

The ventromedial hypothalamus (VMH) projects to the periaqueductal gray (PAG) and anterior hypothalamic nucleus (AHN), mediating freezing and escape behaviors, respectively. We investigated VMH collateral (VMH-coll) neurons, which innervate both PAG and AHN, to elucidate their role in postsynaptic processing and defensive behavior plasticity. Using all-optical voltage imaging of 22,151 postsynaptic neurons ex vivo, we found that VMH-coll neurons engage inhibitory mechanisms at both synaptic ends and can induce synaptic circuit plasticity. In vivo optogenetic activation of the VMH-coll somas induced escape behaviors. We identified an Esr1-expressing VMH-coll subpopulation with postsynaptic connectome resembling that of wild-type collaterals on the PAG side. Activation of Esr1+VMH-coll neurons evoked freezing and unexpected flattening behavior, previously not linked to the VMH. Neuropeptides such as PACAP and dynorphin modulated both Esr1+VMH-coll connectomes. In vivo κ-opioid receptor antagonism impaired Esr1+VMH-coll-mediated defensive behaviors. These findings unveiled the central role of VMH-coll pathways in innate defensive behavior plasticity.

}, doi = {10.1101/2025.01.10.632334}, url = {https://www.biorxiv.org/content/early/2025/01/11/2025.01.10.632334}, author = {Csillag, Veronika and Forastieri, Chiara and Sz{\"u}cs, Gr{\'e}ta Martina and Vidal, In{\'e}s Talaya and Bizzozzero, Marianne Hiriart and Lavis, Luke D. and Calvigioni, Daniela and Fuzik, J{\'a}nos} } @article {70130, title = {Combinatorial protein barcodes enable self-correcting neuron tracing with nanoscale molecular context}, journal = {bioRxiv}, year = {2025}, month = {2025 Sep 28}, abstract = {

Mapping nanoscale neuronal morphology with molecular annotations is critical for understanding healthy and dysfunctional brain circuits. Current methods are constrained by image segmentation errors and by sample defects (e.g., signal gaps, section loss). Genetic strategies promise to overcome these challenges by using easily distinguishable cell identity labels. However, multicolor approaches are spectrally limited in diversity, whereas nucleic acid barcoding lacks a cell-filling morphology signal for segmentation. Here, we introduce PRISM (Protein-barcode Reconstruction via Iterative Staining with Molecular annotations), a platform that integrates combinatorial delivery of antigenically distinct, cell-filling proteins with tissue expansion, multi-cycle imaging, barcode-augmented reconstruction, and molecular annotation. Protein barcodes increase label diversity by \>750-fold over multicolor labeling and enable morphology reconstruction with intrinsic error correction. We acquired a \~10 million μm3 volume of mouse hippocampal area CA2/3, multiplexed across 23 barcode antigen and synaptic marker channels. By combining barcodes with shape information we achieve an 8x increase in automatic tracing accuracy of genetically labelled neurons. We demonstrate PRISM supports automatic proofreading across micron-scale spatial gaps and reconnects neurites across discontinuities spanning hundreds of microns. Using PRISM{\textquoteright}s molecular annotation capability, we map the distribution of synapses onto traced neural morphology, characterizing challenging synaptic structures such as thorny excrescences (TEs), and discovering a size correlation among spatially proximal TEs on the same dendrite. PRISM thus supports self-correcting neuron reconstruction with molecular context.

}, doi = {10.1101/2025.09.26.678648}, url = {https://www.biorxiv.org/content/early/2025/09/28/2025.09.26.678648}, author = {Park, Sung Yun and Sheridan, Arlo and An, Bobae and Jarvis, Erin and Lyudchik, Julia and Patton, William and Axup, Jun Y. and Chan, Stephanie W. and Damstra, Hugo G.J. and Leible, Daniel and Leung, Kylie S. and Magno, Clarence A. and Meeran, Aashir and Michalska, Julia M. and Rieger, Franz and Wang, Claire and Wu, Michelle and Church, George M. and Funke, Jan and Huffman, Todd and Leeper, Kathleen G.C. and Truckenbrodt, Sven and Winnubst, Johan and Kornfeld, Joergen M.R. and Boyden, Edward S. and Rodriques, Samuel G. and Payne, Andrew C.} } @article {69794, title = {Combining sampling methods with attractor dynamics in spiking models of head-direction systems}, journal = {bioRxiv}, year = {2025}, month = {2025 Feb 26}, abstract = {

Uncertainty is a fundamental aspect of the natural environment, requiring the brain to infer and integrate noisy signals to guide behavior effectively. Sampling-based inference has been proposed as a mechanism for dealing with uncertainty, particularly in early sensory processing. However, it is unclear how to reconcile sampling-based methods with operational principles of higher-order brain areas, such as attractor dynamics of persistent neural representations. In this study, we present a spiking neural network model for the head-direction (HD) system that combines sampling-based inference with attractor dynamics. To achieve this, we derive the required spiking neural network dynamics and interactions to perform sampling from a large family of probability distributions - including variables encoded with Poisson noise. We then propose a method that allows the network to update its estimate of the current head direction by integrating angular velocity samples - derived from noisy inputs - with a pull towards a circular manifold, thereby maintaining consistent attractor dynamics. This model makes specific, testable predictions about the HD system that can be examined in future neurophysiological experiments: it predicts correlated subthreshold voltage fluctuations; distinctive short- and long-term firing correlations among neurons; and characteristic statistics of the movement of the neural activity "bump" representing the head direction. Overall, our approach extends previous theories on probabilistic sampling with spiking neurons, offers a novel perspective on the computations responsible for orientation and navigation, and supports the hypothesis that sampling-based methods can be combined with attractor dynamics to provide a viable framework for studying neural dynamics across the brain.

}, doi = {10.1101/2025.02.25.640158}, url = {https://www.biorxiv.org/content/early/2025/02/26/2025.02.25.640158}, author = {Pjanovic, Vojko and Zavatone-Veth, Jacob A and Masset, Paul and Keemink, Sander W and Nardin, Michele} } @article {69854, title = {Combining spatial transcriptomics and ECM imaging in 3D for mapping cellular interactions in the tumor microenvironment.}, journal = {Cell Syst}, year = {2025}, month = {2025 Apr 09}, pages = {101261}, abstract = {

Tumors are complex ecosystems composed of malignant and non-malignant cells embedded in a dynamic extracellular matrix (ECM). In the tumor microenvironment, molecular phenotypes are controlled by cell-cell and ECM interactions in 3D cellular neighborhoods (CNs). While their inhibition can impede tumor progression, routine molecular tumor profiling fails to capture cellular interactions. Single-cell spatial transcriptomics (ST) maps receptor-ligand interactions but usually remains limited to 2D tissue sections and lacks ECM readouts. Here, we integrate 3D ST with ECM imaging in serial sections from one clinical lung carcinoma to systematically quantify molecular states, cell-cell interactions, and ECM remodeling in CN. Our integrative analysis pinpointed known immune escape and tumor invasion mechanisms, revealing several druggable drivers of tumor progression in the patient under study. This proof-of-principle study highlights the potential of in-depth CN profiling in routine clinical samples to inform microenvironment-directed therapies. A record of this paper{\textquoteright}s transparent peer review process is included in the supplemental information.

}, issn = {2405-4720}, doi = {10.1016/j.cels.2025.101261}, url = {https://doi.org10.1016/j.cels.2025.101261}, author = {Pentimalli, Tancredi Massimo and Schallenberg, Simon and Le{\'o}n-Peri{\~n}{\'a}n, Daniel and Legnini, Ivano and Theurillat, Ilan and Thomas, Gwendolin and Boltengagen, Anastasiya and Fritzsche, Sonja and Nimo, Jose and Ruff, Lukas and Dernbach, Gabriel and Jurmeister, Philipp and Murphy, Sarah and Gregory, Mark T and Liang, Yan and Cordenonsi, Michelangelo and Piccolo, Stefano and Coscia, Fabian and Woehler, Andrew and Karaiskos, Nikos and Klauschen, Frederick and Rajewsky, Nikolaus} } @article {69881, title = {Comparative connectomics of Drosophila descending and ascending neurons.}, journal = {Nature}, year = {2025}, month = {2025 Apr 30}, abstract = {

In most complex nervous systems there is a clear anatomical separation between the nerve cord, which contains most of the final motor outputs necessary for behaviour, and the brain. In insects, the neck connective is both a physical and an information bottleneck connecting the brain and the ventral nerve cord (an analogue of the spinal cord) and comprises diverse populations of descending neurons (DNs), ascending neurons (ANs) and sensory ascending neurons, which are crucial for sensorimotor signalling and control. Here, by integrating three separate electron microscopy (EM) datasets, we provide a complete connectomic description of the ANs and DNs of the Drosophila female nervous system and compare them with neurons of the male nerve cord. Proofread neuronal reconstructions are matched across hemispheres, datasets and sexes. Crucially, we also match 51\% of DN cell types to light-level data defining specific driver lines, as well as classifying all ascending populations. We use these results to reveal the anatomical and circuit logic of neck connective neurons. We observe connected chains of DNs and ANs spanning the neck, which may subserve motor sequences. We provide a complete description of sexually dimorphic DN and AN populations, with detailed analyses of selected circuits for reproductive behaviours, including male courtship (DNa12; also known as aSP22) and song production (AN neurons from hemilineage 08B) and female ovipositor extrusion (DNp13). Our work provides EM-level circuit analyses that span the entire central nervous system of an adult animal.

}, issn = {1476-4687}, doi = {10.1038/s41586-025-08925-z}, url = {https://doi.org/10.1038/s41586-025-08925-z}, author = {St{\"u}rner, Tomke and Brooks, Paul and Serratosa Capdevila, Laia and Morris, Billy J and Javier, Alexandre and Fang, Siqi and Gkantia, Marina and Cachero, Sebastian and Beckett, Isabella R and Marin, Elizabeth C and Schlegel, Philipp and Champion, Andrew S and Moitra, Ilina and Richards, Alana and Klemm, Finja and Kugel, Leonie and Namiki, Shigehiro and Cheong, Han S J and Kovalyak, Julie and Tenshaw, Emily and Parekh, Ruchi and Phelps, Jasper S and Mark, Brandon and Dorkenwald, Sven and Bates, Alexander S and Matsliah, Arie and Yu, Szi-Chieh and McKellar, Claire E and Sterling, Amy and Seung, H Sebastian and Murthy, Mala and Tuthill, John C and Lee, Wei-Chung Allen and Card, Gwyneth M and Costa, Marta and Jefferis, Gregory S X E and Eichler, Katharina} } @article {70013, title = {Compartmentalization of the endoplasmic reticulum in mouse kidney proximal tubule epithelial cells}, journal = {Physiology}, volume = {40}, year = {2025}, month = {2025 May 12}, pages = {1280}, abstract = {

The renal proximal tubule plays a critical role in water and solute reabsorption. Recently we generated a high resolution 3D, quantifiable volume microscopic identification of the ultrastructure of kidney Proximal Tubule (PT) cells using enhanced Focused Ion Beam Scanning Electron Microscopy (eFIB-SEM) and machine learning-based segmentation approaches. This analysis revealed that, in a volume of 70x60x177 {\textmu}m3 of mouse kidney tissue, the mean volume of PT cells is 1980.25 {\textmu}m3 {\textpm} 491.28 μm3. In an analysis of 25 PT cells, mitochondria (MITO) and endoplasmic reticulum (ER) accounted for an average of 26.4\% and 6.3\% of cell volume, respectively. Importantly, 91\% of the total ER volume appeared to be comprised of a single contiguous ER structure as determined by tracing the ER surface. Using semi-thin sections (0.5 {\textmu}m) of mouse kidney and antibodies directed against ER proteins we assessed the functional compartmentalization of the ER in PT cells by immunofluorescence microscopy. We find that ER proteins that participate in maintaining ER structure and lipid exchange, such as CLIMP-63 and VAP-A, localize to regions of the ER that are in close apposition to the basolateral plasma membrane (BL PM) of the PT cell. This distribution is confirmed by co-staining with an antibody directed against the Na, K-ATPase, a marker of the BL PM. In contrast, regions of the ER that are involved in calcium ion storage, as detected by staining for the SERCA calcium ATPase, are distributed broadly through the cytoplasm in the area of the cell that is rich in MITO. Staining for mitofilin, a MITO outer membrane protein, confirmed the abundance and distribution of the MITO in all of the PT cells. PDI, a protein that regulates proper folding and maturation of newly synthesized proteins in the lumen of the ER, resides primarily in portions of the ER that surround the nucleus and extend into the apical regions of the cell. PDI is mostly absent from the BL portions of the PT cells. Interestingly, calreticulin, which participates both in ER calcium storage and newly synthesized protein folding and quality control processes, is heavily concentrated in the subapical region of the cell. Using the machine learning algorithm to segment the lumen of the seemingly continuous ER structure demonstrates that, within the limit of resolution of this technique, continuity of ER lumens is limited to discrete patches. The defined distributions of these ER markers demonstrates that the extensive ER network in proximal tubule cells is divided into subdomains with distinct functional capacities and properties. NIH-RC2 DK120534. RDP and EML conributed equally. OAW and MJC contributed equally. This abstract was presented at the American Physiology Summit 2025 and is only available in HTML format. There is no downloadable file or PDF version. The Physiology editorial board was not involved in the peer review process.

}, doi = {10.1152/physiol.2025.40.S1.1280}, url = {https://doi.org/10.1152/physiol.2025.40.S1.1280}, author = {Reyna-Neyra, Andrea and Pandya, Raj D. and Lackner, Emily M. and Pang, Song and Li, Wei-Ping and Xu, C. Shan and Zugates, Christopher and Burdyniuk, Mariia and Pandya, Vraj D. and Weisz, Ora A. and Caplan, Michael J.} } @article {68955, title = {A competitive disinhibitory network for robust optic flow processing in Drosophila}, journal = {Nat Neurosci.}, year = {2025}, month = {2025 may 1}, abstract = {

Many animals navigate using optic flow, detecting rotational image velocity differences between their eyes to adjust direction. Forward locomotion produces strong symmetric translational optic flow that can mask these differences, yet the brain efficiently extracts these binocular asymmetries for course control. In Drosophila melanogaster, monocular horizontal system neurons facilitate detection of binocular asymmetries and contribute to steering. To understand these functions, we reconstructed horizontal system cells{\textquoteright} central network using electron microscopy datasets, revealing convergent visual inputs, a recurrent inhibitory middle layer and a divergent output layer projecting to the ventral nerve cord and deeper brain regions. Two-photon imaging, GABA receptor manipulations and modeling, showed that lateral disinhibition reduces the output{\textquoteright}s translational sensitivity while enhancing its rotational selectivity. Unilateral manipulations confirmed the role of interneurons and descending outputs in steering. These findings establish competitive disinhibition as a key circuit mechanism for detecting rotational motion during translation, supporting navigation in dynamic environments.

Preprint:\ https://doi.org/10.1101/2023.08.06.552150

}, doi = {10.1038/s41593-025-01948-9}, url = {https://doi.org/10.1038/s41593-025-01948-9}, author = {Mert Erginkaya and Tom{\'a}s Cruz and Margarida Brotas and Kathrin Steck and Aljoscha Nern and Filipa Torr{\~a}o and N{\'e}lia Varela and Davi Bock and Michael Reiser and M Eugenia Chiappe} } @article {70118, title = {Composing trajectories for rapid inference of navigational goals}, journal = {bioRxiv}, year = {2025}, month = {2025 Sep 24}, abstract = {

Animals efficiently learn to navigate their environment. In the laboratory, naive mice explore their environment via highly structured trajectories and can learn to localize new spatial targets in as few as a handful of trials. It is unclear how such efficient learning is possible, since existing computational models of spatial navigation require far more experience to achieve comparable performance and do not attempt to explain the evolving structure of animal behavior during learning. To inform a new algorithm for rapid learning of navigational goals, we took inspiration from the reliable structure of behavior as mice learned to intercept hidden spatial targets. We designed agents that generate behavioral trajectories by controlling the speed and angular velocity of smooth path segments between anchor points. To rapidly learn good anchors, we use Bayesian inference on the history of rewarded and unrewarded trajectories to infer the probability that an anchor will be successful, and active sampling to trim hypothesized anchors. Agents learn within tens of trials to generate compact trajectories that intercept a target, capturing the evolution of behavioral structure and matching the upper limits of learning efficiency observed in mice. We further show that this algorithm can explain how mice avoid obstacles and rapidly adapt to target switches. Finally, we show that this framework naturally encompasses both egocentric and allocentric strategies for navigation.

}, doi = {10.1101/2025.09.24.678123}, url = {https://www.biorxiv.org/content/early/2025/09/24/2025.09.24.678123}, author = {AbdelRahman, Nada Y and Jiang, Wanchen and Coddington, Luke T and Gong, Sheng and Dudman, Joshua T and Hermundstad, Ann M} } @article {69957, title = {Compressive streak microscopy for fast sampling of fluorescent reporters of neural activity.}, journal = {Neurophotonics}, volume = {12}, year = {2025}, month = {2025 Apr 12}, pages = {025013}, abstract = {

SIGNIFICANCE: one-photon fluorescence imaging of calcium and voltage indicators expressed in neurons enables noninvasive recordings of neural activity with submillisecond precision. However, data acquisition speed is limited by the frame rate of cameras.

AIM: We developed a compressive streak fluorescence microscope to record fluorescence in individual neurons at high speeds ( frames per second) exceeding the nominal frame rate of the camera by trading off spatial pixels for temporal resolution.

APPROACH: Our microscope leverages a digital micromirror device for targeted illumination, a galvo mirror for temporal scanning, and a ridge regression algorithm for fast computational reconstruction of fluorescence traces with high temporal resolution.

RESULTS: In simulations, the ridge regression algorithm reconstructs traces of high temporal resolution with limited signal loss. Validation experiments with fluorescent beads and experiments in larval zebrafish demonstrate accurate reconstruction with a data compression ratio of 10 and accurate recordings of neural activity with 200- to 400-Hz sampling speeds.

CONCLUSIONS: Our compressive microscopy enables new experimental capabilities to monitor activity at a sampling speed that outpaces the nominal frame rate of the camera.

}, issn = {2329-423X}, doi = {10.1117/1.NPh.12.2.025013}, url = {https://doi.org/10.1117/1.nph.12.2.025013}, author = {Cai, Changjia and Traubert, Owen and Tormes-Vaquerano, Jovan and Eybposh, M Hossein and Turaga, Srinivas C and Rodriguez-Romaguera, Jose and Naumann, Eva A and P{\'e}gard, Nicolas C} } @article {69748, title = {Conjoint specification of action by neocortex and striatum}, journal = {Neuron}, year = {2025}, month = {2025 Jan 20}, abstract = {

Summary The interplay between two major forebrain structures{\textemdash}cortex and subcortical striatum{\textemdash}is critical for flexible, goal-directed action. Traditionally, it has been proposed that striatum is critical for selecting what type of action is initiated, while the primary motor cortex is involved in specifying the continuous parameters of an upcoming/ongoing movement. Recent data indicate that striatum may also be involved in specification. These alternatives have been difficult to reconcile because comparing very distinct actions, as is often done, makes essentially indistinguishable predictions. Here, we develop quantitative models to reveal a somewhat paradoxical insight: only comparing neural activity across similar actions makes strongly distinguishing predictions. We thus developed a novel reach-to-pull task in which mice reliably selected between two similar but distinct reach targets and pull forces. Simultaneous cortical and subcortical recordings were uniquely consistent with a model in which cortex and striatum jointly specify continuous parameters governing movement execution.

}, keywords = {action selection, action specification, Basal Ganglia, computational model, motor control, Motor Cortex, neuropixels, Optogenetics, reinforcement learning, striatum}, issn = {0896-6273}, doi = {https://doi.org/10.1016/j.neuron.2024.12.024}, url = {https://www.sciencedirect.com/science/article/pii/S089662732400922X}, author = {Junchol Park and Peter Polidoro and Catia Fortunato and Jon Arnold and Brett Mensh and Juan A. Gallego and Joshua T. Dudman} } @article {70138, title = {The connectome interpreter toolkit}, journal = {bioRxiv}, year = {2025}, month = {2025 Sep 30}, abstract = {

Complete synaptic wiring diagrams, or connectomes, of whole brains open new opportunities for studying the structure-function relationship of neural circuits. However, the large number of nodes and edges in the graphs makes the analysis challenging. Here, we present the Connectome Interpreter (https://github.com/YijieYin/connectome_interpreter), an open-source software toolkit for efficient graph traversal to find polysynaptic pathways, compute the effective connectivity and receptive fields for arbitrarily deep neurons, slice out subcircuits, and non-linear but differentiable circuit modeling, implemented using efficient approaches tailored to the high density and size of connectomes such as that of the fruit fly Drosophila melanogaster. Our approach delivers results orders of magnitude faster than conventional methods in consumer computer hardware. We demonstrate the capabilities of our toolkit with select applications, including quantifying the density of polysynaptic connections in the whole adult fruit fly brain, exploring the necessity for non-linearities in circuit modeling, and combining known function of neurons with the connectome to aid in formulating hypotheses of circuit function.

}, doi = {10.1101/2025.09.29.679410}, url = {https://www.biorxiv.org/content/early/2025/09/30/2025.09.29.679410}, author = {Yin, Yijie and Hoeller, Judith and Mathiasen, Alexander and Tsang, Joanna and Charrier, Monique Estelle and Cardona, Albert} } @article {69997, title = {A connectomic resource for neural cataloguing and circuit dissection of the larval zebrafish brain}, journal = {bioRxiv}, year = {2025}, month = {2025 Jun 16}, abstract = {

We present a correlated light and electron microscopy (CLEM) dataset from a 7-day-old larval zebrafish, integrating confocal imaging of genetically labeled excitatory (vglut2a) and inhibitory (gad1b) neurons with nanometer-resolution serial section EM. The dataset spans the brain and anterior spinal cord, capturing \>180,000 segmented soma, \>40,000 molecularly annotated neurons, and 30 million synapses, most of which were classified as excitatory, inhibitory, or modulatory. To characterize the directional flow of activity across the brain, we leverage the synaptic and cell body annotations to compute region-wise input and output drive indices at single cell resolution. We illustrate the dataset{\textquoteright}s utility by dissecting and validating circuits in three distinct systems: water flow direction encoding in the lateral line, recurrent excitation and contralateral inhibition in a hindbrain motion integrator, and functionally relevant targeted long-range projections from a tegmental excitatory nucleus, demonstrating that this resource enables rigorous hypothesis testing as well as exploratory-driven circuit analysis. The dataset is integrated into an open-access platform optimized to facilitate community reconstruction and discovery efforts throughout the larval zebrafish brain.

Preprint: https://www.biorxiv.org/content/early/2025/06/15/2025.06.10.658982

}, doi = {10.1101/2025.06.10.658982}, url = {https://www.biorxiv.org/content/early/2025/06/15/2025.06.10.658982}, author = {Petkova, Mariela D. and Januszewski, Micha{\l} and Blakely, Tim and Herrera, Kristian J. and Schuhknecht, Gregor F.P. and Tiller, Robert and Choi, Jinhan and Schalek, Richard L. and Boulanger-Weill, Jonathan and Peleg, Adi and Wu, Yuelong and Wang, Shuohong and Troidl, Jakob and Kumar Vohra, Sumit and Wei, Donglai and Lin, Zudi and Bahl, Armin and Tapia, Juan Carlos and Iyer, Nirmala and Miller, Zachary T. and Hebert, Kathryn B. and Pavarino, Elisa C. and Taylor, Milo and Deng, Zixuan and Stingl, Moritz and Hockling, Dana and Hebling, Alina and Wang, Ruohong C. and Zhang, Lauren L. and Dvorak, Sam and Faik, Zainab and King, Kareem I. and Goel, Pallavi and Wagner-Carena, Julian and Aley, David and Chalyshkan, Selimzhan and Contreas, Dominick and Li, Xiong and Muthukumar, Akila V. and Vernaglia, Marina S. and Carrasco, Teodoro Tapia and Melnychuck, Sofia and Yan, TingTing and Dalal, Ananya and DiMartino, James M. and Brown, Sam and Safo-Mensa, Nana and Greenberg, Ethan and Cook, Michael and Finley-May, Samantha and Flynn, Miriam A. and Hopkins, Gary Patrick and Kovalyak, Julie and Leonard, Meghan and Lohff, Alanna and Ordish, Christopher and Scott, Ashley L. and Takemura, Satoko and Walsh, Claire and Walsh, John J. and Berger, Daniel R. and Pfister, Hanspeter and Berg, Stuart and Knecht, Christopher and Meissner, Geoffrey W. and Korff, Wyatt and Ahrens, Misha B. and Jain, Viren and Lichtman, Jeff W. and Engert, Florian} } @article {70134, title = {COOKIE-Pro: covalent inhibitor binding kinetics profiling on the proteome scale.}, journal = {Nat Commun}, volume = {16}, year = {2025}, month = {2025 Sep 30}, pages = {8373}, abstract = {

Covalent inhibitors are an emerging class of therapeutics, but methods to comprehensively profile their binding kinetics and selectivity across the proteome have been limited. Here we introduce COOKIE-Pro (COvalent Occupancy KInetic Enrichment via Proteomics), an unbiased method for quantifying irreversible covalent inhibitor binding kinetics on a proteome-wide scale. COOKIE-Pro uses a two-step incubation process with mass spectrometry-based proteomics to determine k and K values for covalent inhibitors against both on-target and off-target proteins. We validated COOKIE-Pro using BTK inhibitors spebrutinib and ibrutinib, accurately reproducing known kinetic parameters and identifying both expected and unreported off-targets. The method revealed that spebrutinib has over 10-fold higher potency for TEC kinase compared to its intended target BTK. To demonstrate the method{\textquoteright}s utility for high-throughput screening, we applied a streamlined two-point strategy to a library of 16 covalent fragments. This approach successfully generated thousands of kinetic profiles, enabling the quantitative decoupling of intrinsic chemical reactivity from binding affinity at scale and validating the method{\textquoteright}s broad applicability. By providing a comprehensive view of covalent inhibitor binding across the proteome, COOKIE-Pro represents a powerful tool for optimizing the potency and selectivity of covalent drugs during preclinical development.

bioRxiv preprint: https://doi.org/10.1101/2025.06.19.660637

}, keywords = {Adenine, Agammaglobulinaemia Tyrosine Kinase, High-Throughput Screening Assays, Humans, Kinetics, Mass Spectrometry, Piperidines, Protein Binding, Protein Kinase Inhibitors, Proteome, Proteomics, Pyrazoles, Pyrimidines}, issn = {2041-1723}, doi = {10.1038/s41467-025-63491-2}, url = {https://doi.org/10.1038/s41467-025-63491-2}, author = {Lin, Hanfeng and Yang, Bin and Ding, Lang and Yang, Yen-Yu and Holt, Matthew V and Jung, Sung Yun and Zhang, Bing and Wang, Meng C and Wang, Jin} } @article {69783, title = {Cortical control of innate behavior from subcortical demonstration}, journal = {bioRxiv}, year = {2025}, month = {2025 Feb 13}, abstract = {

Motor control in mammals is traditionally viewed as a hierarchy of descending spinal-targeting pathways, with frontal cortex at the top 1{\textendash}3. Many redundant muscle patterns can solve a given task, and this high dimensionality allows flexibility but poses a problem for efficient learning 4. Although a feasible solution invokes subcortical innate motor patterns, or primitives, to reduce the dimensionality of the control problem, how cortex learns to utilize such primitives remains an open question 5{\textendash}7. To address this, we studied cortical and subcortical interactions as head-fixed mice learned contextual control of innate hindlimb extension behavior. Na{\"\i}ve mice performed reactive extensions to turn off a cold air stimulus within seconds and, using predictive cues, learned to avoid the stimulus altogether in tens of trials. Optogenetic inhibition of large areas of rostral cortex completely prevented avoidance behavior, but did not impair hindlimb extensions in reaction to the cold air stimulus. Remarkably, mice covertly learned to avoid the cold stimulus even without any prior experience of successful, cortically-mediated avoidance. These findings support a dynamic, heterarchical model in which the dominant locus of control can change, on the order of seconds, between cortical and subcortical brain areas. We propose that cortex can leverage periods when subcortex predominates as demonstrations, to learn parameterized control of innate behavioral primitives.

}, doi = {10.1101/2025.02.12.637930}, url = {https://www.biorxiv.org/content/early/2025/02/13/2025.02.12.637930}, author = {Keller, Jason A. and Kwak, Iljung S. and Stark, Alyssa K. and Pachitariu, Marius and Branson, Kristin and Dudman, Joshua T.} } @article {69458, title = {Courtship song differs between African and European populations of Drosophila melanogaster and involves a strong effect locus}, journal = {G3 Genes|Genomes|Genetics}, year = {2025}, month = {2025 Mar 07}, abstract = {

The courtship song of\ Drosophila melanogaster\ has long served as an excellent model system for studies of animal communication and differences in courtship song have been demonstrated among populations and between species. Here, we report that flies of African and European origin, which diverged approximately 13,000 years ago, show significant genetic differentiation in the use of slow versus fast pulse song. Using a combination of quantitative trait mapping and population genetic analysis we detected a single strong QTL underlying this trait and we identified candidate genes that may contribute to the evolution of this trait. Song trait variation between parental strains of our recombinant inbred panel enabled detection of genomic intervals associated with six additional song traits, some of which include known courtship-related genes. These findings improve the prospects for further genetic insights into the evolution of reproductive behavior and the biology underlying courtship song.

bioRxiv Preprint:\ https://www.biorxiv.org/content/early/2024/05/17/2024.05.14.594231

}, doi = {10.1093/g3journal/jkaf050}, url = {https://doi.org/10.1093/g3journal/jkaf050}, author = {Lollar, Matthew J. and Kim, Elizabeth and Stern, David L. and Pool, John E.} } @article {69732, title = {A critical initialization for biological neural networks}, journal = {bioRxiv}, year = {2025}, month = {01/2025}, abstract = {

Artificial neural networks learn faster if they are initialized well. Good initializations can generate high-dimensional macroscopic dynamics with long timescales. It is not known if biological neural networks have similar properties. Here we show that the eigenvalue spectrum and dynamical properties of large-scale neural recordings in mice (two-photon and electrophysiology) are similar to those produced by linear dynamics governed by a random symmetric matrix that is critically normalized. An exception was hippocampal area CA1: population activity in this area resembled an efficient, uncorrelated neural code, which may be optimized for information storage capacity. Global emergent activity modes persisted in simulations with sparse, clustered or spatial connectivity. We hypothesize that the spontaneous neural activity reflects a critical initialization of whole-brain neural circuits that is optimized for learning time-dependent tasks.

}, doi = {10.1101/2025.01.10.632397}, url = {https://www.biorxiv.org/content/early/2025/01/10/2025.01.10.632397}, author = {Pachitariu, Marius and Zhong, Lin and Gracias, Alexa and Minisi, Amanda and Lopez, Crystall and Stringer, Carsen} } @article {69985, title = {Cross-species comparative connectomics reveals the evolution of an olfactory circuit}, journal = {bioRxiv}, year = {2025}, month = {2025 Jun 11}, abstract = {

Animal behavioural diversity ultimately stems from variation in neural circuitry, yet how central neural circuits evolve remains poorly understood. Studies of neural circuit evolution often focus on a few elements within a network. However, addressing fundamental questions in evolutionary neuroscience, such as whether some elements are more evolvable than others, requires a more global and unbiased approach. Here, we used synapse-level comparative connectomics to examine how an entire olfactory circuit evolves. We compared the full antennal lobe connectome of the larvae of two closely related Drosophila species, D. melanogaster and D. erecta, which differ in their ecological niches and odour-driven behaviours. We found that evolutionary change is unevenly distributed across the network. Some features, including neuron types, neuron numbers and interneuron-to-interneuron connectivity, are highly conserved. These conserved elements delineate a core circuit blueprint presumably required for fundamental olfactory processing. Superimposed on this scaffold, we find rewiring changes that mirror each species ecologies, including a systematic shift in the excitation-to-inhibition balance in the feedforward pathways. We further show that some neurons have changed more than others, and that even within individual neurons some synaptic elements remain conserved while others display major species-specific changes, suggesting evolutionary hot-spots within the circuit. Our findings reveal constrained and adaptable elements within olfactory networks, and establish a framework for identifying general principles in the evolution of neural circuits underlying behaviour.

}, doi = {10.1101/2025.06.11.659158}, url = {https://www.biorxiv.org/content/early/2025/06/11/2025.06.11.659158}, author = {Roberts, Ruairi and Giez, Christoph and Dhawan, Serene and Pang, Song and Randel, Nadine and Zhiyuan, Lu and Gong, Hui and Dekens, Leonard and DiFrisco, James and Xu, C Shan and Hess, Harald and Zlatic, Marta and Cardona, Albert and Prieto-Godino, Lucia L.} } @article {69613, title = {Cross-Tissue Coordination between SLC Nucleoside Transporters Regulates Reproduction in Caenorhabditis elegans}, journal = {PLoS Genet}, year = {2025}, month = {2025 May 30}, abstract = {

Metabolism is fundamental to organism physiology and pathology. From the intricate network of metabolic reactions, diverse chemical molecules, collectively termed as metabolites, are produced. In multicellular organisms, metabolite communication between different tissues is vital for maintaining homeostasis and adaptation. However, the molecular mechanisms mediating these metabolite communications remain poorly understood. Here, we focus on nucleosides and nucleotides, essential metabolites involved in multiple cellular processes, and report the pivotal role of the SLC29A family of transporters in mediating nucleoside coordination between the soma and the germline. Through genetic analysis, we discovered that two Caenorhabditis elegans homologs of SLC29A transporters, Equilibrative Nucleoside Transporter ENT-1 and ENT-2, act in the germline and the intestine, respectively, to regulate reproduction. Their knockdown synergistically results in sterility. Further single-cell transcriptomic and targeted metabolomic profiling revealed that the ENT double knockdown specifically affects genes in the purine biosynthesis pathway and reduces the ratio of guanosine to adenosine levels. Importantly, guanosine supplementation into the body cavity/pseudocoelom through microinjection rescued the sterility caused by the ENT double knockdown, whereas adenosine microinjection had no effect. Together, these studies support guanosine as a rate limiting factor in the control of reproduction, uncover the previously unknown nucleoside/nucleotide communication between the soma and the germline essential for reproductive success, and highlight the significance of SLC-mediated cell-nonautonomous metabolite coordination in regulating organism physiology.

Preprint:\ https://doi.org/10.1101/2024.09.12.612591

}, doi = {10.1371/journal.pgen.1011425}, url = {https://doi.org/10.1371/journal.pgen.1011425}, author = {Guan, Youchen and Yu, Yong and Gao, Shihong Max and Ding, Lang and Zhao, Qian and Wang, Meng} } @article {70048, title = {Cryo-electron Microscopy of Vitreous Sections (CEMOVIS) application for model organisms}, journal = {Microscopy and Microanalysis}, volume = {31}, year = {2025}, month = {2025 Jul 25}, pages = {ozaf048.484}, abstract = {

Cryo-ultramicrotomy, developed by Bernhard in 1965 [1], has long been regarded as the pinnacle of achievement for electron microscopists. This technique allows biological samples to be sliced into ultrathin sections and examined in a cryo-electron microscope, revealing the most intricate subcellular structures without chemical fixation or staining. The advent of vitrification [2,3] and high-pressure freezing (HPF) technology [4,5] provided reliable methods for preserving cellular structures, and the introduction of diamond knife to cryo-ultramicrotomy [6] offering cryo-ultramicrotomists reassurance in consistency of the quality [7].

}, issn = {1431-9276}, doi = {10.1093/mam/ozaf048.484}, url = {https://doi.org/10.1093/mam/ozaf048.484}, author = {Uryu, Kunihiro and Zhao, Xiaowei and Shiozaki, Momoko and Yu, Zhiheng} } @article {69722, title = {Days-old zebrafish rapidly learn to recognize threatening agents through noradrenergic and forebrain circuits.}, journal = {Curr Biol}, volume = {35}, year = {2025}, month = {12/2024}, pages = {163-176.e4}, abstract = {

Animals need to rapidly learn to recognize and avoid predators. This ability may be especially important for young animals due to their increased vulnerability. It is unknown whether, and how, nascent vertebrates are capable of such rapid learning. Here, we used a robotic predator-prey interaction assay to show that 1\ week after fertilization-a developmental stage where they have approximately 1\% the number of neurons of adults-zebrafish larvae rapidly and robustly learn to recognize a stationary object as a threat after the object pursues the fish for \~{}1\ min. Larvae continue to avoid the threatening object after it stops moving and can learn to distinguish threatening from non-threatening objects of a different color. Whole-brain functional imaging revealed the multi-timescale activity of noradrenergic neurons and forebrain circuits that encoded the threat. Chemogenetic ablation of those populations prevented the learning. Thus, a noradrenergic and forebrain multiregional network underlies the ability of young vertebrates to rapidly learn to recognize potential predators within their first week of life.

}, keywords = {Adrenergic Neurons, Animals, Larva, Learning, Predatory Behavior, Prosencephalon, Zebrafish}, issn = {1879-0445}, doi = {10.1016/j.cub.2024.11.057}, author = {Zocchi, Dhruv and Nguyen, Millen and Marquez-Legorreta, Emmanuel and Siwanowicz, Igor and Singh, Chanpreet and Prober, David A and Hillman, Elizabeth M C and Ahrens, Misha B} } @article {69719, title = {Deep learning-based aberration compensation improves contrast and resolution in fluorescence microscopyAbstract}, journal = {Nature Communications}, volume = {16}, year = {2025}, month = {Jan-12-2025}, abstract = {

Optical aberrations hinder fluorescence microscopy of thick samples, reducing image signal, contrast, and resolution. Here we introduce a deep learning-based strategy for aberration compensation, improving image quality without slowing image acquisition, applying additional dose, or introducing more optics. Our method (i) introduces synthetic aberrations to images acquired on the shallow side of image stacks, making them resemble those acquired deeper into the volume and (ii) trains neural networks to reverse the effect of these aberrations. We use simulations and experiments to show that applying the trained {\textquoteleft}de-aberration{\textquoteright} networks outperforms alternative methods, providing restoration on par with adaptive optics techniques; and subsequently apply the networks to diverse datasets captured with confocal, light-sheet, multi-photon, and super-resolution microscopy. In all cases, the improved quality of the restored data facilitates qualitative image inspection and improves downstream image quantitation, including orientational analysis of blood vessels in mouse tissue and improved membrane and nuclear segmentation in\ C. elegans\ embryos.

}, doi = {10.1038/s41467-024-55267-x}, url = {https://www.nature.com/articles/s41467-024-55267-xhttps://www.nature.com/articles/s41467-024-55267-x.pdfhttps://www.nature.com/articles/s41467-024-55267-x.pdfhttps://www.nature.com/articles/s41467-024-55267-x}, author = {Guo, Min and Wu, Yicong and Hobson, Chad M. and Su, Yijun and Qian, Shuhao and Krueger, Eric and Christensen, Ryan and Kroeschell, Grant and Bui, Johnny and Chaw, Matthew and Zhang, Lixia and Liu, Jiamin and Hou, Xuekai and Han, Xiaofei and Lu, Zhiye and Ma, Xuefei and Zhovmer, Alexander and Combs, Christian and Moyle, Mark and Yemini, Eviatar and Liu, Huafeng and Liu, Zhiyi and Benedetto, Alexandre and La Riviere, Patrick and Col{\'o}n-Ramos, Daniel and Shroff, Hari} } @article {69880, title = {DeepPD: Joint phase and object estimation from phase diversity with neural calibration of a deformable mirror}, journal = {arXiv}, year = {2025}, month = {2025 Apr 19}, abstract = {

Sample-induced aberrations and optical imperfections limit the resolution of fluorescence microscopy. Phase diversity is a powerful technique that leverages complementary phase information in sequentially acquired images with deliberately introduced aberrations--the phase diversities--to enable phase and object reconstruction and restore diffraction-limited resolution. These phase diversities are typically introduced into the optical path via a deformable mirror. Existing phase-diversity-based methods are limited to Zernike modes, require large numbers of diversity images, or depend on accurate mirror calibration--which are all suboptimal. We present DeepPD, a deep learning-based framework that combines neural representations of the object and wavefront with a learned model of the deformable mirror to jointly estimate both object and phase from only five images. DeepPD improves robustness and reconstruction quality over previous approaches, even under severe aberrations. We demonstrate its performance on calibration targets and biological samples, including immunolabeled myosin in fixed PtK2 cells.

}, doi = {10.48550/arxiv.2504.14157}, url = {https://doi.org/10.48550/arxiv.2504.14157}, author = {Magdalena C. Schneider and Courtney Johnson and C{\'e}dric Allier and Larissa Heinrich and Diane Adjavon and Joren Husic and Patrick La Riviere and Stephan Saalfeld and Hari Shroff} } @article {69457, title = {Deep-tissue transcriptomics and subcellular imaging at high spatial resolution}, journal = {Science}, year = {2025}, month = {2025 Feb 20}, abstract = {

Limited color channels in fluorescence microscopy have long constrained spatial analysis in biological specimens. Here, we introduce cycle Hybridization Chain Reaction (HCR), a method that integrates multicycle DNA barcoding with HCR to overcome this limitation. cycleHCR enables highly multiplexed imaging of RNA and proteins using a unified barcode system. Whole-embryo transcriptomics imaging achieved precise three-dimensional gene expression and cell fate mapping across a specimen depth of ~310 μm. When combined with expansion microscopy, cycleHCR revealed an intricate network of 10 subcellular structures in mouse embryonic fibroblasts. In mouse hippocampal slices, multiplex RNA and protein imaging uncovered complex gene expression gradients and cell-type-specific nuclear structural variations. cycleHCR provides a quantitative framework for elucidating spatial regulation in deep tissue contexts for research and potentially diagnostic applications.

Preprint: https://doi.org/10.1101/2024.05.17.594641

}, doi = { 10.1126/science.adq2084}, url = {https://www.science.org/doi/10.1126/science.adq2084}, author = {Gandin, Valentina and Kim, Jun and Yang, Liang-Zhong and Lian, Yumin and Kawase, Takashi and Hu, Amy and Rokicki, Konrad and Fleishman, Greg and Tillberg, Paul and Aguilera Castrejon, Alejandro and Stringer, Carsen and Preibisch, Stephan and Liu, Zhe J.} } @article {69841, title = {DELTA: A method for brain-wide measurement of synaptic protein turnover reveals localized plasticity during learning.}, journal = {Nat Neurosci}, year = {2025}, month = {2025 Mar 31}, abstract = {

Synaptic plasticity alters neuronal connections in response to experience, which is thought to underlie learning and memory. However, the loci of learning-related synaptic plasticity, and the degree to which plasticity is localized or distributed, remain largely unknown. Here we describe a new method, DELTA, for mapping brain-wide changes in synaptic protein turnover with single-synapse resolution, based on Janelia Fluor dyes and HaloTag knock-in mice. During associative learning, the turnover of the ionotropic glutamate receptor subunit GluA2, an indicator of synaptic plasticity, was enhanced in several brain regions, most markedly hippocampal area CA1. More broadly distributed increases in the turnover of synaptic proteins were observed in response to environmental enrichment. In CA1, GluA2 stability was regulated in an input-specific manner, with more turnover in layers containing input from CA3 compared to entorhinal cortex. DELTA will facilitate exploration of the molecular and circuit basis of learning and memory and other forms of plasticity at scales ranging from single synapses to the entire brain.

}, issn = {1546-1726}, doi = {10.1038/s41593-025-01923-4}, url = {https://doi.org/10.1038/s41593-025-01923-4}, author = {Mohar, Boaz and Michel, Gabriela and Wang, Yi-Zhi and Hernandez, Veronica and Grimm, Jonathan B and Park, Jin-Yong and Patel, Ronak and Clarke, Morgan and Brown, Timothy A and Bergmann, Cornelius and Gebis, Kamil K and Wilen, Anika P and Liu, Bian and Johnson, Richard and Graves, Austin and Tchumatchenko, Tatjana and Savas, Jeffrey N and Fornasiero, Eugenio F and Huganir, Richard L and Tillberg, Paul W and Lavis, Luke D and Svoboda, Karel and Spruston, Nelson} } @article {69460, title = {Dendritic excitations govern back-propagation via a spike-rate accelerometer}, journal = {Nature Communications}, volume = {16}, year = {2025}, month = {2025 Feb 04}, abstract = {

Dendrites on neurons support nonlinear electrical excitations, but the computational significance of these events is not well understood. We developed molecular, optical, and analytical tools to map sub-millisecond voltage dynamics throughout the dendritic trees of CA1 pyramidal neurons under diverse optogenetic and synaptic stimulus patterns, in acute brain slices. We observed history-dependent spike back-propagation in distal dendrites, driven by locally generated Na+ spikes (dSpikes). Dendritic depolarization created a transient window for dSpike propagation, opened by A-type KV channel inactivation, and closed by slow NaV inactivation. Collisions of dSpikes with synaptic inputs triggered calcium channel and N-methyl-D-aspartate receptor (NMDAR)-dependent plateau potentials, with accompanying complex spikes at the soma. This hierarchical ion channel network acts as a spike-rate accelerometer, providing an intuitive picture of how dendritic excitations shape associative plasticity rules.

}, doi = {10.1038/s41467-025-55819-9}, url = {https://www.biorxiv.org/content/early/2024/05/18/2023.06.02.543490}, author = {Park, Pojeong and Wong-Campos, David and Itkis, Daniel G. and Lee, Byung Hun and Qi, Yitong and Davis, Hunter and Antin, Benjamin and Pasarkar, Amol and Grimm, Jonathan B. and Plutkis, Sarah E. and Holland, Katie L. and Paninski, Liam and Lavis, Luke D. and Cohen, Adam E.} } @article {69731, title = {Dense-core vesicles contain exosomes in secretory cells.}, journal = {Biophys J}, year = {2025}, month = {2025 Jun 03}, abstract = {

Dense-core vesicles (DCVs) are found in various types of cells, such as neurons, pancreatic β-cells, and chromaffin cells. These vesicles release transmitters, peptides, and hormones to regulate diverse functions, such as the stress response, immune response, behavior, and blood glucose levels. In traditional electron microscopy after chemical fixation, it is often reported that the dense cores occupy a portion of the vesicle towards the center and are surrounded by a clear halo. With electron microscopy following cryo-fixation in adrenal chromaffin cells, we report here that we did not observe halos, but dense cores filling up the entire vesicles suggesting that halos are likely the product of chemical fixation. More importantly, we observed that a fraction of DCVs contained 36-168 nm clear-core vesicles. A similar fraction of DCVs labeled with fluorescent false neurotransmitter FFN 511 or the dense-core matrix protein chromogranin A (CGA) were colocalized with fluorescently labeled or endogenous CD63 or ALIX, the membrane or lumen marker of \~{}40-160 nm exosomes. These results suggest that DCVs contain exosomes. Since exosomes are generally thought to reside within multivesicular bodies in the cytosol and are released to the extracellular space to mediate diverse cell-to-cell communications, our findings suggest that dense-core vesicle fusion from many cell types is a new source for releasing exosomes to mediate intercellular communications. Given that dense-core vesicle fusion mediates many physiological functions, such as stress responses, immune responses, behavior regulation, and blood glucose regulation, exosome release from dense-core vesicle fusion might contribute to mediating these important functions.

}, issn = {1542-0086}, doi = {10.1016/j.bpj.2025.01.003}, author = {Wang, Xin and Arpino, Gianvito and Mohseni, Ammar and Bleck, Christopher K E and Wu, Ling-Gang} } @article {69801, title = {De-risking transformative microscopy technologies for broad adoption.}, journal = {J Microsc}, year = {2025}, month = {2025 Feb 27}, abstract = {

The past 20 years have seen a paradigm-shifting explosion of new optical microscopy technologies aimed at uncovering fundamental biological insights. Yet only a small portion {\textquoteright}cross the finish line{\textquoteright} into wide adoption by the life science community. We contend that this is not primarily due to a lack of technical prowess or utility. Rather, many risks can conspire to derail the adoption of potentially disruptive technologies. One way to address these challenges is to de-risk paradigm-shifting inventions within open-access technology incubators. Here we detail the framework needed to shepherd innovative microscopy techniques through the often-treacherous adoption landscape to enable transformative scientific output.

}, issn = {1365-2818}, doi = {10.1111/jmi.13400}, author = {Aaron, Jesse and Chew, Teng-Leong} } @article {69718, title = {Design and Generation of TEMPO Reagents for Sequential Labeling and Manipulation of Vertebrate Cell Lineages.}, journal = {Methods Mol Biol}, volume = {2886}, year = {2025}, month = {01/2025}, pages = {327-353}, abstract = {

During development, cells undergo a sequence of specification events to form functional tissues and organs. To investigate complex tissue development, it is crucial to visualize how cell lineages emerge and to be able to manipulate regulatory factors with temporal control. We recently developed TEMPO (Temporal Encoding and Manipulation in a Predefined Order), a genetic tool to label with different colors and genetically manipulate consecutive cell generations in vertebrates. TEMPO relies on CRISPR to activate a cascade of fluorescent proteins which can be imaged in vivo. Here, we explain the steps to design, generate, and express TEMPO constructs in zebrafish and mice.

}, keywords = {Animals, Cell Lineage, CRISPR-Cas Systems, Luminescent Proteins, Mice, Staining and Labeling, Zebrafish}, issn = {1940-6029}, doi = {10.1007/978-1-0716-4310-5_17}, author = {Espinosa-Medina, Isabel} } @article {70054, title = {Design of Orthogonal Far-Red, Orange and Green Fluorophore-binding Proteins for Multiplex Imaging}, journal = {bioRxiv}, year = {2025}, month = {2025 Aug 03}, abstract = {

Fluorescent proteins have transformed biological imaging, yet their limited photostability and brightness restrict their applications. We used deep learning-based de novo protein design methods to design binders to three bright, stable and cell-permeable dyes spanning the imaging spectrum: JF657 (far red), JF596 (orange-red) and JF494 (green). We obtain highly specific dye-binding proteins with low nanomolar affinities for the intended target; a crystal structure of one binder confirms close resemblance to the design model. Simultaneous labeling of mammalian cells expressing three dye-specific binders at different subcellular compartments demonstrates the utility in multiplex imaging. We further expand the functionality of the binder by incorporating an active site that carries out nucleophilic aromatic substitution to form a covalent linkage with the dye, and develop split versions which reconstitute fluorescence at subcellular locations where both halves are present towards monitoring in-cell protein interactions and chemically induced dimerization. Our designed high affinity and specificity dye binders open up new opportunities for multiplexed biological imaging.

}, doi = {10.1101/2025.08.03.668343}, url = {https://www.biorxiv.org/content/early/2025/08/03/2025.08.03.668343}, author = {Tran, Long and Sharma, Shajesh and Klein, Steffen and Jurgens, David and Decarreau, Justin and Liu, Bingxu and Wang, Yujia and Bera, Asim K. and Kang, Alex and Woods, Jon and Joyce, Emily and Vafeados, Dionne K and Roullier, Nicole and Chen, Wei and Lee, Gyu Rie and Mahamid, Julia and Lavis, Luke D. and An, Linna and Baker, David} } @article {70171, title = {Design principles of ciliary signaling.}, journal = {J Cell Sci}, volume = {138}, year = {2025}, month = {2025 Oct 15}, abstract = {

Primary cilia are microtubule-based sensory organelles that have been conserved throughout eukaryotic evolution. As discussed in this Review, a cilium is an elongated and highly specialized structure, and, together with its ability to selectively traffic and concentrate proteins, lipids and second messengers, it creates a signaling environment distinct from the cell body. Ciliary signaling pathways adopt a bow-tie network architecture, in which diverse inputs converge on shared effectors and second messengers before diverging to multiple outputs. Unlike other cellular bow-tie systems, cells exploit ciliary geometry, compartmentalization and infrastructure to enhance sensitivity at multiple scales, from individual molecular reactions to entire signaling pathways. In cilia, integration of the bow-tie network architecture with their specialized structure and unique environment confers robustness and evolvability, which enables cilia to acquire diverse signaling roles. However, this versatility comes with vulnerability - rare mutations that disrupt the features most essential for cilia robustness cause multisystem ciliopathies.

}, keywords = {Animals, Cilia, Ciliopathies, Humans, Signal Transduction}, issn = {1477-9137}, doi = {10.1242/jcs.264325}, url = {https://doi.org/10.1242/jcs.264325}, author = {Ott, Carolyn M and Lippincott-Schwartz, Jennifer} } @article {69772, title = {Discovering symbolic cognitive models from human and animal behavior.}, journal = {bioRxiv}, year = {2025}, month = {2025 Feb 13}, abstract = {

Symbolic models play a key role in cognitive science, expressing computationally precise hypotheses about how the brain implements a cognitive process. Identifying an appropriate model typically requires a great deal of effort and ingenuity on the part of a human scientist. Here, we adapt FunSearch\ Romera-Paredes et al. (2024), a recently developed tool that uses Large Language Models (LLMs) in an evolutionary algorithm, to automatically discover symbolic cognitive models that accurately capture human and animal behavior. We consider datasets from three species performing a classic reward-learning task that has been the focus of substantial modeling effort, and find that the discovered programs outperform state-of-the-art cognitive models for each. The discovered programs can readily be interpreted as hypotheses about human and animal cognition, instantiating interpretable symbolic learning and decision-making algorithms. Broadly, these results demonstrate the viability of using LLM-powered program synthesis to propose novel scientific hypotheses regarding mechanisms of human and animal cognition.

}, doi = {10.1101/2025.02.05.636732}, url = {https://doi.org/10.1101/2025.02.05.636732}, author = {Castro, P. S. and Tomasev, N. and Anand, A. and Sharma, N. and Mohanta, R. and Perlin, K. and Jain, S. and Levin, K. and {\'E}ltet{\H o}, N. and Dabney, W. and Novikov, A. and Eckstein, M. K. and Daw, N. D. and Miller, K. J. and Stachenfeld, K. L.} } @article {69603, title = {Disrupted developmental signaling induces novel transcriptional states}, journal = {Proc Natl Acad Sci U S A}, year = {2025}, month = {2025 October 28}, abstract = {

Signaling pathways induce stereotyped transcriptional changes as stem cells progress into mature cell types during embryogenesis. Signaling perturbations are necessary to discover which genes are responsive or insensitive to pathway activity. However, gene regulation is additionally dependent on cell state-specific factors like chromatin modifications or transcription factor binding. Thus, transcriptional profiles need to be assayed in single cells to identify potentially multiple, distinct perturbation responses among heterogeneous cell states in an embryo. In perturbation studies, comparing heterogeneous transcriptional states among experimental conditions often requires samples to be collected over multiple independent experiments, which can introduce confounding batch effects. We present Design-Aware Integration of Single Cell ExpEriments (DAISEE), a new algorithm that models perturbation responses in single-cell datasets collected according to complex experimental designs. We demonstrate that DAISEE improves upon a previously available integrative nonnegative matrix factorization framework, more efficiently separating perturbation responses from confounding variation. We use DAISEE to integrate newly collected single-cell RNA sequencing datasets from 5-h-old zebrafish embryos expressing optimized photoswitchable MEK (psMEK), which globally activates the extracellular signal-regulated kinase (ERK), a signaling molecule involved in many cell specification events. psMEK drives some cells that are normally not exposed to ERK signals toward other wild type states and induces novel states expressing early-acting endothelial genes. Overactive signaling is therefore capable of producing unexpected gene expression states in developing embryos.

bioRxiv preprint:\ https://www.doi.org/10.1101/2024.09.05.610903

}, doi = {10.1073/pnas.2418351122}, url = {https://doi.org/10.1073/pnas.2418351122}, author = {Patel, Aleena and Gonzalez, Vanessa and Menon, Triveni and Shvartsman, Stanislav Y. and Burdine, Rebecca and Avdeeva, Maria} } @article {70047, title = {Distributed control circuits across a brain-and-cord connectome}, journal = {bioRxiv}, year = {2025}, month = {2025 Aug 02}, abstract = {

Just as genomes revolutionized molecular genetics, connectomes (maps of neurons and synapses) are transforming neuroscience. To date, the only species with complete connectomes are worms\ and sea squirts\ (103-104 synapses). By contrast, the fruit fly is more complex (108 synaptic connections), with a brain that supports learning and spatial memory and an intricate ventral nerve cord analogous to the vertebrate spinal cord. Here we report the first adult fly connectome that unites the brain and ventral nerve cord, and we leverage this resource to investigate principles of neural control. We show that effector cells (motor neurons, endocrine cells and efferent neurons targeting the viscera) are primarily influenced by local sensory cells in the same body part, forming local feedback loops. These local loops are linked by long-range circuits involving ascending and descending neurons organized into behavior-centric modules. Single ascending and descending neurons are often positioned to influence the voluntary movements of multiple body parts, together with endocrine cells or visceral organs that support those movements. Brain regions involved in learning and navigation supervise these circuits. These results reveal an architecture that is distributed, parallelized and embodied (tightly connected to effectors), reminiscent of distributed control architectures in engineered systems.

}, doi = {10.1101/2025.07.31.667571}, url = {https://www.biorxiv.org/content/early/2025/08/02/2025.07.31.667571}, author = {Bates, Alexander Shakeel and Phelps, Jasper S. and Kim, Minsu and Yang, Helen H. and Matsliah, Arie and Ajabi, Zaki and Perlman, Eric and Delgado, Kevin M. and Osman, Mohammed Abdal Monium and Salmon, Christopher K. and Gager, Jay and Silverman, Benjamin and Renauld, Sophia and Collie, Matthew F. and Fan, Jingxuan and Pacheco, Diego A. and Zhao, Yunzhi and Patel, Janki and Zhang, Wenyi and Serratosa Capdevilla, Laia and Roberts, Ruair{\'\i} J.V. and Munnelly, Eva J. and Griggs, Nina and Langley, Helen and Moya-Llamas, Borja and Maloney, Ryan T. and Yu, Szi-Chieh and Sterling, Amy R. and Sorek, Marissa and Kruk, Krzysztof and Serafetinidis, Nikitas and Dhawan, Serene and St{\"u}rner, Tomke and Klemm, Finja and Brooks, Paul and Lesser, Ellen and Jones, Jessica M. and Pierce-Lundgren, Sara E. and Lee, Su-Yee and Luo, Yichen and Cook, Andrew P. and McKim, Theresa H. and Kophs, Emily C. and Falt, Tjalda and Negr{\'o}n Morales, Alexa M. and Burke, Austin and Hebditch, James and Willie, Kyle P. and Willie, Ryan and Popovych, Sergiy and Kemnitz, Nico and Ih, Dodam and Lee, Kisuk and Lu, Ran and Halageri, Akhilesh and Bae, J. Alexander and Jourdan, Ben and Schwartzman, Gregory and Demarest, Damian D. and Behnke, Emily and Bland, Doug and Kristiansen, Anne and Skelton, Jaime and Stocks, Tom and Garner, Dustin and Salman, Farzaan and Daly, Kevin C. and Hernandez, Anthony and Kumar, Sandeep and The BANC-FlyWire Consortium and Dorkenwald, Sven and Collman, Forrest and Suver, Marie P. and Fenk, Lisa M. and Pankratz, Michael J. and Jefferis, Gregory S.X.E. and Eichler, Katharina and Seeds, Andrew M. and Hampel, Stefanie and Agrawal, Sweta and Zandawala, Meet and Macrina, Thomas and Adjavon, Diane-Yayra and Funke, Jan and Tuthill, John C. and Azevedo, Anthony and Seung, H. Sebastian and de Bivort, Benjamin L. and Murthy, Mala and Drugowitsch, Jan and Wilson, Rachel I. and Lee, Wei-Chung Allen} } @article {70199, title = {The efficacy of longevity interventions in Caenorhabditis elegans is determined by the early life activity of RNA splicing factors.}, journal = {PLoS Biol}, volume = {23}, year = {2025}, month = {2025 Nov 21}, pages = {e3003504}, abstract = {

Geroscience aims to target the aging process to extend healthspan. However, even isogenic individuals show heterogeneity in natural aging rate and responsiveness to pro-longevity interventions, limiting translational potential. Using RNAseq analysis of young, isogenic, subpopulations of Caenorhabditis elegans selected solely on the basis of the splicing pattern of an in vivo minigene reporter that is predictive of future life expectancy, we find a strong correlation in young animals between predicted life span and alternative splicing of mRNAs related to lipid metabolism. The activity of two RNA splicing factors, Reversed Polarity-1 (REPO-1) and Splicing Factor 1 (SFA-1), early in life is necessary for C. elegans response to specific longevity interventions and leads to context-specific changes to fat content that is mirrored by knockdown of their direct target POD-2/ACC1. Moreover, POD-2/ACC1 is required for the same longevity interventions as REPO-1/SFA-1. In addition, early inhibition of REPO-1 renders animals refractory to late onset suppression of the TORC1 pathway. Together, we propose that splicing factor activity establishes a cellular landscape early in life that enables responsiveness to specific longevity interventions and may explain variance in efficacy between individuals.

}, issn = {1545-7885}, doi = {10.1371/journal.pbio.3003504}, url = {https://doi.org/10.1371/journal.pbio.3003504}, author = {Dutta, Sneha and Perez Matos, Maria Camila and Heintz, Caroline and Mutlu, Ayse Sena and Piper, Mary and Mistry, Meeta and Sharma, Arpit and Morrow, Christopher S and Smith, Hannah and Howell, Porsha and Sehgal, Rohan and Lanjuin, Anne and Wang, Meng C and Mair, William B} } @article {70017, title = {Efficient planning and implementation of optimal foraging strategies under energetic constraints}, journal = {PNAS Nexus}, year = {2025}, month = {2026 Jan 17}, abstract = {

To successfully forage for food, animals must balance the energetic cost of searching for food sources with the energetic benefit of exploiting those sources. While the Marginal Value Theorem provides one normative account of this balance by specifying that a forager should leave a food patch when its energetic yield falls below the average yield of other patches in the environment, it assumes the presence of other readily reachable patches. In natural settings, however, a forager does not know whether it will encounter additional food patches, and it must balance potential energetic costs and benefits accordingly. Upon first encountering a patch of food, it faces a decision of whether and when to leave the patch in search of better options, and when to return if no better options are found. Here, we explore how a forager should structure its search for new food patches when the existence of those patches is unknown, and when searching for those patches requires energy that can only be harvested from a single known food patch. We identify conditions under which it is more favorable to explore the environment in several successive trips rather than in a single long exploration, and we show how the optimal sequence of trips depends on the forager{\textquoteright}s beliefs about the distribution and nutritional content of food patches in the environment. This optimal strategy is well approximated by a local decision that can be implemented by a simple neural circuit architecture. Together, this work highlights how energetic constraints and prior beliefs shape optimal foraging strategies, and how such strategies can be approximated by simple neural networks that implement local decision rules.

}, issn = {2692-8205}, doi = {10.1093/pnasnexus/pgag009}, url = {https://doi.org/10.1093/pnasnexus/pgag009}, author = {Guo, Yipei and Hermundstad, Ann M} } @article {70148, title = {Emergence of Functional Heart-Brain Circuits in a Vertebrate.}, journal = {eLife}, year = {2025}, month = {2025 Dec 22}, abstract = {

The early formation of sensorimotor circuits is essential for survival. While the development and function of exteroceptive circuits and their associated motor pathways are well characterized, far less is known about the circuits that convey viscerosensory inputs to the brain and transmit visceromotor commands from the central nervous system to internal organs. Technical limitations, such as the\ in utero\ development of viscerosensory and visceromotor circuits and the invasiveness of procedures required to access them, have hindered studies of their functional development in mammals. Using larval zebrafish{\textemdash}which are genetically accessible and optically transparent{\textemdash}we tracked,\ in vivo, how cardiosensory and cardiomotor neural circuits assemble and begin to function. We uncovered a staged program. First, a minimal efferent circuit suffices for heart-rate control: direct brain-to-heart vagal motor innervation is required, intracardiac neurons are not, and heart rate is governed exclusively by the motor vagus nerve. Within the hindbrain, we functionally localize a vagal premotor population that drives this early efferent control. Second, sympathetic innervation arrives and enhances the dynamics and amplitude of cardiac responses, as neurons in the most anterior sympathetic ganglia acquire the ability to drive cardiac acceleration. These neurons exhibit proportional, integral, and derivative{\textendash}like relationships to heart rate, consistent with controller motifs that shape gain and dynamics. Third, vagal sensory neurons innervate the heart. Distinct subsets increase activity when heart rate falls or rises, and across spontaneous fluctuations, responses to aversive stimuli, and optogenetically evoked cardiac perturbations, their dynamics are captured by a single canonical temporal kernel with neuron-specific phase offsets, supporting a population code for heart rate. This temporally segregated maturation isolates three experimentally tractable regimes{\textemdash}unidirectional brain-to-heart communication, dual efferent control, and closed-loop control after sensory feedback engages{\textemdash}providing a framework for mechanistic dissection of organism-wide heart{\textendash}brain circuits.

}, issn = {2692-8205}, doi = {10.1101/2025.09.22.677693}, url = {https://doi.org/10.7554/eLife.109362.1}, author = {Hernandez-Nunez, L and Avrami, J and Shi, S and Markarian, A and Ruetten, Virginia M.S. and Boulanger-Weill, J and Zarghani-Shiraz, A and Ahrens, M and Engert, F and Fishman, M C} } @article {69745, title = {Encoding of cerebellar dentate neuron activity during visual attention in rhesus macaques.}, journal = {Elife}, volume = {13}, year = {2025}, month = {2025 Jan 16}, abstract = {

The role of cerebellum in controlling eye movements is well established, but its contribution to more complex forms of visual behavior has remained elusive. To study cerebellar activity during visual attention we recorded extracellular activity of dentate nucleus (DN) neurons in two non-human primates (NHPs). NHPs were trained to read the direction indicated by a peripheral visual stimulus while maintaining fixation at the center, and report the direction of the cue by performing a saccadic eye movement into the same direction following a delay. We found that single-unit DN neurons modulated spiking activity over the entire time course of the task, and that their activity often bridged temporally separated intra-trial events, yet in a heterogeneous manner. To better understand the heterogeneous relationship between task structure, behavioral performance, and neural dynamics, we constructed a behavioral, an encoding, and a decoding model. Both NHPs showed different behavioral strategies, which influenced the performance. Activity of the DN neurons reflected the unique strategies, with the direction of the visual stimulus frequently being encoded long before an upcoming saccade. Moreover, the latency of the ramping activity of DN neurons following presentation of the visual stimulus was shorter in the better performing NHP. Labeling with the retrograde tracer Cholera Toxin B in the recording location in the DN indicated that these neurons predominantly receive inputs from Purkinje cells in the D1 and D2 zones of the lateral cerebellum as well as neurons of the principal olive and medial pons, all regions known to connect with neurons in the prefrontal cortex contributing to planning of saccades. Together, our results highlight that DN neurons can dynamically modulate their activity during a visual attention task, comprising not only sensorimotor but also cognitive attentional components.

}, keywords = {Animals, Attention, Cerebellar Nuclei, Macaca mulatta, Male, Neurons, Photic Stimulation, Saccades, Visual Perception}, issn = {2050-084X}, doi = {10.7554/eLife.99696}, author = {Flierman, Nico A and Koay, Sue Ann and van Hoogstraten, Willem S and Ruigrok, Tom J H and Roelfsema, Pieter and Badura, Aleksandra and De Zeeuw, Chris I} } @article {70228, title = {Energy minimization for skyrmions on planar thin films}, journal = {arXiv}, year = {2025}, month = {2025 Sep 27}, abstract = {

We consider an energy functional that arises in micromagnetic and liquid crystal theory on thin films. In particular, our energy comprises a non-convex term that models anti-symmetric exchange as well as an anisotropy term. We devise an algorithm for energy minimization in the continuous case and show weak convergence of a subsequence towards a solution of the corresponding Euler--Lagrange equation. Furthermore, an algorithm for numerical energy minimization is presented. We show empirically that this numerical algorithm converges to the correct solutions for a benchmark problem without the need for user-supplied parameters, and present a rigorous convergence analysis for important special cases.

}, doi = {10.48550/arXiv.2509.23495}, url = {https://doi.org/10.48550/arXiv.2509.23495}, author = {Giovanni Di Fratta and Michael Innerberger and Dirk Praetorius and Valeriy Slastikov} } @article {70223, title = {Environmental dynamics impact whether matching is optimal}, journal = {PNAS Nexus}, year = {2025}, month = {2025 Dec 17}, pages = {pgaf392}, abstract = {

Foraging animals often sample options that yield rewards with different probabilities. In such scenarios, many animals exhibit {\textquotedblleft}matching{\textquotedblright}, whereby they allocate their choices such that the fraction of rewarded samples is equal across options. While matching can be optimal in environments with diminishing returns, this condition alone is not sufficient to determine optimality. Moreover, diminishing returns arise when resources deplete and replenish over time, but their form depends on the temporal structure and statistics of replenishment. Here, we investigate how these environmental properties influence whether matching is optimal. We consider an agent that samples options at fixed rates and derive the resulting reward probabilities across different types of environments. This allows us to analytically determine conditions under which the optimal policy exhibits matching. When all options share the same replenishment dynamics, matching emerges as optimal across a wide range of environments. However, when dynamics differ across options, optimal policies can deviate from matching. In such cases, the rank-ordering of observed reward probabilities depends only on the qualitative nature of the replenishment process, and not on the specific replenishment rates. As a result, the optimal policy can exhibit under- or over-matching depending on which options are more rewarding. We use this result to identify environments where performance differs substantially between matching and optimality. Finally, we show that fluctuations in replenishment rates{\textemdash}representing environmental stochasticity or internal uncertainty{\textemdash}can amplify deviations from matching. These findings deepen our understanding of the relationship between environmental variability and behavioral optimality, and provide testable predictions across diverse settings.

}, issn = {2752-6542}, doi = {10.1093/pnasnexus/pgaf392}, url = {https://doi.org/10.1093/pnasnexus/pgaf392}, author = {Guo, Yipei and Hermundstad, Ann M} } @article {69840, title = {EPSILON: A method for pulse-chase labeling to probe synaptic AMPAR exocytosis during memory formation.}, journal = {Nat Neurosci}, year = {2025}, month = {2025 Mar 31}, abstract = {

A tool to map changes in synaptic strength during a defined time window could provide powerful insights into the mechanisms of learning and memory. Here we developed a technique, Extracellular Protein Surface Labeling in Neurons (EPSILON), to map α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) exocytosis in vivo by sequential pulse-chase labeling of surface AMPARs with membrane-impermeable dyes. This approach yields synaptic-resolution maps of AMPAR exocytosis, a proxy for synaptic potentiation, in genetically targeted neurons during memory formation. In mice undergoing contextual fear conditioning, we investigated the relationship between synapse-level AMPAR exocytosis in CA1 pyramidal neurons and cell-level expression of the immediate early gene product cFos, a frequently used marker of engram neurons. We observed a strong correlation between AMPAR exocytosis and cFos expression, suggesting a synaptic mechanism for the association of cFos expression with memory engrams. The EPSILON technique is a useful tool for mapping synaptic plasticity and may be extended to investigate trafficking of other transmembrane proteins.

}, issn = {1546-1726}, doi = {10.1038/s41593-025-01922-5}, url = {https://doi.org/10.1038/s41593-025-01922-5}, author = {Kim, Doyeon and Park, Pojeong and Li, Xiuyuan and Wong-Campos, J David and Tian, He and Moult, Eric M and Grimm, Jonathan B and Lavis, Luke D and Cohen, Adam E} } @article {70178, title = {ER-to-Golgi trafficking is a nutrient-sensitive checkpoint linking glucose starvation to cell surface remodeling}, journal = {bioRxiv}, year = {2025}, month = {2025 October 31}, abstract = {

Cancer cells adapt to nutrient stress by remodeling the repertoire of proteins on their surface, enabling survival and progression under starvation conditions. However, the molecular mechanisms by which nutrient cues reshape the cell surface proteome to influence cell behavior remain largely unresolved. Here, we show that acute glucose starvation, but not amino acid deprivation or mTOR inhibition, selectively impairs ER-to-Golgi export of specific cargoes, such as E-cadherin, in a SEC24C-dependent manner. Quantitative cell surface proteomics reveal that glucose deprivation remodels the cell surface proteome, notably reducing surface expression of key adhesion molecules. This nutrient-sensitive reprogramming enhances cell migration in vitro and promotes metastasis in vivo. Mechanistically, we show that AMPK and ULK1 signaling orchestrate this process independent of autophagy, with ULK1-mediated phosphorylation of SEC31A driving SEC24C-dependent COPII reorganization. These findings establish ER-to-Golgi trafficking as a nutrient-sensitive regulatory node that links metabolic stress to cell surface remodeling and metastatic potential.

}, doi = {10.1101/2025.10.31.685804}, url = {https://www.biorxiv.org/content/early/2025/11/01/2025.10.31.685804}, author = {Joo, Joung Hyuck and Kasberg, William and Douglas, Spencer and Udoh, Uwemedimo and Carisey, Alexandre and Messing, James and Wang, Yong-Dong and Narina, Shilpa and Pruett-Miller, Shondra M. and Labelle, Myriam and Lippincott-Schwartz, Jennifer and Chang, Chi-Lun and Kundu, Mondira} } @article {68117, title = {An essential experimental control for functional connectivity mapping with optogenetics.}, journal = {Genetics}, volume = {231}, year = {2025}, month = {2025 Nov 12}, abstract = {

To establish functional connectivity between two candidate neurons that might form a circuit element, a common approach is to activate an optogenetic tool such as Chrimson in the candidate pre-synaptic neuron and monitor fluorescence of the calcium-sensitive indicator GCaMP in a candidate post-synaptic neuron. While performing such experiments in Drosophila, we found that low levels of leaky Chrimson expression can lead to strong artifactual GCaMP signals in presumptive postsynaptic neurons even when Chrimson is not intentionally expressed in any particular neurons. Withholding all-trans retinal, the chromophore required as a co-factor for Chrimson response to light, eliminates GCaMP signal but does not provide an experimental control for leaky Chrimson expression. Leaky Chrimson expression appears to be an inherent feature of current Chrimson transgenes, since artifactual connectivity was detected with Chrimson transgenes integrated into multiple genomic locations. While these false-positive signals may complicate the interpretation of functional connectivity experiments, we illustrate how a no-Gal4 negative control improves interpretability of functional connectivity assays. We also propose a simple but effective procedure to identify experimental conditions that minimize potentially incorrect interpretations caused by leaky Chrimson expression.

}, doi = {10.1093/genetics/iyaf174}, url = {https://doi.org/10.1093/genetics/iyaf174}, author = {David Tadres and Hiroshi M. Shiozaki and Ibrahim Tastekin and David L. Stern and Matthieu Louis} } @article {70120, title = {Establishing a continuum of cell types in the visual cortex}, journal = {bioRxiv}, year = {2025}, month = {2025 Sep 22}, abstract = {

The mammalian cerebral cortex is composed of neurons whose properties vary in a continuous fashion rather than falling into discrete cell types. In the mouse visual cortex, excitatory neurons in layer 2 and 3 (L2/3) form such a continuum along cortical depth, patterned by the graded expression of hundreds of genes. Here we sought to understand how this continuum develops and contributes to cortical wiring. Using single-nucleus multiomics (RNA- and ATAC-Seq) and spatial transcriptomics, we show that the L2/3 continuum is established in two phases. During the first postnatal week, a genetically hardwired program establishes a primitive continuum of cell identities spanning the depth of L2/3. The second program, promoted by visual experience, is later superimposed upon the preexisting continuum. This second phase is driven by activity-regulated transcription factors that drive the L2/3 depth-dependent expression of genes linked to synaptic function and plasticity. We show that neurons at different positions along the L2/3 continuum project preferentially to distinct higher visual areas and that visual deprivation disrupts targeting to some higher visual areas while sparing others. Thus, cortical continua emerge through a stepwise process in which genetic programs and sensory experience specify neuronal identity and sculpt intracortical wiring specificity.

}, doi = {10.1101/2025.09.22.677893}, url = {https://www.biorxiv.org/content/early/2025/09/22/2025.09.22.677893}, author = {Yoo, Juyoun and Xie, Fangming and Butrus, Salwan and Xu, Runzhe and Tan, Zhiqun and Gorzek, Ryan and Mirshahidi, Parmis and Tring, Elaine and Suresh, Sanjana and Kim, Jinho and Fleishman, Greg and Tan, Liming and Ringach, Dario and Trachtenberg, Joshua and Xu, Xiangmin and Zipursky, S. Lawrence and Shekhar, Karthik and Jain, Saumya} } @article {70083, title = {An expanded palette of bright and photostable organellar Ca2+ sensors}, journal = {eLife}, year = {2025}, month = {2025 Aug 26}, abstract = {

The use of fluorescent sensors for functional imaging has revolutionized the study of organellar Ca2+\ signaling. However, understanding the dynamic interplay between intracellular Ca2+\ sinks and sources has been hindered by the lack of bright, photostable, and multiplexed measurements in different organelles, limiting our ability to define how Ca2+\ shapes cell physiology across fields of biology. Here we introduce a new toolkit of chemigenetic organellar Ca2+\ indicators whose color is tunable by reconstituting their fluorescence with different exogenous rhodamine dye-ligands, which significantly expand the capacity for multiplexing organellar Ca2+\ measurements. These sensors, which we named ER-HaloCaMP and Mito-HaloCaMP, are optimized to report Ca2+dynamics in the endoplasmic reticulum (ER) and mitochondria of mammalian cells and neurons, and show significantly improved brightness, photostability and responsiveness when compared to current best-in-class alternatives. Using either red or far-red dye-ligands, both ER-HaloCaMP and Mito-HaloCaMP enable visualizing ER and mitochondrial Ca2+\ dynamics in neuronal axons, a subcellular location that only contains a few ER tubules and small mitochondria, structural limitations that have impaired measurements with previous red sensors. To show the expanded multiplexing capacities of our toolkit, we measured interorganellar Ca2+\ fluxes simultaneously in three different subcellular compartments in live cells, revealing that the amplitude of ER Ca2+release controls the efficacy of ER-mitochondria Ca2+\ coupling in a cooperative manner. Organellar HaloCaMPs enable also measuring Ca2+\ dynamics in intact brain tissue from flies and rodents, demonstrating their versatility across biological models. Our new toolkit provides an expanded palette of bright, photostable and responsive organellar Ca2+\ sensors, which will facilitate future studies of intracellular Ca2+\ signaling across fields of biology in health and disease.

}, doi = {10.7554/elife.107845.1}, url = {http://dx.doi.org/10.7554/eLife.107845.1}, author = {Moret, Agathe and Farrants, Helen and Fan, Ruolin and Zingg, Kelsey G and Silva, Bryon and Roselli, Camilla and Oertner, Thomas G and Gee, Christine E and Hadjieconomou, Dafni and Rangaraju, Vidhya and Schreiter, Eric R and de Juan-Sanz, Jaime} } @article {69846, title = {Far-red fluorescent genetically encoded calcium ion indicators.}, journal = {Nat Commun}, volume = {16}, year = {2025}, month = {2025 Apr 07}, pages = {3318}, abstract = {

Genetically encoded calcium ion (Ca) indicators (GECIs) are widely-used molecular tools for functional imaging of Ca dynamics and neuronal activities with single-cell resolution. Here we report the design and development of two far-red fluorescent GECIs, FR-GECO1a and FR-GECO1c, based on the monomeric far-red fluorescent proteins mKelly1 and mKelly2. FR-GECOs have excitation and emission maxima at ~596 nm and ~644 nm, respectively, display large responses to Ca in vitro (ΔF/F = 6 for FR-GECO1a, 18 for FR-GECO1c), are bright under both one-photon and two-photon illumination, and have high affinities (apparent K = 29 nM for FR-GECO1a, 83 nM for FR-GECO1c) for Ca. FR-GECOs offer sensitive and fast detection of single action potentials in neurons, and enable in vivo all-optical manipulation and measurement of cellular activities in combination with optogenetic actuators.

Preprint:\ https://doi.org/10.1101/2020.11.12.380089

}, keywords = {Action Potentials, Animals, Calcium, Fluorescent Dyes, HEK293 Cells, Humans, Luminescent Proteins, Mice, Neurons, Optogenetics, Red Fluorescent Protein}, issn = {2041-1723}, doi = {10.1038/s41467-025-58485-z}, url = {https://doi.org/10.1038/s41467-025-58485-z}, author = {Dalangin, Rochelin and Jia, Bill Z and Qi, Yitong and Aggarwal, Abhi and Sakoi, Kenryo and Drobizhev, Mikhail and Molina, Rosana S and Patel, Ronak and Abdelfattah, Ahmed S and Zheng, Jihong and Reep, Daniel and Hasseman, Jeremy P and Zhao, Yufeng and Wu, Jiahui and Podgorski, Kaspar and Tebo, Alison G and Schreiter, Eric R and Hughes, Thomas E and Terai, Takuya and Paquet, Marie-Eve and Megason, Sean G and Cohen, Adam E and Shen, Yi and Campbell, Robert E} } @article {69847, title = {Fast, accurate, and versatile data analysis platform for the quantification of molecular spatiotemporal signals.}, journal = {Cell}, year = {2025}, month = {2025 Apr 04}, abstract = {

Optical recording of intricate molecular dynamics is becoming an indispensable technique for biological studies, accelerated by the development of new or improved biosensors and microscopy technology. This creates major computational challenges to extract and quantify biologically meaningful spatiotemporal patterns embedded within complex and rich data sources, many of which cannot be captured with existing methods. Here, we introduce activity quantification and analysis (AQuA2), a fast, accurate, and versatile data analysis platform built upon advanced machine-learning techniques. It decomposes complex live-imaging-based datasets into elementary signaling events, allowing accurate and unbiased quantification of molecular activities and identification of consensus functional units. We demonstrate applications across a wide range of biosensors, cell types, organs, animal models, microscopy techniques, and imaging approaches. As exemplar findings, we show how AQuA2 identified drug-dependent interactions between neurons and astroglia, as well as distinct sensorimotor signal propagation patterns in the mouse spinal cord.

Preprint:\ https://doi.org/10.1101/2024.05.02.592259

}, issn = {1097-4172}, doi = {10.1016/j.cell.2025.03.012}, url = {https://doi.org/10.1016/j.cell.2025.03.012}, author = {Mi, Xuelong and Chen, Alex Bo-Yuan and Duarte, Daniela and Carey, Erin and Taylor, Charlotte R and Braaker, Philipp N and Bright, Mark and Almeida, Rafael G and Lim, Jing-Xuan and Ruetten, Virginia M S and Wang, Yizhi and Wang, Mengfan and Zhang, Weizhan and Zheng, Wei and Reitman, Michael E and Huang, Yongkang and Wang, Xiaoyu and Li, Lei and Deng, Hanfei and Shi, Song-Hai and Poskanzer, Kira E and Lyons, David A and Nimmerjahn, Axel and Ahrens, Misha B and Yu, Guoqiang} } @article {69865, title = {FilaBuster: A strategy for rapid, specific, and spatiotemporally controlled intermediate filament disassembly}, journal = {bioRxiv}, year = {2025}, month = {2025 Apr 20}, abstract = {

Intermediate filaments (IFs) play key roles in cellular mechanics, signaling, and organization, but tools for their rapid, selective disassembly remain limited. Here, we introduce FilaBuster, a photochemical approach for efficient and spatiotemporally controlled IF disassembly in living cells. FilaBuster uses a three-step strategy: (1) targeting HaloTag to IFs, (2) labeling with a covalent photosensitizer ligand, and (3) light-induced generation of localized reactive oxygen species to trigger filament disassembly. This modular strategy applies broadly across IF subtypes{\textemdash}including vimentin, GFAP, desmin, peripherin, and keratin 18{\textemdash}and is compatible with diverse dyes and imaging platforms. Using vimentin IFs as a model system, we establish a baseline implementation in which vimentin-HaloTag labeled with a photosensitizer HaloTag ligand triggers rapid and specific IF disassembly upon light activation. We then refine this approach by (i) expanding targeting strategies to include a vimentin nanobody-HaloTag fusion, (ii) broadening the range of effective photosensitizers, and (iii) optimizing irradiation parameters to enable precise spatial control over filament disassembly. Together, these findings position FilaBuster as a robust platform for acute, selective, and spatiotemporally precise disassembly of IF networks, enabling new investigations into their structural and functional roles in cell physiology and disease.

}, doi = {10.1101/2025.04.20.649718}, url = {https://www.biorxiv.org/content/early/2025/04/21/2025.04.20.649718}, author = {Moore, Andrew S. and Krug, Tommy and Hansen, Simon B. and Ludlow, Alexander V. and Grimm, Jonathan B. and Ayala, Anthony X. and Plutkis, Sarah E. and Wang, Nan and Goldman, Robert D. and Medalia, Ohad and Lavis, Luke D. and Weitz, David A. and Lippincott-Schwartz, Jennifer} } @article {69723, title = {The first complete 3D reconstruction and morphofunctional mapping of an insect eye}, year = {2025}, month = {01/2025}, doi = {10.7554/elife.103247.1}, url = {http://dx.doi.org/10.7554/eLife.103247.1}, author = {Makarova, Anastasia A and Chua, Nicholas J and Diakova, Anna V and Desyatirkina, Inna A and Gunn, Pat and Pang, Song and Xu, C Shan and Hess, Harald and Chklovskii, Dmitri B and Polilov, Alexey A} } @article {69629, title = {The first complete 3D reconstruction and morphofunctional mapping of an insect eye}, journal = {eLife}, year = {2025}, month = {2025 May 1}, abstract = {

The structure of compound eyes in arthropods has been the subject of many studies, revealing important biological principles. Until recently, these studies were constrained by the two-dimensional nature of available ultrastructural data. By taking advantage of the novel three-dimensional ultrastructural dataset obtained using volume electron microscopy, we present the first cellular-level reconstruction of the whole compound eye of an insect, the miniaturized parasitoid wasp\ Megaphragma viggianii. The compound eye of the female\ M. viggianii\ consists of 29 ommatidia and contains 478 cells. Despite the almost anucleate brain, all cells of the compound eye contain nuclei. As in larger insects, the dorsal rim area of the eye in\ M. viggianii\ contains ommatidia that are believed to be specialized in polarized light detection as reflected in their corneal and retinal morphology. We report the presence of three {\textquoteright}ectopic{\textquoteright} photoreceptors. Our results offer new insights into the miniaturization of compound eyes and scaling of sensory organs in general.

Preprint: \ https://doi.org 10.1101/2024.09.30.615804

}, doi = {10.7554/elife.103247}, url = {https://doi.org/10.7554/elife.103247}, author = {Makarova, Anastasia A. and Chua, Nicholas J. and Diakova, Anna V. and Desyatirkina, Inna A. and Gunn, Pat and Pang, Song and Xu, C Shan and Hess, Harald F and Chklovskii, Dmitri B. and Polilov, Alexey A.} } @article {70031, title = {Fishexplorer: A multimodal cellular atlas platform for neuronal circuit dissection in larval zebrafish}, journal = {bioRxiv}, year = {2025}, month = {2025 Jul 14}, abstract = {

Understanding how neural circuits give rise to behavior requires comprehensive knowledge of neuronal morphology, connectivity, and function. Atlas platforms play a critical role in enabling the visualization, exploration, and dissemination of such information. Here, we present FishExplorer, an interactive and expandable community platform designed to integrate and analyze multimodal brain data from larval zebrafish. FishExplorer supports datasets acquired through light microscopy (LM), electron microscopy (EM), and X-ray imaging, all co-registered within a unified spatial coordinate system which enables seamless comparison of neuronal morphologies and synaptic connections. To further assist circuit analysis, FishExplorer includes a suite of tools for querying and visualizing connectivity at the whole-brain scale. By integrating data from recent large-scale EM reconstructions (presented in companion studies), FishExplorer enables researchers to validate circuit models, explore wiring principles, and generate new hypotheses. As a continuously evolving resource, FishExplorer is designed to facilitate collaborative discovery and serve the growing needs of the teleost neuroscience community.

}, doi = {10.1101/2025.07.14.664689}, url = {https://www.biorxiv.org/content/early/2025/07/15/2025.07.14.664689}, author = {Vohra, Sumit K. and Eberle, Maren and Boulanger-Weill, Jonathan and Petkova, Mariela D. and Schuhknecht, Gregor F. P. and Herrera, Kristian J. and K{\"a}mpf, Florian and Ruetten, Virginia M. S. and Lichtman, Jeff W. and Engert, Florian and Randlett, Owen and Bahl, Armin and Isoe, Yasuko and Hege, Hans-Christian and Baum, Daniel} } @article {70145, title = {Foraging as an ethological framework for neuroscience.}, journal = {Trends Neurosci}, year = {2025}, month = {2025 Oct 06}, abstract = {

The study of foraging is central to a renewed interest in naturalistic behavior in neuroscience. Applying a foraging framework grounded in behavioral ecology has enabled probing of the mechanisms underlying cognitive processes such as decision-making within a more ecological context. Yet, foraging also involves myriad other aspects, including navigation of complex environments, sensory processing, and social interactions. Here, we first provide a brief overview of the neuroscience of foraging decisions, and then combine insights from behavioral ecology and neuroscience to review the role of these additional dimensions of foraging. We conclude by highlighting four opportunities for the continued development of foraging as an ethological framework for neuroscience: integrating normative and implementation-level models, developing new tools, enabling cross-species comparisons, and fostering interdisciplinary collaboration.

}, issn = {1878-108X}, doi = {10.1016/j.tins.2025.08.006}, url = {https://doi.org/10.1016/j.tins.2025.08.006}, author = {Grima, Laura L and Haberkern, Hannah and Mohanta, Rishika and Morimoto, Mai M and Rajagopalan, Adithya E and Scholey, Emma V} } @article {70200, title = {Form and function of actin impacts actin health and aging}, journal = {bioRxiv}, year = {2025}, month = {2025 Nov 23 }, abstract = {

The actin cytoskeleton is a fundamental and highly conserved structure that functions in diverse cellular processes, yet its direct contribution to organismal aging remains unclear. Here, we systematically interrogated how genetic and pharmacologic perturbations of actin structure and function influence lifespan and various hallmarks of aging in Caenorhabditis elegans. Whole-animal and tissue-specific knockdown of actin and key actin-binding proteins (ABPs) - arx-2 (Arp2/3), unc-60 (cofilin), and lev-11 (tropomyosin) - led to premature disruption of filament organization, reduced lifespan, and tissue-specific physiological defects. Bulk and single-nucleus RNA-sequencing revealed that ABP knockdowns elicited a strongly {\textquotedblleft}aged{\textquotedblright} transcriptome. Actin dysfunction broadly exacerbated many age-associated phenotypes, including mitochondrial dysfunction, lipid dysregulation, loss of proteostasis, impaired autophagy, and intestinal barrier failure. Pharmacological destabilization with Latrunculin A mirrored genetic knockdowns, while mild stabilization with Jasplakinolide modestly extended lifespan, emphasizing that optimal and finely-tuned actin function is critical for healthy aging. Finally, analysis of human genome-wide association data revealed that common ACTB polymorphisms correlate with differences in age-related decline in gait speed, suggesting evolutionary conservation of actin{\textquoteright}s role in healthy aging. Taken together, our results provide a comprehensive and publicly accessible resource that maps, for the first time, how actin integrity intersects with diverse aging pathways across tissues and scales. This descriptive framework is intended to enable future mechanistic discovery by offering a deep, unbiased dataset that can be integrated with emerging studies to define how actin dynamics contribute to aging.

}, doi = {10.1101/2025.11.22.689949}, url = {https://www.biorxiv.org/content/early/2025/11/23/2025.11.22.689949}, author = {Averbukh, Maxim and Nelson, Hunter and Wang, Tiffany and Lange, Caitlin M and Alcala, Athena and Nair, Tripti and Kim, Juri and Suh, Daniella and Vega, Matthew and Gao, Shihong Max and Dutta, Naibedya and Aviles Barahona, Rebecca and Coakley, Aeowynn J and Gerke, Joe A. and Odron, Sofia F. and Clarke, Jacqueline G. and Singh, Navjot and Nickel, Matthew S. and Peterson, Jacob C. and Lam-Truong, Hannah L. and Moaddeli, Darius and Castro Torres, Toni and Oorloff, Maria and Peruch, Melissa and Mehta, Hemal and Thorwald, Max A. and Curran, Sean P. and Wang, Meng C and Johnson, Tyler A. and Crimmins, Eileen M. and Arpawong, Thalida Em and Kumsta, Caroline and Garcia, Gilberto and Higuchi-Sanabria, Ryo} } @article {69838, title = {Fourier-Based 3D Multistage Transformer for Aberration Correction in Multicellular Specimens}, journal = {Research Square}, year = {2025}, month = {2025 Apr 02}, abstract = {

High-resolution tissue imaging is often compromised by sample-induced optical aberrations that degrade resolution and contrast. While wavefront sensor-based adaptive optics (AO) can measure these aberrations, such hardware solutions are typically complex, expensive to implement, and slow when serially mapping spatially varying aberrations across large fields of view. Here, we introduce AOViFT (Adaptive Optical Vision Fourier Transformer)---a machine learning-based aberration sensing framework built around a 3D multistage Vision Transformer that operates on Fourier domain embeddings. AOViFT infers aberrations and restores diffraction-limited performance in puncta-labeled specimens with substantially reduced computational cost, training time, and memory footprint compared to conventional architectures or real-space networks. We validated AOViFT on live gene-edited zebrafish embryos, demonstrating its ability to correct spatially varying aberrations using either a deformable mirror or post-acquisition deconvolution. By eliminating the need for the guide star and wavefront sensing hardware and simplifying the experimental workflow, AOViFT lowers technical barriers for high-resolution volumetric microscopy across diverse biological samples.

}, doi = {10.21203/rs.3.rs-6273247/v1}, url = {https://doi.org/10.21203/rs.3.rs-6273247/v1}, author = {Thayer Alshaabi and Daniel Milkie and Gaoxiang Liu and Cyna Shirazinejad and Jason Hong and Kemal Achour and Frederik G{\"o}rlitz and Ana Milunovic-Jevtic and Cat Simmons and Ibrahim Abuzahriyeh and Erin Hong and Samara Williams and Nathanael Harrison and Evan Huang and Eun Bae and Alison Killilea and David Drubin and Ian Swinburne and Srigokul Upadhyayula and Eric Betzig} } @article {70132, title = {Fourier-based three-dimensional multistage transformer for aberration correction in multicellular specimens.}, journal = {Nat Methods}, year = {2025}, month = {2025 Oct 01}, abstract = {

High-resolution tissue imaging is often compromised by sample-induced optical aberrations that degrade resolution and contrast. Although wavefront sensor-based adaptive optics (AO) can measure these aberrations, such hardware solutions are typically complex, expensive to implement and slow when serially mapping spatially varying aberrations across large fields of view. Here we introduce AOVIFT (adaptive optical vision Fourier transformer)-a machine learning-based aberration sensing framework built around a three-dimensional multistage vision transformer that operates on Fourier domain embeddings. AOVIFT infers aberrations and restores diffraction-limited performance in puncta-labeled specimens with substantially reduced computational cost, training time and memory footprint compared to conventional architectures or real-space networks. We validated AOVIFT on live gene-edited zebrafish embryos, demonstrating its ability to correct spatially varying aberrations using either a deformable mirror or postacquisition deconvolution. By eliminating the need for the guide star and wavefront sensing hardware and simplifying the experimental workflow, AOVIFT lowers technical barriers for high-resolution volumetric microscopy across diverse biological samples.

Preprint: https://doi.org/10.48550/arXiv.2503.12593

}, issn = {1548-7105}, doi = {10.1038/s41592-025-02844-7}, url = {https://doi.org/10.1038/s41592-025-02844-7}, author = {Alshaabi, Thayer and Milkie, Daniel E and Liu, Gaoxiang and Shirazinejad, Cyna and Hong, Jason L and Achour, Kemal and G{\"o}rlitz, Frederik and Milunovic-Jevtic, Ana and Simmons, Cat and Abuzahriyeh, Ibrahim S and Hong, Erin and Williams, Samara Erin and Harrison, Nathanael and Huang, Evan and Bae, Eun Seok and Killilea, Alison N and Swinburne, Ian A and Drubin, David G and Upadhyayula, Srigokul and Betzig, Eric} } @article {70157, title = {Functional MRI signals as fast as 1Hz are coupled to brain states and predict spontaneous neural activity}, journal = {bioRxiv}, year = {2025}, month = {2025 Oct 14}, abstract = {

fMRI signals were traditionally seen as slow and sampled in the order of seconds, but recent technological advances have enabled much faster sampling rates. We hypothesized that high-frequency fMRI signals can capture spontaneous neural activity that index brain states. Using fast fMRI (TR=378ms) and simultaneous EEG in 27 humans drifting between sleep and wakefulness, we found that fMRI spectral power increased during NREM sleep (compared to wakefulness) across several frequency ranges as fast as 1Hz. This fast fMRI power was correlated with canonical arousal-linked EEG rhythms (alpha and delta), with spatiotemporal correlation patterns for each rhythm reflecting a combination of shared arousal dynamics and rhythm-specific neural signatures. Using machine learning, we found that alpha and delta EEG rhythms can be decoded from fast fMRI signals, in subjects held-out from the training set, showing that fMRI as fast as 0.9Hz (alpha) and 0.7Hz (delta) contains reliable neurally-coupled information that generalizes across individuals. Finally, we demonstrate that this fast fMRI acquisition allows for EEG rhythms to be decoded from 3.8s windows of fMRI data. These results reveal that high-frequency fMRI signals are coupled to dynamically varying brain states, and that fast fMRI sampling allows for more temporally precise quantification of spontaneous neural activity than previously thought possible.

}, doi = {10.1101/2025.10.13.681720}, url = {https://www.biorxiv.org/content/early/2025/10/14/2025.10.13.681720}, author = {Jacob, Leandro P. L. and Bailes, Sydney M and Stringer, Carsen and Polimeni, Jonathan R and Lewis, Laura D} } @article {70101, title = {Functional synapses between neurons and small cell lung cancer.}, journal = {Nature}, year = {2025}, month = {2025 Sep 10}, abstract = {

Small\ cell lung cancer (SCLC) is a highly aggressive type of lung cancer, characterized by rapid proliferation, early metastatic spread, frequent early relapse and a high mortality rate. Recent evidence has suggested that innervation has an important role in the development and progression of several types of cancer. Cancer-to-neuron synapses have been reported in gliomas, but whether peripheral tumours can form such structures is unknown. Here we show that SCLC cells can form functional synapses and receive synaptic transmission. Using in vivo insertional mutagenesis screening in conjunction with cross-species genomic and transcriptomic validation, we identified neuronal, synaptic and glutamatergic signalling gene sets in mouse and human SCLC. Further experiments revealed the ability of SCLC cells to form synaptic structures with neurons in vitro and in vivo. Electrophysiology and optogenetic experiments confirmed that cancer cells can receive NMDA receptor- and GABA receptor-mediated synaptic inputs. Fitting with a potential oncogenic role of neuron-SCLC interactions, we showed that SCLC cells derive a proliferation advantage when co-cultured with vagal sensory or cortical neurons. Moreover, inhibition of glutamate signalling had therapeutic efficacy in an autochthonous mouse model of SCLC. Therefore, following malignant transformation, SCLC cells seem to hijack synaptic signalling to promote tumour growth, thereby exposing a new route for therapeutic intervention.

}, issn = {1476-4687}, doi = {10.1038/s41586-025-09434-9}, url = {https://doi.org/10.1038/s41586-025-09434-9}, author = {Sakthivelu, Vignesh and Schmitt, Anna and Odenthal, Franka and Ndoci, Kristiano and Touet, Marian and Shaib, Ali H and Chihab, Abdulla and Wani, Gulzar A and Nieper, Pascal and Hartmann, Griffin G and Pintelon, Isabel and Kisis, Ilmars and Boecker, Maike and Eckert, Naja M and Iannicelli Caiaffa, Manoela and Ibruli, Olta and Weber, Julia and Maresch, Roman and Bebber, Christina M and Chitsaz, Ali and L{\"u}tz, Anna and Kim Alves Carpinteiro, Mira and Morris, Kaylee M and Franchino, Camilla A and Benz, Jonas and P{\'e}rez-Revuelta, Laura and Soriano-Campos, Jorge A and Huetzen, Maxim A and Goergens, Jonas and Jevtic, Milica and Jahn-Kelleter, Hannah M and Zempel, Hans and Placzek, Aleksandra and Hennrich, Alexandru A and Conzelmann, Karl-Klaus and Tumbrink, Hannah L and Hunold, Pascal and Isensee, Joerg and Werr, Lisa and Gaedke, Felix and Schauss, Astrid and Min{\`e}re, Marielle and M{\"u}ller, Marie and Fenselau, Henning and Liu, Yin and Heimsoeth, Alena and G{\"u}lc{\"u}ler Balta, G{\"u}lce S and Walczak, Henning and Frezza, Christian and Jachimowicz, Ron D and George, Julie and Schmiel, Marcel and Br{\"a}gelmann, Johannes and Hucho, Tim and von Karstedt, Silvia and Peifer, Martin and Annibaldi, Alessandro and H{\"a}nsel-Hertsch, Robert and Persigehl, Thorsten and Gr{\"u}ll, Holger and Sos, Martin L and Reifenberger, Guido and Fischer, Matthias and Adriaensen, Dirk and B{\"u}ttner, Reinhard and Sage, Julien and Brouns, Inge and Rad, Roland and Thomas, Roman K and Anst{\"o}tz, Max and Rizzoli, Silvio O and Bergami, Matteo and Motori, Elisa and Reinhardt, Hans Christian and Beleggia, Filippo} } @article {70122, title = {GABAergic neuronal dysfunction underlies tremor in a Drosophila model of Spinocerebellar ataxia 3}, journal = {Dis Model Mech}, year = {2025}, month = {2025 Sep 18}, abstract = {

Tremor is a common movement disorder associated with several neurodegenerative diseases, yet its mechanisms are not well understood. Using a machine learning method, FLLIT, we previously characterised gait and tremor signatures in the Drosophila model for Spinocerebellar ataxia 3 (SCA3), and found them to be analogous to human SCA3. Here, we carried out a functional screen for neuronal populations that underlie tremor, and found that dysfunction of a specific population of neurons in the ventral nerve cord (VNC) is necessary and sufficient for tremor. Adult-onset expression of mutant ATXN3 in or genetic hypo-activation of these neurons leads to tremor, indicating their important role in adult motor control. RNAseq and functional experiments showed that dysfunction of GABAergic neurons, and not other neurotransmitter populations tested, causes tremor. Finally, we identified a small subset of approximately 30 predominantly GABAergic neurons within the adult VNC that are essential for smooth walking. This study demonstrates that tremor in SCA3 flies arises from GABAergic dysfunction, and that FLLIT can be used to dissect motor control mechanisms.

}, issn = {1754-8411}, doi = {10.1242/dmm.052329}, url = {https://doi.org/10.1242/dmm.052329}, author = {Banerjee, Animesh and Chatterjee, Moumita and Tan, Kah Junn and Tay, Shermaine and Duan, Kaibo and Andiappan, Anand Kumar and Howland, Shanshan Wu and Aso, Yoshinori and Aw, Sherry Shiying} } @article {70007, title = {A genetic driver of epileptic encephalopathy impairs gating of synaptic glycolysis}, journal = {bioRxiv}, year = {2025}, month = {2025 Jun 19}, abstract = {

The brain is a disproportionately large consumer of fuel, estimated to expend \~20\% of the whole-body energy budget, and therefore it is critical to adequately control brain fuel expenditures while satisfying its on-demand needs for continued function. The brain is also metabolically vulnerable as the inability to adequately fuel cellular processes that support information transfer between cells leads to rapid neurological impairment. We show here that a genetic driver of early onset epileptic encephalopathy (EOEE), SLC13A5, a Na+/citrate cotransporter (NaCT), is critical for gating the activation of local presynaptic glycolysis. We show that SLC13A5 is in part localized to a presynaptic pool of membrane-bound organelles and acts to transiently clear axonal citrate during electrical activity, in turn activating phosphofructokinase 1. We show that loss of SLC13A5 or mistargeting to the plasma membrane results in suppressed glycolytic gating, activity dependent presynaptic bioenergetic deficits and synapse dysfunction.

}, doi = {10.1101/2025.06.17.660213}, url = {https://www.biorxiv.org/content/early/2025/06/19/2025.06.17.660213}, author = {Koshenov, Zhanat and Kokotos, Alexandros C. and Benedetti, Lorena and Schwartz, Jennifer Lippincott and Ryan, Timothy A.} } @article {69856, title = {Glutamate indicators with increased sensitivity and tailored deactivation rates}, journal = {Research Square}, year = {2025}, month = {2025 Apr 8}, abstract = {

Identifying the input-output operations of neurons requires measurements of synaptic transmission simultaneously at many of a neuron{\textquoteright}s thousands of inputs in the intact brain. To facilitate this goal, we engineered and screened 3365 variants of the fluorescent protein glutamate indicator iGluSnFR3 in neuron culture, and selected variants in the mouse visual cortex. Two variants have high sensitivity, fast activation (\< 2 ms) and deactivation times tailored for recording large populations of synapses (iGluSnFR4s, 153 ms) or rapid dynamics (iGluSnFR4f, 26 ms). By imaging action-potential evoked signals on axons and visually-evoked signals on dendritic spines, we show that iGluSnFR4s/4f primarily detect local synaptic glutamate with single-vesicle sensitivity. The indicators detect a wide range of naturalistic synaptic transmission, including in the vibrissal cortex layer 4 and in hippocampal CA1 dendrites. iGluSnFR4 increases the sensitivity and scale (4s) or speed (4f) of tracking information flow in neural networks in vivo.

}, doi = {10.21203/rs.3.rs-6257403/v1}, url = {https://doi.org/10.21203/rs.3.rs-6257403/v1}, author = {Podgorski, Kaspar and Aggarwal, Abhi and Negrean, Adrian and Chen, Yang and Iyer, Rishyashring and Reep, Daniel and Liu, Anyi and Palutla, Anirudh and Xie, Michael and Maclennan, Bryan and Hagihara, Kenta and Kinsey, Lucas and Sun, Julianna and Yao, Pantong and Zheng, Jihong and Tsang, Arthur and Tsegaye, Getahun and Zhang, Yonghai and Patel, Ronak and Hasseman, Jeremy} } @article {69833, title = {Glutamate indicators with increased sensitivity and tailored deactivation rates}, journal = {Nat Methods}, year = {2025}, month = {2025 Dec 23}, abstract = {

Understanding how neurons integrate signals from thousands of input synapses requires methods to monitor neurotransmission across many sites simultaneously. The fluorescent protein glutamate indicator iGluSnFR enables visualization of synaptic signaling, but the sensitivity, scale and speed of such measurements are limited by existing variants. Here we developed two highly sensitive fourth-generation iGluSnFR variants with fast activation and tailored deactivation rates: iGluSnFR4f for tracking rapid dynamics, and iGluSnFR4s for recording from large populations of synapses. These indicators detect glutamate with high spatial specificity and single-vesicle sensitivity in vivo. We used them to record natural patterns of synaptic transmission across multiple experimental contexts in mice, including two-photon imaging in cortical layers 1{\textendash}4 and hippocampal CA1, and photometry in the midbrain. The iGluSnFR4 variants extend the speed, sensitivity and scalability of glutamate imaging, enabling direct observation of information flow through neural networks in the intact brain.

}, doi = {10.1038/s41592-025-02965-z}, url = {https://doi.org/10.1038/s41592-025-02965-z}, author = {Aggarwal, Abhi and Negrean, Adrian and Chen, Yang and Iyer, Rishyashring and Reep, Daniel and Liu, Anyi and Palutla, Anirudh and Xie, Michael E. and MacLennan, Bryan J. and Hagihara, Kenta M. and Kinsey, Lucas W. and Sun, Julianna L. and Yao, Pantong and Zheng, Jihong and Tsang, Arthur and Tsegaye, Getahun and Zhang, Yonghai and Patel, Ronak H. and Arthur, Benjamin J. and Hiblot, Julien and Leippe, Philipp and Tarnawski, Miroslaw and Marvin, Jonathan S. and Vevea, Jason D. and Turaga, Srinivas C. and Tebo, Alison G. and Carandini, Matteo and Rossi, L. F. and Kleinfeld, David and Konnerth, Arthur and Svoboda, Karel and Turner, Glenn C. and Hasseman, Jeremy and Podgorski, Kaspar} } @article {69720, title = {HD2Net: A deep learning framework for simultaneous denoising and deaberration in fluorescence microscopy}, journal = {bioRxiv}, year = {2025}, month = {01/2025}, abstract = {

Fluorescence microscopy is essential for biological research, offering high-contrast imaging of microscopic structures. However, the quality of these images is often compromised by optical aberrations and noise, particularly in low signal-to-noise ratio (SNR) conditions. While adaptive optics (AO) can correct aberrations, it requires costly hardware and slows down imaging; whereas current denoising approaches boost the SNR but leave out the aberration compensation. To address these limitations, we introduce HD2Net, a deep learning framework that enhances image quality by simultaneously denoising and suppressing the effect of aberrations without the need for additional hardware. Building on our previous work, HD2Net incorporates noise estimation and aberration removal modules, effectively restoring images degraded by noise and aberrations. Through comprehensive evaluation of synthetic phantoms and biological data, we demonstrate that HD2Net outperforms existing methods, significantly improving image resolution and contrast. This framework offers a promising solution for enhancing biological imaging, particularly in challenging aberrating and low-light conditions.

}, doi = {10.1101/2025.01.06.631475}, url = {https://www.biorxiv.org/content/early/2025/01/08/2025.01.06.631475}, author = {Hou, Xuekai and Li, Yue and Hobson, Chad M. and Shroff, Hari and Guo, Min and Liu, Huafeng} } @article {69734, title = {HD2Net: A Deep Learning Framework for Simultaneous Denoising and Deaberration in Fluorescence Microscopy}, journal = {bioRxiv}, year = {2025}, month = {2025 Jan 8}, abstract = {

Fluorescence microscopy is essential for biological research, offering high-contrast imaging of microscopic structures. However, the quality of these images is often compromised by optical aberrations and noise, particularly in low signal-to-noise ratio (SNR) conditions. While adaptive optics (AO) can correct aberrations, it requires costly hardware and slows down imaging; whereas current denoising approaches boost the SNR but leave out the aberration compensation. To address these limitations, we introduce HD2Net, a deep learning framework that enhances image quality by simultaneously denoising and suppressing the effect of aberrations without the need for additional hardware. Building on our previous work, HD2Net incorporates noise estimation and aberration removal modules, effectively restoring images degraded by noise and aberrations. Through comprehensive evaluation of synthetic phantoms and biological data, we demonstrate that HD2Net outperforms existing methods, significantly improving image resolution and contrast. This framework offers a promising solution for enhancing biological imaging, particularly in challenging aberrating and low-light conditions.

}, doi = {10.1101/2025.01.06.631475}, url = {https://www.biorxiv.org/content/early/2025/01/08/2025.01.06.631475}, author = {Hou, Xuekai and Li, Yue and Hobson, Chad M. and Shroff, Hari and Guo, Min and Liu, Huafeng} } @article {69842, title = {Hedonic eating is controlled by dopamine neurons that oppose GLP-1R satiety.}, journal = {Science}, volume = {387}, year = {2025}, month = {2025 Mar 28}, pages = {eadt0773}, abstract = {

Hedonic eating is defined as food consumption driven by palatability without physiological need. However, neural control of palatable food intake is poorly understood. We discovered that hedonic eating is controlled by a neural pathway from the peri-locus ceruleus to the ventral tegmental area (VTA). Using photometry-calibrated optogenetics, we found that VTA dopamine (VTA) neurons encode palatability to bidirectionally regulate hedonic food consumption. VTA neuron responsiveness was suppressed during food consumption by semaglutide, a glucagon-like peptide receptor 1 (GLP-1R) agonist used as an antiobesity drug. Mice recovered palatable food appetite and VTA neuron activity during repeated semaglutide treatment, which was reversed by consumption-triggered VTA neuron inhibition. Thus, hedonic food intake activates VTA neurons, which sustain further consumption, a mechanism that opposes appetite reduction by semaglutide.

}, keywords = {Animals, Anti-Obesity Agents, Appetite, Dopaminergic Neurons, Eating, Glucagon-Like Peptide 1, Glucagon-Like Peptide-1 Receptor, Glucagon-Like Peptides, Male, Mice, Mice, Inbred C57BL, Neural Pathways, Optogenetics, Satiation, Satiety Response, Ventral Tegmental Area}, issn = {1095-9203}, doi = {10.1126/science.adt0773}, url = {https://doi.org/10.1126/science.adt0773}, author = {Zhu, Zhenggang and Gong, Rong and Rodriguez, Vicente and Quach, Kathleen T and Chen, Xinyu and Sternson, Scott M} } @article {69954, title = {High-resolution imaging of RNA and proteins in thick tissues using cycleHCR.}, journal = {Nat Rev Genet}, year = {2025}, month = {2025 May 28}, issn = {1471-0064}, doi = {10.1038/s41576-025-00860-z}, url = {https://doi.org/10.1038/s41576-025-00860-z}, author = {Kim, Jun and Liu, Zhe J} } @article {69905, title = {History of hypoxia exposure aids future cell invasion according to cell type and collagen density.}, journal = {Mol Biol Cell}, year = {2025}, month = {2025 May 06}, pages = {mbcE24120580}, abstract = {

In cancer progression, tumor microenvironments progressively become denser and hypoxic, and cell migrate toward higher oxygen levels as they invade across the tumor-stromal boundary. While cell invasion dependence on optimal collagen density is well appreciated, it remains unclear whether past oxygen conditions alter future invasion phenotype of cells. Here, we show that normal human mammary epithelial cells (MCF10A) and leader-like human breast tumor cells (BT549) undergo higher rates of invasion and collagen deformation after past exposure to hypoxia, compared to normoxia controls. Upon increasing collagen density by \~{}50\%, cell invasion under normoxia reduced, as expected due to the increased matrix crowding. However, surprisingly, past hypoxia increased cell invasion in future normoxic dense collagen, with more pronounced invasion of cancer cells. This culmination of cancer-related conditions of hypoxia history, tumor cell, and denser collagen led to more aggressive invasion phenotypes. We found that hypoxia-primed cancer cells produce laminin332, a basement membrane protein required for cell-matrix adhesions, which could explain the additional adhesion feedback from the matrix that led to invasion after hypoxia priming. Depletion of Cdh3 disrupts the hypoxia-dependent laminin production and thus disables the rise in rates of cancer cell invasion and collagen deformation caused by hypoxia memory. These findings highlight the importance of considering past oxygen conditions in combination with current mechanical composition of tissues to better understand tumor invasion in physically evolving tumor microenvironments.

}, issn = {1939-4586}, doi = {10.1091/mbc.E24-12-0580}, url = {https://doi.org/10.1091/mbc.e24-12-0580}, author = {Almeida, Jos{\'e} A and Avila, Diego B and Longmore, Gregory D and Pathak, Amit} } @article {69825, title = {HortaCloud: An open and collaborative platform for whole brain neuronal reconstructions}, journal = {bioRxiv}, year = {2025}, month = {2025 Mar 13}, abstract = {

HortaCloud is a cloud-based, open-source platform designed to facilitate the collaborative reconstruction of long-range projection neurons from whole-brain light microscopy data. By providing virtual environments directly within the cloud, it eliminates the need for costly and time-consuming data downloads, allowing researchers to work efficiently with terabyte- scale volumetric datasets. Standardization of computational resources in the cloud make deployment easier and more predictable. The pay-as-you-go cloud model reduces adoption barriers by eliminating upfront investments in expensive hardware. Finally, HortaCloud{\textquoteright}s decentralized architecture enables global collaboration between researchers and between institutions.

}, doi = {10.1101/2025.03.13.642887}, url = {https://www.biorxiv.org/content/early/2025/03/14/2025.03.13.642887}, author = {Rokicki, Konrad and Schauder, David and Olbris, Donald J. and Goina, Cristian and Clements, Jody and Edson, Patrick and Kawase, Takashi and Svirskas, Robert and Arshadi, Cameron and Feng, David and Chandrashekar, Jayaram and Ferreira, Tiago A. and MouseLight Project Team} } @article {70016, title = {How short peptides disassemble tau fibrils in Alzheimer{\textquoteright}s disease}, journal = {Nature}, year = {2025}, month = {2025 Jul 09}, abstract = {

Reducing fibrous aggregates of the protein tau is a possible strategy for halting the progression of Alzheimer{\textquoteright}s disease (AD). Previously, we found that in vitro, the D-enantiomeric peptide (D-peptide) D-TLKIVWC disassembles ultra-stable tau fibrils extracted from the autopsied brains of individuals with AD (hereafter, these tau fibrils are referred to as AD-tau) into benign segments, with no energy source other than ambient thermal agitation. To consider D-peptide-mediated disassembly as a potential route to therapeutics for AD, it is essential to understand the mechanism and energy source of the disassembly action. Here, we show that the assembly of D-peptides into amyloid-like ({\textquoteright}mock-amyloid{\textquoteright}) fibrils is essential for AD-tau disassembly. These mock-amyloid fibrils have a right-handed twist but are constrained to adopt a left-handed twist when templated in complex with AD-tau. The release of strain that accompanies the conversion of left-twisted to right-twisted, relaxed mock-amyloid produces a torque that is sufficient to break the local hydrogen bonding between tau molecules, and leads to the fragmentation of AD-tau. This strain-relief mechanism seems to operate in other examples of amyloid fibril disassembly, and could inform the development of first-in-class therapeutics for amyloid diseases.

Preprint:\ https://doi.org/10.1101/2024.03.25.586668

}, issn = {1476-4687}, doi = {10.1038/s41586-025-09244-z}, url = {https://doi.org/10.1038/s41586-025-09244-z}, author = {Hou, Ke and Ge, Peng and Sawaya, Michael R and Lutter, Liisa and Dolinsky, Joshua L and Yang, Yuan and Jiang, Yi Xiao and Boyer, David R and Cheng, Xinyi and Pi, Justin and Zhang, Jeffrey and Lu, Jiahui and Abskharon, Romany and Yang, Shixin and Yu, Zhiheng and Feigon, Juli and Eisenberg, David S} } @article {69831, title = {iGABASnFR2: Improved genetically encoded protein sensors of GABA}, journal = {bioRxiv}, year = {2025}, month = {2025 Mar 25}, abstract = {

Monitoring GABAergic inhibition in the nervous system has been enabled by development of an intensiometric molecular sensor that directly detects GABA. However the first generation iGABASnFR exhibits low signal-to-noise and suboptimal kinetics, making in vivo experiments challenging. To improve sensor performance, we targeted several sites in the protein for near-saturation mutagenesis, and evaluated the resulting sensor variants in a high throughput screening system using evoked synaptic release in primary cultured neurons. This identified a sensor variant, iGABASnFR2, with 4.2-fold improved sensitivity and 20\% faster kinetics, and binding affinity that remained in a range sensitive to changes in GABA concentration at synapses. We also identified sensors with an inverted response, decreasing fluorescence intensity upon GABA binding. We termed the best such negative-going sensor iGABASnFR2n, which can be used to corroborate observations with the positive-going sensor. These improvements yielded a qualitative enhancement of in vivo performance, enabling us to make the first measurements of direction selective GABA release in the retina and confirm a longstanding hypothesis for how sensitivity to motion arises in the visual system.

}, doi = {10.1101/2025.03.25.644953}, url = {https://www.biorxiv.org/content/early/2025/03/26/2025.03.25.644953}, author = {Kolb, Ilya and Hasseman, Jeremy P. and Matsumoto, Akihiro and Arthur, Benjamin J. and Zhang, Yan and Tsang, Arthur and Reep, Daniel and Tsegaye, Getahun and Zheng, Jihong and Patel, Ronak and Looger, Loren L. and Marvin, Jonathan S. and Korff, Wyatt L. and Yonehara, Keisuke and Turner, Glenn C.} } @article {70182, title = {iGlucoSnFR2: A genetically encoded fluorescent sensor for measuring intracellular or extracellular glucose in vivo in mouse brain.}, journal = {Sci Adv}, volume = {11}, year = {2025}, month = {2025 Nov 14}, pages = {eadz3889}, abstract = {

Continuous glucose monitors have proven invaluable for monitoring blood glucose levels for diabetics, but they are of limited use for observing glucose dynamics at the cellular (or subcellular) level. We have developed a second generation, genetically encoded intensity-based glucose sensing fluorescent reporter (iGlucoSnFR2). We show that when it is targeted to the cytosol, it reports intracellular glucose consumption and gluconeogenesis in cell culture, along with efflux from the endoplasmic reticulum. It outperforms the original iGlucoSnFR in vivo when observed by fiber photometry in mouse brain and reports transient increase in glucose concentration when stimulated by noradrenaline or electrical stimulation. Last, we demonstrate that membrane localized iGlucoSnFR2 can be calibrated in vivo to indicate absolute changes in extracellular glucose concentration in awake mice. We anticipate iGlucoSnFR2 facilitating previously unobservable measurements of glucose dynamics with high spatial and temporal resolution in living mammals and other experimental organisms.

}, issn = {2375-2548}, doi = {10.1126/sciadv.adz3889}, url = {https://doi.org/10.1126/sciadv.adz3889}, author = {Marvin, Jonathan S and M{\"a}chler, Philipp and Meng, Chengbo and Ates, Tayfun and Patel, Ronak H and Adhikari, Raghabendra and Makurath, Monika A and Ku, Zaneta and Feliciano, Daniel and Atasoy, Deniz and Cui, Guohong and Kleinfeld, David and Brown, Timothy A} } @article {70147, title = {Illuminating renal proximal tubule architecture through high-resolution volume em and machine learning analysis.}, journal = {J Am Soc Nephrol}, year = {2025}, month = {2025 Oct 06}, abstract = {

BACKGROUND: Kidney epithelial cells perform complex vectorial fluid and solute transport at high volumes and rapid rates. Their structural organization both reflects and enables these sophisticated physiological functions. However, our understanding of the nanoscale spatial organization and intracellular ultrastructure that underlies these crucial cellular functions remains limited.

METHODS: To address this knowledge gap, we generated and reconstructed an extensive electron microscopic dataset of renal proximal tubule (PT) epithelial cells at isotropic resolutions down to 4nm. We employed artificial intelligence-based segmentation tools to identify, trace, and measure all major subcellular components. We complemented this analysis with immunofluorescence microscopy to connect subcellular architecture to biochemical function.

RESULTS: Our ultrastructural analysis revealed complex organization of membrane-bound compartments in proximal tubule cells. The apical endocytic system featured deep invaginations connected to an anastomosing meshwork of dense apical tubules, rather than discrete structures. The endoplasmic reticulum displayed distinct structural domains: fenestrated sheets in the basolateral region and smaller, disconnected clusters in the subapical region. We identified, quantified, and visualized membrane contact sites between endoplasmic reticulum, plasma membrane, mitochondria, and apical endocytic compartments. Immunofluorescence microscopy demonstrated distinct localization patterns for endoplasmic reticulum resident proteins at mitochondrial and plasma membrane interfaces.

CONCLUSIONS: This study provides novel insights into proximal tubule cell organization, revealing specialized compartmentalization and unexpected connections between membrane-bound organelles. We identified previously uncharacterized structures, including mitochondria-plasma membrane bridges and an interconnected endocytic meshwork, suggesting mechanisms for efficient energy distribution, cargo processing and structural support. Morphological differences between 4nm and 8nm datasets indicate subsegment-specific specializations within the proximal tubule. This comprehensive open-source dataset provides a foundation for understanding how subcellular architecture supports specialized epithelial function in health and disease.

}, issn = {1533-3450}, doi = {10.1681/ASN.0000000884}, url = {https://doi.org/10.1681/asn.0000000884}, author = {Pandya, Raj D and Lackner, Emily M and Xu, C Shan and Zugates, Christopher and Burdyniuk, Mariia and Reyna-Neyra, Andrea and Pandya, Vraj D and Li, Wei-Ping and Pang, Song and Weisz, Ora A and Caplan, Michael J} } @article {70084, title = {Imaging cellular activity simultaneously across all organs of a vertebrate reveals body-wide circuits}, journal = {bioRxiv}, year = {2025}, month = {2025 August 22}, abstract = {

All cells in an animal collectively ensure, moment-to-moment, the survival of the whole organism in the face of environmental stressors1,2. Physiology seeks to elucidate the intricate network of interactions that sustain life, which often span multiple organs, cell types, and timescales, but a major challenge lies in the inability to simultaneously record time-varying cellular activity throughout the entire body.We developed WHOLISTIC, a method to image second-timescale, time-varying intracellular dynamics across cell-types of the vertebrate body. By advancing and integrating volumetric fluorescence microscopy, machine learning, and pancellular transgenic expression of calcium sensors in transparent young Danio rerio (zebrafish) and adult Danionella, the method enables real-time recording of cellular dynamics across the organism. Calcium is a universal intracellular messenger, with a large array of cellular processes depending on changes in calcium concentration across varying time-scales, making it an ideal proxy of cellular activity3.Using this platform to screen the dynamics of all cells in the body, we discovered unexpected responses of specific cell types to stimuli, such as chondrocyte reactions to cold, meningeal responses to ketamine, and state-dependent activity, such as oscillatory ependymal-cell activity during periods of extended motor quiescence. At the organ scale, the method uncovered pulsating traveling waves along the kidney nephron. At the multi-organ scale, we uncovered muscle synergies and independencies, as well as muscle-organ interactions. Integration with optogenetics allowed us to all-optically determine the causal direction of brain-body interactions. At the whole-organism scale, the method captured the rapid brainstem-controlled redistribution of blood flow across the body.Finally, we advanced Whole-Body Expansion Microscopy4 to provide ground-truth molecular and ultrastructural anatomical context, explaining the spatiotemporal structure of activity captured by WHOLISTIC. Together, these innovations establish a new paradigm for systems biology, bridging cellular and organismal physiology, with broad implications for both fundamental research and drug discovery.

}, doi = {10.1101/2025.08.20.670374}, url = {https://www.biorxiv.org/content/early/2025/08/22/2025.08.20.670374.1}, author = {Ruetten, Virginia M. S. and Zheng, Wei and Siwanowicz, Igor and Mensh, Brett D. and Eddison, Mark and Hu, Amy and Chi, Yunfeng and Lemire, Andrew L. and Guo, Caiying and Kadobianskyi, Mykola and Renz, Marc and Lelek-Greskovic, Sara and He, Yisheng and Close, Kari and Ihrke, Gudrun and Dev, Aparna and Petruncio, Alyson and Wan, Yinan and Engert, Florian and Fishman, Mark C. and Judkewitz, Benjamin and Rubinov, Mikail and Keller, Philipp J. and Satou, Chie and Yu, Guoqiang and Tillberg, Paul W. and Sahani, Maneesh and Ahrens, Misha B.} } @article {69110, title = {Imaging neuronal voltage beyond the scattering limit}, journal = {Nat Methods}, year = {2025}, month = {2025 May 19}, abstract = {

Voltage imaging is a promising technique for high-speed recording of neuronal population activity. However, tissue scattering severely limits its application in dense neuronal populations. Here, we adopted the principle of localization microscopy, a technique that enables super-resolution imaging of single-molecules, to resolve dense neuronal activities\ in vivo. Leveraging the sparse activation of neurons during action potentials (APs), we precisely localize the fluorescence change associated with each AP, creating a super-resolution image of neuronal activities. This approach, termed\ Activity\ Localization\ Imaging (ALI), identifies overlapping neurons and separates their activities with over 10-fold greater precision than what tissue scattering permits. Using ALI, we simultaneously recorded over a hundred densely-labeled CA1 neurons, creating a map of hippocampal theta oscillation at single-cell and single-cycle resolution.

Preprint:\ https://doi.org/10.1101/2023.12.03.56840

}, doi = {10.1038/s41592-025-02692-5}, url = {https://doi.org/10.1038/s41592-025-02692-5}, author = {Tsai-Wen Chen and Xian-Bin Huang and Sarah E. Plutkis and Katie L. Holland and Luke D. Lavis and Bei-Jung Lin} } @article {70190, title = {Imp1 acts as a dosage- and stage-dependent temporal rheostat orchestrating radial glial fate transitions and cortical morphogenesis}, journal = {bioRxiv}, year = {2025}, month = {2025 Nov 18}, abstract = {

Cortical neurogenesis proceeds through a precise temporal program in which radial glia sequentially generate distinct neuronal subtypes and later glia, yet how post-transcriptional regulators coordinate these transitions remain poorly understood. We previously identified that a decreasing temporal gradient of the RNA-binding protein Imp encodes neural stem cell age in Drosophila. In this work, we extend our investigation to Imp1, a mammalian homologue of Imp, and its role in murine neocortical development. Using TEMPO to track birth-order dynamics, we demonstrate that sustained Imp1 overexpression during early neurogenesis arrests temporal fate progression, shifting neuronal populations toward deeper cortical layers V-VI. Immunostaining with layer-specific transcription factors Cux1 and Ctip2 confirmed that laminar repositioning results from genuine changes in neuronal identity rather than migratory defects, with neurons adopting molecular identities matching their final positions. Temporal window-specific manipulations reveal distinct stage-specific effects where early-stage Imp1 induction produces cascading effects on fate specification and moderately delays the neuronal-to-gliogenic transition, while mid-stage induction induces neuronal accumulation in the subplate region. Live imaging of organotypic cultures reveals continuous neuronal recruitment within intermediate and ventricular zones, with mid-stage-born neurons accumulating at significantly faster rates than earlier cohorts. Strikingly, mid-stage Imp1 overexpression also induces ectopic glial-like foci distributed throughout the cortical plate, featuring dramatic cellular expansion and morphological heterogeneity. These findings establish Imp1 as a dosage- and stage-dependent temporal rheostat orchestrating developmental transitions in radial glial progenitors, controlling neuronal fate decisions and spatial organization. This work advances our understanding of molecular timing mechanisms governing neuronal diversity in the mammalian cortex.

}, doi = {10.1101/2025.11.18.688993}, url = {https://www.biorxiv.org/content/early/2025/11/18/2025.11.18.688993}, author = {Azur, Romie Angelo G. and Feliciano, Daniel and Espinosa-Medina, Isabel and Adhikari, Raghabendra and Lilao-Garz{\'o}n, Joaquin and Jensen, Ella and Yang, Ching-Po and Lee, Tzumin} } @article {69709, title = {In vivo multiplex imaging of dynamic neurochemical networks with designed far-red dopamine sensors}, journal = {Science}, year = {2025}, month = {2025 Jun 05}, abstract = {

Neurochemical signals like dopamine (DA) play a crucial role in a variety of brain functions through intricate interactions with other neuromodulators and intracellular signaling pathways. However, studying these complex networks has been hindered by the challenge of detecting multiple neurochemicals in vivo simultaneously. To overcome this limitation, we developed a single-protein chemigenetic DA sensor, HaloDA1.0, which combines a cpHaloTag-chemical dye approach with the G protein-coupled receptor activation-based (GRAB) strategy, providing high sensitivity for DA, sub-second response kinetics, and an extensive spectral range from far-red to near-infrared. When used together with existing green and red fluorescent neuromodulator sensors, Ca2+ indicators, cAMP sensors, and optogenetic tools, HaloDA1.0 provides high versatility for multiplex imaging in cultured neurons, brain slices, and behaving animals, facilitating in-depth studies of dynamic neurochemical networks.

}, doi = {10.1126/science.adt7705}, url = {https://doi.org/10.1126/science.adt7705}, author = {Zheng, Yu and Cai, Ruyi and Wang, Kui and Zhang, Junwei and Zhuo, Yizhou and Dong, Hui and Zhang, Yuqi and Wang, Yifan and Deng, Fei and Ji, En and Cui, Yiwen and Fang, Shilin and Zhang, Xinxin and Zhang, Kecheng and Wang, Jinxu and Li, Guochuan and Miao, Xiaolei and Wang, Zhenghua and Yang, Yuqing and Li, Shaochuang and Grimm, Jonathan and Johnsson, Kai and Schreiter, Eric and Lavis, Luke and Chen, Zhixing and Mu, Yu and Li, Yulong} } @article {70214, title = {Innovative In Vivo Imaging and Single Cell Expression from Tumor Bulk and Corpus Callosum Reveal Glioma Stem Cells with Unique Regulatory Programs}, journal = {Cancers}, volume = {17}, year = {2025}, month = {2025 Nov 30}, pages = {3851}, abstract = {

Background/Objectives: High-grade gliomas (HGGs), including glioblastomas, are among the most aggressive brain tumors due to their high intratumoral heterogeneity and extensive infiltration. Glioma stem-like cells (GSCs) frequently invade along white matter tracts such as the corpus callosum, but the molecular programs driving this region-specific invasion remain poorly defined. The aim of this study was to identify transcriptional signatures associated with GSC infiltration into the corpus callosum. Methods: We established an orthotopic xenograft model by implanting fluorescently labeled human GSCs into nude mouse brains. Tumor growth and invasion patterns were assessed using tissue clearing, light-sheet fluorescence microscopy, and histological analyses. To characterize region-specific molecular profiles, we performed microfluidic-based single-cell RNA expression analysis of 48 invasion- and stemness-related genes in cells isolated from the tumor bulk (TB) and corpus callosum (CC). Results: By six weeks post-implantation, GSCs displayed marked tropism for the corpus callosum, with distinct infiltration patterns captured by three-dimensional imaging. Single-cell gene expression profiling revealed significant differences in 7 of the 48 genes (14.6\%) between TB- and CC-derived GSCs. These genes{\textemdash}NES, CCND1, GUSB, NOTCH1, E2F1, EGFR, and TGFB1{\textemdash}collectively defined a {\textquotedblleft}corpus callosum invasion signature{\textquotedblright} (CC-Iv). CC-derived cells showed a unimodal, high-expression profile of CC-Iv genes, whereas TB cells exhibited bimodal distributions, suggesting heterogeneous transcriptional states. Importantly, higher CC-Iv expression correlated with worse survival in patients with low-grade gliomas. Conclusions: This multimodal approach identified a corpus callosum-specific invasion signature in glioma stem-like cells, revealing how local microenvironmental cues shape transcriptional reprogramming during infiltration. These findings provide new insights into the spatial heterogeneity of gliomas and highlight potential molecular targets for therapies designed to limit tumor spread through white matter tracts.

}, issn = {2072-6694}, doi = {10.3390/cancers17233851}, url = {https://www.mdpi.com/2072-6694/17/23/3851}, author = {Dos Santos, Nat{\'a}lia and Aquino, Aline and Preu{\ss}er, Friedrich and Rusak, Fabio Rojas and Jandrey, Elisa Helena Farias and Uno, Miyuki and Furuya, Tatiane Katsue and Lancellotti, Carmen Lucia Penteado and Maldaun, Marcos Vinicius Calfat and Chammas, Roger and Preibisch, Stephan and Camargo, Anamaria Aranha and Masotti, Cibele and Costa, {\'E}rico Tosoni} } @article {70207, title = {Innovative In Vivo Imaging and Single Cell Expression from Tumor Bulk and Corpus Callosum Reveal Glioma Stem Cells with Unique Regulatory Programs}, journal = {Cancers}, volume = {17}, year = {2025}, month = {2025 Nov 30}, pages = {3851}, abstract = {

Background/Objectives: High-grade gliomas (HGGs), including glioblastomas, are among the most aggressive brain tumors{\r a} due to their high intratumoral heterogeneity and extensive infiltration. Glioma stem-like cells (GSCs) frequently invade along white matter tracts such as the corpus callosum, but the molecular programs driving this region-specific invasion remain poorly defined. The aim of this study was to identify transcriptional signatures associated with GSC infiltration into the corpus callosum. Methods: We established an orthotopic xenograft model by implanting fluorescently labeled human GSCs into nude mouse brains. Tumor growth and invasion patterns were assessed using tissue clearing, light-sheet fluorescence microscopy, and histological analyses. To characterize region-specific molecular profiles, we performed microfluidic-based single-cell RNA expression analysis of 48 invasion- and stemness-related genes in cells isolated from the tumor bulk (TB) and corpus callosum (CC). Results: By six weeks post-implantation, GSCs displayed marked tropism for the corpus callosum, with distinct infiltration patterns captured by three-dimensional imaging. Single-cell gene expression profiling revealed significant differences in 7 of the 48 genes (14.6\%) between TB- and CC-derived GSCs. These genes{\textemdash}NES, CCND1, GUSB, NOTCH1, E2F1, EGFR, and TGFB1{\textemdash}collectively defined a {\textquotedblleft}corpus callosum invasion signature{\textquotedblright} (CC-Iv). CC-derived cells showed a unimodal, high-expression profile of CC-Iv genes, whereas TB cells exhibited bimodal distributions, suggesting heterogeneous transcriptional states. Importantly, higher CC-Iv expression correlated with worse survival in patients with low-grade gliomas. Conclusions: This multimodal approach identified a corpus callosum-specific invasion signature in glioma stem-like cells, revealing how local microenvironmental cues shape transcriptional reprogramming during infiltration. These findings provide new insights into the spatial heterogeneity of gliomas and highlight potential molecular targets for therapies designed to limit tumor spread through white matter tracts.

}, issn = {2072-6694}, doi = {10.3390/cancers17233851}, url = {https://www.mdpi.com/2072-6694/17/23/3851}, author = {Dos Santos, Nat{\'a}lia and Aquino, Aline and Preu{\ss}er, Friedrich and Rusak, Fabio Rojas and Jandrey, Elisa Helena Farias and Uno, Miyuki and Furuya, Tatiane Katsue and Lancellotti, Carmen Lucia Penteado and Maldaun, Marcos Vinicius Calfat and Chammas, Roger and Preibisch, Stephan and Camargo, Anamaria Aranha and Masotti, Cibele and Costa, {\'E}rico Tosoni} } @article {70139, title = {In-situ glial cell-surface proteomics identifies pro-longevity factors in Drosophila}, journal = {eLife}, year = {2025}, month = {2025 Dec 12}, abstract = {

Much focus has shifted towards understanding how glial dysfunction contributes to age-related neurodegeneration due to the critical roles glial cells play in maintaining healthy brain function. Cell-cell interactions, which are largely mediated by cell-surface proteins, control many critical aspects of development and physiology; as such, dysregulation of glial cell-surface proteins in particular is hypothesized to play an important role in age-related neurodegeneration. However, it remains technically difficult to profile glial cell-surface proteins in intact brains. Here, we applied a cell-surface proteomic profiling method to glial cells from intact brains in\ Drosophila,\ which enabled us to fully profile cell-surface proteomes\ in-situ, preserving native cell-cell interactions that would otherwise be omitted using traditional proteomics methods. Applying this platform to young and old flies, we investigated how glial cell-surface proteomes change during aging. We identified candidate genes predicted to be involved in brain aging, including several associated with neural development and synapse wiring molecules not previously thought to be particularly active in glia. Through a functional genetic screen, we identified one surface protein, DIP-β, which is down-regulated in old flies and can increase fly lifespan when overexpressed in adult glial cells. We further performed whole-head single-nucleus RNA-seq, and revealed that DIP-β overexpression mainly impacts glial and fat cells. We also found that glial DIP-β overexpression was associated with improved cell-cell communication, which may contribute to the observed lifespan extension. Our study is the first to apply\ in-situ\ cell-surface proteomics to glial cells in\ Drosophila, and to identify DIP-β as a potential glial regulator of brain aging.

}, doi = {10.7554/eLife.109422.1}, url = {https://doi.org/10.7554/eLife.109422.1}, author = {Marques, Madeline P. and Sun, Bo and Park, Ye-Jin and Jackson, Tyler and Lu, Tzu-Chiao and Qi, Yanyan and Harrison, Erin and Wang, Miranda C. and Venkatachalam, Kartik and Pasha, Omar Moussa and Varanasi, Amogh and Carey, Dominique Kiki and Mani, D.R. and Zirin, Jonathan and Qadiri, Mujeeb and Hu, Yanhui and Perrimon, Norbert and Carr, Steven A. and Udeshi, Namrata D. and Luo, Liqun and Li, Jiefu and Li, Hongjie} } @conference {70301, title = {An investigation of unsupervised cell tracking and interactive fine-tuning}, booktitle = {2025 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW)}, year = {2025}, month = {2026 Feb 23}, abstract = {

Most existing deep learning-based cell tracking methods rely on supervised learning, requiring large-scale annotated datasets that are often unavailable in real-world scenarios. Moreover, many approaches lack tools and methods for correcting mispredicted links or incorporating corrections through fine-tuning. These limitations contribute to the limited adoption of deep learning-based tracking methods in the life sciences, where manual tracking remains the predominant approach. To reduce the annotation burden and enable model training without extensive labeled data, we introduce a loss function for unsupervised training. Our method leverages the predictable dynamics inherent in many biological processes, providing an initialization that does not require an annotated dataset. We further investigate how minimal user-provided annotations can refine tracking accuracy. To this end, we propose an active learning framework that selectively identifies uncertain decisions within the tracking graph, allowing for efficient annotation of the most informative data points. We evaluate our approach on two microscopy datasets, demonstrating the effectiveness of both our unsupervised training strategy and active learning scheme in improving tracking performance. Our implementation and reproducible experiments are available at github.com/funkelab/attrackt and github.com/funkelab/attrackt_experiments, respectively.

}, keywords = {Active learning, Annotations, Cell Tracking, Computer vision, Conferences, Data models, Fine-Tuning, Life sciences, Manuals, Microscopy, Supervised learning, Training, Unsupervised Deep Learning}, doi = {10.1109/ICCVW69036.2025.00610}, url = {https://doi.org/10.1109/ICCVW69036.2025.00610}, author = {Lalit, Manan and Funke, Jan} } @article {70055, title = {(Invited) Nanoscale Insights into Dopamine Release: Single-Strand DNA Functionalized SWCNTs in Neuroscience}, journal = {ECS Meeting Abstracts}, volume = {MA2025-01}, year = {2025}, month = {2025 July 01}, pages = {933}, abstract = {

Single-stranded DNA (ssDNA)-functionalized single-wall carbon nanotubes (SWCNTs) exhibit exceptional optical sensitivity to catecholamines, including dopamine and norepinephrine{\textemdash}key signaling molecules that play vital roles in brain function. This unique capability positions SWCNTs as powerful tools for advancing our understanding of neurochemical processes involving dopaminergic and noradrenergic neurons. In this presentation, I will highlight how our lab has leveraged SWCNT nanosensors to push the boundaries of dopamine neuroscience. For studies in cultured neurons, we developed a composite nanofilm strategy that enabled us to visualize dopamine release with exceptional resolution, capturing single bouton activity with quantal sensitivity while monitoring thousands of release sites simultaneously in large imaging fields of view. By combining SWCNT-based activity imaging with immunofluorescence, electron microscopy, and cutting-edge molecular, cellular and genetic techniques, we have gained new insights into neurobiological properties of dopamine release sites in dopaminergic neurons that had heretofore been inaccessible with conventional methods of inquiry. Building on these advances, I will discuss recent progress in the development of in vivo-compatible dopamine nanosensors. These innovations have allowed us to monitor dopamine dynamics in awake and behaving mice, bridging the gap between molecular-scale imaging and real-time behavior analysis. Furthermore, I will discuss methodological developments that enabled the deployment of these nanosensors in vivo. Looking ahead, these SWCNT-enabled technological advancements hold potential for the study of neurochemical signaling, offering deeper insights into both normal brain function and the pathophysiology of disorders involving catecholamines. Future work aims to expand the applications of these nanosensors to other neural circuits and neuromodulators, ultimately advancing our ability to decode the brain{\textquoteright}s chemical language.

}, doi = {10.1149/MA2025-0111933mtgabs}, url = {https://dx.doi.org/10.1149/MA2025-0111933mtgabs}, author = {Beyene, Abraham G.} } @article {70116, title = {stk32a links sleep homeostasis to suppression of sensory and motor systems}, journal = {bioRxiv}, year = {2025}, month = {2025 Sep 11}, abstract = {

Sleep is regulated by a homeostatic process and associated with an increased arousal threshold, but the genetic and neuronal mechanisms that implement these essential features of sleep remain poorly understood. To address these fundamental questions, we performed a zebrafish genetic screen informed by human genome-wide association studies. We found that mutation of serine/threonine kinase 32a (stk32a) results in increased sleep and impaired sleep homeostasis in both zebrafish and mice, and that stk32a acts downstream of neurotensin signaling and the serotonergic raphe in zebrafish. stk32a mutation reduces phosphorylation of neurofilament proteins, which are co-expressed with stk32a in neurons that regulate motor activity and in lateral line hair cells that detect environmental stimuli, and ablating these cells phenocopies stk32a mutation. Neurotensin signaling inhibits specific sensory and motor populations, and blocks stimulus-evoked responses of neurons that relay sensory information from hair cells to the brain. Our work thus shows that stk32a is an evolutionarily conserved sleep regulator that links neuropeptidergic and neuromodulatory systems to homeostatic sleep drive and changes in arousal threshold, which are implemented through suppression of specific sensory and motor systems.

}, doi = {10.1101/2025.09.09.675098}, url = {https://www.biorxiv.org/content/early/2025/09/11/2025.09.09.675098}, author = {Tran, Steven and Emtage, Jasmine and Zhang, Chaodong and Liu, Xiaoyao and Lecoeuche, Marina and Andreev, Andrey and Oikonomou, Grigorios and Narayan, Sujatha and Garcia, Brianna and Cammidge, Tasha and Gonzales, Cristina and Hurley, Hannah and Yap, Misha and Li, Shan and Wang, Feng and Wang, Ting-Yu and Ahrens, Misha B. and Chou, Tsui-Fen and Xu, Min and Liu, Qinghua and Prober, David A.} } @article {70154, title = {LARGE1 processively polymerizes length-controlled matriglycan on prodystroglycan.}, journal = {Nat Commun}, volume = {16}, year = {2025}, month = {2025 Oct 10}, pages = {9028}, abstract = {

Matriglycan is a linear glycan (xylose-β1,3-glucuronate), which binds proteins in the extracellular matrix that contain laminin-globular domains and Lassa Fever Virus. It is indispensable for neuromuscular function. Matriglycan of insufficient length can cause muscular dystrophy with abnormal brain and eye development. LARGE1 (Like-acetylglucosaminyltransferase-1) uniquely synthesizes matriglycan on dystroglycan. The mechanism of matriglycan synthesis is not obvious from cryo-EM reconstructions of LARGE1. However, by reconstituting activity in vitro on recombinant prodystroglycan we show that the presence of the dystroglycan N-terminal domain (DGN), phosphorylated core M3, and a xylose-glucuronate primer are necessary for matriglycan polymerization by LARGE1. By introducing active site mutations, we demonstrate that LARGE1 processively polymerizes matriglycan on prodystroglycan, with its length regulated by the dystroglycan prodomain, DGN. Our enzymatic analysis of LARGE1 uncovers the mechanism of matriglycan synthesis on dystroglycan, which can form the basis for therapeutic strategies to treat matriglycan-deficient neuromuscular disorders and arenaviral infections.

}, keywords = {Animals, Catalytic Domain, Cryoelectron Microscopy, Dystroglycans, Humans, N-Acetylglucosaminyltransferases, Polymerization, Polysaccharides}, issn = {2041-1723}, doi = {10.1038/s41467-025-64080-z}, url = {https://doi.org/10.1038/s41467-025-64080-z}, author = {Joseph, Soumya and Schnicker, Nicholas J and Spellmon, Nicholas and Xu, Zhen and Yan, Rui and Yu, Zhiheng and Davulcu, Omar and Yang, Tiandi and Hopkins, Jesse and Anderson, Mary E and Venzke, David and Campbell, Kevin P} } @article {70006, title = {Large-scale high-density brain-wide neural recording in nonhuman primates.}, journal = {Nat Neurosci}, year = {2025}, month = {2025 Jun 23}, abstract = {

High-density silicon probes have transformed neuroscience by enabling large-scale neural recordings at single-cell resolution. However, existing technologies have provided limited functionality in nonhuman primates (NHPs) such as macaques. In the present report, we describe the design, fabrication and performance of Neuropixels 1.0 NHP, a high-channel electrode array designed to enable large-scale acute recording throughout large animal brains. The probe features 4,416 recording sites distributed along a 45-mm shank. Experimenters can programmably select 384 recording channels, enabling simultaneous multi-area recording from thousands of neurons with single or multiple probes. This technology substantially increases scalability and recording access relative to existing technologies and enables new classes of experiments that involve electrophysiological mapping of brain areas at single-neuron and single-spike resolution, measurement of spike-spike correlations between cells and simultaneous brain-wide recordings at scale.

Preprint: https://doi.org/10.1101/2023.02.01.526664\ 

}, issn = {1546-1726}, doi = {10.1038/s41593-025-01976-5}, url = {https://doi.org/10.1038/s41593-025-01976-5}, author = {Trautmann, Eric M and Hesse, Janis K and Stine, Gabriel M and Xia, Ruobing and Zhu, Shude and O{\textquoteright}Shea, Daniel J and Karsh, Bill and Colonell, Jennifer and Lanfranchi, Frank F and Vyas, Saurabh and Zimnik, Andrew and Amematsro, Elom and Steinemann, Natalie A and Wagenaar, Daniel A and Pachitariu, Marius and Andrei, Alexandru and Lopez, Carolina Mora and O{\textquoteright}Callaghan, John and Putzeys, Jan and Raducanu, Bogdan C and Welkenhuysen, Marleen and Churchland, Mark and Moore, Tirin and Shadlen, Michael and Shenoy, Krishna and Tsao, Doris and Dutta, Barundeb and Harris, Timothy} } @article {68938, title = {Learning produces an orthogonalized state machine in the hippocampus.}, journal = {Nature}, volume = {640}, year = {2025}, month = {2025 February 12}, abstract = {

Cognitive maps confer animals with flexible intelligence by representing spatial, temporal and abstract relationships that can be used to shape thought, planning and behaviour. Cognitive maps have been observed in the hippocampus1, but their algorithmic form and learning mechanisms remain obscure. Here we used large-scale, longitudinal two-photon calcium imaging to record activity from thousands of neurons in the CA1 region of the hippocampus while mice learned to efficiently collect rewards from two subtly different linear tracks in virtual reality. Throughout learning, both animal behaviour and hippocampal neural activity progressed through multiple stages, gradually revealing improved task representation that mirrored improved behavioural efficiency. The learning process involved progressive decorrelations in initially similar hippocampal neural activity within and across tracks, ultimately resulting in orthogonalized representations resembling a state machine capturing the inherent structure of the task. This decorrelation process was driven by individual neurons acquiring task-state-specific responses (that is, {\textquoteright}state cells{\textquoteright}). Although various standard artificial neural networks did not naturally capture these dynamics, the clone-structured causal graph, a hidden Markov model variant, uniquely reproduced both the final orthogonalized states and the learning trajectory seen in animals. The observed cellular and population dynamics constrain the mechanisms underlying cognitive map formation in the hippocampus, pointing to hidden state inference as a fundamental computational principle, with implications for both biological and artificial intelligence.

}, doi = {10.1038/s41586-024-08548-w}, url = {https://doi.org/10.1038/s41586-024-08548-w}, author = {Sun, Weinan and Winnubst, Johan and Natrajan, Maanasa and Lai, Chongxi and Kajikawa, Koichiro and Michaelos, Michalis and Gattoni, Rachel and Stringer, Carsen and Flickinger, Daniel and Fitzgerald, James E and Spruston, Nelson} } @article {69577, title = {Learning reshapes the hippocampal representation hierarchy}, journal = {Proc. Natl. Acad. Sci. U.S.A.}, year = {2025}, month = {2025 Mar 10}, abstract = {

Biological neural networks seem to efficiently select and represent task-relevant features of their inputs, an ability that is highly sought after also in artificial networks. A lot of work has gone into identifying such representations in both sensory and motor systems; however, less is understood about how representations form during complex learning conditions to support behavior, especially in higher associative brain areas. Our work shows that the hippocampus maintains a robust hierarchical representation of task variables and that this structure can support new learning through minimal changes to the neural representations.

Preprint:\ https://www.doi.org/10.1101/2024.08.21.608911

}, doi = {10.1073/pnas.2417025122}, url = {https://doi.org/10.1073/pnas.2417025122}, author = {Chiossi, Heloisa S. C. and Nardin, Michele and Tka{\v c}ik, Ga{\v s}per and Csicsvari, Jozsef L.} } @article {69624, title = {Leg compliance is required to explain the ground reaction force patterns and speed ranges in different gaits}, journal = {Royal Society of Open Science}, year = {2025}, month = {2025 October 15}, abstract = {

Two simple models{\textemdash}vaulting over stiff legs and rebounding over compliant legs{\textemdash}are employed to describe the mechanics of legged locomotion. It is agreed that compliant legs are necessary for describing running, and that leg compliance is also present during walking. Stiff legs continue to be employed to model walking under the assumption that the compliance of the leg during walking is low enough to be considered stiff. Here we study gait choice and walk-to-run transition in a biped with compliance and show that the principles underlying gait choice and transition are completely different from stiff legs. Two findings underpin our conclusions: First, at the same speed, step length and stance duration, multiple gaits that differ in the number of times the leg expands and contracts during a single stance are possible. Among them, humans and other animals choose the (normal) gait with M-shaped vertical ground reaction forces (vGRF) not just because of energy considerations but also constraints from forces. Second, the transition from walking to running occurs because of three factors: vGRF minimum at mid-stance characteristic of normal walking, synchronization of horizontal and vertical motions during single support, and velocity redirection during the double support. The insight above required an analytical approximation of the double spring-loaded pendulum (DSLIP) model describing the intricate oscillatory dynamics that relate single and double support phases. Additionally, we also examined DSLIP as a quantitative model for locomotion and conclude that DSLIP speed range is limited. However, insights gleaned from the analytical treatment of DSLIP are general and will inform the construction of more accurate models of walking.

bioRxiv preprint:\ https://doi.org/10.1101/2024.09.23.612940

}, doi = {10.1098/rsos.250527}, url = {https://doi.org/10.1098/rsos.250527}, author = {Safa, Ali Tehrani and Biswas, Tirthabir and Ramakrishnan, Arun and Bhandawat, Vikas} } @article {69656, title = {Leukocytes use endothelial membrane tunnels to extravasate the vasculature}, journal = {Cell Rep}, year = {2025}, month = {2025 Sep 04}, abstract = {

Upon inflammation, leukocytes extravasate through endothelial cells. When they extravasate, it is generally accepted that neighboring endothelial cells disconnect. Careful examination of endothelial junctions showed a partial membrane overlap beyond VE-cadherin distribution. These overlaps are regulated by actin polymerization and, although marked by, do not require PECAM-1, nor VE-cadherin. Neutrophils prefer wider membrane overlaps as exit sites. Detailed 3D analysis of neutrophil transmigration in real time at high spatiotemporal resolution revealed that overlapping endothelial membranes form a tunnel during neutrophil transmigration. These tunnels are formed by the neutrophil lifting the membrane of the upper endothelial cell while indenting and crawling over the membrane of the underlying endothelial cell. Our work shows that endothelial cells do not simply retract upon the passage of neutrophils but provide membrane tunnels, allowing neutrophils to extravasate. This discovery defines the 3D multicellular architecture in which the paracellular transmigration of neutrophils occurs.

}, doi = {10.1016/j.celrep.2025.116242}, url = {https://doi.org/10.1016/j.celrep.2025.116242}, author = {van der Meer, Werner and van Steen, Abraham C.I. and Mahlandt, Eike and Rolas, Loic and Wang, Haitao and Arts, Janine and Kempers, Lanette and Gr{\"o}nloh, Max and Schoon, Rianne M. and Driessen, Amber and van Rijssel, Jos and Klaassen, Ingeborg and Schlingemann, Reinier O. and Manavski, Yosif and Hoogenboezem, Mark and Boon, Reinier A. and Khuon, Satya and Wait, Eric and Heddleston, John and Chew, Teng-Leong and Nolte, Martijn A and Nourshargh, Sussan and Goedhart, Joachim and van Buul, Jaap D} } @article {69773, title = {Live imaging of the extracellular matrix with a glycan-binding fluorophore.}, journal = {Nat Methods}, year = {2025}, month = {2025 Feb 06}, abstract = {

All multicellular systems produce and dynamically regulate extracellular matrices (ECMs) that play essential roles in both biochemical and mechanical signaling. Though the spatial arrangement of these extracellular assemblies is critical to their biological functions, visualization of ECM structure is challenging, in part because the biomolecules that compose the ECM are difficult to fluorescently label individually and collectively. Here, we present a cell-impermeable small-molecule fluorophore, termed Rhobo6, that turns on and red shifts upon reversible binding to glycans. Given that most ECM components are densely glycosylated, the dye enables wash-free visualization of ECM, in systems ranging from in vitro substrates to in vivo mouse mammary tumors. Relative to existing techniques, Rhobo6 provides a broad substrate profile, superior tissue penetration, non-perturbative labeling, and negligible photobleaching. This work establishes a straightforward method for imaging the distribution of ECM in live tissues and organisms, lowering barriers for investigation of extracellular biology.

}, issn = {1548-7105}, doi = {10.1038/s41592-024-02590-2}, url = {https://doi.org/10.1038/s41592-024-02590-2}, author = {Fiore, Antonio and Yu, Guoqiang and Northey, Jason J and Patel, Ronak and Ravenscroft, Thomas A. and Ikegami, Richard and Kolkman, W and Pratik Kumar and Dilan, Tanya L and Ruetten, Virginia M.S. and Ahrens, Misha B and Shroff, Hari and Wang, Shaohe and Weaver, Valarie M and Pedram, Kayvon} } @article {69423, title = {Live-cell single-molecule fluorescence microscopy for protruding organelles reveals regulatory mechanisms of MYO7A-driven cargo transport in stereocilia of inner ear hair cells}, journal = {Nat Commun}, year = {2025}, month = {2025 Sep 01}, abstract = {

Stereocilia are F-actin-based cylindrical protrusions on the apical surface of inner ear hair cells that function as biological mechanosensors of sound and acceleration. During stereocilia development, specific unconventional myosins transport proteins and phospholipids as cargo and mediate elongation, differentiation and acquisition of the mechanoelectrical transduction (MET). How unconventional myosins localize themselves and cargo in stereocilia using energy from ATP hydrolysis is only partially understood. Here, we developed STELLA-SPIM microscopy to visualize movement of single myosin molecules in live hair cell stereocilia. STELLA-SPIM demonstrated that MYO7A, a component of MET machinery, shows processive movement toward stereocilia tips when chemically dimerized or constitutively activated by missense mutations disabling tail-mediated autoinhibition. Conversely, MYO7A shows step-wise but not processive movement in stereocilia when its tail is tethered to the plasma membrane or F-actin in the presence of MYO7A interacting partners. We posit that MYO7A dimerizes and moves processively in stereocilia when unleashed from autoinhibition.

}, doi = {10.1038/s41467-025-63102-0}, url = {https://doi.org/10.1038/s41467-025-63102-0}, author = {Takushi Miyoshi and Harshad D Vishwasrao and Inna A Belyantseva and Mrudhula Sajeevadathan and Yasuko Ishibashi and Samuel M Adadey and Narinobu Harada and Hari Shroff and Thomas B Friedman} } @article {69956, title = {Lysosomes signal through epigenome to regulate longevity across generations}, journal = {bioRxiv}, year = {2025}, month = {2025 May 23}, abstract = {

Epigenome is sensitive to metabolic inputs and crucial for aging. Lysosomes emerge as a signaling hub to sense metabolic cues and regulate longevity. We unveil that lysosomal metabolic pathways signal through the epigenome to regulate transgenerational longevity in Caenorhabditis elegans. We discovered that the induction of lysosomal lipid signaling and lysosomal AMP-activated protein kinase (AMPK), or the reduction of lysosomal mechanistic-target-of-rapamycin (mTOR) signaling, increases the expression of histone H3.3 variant and elevates H3K79 methylation, leading to lifespan extension across multiple generations. This transgenerational pro-longevity effect requires intestine-to-germline transportation of H3.3 and a germline-specific H3K79 methyltransferase, and can be recapitulated by overexpressing H3.3 or the H3K79 methyltransferase. This work uncovers a lysosome-epigenome signaling axis linking soma and germline to mediate the transgenerational inheritance of longevity.Competing Interest StatementThe authors have declared no competing interest.National Institutes of Health, RF1AG074540, DP1DK113644Howard Hughes Medical Institute, https://ror.org/006w34k90

}, doi = {10.1101/2025.05.21.652954}, url = {https://www.biorxiv.org/content/early/2025/05/23/2025.05.21.652954}, author = {Zhang, Qinghao and Dang, Weiwei and Wang, Meng C.} } @article {69955, title = {Lysosomes Signal through Epigenome to Regulate Longevity across Generations}, journal = {Science}, volume = {389}, year = {2025}, month = {2025 Sep 25}, abstract = {

Epigenome is sensitive to metabolic inputs and crucial for aging. Lysosomes emerge as a signaling hub to sense metabolic cues and regulate longevity. We unveil that lysosomal metabolic pathways signal through the epigenome to regulate transgenerational longevity in Caenorhabditis elegans. We discovered that the induction of lysosomal lipid signaling and lysosomal AMP-activated protein kinase (AMPK), or the reduction of lysosomal mechanistic-target-of-rapamycin (mTOR) signaling, increases the expression of histone H3.3 variant and elevates H3K79 methylation, leading to lifespan extension across multiple generations. This transgenerational pro-longevity effect requires intestine-to-germline transportation of H3.3 and a germline-specific H3K79 methyltransferase, and can be recapitulated by overexpressing H3.3 or the H3K79 methyltransferase. This work uncovers a lysosome-epigenome signaling axis linking soma and germline to mediate the transgenerational inheritance of longevity.

bioRxiv preprint: https://www.biorxiv.org/content/early/2025/05/23/2025.05.21.652954

}, doi = {10.1126/science.adn8754}, url = {https://doi.org/10.1126/science.adn8754}, author = {Zhang, Qinghao and Dang, Weiwei and Wang, Meng C.} } @conference {70314, title = {Machine learning and neural representations for enhancing phase diversity-based adaptive optics}, booktitle = {Optica Biophotonics Congress 2025}, year = {2025}, month = {2025 Apr 21}, publisher = {Optica Publishing Group}, organization = {Optica Publishing Group}, abstract = {

Using phase-diversity wavefront sensing, machine learning-based deformable mirror control, and neural representations of the unknown sample and phase aberration, we demonstrate precise reconstruction of sample structures in fluorescence microscopy, even under severe, high-order aberrations.Full-text article not available; see video presentation

}, keywords = {Adaptive optics, Deformable mirrors, Fluorescence microscopy, Machine Learning, Phase diversity, Wave front sensing}, doi = {10.1364/NTM.2025.NTu4C.1}, url = {https://opg.optica.org/abstract.cfm?URI=NTM-2025-NTu4C.1}, author = {Magdalena Schneider} } @article {69945, title = {Macrophages release neuraminidase and cleaved calreticulin for programmed cell removal.}, journal = {Proc Natl Acad Sci U S A}, volume = {122}, year = {2025}, month = {2025 May 27}, pages = {e2426644122}, abstract = {

Calreticulin (CALR) is primarily an endoplasmic reticulum chaperone protein that also plays a key role in facilitating programmed cell removal (PrCR) by acting as an "eat-me" signal for macrophages, directing their recognition and engulfment of dying, diseased, or unwanted cells. Recent findings have demonstrated that macrophages can transfer their own CALR onto exposed asialoglycans on target cells, marking them for PrCR. Despite the critical role CALR plays in this process, the molecular mechanisms behind its secretion by macrophages and the formation of binding sites on target cells remain unclear. Our findings show that CALR undergoes C-terminal cleavage upon secretion, producing a truncated form that functions as the active eat-me signal detectable on target cells. We identify cathepsins as potential proteases involved in this cleavage process. Furthermore, we demonstrate that macrophages release neuraminidases, which modify the surface of target cells and facilitate CALR binding. These insights reveal a coordinated mechanism through which lipopolysaccharide (LPS)-activated macrophages regulate CALR cleavage and neuraminidase activity to mark target cells for PrCR. How they recognize the cells to be targeted remains unknown.

}, keywords = {Animals, Apoptosis, Calreticulin, Humans, Lipopolysaccharides, Macrophages, Mice, Neuraminidase}, issn = {1091-6490}, doi = {10.1073/pnas.2426644122}, url = {https://doi.org/10.1073/pnas.2426644122}, author = {Banuelos, Allison and Baez, Michelle and Zhang, Allison and Y{\i}lmaz, Leyla and Kasberg, William and Volk, Regan and Georgeos, Nardin and Koren-Sedova, Elle and Le, Uyen and Burden, Andrew T and Marjon, Kristopher D and Lippincott-Schwartz, Jennifer and Zaro, Balyn W and Weissman, Irving L} } @article {69782, title = {Melanocortin 3 receptor regulates hepatic autophagy and systemic adiposity.}, journal = {Nat Commun}, volume = {16}, year = {2025}, month = {2025 Feb 16}, pages = {1690}, abstract = {

Systemic lipid homeostasis requires hepatic autophagy, a major cellular program for intracellular fat recycling. Here, we find melanocortin 3 receptor (MC3R) regulates hepatic autophagy in addition to its previously established CNS role in systemic energy partitioning and puberty. Mice with Mc3r deficiency develop obesity with hepatic triglyceride accumulation and disrupted hepatocellular autophagosome turnover. Mice with partially inactive human MC3R due to obesogenic variants demonstrate similar hepatic autophagic dysfunction. In vitro and in vivo activation of hepatic MC3R upregulates autophagy through LC3II activation, TFEB cytoplasmic-to-nuclear translocation, and subsequent downstream gene activation. MC3R-deficient hepatocytes had blunted autophagosome-lysosome docking and lipid droplet clearance. Finally, the liver-specific rescue of Mc3r was sufficient to restore hepatocellular autophagy, improve hepatocyte mitochondrial function and systemic energy expenditures, reduce adipose tissue lipid accumulation, and partially restore body weight in both male and female mice. We thus report a role for MC3R in regulating hepatic autophagy and systemic adiposity.

}, keywords = {Adiposity, Animals, Autophagosomes, Autophagy, Basic Helix-Loop-Helix Leucine Zipper Transcription Factors, Female, Hepatocytes, Humans, Lipid Metabolism, Liver, Male, Mice, Mice, Inbred C57BL, Mice, Knockout, Microtubule-Associated Proteins, Obesity, Receptor, Melanocortin, Type 3, Triglycerides}, issn = {2041-1723}, doi = {10.1038/s41467-025-56936-1}, author = {Patel, Tushar P and Jun, Joo Yun and Seo, Arnold Y and Levi, Noah J and Elizondo, Diana M and Chen, Jocelyn and Wong, Adrian M and Tugarinov, Nicol and Altman, Elizabeth K and Gehle, Daniel B and Jung, Sun Min and Patel, Pooja and Ericson, Mark and Haskell-Luevano, Carrie and Demby, Tamar C and Cougnoux, Antony and Wolska, Anna and Yanovski, Jack A} } @article {70202, title = {Memory traces bias new learning for hippocampal generalization}, journal = {bioRxiv}, year = {2025}, month = {2025 Nov 25}, abstract = {

The ability to use generalized prior experience to guide behavior in novel situations is a fundamental cognitive function. While recent evidence suggests that the hippocampus supports generalization how this is accomplished is poorly understood. Here we combined longitudinal optical imaging in head-fixed mice with computational modeling to examine generalization in hippocampal area CA1. We found that prior training accelerated behavioral adaptation to a novel environment and that this was accompanied by highly stable hippocampal representations. We identified putative memory traces from prior experience that enabled this generalization at multiple levels. At the population level, novel-context network dynamics rapidly aligned with low-dimensional neural subspaces established during prior experience. At the cellular level, spatially-informative weak "residual" activity reflecting generalizable information about the task structure appeared to bias which neurons form place fields (PFs) and where via behavioral timescale synaptic plasticity (BTSP). Finally, this was an active process as many PFs changed their reference frame in the novel environment to reflect the consistent task structure. In sum, the influence of memory traces on new PF formation may allow past experience to guide new learning such that representations are based on generalizable features, thus enabling rapid adaptive behavior in new contexts.

}, doi = {10.1101/2025.11.24.690297}, url = {https://www.biorxiv.org/content/early/2025/11/25/2025.11.24.690297}, author = {Qian, Fish Kunxun and Li, Guanchun and Lipshutz, David and Romani, Sandro and Magee, Jeffrey Charles} } @article {70161, title = {Mesoscale volumetric fluorescence imaging at nanoscale resolution by photochemical sectioning}, journal = {Science}, volume = {390}, year = {2025}, month = {2025 Oct 16}, pages = {eadr9109}, abstract = {

Optical nanoscopy of intact biological specimens has been transformed by recent advancements in hydrogel-based tissue clearing and expansion, enabling the imaging of cellular and subcellular structures with molecular contrast. However, existing high-resolution fluorescence microscopes are physically limited by objective-to-specimen distance, which prevents the study of whole-mount specimens without physical sectioning. To address this challenge, we developed a photochemical strategy for spatially precise sectioning of specimens. By combining serial photochemical sectioning with lattice light-sheet imaging and petabyte-scale computation, we imaged and reconstructed axons and myelin sheaths across entire mouse olfactory bulbs at nanoscale resolution. An olfactory bulb{\textendash}wide analysis of myelinated and unmyelinated axons revealed distinctive patterns of axon degeneration and de-/dysmyelination in the neurodegenerative brain, highlighting the potential for peta- to exabyte-scale super-resolution studies using this approach. High-resolution microscopes have a short working distance, making it difficult to see deep within large biological samples such as an intact brain. Slicing the tissue with a blade can reach deeper, but this often distorts or destroys the fine structures that scientists want to study. By embedding a sample in a light-sensitive hydrogel, Wang et al. demonstrated a gentler approach using a precise ray or sheet of light to dissolve or cut away tissue layer by layer. After each layer is removed, the newly exposed surface is imaged, allowing for a complete, high-resolution, three-dimensional reconstruction without damaging physical contact.\ 

bioRxiv preprint: https://www.biorxiv.org/content/10.1101/2024.08.01.605857v1

}, doi = {10.1126/science.adr9109}, url = {https://www.science.org/doi/abs/10.1126/science.adr9109}, author = {Wei Wang and Xiongtao Ruan and Gaoxiang Liu and Daniel E. Milkie and Wenping Li and Eric Betzig and Srigokul Upadhyayula and Ruixuan Gao} } @article {70050, title = {Michael Patrick Sheetz, 1946{\textendash}2025, a devotee of and major contributor to membrane and cytoskeletal biology}, journal = {Molecular Biology of the Cell}, volume = {36}, year = {2025}, month = {2025 Jul 31}, pages = {fe1}, abstract = {

Michael P. Sheetz (1946{\textendash}2025) advanced the field of mechanobiology through his creative experiments, new methodologies, and keen insights. His research touched many fields of cell biology, including membrane biophysics, motor proteins, the cytoskeleton, cell migration, and cellular senescence. In addition to his research, Sheetz was a leader who built vibrant academic departments and institutes and advanced the careers of many trainees.

}, doi = {10.1091/mbc.E25-05-0208}, url = {https://doi.org/10.1091/mbc.E25-05-0208}, author = {Kenney, Linda J. and Vale, Ronald D. and Spudich, James A.} } @article {70039, title = {MicroSplit: Semantic Unmixing of Fluorescent Microscopy Data}, journal = {bioRxiv}, year = {2025}, month = {2025 Jul 21}, abstract = {

Fluorescence microscopy, a key driver for progress in the life sciences, faces limitations due to the microscope{\textquoteright}s optics, fluorophore chemistry, and photon exposure limits, necessitating trade-offs in imaging speed, resolution, and depth. Here, we introduce MicroSplit, a computational multiplexing technique based on deep learning that allows multiple cellular structures to be imaged in a single fluorescent channel and then unmixed computationally, allowing faster imaging and reduced photon exposure. We show that MicroSplit efficiently separates up to four superimposed noisy structures into distinct denoised fluorescent image channels. Furthermore, using Variational Splitting Encoder-Decoder (VSE) networks, our approach can sample diverse predictions from a trained posterior of solutions. The diversity of these samples scales with the uncertainty in a given input, allowing us to estimate the true prediction errors by computing the variability between posterior samples. We demonstrate the robustness of MicroSplit across various datasets and noise levels and show its utility to image more, image faster, and improve downstream analysis. We provide MicroSplit along with all associated training and evaluation datasets as open resources, enabling life scientists to benefit from the potential of computational multiplexing and accelerate the pace of scientific discovery.

}, doi = {10.1101/2025.02.10.637323}, url = {https://www.biorxiv.org/content/early/2025/07/21/2025.02.10.637323}, author = {Ashesh, Ashesh and Carrara, Federico and Zubarev, Igor and Galinova, Vera and Croft, Melisande and Pezzotti, Melissa and Gong, Daozheng and Casagrande, Francesca and Colombo, Elisa and Giussani, Stefania and Restelli, Elena and Cammarota, Eugenia and Battagliotti, Juan Manuel and Klena, Nikolai and Di Sante, Moises and Adhikari, Raghabendra and Feliciano, Daniel and Pigino, Gaia and Taverna, Elena and Harschnitz, Oliver and Maghelli, Nicola and Scherer, Norbert and Dalle Nogare, Damian Edward and Deschamps, Joran and Pasqualini, Francesco and Jug, Florian} } @article {69862, title = {Mitochondrial complexity is regulated at ER-mitochondria contact sites via PDZD8-FKBP8 tethering.}, journal = {Nat Commun}, volume = {16}, year = {2025}, month = {2025 Apr 17}, pages = {3401}, abstract = {

Mitochondria-ER membrane contact sites (MERCS) represent a fundamental ultrastructural feature underlying unique biochemistry and physiology in eukaryotic cells. The ER protein PDZD8 is required for the formation of MERCS in many cell types, however, its tethering partner on the outer mitochondrial membrane (OMM) is currently unknown. Here we identify the OMM protein FKBP8 as the tethering partner of PDZD8 using a combination of unbiased proximity proteomics, CRISPR-Cas9 endogenous protein tagging, Cryo-electron tomography, and correlative light-electron microscopy. Single molecule tracking reveals highly dynamic diffusion properties of PDZD8 along the ER membrane with significant pauses and captures at MERCS. Overexpression of FKBP8 is sufficient to narrow the ER-OMM distance, whereas independent versus combined deletions of these two proteins demonstrate their interdependence for MERCS formation. Furthermore, PDZD8 enhances mitochondrial complexity in a FKBP8-dependent manner. Our results identify a novel ER-mitochondria tethering complex that regulates mitochondrial morphology in mammalian cells.

Preprint:\ 10.1101/2025.02.22.639343

}, keywords = {Animals, CRISPR-Cas Systems, Cryoelectron Microscopy, Endoplasmic Reticulum, HEK293 Cells, Hela Cells, Humans, Membrane Proteins, Mitochondria, Mitochondrial Membranes, Proteomics, Tacrolimus Binding Proteins}, issn = {2041-1723}, doi = {10.1038/s41467-025-58538-3}, url = {https://doi.org/10.1038/s41467-025-58538-3}, author = {Nakamura, Koki and Aoyama-Ishiwatari, Saeko and Nagao, Takahiro and Paaran, Mohammadreza and Obara, Christopher J and Sakurai-Saito, Yui and Johnston, Jake and Du, Yudan and Suga, Shogo and Tsuboi, Masafumi and Nakakido, Makoto and Tsumoto, Kouhei and Kishi, Yusuke and Gotoh, Yukiko and Kwak, Chulhwan and Rhee, Hyun-Woo and Seo, Jeong Kon and Kosako, Hidetaka and Potter, Clint and Carragher, Bridget and Lippincott-Schwartz, Jennifer and Polleux, Franck and Hirabayashi, Yusuke} } @article {69747, title = {Molecular determinants of optical modulation in ssDNA{\textendash}carbon nanotube biosensors}, journal = {ACS Nano}, year = {2025}, month = {01/2025}, abstract = {

Most traditional optical biosensors operate through molecular recognition, where ligand binding causes conformational changes that lead to optical perturbations in the emitting motif. Optical sensors developed from single-stranded DNA-functionalized single-walled carbon nanotubes (ssDNA{\textendash}SWCNTs) have started to make useful contributions to biological research. However, the mechanisms underlying their function have remained poorly understood. In this study, we combine experimental and computational approaches to show that ligand binding alone is not sufficient for optical modulation in this class of synthetic biosensors. Instead, the optical response that occurs after ligand binding is highly dependent on the chemical properties of the ligands, resembling mechanisms seen in activity-based biosensors. Specifically, we show that in ssDNA{\textendash}SWCNT catecholamine sensors, the optical response correlates positively with the electron density on the aryl motif, even among ligands with similar ligand binding affinities. Importantly, despite the strong correlations with electrochemical properties, we find that catechol oxidation itself is not necessary to drive the sensor optical response. We discuss how these findings could serve as a framework for tuning the performance of existing sensors and guiding the development of new biosensors of this class.

}, doi = {10.1021/acsnano.4c13814}, url = {https://doi.org/10.1021/acsnano.4c13814}, author = {Krasley, Andrew T. and Chakraborty, Sayantani and Vukovi{\'c}, Lela and Beyene, Abraham G.} } @article {69882, title = {Molecular organization of central cholinergic synapses.}, journal = {Proc Natl Acad Sci U S A}, volume = {122}, year = {2025}, month = {2025 Apr 29}, pages = {e2422173122}, abstract = {

Synapses have undergone significant diversification and adaptation, contributing to the complexity of the central nervous system. Understanding their molecular architecture is essential for deciphering the brain{\textquoteright}s functional evolution. While nicotinic acetylcholine receptors (nAchRs) are widely distributed across metazoan brains, their associated protein networks remain poorly characterized. Using in vivo proximity labeling, we generated proteomic maps of subunit-specific nAchR interactomes in developing and mature brains. Our findings reveal a developmental expansion and reconfiguration of the nAchR interactome. Proteome profiling with genetic perturbations showed that removing individual nAchR subunits consistently triggers compensatory shifts in receptor subtypes, highlighting mechanisms of synaptic plasticity. We also identified the Rho-GTPase regulator Still life (Sif) as a key organizer of cholinergic synapses, with loss of Sif disrupting their molecular composition and structural integrity. These results provide molecular insights into the development and plasticity of central cholinergic synapses, advancing our understanding of synaptic identity conservation and divergence.

}, keywords = {Animals, Brain, Cholinergic Neurons, Drosophila melanogaster, Drosophila Proteins, Neuronal Plasticity, Proteome, Proteomics, Receptors, Nicotinic, Synapses}, issn = {1091-6490}, doi = {10.1073/pnas.2422173122}, url = {https://doi.org/10.1073/pnas.2422173122}, author = {Rosenthal, Justin S and Zhang, Dean and Yin, Jun and Long, Caixia and Yang, George and Li, Yan and Lu, Zhiyuan and Li, Wei-Ping and Yu, Zhiheng and Li, Jiefu and Yuan, Quan} } @article {69746, title = {Multicilia dynamically transduce Sonic Hedgehog signaling to regulate choroid plexus functions}, journal = {Cell Reports}, year = {2025}, month = {2025 Mar 25}, abstract = {

The choroid plexus is a major site for cerebrospinal fluid (CSF) production, characterized by a multiciliated epithelial monolayer that regulates CSF production. We demonstrate that defective choroid plexus ciliogenesis or intraflagellar transport yields neonatal hydrocephalus, at least in part due to increased water channel Aqp1 and ion transporter Atp1a2 expression. We demonstrate choroid plexus multicilia as sensory cilia, transducing both canonical and non-canonical Sonic Hedgehog (Shh) signaling. Interestingly, it is the non-canonical Shh signaling that represses Aqp1 and Atp1a2 expression by the Smoothened (Smo)/Gαi/cyclic AMP (cAMP) pathway. Choroid plexus multicilia exhibit unique ciliary ultrastructure, carrying features of both primary and motile cilia. Unlike most cilia that elongate during maturation, choroid plexus ciliary length decreases during development, causing a decline of Shh signaling intensity in the developing choroid plexus, a derepression of Aqp1 and Atp1a2, and, ultimately, increased CSF production. Hence, the developmental dynamics of choroid plexus multicilia dampens the Shh signaling intensity to promote CSF production.

bioRxiv Preprint:\ https://www.biorxiv.org/content/early/2025/01/22/2025.01.21.633415

}, doi = {10.1016/j.celrep.2025.115383}, url = {https://doi.org/10.1016/j.celrep.2025.115383}, author = {Mao, Suifang and Song, Rui and Jin, Shibo and Pang, Song and Jovanovic, Aleksandra and Zimmerman, Adam and Li, Peng and Wu, Xinying and Wendland, Michael F. and Lin, Kerry and Chen, Wei-Chi and Choksi, Semil P. and Chen, Gang and Holtzman, Michael J. and Reiter, Jeremy F. and Wan, Ying and Xuan, Zhenyu and Xiang, Yang K. and Xu, C Shan and Upadhyayula, Srigokul and Hess, Harald F. and He, Lin} } @article {69994, title = {A multimodal adaptive optical microscope for in vivo imaging from molecules to organisms}, journal = {bioRxiv}, year = {2025}, month = {2025 Jun 16}, abstract = {

Understanding biological systems requires observing features and processes across vast spatial and temporal scales, spanning nanometers to centimeters and milliseconds to days, often using multiple imaging modalities within complex native microenvironments. Yet, achieving this comprehensive view is challenging because microscopes optimized for specific tasks typically lack versatility due to inherent optical and sample handling trade-offs, and frequently suffer performance degradation from sample-induced optical aberrations in multicellular contexts. Here, we present MOSAIC, a reconfigurable microscope that integrates multiple advanced imaging techniques including light-sheet, label-free, super-resolution, and multi-photon, all equipped with adaptive optics. MOSAIC enables non-invasive imaging of subcellular dynamics in both cultured cells and live multicellular organisms, nanoscale mapping of molecular architectures across millimeter-scale expanded tissues, and structural/functional neural imaging within live mice. MOSAIC facilitates correlative studies across biological scales within the same specimen, providing an integrated platform for broad biological investigation.

Preprint:\ https://www.biorxiv.org/content/early/2025/06/13/2025.06.02.657494

}, doi = {10.1101/2025.06.02.657494}, url = {https://www.biorxiv.org/content/early/2025/06/13/2025.06.02.657494}, author = {Fu, Tian-Ming and Liu, Gaoxiang and Milkie, Daniel E. and Ruan, Xiongtao and G{\"o}rlitz, Frederik and Shi, Yu and Ferro, Valentina and Divekar, Nikita S. and Wang, Wei and York, Harrison M. and Kilic, Velat and Mueller, Matthew and Liang, Yajie and Daugird, Timothy A. and Gacha-Garay, Maria J. and Larkin, Kathryn A. and Adikes, Rebecca C. and Harrison, Nathaniel and Shirazinejad, Cyna and Williams, Samara and Nourse, Jamison L. and Sheu, Shu-Hsien and Gao, Liang and Li, Tongchao and Mondal, Chandrani and Achour, Kemal and Hercule, Wilmene and Stabley, Daniel and Emmerich, Kevin and Dong, Peng and Drubin, David and Liu, Zhe J. and Clapham, David and Mumm, Jeff S. and Koyama, Minoru and Killilea, Alison and Bravo-Cordero, Jose Javier and Keene, C. Dirk and Luo, Liqun and Kirchhausen, Tom and Pathak, Medha M. and Arumugam, Senthil and Nunez, James K. and Gao, Ruixuan and Matus, David Q. and Martin, Benjamin L. and Swinburne, Ian A. and Betzig, Eric and Legant, Wesley R. and Upadhyayula, Srigokul} } @article {70191, title = {Multimodal cell lineage reconstruction in the hindbrain reveals a link between progenitor origin and activity patterning}, journal = {bioRxiv}, year = {2025}, month = {2025 Nov 14}, abstract = {

The vertebrate brain develops through a precisely orchestrated sequence of events, where neural progenitors generate neuronal diversity. However, the importance of stem cell origin in the acquisition of functional characteristics and the assembly into circuits are largely unknown. Here, by multimodal cell lineage reconstruction we reveal a link between progenitor origin and excitatory and inhibitory activity in the hindbrain. By combining progenitor intersectional fate mapping with newly developed computational tools and CRISPR/Cas9-based loss-of-function experiments, we discovered the differential temporal contribution of distinct progenitor pools {\textendash}defined by proneural gene expression{\textendash} to both glutamatergic and GABAergic neurons. Whereas neurog1-progenitors contribute to both lineages in early embryonic stages, later, other progenitor pools either also assume this role or take over. Using calcium imaging in combination with genetic perturbations, we unveiled that spatiotemporally defined stem cell origin determines specific neuronal activity features. Overall, we provide in vivo evidence for a link between cell ontogeny and functionality in the vertebrate hindbrain.For more information or any specific tool, you can contact us.

}, doi = {10.1101/2025.11.14.688499}, url = {https://www.biorxiv.org/content/early/2025/11/14/2025.11.14.688499}, author = {Blanc, Matthias and Meister, Lydvina and Lemon, William C. and Fiuza, Ulla-Maj and Keller, Philipp J. and Espinosa-Medina, Isabel and Pujades, Cristina} } @article {70137, title = {A multi-muscular, redundant strategy for free-flight roll stability}, journal = {bioRxiv}, year = {2025}, month = {2025 Oct 01}, abstract = {

Whether recovering after a gust of wind, or rapidly saccading away from an oncoming predator, fruit flies show remarkable aerial dexterity about their body roll axis. Here, we investigated the detailed wing kinematic changes during free-flight roll motion and probed the neuromuscular basis for such changes. Consistent with previous work, we observed that flies manipulated the stroke amplitude difference between their wings to control their roll angle. Here, we show that flies are capable of achieving such changes by altering the stroke amplitude of either or both of their wings. Further we found that during corrections flies can also take advantage of an aerodynamically significant change in the angle of attack of their uppermost wing. Curiously, these corrective wing changes cannot be eliminated when motor neurons hypothesized to be used during roll maneuvers (i1, i2, b1, b2, and b3) are individually inhibited. However, free-flight optogenetic manipulations and quasi-steady aerodynamic calculations show that each of these motor neurons individually can effect kinematic changes consistent with a roll correction. Combining this evidence with an analysis of haltere inputs found in the BANC connectome, we propose that the observed robustness could be the result of two sets of muscular redundancies that receive shared inputs from haltere sensory afferents: one set, containing b1 and b2, is able to increase the stroke amplitude of the lower wing; while the other set, containing i1, i2, and b3, is able to decrease the stroke amplitude and wing pitch angle of the upper wing. Because of the redundancy in the input sensory information and output wing motion in the muscles in each cluster, the fly is able to perform roll stability maneuvers even when one of the constituent motor neurons is inhibited. This framework proposes new ways fast aerial maneuverability can be implemented when dealing with the fly{\textquoteright}s most unstable rotational degree of freedom.

}, doi = {10.1101/2025.09.29.679272}, url = {https://www.biorxiv.org/content/early/2025/10/01/2025.09.29.679272.1}, author = {Ludlow, B. Kemper and Dhawan, Serene and Whitehead, Samuel C and Teoh, Han Kheng and Ehrhardt, Erica and Cowan, Noah and Dickerson, Bradley H and Cohen, Itai} } @article {69947, title = {Multiplex Detection of Gene Expression in the Intact Drosophila Brain Using Expansion-Assisted Iterative Fluorescence In Situ Hybridization.}, journal = {J Vis Exp}, year = {2025}, month = {2025 May 02}, abstract = {

Understanding gene expression is essential for deciphering cellular functions. However, methods for analyzing the expression of numerous genes in situ within a given tissue remain limited. The EASI-FISH protocol described here has been adapted to detect the expression of dozens of genes in the intact adult Drosophila central nervous system (CNS) using commercially available reagents. This protocol includes a new gel formulation that enhances gel robustness, enabling multiple rounds of hybridization and allowing the embedding of multiple brains per gel. This improvement increases throughput, facilitates optimal comparison of experimental conditions, and reduces reagent costs. Additionally, by employing the GAL4-UAS system for co-detection of green fluorescent protein (GFP), gene expression can be visualized in specific neuronal or glial cell types. Notably, the high resolution achieved through expansion microscopy, combined with the sensitivity of the method, allows for the detection of single RNA transcripts. This approach effectively integrates high image quality with high throughput, making it a powerful tool for studying gene expression throughout the intact fly brain.

}, keywords = {Animals, Brain, Drosophila, Green Fluorescent Proteins, In Situ Hybridization, Fluorescence}, issn = {1940-087X}, doi = {10.3791/67656}, url = {https://doi.org/10.3791/67656}, author = {Close, Kari and He, Yisheng and Jeter, Jennifer and Ihrke, Gudrun and Eddison, Mark} } @article {70213, title = {Multiscale structure of chromatin condensates explains phase separation and material properties.}, journal = {Science}, volume = {390}, year = {2025}, month = {2025 Dec 04}, pages = {eadv6588}, abstract = {

The structure and interaction networks of molecules within biomolecular condensates are poorly understood. Using cryo-electron tomography and molecular dynamics simulations, we elucidated the structure of phase-separated chromatin condensates across scales, from individual amino acids to network architecture. We found that internucleosomal DNA linker length controls nucleosome arrangement and histone tail interactions, shaping the structure of individual chromatin molecules within and outside condensates. This structural modulation determines the balance between intra- and intermolecular interactions, which governs the molecular network, thermodynamic stability, and material properties of chromatin condensates. Mammalian nuclei contain dense clusters of nucleosomes whose nonrandom organization is mirrored by the reconstituted condensates. Our work explains how the structure of individual chromatin molecules determines physical properties of chromatin condensates and cellular chromatin organization.

}, keywords = {Animals, Biomolecular Condensates, Chromatin, Cryoelectron Microscopy, DNA, Electron Microscope Tomography, Histones, Humans, Molecular Dynamics Simulation, Nucleosomes, Phase Separation, Thermodynamics}, issn = {1095-9203}, doi = {10.1126/science.adv6588}, url = {https://doi.org/10.1126/science.adv6588}, author = {Zhou, Huabin and Huertas, Jan and Maristany, M Julia and Russell, Kieran and Hwang, June Ho and Yao, Run-Wen and Samanta, Nirnay and Hutchings, Joshua and Billur, Ramya and Shiozaki, Momoko and Zhao, Xiaowei and Doolittle, Lynda K and Gibson, Bryan A and Soranno, Andrea and Riggi, Margot and Espinosa, Jorge R and Yu, Zhiheng and Villa, Elizabeth and Collepardo-Guevara, Rosana and Rosen, Michael K} } @article {69960, title = {Myocardium and endocardium of the early mammalian heart tube arise from independent multipotent lineages specified at the primitive streak}, journal = {Dev Cell}, year = {2025}, month = {2025 May 20}, abstract = {

The formation of the primitive heart tube from cardiomyocytes and endocardial cells is a key event in mammalian development. Previous studies suggested that cardiomyocytes and endocardial cells segregate from a shared cardiac progenitor around the onset of gastrulation, yet their lineage relationship with other mesodermal tissues remains unclear. Using retrospective and prospective clonal analyses in mouse embryos, we traced cardiomyocyte and endocardial progenitors from the primitive streak to the heart tube. Our results identify two independent mesodermal populations specified around gastrulation onset. While each of these populations is unipotent in producing cardiomyocytes or endocardium, they retain multipotency and contribute to different subsets of non-cardiac mesoderm. Nonetheless, live imaging identifies simultaneous ingression and intermingling of these two mesodermal lineages in the primitive streak, showing their coordinated specification and migration. The proposed model for cardiac progenitor specification will help understanding the origins of congenital heart diseases and designing tissue engineering strategies.

}, issn = {1878-1551}, doi = {10.1016/j.devcel.2025.05.002}, url = {https://doi.org/10.1016/j.devcel.2025.05.002}, author = {Sendra, Miquel and McDole, Katie and de Dios Hourcade, Juan and Temi{\~n}o, Susana and Raiola, Morena and Guignard, Leo and Keller, Philipp J and Dom{\'\i}nguez, Jorge N and Torres, Miguel} } @article {70170, title = {NanoBlocks: creating fluorescent biosensors from affinity binders using competitive binding}, journal = {bioRxiv}, year = {2025}, month = {2025 October 28}, abstract = {

Genetically-encoded fluorescent biosensors have revolutionized our understanding of complex systems by permitting the in situ observation of chemical activities. However, only a comparatively small set of chemical activities can be monitored, largely due to the need to identify protein domains that undergo conformational and/or association changes in response to a stimulus. Here, we present a strategy that can convert {\textquoteright}simple{\textquoteright} affinity binders such as nanobodies into biosensors for their innate targets by introducing a peptide sequence that competes for the binding site. We demonstrate proof-of-concept implementations of this {\textquoteright}NanoBlock{\textquoteright} design, developing sensors based on the ALFA nanobody and on the PDZ domain of Erbin. We show that these sensors can reliably detect their targets in vitro, in mammalian cells, and as part of fluorescence-activated cell sorting (FACS) experiments. In doing so, our strategy offers a way to strongly expand the range of cellular processes that can be probed using fluorescent biosensors.

}, doi = {10.1101/2025.10.28.685015}, url = {https://www.biorxiv.org/content/early/2025/10/28/2025.10.28.685015}, author = {Denis, Silke and Van Deuren, Vincent and Frecot, Desiree I. and Rothbauer, Ulrich and Ismail, Shehab and Tebo, Alison G. and Dedecker, Peter} } @article {70156, title = {Natural evolution of intermale sexual behavior by multiple pheromone switches among Drosophila species}, journal = {bioRxiv}, year = {2025}, month = {2025 Oct 14}, abstract = {

We have identified a Drosophila species in which males exhibit spontaneous, elaborate, and robust intermale sexual behavior. Males of D. santomea, a West African island endemic, distinguish conspecific sexes but court males and females promiscuously and seldom attack. Elevated intermale courtship derives from at least three changes in two separate pheromone systems. In males, the sexually monomorphic cuticular pheromone 7-tricosene promotes rather than inhibits courtship and the courtship-inhibiting olfactory pheromone cVA is reduced 84-92\% compared to close relatives, including the sibling species D. yakuba. The third change is surprisingly in D. santomea females, where cVA suppresses rather than promotes sexual receptivity. The female cVA switch and male cVA reduction may have co-evolved to maintain efficient intraspecific mating in D. santomea but prevent sympatric hybridization with D. yakuba, or to reduce intraspecific aggression. We find that high intermale courtship and low cVA also co-occur and appear selectively derived in a distant monomorphic species D. persimilis, implying pheromonal and behavioral convergence in the two recently speciated taxa. The data suggest that sequential changes in the behavioral valence and levels of pheromones explain the recent evolutionary emergence of intermale sexual behavior in Drosophila.

}, doi = {10.1101/2025.10.14.682417}, url = {https://www.biorxiv.org/content/early/2025/10/15/2025.10.14.682417}, author = {Ouadah, Youcef and Naragon, Thomas H. and Smihula, Hayley and Behrman, Emily L. and Khallaf, Mohammed A. and Ding, Yun and Stern, David L. and Parker, Joseph and Anderson, David J.} } @article {70162, title = {Networks of sexually dimorphic neurons that regulate social behaviors in Drosophila}, journal = {bioRxiv}, year = {2025}, month = {2025 Oct 21}, abstract = {

Neural mechanisms underlying sexually dimorphic social behaviors remain enigmatic in most species. In Drosophila, sexually dimorphic P1/pC1x neurons have been described as a site of sensory integration that regulates mating and aggressive behaviors. We show that the male P1/pC1x population forms a highly intertwined network with male-specific mAL and aSP-a neurons that is poised to regulate male behavior. The 48 P1/pC1x cell types exhibit heterogeneous synaptic connections with a subset receiving strong input from identified sensory pathways. We also describe circuit motifs by which P1 and sexually dimorphic aIPg neurons co-regulate social behaviors. Genetic driver lines for these cell types were generated and used to discover distinct roles for P1/pC1x cell types in promoting social acoustic signaling and male-male interactions. Our results reveal unexpected diversity in the connectivity and behavioral roles of the P1/pC1x cell types and provide essential genetic tools for interrogating their neurophysiological and behavioral functions.

}, doi = {10.1101/2025.10.21.683766}, url = {https://www.biorxiv.org/content/early/2025/10/22/2025.10.21.683766}, author = {Rubin, Gerald M. and Managan, Claire and Dreher, Marisa and Kim, Elizabeth and Miller, Scott and Boone, Kaitlyn and Robie, Alice and Taylor, Adam L. and Branson, Kristin and Schretter, Catherine E. and Otopalik, Adriane G.} } @article {70201, title = {Neural dynamics outside task-coding dimensions drive decision trajectories through transient amplification}, journal = {bioRxiv}, year = {2025}, month = {2025 Nov 22}, abstract = {

Most behaviors involve neural dynamics in high-dimensional activity spaces. A common approach is to extract dimensions that capture task-related variability, such as those separating stimuli or choices, yielding low-dimensional, task-aligned neural activity subspaces ({\textquotedblleft}coding dimensions{\textquotedblright}). However, whether these dimensions actively drive decisions or merely reflect underlying computations remains unclear. Moreover, neural activity outside these coding subspaces ({\textquotedblleft}residual dimensions{\textquotedblright}) is often ignored, though it could also causally shape neural dynamics driving behavior. We developed a recurrent neural network model that fits population activity and uncovers the dynamic interactions between coding and residual subspaces on single trials. Applied to electrophysiological recordings from the anterior lateral motor cortex (ALM) and motor thalamus in mice performing a delayed response task, our model demonstrates that perturbations of residual dimensions reliably alter behavioral choices, whereas perturbations of the choice dimension, which strongly encodes the animal{\textquoteright}s upcoming decision, are largely ineffective. These perturbation effects arise because residual dimensions drive transient amplification across an intermediate number of coding and residual dimensions (\~10), before the dynamics collapse into discrete attractor states corresponding to the animal{\textquoteright}s choice. By dissecting the low-dimensional variability underlying error trials, we find that it primarily shifts trajectories along residual dimensions, biasing single decisions. Residual activity in thalamus shapes cortical decision dynamics, implicating weakly selective thalamic populations in the emergence of cortical selectivity. Our findings challenge the conventional focus on low-dimensional coding subspaces as sufficient framework for understanding neural computations, demonstrating that dimensions previously considered task-irrelevant and accounting for little variance can have a critical role in driving behavior.

}, doi = {10.1101/2025.11.20.689599}, url = {https://www.biorxiv.org/content/early/2025/11/22/2025.11.20.689599}, author = {Pereira-Obilinovic, Ulises and Daie, Kayvon and Chen, Susu and Svoboda, Karel and Darshan, Ran} } @article {69996, title = {Neural substrates of cold nociception in Drosophila larva}, journal = {eLife}, volume = {12}, year = {2025}, month = {2025 Jun 13}, pages = {RP91582}, abstract = {

Metazoans detect and differentiate between innocuous (non-painful) and/or noxious (harmful) environmental cues using primary sensory neurons, which serve as the first node in a neural network that computes stimulus-specific behaviors to either navigate away from injury-causing conditions or to perform protective behaviors that mitigate extensive injury. The ability of an animal to detect and respond to various sensory stimuli depends upon molecular diversity in the primary sensors and the underlying neural circuitry responsible for the relevant behavioral action selection. Recent studies in Drosophila larvae have revealed that somatosensory class III multidendritic (CIII md) neurons function as multimodal sensors regulating distinct behavioral responses to innocuous mechanical and nociceptive thermal stimuli. Recent advances in circuit bases of behavior have identified and functionally validated \Drosophila larval somatosensory circuitry involved in innocuous (mechanical) and noxious (heat and mechanical) cues. However, central processing of cold nociceptive cues remained unexplored. We implicate multisensory integrators (Basins), premotor (Down-and-Back), and projection (A09e and TePns) neurons as neural substrates required for cold-evoked behavioral and calcium responses. Neural silencing of cell types downstream of CIII md neurons led to significant reductions in cold-evoked behaviors, and neural co-activation of CIII md neurons plus additional cell types facilitated larval contraction (CT) responses. Further, we demonstrate that optogenetic activation of CIII md neurons evokes calcium increases in these neurons. Finally, we characterize the premotor to motor neuron network underlying cold-evoked CT and delineate the muscular basis of CT response. Collectively, we demonstrate how Drosophila larvae process cold stimuli through functionally diverse somatosensory circuitry responsible for generating stimulus-specific behaviors.

}, keywords = {cold nociception, somatosensory circuits, thermosensation, \textitDrosophila}, issn = {2050-084X}, doi = {10.7554/eLife.91582}, url = {https://doi.org/10.7554/eLife.91582}, author = {Patel, Atit A and Cardona, Albert and Cox, Daniel N}, editor = {Tuthill, John C and Sen, Sonia Q} } @article {69946, title = {Neuronal growth patterns and synapse formation are mediated by distinct activity-dependent mechanisms.}, journal = {Sci Rep}, volume = {15}, year = {2025}, month = {2025 May 19}, pages = {17338}, abstract = {

All brain functions in animals rely upon neuronal connectivity that is established during early development. Although the activity-dependent mechanisms are deemed important for brain development and adult synaptic plasticity, the precise cellular and molecular mechanisms remain however, largely unknown. This lack of fundamental knowledge regarding developmental neuronal assembly owes its existence to the complexity of the mammalian brain as cell-cell interactions between individual neurons cannot be investigated directly. Here, we used individually identified synaptic partners from Lymnaea stagnalis to interrogate the role of neuronal activity patterns over an extended time period during various growth time points and synaptogenesis. Using intracellular recordings, microelectrode arrays, and time-lapse imaging, we identified unique patterns of activity throughout neurite outgrowth and synapse formation. Perturbation of voltage-gated Ca channels compromised neuronal growth patterns which also invoked a protein kinase A mediated pathway. Our findings underscore the importance of unique activity patterns in regulating neuronal growth, neurite branching, and synapse formation, and identify the underlying cellular and molecular mechanisms.

}, keywords = {Animals, Cyclic AMP-Dependent Protein Kinases, Lymnaea, Neurites, Neurogenesis, Neuronal Outgrowth, Neuronal Plasticity, Neurons, Synapses}, issn = {2045-2322}, doi = {10.1038/s41598-025-00806-9}, url = {https://doi.org/10.1038/s41598-025-00806-9}, author = {Yacoub, Matthew and Iqbal, Fahad and Khan, Zainab and Syeda, Atika and Lijnse, Thomas and Syed, Naweed I} } @article {69774, title = {Neuropixels Opto: Combining high-resolution electrophysiology and optogenetics}, journal = {bioRxiv}, year = {2025}, month = {2025 Feb 06}, abstract = {

High-resolution extracellular electrophysiology is the gold standard for recording spikes from distributed neural populations, and is especially powerful when combined with optogenetics for manipulation of specific cell types with high temporal resolution. We integrated these approaches into prototype Neuropixels Opto probes, which combine electronic and photonic circuits. These devices pack 960 electrical recording sites and two sets of 14 light emitters onto a 1 cm shank, allowing spatially addressable optogenetic stimulation with blue and red light. In mouse cortex, Neuropixels Opto probes delivered high-quality recordings together with spatially addressable optogenetics, differentially activating or silencing neurons at distinct cortical depths. In mouse striatum and other deep structures, Neuropixels Opto probes delivered efficient optotagging, facilitating the identification of two cell types in parallel. Neuropixels Opto probes represent an unprecedented tool for recording, identifying, and manipulating neuronal populations.

}, doi = {10.1101/2025.02.04.636286}, url = {https://www.biorxiv.org/content/early/2025/02/06/2025.02.04.636286}, author = {Lakunina, Anna and Socha, Karolina Z and Ladd, Alexander and Bowen, Anna J and Chen, Susu and Colonell, Jennifer and Doshi, Anjal and Karsh, Bill and Krumin, Michael and Kulik, Pavel and Li, Anna and Neutens, Pieter and O{\textquoteright}Callaghan, John and Olsen, Meghan and Putzeys, Jan and Tilmans, Harrie AC and Ye, Zhiwen and Welkenhuysen, Marleen and H{\"a}usser, Michael and Koch, Christof and Ting, Jonathan T. and Neuropixels Opto Consortium and Dutta, Barun and Harris, Timothy D and Steinmetz, Nicholas A and Svoboda, Karel and Siegle, Joshua H and Carandini, Matteo} } @article {70226, title = {Octopamine instructs head direction plasticity}, journal = {bioRxiv}, year = {2025}, month = {2025 Dec 15}, abstract = {

Many plasticity rules rely on adjusting the strength of synapses between pairs of cells based on their coincident activity. We uncovered a new mechanism for coincidence detection in the Drosophila head direction network. To maintain an accurate sense of direction, head direction neurons that signal orientation during navigation must learn to anchor to relevant external sensory cues in novel environments. Yet the synaptic mechanism for this form of unsupervised learning is unknown in any organism. In Drosophila, GABAergic visual inputs converge onto head direction neurons, and these inhibitory synapses change strength with experience to learn the relationship between visual landmarks and head direction. However, how coincident pre- and postsynaptic activity is detected across this inhibitory synapse is not understood. We discovered that neurons which release the monoamine octopamine close a feedback loop that conveys postsynaptic head direction activity onto presynaptic terminals of visual inputs. This octopamine pathway is required for anchoring the head direction network to visual cues. Furthermore, pairing structured activation of octopamine neurons with a visual cue is sufficient to drive rapid plasticity, even without postsynaptic head direction cell activity. Previous work has extensively characterized coincidence detection mechanisms at excitatory synapses; our work defines a novel mechanism for coincidence detection at an inhibitory synapse, in which postsynaptic activity is relayed via a neuromodulatory neuron onto presynaptic terminals

}, doi = {10.64898/2025.12.11.693783}, url = {https://www.biorxiv.org/content/early/2025/12/15/2025.12.11.693783}, author = {Plitt, Mark H. and Turner-Evans, Daniel B. and Co, Jessica C. and Layden, Aryanna and Eddison, Mark and Ray, Robert P. and Jayaraman, Vivek and Fisher, Yvette E.} } @article {70169, title = {Optimizing multifunctional fluorescent ligands for intracellular labeling.}, journal = {Proc Natl Acad Sci USA}, volume = {122}, year = {2025}, month = {2025 Nov 04}, pages = {e2510046122}, abstract = {

Enzyme-based self-labeling tags enable the covalent attachment of synthetic molecules to proteins inside living cells. A frontier of this field is designing cell-permeable multifunctional ligands that contain fluorophores in combination with affinity tags or pharmacological agents. This is challenging since attachment of additional chemical moieties onto fluorescent ligands can adversely affect membrane permeability. To address this problem, we examined the chemical properties of rhodamine-based self-labeling tag ligands through the lens of medicinal chemistry. We found that the lactone-zwitterion equilibrium constant () of rhodamines inversely correlates with their distribution coefficients (log), suggesting that ligands based on dyes exhibiting low and high log values, such as Si-rhodamines, would efficiently enter cells. We designed cell-permeable multifunctional HaloTag ligands with a biotin moiety to purify mitochondria or a JQ1 appendage to translocate BRD4 within the nucleus. We found that translocation of BRD4 to constitutive heterochromatin in cells leads to apparent increases in transcriptional activity. These fluorescent reagents enable affinity capture and translocation of intracellular proteins in living cells, and our general design concepts will facilitate the design of multifunctional chemical tools for biology.

Preprint:\ https://doi.org/10.1101/2022.07.02.498544
Preprint:\ https://doi.org/10.32388/0xcyuc

}, keywords = {Bromodomain Containing Proteins, Cell Cycle Proteins, Fluorescent Dyes, Humans, Ligands, Mitochondria, Nuclear Proteins, Rhodamines, Staining and Labeling, Transcription Factors}, issn = {1091-6490}, doi = {10.1073/pnas.2510046122}, url = {https://doi.org/10.1073/pnas.2510046122}, author = {Kumar, Pratik and Vevea, Jason D and Tkachuk, Ariana N and Campbell, Kirby R and Watson, Emma T and Ayala, Anthony X and Grimm, Jonathan B and Chapman, Edwin R and Solecki, David J and Lavis, Luke D} } @article {70243, title = {The organization of visual pathways in the Drosophila brain}, journal = {bioRxiv}, year = {2025}, month = {2025 Dec 26}, abstract = {

Visual systems across species transform photoreceptor inputs into diverse perceptual representations through hierarchical networks that extract features via parallel pathways. In Drosophila, the optic lobes are layered, retinotopic visual processing centers that contain two-thirds of the brain{\textquoteright}s neurons and support diverse visually guided behaviors. Although this architecture has long suggested hierarchical and parallel organization, a system-wide account of how behaviorally relevant visual features are routed and integrated across a complete visual system{\textemdash}in any animal{\textemdash}has remained elusive. The new male fly connectome now provides the synapse-level wiring needed to trace visual information from photoreceptors through the optic lobes and across the central brain. Applying a network-based analysis of information flow, we reveal a multi-layered architecture organized into distinct, functionally interpretable pathways. Using this framework to propagate signals through these pathways predicts receptive-field structure and feature selectivity consistent with physiological data, enabling large-scale functional annotation of thousands of neuron types. We find that distinct visual input channels are broadly distributed throughout the brain, yet converge in focal regions of feature specificity and acute spatial vision. Together, these analyses provide a neuron-level, connectome-based view of how a brain organizes and transforms visual input.

}, doi = {10.64898/2025.12.22.696097}, url = {https://www.biorxiv.org/content/early/2025/12/26/2025.12.22.696097}, author = {Hoeller, Judith and Zhao, Arthur and Nern, Aljoscha and Rogers, Edward M and Romani, Sandro and Reiser, Michael B} } @article {70225, title = {Parallel neuronal ensembles control behavior across sensorimotor levels in Drosophila}, journal = {bioRxiv}, year = {2025}, month = {2025 Dec 16}, abstract = {

Nervous systems can process information in serial or in parallel, trading off efficiency for flexibility and speed. How these network architectures are implemented across sensorimotor pathways to control behavior is unclear. We investigate this tradeoff directly in Drosophila by comparing neuronal circuits underlying landing and takeoff, behaviors transforming similar visual cues to whole-body motor output. Using a whole-CNS connectome, electrophysiology, and behavioral analysis, we reconstruct the complete feedforward pathway for landing, including visual feature detectors, a dedicated ensemble of descending neurons (DNs), and a core premotor circuit in the nerve cord. Comparison to the takeoff pathway reveals that, despite encoding the same sensory feature and engaging similar muscle groups, neuronal circuits controlling the two behaviors are separated at every sensorimotor level. Extending this analysis to the complete DN population reveals a blueprint for descending motor control: DNs across the behavioral space utilized by the fly are organized as a set of parallel, loosely-overlapping ensembles that form a continuum from command-like control, with individual DNs determining behavioral output, to population coding, with multiple DNs controlling behavior synergistically. Distinct combinations of sensory feature detectors differentially recruit DN ensembles to enable flexible, context-dependent behavioral control.

}, doi = {10.64898/2025.12.13.693955}, url = {https://www.biorxiv.org/content/early/2025/12/16/2025.12.13.693955}, author = {Liessem, Sander and Asinof, Samuel K. and Nern, Aljoscha and Sumathipala, Marissa and Rogers, Edward and Erginkaya, Mert and Dallmann, Chris J. and Card, Gwyneth M and Ache, Jan M.} } @article {68716, title = {PEELing: an integrated and user-centric platform for cell-surface proteomics analysis}, journal = {Bioinformatics}, year = {2025}, month = {2025 Aug 06}, abstract = {

Summary:\ Molecular compartmentalization is vital for cellular physiology. Spatially-resolved proteomics allows biologists to survey protein composition and dynamics with subcellular resolution. Here we present PEELing, an integrated package and user-friendly web service for analyzing spatially-resolved proteomics data. PEELing assesses data quality using curated or user-defined references, performs cutoff analysis to remove contaminants, connects to databases for functional annotation, and generates data visualizations-providing a streamlined and reproducible workflow to explore spatially-resolved proteomics data.

Availability and implementation:\ PEELing and its tutorial are publicly available at https://peeling.janelia.org/ (Zenodo DOI: 10.5281/zenodo.15692517). A Python package of PEELing is available at https://github.com/JaneliaSciComp/peeling/ (Zenodo DOI: 10.5281/zenodo.15692434).

Contact:Technical support for PEELing: peeling@janelia.hhmi.org.

bioRxiv Preprint:\ https://doi.org/10.1101/2023.04.21.537871

}, doi = {10.1093/bioinformatics/btaf439}, url = {https://doi.org/10.1093/bioinformatics/btaf439}, author = {Xi Peng and Jody Clements and Zuzhi Jiang and Stephan Preibisch and Jiefu Li} } @article {70194, title = {Pericyte and Endothelial Primary Cilia and Centrioles have Disparate Organization Across the Brain Microvasculature}, journal = {bioRxiv}, year = {2025}, month = {2025 Nov 19}, abstract = {

The brain microvascular functions are strongly influenced by the local microenvironment and cellular organization. Intracellular organelles, including primary cilia and centrioles, play critical roles in sensing and transmitting environmental cues and maintaining vascular integrity. However, their distribution across the brain vasculature remains poorly understood. In this study, we utilized publicly available large-volume electron microscopy datasets encompassing the cerebral vasculature from pial arterioles through parenchymal capillaries to pial venules. We systematically analyzed the cellular organization and characterized the distribution of primary cilia and centrioles in the mouse and human brain microvasculature. We found primary cilia exclusively on human cortical endothelial cells (ECs), indicating inter-species differences between mouse and human. Primary cilia were frequently present on mural cells (MCs, smooth muscle cells or pericytes) surrounding venules and capillaries but rarely observed on arterioles in both mouse and human brains. These MC primary cilia exhibited heterogeneity in ciliogenesis, including cells with ciliary pockets, surface cilia, and a hybrid configuration we refer as a partial pocket. In the mouse brain, many MC primary cilia were closely ensheathed by astrocytic endfeet and occasionally extended between them to establish proximity to synapses, whereas all primary cilia in the human brain were confined within the basal lamina. Our analysis of cellular density revealed similar EC densities between arterioles and venules in mice, but not in human. EC centrioles were consistently positioned against the direction of blood flow relative to the nuclei, suggesting that they may serve as a structural marker for flow direction. Collectively, these findings provide a comprehensive characterization of primary cilia and centrioles, highlighting distinct interspecies differences between mouse and human brain microvasculature. The proximity to neural cells and gradient distribution of these subcellular structures suggest that they may act as antennae for sensing mechanical and chemical signals within the brain microvascular environment.

}, doi = {10.1101/2025.11.19.689283}, url = {https://www.biorxiv.org/content/early/2025/11/19/2025.11.19.689283}, author = {Grubb, Soren and Chanddha, Vanshika and Lippincott-Schwartz, Jennifer and Ott, Carolyn and Mughal, Amreen} } @article {69756, title = {Periodic ER-plasma membrane junctions support long-range Ca signal integration in dendrites.}, journal = {Cell}, volume = {188}, year = {2025}, month = {01/2025}, pages = {484-500.e22}, abstract = {

Neuronal dendrites must relay synaptic inputs over long distances, but the mechanisms by which activity-evoked intracellular signals propagate over macroscopic distances remain unclear. Here, we discovered a system of periodically arranged endoplasmic reticulum-plasma membrane (ER-PM) junctions tiling the plasma membrane of dendrites at \~{}1\ μm intervals, interlinked by a meshwork of ER tubules patterned in a ladder-like array. Populated with Junctophilin-linked plasma membrane voltage-gated Ca channels and ER Ca-release channels (ryanodine receptors), ER-PM junctions are hubs for ER-PM crosstalk, fine-tuning of Ca homeostasis, and local activation of the Ca/calmodulin-dependent protein kinase II. Local spine stimulation activates the Ca modulatory machinery, facilitating signal transmission and ryanodine-receptor-dependent Ca release at ER-PM junctions over 20\ μm away. Thus, interconnected ER-PM junctions support signal propagation and Ca release from the spine-adjacent ER. The capacity of this subcellular architecture to modify both local and distant membrane-proximal biochemistry potentially contributes to dendritic computations.

}, keywords = {Animals, Calcium, Calcium Signaling, Calcium-Calmodulin-Dependent Protein Kinase Type 2, Cell Membrane, Dendrites, Endoplasmic Reticulum, Hippocampus, Humans, Male, Mice, Rats, Ryanodine Receptor Calcium Release Channel}, issn = {1097-4172}, doi = {10.1016/j.cell.2024.11.029}, author = {Benedetti, Lorena and Fan, Ruolin and Weigel, Aubrey V and Moore, Andrew S and Houlihan, Patrick R and Kittisopikul, Mark and Park, Grace and Petruncio, Alyson and Hubbard, Philip M and Pang, Song and Xu, C Shan and Hess, Harald F and Saalfeld, Stephan and Rangaraju, Vidhya and Clapham, David E and De Camilli, Pietro and Ryan, Timothy A and Lippincott-Schwartz, Jennifer} } @article {70164, title = {Place-cell heterogeneity underlies power-laws in hippocampal activity}, journal = {arXiv}, year = {2025}, month = {2025 Jul 30}, abstract = {

Power-law scaling in coarse-grained data suggests critical dynamics, but the true source of this scaling often remains unclear. Here, we analyze neural activity recorded during spatial navigation, reproducing power-law scaling under a phenomenological renormalization group (PRG) procedure that clusters units by activity similarity. Such scaling was previously linked to criticality. Here, we show that the iterative nature of the procedure itself leads to the emergence of power laws when applied to heterogeneous, non-interacting units obeying spatially structured activity without requiring critical interactions. Furthermore, the scaling exponents produced by heteregeneous non-interacting units match the observed exponents in recorded neural data. A simplified version of the PRG further reveals how heterogeneity smooths transitions across scales, mimicking critical behavior. The resulting exponents depend systematically on system and population size, predictions confirmed by subsampling the data.

}, doi = {10.48550/arXiv.2507.23030}, url = {https://arxiv.org/abs/2507.23030}, author = {John J. Briguglio and Jaesung Lee and Albert K. Lee and Vincent Hakim and Sandro Romani} } @article {70193, title = {Population morphology implies a common developmental blueprint for Drosophila motion detectors}, journal = {bioRxiv}, year = {2025}, month = {2025 Nov 15}, abstract = {

Quantitative analysis of neuron morphology is essential in order to develop our understanding of circuit organisation and development. The recent acquisition of whole-brain electron microscopy-based (EM) reconstructions of the Drosophila melanogaster nervous system now provide the resolution needed to examine morphology at scale. Utilising these data, together with new computational tools, we extract and analyse the dendrites of all T4 and T5 neurons within one hemisphere (n \~ 6000).T4 and T5 neurons are the first uniquely direction-selective neurons in the visual pathway, and are classified into four subtypes (a,b,c, and d). Each subtype encodes one of four cardinal motion directions (up, down, forwards, backwards). The dendrites of these neurons form in two distinct neuropils, the Medulla (T4) and the Lobula (T5), and are asymmetrically oriented in a direction inverse to the direction of motion which they encode. However, their densely overlapping and compact arbours has made rigorous morphological quantification challenging. The presence of differences beyond their characteristic orientation, both between T4 and T5, as well as within subtypes, has remained poorly understood.Our analysis reveals a high degree of structural similarity across both types and subtypes. Particularly, measures of geometry and graph topology show only minor variation, with no consistent separation between T4 and T5, or their subtypes.These results indicate that, despite forming in different neuropils, and serving distinct motion directions, T4 and T5 dendrites follow closely aligned morphological patterns. This suggests that their arborization may be governed by shared developmental constraints and mechanisms.

}, doi = {10.1101/2025.11.15.688637}, url = {https://www.biorxiv.org/content/early/2025/11/16/2025.11.15.688637}, author = {Drummond, Nikolas and Zhao, Arthur and Borst, Alexander} } @article {70119, title = {A priming circuit controls the olfactory response and memory in Drosophila}, journal = {eLife}, year = {2025}, month = {2025 Sep 23}, abstract = {

Priming is a process by which exposure to a stimulus affects the response to a subsequent stimulus in humans. In this study we found that in\ Drosophila, a prior encounter with an aversive stimulus results in enhanced preference for a following novel odor, while an appetitive stimulus leads to reduced preference for a new odor. This priming behavior of flies relies on the well-studied olfactory memory circuits including Kenyon cells (KC), dopaminergic neurons (DANs), and mushroom body output neurons (MBONs). Aversive stimulus results in increased odor responses in reward DANs that innervate the γ4 lobe of the mushroom body (MB) and decreased odor responses in a γ4γ5-innvervating repulsive MBON. We concluded that these neurons are required for the priming effects in flies. These results characterized the newly found priming behavior in flies and demonstrated the sheer influence of unconditioned stimulus on odor perception during associative learning.

}, doi = {10.7554/elife.107736.1}, url = {http://dx.doi.org/10.7554/eLife.107736.1}, author = {Yang, He and Jiang, Yang and Kunes, Samuel} } @article {70022, title = {Programmable Liposome Organization via DNA Origami Templates.}, journal = {J Am Chem Soc}, volume = {147}, year = {2025}, month = {2025 Jul 16}, pages = {24548-24554}, abstract = {

Liposomes are essential vehicles for membrane protein reconstitution and drug delivery, making them vital tools in both in vivo and in vitro studies. However, the lack of robust techniques for the precise arrangement of these synthetic vesicles limits their potential applications. Here, we present a modular polymerization platform based on square DNA origami to template the formation and organization of liposomes. By programming the sequence, number, position, chirality, and flexibility of sticky ends on each square, we assemble uniformly sized liposomes into diverse two-dimensional (2D) arrays, as well as finite lattices and rings. Additionally, we demonstrate stepwise assembly and targeted disassembly, enabling dynamic structural control. These complex liposome architectures represent a significant advancement in the fields of biotechnology, nanotechnology, and bottom-up biology.

}, keywords = {DNA, Liposomes, Nucleic Acid Conformation}, issn = {1520-5126}, doi = {10.1021/jacs.5c05196}, url = {https://doi.org/10.1021/jacs.5c05196}, author = {Zhang, Zhao and Feng, Zhaomeng and Zhao, Xiaowei and Yu, Zhiheng and Chapman, Edwin R} } @article {70011, title = {Programmable Liposome Organization via DNA Origami Templates.}, journal = {J Am Chem Soc}, year = {2025}, month = {2025 Jul 02}, abstract = {

Liposomes are essential vehicles for membrane protein reconstitution and drug delivery, making them vital tools in both in vivo and in vitro studies. However, the lack of robust techniques for the precise arrangement of these synthetic vesicles limits their potential applications. Here, we present a modular polymerization platform based on square DNA origami to template the formation and organization of liposomes. By programming the sequence, number, position, chirality, and flexibility of sticky ends on each square, we assemble uniformly sized liposomes into diverse two-dimensional (2D) arrays, as well as finite lattices and rings. Additionally, we demonstrate stepwise assembly and targeted disassembly, enabling dynamic structural control. These complex liposome architectures represent a significant advancement in the fields of biotechnology, nanotechnology, and bottom-up biology.

}, issn = {1520-5126}, doi = {10.1021/jacs.5c05196}, url = {https://doi.org/10.1021/jacs.5c05196}, author = {Zhang, Zhao and Feng, Zhaomeng and Zhao, Xiaowei and Yu, Zhiheng and Chapman, Edwin R} } @article {70082, title = {A protein tunnel helps stressed lysosomes swell.}, journal = {Science}, volume = {389}, year = {2025}, month = {2025 Aug 21}, pages = {782-783}, abstract = {

The endoplasmic reticulum donates lipids through a tunnel-like protein to help lysosomes expand.

}, keywords = {Adaptor Proteins, Signal Transducing, Animals, Endoplasmic Reticulum, Humans, Lipid Metabolism, Lysosomes}, issn = {1095-9203}, doi = {10.1126/science.aea5377}, url = {https://doi.org/10.1126/science.aea5377}, author = {Lippincott-Schwartz, Jennifer} } @article {69755, title = {Quantitative profiling pH heterogeneity of acidic endolysosomal compartments using fluorescence lifetime imaging microscopy.}, journal = {Mol Biol Cell}, year = {2025}, month = {2025 Jan 29}, pages = {mbcE23060220}, abstract = {

The endo-lysosomal system plays a crucial role in maintaining cellular homeostasis and promoting organism fitness. The pH of its acidic compartments is a crucial parameter for proper function, and it is dynamically influenced by both intracellular and environmental factors. Here, we present a method based on fluorescence lifetime imaging microscopy (FLIM) for quantitatively analyzing the pH profiles of acidic endolysosomal compartments in diverse types of primary mammalian cells and in live organism . This FLIM-based method exhibits high sensitivity in resolving subtle pH differences, thereby revealing heterogeneity within a cell and across cell types. This method enables rapid measurement of pH changes in the acidic endolysosomal system in response to various environmental stimuli. Furthermore, the fast FLIM measurement of pH-sensitive dyes circumvents the need for transgenic reporters and mitigates potential confounding factors associated with varying dye concentrations or excitation light intensity. This FLIM approach offers absolute pH quantification and highlights the significance of pH heterogeneity and dynamics, offering a valuable tool for investigating lysosomal functions and their regulation in various physiological and pathological contexts.

}, issn = {1939-4586}, doi = {10.1091/mbc.E23-06-0220}, author = {Deng, Dinghuan and Guan, Youchen and Mutlu, Ayse Sena and Wang, Baiping and Gao, Shihong Max and Zheng, Hui and Wang, Meng C} } @article {69904, title = {Quantitative spatial analysis of chromatin biomolecular condensates using cryoelectron tomography.}, journal = {Proc Natl Acad Sci U S A}, volume = {122}, year = {2025}, month = {2025 May 13}, pages = {e2426449122}, abstract = {

Phase separation is an important mechanism to generate certain biomolecular condensates and organize the cell interior. Condensate formation and function remain incompletely understood due to difficulties in visualizing the condensate interior at high resolution. Here, we analyzed the structure of biochemically reconstituted chromatin condensates through cryoelectron tomography. We found that traditional blotting methods of sample preparation were inadequate, and high-pressure freezing plus focused ion beam milling was essential to maintain condensate integrity. To identify densely packed molecules within the condensate, we integrated deep learning-based segmentation with context-aware template matching. Our approaches were developed on chromatin condensates and were also effective on condensed regions of in situ native chromatin. Using these methods, we determined the average structure of nucleosomes to 6.1 and 12 {\r A} resolution in reconstituted and native systems, respectively, found that nucleosomes form heterogeneous interaction networks in both cases, and gained insight into the molecular origins of surface tension in chromatin condensates. Our methods should be applicable to biomolecular condensates containing large and distinctive components in both biochemical reconstitutions and certain cellular systems.

Preprint:\ https://www.biorxiv.org/content/10.1101/2024.12.01.626131v2

}, keywords = {Animals, Biomolecular Condensates, Chromatin, Cryoelectron Microscopy, Electron Microscope Tomography, Nucleosomes}, issn = {1091-6490}, doi = {10.1073/pnas.2426449122}, url = {https://doi.org/10.1073/pnas.2426449122}, author = {Zhou, Huabin and Hutchings, Joshua and Shiozaki, Momoko and Zhao, Xiaowei and Doolittle, Lynda K and Yang, Shixin and Yan, Rui and Jean, Nikki and Riggi, Margot and Yu, Zhiheng and Villa, Elizabeth and Rosen, Michael K} } @article {70080, title = {RABGAP1 is a sensor that facilitates the sorting and processing of amyloid precursor protein}, journal = {The EMBO Journal}, year = {2025}, month = {2026 Aug 26}, pages = {1-20}, abstract = {

A hallmark of Alzheimer{\textquoteright}s disease (AD) is the accumulation of extracellular amyloid-β plaques in the brain. Amyloid-β is a 40{\textendash}42 amino acid peptide generated by proteolytic processing of amyloid precursor protein (APP) via membrane-bound proteases. APP is a transmembrane protein, and its trafficking to sites of proteolysis represents a rate-limiting step in AD progression. Although APP processing has been well-studied, its trafficking itinerary and machinery remain incompletely understood. To address this, we performed an unbiased interaction screen for interactors of the APP cytosolic tail. We identified previously characterised APP binders as well as novel interactors, including RABGAP1. We demonstrated that RABGAP1 partially co-localises with APP and directly interacts with a YENPTY motif in the APP cytosolic tail. Depletion or overexpression of RABGAP1 caused mistrafficking and misprocessing of endogenous APP in human and rodent neurons. This effect is dependent on the GAP activity of RABGAP1, demonstrating that RABGAP1 affects the trafficking of APP by modulating RAB activity on endosomal subdomains. This novel trafficking mechanism has implications for other NPXY cargoes and presents a possible therapeutic avenue to explore.

}, keywords = {Alzheimer{\textquoteright}s Disease, APP, RABGAP1, Trafficking}, doi = {10.1038/s44318-025-00530-0}, url = {https://www.embopress.org/doi/abs/10.1038/s44318-025-00530-0}, author = {Eden, Jessica and Kaufman, Jonathan G G and Pereira, Concei{\c c}{\~a}o and Fox, Eleanor and Cattin-Ortol{\'a}, Jerome and Benedetti, Lorena and Nieuwenhuis, Bart and Owen, David J and Lippincott-Schwartz, Jennifer and Munro, Sean and Gershlick, David C} } @article {70229, title = {Reclassifying therapeutic strategies: The 5R model and role of acupuncture}, journal = {Journal of Traditional Chinese Medical Sciences}, year = {2025}, month = {2025 Dec 11}, abstract = {

Mainstream medicine commonly categorizes acupuncture as {\textquotedblleft}alternative and complementary,{\textquotedblright} a designation that reflects conceptual gaps in existing treatment classification systems. Integrating complementary medicine into the mainstream medical system requires a conceptual adjustment. Here, I propose a mechanism-based 5R classification{\textemdash}Removing, Repairing, Replacing, Replenishing, Regulating{\textemdash}to systematically categorize therapies. Based on this classification, acupuncture and its related interventions fall under functional regulation therapy. This framework offers a unified, functional perspective that facilitates the integration of complementary medicine into mainstream medical taxonomy.

}, keywords = {Acupuncture, Alternative and complementary medicine, Therapy}, issn = {2095-7548}, doi = {10.1016/j.jtcms.2025.12.003}, url = {https://doi.org/10.1016/j.jtcms.2025.12.003}, author = {Weixing Pan} } @article {70222, title = {Reconstructing a physiological state space via chronic jugular microdialysis in freely moving mice}, journal = {bioRxiv}, year = {2025}, month = {2025 Dec 11}, abstract = {

Maintaining physiological homeostasis requires a complex interplay among endocrine organs, peripheral tissues, and distributed neuroendocrine control circuits, all of which are coupled through feedback loops that operate over minutes to hours. Although many physiological needs are broadcast through hormones, metabolites, and other chemical compounds circulating in the bloodstream, we rarely observe more than a few of these messengers together and at high cadence during behavior. To address this, we developed a minimally disruptive workflow to measure the free fraction of hundreds of amines and small peptides at a 7.5-minute cadence for \~8 hrs in freely moving mice using chronic jugular microdialysis implants and chemical isotope labeling Liquid Chromatography-Mass Spectrometry. Single-compound profiles behave according to known physiology, such as purine turnover correlating with movement, delayed histamine/5-HIAA changes, and coordinated amino-acid dynamics. Our multiplexed measures enable high-dimensional analyses that uncover properties of the underlying dynamics. For example, systems-level analyses show that 10 dimensions explain over 70\% of the variance in hormone/metabolite covariation, consistent with a low rank description of the physiological state space, with projections aligned to locomotion state transitions. Our work opens avenues for the discovery of hormonal dynamics, compound interactions, and their effects on behavior.

}, doi = {10.64898/2025.12.08.692974}, url = {https://www.biorxiv.org/content/early/2025/12/11/2025.12.08.692974}, author = {Nardin, Michele and Wang, Nan and Elziny, Soad and Boyer, Claire and Pjanovic, Vojko and Schuster, Luisa and Boklund, Peter and Lindo, Sarah and Morris, Kendra and Ilanges, Anoj and Voigts, Jakob and Dennis, Emily Jane} } @article {69781, title = {Recovery of plasma membrane tension after a hyperosmotic shock.}, journal = {Mol Biol Cell}, year = {2025}, month = {2025 Feb 19}, pages = {mbcE24100436}, abstract = {

Maintaining proper tension is critical for the organization and function of the plasma membrane. To study the mechanisms by which yeast restores normal plasma membrane tension, we used a microfluidics device to expose yeast to hyperosmotic conditions, which reduced cell volume and caused a \~{}20\% drop in cell surface area. The resulting low tension plasma membrane exhibited large clusters of negatively-charged glycerophospholipids together with nutrient transporters, suggesting phase segregation of the membrane. We found that endocytosis was blocked by the phase segregation and thus was not involved in removing excess membrane. In contrast, rapid recovery of plasma membrane tension was dependent on 1) eisosome morphology changes that were able to absorb most of the excess surface area and 2) lipid transport from the plasma membrane to the endoplasmic reticulum, where lipids were shunted into newly formed lipid droplets.

}, issn = {1939-4586}, doi = {10.1091/mbc.E24-10-0436}, author = {Phan, Jasmine and Silva, Malan and Kohlmeyer, Robin and Ruethemann, Romy and Gay, Lincoln and Jorgensen, Erik and Babst, Markus} } @article {70203, title = {Redefining colocalization analysis with a novel Phasor Mixing Coefficient.}, journal = {J Cell Sci}, year = {2025}, month = {2025 Nov 24}, abstract = {

The first step to probing any potential interaction between two biomolecules is to determine their spatial association. In other words, if two biomolecules localize similarly within a cell, then it is plausible they could interact. Traditionally, this is quantified through various colocalization metrics. These measures infer this association by estimating the degree to which fluorescent signals from each biomolecule overlap or correlate. However, these metrics are, at best, proxies, and they depend strongly on various experimental choices. Alternatively, here we define a new strategy which leverages multispectral imaging and phasor analysis, termed the Phasor Mixing Coefficient (PMC). PMC measures the precise mixing of fluorescent signals in each pixel. We demonstrate how PMC captures complex biological subtlety by offering two distinct values, a global measure of overall color mixing and the homogeneity thereof. We additionally show that PMC exhibits less sensitivity to signal-to-noise ratio, intensity threshold, and background signal compared to canonical methods. Moreover, this method provides a means to visualize color mixing at each pixel. We show that PMC offers users a nuanced and robust metric to quantify biological association.

}, issn = {1477-9137}, doi = {10.1242/jcs.264388}, url = {https://doi.org/10.1242/jcs.264388}, author = {Puls, Owen F and Aaron, Jesse S and Quarles, Ellen K and Khuon, Satya and Eisenman, Leanna R and Kamaid, Andres and Malacrida, Leonel and Chew, Teng-Leong} } @article {70198, title = {Redefining colocalization analysis with a novel Phasor Mixing Coefficient.}, journal = {J Cell Sci}, year = {2025}, month = {2025 Nov 24}, abstract = {

The first step to probing any potential interaction between two biomolecules is to determine their spatial association. In other words, if two biomolecules localize similarly within a cell, then it is plausible they could interact. Traditionally, this is quantified through various colocalization metrics. These measures infer this association by estimating the degree to which fluorescent signals from each biomolecule overlap or correlate. However, these metrics are, at best, proxies, and they depend strongly on various experimental choices. Alternatively, here we define a new strategy which leverages multispectral imaging and phasor analysis, termed the Phasor Mixing Coefficient (PMC). PMC measures the precise mixing of fluorescent signals in each pixel. We demonstrate how PMC captures complex biological subtlety by offering two distinct values, a global measure of overall color mixing and the homogeneity thereof. We additionally show that PMC exhibits less sensitivity to signal-to-noise ratio, intensity threshold, and background signal compared to canonical methods. Moreover, this method provides a means to visualize color mixing at each pixel. We show that PMC offers users a nuanced and robust metric to quantify biological association.

}, issn = {1477-9137}, doi = {10.1242/jcs.264388}, author = {Puls, Owen F and Aaron, Jesse S and Quarles, Ellen K and Khuon, Satya and Eisenman, Leanna R and Kamaid, Andres and Malacrida, Leonel and Chew, Teng-Leong} } @article {70189, title = {Relative phase of membrane potential theta oscillations between individual hippocampal neurons code space}, journal = {bioRxiv}, year = {2025}, month = {2025 Nov 14}, abstract = {

The timing of spikes dictates a neuron{\textquoteright}s impact on downstream circuits and behavior, and spike timing is determined by the membrane potential (Vm). However, due to technical challenges, it has been impossible to analyze the relative timing of Vm dynamics between neurons during behavior. Using large scale membrane voltage imaging, we simultaneously recorded Vm from many individual hippocampal neurons in animals engaged in a virtual spatial task. We found that relative phase of Vm theta oscillations across neurons exhibit gradual or discrete shifts depending on spatial position. This finding extends beyond previous studies showing Vm dynamics in single neurons or spiking activity in multiple neurons, revealing previously unknown evidence for consistent coding of space by spike-independent relative phase of Vm theta dynamics between neurons.

}, doi = {10.1101/2025.11.14.688496}, url = {https://www.biorxiv.org/content/early/2025/11/14/2025.11.14.688496}, author = {Athif, Mohamed and Malmberg, Samantha and Mount, Rebecca and Patel, Kush and Wang, Yangyang and Shaw, Dana and Ravasio, Cara and Xiao, Sheng and Rillosi, Enrico and Tseng, Hua-An and Plutkis, Sarah E. and Grimm, Jonathan B. and Lavis, Luke D. and Mertz, Jerome and Han, Xue and Hasselmo, Michael E.} } @article {69959, title = {Resolution in super-resolution microscopy - facts, artifacts, technological advancements and biological applications}, journal = {J Cell Sci}, volume = {138}, year = {2025}, month = {2025 May 27}, abstract = {

Super-resolution microscopy (SRM) has undeniable potential for scientific discovery, yet still presents many challenges that hinder its widespread adoption, including technical trade-offs between resolution, speed and photodamage, as well as limitations in imaging live samples and larger, more complex biological structures. Furthermore, SRM often requires specialized expertise and complex instrumentation, which can deter biologists from fully embracing the technology. In this Perspective, a follow-up to our recent Q\&A article, we aim to demystify these challenges by addressing common questions and misconceptions surrounding SRM. Experts offer practical insights into how biologists can maximize the benefits of SRM while navigating issues such as photobleaching, image artifacts and the limitations of existing techniques. We also highlight recent developments in SRM that continue to push the boundaries of resolution. Our goal is to equip researchers with the crucial knowledge they need to harness the full potential of SRM.

}, keywords = {Animals, Artifacts, Humans, Microscopy, Microscopy, Fluorescence}, issn = {1477-9137}, doi = {10.1242/jcs.263567}, url = {https://doi.org/10.1242/jcs.263567}, author = {Prakash, Kirti and Baddeley, David and Eggeling, Christian and Fiolka, Reto and Heintzmann, Rainer and Manley, Suliana and Radenovic, Aleksandra and Shroff, Hari and Smith, Carlas and Schermelleh, Lothar} } @article {70176, title = {Revisiting PSF models: Unifying framework and high-performance implementation.}, journal = {J Microsc}, year = {2025}, month = {2025 Nov 04}, abstract = {

Localisation microscopy often relies on detailed models of point-spread functions. For applications such as deconvolution or PSF engineering, accurate models for light propagation in imaging systems with a high numerical aperture are required. Different models have been proposed based on 2D Fourier transforms or 1D Bessel integrals. The most precise ones combine a vectorial description of the electric field and accurate aberration models. However, it may be unclear which model to choose as there is no comprehensive comparison between the Fourier and Bessel approaches yet. Moreover, many existing libraries are written in Java (e.g., our previous PSF generator software) or MATLAB, which hinders their integration into deep learning algorithms. In this work, we start from the original Richards-Wolf integral and revisit both approaches in a systematic way. We present a unifying framework in which we prove the equivalence between the Fourier and Bessel strategies and detail a variety of correction factors applicable to both of them. Then, we provide a high-performance implementation of our theoretical framework in the form of an open-source library that is built on top of PyTorch, a popular library for deep learning. It enables us to benchmark the accuracy and computational speed of different models and allows for an in-depth comparison of the existing models for the first time. We show that the Bessel strategy is optimal for axisymmetric beams, while the Fourier approach can be applied to more general scenarios. Our work enables the efficient computation of a point-spread function on CPU or GPU, which can then be included in simulation and optimisation\ pipelines.

}, issn = {1365-2818}, doi = {10.1111/jmi.70045}, url = {https://doi.org/10.1111/jmi.70045}, author = {Liu, Yan and Stergiopoulou, Vasiliki and Chuah, Jonathan and Bezzam, Eric and Both, Gert-Jan and Unser, Michael and Sage, Daniel and Dong, Jonathan} } @article {70100, title = {A roadmap for the widespread adoption of frugal microscopes.}, journal = {Nat Commun}, volume = {16}, year = {2025}, month = {2025 Sep 08}, pages = {8241}, abstract = {

Microscopy drives biological discovery, yet high costs limit its access to resource-limited regions. We highlight examples of successful frugal microscopes that have overcome adoption barriers, offering a roadmap to expand affordable, quantitative imaging tools and foster impactful research in resource-limited settings.

}, issn = {2041-1723}, doi = {10.1038/s41467-025-63691-w}, url = {https://doi.org/10.1038/s41467-025-63691-w}, author = {Rahmoon, Mai A and Hobson, Chad M and Chew, Teng-Leong and Aaron, Jesse S} } @article {69993, title = {RubyACRs enable red-shifted optogenetic inhibition in freely behaving Drosophila}, journal = {eLife}, year = {2025}, month = {2025 Sep 05}, abstract = {

Optogenetic activators with red-shifted excitation spectra, such as Chrimson, have significantly advanced Drosophila neuroscience. However, until recently, available optogenetic inhibitors required shorter activation wavelengths, which don{\textquoteright}t penetrate tissue as effectively and are stronger visual stimuli to the animal, potentially confounding behavioral results. Here, we assess the efficacy of two newly identified anion-conducting channelrhodopsins with spectral sensitivities similar to Chrimson: A1ACR and HfACR (RubyACRs). Electrophysiology and functional imaging confirmed that RubyACRs effectively hyperpolarize neurons, with stronger and faster effects than the widely used inhibitor GtACR1. Activation of RubyACRs led to circuit-specific behavioral changes in three different neuronal groups. In glutamatergic motor neurons, activating RubyACRs suppressed adult locomotor activity. In PPL1-γ1pedc dopaminergic neurons, pairing odors with RubyACR activation during learning produced odor responses consistent with synaptic silencing. Finally, activation of RubyACRs in the pIP10 neuron suppressed pulse song during courtship. Together, these results demonstrate that RubyACRs are effective and reliable tools for neuronal inhibition in Drosophila, expanding the optogenetic toolkit for circuit dissection in freely behaving animals.

Preprint: https://www.biorxiv.org/content/early/2025/06/15/2025.06.13.659144

}, doi = {10.7554/eLife.108210.1}, url = {https://doi.org/10.7554/eLife.108210.1}, author = {Bushey, Daniel and Shiozaki, Hiroshi and Shuai, Yichun and Zheng, Jihong and Jayaraman, Vivek and Hasseman, Jeremy P. and Kolb, Ilya and GENIE Project Team and Turner, Glenn C.} } @article {69915, title = {A Salmonella subset exploits erythrophagocytosis to subvert SLC11A1-imposed iron deprivation}, journal = {Cell Host \& Microbe}, volume = {33}, year = {2025}, month = {2025 May 14}, pages = {632-642.e4}, abstract = {

Summary Solute carrier family 11 member 1 (SLC11A1) is critical for host resistance to diverse intracellular pathogens. During infection, SLC11A1 limits Salmonella{\textquoteright}s access to iron, zinc, and magnesium, but only magnesium deprivation significantly impairs Salmonella replication. To understand the unexpected minor impact of iron, we determined Salmonella{\textquoteright}s iron access in infected SLC11A1-deficient and normal mice. Using reporter strains and mass spectrometry of Salmonella purified from the spleen, we found that SLC11A1 caused growth-restricting iron deprivation in a subset of Salmonella. Volume electron microscopy revealed that another Salmonella subset circumvented iron restriction by targeting iron-rich endosomes in macrophages degrading red blood cells (erythrophagocytosis). These iron-replete bacteria dominated overall Salmonella growth, masking the effects of the other Salmonella subset{\textquoteright}s iron deprivation. Thus, SLC11A1 effectively sequesters iron, but heterogeneous Salmonella populations partially bypass this nutritional immunity by targeting iron-rich tissue microenvironments.

}, keywords = {bacterial infection, heterogeneity, iron limitation, iron transport, NRAMP1, nutritional immunity, Slc11A1}, issn = {1931-3128}, doi = {https://doi.org/10.1016/j.chom.2025.04.013}, url = {https://www.sciencedirect.com/science/article/pii/S1931312825001465}, author = {B{\'e}atrice Roche and Beatrice Claudi and Olivier Cunrath and Christopher K.E. Bleck and Minia Antelo-Varela and Jiagui Li and Dirk Bumann} } @article {69712, title = {Scalable image-based visualization and alignment of spatial transcriptomics datasets}, journal = {Cell Syst}, year = {2025}, month = {2025 Apr 17}, abstract = {

We present the "spatial transcriptomics imaging framework" (STIM), an imaging-based computational framework focused on visualizing and aligning high-throughput spatial sequencing datasets. STIM is built on the powerful, scalable ImgLib2 and BigDataViewer (BDV) image data frameworks and thus enables novel development or transfer of existing computer vision techniques to the sequencing domain characterized by datasets with irregular measurement-spacing and arbitrary spatial resolution, such as spatial transcriptomics data generated by multiplexed targeted hybridization or spatial sequencing technologies. We illustrate STIM{\textquoteright}s capabilities by representing, interactively visualizing, 3D rendering, automatically registering, and segmenting publicly available spatial sequencing data from 13 serial sections of mouse brain tissue and from 19 sections of a human metastatic lymph node. We demonstrate that the simplest alignment mode of STIM achieves human-level accuracy.

Preprint:\ www.biorxiv.org/content/early/2024/10/07/2021.12.07.471629

}, doi = {10.1016/j.cels.2025.101264}, url = {https://doi.org/10.1016/j.cels.2025.101264}, author = {Preibisch, Stephan and Innerberger, Michael and Le{\'o}n-Peri{\~n}{\'a}n, Daniel and Karaiskos, Nikos and Rajewsky, Nikolaus} } @article {70044, title = {A sensitive orange fluorescent calcium ion indicator for imaging neural activity}, journal = {bioRxiv}, year = {2025}, month = {2025 Jul 31}, abstract = {

Genetically encoded calcium indicators (GECIs) are vital tools for fluorescence-based visualization of neuronal activity with high spatial and temporal resolution. However, current highest-performance GECIs are predominantly green or red fluorescent, limiting multiplexing options and efficient excitation with fixed-wavelength femtosecond lasers operating at 1030 nm. Here, we introduce OCaMP (also known as O-GECO2), an orange fluorescent GECI engineered from O-GECO1 through targeted substitutions to improve calcium affinity while retaining the favorable photophysical properties of mOrange2. OCaMP exhibits improved two-photon cross-section, responsiveness, photostability, and calcium affinity relative to O-GECO1. In cultured neurons, zebrafish, and mouse cortex, OCaMP outperforms the red GECIs jRCaMP1a and jRGECO1a in sensitivity, kinetics, and signal-to-noise ratio. These properties establish OCaMP as a robust tool for high-fidelity neural imaging optimized for 1030 nm excitation and a compromise-free option within the spectral gap between existing green and red GECIs.

}, doi = {10.1101/2025.07.28.667269}, url = {https://www.biorxiv.org/content/early/2025/07/31/2025.07.28.667269}, author = {Aggarwal, Abhi and Baker, Heather A. and D{\"u}rst, C{\'e}line D. and Chen, I-Wen and de Chambrier, Pablo and Gonzales, Julia Marie and Marvin, Jonathan S. and Vandal, Mil{\`e}ne and Lundberg, Torgny and Sakoi, Kenryo and Patel, Ronak and Wang, Ching-Yao and Visser, Frank and Fouad, Yannick and Sunil, Smrithi and Wiens, Matthew and Terai, Takuya and Takahashi-Yamashiro, Kei and Thompson, Roger J. and Brown, Timothy A. and Nasu, Yusuke and Nguyen, Minh Dang and Gordon, Grant R. J. and McFarlane, Sarah and Podgorski, Kaspar and Holtmaat, Antonius and Campbell, Robert E. and Lohman, Alexander W.} } @article {70155, title = {Sexual dimorphism in the complete connectome of the Drosophila male central nervous system}, journal = {bioRxiv}, year = {2025}, month = {2025 Oct 09}, abstract = {

Sex differences in behaviour exist across the animal kingdom, typically under strong genetic regulation. In Drosophila, previous work has shown that fruitless and doublesex transcription factors identify neurons driving sexually dimorphic behaviour. However, the organisation of dimorphic neurons into functional circuits remains unclear.We now present the connectome of the entire Drosophila male central nervous system. This contains 166,691 neurons spanning the brain and ventral nerve cord, fully proofread and comprehensively annotated including fruitless and doublesex expression and 11,691 cell types. By comparison with a previous female brain connectome, we provide the first comprehensive description of the differences between male and female brains to synaptic resolution. Of 7,319 cross-matched cell types in the central brain, 114 are dimorphic with an additional 262 male- and 69 female-specific (totalling 4.8\% of neurons in males and 2.4\% in females).This resource enables analysis of full sensory-to-motor circuits underlying complex behaviours as well as the impact of dimorphic elements. Sex-specific and dimorphic neurons are concentrated in higher brain centres while the sensory and motor periphery are largely isomorphic. Within higher centres, male-specific connections are organised into hotspots defined by male-specific neurons or the presence of male-specific arbours on neurons that are otherwise similar between sexes. Numerous circuit switches reroute sensory information to form conserved, antagonistic circuits controlling opposing behaviours.

}, doi = {10.1101/2025.10.09.680999}, url = {https://www.biorxiv.org/content/early/2025/10/09/2025.10.09.680999}, author = {Berg, Stuart and Beckett, Isabella R and Costa, Marta and Schlegel, Philipp and Januszewski, Micha{\l} and Marin, Elizabeth C and Nern, Aljoscha and Preibisch, Stephan and Qiu, Wei and Takemura, Shin-ya and Fragniere, Alexandra MC and Champion, Andrew S and Adjavon, Diane-Yayra and Cook, Michael and Gkantia, Marina and Hayworth, Kenneth J and Huang, Gary B and Katz, William T and K{\"a}mpf, Florian and Lu, Zhiyuan and Ordish, Christopher and Paterson, Tyler and St{\"u}rner, Tomke and Trautman, Eric T and Whittle, Catherine R and Burnett, Laura E and Hoeller, Judith and Li, Feng and Loesche, Frank and Morris, Billy J and Pietzsch, Tobias and Pleijzier, Markus W and Silva, Valeria and Yin, Yijie and Ali, Iris and Badalamente, Griffin and Bates, Alexander Shakeel and Bogovic, John and Brooks, Paul and Cachero, Sebastian and Canino, Brandon S and Chaisrisawatsuk, Bhumpanya and Clements, Jody and Crowe, Arthur and de Haan Vicente, In{\^e}s and Dempsey, Georgia and Don{\`a}, Erika and dos Santos, M{\'a}rcia and Dreher, Marisa and Dunne, Christopher R and Eichler, Katharina and Finley-May, Samantha and Flynn, Miriam A and Hameed, Imran and Hopkins, Gary Patrick and Hubbard, Philip M and Kiassat, Ladann and Kovalyak, Julie and Lauchie, Shirley A and Leonard, Meghan and Lohff, Alanna and Longden, Kit D and Maldonado, Charli A and Mitletton, Myrto and Moitra, Ilina and Moon, Sung Soo and Mooney, Caroline and Munnelly, Eva J and Okeoma, Nneoma and Olbris, Donald J and Pai, Anika and Patel, Birava and Phillips, Emily M and Plaza, Stephen M and Richards, Alana and Rivas Salinas, Jennifer and Roberts, Ruair{\'\i} Jv and Rogers, Edward M and Scott, Ashley L and Scuderi, Louis A and Seenivasan, Pavithraa and Serratosa Capdevila, Laia and Smith, Claire and Svirskas, Rob and Takemura, Satoko and Tastekin, Ibrahim and Thomson, Alexander and Umayam, Lowell and Walsh, John J and Whittome, Holly and Xu, C Shan and Yakal, Emily A and Yang, Tansy and Zhao, Arthur and George, Reed and Jain, Viren and Jayaraman, Vivek and Korff, Wyatt and Meissner, Geoffrey W and Romani, Sandro and Funke, Jan and Knecht, Christopher and Saalfeld, Stephan and Scheffer, Louis K and Waddell, Scott and Card, Gwyneth M and Ribeiro, Carlos and Reiser, Michael B and Hess, Harald F and Rubin, Gerald M and Jefferis, Gregory Sxe} } @article {70012, title = {Sexually-dimorphic neurons in the Drosophila whole-brain connectome}, journal = {Research Square}, year = {2025}, month = {2025 Jun 26}, abstract = {

Sexual dimorphisms are present across brains. Male and female brains contain sets of cell types with differences in cell number, morphology, or synaptic connectivity between the two sexes. These differences are driven by differentially-expressed transcription factors, which set the stage for disparate sexual and social behaviors observed between males and females, such as courtship, aggression, receptivity, and mating. In the Drosophila brain, sexual dimorphisms result from differential expression of two transcription factors, Fruitless (Fru) and Doublesex (Dsx), and genetic reagents driven by enhancers for Fru and Dsx label sexually-dimorphic neurons in both male and female brains. The recent release of the first whole-brain connectome for Drosophila provides a unique opportunity to study the connectivity between these neurons as well as their integration into the larger brain network. Here, we identify 91 putative Fru or Dsx cell types, comprising ~1400 neurons, within the whole-brain connectome, using morphological similarity between electron microscopic (EM) reconstructions and light microscopic (LM) images of known Fru and Dsx neurons. We discover that while Fru and Dsx neurons are highly interconnected, each cell type typically receives more inputs from and sends more outputs to non-Fru/Dsx neurons. We characterize the connectivity in the Fru/Dsx networks to predict the function of cell types not previously characterized, we measure distances to the sensory periphery and uncover multisensory interactions, and we map connections to descending neurons that drive behavior. All Fru and Dsx labels reported here are shared within FlyWire Codex (codex.flywire.ai; gene==Fruitless or Doublesex); this work is a critical first step towards deciphering the neural basis of sexually-dimorphic behaviors and for making comparisons with future connectomes of the male brain.

}, doi = {10.21203/rs.3.rs-6881911/v1}, url = {https://doi.org/10.21203/rs.3.rs-6881911/v1}, author = {Deutsch, David and Matsliah, Arie and Wang, Kaiyu and Dorkenwald, Sven and Mondal, Arpita and Burke, Austin and Hebditch, James and Gager, Jay and Yu, Szi-Chieh and Sterling, Amy and McKellar, Amy and Schlegel, Philipp and Gerhard, Stephan and Sterne, Gabriella and Costa, Marta and Eichler, Katharina and Yin, Yijie and Jefferis, Gregory and Dickson, Barry and Seung, H Sebastian and Murthy, Mala} } @article {69398, title = {Shorter-duration escapes driven by Drosophila giant interneurons promote survival during predation}, journal = {Proc Biol Sci}, year = {2025}, month = {2025 May 28}, abstract = {

Large axon-diameter descending neurons are metabolically costly but transmit information rapidly from sensory neurons in the brain to motor neurons in the nerve cord. They have thus endured as a common feature of escape circuits in many animal species where speed is paramount. Though often considered isolated command neurons triggering fast-reaction-time, all-or-none escape responses, giant neurons are just one of multiple parallel pathways enabling selection between behavioral alternatives. Such degeneracy among escape circuits makes it unclear if and how giant neurons benefit prey fitness. Here we competed Drosophila melanogaster flies with genetically-silenced Giant Fibers (GFs) against flies with functional GFs in an arena with wild-caught damselfly predators and find that GF silencing decreases prey survival. Kinematic analysis of damselfly attack trajectories shows that decreased prey survival fitness results from GF-silenced flies failing to escape during predator attack speeds and approach distances that would normally elicit successful escapes. When challenged with a virtual looming predator, fly GFs promote survival by enforcing selection of a short-duration takeoff sequence as opposed to reducing reaction time. Our findings support a role for the GFs in promoting prey survival by influencing action selection as a means to enhance escape performance during realistically complex predation scenarios.

Preprint:\ https://www.biorxiv.org/content/early/2024/05/01/2024.04.30.591368

}, doi = {10.1098/rspb.2024.1724}, url = {https://doi.org/10.1098/rspb.2024.1724}, author = {Cynthia M. Chai and Carmen Morrow and Dhyey D. Parikh and Catherine R. von Reyn and Anthony Leonardo and Gwyneth M Card} } @article {70215, title = {Signatures of remote planning in hippocampal replay}, journal = {bioRxiv}, year = {2025}, month = {2025 Dec 04}, abstract = {

During brief, intermittent {\textquotedblleft}replay{\textquotedblright} events, hippocampal activity can express navigational trajectories disconnected from both when and where they originally occurred. While replay biased toward immediate future goals has been observed, there is no evidence yet linking replay to planning beyond the next action. Here, we designed a sequential spatial working memory task which required rats to utilize information across multiple temporally separated actions. Remote replay events matched the animal{\textquoteright}s future navigational choices made after completing an intervening subtask. Critically, this occurred only when the replayed information was useful for reducing memory load, consistent with it being an active process. Our findings suggest these remote replay events are a neural correlate of episodic forethought, allowing animals to use memories to plan beyond their immediate surroundings.

}, doi = {10.64898/2025.12.02.691753}, url = {https://www.biorxiv.org/content/early/2025/12/04/2025.12.02.691753}, author = {Lustig, Brian and Wang, Yingxue and Romani, Sandro and Pastalkova, Eva and Lee, Albert K.} } @article {69514, title = {A simplified minimodel of visual cortical neurons}, journal = {Nat Commun}, year = {2025}, month = {2025 Jul 01}, abstract = {

Artificial neural networks (ANNs) have been shown to predict neural responses in primary visual cortex (V1) better than classical models. However, this performance often comes at the expense of simplicity and interpretability. Here we introduce a new class of simplified ANN models that can predict over 70\% of the response variance of V1 neurons. To achieve this high performance, we first recorded a new dataset of over 29,000 neurons responding to up to 65,000 natural image presentations in mouse V1. We found that ANN models required only two convolutional layers for good performance, with a relatively small first layer. We further found that we could make the second layer small without loss of performance, by fitting individual "minimodels" to each neuron. Similar simplifications applied for models of monkey V1 neurons. We show that the minimodels can be used to gain insight into how stimulus invariance arises in biological neurons.

Preprint:\ https://www.biorxiv.org/content/early/2024/07/02/2024.06.30.601394

}, doi = {10.1038/s41467-025-61171-9}, url = {https://doi.org/10.1038/s41467-025-61171-9}, author = {Du, Fengtong and N{\'u}{\~n}ez-Ochoa, Miguel Angel and Pachitariu, Marius and Stringer, Carsen} } @article {70136, title = {A single residue in the yellow fever virus envelope protein modulates virion architecture and antigenicity.}, journal = {Nat Commun}, volume = {16}, year = {2025}, month = {2025 Sep 26}, pages = {8449}, abstract = {

Yellow fever virus (YFV) is a re-emerging flavivirus that causes severe hepatic disease and mortality in humans. Despite being researched for over a century, the structure of YFV has remained elusive. Here we use a chimeric virus platform to resolve the first high resolution cryo-EM structures of YFV. Stark differences in particle morphology and homogeneity are observed between vaccine and virulent strains of YFV, and these are found to have significant implications on antibody recognition and neutralisation. We identify a single residue (R380) in the YFV envelope protein that stabilises the virion surface, and leads to reduced exposure of the cross-reactive fusion loop epitope. The differences in virion morphology between YFV strains also contribute to the reduced sensitivity of the virulent YFV virions to vaccine-induced antibodies. These findings have significant implications for YFV biology, vaccinology and structure-based flavivirus antigen design.

}, keywords = {Animals, Antibodies, Neutralizing, Antibodies, Viral, Antigens, Viral, Cross Reactions, Cryoelectron Microscopy, Epitopes, Humans, Viral Envelope Proteins, Virion, Yellow Fever, Yellow Fever Vaccine, Yellow fever virus}, issn = {2041-1723}, doi = {10.1038/s41467-025-63038-5}, url = {https://doi.org/10.1038/s41467-025-63038-5}, author = {Bibby, Summa and Jung, James and Low, Yu Shang and Amarilla, Alberto A and Newton, Natalee D and Scott, Connor A P and Balk, Jessica and Ting, Yi Tian and Freney, Morgan E and Liang, Benjamin and Grant, Timothy and Coulibaly, Fass{\'e}li and Young, Paul and Hall, Roy A and Hobson-Peters, Jody and Modhiran, Naphak and Watterson, Daniel} } @article {70181, title = {Single-cell synaptome mapping of endogenous protein subpopulations in mammalian brain.}, journal = {Nat Commun}, volume = {16}, year = {2025}, month = {2025 Nov 11}, pages = {9705}, abstract = {

Different spatial or temporal protein populations, such as cell-surface/intracellular or pre-existing/nascent subpopulations, determine the basal and activity-induced functions of individual synapses within a neuron in vivo. Here, we developed a simple and generalizable platform to image different spatial and temporal subpopulations of endogenous proteins at thousands of synapses in single neurons in the mammalian brain. The platform is based on the development, improvement and integration of CRISPR-Cas9-mediated protein labeling methods, chemical tag labeling techniques, and a semi-automatic analytical pipeline. The combined platform enables whole-cell mapping of total, cell-surface, intracellular, pre-existing, nascent or nascent-and-surface populations of endogenous proteins, such as receptor, scaffold and signaling proteins, at thousands of synapses in individual neurons in living or fixed mouse brain. Our single-cell "synaptome" mapping of endogenous protein subpopulations comprehensively visualizes the spatial representation of synapse diversity in protein localization, trafficking and turnover, providing valuable insights into single-cell organization and computations in the brain.

}, keywords = {Animals, Brain, CRISPR-Cas Systems, Mice, Mice, Inbred C57BL, Neurons, Single-Cell Analysis, Synapses}, issn = {2041-1723}, doi = {10.1038/s41467-025-65813-w}, url = {https://doi.org/10.1038/s41467-025-65813-w}, author = {Uchigashima, Motokazu and Iguchi, Risa and Fujii, Kazuma and Shiku, Kaito and Kumar, Pratik and Liu, Xinyi and Isogai, Mari and Hoshino, Chiaki and Abe, Manabu and Nozumi, Motohiro and Okamura, Yosuke and Igarashi, Michihiro and Sakimura, Kenji and Bise, Ryoma and Lavis, Luke D and Mikuni, Takayasu} } @article {68799, title = {Single-cell type analysis of wing premotor circuits in the ventral nerve cord of Drosophila melanogaster}, journal = {eLife}, year = {2025}, month = {2025 May 06}, abstract = {

To perform most behaviors, animals must send commands from higher-order processing centers in the brain to premotor circuits that reside in ganglia distinct from the brain, such as the mammalian spinal cord or insect ventral nerve cord. How these circuits are functionally organized to generate the great diversity of animal behavior remains unclear. An important first step in unraveling the organization of premotor circuits is to identify their constituent cell types and create tools to monitor and manipulate these with high specificity to assess their functions. This is possible in the tractable ventral nerve cord of the fly. To generate such a toolkit, we used a combinatorial genetic technique (split-GAL4) to create 195 sparse transgenic driver lines targeting 196 individual cell types in the ventral nerve cord. These included wing and haltere motoneurons, modulatory neurons, and interneurons. Using a combination of behavioral, developmental, and anatomical analyses, we systematically characterized the cell types targeted in our collection. In addition, we identified correspondences between the cells in this collection and a recent connectomic data set of the ventral nerve cord. Taken together, the resources and results presented here form a powerful toolkit for future investigations of neuronal circuits and connectivity of premotor circuits while linking them to behavioral outputs.

}, doi = {10.7554/eLife.106548.1}, url = {https://doi.org/10.7554/eLife.106548.1}, author = {Erica Ehrhardt and Samuel C Whitehead and Shigehiro Namiki and Ryo Minegishi and Igor Siwanowicz and Kai Feng and Hideo Otsuna and FlyLight Project Team and Geoffrey W Meissner and David Stern and Jim Truman and David Shepherd and Michael H. Dickinson and Kei Ito and Barry J Dickson and Itai Cohen and Gwyneth M Card and Wyatt Korff} } @article {69998, title = {Single-Particle Tracking of AMPA Receptor-Containing Vesicles}, journal = {Bio-protocol}, volume = {15}, year = {2025}, month = {2025 Jun 05}, abstract = {

AMPA-type receptors are transported large distances to support synaptic plasticity at distal dendritic locations. Studying the motion of AMPA receptor+\ vesicles can improve our understanding of the mechanisms that underlie learning and memory. Nevertheless, technical challenges that prevent the visualization of AMPA receptor+vesicles limit our ability to study how these vesicles are trafficked. Existing methods rely on the overexpression of fluorescent protein-tagged AMPA receptors from plasmids, resulting in a saturated signal that obscures vesicles. Photobleaching must be applied to detect individual AMPA receptor+\ vesicles, which may eliminate important vesicle populations from analysis. Here, we present a protocol to study AMPA receptor+\ vesicles that addresses these challenges by 1) tagging AMPA receptors expressed from native loci with HaloTag and 2) employing a block-and-chase strategy with Janelia Fluor-conjugated HaloTag ligand to achieve sparse AMPA receptor labeling that obviates the need for photobleaching. After timelapse imaging is performed, AMPA receptor+\ vesicles can be identified during image analysis, and their motion can be characterized using a single-particle tracking pipeline.

Key features

{\textbullet} Track and characterize the motion of AMPAR GluA1+\ vesicles in cultured rat hippocampal neurons.

{\textbullet} GluA1 tagged with HaloTag (GluA1-HT) is expressed from native\ Gria1\ loci to avoid overexpression.

{\textbullet} Sparse GluA1-HT labeling densities can be achieved without photobleaching via a block-and-chase strategy that utilizes Janelia Fluor (JF) dyes conjugated to HaloTag ligand (HTL).

{\textbullet} GluA1-HT+\ vesicles are identified during image analysis, and their motion is characterized using single-particle tracking (SPT) and hidden Markov modeling with Bayesian model selection (HMM-Bayes).

}, doi = {10.21769/BioProtoc.5325}, url = {https://doi.org/10.21769/BioProtoc.5325}, author = {Wong, Victor C. and Walpita, Deepika and Liu, Zhe and O{\textquoteright}Shea, Erin K} } @article {69995, title = {Skin health and biological aging.}, journal = {Nat Aging}, year = {2025}, month = {2025 Jun 17}, abstract = {

Accumulating evidence indicates that biological aging can be accelerated by environmental exposures, collectively called the {\textquoteright}exposome{\textquoteright}. The skin, as the largest and most exposed organ, can be viewed as a {\textquoteright}window{\textquoteright} for the deep exploration of the exposome and its effects on systemic aging. The complex interplay across hallmarks of aging in the skin and systemic biological aging suggests that physiological processes associated with skin aging influence, and are influenced by, systemic hallmarks of aging. This bidirectional relationship provides potential avenues for the prevention of accelerated biological aging and the identification of therapeutic targets. We provide a review of the interactions between skin exposure, aging hallmarks in the skin and associated systemic changes, and their implications in treatment and disease. We also discuss key questions that need to be addressed to maintain skin and overall health, highlighting the need for the development of precise biomarkers and advanced skin models.

}, issn = {2662-8465}, doi = {10.1038/s43587-025-00901-6}, url = {https://doi.org/10.1038/s43587-025-00901-6}, author = {Furman, David and Auwerx, Johan and Bulteau, Anne-Laure and Church, George and Couturaud, Virginie and Crabbe, Laure and Davies, Kelvin J A and Decottignies, Anabelle and Gladyshev, Vadim N and Kennedy, Brian K and Neretti, Nicola and Nizard, Carine and Pays, Karl and Robinton, Daisy and Sebastiano, Vittorio and Watson, Rachel E B and Wang, Meng C and Woltjen, Knut} } @article {70004, title = {SLAy-ing oversplitting errors in high-density electrophysiology spike sorting}, journal = {bioRxiv}, year = {2025}, month = {2025 Jun 25}, abstract = {

The growing channel count of silicon probes has substantially increased the number of neurons recorded in electrophysiology (ephys) experiments, rendering traditional manual spike sorting impractical. Instead, modern ephys recordings are processed with automated methods that use waveform template matching to isolate putative single neurons. While scalable, automated methods are subject to assumptions that often fail to account for biophysical changes in action potential waveforms, leading to systematic errors. Consequently, manual curation of these errors, which is both time-consuming and lacks reproducibility, remains necessary. To improve efficiency and reproducibility in the spike-sorting pipeline, we introduce here the Spike-sorting Lapse Amelioration System (SLAy), an algorithm that automatically merges oversplit spike clusters. SLAy employs two novel metrics: (1) a waveform similarity metric that uses a neural network to obtain spatially informed, time-shift invariant low-dimensional waveform representations, and (2) a cross-correlogram significance metric based on the earth-movers distance between the observed and null cross-correlograms. We demonstrate that SLAy achieves 85\% agreement with human curators across a diverse set of animal models, brain regions, and probe geometries. To illustrate the impact of spike sorting errors on downstream analyses, we develop a new burst-detection algorithm and show that SLAy fixes spike sorting errors that preclude the accurate detection of bursts in neural data. SLAy leverages GPU parallelization and multithreading for computational efficiency, and is compatible with Phy and NeuroData Without Borders, making it a practical and flexible solution for large-scale ephys data analysis.

}, doi = {10.1101/2025.06.20.660590}, url = {https://www.biorxiv.org/content/early/2025/06/25/2025.06.20.660590}, author = {Koukuntla, Sai and DeWeese, Tate and Cheng, Alexandra and Mildren, Robyn and Lawrence, Aamna and Graves, Austin R and Colonell, Jennifer and Harris, Timothy D and Charles, Adam S} } @article {70005, title = {Sleep need-dependent plasticity of a thalamic circuit promotes homeostatic recovery sleep.}, journal = {Science}, volume = {388}, year = {2025}, month = {2025 Jun 19}, pages = {eadm8203}, abstract = {

Prolonged wakefulness leads to persistent, deep recovery sleep (RS). However, the neuronal circuits that mediate this process remain elusive. From a circuit screen in mice, we identified a group of thalamic nucleus reuniens (RE) neurons activated during sleep deprivation (SD) and required for sleep homeostasis. Optogenetic activation of RE neurons leads to an unusual phenotype: presleep behaviors (grooming and nest organizing) followed by prolonged, intense sleep that resembles RS. Inhibiting RE activity during SD impairs subsequent RS, which suggests that these neurons signal sleep need. RE neurons act upstream of sleep-promoting zona incerta cells, and SD triggers plasticity of this circuit to strengthen their connectivity. These findings reveal a circuit mechanism by which sleep need transforms the functional coupling of a sleep circuit to promote persistent, deep sleep.

}, keywords = {Animals, Homeostasis, Male, Mice, Mice, Inbred C57BL, Midline Thalamic Nuclei, Neuronal Plasticity, Neurons, Optogenetics, Sleep Deprivation, Sleep, Slow-Wave, Wakefulness}, issn = {1095-9203}, doi = {10.1126/science.adm8203}, url = {https://doi.org/10.1126/science.adm8203}, author = {Lee, Sang Soo and Liu, Qiang and Cheng, Alexandra H R and Kim, Dong Won and Boudreau, Daphne M and Mehta, Anuradha and Keles, Mehmet F and Fejfer, Rafal and Palmer, Isabelle and Park, Kristen H and M{\"u}nzberg, Heike and Harris, Timothy D and Graves, Austin R and Blackshaw, Seth and Wu, Mark N} } @article {70117, title = {Spatial predictive coding in visual cortical neurons}, journal = {bioRxiv}, year = {2025}, month = {2025 Sep 19}, abstract = {

Predictive coding is a theoretical framework that can explain how animals build internal models of their sensory environments by predicting sensory inputs. Predictive coding may capture either spatial or temporal relationships between sensory objects. While the original theory by Rao and Ballard, 1999 described spatial predictive coding, much of the recent experimental data has been interpreted as evidence for temporal predictive coding. Here we directly tested whether the {\textquotedblleft}mismatch{\textquotedblright} neural responses in sensory cortex are due to a spatial or a temporal internal model. We adopted two common paradigms to study predictive coding: one based on virtual-reality and one based on static images. After training mice with repeated visual stimulation for several days, we performed multiple manipulations, including: 1) we introduced a novel stimulus, 2) we replaced a stimulus with a novel gray wall, 3) we duplicated a trained stimulus, or 4) we altered the order of the stimuli. The first two manipulations induced a substantial mismatch response in neural populations of up to 20,000 neurons recorded across primary and higher-order visual cortex, while the third and fourth ones did not. Thus, a mismatch response only occurred if a new spatial {\textendash} not temporal {\textendash} pattern was introduced.

}, doi = {10.1101/2025.09.17.676794}, url = {https://www.biorxiv.org/content/early/2025/09/19/2025.09.17.676794}, author = {Zhang, Qingqing and Gr{\o}dem, Sverre and Gracias, Alexa and Lensj{\o}, Kristian K. and Fyhn, Marianne and Stringer, Carsen and Pachitariu, Marius} } @article {69984, title = {Spatial reasoning via recurrent neural dynamics in mouse retrosplenial cortex}, journal = {Nat Neurosci}, volume = {28}, year = {2025}, month = {2025 Jun 06}, pages = {1293-1299}, abstract = {

From visual perception to language, sensory stimuli change their meaning depending on previous experience. Recurrent neural dynamics can interpret stimuli based on externally cued context, but it is unknown whether they can compute and employ internal hypotheses to resolve ambiguities. Here we show that mouse retrosplenial cortex (RSC) can form several hypotheses over time and perform spatial reasoning through recurrent dynamics. In our task, mice navigated using ambiguous landmarks that are identified through their mutual spatial relationship, requiring sequential refinement of hypotheses. Neurons in RSC and in artificial neural networks encoded mixtures of hypotheses, location and sensory information, and were constrained by robust low-dimensional dynamics. RSC encoded hypotheses as locations in activity space with divergent trajectories for identical sensory inputs, enabling their correct interpretation. Our results indicate that interactions between internal hypotheses and external sensory data in recurrent circuits can provide a substrate for complex sequential cognitive reasoning.

Preprint: https://doi.org/10.1101/2022.04.12.488024v1

}, keywords = {Animals, Cerebral Cortex, Gyrus Cinguli, Male, Mice, Mice, Inbred C57BL, Models, Neurological, Neural Networks, Computer, Neurons, Photic Stimulation, Space Perception}, issn = {1546-1726}, doi = {10.1038/s41593-025-01944-z}, url = {https://doi.org/10.1038/s41593-025-01944-z}, author = {Voigts, Jakob and Kanitscheider, Ingmar and Miller, Nicholas J and Toloza, Enrique H S and Newman, Jonathan P and Fiete, Ila R and Harnett, Mark T} } @article {69490, title = {Spatial transcriptomics reveals human cortical layer and area specification}, journal = {Nature}, year = {2025}, month = {2025 May 14}, abstract = {

The human cerebral cortex, pivotal for advanced cognitive functions, is composed of six distinct layers and dozens of functionally specialized areas. The layers and areas are distinguished both molecularly, by diverse neuronal and glial cell subtypes, and structurally, through intricate spatial organization3,4. While single-cell transcriptomics studies have advanced molecular characterization of human cortical development, a critical gap exists due to the loss of spatial context during cell dissociation. Here, we utilized multiplexed error-robust fluorescence in situ hybridization (MERFISH)9, augmented with deep-learning-based cell segmentation, to examine the molecular, cellular, and cytoarchitectural development of human fetal cortex with spatially resolved single-cell resolution. Our extensive spatial atlas, encompassing 16 million single cells, spans eight cortical areas across four time points in the second and third trimesters. We uncovered an early establishment of the six-layer structure, identifiable in the laminar distribution of excitatory neuronal subtypes by mid-gestation, long before the emergence of cytoarchitectural layers. Notably, while anterior-posterior gradients of neuronal subtypes were generally observed in most cortical areas, a striking exception was the sharp molecular border between primary (V1) and secondary visual cortices (V2) at gestational week 20. Here we discovered an abrupt binary shift in neuronal subtype specification at the earliest stages, challenging the notion that continuous morphogen gradients dictate mid-gestation cortical arealization. Moreover, integrating single-nuclei RNA-sequencing and in situ whole transcriptomics revealed an early upregulation of synaptogenesis in V1-specific Layer 4 neurons, suggesting a role of synaptogenesis in this discrete border formation. Collectively, our findings underscore the crucial role of spatial relationships in determining the molecular specification of cortical layers and areas. This work not only provides a valuable resource for the field, but also establishes a spatially resolved single-cell analysis paradigm that paves the way for a comprehensive developmental atlas of the human brain.

Preprint:\ https://www.biorxiv.org/content/early/2024/06/10/2024.06.05.597673

}, doi = {10.1038/s41586-025-09010-1}, url = {https://doi.org/10.1038/s41586-025-09010-1}, author = {Qian, Xuyu and Coleman, Kyle and Jiang, Shunzhou and Kriz, Andrea J. and Marciano, Jack H. and Luo, Chunyu and Cai, Chunhui and Manam, Monica Devi and Caglayan, Emre and Otani, Aoi and Ghosh, Urmi and Shao, Diane D. and Andersen, Rebecca E. and Neil, Jennifer E. and Johnson, Robert and LeFevre, Alexandra and Hecht, Jonathan L. and Miller, Michael B. and Sun, Liang and Stringer, Carsen and Li, Mingyao and Walsh, Christopher A.} } @article {69721, title = {A split-GAL4 driver line resource for Drosophila neuron types}, year = {2025}, month = {01/2025}, doi = {10.7554/elife.98405.3}, url = {http://dx.doi.org/10.7554/eLife.98405.3}, author = {Meissner, Geoffrey W and Vannan, Allison and Jeter, Jennifer and Close, Kari and Depasquale, Gina M and Dorman, Zachary and Forster, Kaitlyn and Beringer, Jaye Anne and Gibney, Theresa V and Hausenfluck, Joanna H and He, Yisheng and Henderson, Kristin and Johnson, Lauren and Johnston, Rebecca M and Ihrke, Gudrun and Iyer, Nirmala and Lazarus, Rachel and Lee, Kelley and Li, Hsing-Hsi and Liaw, Hua-Peng and Melton, Brian and Miller, Scott and Motaher, Reeham and Novak, Alexandra and Ogundeyi, Omotara and Petruncio, Alyson and Price, Jacquelyn and Protopapas, Sophia and Tae, Susana and Taylor, Jennifer and Vorimo, Rebecca and Yarbrough, Brianna and Zeng, Kevin Xiankun and Zugates, Christopher T and Dionne, Heather and Angstadt, Claire and Ashley, Kelly and Cavallaro, Amanda and Dang, Tam and Gonzalez, Guillermo A and Hibbard, Karen L and Huang, Cuizhen and Kao, Jui-Chun and Laverty, Todd and Mercer, Monti and Perez, Brenda and Pitts, Scarlett and Ruiz, Danielle and Vallanadu, Viruthika and Zheng, Grace Zhiyu and Goina, Cristian and Otsuna, Hideo and Rokicki, Konrad and Svirskas, Robert R and Cheong, Han Sj and Dolan, Michael-John and Ehrhardt, Erica and Feng, Kai and El Galfi, Basel and Goldammer, Jens and Huston, Stephen J and Hu, Nan and Ito, Masayoshi and McKellar, Claire and minegishi, ryo and Namiki, Shigehiro and Nern, Aljoscha and Schretter, Catherine E and Sterne, Gabriella R and Venkatasubramanian, Lalanti and Wang, Kaiyu and Wolff, Tanya and Wu, Ming and George, Reed and Malkesman, Oz and Aso, Yoshinori and Card, Gwyneth M and Dickson, Barry J and Korff, Wyatt and Ito, Kei and Truman, James W and Zlatic, Marta and Rubin, Gerald M} } @article {70224, title = {SpotDMix: informed mRNA transcript assignment using mixture models}, journal = {bioRxiv}, year = {2025}, month = {2025 Dec 18}, abstract = {

Unveiling the genetic profiles of spatially distinguished cells is an important aspect in many areas of brain research, as the genetic identity contains information about a cell{\textquoteright}s physiological properties and internal state. On top of this, knowledge of the genetic details of each cell can reveal structural organization within tissue. As image-based spatial transcriptomics moves toward applications in tissues with dense cellular packing, accurate assignment of detected mRNA transcripts ("spots") to correct segmented cells becomes increasingly difficult, rendering simple methods insufficient with many incorrect assignments to neighboring cells. Here we introduce SpotDMix, a statistical model for assigning spots to cells by modeling spots as coming from a mixture model of distributions matching segmented cell shapes, with assignment probabilities and shape parameters optimized using the Expectation Maximization algorithm. Performance is assessed and compared against several simple methods in various scenarios on both surrogate data and larval zebrafish data. In all tested scenarios SpotDMix outperforms the simple methods on all evaluated metrics, including individual transcript assignment accuracy, total assigned number of spots per cell error and cell type classification. Further, SpotDMix produces a higher degree of exclusivity between genes which are known to not or rarely co-express.

}, doi = {10.64898/2025.12.15.693918}, url = {https://www.biorxiv.org/content/early/2025/12/18/2025.12.15.693918}, author = {Smeets, Kasper and Hesselink, Luuk W and Marquez-Legorreta, Emmanuel and Fleishman, Greg M and Eddison, Mark and Tillberg, Paul W and Ahrens, Misha B and Englitz, Bernhard} } @article {70183, title = {Stability through plasticity: Finding robust memories through representational drift.}, journal = {Proc Natl Acad Sci USA}, volume = {122}, year = {2025}, month = {2025 Nov 11}, pages = {e2500077122}, abstract = {

Memories are believed to be stored in synapses and retrieved by reactivating neural ensembles. Learning alters synaptic weights, which can interfere with previously stored memories that share the same synapses, creating a trade-off between plasticity and stability. Interestingly, neural representations change even in stable environments, without apparent learning or forgetting-a phenomenon known as representational drift. Theoretical studies have suggested that multiple neural representations can correspond to a memory, with postlearning exploration of these representation solutions driving drift. However, it remains unclear whether representations explored through drift differ from those learned or offer unique advantages. Here, we show that representational drift uncovers noise-robust representations that are otherwise difficult to learn. We first define the nonlinear solution space manifold of synaptic weights for fixed input-output mappings, which allows us to disentangle drift from learning and forgetting and simulate drift as diffusion within this manifold. Solutions explored by drift have many inactive and saturated neurons, making them robust to weight perturbations due to noise or continual learning. Such solutions are prevalent and entropically favored by drift, but their lack of gradients makes them difficult to learn and nonconducive to future learning. To overcome this, we introduce an allocation procedure that selectively shifts representations for new stimuli into a learning-conducive regime. By combining allocation with drift, we resolve the trade-off between learnability and robustness.

}, keywords = {Humans, Learning, Memory, Models, Neurological, Neuronal Plasticity, Neurons, Synapses}, issn = {1091-6490}, doi = {10.1073/pnas.2500077122}, url = {https://doi.org/10.1073/pnas.2500077122}, author = {Natrajan, Maanasa and Fitzgerald, James E} } @article {69785, title = {Stars by the pocketful}, journal = {ACS Central Science}, year = {2025}, month = {2025 Feb 12}, abstract = {

Fluorescence is magical. Shine one color of light on a fluorophore and it glows in another color. This property allows imaging of biological systems with high sensitivity-we can visualize individual fluorescent molecules in an ocean of nonfluorescent ones.

Fluorescence microscopy has long been used to study isolated cells, both living and dead, but the development of newer, tailored fluorophores is swiftly expanding the use of fluorescence imaging to more complicated systems such as intact animals. In the latest in a long string of transformative work, Sletten and co-workers introduce dyes shrouded with multiple polymer chains-effectively star polymers with a bright fluorophore at the center.

}, doi = {10.1021/acscentsci.5c00223}, author = {Lavis, Luke and Lavis, Clara} } @article {69975, title = {Statistical signature of subtle behavioral changes in large-scale assays.}, journal = {PLoS Comput Biol}, volume = {21}, year = {2025}, month = {2025 Apr 21}, pages = {e1012990}, abstract = {

The central nervous system can generate various behaviors, including motor responses, which we can observe through video recordings. Recent advances in gene manipulation, automated behavioral acquisition at scale, and machine learning enable us to causally link behaviors to their underlying neural mechanisms. Moreover, in some animals, such as the Drosophila melanogaster larva, this mapping is possible at the unprecedented scale of single neurons, allowing us to identify the neural microcircuits generating particular behaviors. These high-throughput screening efforts, linking the activation or suppression of specific neurons to behavioral patterns in millions of animals, provide a rich dataset to explore the diversity of nervous system responses to the same stimuli. However, important challenges remain in identifying subtle behaviors, including immediate and delayed responses to neural activation or suppression, and understanding these behaviors on a large scale. We here introduce several statistically robust methods for analyzing behavioral data in response to these challenges: 1) A generative physical model that regularizes the inference of larval shapes across the entire dataset. 2) An unsupervised kernel-based method for statistical testing in learned behavioral spaces aimed at detecting subtle deviations in behavior. 3) A generative model for larval behavioral sequences, providing a benchmark for identifying higher-order behavioral changes. 4) A comprehensive analysis technique using suffix trees to categorize genetic lines into clusters based on common action sequences. We showcase these methodologies through a behavioral screen focused on responses to an air puff, analyzing data from 280 716 larvae across 569 genetic lines.

Preprint:\ https://www.biorxiv.org/content/10.1101/2024.05.03.591825v1

}, keywords = {Animals, Behavior, Animal, Computational Biology, Drosophila melanogaster, Larva, Machine Learning, Models, Neurological, Models, Statistical, Neurons}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1012990}, url = {https://doi.org/10.1371/journal.pcbi.1012990}, author = {Blanc, Alexandre and Laurent, Francois and Barbier-Chebbah, Alex and Van Assel, Hugues and Cocanougher, Benjamin T and Jones, Benjamin M W and Hague, Peter and Zlatic, Marta and Chikhi, Rayan and Vestergaard, Christian L and Jovanic, Tihana and Masson, Jean-Baptiste and Barre, Chloe} } @article {69702, title = {Structural dynamics and binding of Caenorhabditis elegans lifespan-extending lipid binding protein-3 to polyunsaturated fatty acids.}, journal = {Protein Sci}, volume = {34}, year = {2025}, month = {2025 Jan 01}, pages = {e5249}, abstract = {

Intracellular lipid binding proteins (iLBPs) play crucial roles in lipid transport and cellular metabolism across the animal kingdom. Recently, a fat-to-neuron axis was described in Caenorhabditis elegans, in which lysosomal activity in the fat liberates polyunsaturated fatty acids (PUFAs) that signal to neurons and extend lifespan with durable fecundity. In this study, we investigate the structure and binding mechanisms of a lifespan-extending lipid chaperone, lipid binding protein-3 (LBP-3), which shuttles dihomo-γ-linolenic (DGLA) acid from intestinal fat to neurons. We present the first high-resolution crystal structure of LBP-3, which reveals a classic iLBP fold with an unexpected and unique homodimeric arrangement via interstrand interactions that is incompatible with ligand binding. We identify key ionic interactions that mediate DGLA binding within the lipid binding pocket. Molecular dynamics simulations further elucidate LBP-3{\textquoteright}s preferential binding to DGLA due to its rotational freedom and access to favorable binding conformations compared to other 20-carbon PUFAs. We also propose that LBP-3 dimerization may be a unique regulatory mechanism for lipid chaperones.

}, keywords = {Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Crystallography, X-Ray, Fatty Acid-Binding Proteins, Fatty Acids, Unsaturated, Molecular Dynamics Simulation, Protein Binding}, issn = {1469-896X}, doi = {10.1002/pro.5249}, url = {https://doi.org/10.1002/pro.5249}, author = {Cuevas, Andr{\'e} R and Tillman, Matthew C and Wang, Meng C and Ortlund, Eric A} } @article {70195, title = {Structural dynamics and neural representation of wing deformation.}, journal = {Proc Natl Acad Sci USA}, volume = {122}, year = {2025}, month = {2025 Nov 18}, pages = {e2518032122}, abstract = {

Locomotor control is facilitated by mechanosensory inputs that report how the body interacts with a physical medium. Effective representation of compliant wing deformations is particularly challenging due to the many degrees of freedom. Structural configurations can constrain the stimulus space, and strategic placement of sensors can simplify computation. Here, we measured and modeled wing displacement fields and characterized spatiotemporal encoding of the wing mechanosensors. Our data show how dragonfly wing architecture prescribes deformation modes consistent across models and measurements. We found that the wing{\textquoteright}s state under normal flapping conditions is detected by the spike timing of few sensors, with additional sensors recruited under perturbation. The functional integration of wing biomechanics and sensor placement enables a straightforward solution for information transfer.

}, keywords = {Animals, Biomechanical Phenomena, Flight, Animal, Models, Biological, Odonata, Wings, Animal}, issn = {1091-6490}, doi = {10.1073/pnas.2518032122}, url = {https://doi.org/10.1073/pnas.2518032122}, author = {Yarger, Alexandra M and Maeda, Masateru and Siwanowicz, Igor and Kajiyama, Haruhiro and Walker, Simon M and Bomphrey, Richard J and Lin, Huai-Ti} } @article {70081, title = {Supraspinal commands have a modular organization that is behavioral context specific.}, journal = {Curr Biol}, year = {2025}, month = {2025 Aug 21}, abstract = {

Animals generate a range of locomotor patterns that subserve diverse behaviors, and in vertebrates, the required supraspinal commands derive from reticulospinal neurons in the brainstem. Yet how these commands are encoded across the reticulospinal population is unknown, making it unclear whether a universal control logic generates the full locomotor repertoire or if distinct sets of command modules might compose movement in different behavioral contexts. Here, we used calcium imaging, high-resolution behavior tracking, and statistical modeling to comprehensively survey reticulospinal activity and relate single-cell activity to movement kinematics as larval zebrafish generated a broad diversity of swim types. We found that reticulospinal population activity had a low-dimensional organization and identified 8 functional archetypes that provided a succinct and robust encoding of the full range of locomotor actions. Across much of locomotor space, 5 functional archetypes supported multiplexed control of swim speed and independent control of direction, whereas an independent set of 3 functional archetypes controlled the specialized swims that zebrafish use during hunting to orient toward prey. Overall, our study reveals a modular supraspinal control architecture that is partitioned according to behavioral context.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2025.07.066}, author = {Lau, Joanna Y N and Fitzgerald, James E and Bianco, Isaac H} } @article {70094, title = {Surrogate selection oversamples expanded T cell clonotypes}, journal = {The Annals of Applied Statistics}, volume = {19}, year = {2025}, month = {2025 Sept 01}, pages = {1884 {\textendash} 1907}, abstract = {

Surrogate selection is an experimental design that without sequencing any DNA can restrict a sample of cells to those carrying certain genomic mutations. In immunological disease studies, this design may provide a relatively easy approach to enrich a lymphocyte sample with cells relevant to the disease response because the emergence of neutral mutations associates with the proliferation history of clonal subpopulations. A statistical analysis of clonotype sizes provides a structured, quantitative perspective on this useful property of surrogate selection. Our model specification couples within-clonotype birth-death processes with an exchangeable model across clonotypes. Beyond enrichment questions about the surrogate selection design, our framework enables a study of sampling properties of elementary sample diversity statistics; it also points to new statistics that may usefully measure the burden of somatic genomic alterations associated with clonal expansion. We examine statistical properties of immunological samples governed by the coupled model specification, and we illustrate calculations in surrogate selection studies of melanoma and in single-cell genomic studies of T cell repertoires.

}, keywords = {Bayes{\textquoteright} rule, clonal expansion, diversity statistic, enrichment, exchangeable birth-death processes, Experimental design, single cell sequencing, size bias, somatic mutation}, doi = {10.1214/25-AOAS2032}, url = {https://doi.org/10.1214/25-AOAS2032}, author = {Peng Yu and Yumin Lian and Elliot Xie and Cindy L. Zuleger and Richard J. Albertini and Mark R. Albertini and Michael A. Newton} } @article {69771, title = {Symposia report of The Annual Biological Sciences Section Meeting of the Gerontological Society of America 2023, Tampa, Florida.}, journal = {J Gerontol A Biol Sci Med Sci}, year = {2025}, month = {2025 Feb 11}, abstract = {

The aging process is universal, and it is characterized by a progressive deterioration and decrease in physiological function leading to decline on the organismal level. Nevertheless, a number of genetic and non-genetic interventions have been described, which successfully extend healthspan and lifespan in different species. Furthermore, a number of clinical trials have been evaluating the feasibility of different interventions to promote human health. The goal of the annual Biological Sciences Section of the Gerontological Society of America meeting was to share current knowledge of different topics in aging research and provide a vision of the future of aging research. The meeting gathered international experts in diverse areas of aging research including basic biology, demography, and clinical and translational studies. Specific topics included metabolism, inflammaging, epigenetic clocks, frailty, senescence, neuroscience, stem cells, reproductive aging, inter-organelle crosstalk, comparative transcriptomics of longevity, circadian clock, metabolomics, and biodemography.

}, issn = {1758-535X}, doi = {10.1093/gerona/glaf026}, url = {https://doi.org/10.1093/gerona/glaf026}, author = {Rogina, Blanka and Anderson, Rozalyn and Lebrasseur, Nathan and Curan, Sean and Yousefzadeh, Matthew J and Ghosh, Bhaswati and Duque, Gustavo and Howlett, Susan and Austad, Steven and Demuth, Ilja and Gerstorf, Denis and Korfhage, Justin and Lombard, David B and Abadir, Peter and Christensen, Kaare and Carey, James R and Alberts, Susan C and Campos, Fernando and Palavicini, Juan Pablo and Palmer, Allyson and Bell, Justice and Basisty, Nathan and de Cabo, Rafael and Gomes, Ana and Dixit, Vishwa Deep and Sen, Payel and Baur, Joseph A and Imai, Shin-Ichiro and Li, Xiaoling and Valdez, Gregorio and Orr, Miranda E and Pletcher, Scott and Andersen, Julie and Jones, Leanne and Castillo-Azofeida, David and Bonaguidi, Michael and Suh, Yousin and Duncan, Francesca E and Murray, Anna and Burkewitz, Kristopher and Henne, Mike and Zhou, Kai and Bouhrara, Mustapha and Benjamini, Dan and Kolind, Shannon and Walker, Keenan A and Reiter, David A and Dean Iii, Doug and Gorbunova, Vera and Gladyshev, Vadim N and Palovics, Robert and Niedernhofer, Laura J and Fan, Rong and Bueckle, Andreas D and Hurley, Jennifer and Esser, Karyn A and Kapahi, Pankaj and Sato, Shogo and Jiang, Nisi and Ashiqueali, Sarah A and Diaz, Jose and Mishra, Sidharth Prasad and Ralmundo, Nuno and Banarjee, Reema and Allsopp, Richard and Reynolds, Lindsay M and Zhang, Bohan and Sebastiani, Paola and Monti, Stefano and Schork, Nicholas and Rappaport, Noa} } @article {70163, title = {Synapse detection efficiency in EM Drosophila connectomics}, journal = {bioRxiv}, year = {2025}, month = {2025 Oct 16}, abstract = {

Researchers have long noted the differences in synapse count between different EM reconstructions of similar circuitry. In this paper we attempt to determine the portion of these differences that may be due to different sample preparation and imaging techniques, in particular serial-section transmission imaging (SS-TEM) compared to focused ion beam with scanning electron microscopy (FIB-SEM). To do this, we compare synapse detection in the major Drosophila EM reconstructions - FANC, MANC, FAFB (with original and new synapses), male CNS, BANC, and HemiBrain, plus several smaller reconstructions. We look at raw synapse counts to avoid any dependence on proofreading, and compensate insofar as possible for the confounds of sample sizes differences and different software detection efficiency. The result are estimates, per compartment and for the sample as a whole, of the number of synapses that would be visible to a skilled human observer. These are then compared across all samples, using regions which are reconstructed in common for each sample pair. We find that in almost all known cases where a volume has been reconstructed by both techniques, isotropic FIB-SEM reconstructions show more human-visible synapses than microtome sliced reconstructions, typically by more than 40\%. This strongly suggests, but does not conclusively prove, that synapses are easier to see in isotropic FIB-SEM data.

}, doi = {10.1101/2025.10.16.682869}, url = {https://www.biorxiv.org/content/early/2025/10/19/2025.10.16.682869}, author = {Scheffer, Louis K.} } @article {70091, title = {Synaptic targets of circadian clock neurons influence core clock parameters.}, journal = {Sci Adv}, volume = {11}, year = {2025}, month = {2025 Sep 05}, pages = {eadw4666}, abstract = {

Neuronal connectivity in the circadian clock network is essential for robust endogenous timekeeping. In the circadian clock network, the small ventral lateral neurons (sLNs) serve as critical pacemakers. Peptidergic communication mediated by the neuropeptide (PDF), released by sLNs, has been well characterized. In contrast, little is known about the role of the synaptic connections that sLNs form with downstream neurons. Connectomic analyses revealed that the sLNs form strong synaptic connections with previously uncharacterized neurons called superior lateral protocerebrum 316 (SLP316). Here, we show that silencing the synaptic output from the SLP316 neurons via tetanus toxin expression shortened the free-running period, whereas hyperexciting them by expressing the bacterial voltage-gated sodium channel resulted in period lengthening. Under light-dark cycles, silencing SLP316 neurons caused lower daytime activity and higher daytime sleep. Our results reveal that the main postsynaptic partners of key pacemaker neurons are a nonclock neuronal cell type that regulates the timing of sleep and activity.

}, keywords = {Animals, Circadian Clocks, Circadian Rhythm, Drosophila melanogaster, Drosophila Proteins, Neurons, Neuropeptides, Sleep, Synapses, Tetanus Toxin}, issn = {2375-2548}, doi = {10.1126/sciadv.adw4666}, url = {https://doi.org/10.1126/sciadv.adw4666}, author = {Scholz-Carlson, Eva and Iyer, Aishwarya R and Nern, Aljoscha and Ewer, John and Fernandez, Maria P} } @article {69205, title = {Synchronous ensembles of hippocampal CA1 pyramidal neurons associated with theta but not ripple oscillations during novel exploration.}, journal = {eLife}, year = {2025}, month = {2025 Apr 1}, abstract = {

Synchronous neuronal ensembles play a pivotal role in the consolidation of long-term memory in the hippocampus. However, their organization during the acquisition of spatial memory remains less clear. In this study, we used neuronal population voltage imaging to investigate the synchronization patterns of CA1 pyramidal neuronal ensembles during the exploration of a new environment, a critical phase for spatial memory acquisition. We found synchronous ensembles comprising approximately 40\% of CA1 pyramidal neurons, firing simultaneously in brief windows (\~{}25ms) during immobility and locomotion in novel exploration. Notably, these synchronous ensembles were not associated with ripple oscillations but were instead phase-locked to local field potential theta waves. Specifically, the subthreshold membrane potentials of neurons exhibited coherent theta oscillations with a depolarizing peak at the moment of synchrony. Among newly formed place cells, pairs with more robust synchronization during locomotion displayed more distinct place-specific activities. These findings underscore the role of synchronous ensembles in coordinating place cells of different place fields.

}, doi = {10.7554/elife.96718.2}, url = {https://doi.org/10.7554/elife.96718.2}, author = {Bei-Jung Lin and Tsai-Wen Chen and En-Li Chen and Eric R. Schreiter} } @article {70025, title = {Synchronous Ensembles of Hippocampal CA1 Pyramidal Neurons During Novel Exploration}, journal = {eLife}, year = {2025}, month = {2025 Jul 10}, abstract = {

Synchronous neuronal ensembles play a pivotal role in the consolidation of long-term memory in the hippocampus. However, their organization during the acquisition of spatial memory remains less clear. In this study, we used neuronal population voltage imaging to investigate the synchronization patterns of CA1 pyramidal neuronal ensembles during the exploration of a new environment, a critical phase for spatial memory acquisition. We found synchronous ensembles comprising approximately 40\% of CA1 pyramidal neurons, firing simultaneously in brief windows (\~{}25ms) during immobility and locomotion in novel exploration. Notably, these synchronous ensembles were not associated with contralateral ripple oscillations but were instead phase-locked to theta waves recorded in the contralateral CA1 region. Moreover, the subthreshold membrane potentials of neurons exhibited coherent intracellular theta oscillations with a depolarizing peak at the moment of synchrony. Among newly formed place cells, pairs with more robust synchronization during locomotion displayed more distinct place-specific activities. These findings underscore the role of synchronous ensembles in coordinating place cells of different place fields.

}, doi = {10.7554/elife.96718.4}, url = {http://dx.doi.org/10.7554/eLife.96718.4}, author = {Chen, En-Li and Chen, Tsai-Wen and Schreiter, Eric R and Lin, Bei-Jung} } @article {70092, title = {Taking down the primary cilium: Pathways for disassembly in differentiating cells.}, journal = {Bioessays}, year = {2025}, month = {2025 Sep 01}, pages = {e70060}, abstract = {

Primary cilia are customized subcellular signaling compartments leveraged to detect signals in diverse physiological contexts. Although prevalent throughout mammalian tissues, primary cilia are not universal. Many non-ciliated cells derive from developmental lineages that include ciliated progenitors; however, little is known about how primary cilia are lost as cells differentiate. Here, we examine how ciliated and non-ciliated states emerge during development and are actively maintained. We highlight several pathways for primary cilia loss, including cilia resorption in pre-mitotic cells, cilia deconstruction in post-mitotic cells, cilia shortening via remodeling, and cilia disassembly preceding multiciliogenesis. Lack of ciliogenesis is known to decrease primary cilia frequency and cause ciliopathies. Failure to maintain cilia can also cause primary cilia to be absent. Conversely, defects in primary cilia suppression or disassembly can lead to the presence of primary cilia in non-ciliated cells. We examine how changes in ciliation states could contribute to tumorigenesis and neurodegeneration.

}, issn = {1521-1878}, doi = {10.1002/bies.70060}, url = {https://doi.org/10.1002/bies.70060}, author = {Ott, Carolyn M and Mukhopadhyay, Saikat} } @article {69764, title = {Targets of circadian clock neurons influence core clock parameters}, journal = {bioRxiv}, year = {2025}, month = {2025 Jan 31}, abstract = {

Neuronal connectivity in the circadian clock network is essential for robust endogenous timekeeping. In the\ Drosophila\ circadian clock network, the four pairs of small ventral lateral neurons (sLNvs) serve as main pacemakers. Peptidergic communication via sLNv, which release the key output neuropeptide,\ Pigment Dispersing Factor\ (PDF), has been well characterized. In the absence of PDF, flies become largely arrhythmic, similar to the phenotype associated with the loss of the mammalian circadian peptide, VIP. In contrast, little is known about the role of the synaptic connections that sLNvs form with downstream neurons. Connectomic analyses revealed that despite their role as key pacemaker neurons within the clock network, the sLNvs form few connections with other clock neurons. However, they form strong synaptic connections with a small group of previously uncharacterized neurons, SLP316, which in turn synapse onto dorsal clock neurons. Here, we show that silencing SLP316 neurons via tetanus toxin (TNT) expression shortens the free-running period, whereas hyper-exciting them by expressing the constitutively open Na[+] channel, NaChBac, results in period lengthening. Under light-dark cycles, silencing SLP316 neurons also causes lower daytime activity and higher daytime sleep. Our results revealed that the main postsynaptic partners of the\ Drosophila\ pacemaker neurons are a non-clock neuronal cell type that regulates the timing of sleep and activity.

}, doi = {https://doi.org/10.1101/2025.01.30.635801v1}, author = {Scholz-Carson, E. and Iyer, A. R. and Ewer, J. and Fernandez, Maria P.} } @article {69803, title = {TEMI: Tissue Expansion Mass Spectrometry Imaging}, journal = {Nat Methods}, year = {2025}, month = {2025 Apr 22}, abstract = {

The spatial distribution of diverse biomolecules in multicellular organisms is essential for their physiological functions. High-throughput in situ mapping of biomolecules is crucial for both basic and medical research, and requires high scanning speed, spatial resolution, and chemical sensitivity. Here, we developed a Tissue Expansion method compatible with matrix-assisted laser desorption/ionization Mass spectrometry Imaging (TEMI). TEMI reaches single-cell spatial resolution without sacrificing voxel throughput and enables the profiling of hundreds of biomolecules, including lipids, metabolites, peptides (proteins), and N-glycans. Using TEMI, we mapped the spatial distribution of biomolecules across various mammalian tissues and uncovered metabolic heterogeneity in tumors. TEMI can be easily adapted and broadly applied in biological and medical research, to advance spatial multi-omics profiling.

Preprint:\ 10.1101/2025.02.22.639343

}, doi = {10.1101/2025.02.22.639343}, url = {https://doi.org/ 10.1038/s41592-025-02664-9.}, author = {Zhang, Hua and Ding, Lang and Hu, Amy and Shi, Xudong and Huang, Penghsuan and Lu, Haiyan and Tillberg, Paul W. and Wang, Meng C. and Li, Lingjun} } @article {69802, title = {A theory of rapid behavioral inferences under the pressure of time}, journal = {bioRxiv}, year = {2025}, month = {2025 Mar 03}, abstract = {

To survive, animals must be able quickly infer the state of their surroundings. For example, to successfully escape an approaching predator, prey must quickly estimate the direction of approach from incoming sensory stimuli and guide their behavior accordingly. Such rapid inferences are particularly challenging because the animal has only a brief window of time to gather sensory stimuli, and yet the accuracy of inference is critical for survival. Due to evolutionary pressures, nervous systems have likely evolved effective computational strategies that enable accurate inferences under strong time limitations. Traditionally, the relationship between the speed and accuracy of inference has been described by the {\textquotedblleft}speed-accuracy tradeoff{\textquotedblright} (SAT), which quantifies how the average performance of an ideal observer improves as the observer has more time to collect incoming stimuli. While this trial-averaged description can reasonably account for individual inferences made over long timescales, it does not capture individual inferences on short timescales, when trial-to-trial variability gives rise to diverse patterns of error dynamics. We show that an ideal observer can exploit this single-trial structure by adaptively tracking the dynamics of its belief about the state of the environment, which enables it to speed its own inferences and more reliably track its own error, but also causes it to violate the SAT. We show that these features can be used to improve overall performance during rapid escape. The resulting behavior qualitatively reproduces features of escape behavior in the fruit fly Drosophila melanogaster, whose escapes have presumably been highly optimized by natural selection.

}, doi = {10.1101/2024.08.26.609738}, url = {https://www.biorxiv.org/content/early/2025/03/03/2024.08.26.609738}, author = {Hermundstad, Ann M. and M{\l}ynarski, Wiktor F.} } @article {69616, title = {The tilt illusion arises from an efficient reallocation of neural coding resources at the contextual boundary}, journal = {Proc Natl Acad Sci U S A}, year = {2025}, month = {2025 Apr 29}, abstract = {

The tilt illusion-a bias in the perceived orientation of a center stimulus induced by an oriented surround-illustrates how context shapes visual perception. Although extensively studied for decades, we still lack a comprehensive account of the illusion that connects its behavioral and neural characteristics. Here, we demonstrate that the tilt illusion originates from dynamic changes in neural coding precision induced by the surround context. We simultaneously obtained psychophysical and functional MRI responses from human subjects while they viewed gratings in the absence and presence of an oriented surround and independently extracted sensory encoding precision from their behavioral and neural data. Both measures show that in the absence of an oriented surround, encoding reflects the natural scene statistics of orientation. However, with an oriented surround, encoding precision is significantly increased for stimuli similar to the surround orientation. This local change in encoding is sufficient to predict the behavioral characteristics of the tilt illusion using a Bayesian observer model. The effect of surround modulation increases along the ventral stream and is localized to the portion of the visual cortex with receptive fields at the center-surround boundary. The pattern of change in coding accuracy reflects the surround-conditioned orientation statistics in natural scenes, but cannot be explained by local stimulus configuration. Our results suggest that the tilt illusion naturally emerges from an adaptive coding strategy that efficiently reallocates neural coding resources based on the current stimulus context.

Preprint:\ http://doi.org/10.1101/2024.09.17.613538

}, doi = {10.1073/pnas.2421565122}, url = {https://doi.org/10.1073/pnas.2421565122}, author = {Zhang, Ling-Qi and Mao, Jiang and Aguirre, Geoffrey Karl and Stocker, Alan A} } @article {70220, title = {Time or distance encoding by hippocampal neurons via heterogeneous ramping rates.}, journal = {Nat Commun}, volume = {16}, year = {2025}, month = {2025 Dec 17}, pages = {11083}, abstract = {

To navigate their environments effectively, animals frequently track time elapsed or distance traveled while seeking food and avoiding threats. The hippocampus is implicated in this process, but the neural mechanisms remain unclear. Using virtual reality tasks that require mice to integrate time or distance to collect a reward, we identified two previously unknown functional subpopulations of CA1 pyramidal neurons. Both subpopulations encode time or distance via distinct ramping dynamics. The first subpopulation exhibits a rapid, synchronous rise in activity upon movement-initiated integration. Subsequently, individual neurons ramp down at heterogeneous rates, creating progressively diverging firing rates that encode elapsed time or distance. Closed-loop optogenetic inactivation of somatostatin-positive (SST) interneurons counterintuitively reduced the ramping activity, leading mice to prematurely attempt reward collection, suggesting impaired time/distance estimation. Conversely, the second CA1 subpopulation shows opposite dynamics - an initial rapid suppression followed by a gradual ramp-up. Inactivating parvalbumin-positive (PV) interneurons diminished this initial suppression, resulting in transient attempts to collect reward near integration onset. These findings reveal parallel hippocampal circuits that initiate and maintain time or distance encoding, controlled by PV and SST interneurons, respectively, and provide insights into the neural computations supporting goal-directed navigation.

}, keywords = {Action Potentials, Animals, CA1 Region, Hippocampal, Hippocampus, Interneurons, Male, Mice, Mice, Inbred C57BL, Neurons, Optogenetics, Parvalbumins, Pyramidal Cells, Reward, Somatostatin, Virtual Reality}, issn = {2041-1723}, doi = {10.1038/s41467-025-67038-3}, url = {https://doi.org/10.1038/s41467-025-67038-3}, author = {Heldman, Raphael and Pang, Dongyan and Zhao, Xiaoliang and Mensh, Brett and Wang, Yingxue} } @article {70085, title = {Time-deterministic cryo-optical microscopy.}, journal = {Light Sci Appl}, volume = {14}, year = {2025}, month = {2025 Aug 23}, pages = {275}, abstract = {

Fluorescence microscopy enables the visualization of cellular morphology, molecular distribution, ion distribution, and their dynamic behaviors during biological processes. Enhancing the signal-to-noise ratio (SNR) in fluorescence imaging improves the quantification accuracy and spatial resolution; however, achieving high SNR at fast image acquisition rates, which is often required to observe cellular dynamics, still remains a challenge. In this study, we developed a technique to rapidly freeze biological cells in milliseconds during optical microscopy observation. Compared to chemical fixation, rapid freezing provides rapid immobilization of samples while more effectively preserving the morphology and conditions of cells. This technique combines the advantages of both live-cell and cryofixation microscopy, i.e., temporal dynamics and high SNR snapshots of selected moments, and is demonstrated by fluorescence and Raman microscopy with high spatial resolution and quantification under low temperature conditions. Furthermore, we also demonstrated that intracellular calcium dynamics can be frozen rapidly and visualized using fluorescent ion indicators, suggesting that ion distribution and conformation of the probe molecules can be fixed both spatially and temporally. These results confirmed that our technique can time-deterministically suspend and visualize cellular dynamics while preserving molecular and ionic states, indicating the potential to provide detailed insights into sample dynamics with improved spatial resolution and temporal accuracy in observations.

}, issn = {2047-7538}, doi = {10.1038/s41377-025-01941-8}, url = {https://doi.org/10.1038/s41377-025-01941-8}, author = {Tsuji, Kosuke and Yamanaka, Masahito and Kumamoto, Yasuaki and Tamura, Shoko and Miyamura, Wakana and Kubo, Toshiki and Mizushima, Kenta and Kono, Kakeru and Hirano, Hanae and Shiozaki, Momoko and Zhao, Xiaowei and Xi, Heqi and Sugiura, Kazunori and Fukushima, Shun-Ichi and Kunimoto, Takumi and Tanabe, Yoshino and Nishida, Kentaro and Mochizuki, Kentaro and Harada, Yoshinori and Smith, Nicholas I and Heintzmann, Rainer and Yu, Zhiheng and Wang, Meng C and Nagai, Takeharu and Tanaka, Hideo and Fujita, Katsumasa} } @article {70192, title = {Tissue expansion-enhanced mass-spectrometry imaging decodes biomolecular landscapes.}, journal = {Nat Rev Mol Cell Biol}, year = {2025}, month = {2025 Nov 17}, issn = {1471-0080}, doi = {10.1038/s41580-025-00931-3}, url = {https://doi.org/10.1038/s41580-025-00931-3}, author = {Ding, Lang} } @article {70135, title = {Towards a unified framework for the function of endoplasmic reticulum exit sites.}, journal = {Nat Rev Mol Cell Biol}, year = {2025}, month = {2025 Sep 29}, abstract = {

Endoplasmic reticulum exit sites (ERES) are specialized, ribosome-free ER subdomains that serve as dynamic portals for COPII-mediated export of proteins from the ER. Beyond their role in the secretory pathway, ERES are implicated in diverse processes, including autophagy and the maturation of lipid droplets, highlighting their functional plasticity. ERES integrate cargo load, membrane tension and spatial cues to remodel their architecture and function in real time. This Roadmap synthesizes our current knowledge on the biogenesis, structural diversity and regulatory logic of ERES. We highlight key unanswered questions in the field, particularly concerning how ERES integrate signals to coordinate protein trafficking under varying cellular states. Finally, we propose a multidisciplinary framework - leveraging advances in high-resolution imaging, synthetic reconstitution and computational modelling - to delineate the principles governing the function and plasticity of ERES. Understanding these mechanisms holds significant potential for developing targeted therapeutic strategies in diseases linked to trafficking dysfunction.

}, issn = {1471-0080}, doi = {10.1038/s41580-025-00899-0}, url = {https://doi.org/10.1038/s41580-025-00899-0}, author = {Farhan, Hesso and Raote, Ishier and Campelo, Felix and Ge, Liang and Hirschberg, Koret and Forrester, Alison and Zanetti, Giulia and Lippincott-Schwartz, Jennifer and Pastor-Pareja, Jos{\'e} Carlos and Perez, Franck and Saito, Kota and Malhotra, Vivek} } @article {70030, title = {Transforming descending input into motor output: An analysis of the Drosophila Male Adult Nerve Cord connectome}, journal = {eLife}, year = {2025}, month = {2025 Jul 21}, abstract = {

In most animals, a relatively small number of descending neurons (DNs) connect higher brain centers in the animal{\textquoteright}s head to circuits and motor neurons (MNs) in the nerve cord of the animal{\textquoteright}s body that effect movement of the limbs. To understand how brain signals generate behavior, it is critical to understand how these descending pathways are organized onto the body MNs. In the fly,\ Drosophila melanogaster, MNs controlling muscles in the leg, wing, and other motor systems reside in a ventral nerve cord (VNC), analogous to the mammalian spinal cord. In companion papers, we introduced a densely-reconstructed connectome of the\ Drosophila\ Male Adult Nerve Cord (MANC, (Takemura et al., 2024)), including cell type and developmental lineage annotation (Marin et al., 2024), which provides complete VNC connectivity at synaptic resolution. Here, we present a first look at the organization of the VNC networks connecting DNs to MNs based on this new connectome information. We proofread and curated all DNs and MNs to ensure accuracy and reliability, then systematically matched DN axon terminals and MN dendrites with light microscopy data to link their VNC morphology with their brain inputs or muscle targets. We report both broad organizational patterns of the entire network and fine-scale analysis of selected circuits of interest. We discover that direct DN-MN connections are infrequent and identify communities of intrinsic neurons linked to control of different motor systems, including putative ventral circuits for walking, dorsal circuits for flight steering and power generation, and intermediate circuits in the lower tectulum for coordinated action of wings and legs. Our analysis generates hypotheses for future functional experiments and, together with the MANC connectome, empowers others to investigate these and other circuits of the\ Drosophila\ ventral nerve cord in richer mechanistic detail.

}, doi = {10.7554/elife.96084.2}, url = {http://dx.doi.org/10.7554/eLife.96084.2}, author = {Cheong, Han Sj and Eichler, Katharina and St{\"u}rner, Tomke and Asinof, Samuel K and Champion, Andrew S and Marin, Elizabeth C and Oram, Tess B and Sumathipala, Marissa and Venkatasubramanian, Lalanti and Namiki, Shigehiro and Siwanowicz, Igor and Costa, Marta and Berg, Stuart and Jefferis, Gregory Sxe and Card, Gwyneth M} } @article {70053, title = {Transgene-free generation of mouse post-gastrulation whole embryo models solely from naive ESCs and iPSCs.}, journal = {Cell Stem Cell}, year = {2025}, month = {2025 Aug 06}, abstract = {

The generation of post-gastrulation stem cell-derived mouse embryo models (SEMs) exclusively from naive embryonic stem cells (nESCs) has underscored their ability to give rise to embryonic and extra-embryonic lineages. However, existing protocols for mouse SEMs rely on the separate induction of extra-embryonic lineages and on ectopic expression of transcription factors to induce nESC differentiation into trophectoderm (TE) or primitive endoderm (PrE). Here, we demonstrate that mouse nESCs and naive induced pluripotent stem cells (niPSCs) can be simultaneously co-induced, via signaling pathway modulation, to generate PrE and TE extra-embryonic cells that self-organize into embryonic day (E) 8.5-E8.75 transgene-free (TF) SEMs. We also devised an alternative condition (AC) naive media that in vitro stabilizes TF-SEM-competent OCT4+/NANOG+ nESC colonies that co-express antagonistic CDX2 and/or GATA6 extra-embryonic fate master regulators and self-renew while remaining poised for TE and PrE differentiation, respectively. These findings improve mouse SEM strategies and shed light on amplifying an inherent and dormant extra-embryonic plasticity of mouse naive pluripotent cells in vitro.

}, issn = {1875-9777}, doi = {10.1016/j.stem.2025.07.005}, url = {https://doi.org/10.1016/j.stem.2025.07.005}, author = {Yilmaz, Alperen and Gurhan, Gulben and Comar, Mehmet-Yunus and Viukov, Sergey and Serfaty, Inbal and Gayretli, Mert and Golenchenko, Sergey and Lokshtanov, Dmitry and Ashouokhi, Shahd and Polanco, Angel and Berlad, Idan and Ha, Tae-Won and Aguilera-Castrejon, Alejandro and Tarazi, Shadi and Cohen, Marina and Livnat, Nir and Kumar, Komal and Cholakkal, Hisham and Levy, Nathan and Yosef, Nir and Khatib, Nizar and Kakun, Reli Rachel and Kedmi, Merav and Nachman, Inbal Bolocan and Keren-Shaul, Hadas and Addadi, Yoseph and Orenbuch, Ayelet-Hashahar and Korovin, Karina and Molchadsky, Alina and Hochedlinger, Konrad and Gafni, Ohad and Maza, Itay and Novershtern, Noa and Oldak, Bernardo and Hanna, Jacob H} } @article {69347, title = {A tunable and versatile chemogenetic near infrared fluorescent reporter}, journal = {Nat Commun}, year = {2025}, month = {2025 Mar 16}, abstract = {

Near-infrared (NIR) fluorescent reporters open interesting perspectives for multiplexed imaging with higher contrast and depth using less toxic light. Here, we propose nirFAST, a small (14 kDa) chemogenetic NIR fluorescent reporter, displaying higher cellular brightness compared to top-performing NIR fluorescent proteins. nirFAST binds and stabilizes the fluorescent state of synthetic cell permeant fluorogenic chromophores (so-called fluorogens), otherwise dark when free. nirFAST displays tunable NIR, far-red or red emission through change of fluorogen. nirFAST allows imaging and spectral multiplexing in live cultured mammalian cells, chicken embryo tissues and zebrafish larvae. Its suitability for stimulated emission depletion nanoscopy enabled protein imaging with subdiffraction resolution in live cells. nirFAST enabled the design of a two-color cell cycle indicator for monitoring the different phases of the cell cycle. Finally, bisection of nirFAST allowed the design of a chemically induced dimerization technology with NIR fluorescence readout, enabling the control and visualization of protein proximity.

bioRxiv preprint:\ https://doi.org/10.1101/2024.04.05.588310

}, doi = {10.1038/s41467-025-58017-9}, url = {https://doi.org/10.1038/s41467-025-58017-9}, author = {Lina El Hajji and Benjamin Bunel and Octave Joliot and Chenge Li and Alison G. Tebo and Christine Rampon and Michel Volovitch and Evelyne Fischer and Nicolas Pietrancosta and Franck Perez and Xavier Morin and Sophie Vriz and Arnaud Gautier} } @article {70133, title = {Ultra-high-density Neuropixels probes improve detection and identification in neuronal recordings.}, journal = {Neuron}, volume = {113}, year = {2025}, month = {2025 Dec 3}, abstract = {

To understand the neural basis of behavior, it is essential to sensitively and accurately measure neural activity at single-neuron and single-spike resolution. Extracellular electrophysiology delivers this, but it has biases in the neurons it detects and it imperfectly resolves their action potentials. To minimize these limitations, we developed a silicon probe with much smaller and denser recording sites than previous designs, called Neuropixels Ultra (NP Ultra). Using NP Ultra, neuronal yield in mouse visual cortex recordings increased by more than 2-fold. With ultra-high spatial resolution, we discovered that a feature of extracellular waveforms, the spatial extent or "footprint," distinguished axonal from somatic recordings. In addition, three genetically identified cortical cell types could be discriminated from one another with \~{}80\% accuracy and from other neurons with \~{}85\% accuracy. NP Ultra improves yield, detection of subcellular compartments, and cell type identification to enable a more powerful dissection of neural circuit activity during behavior.

bioRxiv preprint: doi.org/10.1101/2023.08.23.554527

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2025.08.030}, url = {https://doi.org/10.1016/j.neuron.2025.08.030}, author = {Ye, Zhiwen and Shelton, Andrew M and Shaker, Jordan R and Boussard, Julien and Colonell, Jennifer and Birman, Daniel and Manavi, Sahar and Chen, Susu and Windolf, Charlie and Hurwitz, Cole and Yu, Han and Namima, Tomoyuki and Pedraja, Federico and Weiss, Shahaf and Raducanu, Bogdan C and Ness, Torbj{\o}rn V and Jia, Xiaoxuan and Mastroberardino, Giulia and Rossi, L Federico and Carandini, Matteo and H{\"a}usser, Michael and Einevoll, Gaute T and Laurent, Gilles and Sawtell, Nathaniel B and Bair, Wyeth and Pasupathy, Anitha and Mora Lopez, Carolina and Dutta, Barundeb and Paninski, Liam and Siegle, Joshua H and Koch, Christof and Olsen, Shawn R and Harris, Timothy D and Steinmetz, Nicholas A} } @article {70212, title = {Uncertainty quantification for connectomics.}, journal = {Nat Methods}, volume = {22}, year = {2025}, month = {2025 Dec 08}, pages = {2484-2486}, abstract = {

No abstract available.

}, issn = {1548-7105}, doi = {10.1038/s41592-025-02945-3}, url = {https://doi.org/10.1038/s41592-025-02945-3}, author = {Funke, Jan} } @article {69914, title = {Unlocking in vivo metabolic insights with vibrational microscopy.}, journal = {Nat Methods}, volume = {22}, year = {2025}, month = {2025 May 13}, pages = {886-889}, abstract = {

No abstract available.

}, issn = {1548-7105}, doi = {10.1038/s41592-025-02616-3}, url = {https://doi.org/10.1038/s41592-025-02616-3}, author = {Chen, Tao and Savini, Marzia and Wang, Meng C} } @article {69913, title = {Unlocking in vivo metabolic insights with vibrational microscopy.}, journal = {Nat Methods}, volume = {22}, year = {2025}, month = {2025 May 13}, pages = {886-889}, issn = {1548-7105}, doi = {10.1038/s41592-025-02616-3}, url = {https://doi.org/10.1038/s41592-025-02616-3}, author = {Chen, Tao and Savini, Marzia and Wang, Meng C} } @article {69228, title = {Unsupervised pretraining in biological neural networks}, journal = {Nature}, year = {2025}, month = {2025 Jun 18}, abstract = {

Representation learning in neural networks may be implemented with supervised or unsupervised algorithms, distinguished by the availability of instruction. In the sensory cortex, perceptual learning drives neural plasticity1-13, but it is not known whether this is due to supervised or unsupervised learning. Here we recorded populations of up to 90,000 neurons simultaneously from the primary visual cortex (V1) and higher visual areas (HVAs) while mice learned multiple tasks, as well as during unrewarded exposure to the same stimuli. Similar to previous studies, we found that neural changes in task mice were correlated with their behavioural learning. However, the neural changes were mostly replicated in mice with unrewarded exposure, suggesting that the changes were in fact due to unsupervised learning. The neural plasticity was highest in the medial HVAs and obeyed visual, rather than spatial, learning rules. In task mice only, we found a ramping reward-prediction signal in anterior HVAs, potentially involved in supervised learning. Our neural results predict that unsupervised learning may accelerate subsequent task learning, a prediction that we validated with behavioural experiments.

Preprint:\ https://www.biorxiv.org/content/early/2024/02/27/2024.02.25.581990

}, doi = {10.1038/s41586-025-09180-y}, url = {https://doi.org/10.1038/s41586-025-09180-y}, author = {Lin Zhong and Scott Baptista and Rachel Gattoni and Jon Arnold and Daniel Flickinger and Carsen Stringer and Marius Pachitariu} } @article {70123, title = {An updated catalogue of split-GAL4 driver lines for descending neurons in Drosophila melanogaster}, journal = {eLife}, year = {2025}, month = {2025 Sept 19}, abstract = {

Descending neurons (DNs) occupy a key position in the sensorimotor hierarchy, conveying signals from the brain to the rest of the body below the neck. In\ Drosophila melanogaster\ flies, approximately 480 DN cell types have been described from electron-microscopy image datasets. Genetic access to these cell types is crucial for further investigation of their role in generating behaviour. We previously conducted the first large-scale survey of\ Drosophila melanogaster\ DNs, describing 98 unique cell types from light microscopy and generating cell-type-specific split-Gal4 driver lines for 65 of them. Here, we extend our previous work, describing the morphology of 146 additional DN types from light microscopy, bringing the total number DN types identified in light microscopy datasets to 244, or roughly 50\% of all DN types. In addition, we produced 500 new sparse split-Gal4 driver lines and compiled a list of previously published DN lines from the literature for a combined list of 806 split-Gal4 driver lines targeting 190 DN types.

}, doi = {10.7554/elife.107450.1}, url = {http://dx.doi.org/10.7554/eLife.107450.1}, author = {Zung, Jessica L and Namiki, Shigehiro and Meissner, Geoffrey W and Cheong, Han Sj and Costa, Marta and Eichler, Katharina and St{\"u}rner, Tomke and Jefferis, Gregory Sxe and Managan, Claire and Korff, Wyatt and Card, Gwyneth M} } @article {69790, title = {An updated catalogue of split-GAL4 driver lines for descending neurons in Drosophila melanogaster}, journal = {bioRxiv}, year = {2025}, month = {2025 Feb 24}, abstract = {

Descending neurons (DNs) occupy a key position in the sensorimotor hierarchy, conveying signals from the brain to the rest of the body below the neck. In Drosophila melanogaster flies, approximately 480 DN cell types have been described from electron-microscopy image datasets. Genetic access to these cell types is crucial for further investigation of their role in generating behaviour. We previously conducted the first large-scale survey of Drosophila melanogaster DNs, describing 98 unique cell types from light microscopy and generating cell-type-specific split-Gal4 driver lines for 65 of them. Here, we extend our previous work, describing the morphology of 137 additional DN types from light microscopy, bringing the total number DN types identified in light microscopy datasets to 235, or nearly 50\%. In addition, we produced 500 new sparse split-Gal4 driver lines and compiled a list of previously published DN lines from the literature for a combined list of 738 split-Gal4 driver lines targeting 171 DN types.

}, doi = {10.1101/2025.02.22.639679}, url = {https://www.biorxiv.org/content/early/2025/02/24/2025.02.22.639679}, author = {Zung, Jessica L. and Namiki, Shigehiro and Meissner, Geoffrey W. and Costa, Marta and Eichler, Katharina and St{\"u}rner, Tomke and Jefferis, Gregory S.X.E. and Managan, Claire and FlyLight Project Team and Korff, Wyatt and Card, Gwyneth M.} } @article {69824, title = {Vagal sensory circuits of the lower airway in respiratory physiology: Insights from neuronal diversity.}, journal = {Curr Opin Neurobiol}, volume = {92}, year = {2025}, month = {2025 Mar 17}, pages = {103000}, abstract = {

Sensory neurons innervating the lower airway provide essential feedback information that regulates respiratory physiology. These neurons synapse with second-order neurons in the central nervous system, which project directly or indirectly to the respiratory and autonomic centers. Both primary sensory neurons and second-order neurons within these circuits exhibit significant heterogeneity, and the precise roles of individual neuronal subtypes in coding the airway{\textquoteright}s internal states and modulating respiratory and autonomic outputs remain incompletely understood. In this review, we summarize recent advances in understanding the neuronal diversity along sensory circuits of the lower airway and their physiological functions. We also highlight the challenges in elucidating the roles of specific neuronal subtypes due to the extensive molecular and anatomical diversity among these neurons. Improving targeting specificity for neuronal manipulation, combined with the development of a comprehensive connectivity map, will be critical for revealing the coding and wiring logics that underlie the precise control of respiratory physiology.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2025.103000}, author = {Li, Jie and Liu, Yin} } @article {69812, title = {Vimentin filament transport and organization revealed by single-particle tracking and 3D FIB-SEM}, journal = {Journal of Cell Biology}, volume = {224}, year = {2025}, month = {2025 Apr 03}, pages = {e202406054}, abstract = {

Vimentin intermediate filaments (VIFs) form complex, tightly packed networks; due to this density, traditional imaging approaches cannot discern single-filament behavior. To address this, we developed and validated a sparse vimentin-SunTag labeling strategy, enabling single-particle tracking of individual VIFs and providing a sensitive, unbiased, and quantitative method for measuring global VIF motility. Using this approach, we define the steady-state VIF motility rate, showing a constant \~{}8\% of VIFs undergo directed microtubule-based motion irrespective of subcellular location or local filament density. Significantly, our single-particle tracking approach revealed uncorrelated motion of individual VIFs within bundles, an observation seemingly at odds with conventional models of tightly cross-linked bundles. To address this, we acquired high-resolution focused ion beam scanning electron microscopy volumes of vitreously frozen cells and reconstructed three-dimensional VIF bundles, finding that they form only loosely organized, semi-coherent structures from which single VIFs frequently emerge to locally engage neighboring microtubules. Overall, this work demonstrates single VIF dynamics and organization in the cellular milieu for the first time.

bioRxiv Preprint:\ https://doi.org/10.1101/2024.06.10.598346

}, issn = {0021-9525}, doi = {10.1083/jcb.202406054}, url = {https://doi.org/10.1083/jcb.202406054}, author = {Renganathan, Bhuvanasundar and Moore, Andrew S. and Yeo, Wei-Hong and Petruncio, Alyson and Ackerman, David and Weigel, Aubrey V. and Team, The CellMap and Pasolli, H. Amalia and Xu, C. Shan and Shtengel, Gleb and Hess, Harald F. and Serpinskaya, Anna S. and Zhang, Hao F. and Lippincott-Schwartz, Jennifer and Gelfand, Vladimir I.} } @article {70049, title = {Vimentin intermediate filaments as structural and mechanical coordinators of mesenchymal cells.}, journal = {Nat Cell Biol}, year = {2025}, month = {2025 Aug 05}, abstract = {

Vimentin is a cytoskeletal intermediate filament protein that governs the form and function of mesenchymal cells, although the mechanistic details have been poorly understood. Here we highlight recent findings that reveal the diverse role of vimentin in dynamically organizing intracellular architecture and enhancing mechanical resilience. The exceptional deformability of vimentin can now be understood from its high-resolution three-dimensional structure resolved using cryo-electron microscopy. Vimentin also organizes the motion and positioning of numerous organelles, including mitochondria and the nucleus. Furthermore, it synergizes with the actin cytoskeleton to protect cells from extreme mechanical deformations. Finally, vimentin expression in epithelial-mesenchymal transitions has a functional role in tumour invasion analogous to embryonic development and wound healing. These recent developments emphasize the importance of understanding the multifaceted roles of vimentin intermediate filaments in human health and disease.

}, issn = {1476-4679}, doi = {10.1038/s41556-025-01713-x}, url = {https://doi.org/10.1038/s41556-025-01713-x}, author = {Guo, Ming and Wong, Ian Y and Moore, Andrew S and Medalia, Ohad and Lippincott-Schwartz, Jennifer and Weitz, David A and Goldman, Robert D} } @article {69614, title = {Voltage imaging reveals circuit computations in the raphe underlying serotonin-mediated motor vigor learning}, journal = {Neuron}, year = {2025}, month = {2025 Jun 06}, abstract = {

As animals adapt to new situations, neuromodulation is a potent way to alter behavior, yet mechanisms by which neuromodulatory nuclei compute during behavior are underexplored. The serotonergic raphe supports motor learning in larval zebrafish by visually detecting distance traveled during swims, encoding action effectiveness, and modulating motor vigor. We found that swimming opens a gate for visual input to cause spiking in serotonergic neurons, enabling encoding of action outcomes and filtering out learning-irrelevant visual signals. Using light-sheet microscopy, voltage sensors, and neurotransmitter/modulator sensors, we tracked millisecond-timescale neuronal input-output computations during behavior. Swim commands initially inhibited serotonergic neurons via GABA, closing the gate to spiking. Immediately after, the gate briefly opened: voltage increased consistent with post-inhibitory rebound, allowing swim-induced visual motion to evoke firing through glutamate, triggering serotonin secretion and modulating motor vigor. Ablating GABAergic neurons impaired raphe coding and motor learning. Thus, serotonergic neuromodulation arises from action-outcome coincidence detection within the raphe, suggesting the existence of similarly fast and precise circuit computations across neuromodulatory nuclei.

Preprint:\ https://doi.org/10.1101/2024.09.15.613083

}, doi = {10.1016/j.neuron.2025.05.017}, url = {https://doi.org/10.1016/j.neuron.2025.05.017}, author = {Kawashima, Takashi and Wei, Ziqiang and Haruvi, Ravid and Shainer, Inbal and Narayan, Sujatha and Baier, Herwig and Ahrens, Misha B} } @article {69792, title = {Volumetric imaging of the 3D orientation of cellular structures with a polarized fluorescence light-sheet microscope.}, journal = {Proc Natl Acad Sci }, volume = {122}, year = {2025}, month = {2025 Feb 25}, pages = {e2406679122}, abstract = {

Polarized fluorescence microscopy is a valuable tool for measuring molecular orientations in biological samples, but techniques for recovering three-dimensional orientations and positions of fluorescent ensembles are limited. We report a polarized dual-view light-sheet system for determining the diffraction-limited three-dimensional distribution of the orientations and positions of ensembles of fluorescent dipoles that label biological structures. We share a set of visualization, histogram, and profiling tools for interpreting these positions and orientations. We model the distributions based on the polarization-dependent efficiency of excitation and detection of emitted fluorescence, using coarse-grained representations we call orientation distribution functions (ODFs). We apply ODFs to create physics-informed models of image formation with spatio-angular point-spread and transfer functions. We use theory and experiment to conclude that light-sheet tilting is a necessary part of our design for recovering all three-dimensional orientations. We use our system to extend known two-dimensional results to three dimensions in FM1-43-labeled giant unilamellar vesicles, fast-scarlet-labeled cellulose in xylem cells, and phalloidin-labeled actin in U2OS cells. Additionally, we observe phalloidin-labeled actin in mouse fibroblasts grown on grids of labeled nanowires and identify correlations between local actin alignment and global cell-scale orientation, indicating cellular coordination across length scales.

}, keywords = {Actins, Animals, Humans, Imaging, Three-Dimensional, Mice, Microscopy, Fluorescence, Microscopy, Polarization, Xylem}, issn = {1091-6490}, doi = {10.1073/pnas.2406679122}, author = {Chandler, Talon and Guo, Min and Su, Yijun and Chen, Jiji and Wu, Yicong and Liu, Junyu and Agashe, Atharva and Fischer, Robert S and Mehta, Shalin B and Kumar, Abhishek and Baskin, Tobias I and Jaumouill{\'e}, Valentin and Liu, Huafeng and Swaminathan, Vinay and Nain, Amrinder S and Oldenbourg, Rudolf and La Riviere, Patrick J and Shroff, Hari} } @article {69290, title = {Whole-body simulation of realistic fruit fly locomotion with deep reinforcement learning}, journal = {Nature}, volume = {643}, year = {2025}, month = {2025 Jul}, abstract = {

The body of an animal influences how its nervous system generates behavior1. Accurately modeling the neural control of sensorimotor behavior requires an anatomically detailed biomechanical representation of the body. Here, we introduce a whole-body model of the fruit fly Drosophila melanogaster in a physics simulator. Designed as a general-purpose framework, our model enables the simulation of diverse fly behaviors, including both terrestrial and aerial locomotion. We validate its versatility by replicating realistic walking and flight behaviors. To support these behaviors, we develop new phenomenological models for fluid and adhesion forces. Using data-driven, end-to-end reinforcement learning\ we train neural network controllers capable of generating naturalistic locomotion along complex trajectories in response to high-level steering commands. Additionally, we show the use of visual sensors and hierarchical motor control, training a high-level controller to reuse a pre-trained low-level flight controller to perform visually guided flight tasks. Our model serves as an open-source platform for studying the neural control of sensorimotor behavior in an embodied context.

Preprint:\ www.biorxiv.org/content/early/2024/03/14/2024.03.11.584515

}, doi = {10.1038/s41586-025-09029-4}, url = {https://doi.org/10.1038/s41586-025-09029-4}, author = {Roman Vaxenburg and Igor Siwanowicz and Josh Merel and Alice A Robie and Carmen Morrow and Guido Novati and Zinovia Stefanidi and Gwyneth M Card and Michael B Reiser and Matthew M Botvinick and Kristin M Branson and Yuval Tassa and Srinivas C Turaga} } @article {69839, title = {Whole-brain, all-optical interrogation of neuronal dynamics underlying gut interoception in zebrafish}, journal = {bioRxiv}, year = {2025}, month = {2025 Mar 30}, abstract = {

Internal signals from the body and external signals from the environment are processed by brain-wide circuits to guide behavior. However, the complete brain-wide circuit activity underlying interoception{\textemdash}the perception of bodily signals{\textemdash}and its interactions with sensorimotor circuits remain unclear due to technical barriers to accessing whole-brain activity at the cellular level during organ physiology perturbations. We developed an all-optical system for whole-brain neuronal imaging in behaving larval zebrafish during optical uncaging of gut-targeted nutrients and visuo-motor stimulation. Widespread neural activity throughout the brain encoded nutrient delivery, unfolding on multiple timescales across many specific peripheral and central regions. Evoked activity depended on delivery location and occurred with amino acids and D-glucose, but not L-glucose. Many gut-sensitive neurons also responded to swimming and visual stimuli, with brainstem areas primarily integrating gut and motor signals and midbrain regions integrating gut and visual signals. This platform links body-brain communication studies to brain-wide neural computation in awake, behaving vertebrates.

}, doi = {10.1101/2025.03.26.645305}, url = {https://www.biorxiv.org/content/early/2025/03/30/2025.03.26.645305}, author = {Chen, Weiyu and James, Ben and Ruetten, Virginia M. S. and Banala, Sambashiva and Wei, Ziqiang and Fleishman, Greg and Rubinov, Mikail and Fishman, Mark C. and Engert, Florian and Lavis, Luke D. and Fitzgerald, James E. and Ahrens, Misha B.} } @article {69855, title = {Wnt/β-catenin signalling assists cell fate decision making in the early mouse embryo}, journal = {bioRxiv}, year = {2025}, month = {2025 Apr 15}, abstract = {

Cell fate choice is a key event happening during preimplantation mouse development. From embryonic day 3.5 (E3.5) to E4.5, the inner cell mass (ICM) differentiates into epiblast (Epi, NANOG expressing cells) and primitive endoderm (PrE, GATA6, SOX17 and/or GATA4 expressing cells). The mechanism by which ICM cells differentiate into Epi cells and PrE cells remains partially unknown. FGF/ERK has been proposed as the main signalling pathway for this event, but it does not explain co-expression of NANOG and GAT6 or how the cell fate choice is initiated.

In this study, we investigate whether Wnt/β-catenin signalling also plays a role. To this end, we use two\ in vitro\ models based on inducible GATA6 expression: one in 2D, and another in 3D, namely ICM organoids. By combining these\ in vitro\ models with\ in vivo\ mouse embryos, chemical and classical genetics, and quantitative 3D immunofluorescence analyses, we propose a dual role for Wnt/β-catenin signalling.

We find that β-catenin, acting alongside FGF/ERK signalling, helps to guide the cell fate choice towards PrE. Additionally, by regulating GATA6 and GATA4 stability, β-catenin further facilitates this choice. To summarise, we observe that pathway activation promotes PrE differentiation, while its inhibition stalls it.

SUMMARY STATEMENT\ Wnt/β-catenin signalling promotes PrE fate in mouse preimplantation embryos.

}, doi = {10.1101/2025.04.09.647220}, url = {https://www.biorxiv.org/content/early/2025/04/15/2025.04.09.647220}, author = {Lilao-Garz{\'o}n, Joaquin and Corujo-Simon, Elena and Vinyoles, Meritxell and Fischer, Sabine C. and Guill{\'e}n, Jos{\'e} and Balayo, Tina and Mu{\~n}oz-Descalzo, Silvia} } @article {69601, title = {3D nanoscale architecture of the respiratory epithelium reveals motile cilia-rootlets-mitochondria axis of communication}, journal = {bioRxiv}, year = {2024}, month = {2024 Sep 08}, abstract = {

A major frontier in single cell biology is decoding how transcriptional states result in cellular-level architectural changes, ultimately driving function. A remarkable example of this cellular remodelling program is the differentiation of airway stem cells into the human respiratory multiciliated epithelium, a tissue barrier protecting against bacteria, viruses and particulate matter. Here, we present the first isotropic three-dimensional map of the airway epithelium at the nanometre scale unveiling the coordinated changes in cellular organisation, organelle topology and contacts, occurring during multiciliogenesis. This analysis led us to discover a cellular mechanism of communication whereby motile cilia relay mechanical information to mitochondria through striated cytoskeletal fibres, the rootlets, to promote effective ciliary motility and ATP generation. Altogether, this study integrates nanometre-scale structural, functional and dynamic insights to elucidate fundamental mechanisms responsible for airway defence.

}, doi = {10.1101/2024.09.08.611854}, url = {https://www.doi.org/10.1101/2024.09.08.611854}, author = {Vijayakumaran, Aaran and Godbehere, Christopher and Abuammar, Analle and Breusegem, Sophia Y. and Hurst, Leah R. and Morone, Nobuhiro and Llodra, Jaime and Dalbay, Melis T. and Tanvir, Niaj M. and MacLellan-Gibson, K. and O{\textquoteright}Callaghan, Chris and Lorentzen, Esben and , and , and Murray, Andrew J. and Narayan, Kedar and Mennella, Vito} } @article {69594, title = {Activity of nested neural circuits drives different courtship songs in Drosophila.}, journal = {Nat Neurosci}, year = {2024}, month = {2024 Aug 28}, abstract = {

Motor systems implement diverse motor programs to pattern behavioral sequences, yet how different motor actions are controlled on a moment-by-moment basis remains unclear. Here, we investigated the neural circuit mechanisms underlying the control of distinct courtship songs in Drosophila. Courting males rapidly alternate between two types of song: pulse and sine. By recording calcium signals in the ventral nerve cord in singing flies, we found that one neural population is active during both songs, whereas an expanded neural population, which includes neurons from the first population, is active during pulse song. Brain recordings showed that this nested activation pattern is present in two descending pathways required for singing. Connectomic analysis reveals that these two descending pathways provide structured input to ventral nerve cord neurons in a manner consistent with their activation patterns. These results suggest that nested premotor circuit activity, directed by distinct descending signals, enables rapid switching between motor actions.

}, issn = {1546-1726}, doi = {10.1038/s41593-024-01738-9}, url = {https://doi.org/10.1038/s41593-024-01738-9}, author = {Shiozaki, Hiroshi M and Wang, Kaiyu and Lillvis, Joshua L and Xu, Min and Dickson, Barry J and Stern, David L} } @article {69424, title = {Adaptive optical third-harmonic generation microscopy for in vivo imaging of tissues}, journal = {bioRxiv}, year = {2024}, month = {2024 May 05}, abstract = {

Third-harmonic generation microscopy is a powerful label-free nonlinear imaging technique, providing essential information about structural characteristics of cells and tissues without requiring external labelling agents. In this work, we integrated a recently developed compact adaptive optics module into a third-harmonic generation microscope, to measure and correct for optical aberrations in complex tissues. Taking advantage of the high sensitivity of the third-harmonic generation process to material interfaces and thin membranes, along with the 1,300-nm excitation wavelength used here, our adaptive optical third-harmonic generation microscope enabled high-resolution in vivo imaging within highly scattering biological model systems. Examples include imaging of myelinated axons and vascular structures within the mouse spinal cord and deep cortical layers of the mouse brain, along with imaging of key anatomical features in the roots of the model plant Brachypodium distachyon. In all instances, aberration correction led to significant enhancements in image quality.

}, doi = {10.1101/2024.05.02.592275}, url = {https://www.biorxiv.org/content/early/2024/05/05/2024.05.02.592275}, author = {Cristina Rodr{\'\i}guez and Daisong Pan and Ryan G. Natan and Manuel A. Mohr and Max Miao and Xiaoke Chen and Trent R. Northen and John P. Vogel and Na Ji} } @article {69482, title = {Aging atlas reveals cell-type-specific effects of pro-longevity strategies.}, journal = {Nat Aging}, year = {2024}, month = {2024 May 30}, abstract = {

Organismal aging involves functional declines in both somatic and reproductive tissues. Multiple strategies have been discovered to extend lifespan across species. However, how age-related molecular changes differ among various tissues and how those lifespan-extending strategies slow tissue aging in distinct manners remain unclear. Here we generated the transcriptomic Cell Atlas of Worm Aging (CAWA, http://mengwanglab.org/atlas ) of wild-type and long-lived strains. We discovered cell-specific, age-related molecular and functional signatures across all somatic and germ cell types. We developed transcriptomic aging clocks for different tissues and quantitatively determined how three different pro-longevity strategies slow tissue aging distinctively. Furthermore, through genome-wide profiling of alternative polyadenylation (APA) events in different tissues, we discovered cell-type-specific APA changes during aging and revealed how these changes are differentially affected by the pro-longevity strategies. Together, this study offers fundamental molecular insights into both somatic and reproductive aging and provides a valuable resource for in-depth understanding of the diversity of pro-longevity mechanisms.

}, issn = {2662-8465}, doi = {10.1038/s43587-024-00631-1}, author = {Gao, Shihong Max and Qi, Yanyan and Zhang, Qinghao and Guan, Youchen and Lee, Yi-Tang and Ding, Lang and Wang, Lihua and Mohammed, Aaron S and Li, Hongjie and Fu, Yusi and Wang, Meng C} } @article {69642, title = {All-optical reporting of inhibitory receptor driving force in the nervous system}, journal = {Nat Commun}, volume = {15}, year = {2024}, month = {2024 Oct 16}, pages = {8913}, abstract = {

Ionic driving forces provide the net electromotive force for ion movement across receptors, channels, and transporters, and are a fundamental property of all cells. In the nervous system, fast synaptic inhibition is mediated by chloride permeable GABA and glycine receptors, and single-cell intracellular recordings have been the only method for estimating driving forces across these receptors (DF). Here we present a tool for quantifying inhibitory receptor driving force named ORCHID: all-Optical Reporting of CHloride Ion Driving force. We demonstrate ORCHID{\textquoteright}s ability to provide accurate, high-throughput measurements of resting and dynamic DF from genetically targeted cell types over multiple timescales. ORCHID confirms theoretical predictions about the biophysical mechanisms that establish DF, reveals differences in DF between neurons and astrocytes, and affords the first in vivo measurements of intact DF. This work extends our understanding of inhibitory synaptic transmission and demonstrates the potential for all-optical methods to assess ionic driving forces.

}, keywords = {Animals, Astrocytes, Chlorides, Humans, Male, Mice, Neurons, Receptors, GABA-A, Receptors, Glycine, Synaptic Transmission}, issn = {2041-1723}, doi = {10.1038/s41467-024-53074-y}, url = {https://doi.org/10.1038/s41467-024-53074-y}, author = {Selfe, Joshua S and Steyn, Teresa J S and Shorer, Eran F and Burman, Richard J and D{\"u}sterwald, Kira M and Kraitzick, Ariel Z and Abdelfattah, Ahmed S and Schreiter, Eric R and Newey, Sarah E and Akerman, Colin J and Raimondo, Joseph V} } @article {69315, title = {Altruistic feeding and cell-cell signaling during bacterial differentiation actively enhance phenotypic heterogeneity}, journal = {Sci Adv}, volume = {10}, year = {2024}, month = {2024 Oct 18}, pages = {eadq0791}, abstract = {

Starvation triggers bacterial spore formation, a committed differentiation program that transforms a vegetative cell into a dormant spore. Cells in a population enter sporulation nonuniformly to secure against the possibility that favorable growth conditions, which put sporulation-committed cells at a disadvantage, may resume. This heterogeneous behavior is initiated by a passive mechanism: stochastic activation of a master transcriptional regulator. Here, we identify a cell-cell communication pathway containing the proteins ShfA (YabQ) and ShfP (YvnB) that actively promotes phenotypic heterogeneity, wherein Bacillus subtilis cells that start sporulating early use a calcineurin-like phosphoesterase to release glycerol, which simultaneously acts as a signaling molecule and a nutrient to delay nonsporulating cells from entering sporulation. This produced a more diverse population that was better poised to exploit a sudden influx of nutrients compared to those generating heterogeneity via stochastic gene expression alone. Although conflict systems are prevalent among microbes, genetically encoded cooperative behavior in unicellular organisms can evidently also boost inclusive fitness.

}, doi = {10.1126/sciadv.adq0791}, url = {https://doi.org/10.1126/sciadv.adq0791}, author = {Taylor B. Updegrove and Thomas Delerue and V. Anantharaman and Hyomoon Cho and Carissa Chan and Thomas Nipper and Hyoyoung Choo-Wosoba and Lisa Jenkins and Lixia Zhang and Yijun Su and Hari Shroff and Jiji Chen and Carole Bewley and L. Aravind and Kumaran S Ramamurthi} } @article {69371, title = {Amino acid transporter SLC7A5 regulates cell proliferation and secretary cell differentiation and distribution in the mouse intestine}, journal = {Int J Biol Sci}, volume = {20}, year = {2024}, month = {2024 Mar 25}, pages = {2187-2201}, abstract = {

The intestine is critical for not only processing nutrients but also protecting the organism from the environment. These functions are mainly carried out by the epithelium, which is constantly being self-renewed. Many genes and pathways can influence intestinal epithelial cell proliferation. Among them is mTORC1, whose activation increases cell proliferation. Here, we report the first intestinal epithelial cell (IEC)-specific knockout () of an amino acid transporter capable of activating mTORC1. We show that the transporter, SLC7A5, is highly expressed in mouse intestinal crypt and reduces mTORC1 signaling. Surprisingly, adult intestinal crypts have increased cell proliferation but reduced mature Paneth cells. Goblet cells, the other major secretory cell type in the small intestine, are increased in the crypts but reduced in the villi. Analyses with scRNA-seq and electron microscopy have revealed dedifferentiation of Paneth cells in mice, leading to markedly reduced secretory granules with little effect on Paneth cell number. Thus, SLC7A5 likely regulates secretory cell differentiation to affect stem cell niche and indirectly regulate cell proliferation.

}, keywords = {Amino Acid Transport Systems, Animals, Cell Differentiation, Cell Proliferation, Large Neutral Amino Acid-Transporter 1, Mechanistic Target of Rapamycin Complex 1, Mice}, issn = {1449-2288}, doi = {10.7150/ijbs.94297}, author = {Bao, Lingyu and Fu, Liezhen and Su, Yijun and Chen, Zuojia and Peng, Zhaoyi and Sun, Lulu and Gonzalez, Frank J and Wu, Chuan and Zhang, Hongen and Shi, Bingyin and Shi, Yun-Bo} } @article {69668, title = {Analysis methods for large-scale neuronal recordings.}, journal = {Science}, volume = {386}, year = {2024}, month = {2024 Nov 08}, pages = {eadp7429}, abstract = {

Simultaneous recordings from hundreds or thousands of neurons are becoming routine because of innovations in instrumentation, molecular tools, and data processing software. Such recordings can be analyzed with data science methods, but it is not immediately clear what methods to use or how to adapt them for neuroscience applications. We review, categorize, and illustrate diverse analysis methods for neural population recordings and describe how these methods have been used to make progress on longstanding questions in neuroscience. We review a variety of approaches, ranging from the mathematically simple to the complex, from exploratory to hypothesis-driven, and from recently developed to more established methods. We also illustrate some of the common statistical pitfalls in analyzing large-scale neural data.

}, keywords = {Action Potentials, Animals, Humans, Models, Neurological, Neurons, Neurosciences, Software}, issn = {1095-9203}, doi = {10.1126/science.adp7429}, author = {Stringer, Carsen and Pachitariu, Marius} } @article {69455, title = {Analysis of developmental gene expression using smFISH and in silico staging of C. elegans embryos}, journal = {bioRxiv}, year = {2024}, month = {2024 May 16}, abstract = {

Regulation of transcription during embryogenesis is key to development and differentiation. To study transcript expression throughout Caenorhabditis elegans embryogenesis at single-molecule resolution, we developed a high-throughput single-molecule fluorescence in situ hybridization (smFISH) method that relies on computational methods to developmentally stage embryos and quantify individual mRNA molecules in single embryos. We applied our system to sdc-2, a zygotically transcribed gene essential for hermaphrodite development and dosage compensation. We found that sdc-2 is rapidly activated during early embryogenesis by increasing both the number of mRNAs produced per transcription site and the frequency of sites engaged in transcription. Knockdown of sdc-2 and dpy-27, a subunit of the dosage compensation complex (DCC), increased the number of active transcription sites for the X chromosomal gene dpy-23 but not the autosomal gene mdh-1, suggesting that the DCC reduces the frequency of dpy-23 transcription. The temporal resolution from in silico staging of embryos showed that the deletion of a single DCC recruitment element near the dpy-23 gene causes higher dpy-23 mRNA expression after the start of dosage compensation, which could not be resolved using mRNAseq from mixed-stage embryos. In summary, we have established a computational approach to quantify temporal regulation of transcription throughout C. elegans embryogenesis and demonstrated its potential to provide new insights into developmental gene regulation.

}, doi = {10.1101/2024.05.15.594414}, url = {https://www.biorxiv.org/content/early/2024/05/16/2024.05.15.594414}, author = {Breimann, Laura and Bahry, Ella and Zouinkhi, Marwan and Kolyvanov, Klim and Street, Lena Annika and Preibisch, Stephan and Ercan, Sevin{\c c}} } @article {69713, title = {Analysis of developmental gene expression using smFISH and in silico staging of C. elegans embryos}, journal = {bioRxiv}, year = {2024}, month = {05/2024}, abstract = {

Regulation of transcription during embryogenesis is key to development and differentiation. To study transcript expression throughout Caenorhabditis elegans embryogenesis at single-molecule resolution, we developed a high-throughput single-molecule fluorescence in situ hybridization (smFISH) method that relies on computational methods to developmentally stage embryos and quantify individual mRNA molecules in single embryos. We applied our system to sdc-2, a zygotically transcribed gene essential for hermaphrodite development and dosage compensation. We found that sdc-2 is rapidly activated during early embryogenesis by increasing both the number of mRNAs produced per transcription site and the frequency of sites engaged in transcription. Knockdown of sdc-2 and dpy-27, a subunit of the dosage compensation complex (DCC), increased the number of active transcription sites for the X chromosomal gene dpy-23 but not the autosomal gene mdh-1, suggesting that the DCC reduces the frequency of dpy-23 transcription. The temporal resolution from in silico staging of embryos showed that the deletion of a single DCC recruitment element near the dpy-23 gene causes higher dpy-23 mRNA expression after the start of dosage compensation, which could not be resolved using mRNAseq from mixed-stage embryos. In summary, we have established a computational approach to quantify temporal regulation of transcription throughout C. elegans embryogenesis and demonstrated its potential to provide new insights into developmental gene regulation.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2024.05.15.594414}, url = {https://www.biorxiv.org/content/early/2024/05/16/2024.05.15.594414}, author = {Breimann, Laura and Bahry, Ella and Zouinkhi, Marwan and Kolyvanov, Klim and Street, Lena Annika and Preibisch, Stephan and Ercan, Sevin{\c c}} } @article {69284, title = {Analysis of meiotic recombination in Drosophila simulans shows heterozygous inversions do not cause an interchromosomal effect}, journal = {Genetics}, year = {2024}, month = {2024 May 19}, abstract = {

Chromosome inversions are of unique importance in the evolution of genomes and species because when heterozygous with a standard arrangement chromosome, they suppress meiotic crossovers within the inversion. In Drosophila species, heterozygous inversions also cause the interchromosomal effect, whereby the presence of a heterozygous inversion induces a dramatic increase in crossover frequencies in the remainder of the genome within a single meiosis. To date, the interchromosomal effect has been studied exclusively in species that also have high frequencies of inversions in wild populations. We took advantage of a recently developed approach for generating inversions in Drosophila simulans, a species that does not have inversions in wild populations, to ask if there is an interchromosomal effect. We used the existing chromosome 3R balancer and generated a new chromosome 2L balancer to assay for the interchromosomal effect genetically and cytologically. We found no evidence of an interchromosomal effect in D. simulans. To gain insight into the underlying mechanistic reasons, we qualitatively analyzed the relationship between meiotic double-strand break formation and synaptonemal complex assembly. We find that the synaptonemal complex is assembled prior to double-strand break formation as in D. melanogaster; however, we show that the synaptonemal complex is assembled prior to localization of the oocyte determination factor Orb, whereas in D. melanogaster, synaptonemal complex formation does not begin until Orb is localized. Together, our data show heterozygous inversions in D. simulans do not induce an interchromosomal effect and that there are differences in the developmental programming of the early stages of meiosis.

}, doi = {10.1093/genetics/iyae084}, author = {Bowen Man and Elizabeth Kim and Alekhya Vadlakonda and David L Stern and Nicole Crown} } @article {69657, title = {Anti-seizure effects of norepinephrine-induced free fatty acid release.}, journal = {Cell Metab}, year = {2024}, month = {2024 Oct 29}, abstract = {

The brain{\textquoteright}s ability to rapidly transition between sleep, quiet wakefulness, and states of high vigilance is remarkable. Cerebral norepinephrine (NE) plays a key role in promoting wakefulness, but how does the brain avoid neuronal hyperexcitability upon arousal? Here, we show that NE exposure results in the generation of free fatty acids (FFAs) within the plasma membrane from both astrocytes and neurons. In turn, FFAs dampen excitability by differentially modulating the activity of astrocytic and neuronal Na, K, ATPase. Direct application of FFA to the occipital cortex in awake, behaving mice dampened visual-evoked potential (VEP). Conversely, blocking FFA production via local application of a lipase inhibitor heightened VEP and triggered seizure-like activity. These results suggest that FFA release is a crucial step in NE signaling that safeguards against hyperexcitability. Targeting lipid-signaling pathways may offer a novel therapeutic approach for seizure prevention.

}, issn = {1932-7420}, doi = {10.1016/j.cmet.2024.10.011}, url = {https://doi.org/10.1016/j.cmet.2024.10.011}, author = {Li, Baoman and Sun, Qian and Ding, Fengfei and Xu, Qiwu and Kang, Ning and Xue, Yang and Ladron-de-Guevara, Antonio and Hirase, Hajime and Weikop, Pia and Gong, Sheng and Nathan, Smith and Nedergaard, Maiken} } @article {69249, title = {Architecture and flexibility of native kinetochores revealed by structural studies utilizing a thermophilic yeast}, journal = { Curr Biol}, volume = {S0960-9822}, year = {2024}, month = {2024 Aug 07}, pages = {00939-4}, abstract = {

Eukaryotic chromosome segregation requires kinetochores, multi-megadalton protein machines that assemble on the centromeres of chromosomes and mediate attachments to dynamic spindle microtubules. Kinetochores are built from numerous complexes, and there has been progress in structural studies on recombinant subassemblies. However, there is limited structural information on native kinetochore architecture. To address this, we purified functional, native kinetochores from the thermophilic yeast Kluyveromyces marxianus and examined them by electron microscopy (EM), cryoelectron tomography (cryo-ET), and atomic force microscopy (AFM). The kinetochores are extremely large, flexible assemblies that exhibit features consistent with prior models. We assigned kinetochore polarity by visualizing their interactions with microtubules and locating the microtubule binder, Ndc80c. This work shows that isolated kinetochores are more dynamic and complex than what might be anticipated based on the known structures of recombinant subassemblies and provides the foundation to study the global architecture and functions of kinetochores at a structural level.

}, doi = {10.1016/j.cub.2024.07.036}, url = {https://doi.org/10.1016/j.cub.2024.07.036}, author = {Daniel J. Barrero and Sithara S. Wijeratne and Xiaowei Zhao and Grace F. Cunningham and Rui Yan and Christian R. Nelson and Yasuhiro Arimura and Hironori Funabiki and Charles L. Asbury and Zhiheng Yu and Radhika Subramanian and Sue Biggins} } @article {69641, title = {Assembloid model to study loop circuits of the human nervous system}, journal = {bioRxiv}, year = {2024}, month = {2024 Oct 14}, abstract = {

Neural circuits connecting the cerebral cortex, the basal ganglia and the thalamus are fundamental networks for sensorimotor processing and their dysfunction has been consistently implicated in neuropsychiatric disorders1-9. These recursive, loop circuits have been investigated in animal models and by clinical neuroimaging, however, direct functional access to developing human neurons forming these networks has been limited. Here, we use human pluripotent stem cells to reconstruct an in vitro cortico-striatal-thalamic-cortical circuit by creating a four-part loop assembloid. More specifically, we generate regionalized neural organoids that resemble the key elements of the cortico-striatal-thalamic-cortical circuit, and functionally integrate them into loop assembloids using custom 3D-printed biocompatible wells. Volumetric and mesoscale calcium imaging, as well as extracellular recordings from individual parts of these assembloids reveal the emergence of synchronized patterns of neuronal activity. In addition, a multi{\textendash}step rabies retrograde tracing approach demonstrate the formation of neuronal connectivity across the network in loop assembloids. Lastly, we apply this system to study heterozygous loss of ASH1L gene associated with autism spectrum disorder and Tourette syndrome and discover aberrant synchronized activity in disease model assembloids. Taken together, this human multi-cellular platform will facilitate functional investigations of the cortico-striatal-thalamic-cortical circuit in the context of early human development and in disease conditions.

}, doi = {10.1101/2024.10.13.617729}, url = {https://doi.org/10.1101/2024.10.13.617729}, author = {Miura, Yuki and Kim, Ji-il and Jurjut, Ovidiu and Kelley, Kevin W. and Yang, Xiao and Chen, Xiaoyu and Thete, Mayuri Vijay and Revah, Omer and Cui, Bianxiao and Pachitariu, Marius and Pasca, Sergiu P.} } @article {69255, title = {Assessing the impact of Brd2 depletion on chromatin compartmentalization}, journal = {bioRxiv}, year = {2024}, month = {2024 Mar 6}, abstract = {

Recent insights into genome organization have emphasized the importance of A/B chromatin compartments. While our previous research showed that Brd2 depletion weakens compartment boundaries and promotes A/B mixing 1, Hinojosa-Gonzalez et al.2 were unable to replicate the findings. In response, we revisited our Micro-C data and successfully replicated the original results using the default parameters in the cooltools software package. We show that, after correcting inconsistencies with the selection and phasing of the compartment profiles, the decrease in B compartment strength persists but the change in compartment identity is to a much lesser extent than originally reported. To further assess the regulatory role of Brd2, we used saddle plots to determine the strength of compartmentalization and observed a consistent decrease of compartment strength especially at B compartments upon Brd2 depletion. This study highlights the importance of selecting appropriate parameters and analytical tools for compartment analysis and carefully interpreting the results.

}, doi = {10.1101/2024.03.02.583085}, url = {https://www.biorxiv.org/content/early/2024/03/06/2024.03.02.583085}, author = {Advait Athreya and Liangqi Xie and Robert Tjian and Bin Zhang and Zhe J. Liu} } @article {69454, title = {Astrocyte Calcium Signaling}, journal = {Cold Spring Harb Perspect Biol}, year = {2024}, month = {2024 May 20}, abstract = {

Astrocytes are predominant glial cells that tile the central nervous system and participate in well-established functional and morphological interactions with neurons, blood vessels, and other glia. These ubiquitous cells display rich intracellular Ca signaling, which has now been studied for over 30 years. In this review, we provide a summary and perspective of recent progress concerning the study of astrocyte intracellular Ca signaling as well as discussion of its potential functions. Progress has occurred in the areas of imaging, silencing, activating, and analyzing astrocyte Ca signals. These insights have collectively permitted exploration of the relationships of astrocyte Ca signals to neural circuit function and behavior in a variety of species. We summarize these aspects along with a framework for mechanistically interpreting behavioral studies to identify directly causal effects. We finish by providing a perspective on new avenues of research concerning astrocyte Ca signaling.

}, issn = {1943-0264}, doi = {10.1101/cshperspect.a041353}, author = {Ahrens, Misha B and Khakh, Baljit S and Poskanzer, Kira E} } @article {69654, title = {Back to the future - 20 years of progress and developments in photonic microscopy and biological imaging.}, journal = {J Cell Sci}, volume = {137}, year = {2024}, month = {2024 Oct 15}, abstract = {

In 2023, the ImaBio consortium (imabio-cnrs.fr), an interdisciplinary life microscopy research group at the Centre National de la Recherche Scientifique, celebrated its 20th anniversary. ImaBio contributes to the biological imaging community through organization of MiFoBio conferences, which are interdisciplinary conferences featuring lectures and hands-on workshops that attract specialists from around the world. MiFoBio conferences provide the community with an opportunity to reflect on the evolution of the field, and the 2023 event offered retrospective talks discussing the past 20 years of topics in microscopy, including imaging of multicellular assemblies, image analysis, quantification of molecular motions and interactions within cells, advancements in fluorescent labels, and laser technology for multiphoton and label-free imaging of thick biological samples. In this Perspective, we compile summaries of these presentations overviewing 20 years of advancements in a specific area of microscopy, each of which concludes with a brief look towards the future. The full presentations are available on the ImaBio YouTube channel (youtube.com/@gdrimabio5724).

}, keywords = {Animals, Humans, Microscopy, Photons}, issn = {1477-9137}, doi = {10.1242/jcs.262344}, url = {https://doi.org/10.1242/jcs.262344}, author = {Erard, Marie and Favard, Cyril and Lavis, Luke D and Recher, Ga{\"e}lle and Rigneault, Herv{\'e} and Sage, Daniel} } @article {69446, title = {Bacteria-organelle communication in physiology and disease}, journal = {J Cell Biol}, volume = {223}, year = {2024}, month = {2024 May 15}, abstract = {

Bacteria, omnipresent in our environment and coexisting within our body, exert dual beneficial and pathogenic influences. These microorganisms engage in intricate interactions with the human body, impacting both human health and disease. Simultaneously, certain organelles within our cells share an evolutionary relationship with bacteria, particularly mitochondria, best known for their energy production role and their dynamic interaction with each other and other organelles. In recent years, communication between bacteria and mitochondria has emerged as a new mechanism for regulating the host{\textquoteright}s physiology and pathology. In this review, we delve into the dynamic communications between bacteria and host mitochondria, shedding light on their collaborative regulation of host immune response, metabolism, aging, and longevity. Additionally, we discuss bacterial interactions with other organelles, including chloroplasts, lysosomes, and the endoplasmic reticulum (ER).

}, keywords = {Animals, Bacteria, Endoplasmic Reticulum, Host-Pathogen Interactions, Humans, Lysosomes, Mitochondria, Organelles}, issn = {1540-8140}, doi = {10.1083/jcb.202310134}, author = {Lee, Yi-Tang and Senturk, Mumine and Guan, Youchen and Wang, Meng C} } @article {69385, title = {A Bayesian Solution to Count the Number of Molecules within a Diffraction Limited Spot}, journal = {bioRxiv}, year = {2024}, month = {2024 Apr 22}, abstract = {

We address the problem of inferring the number of independently blinking fluorescent light emitters, when only their combined intensity contributions can be observed at each timepoint. This problem occurs regularly in light microscopy of objects that are smaller than the diffraction limit, where one wishes to count the number of fluorescently labelled subunits. Our proposed solution directly models the photo-physics of the system, as well as the blinking kinetics of the fluorescent emitters as a fully differentiable hidden Markov model. Given a trace of intensity over time, our model jointly estimates the parameters of the intensity distribution per emitter, their blinking rates, as well as a posterior distribution of the total number of fluorescent emitters. We show that our model is consistently more accurate and increases the range of countable subunits by a factor of two compared to current state-of-the-art methods, which count based on autocorrelation and blinking frequency, Further-more, we demonstrate that our model can be used to investigate the effect of blinking kinetics on counting ability, and therefore can inform experimental conditions that will maximize counting accuracy.

}, doi = {10.1101/2024.04.18.590066}, url = {https://www.biorxiv.org/content/early/2024/04/22/2024.04.18.590066}, author = {Alexander Hillsley and Johannes Stein and Paul W. Tillberg and David L. Stern and Jan Funke} } @article {69147, title = {Believing is seeing - the deceptive influence of bias in quantitative microscopy.}, journal = {Journal of Cell Science}, volume = {137}, year = {2024}, month = {2024 Jan 10}, abstract = {

The visual allure of microscopy makes it an intuitively powerful research tool. Intuition, however, can easily obscure or distort the reality of the information contained in an image. Common cognitive biases, combined with institutional pressures that reward positive research results, can quickly skew a microscopy project towards upholding, rather than rigorously challenging, a hypothesis. The impact of these biases on a variety of research topics is well known. What might be less appreciated are the many forms in which bias can permeate a microscopy experiment. Even well-intentioned researchers are susceptible to bias, which must therefore be actively recognized to be mitigated. Importantly, although image quantification has increasingly become an expectation, ostensibly to confront subtle biases, it is not a guarantee against bias and cannot alone shield an experiment from cognitive distortions. Here, we provide illustrative examples of the insidiously pervasive nature of bias in microscopy experiments - from initial experimental design to image acquisition, analysis and data interpretation. We then provide suggestions that can serve as guard rails against bias.

}, keywords = {Bias, Humans, Microscopy, Research Personnel}, issn = {1477-9137}, doi = {10.1242/jcs.261567}, author = {Lee, Rachel M and Eisenman, Leanna R and Khuon, Satya and Aaron, Jesse S and Chew, Teng-Leong} } @article {69044, title = {Blue-shifted genetically encoded Ca2+ indicator with enhanced two-photon absorption}, journal = {Neurophotonics}, year = {2024}, month = {2024 Apr 11}, abstract = {

Significance:\ Genetically encoded calcium ion (Ca2+) indicators (GECIs) are powerful tools for monitoring intracellular\ Ca2+\ concentration changes in living cells and model organisms. In particular, GECIs have found particular utility for monitoring the transient increase of\ Ca2+concentration that is associated with the neuronal action potential. However, the palette of highly optimized GECIs for imaging of neuronal activity remains relatively limited. Expanding the selection of available GECIs to include new colors and distinct photophysical properties could create new opportunities for\ in vitro\ and\ in vivo\ fluorescence imaging of neuronal activity. In particular, blue-shifted variants of GECIs are expected to have enhanced two-photon brightness, which would facilitate multiphoton microscopy.

Aim:\ We describe the development and applications of T-GECO1-a high-performance blue-shifted GECI based on the\ Clavularia sp.-derived mTFP1.

Approach:\ We use protein engineering and extensive directed evolution to develop T-GECO1. We characterize the purified protein and assess its performance\ in vitro\ using one-photon excitation in cultured rat hippocampal neurons,\ in vivo\ using one-photon excitation fiber photometry in mice, and\ ex vivo\ using two-photon\ Ca2+\ imaging in hippocampal slices.

Results:\ The\ Ca2+-bound state of T-GECO1 has an excitation peak maximum of 468 nm, an emission peak maximum of 500 nm, an extinction coefficient of\ 49,300M-1cm-1, a quantum yield of 0.83, and two-photon brightness approximately double that of EGFP. The\ Ca2+-dependent fluorescence increase is 15-fold, and the apparent\ Kd\ for\ Ca2+\ is 82 nM. With two-photon excitation conditions at 850 nm, T-GECO1 consistently enabled the detection of action potentials with higher signal-to-noise (SNR) than a late generation GCaMP variant.

Conclusions:\ T-GECO1 is a high-performance blue-shifted GECI that, under two-photon excitation conditions, provides advantages relative to late generation GCaMP variants.

Keywords:\ blue-shifted fluorescence; genetically encoded calcium ion indicator; neuronal activity imaging; protein engineering; two-photon excitation.

}, doi = {10.1117/1.NPh.11.2.024207}, url = {https://doi.org/10.1117/1.NPh.11.2.024207}, author = {Abhi Aggarwal and Smrithi Sunil and Imane Bendifallah and Michael Moon and Mikhail Drobizhev and Landon Zarowny and Jihong Zheng and Sheng-Yi Wu and Alexander W. Lohman and Alison G. Tebo and Valentina Emiliani and Kaspar Podgorski and Yi Shen and Robert E. Campbell} } @article {69185, title = {Brain-wide neural activity underlying memory-guided movement.}, journal = {Cell}, volume = {187}, year = {2024}, month = {2024 Feb 01}, pages = {676-691.e16}, abstract = {

Behavior relies on activity in structured neural circuits that are distributed across the brain, but most experiments probe neurons in a single area at a time. Using multiple Neuropixels probes, we recorded from multi-regional loops connected to the anterior lateral motor cortex (ALM), a circuit node mediating memory-guided directional licking. Neurons encoding sensory stimuli, choices, and actions were distributed across the brain. However, choice coding was concentrated in the ALM and subcortical areas receiving input from the ALM in an ALM-dependent manner. Diverse orofacial movements were encoded in the hindbrain; midbrain; and, to a lesser extent, forebrain. Choice signals were first detected in the ALM and the midbrain, followed by the thalamus and other brain areas. At movement initiation, choice-selective activity collapsed across the brain, followed by new activity patterns driving specific actions. Our experiments provide the foundation for neural circuit models of decision-making and movement initiation.

}, keywords = {Brain, Memory, Movement, Neurons, Thalamus}, issn = {1097-4172}, doi = {10.1016/j.cell.2023.12.035}, author = {Chen, Susu and Liu, Yi and Wang, Ziyue Aiden and Colonell, Jennifer and Liu, Liu D and Hou, Han and Tien, Nai-Wen and Wang, Tim and Harris, Timothy and Druckmann, Shaul and Li, Nuo and Svoboda, Karel} } @article {69148, title = {Bridging gaps in traditional research training with iBiology Courses.}, journal = {PLoS Biology}, volume = {22}, year = {2024}, month = {2024 Jan 11}, pages = {e3002458}, abstract = {

iBiology Courses provide trainees with just-in-time learning resources to become effective researchers. These courses can help scientists build core research skills, plan their research projects and careers, and learn from scientists with diverse backgrounds.

}, issn = {1545-7885}, doi = {10.1371/journal.pbio.3002458}, author = {Schnoes, Alexandra M and Green, Noah H and Nguyen, Thi A and Vale, Ronald D and Goodwin, Sarah S and Behrman, Shannon L} } @article {69557, title = {Bridging tuning and invariance with equivariant neuronal representations}, journal = {bioRxiv}, year = {2024}, month = {2024 Aug 02}, abstract = {

As we move through the world, we see the same visual scenes from different perspectives. Although we experience perspective deformations, our perception of a scene remains stable. This raises the question of which neuronal representations in visual brain areas are perspective-tuned and which are invariant. Focusing on planar rotations, we introduce a mathematical framework based on the principle of equivariance, which asserts that an image rotation results in a corresponding rotation of neuronal representations, to explain how the same representation can range from being fully tuned to fully invariant. We applied this framework to large-scale simultaneous neuronal recordings from four visual cortical areas in mice, where we found that representations are both tuned and invariant but become more invariant across higher-order areas. While common deep convolutional neural networks show similar trends in orientation-invariance across layers, they are not rotation-equivariant. We propose that equivariance is a prevalent computation of populations of biological neurons to gradually achieve invariance through structured tuning.

}, doi = {10.1101/2024.08.02.606398}, url = {https://www.doi.org/10.1101/2024.08.02.606398}, author = {Hoeller, Judith and Zhong, Lin and Pachitariu, Marius and Romani, Sandro} } @article {69445, title = {Building momentum through networks: Bioimaging across the Americas}, journal = {Journal of Microscopy}, volume = {n/a}, year = {2024}, month = {2024 May 15}, abstract = {

In September 2023, the two largest bioimaging networks in the Americas, Latin America Bioimaging (LABI) and BioImaging North America (BINA), came together during a 1-week meeting in Mexico. This meeting provided opportunities for participants to interact closely with decision-makers from imaging core facilities across the Americas. The meeting was held in a hybrid format and attended in-person by imaging scientists from across the Americas, including Canada, the United States, Mexico, Colombia, Peru, Argentina, Chile, Brazil and Uruguay. The aims of the meeting were to discuss progress achieved over the past year, to foster networking and collaborative efforts among members of both communities, to bring together key members of the international imaging community to promote the exchange of experience and expertise, to engage with industry partners, and to establish future directions within each individual network, as well as common goals. This meeting report summarises the discussions exchanged, the achievements shared, and the goals set during the LABIxBINA2023: Bioimaging across the Americas meeting.

}, keywords = {bioimaging networks, BioImaging North America, community-building, imaging scientists, Latin America Bioimaging}, doi = {https://doi.org/10.1111/jmi.13318}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jmi.13318}, author = {De Niz, Mariana and Escobedo Garc{\'\i}a, Rodrigo and Ter{\'a}n Ramirez, Celina and Pakowski, Ysa and Abonza, Yuriney and Bialy, Nikki and Orr, Vanessa L. and Olivera, Andres and Abonza, Victor and Alleva, Karina and Allodi, Silvana and Almeida, Michael F. and Becerril Cuevas, Alexis Ricardo and Bonnet, Frederic and Burgos Solorio, Armando and Chew, Teng-Leong and Chiabrando, Gustavo and Cimini, Beth and Cleret-Buhot, Aur{\'e}lie and Contreras Jim{\'e}nez, Gast{\'o}n and Daza, Laura and De S{\'a}, Vanessa and De Val, Natalia and Delgado-{\'A}lvarez, Diego L. and Eliceiri, Kevin and Fiolka, Reto and Grecco, Hernan and Hanein, Dorit and Hern{\'a}ndez Herrera, Pa{\'u}l and Hockberger, Phil and Hernandez, Haydee O. and Hernandez Guadarrama, Yael and Itano, Michelle and Jacobs, Caron A. and Jim{\'e}nez-Garc{\'\i}a, Luis F. and Jim{\'e}nez Sabinina, Vilma and Kamaid, Andres and Keppler, Antje and Kumar, Abhishek and Lacoste, Judith and Lovy, Alenka and Luby-Phelps, Kate and Mahadevan-Jansen, Anita and Malacrida, Leonel and Mehta, Shalin B. and Miller, Caroline and Miranda, Kildare and Moore, Joshua A. and North, Alison and O{\textquoteright}Toole, Peter and Olivares Urbano, Mariana and Pietrasanta, L{\'\i}a I. and Portugal, Rodrigo V. and Rossi, Andr{\'e}s H. and Sanchez Contreras, Jonathan and Strambio-De-Castilla, Caterina and Soldevila, Gloria and Vale, Bruno and Vazquez, Diana and Wood, Chris and Brown, Claire M. and Guerrero, Adan} } @article {69289, title = {Carbon Nanomaterial Fluorescent Probes and Their Biological Applications}, journal = {Chemical Reviews}, year = {2024}, month = {2024 Mar 13}, abstract = {

Fluorescent carbon nanomaterials have broadly useful chemical and photophysical attributes that are conducive to applications in biology. In this review, we focus on materials whose photophysics allow for the use of these materials in biomedical and environmental applications, with emphasis on imaging, biosensing, and cargo delivery. The review focuses primarily on graphitic carbon nanomaterials including graphene and its derivatives, carbon nanotubes, as well as carbon dots and carbon nanohoops. Recent advances in and future prospects of these fields are discussed at depth, and where appropriate, references to reviews pertaining to older literature are provided.

}, doi = {10.1021/acs.chemrev.3c00581}, url = {https://doi.org/10.1021/acs.chemrev.3c00581}, author = {Krasley, Andrew T. and Li, Eugene and Galeana, Jesus M. and Bulumulla, Chandima and Beyene, Abraham G. and Demirer, Gozde S.} } @article {69297, title = {Cell division machinery drives cell-specific gene activation during differentiation in .}, journal = {Proc Natl Acad Sci U S A}, volume = {121}, year = {2024}, month = {2024 Mar 6}, pages = {e2400584121}, abstract = {

When faced with starvation, the bacterium transforms itself into a dormant cell type called a "spore". Sporulation initiates with an asymmetric division event, which requires the relocation of the core divisome components FtsA and FtsZ, after which the sigma factor σ is exclusively activated in the smaller daughter cell. Compartment-specific activation of σ requires the SpoIIE phosphatase, which displays a biased localization on one side of the asymmetric division septum and associates with the structural protein DivIVA, but the mechanism by which this preferential localization is achieved is unclear. Here, we isolated a variant of DivIVA that indiscriminately activates σ in both daughter cells due to promiscuous localization of SpoIIE, which was corrected by overproduction of FtsA and FtsZ. We propose that the core components of the redeployed cell division machinery drive the asymmetric localization of DivIVA and SpoIIE to trigger the initiation of the sporulation program.

}, issn = {1091-6490}, doi = {10.1073/pnas.2400584121}, author = {Chareyre, Sylvia and Li, Xuesong and Anjuwon-Foster, Brandon R and Updegrove, Taylor B and Clifford, Sarah and Brogan, Anna P and Su, Yijun and Zhang, Lixia and Chen, Jiji and Shroff, Hari and Ramamurthi, Kumaran S} } @article {69569, title = {A Cell Observatory to reveal the subcellular foundations of life.}, journal = {Nat Methods}, year = {2024}, month = {2024 Aug 07}, abstract = {

Imaging the 4D choreography of subcellular events in living multicellular organisms at high spatiotemporal resolution could reveal life{\textquoteright}s fundamental principles. Yet extracting these principles from petabyte-scale image data requires fusing advanced light microscopy and cutting-edge machine learning models with biological insight and expertise.

}, issn = {1548-7105}, doi = {10.1038/s41592-024-02379-3}, url = {https://doi.org/10.1038/s41592-024-02379-3 }, author = {Betzig, Eric} } @article {69650, title = {Cell type-specific driver lines targeting the Drosophila central complex and their use to investigate neuropeptide expression and sleep regulation}, journal = {bioRxiv}, year = {2024}, month = {2024 Oct 21}, abstract = {

The central complex (CX) plays a key role in many higher-order functions of the insect brain including navigation and activity regulation. Genetic tools for manipulating individual cell types, and knowledge of what neurotransmitters and neuromodulators they express, will be required to gain mechanistic understanding of how these functions are implemented. We generated and characterized split-GAL4 driver lines that express in individual or small subsets of about half of CX cell types. We surveyed neuropeptide and neuropeptide receptor expression in the central brain using fluorescent in situ hybridization. About half of the neuropeptides we examined were expressed in only a few cells, while the rest were expressed in dozens to hundreds of cells. Neuropeptide receptors were expressed more broadly and at lower levels. Using our GAL4 drivers to mark individual cell types, we found that 51 of the 85 CX cell types we examined expressed at least one neuropeptide and 21 expressed multiple neuropeptides. Surprisingly, all co-expressed a small neurotransmitter. Finally, we used our driver lines to identify CX cell types whose activation affects sleep, and identified other central brain cell types that link the circadian clock to the CX. The well-characterized genetic tools and information on neuropeptide and neurotransmitter expression we provide should enhance studies of the CX.

}, doi = {10.1101/2024.10.21.619448}, url = {https://doi.org/10.1101/2024.10.21.619448}, author = {Wolff, Tanya and Eddison, Mark and Chen, Nan and Nern, Aljoscha and Sundaramurthi, Preeti and Sitaraman, Divya and Rubin, Gerald M.} } @article {69570, title = {Cell-surface Milieu Remodeling in Human Dendritic Cell Activation.}, journal = {J Immunol}, year = {2024}, month = {2024 Aug 12}, abstract = {

Dendritic cells (DCs) are specialized sentinel and APCs coordinating innate and adaptive immunity. Through proteins on their cell surface, DCs sense changes in the environment, internalize pathogens, present processed Ags, and communicate with other immune cells. By combining chemical labeling and quantitative mass spectrometry, we systematically profiled and compared the cell-surface proteomes of human primary conventional DCs (cDCs) in their resting and activated states. TLR activation by a lipopeptide globally reshaped the cell-surface proteome of cDCs, with \>100 proteins upregulated or downregulated. By simultaneously elevating positive regulators and reducing inhibitory signals across multiple protein families, the remodeling creates a cell-surface milieu promoting immune responses. Still, cDCs maintain the stimulatory-to-inhibitory balance by leveraging a distinct set of inhibitory molecules. This analysis thus uncovers the molecular complexity and plasticity of the cDC cell surface and provides a roadmap for understanding cDC activation and signaling.

}, issn = {1550-6606}, doi = {10.4049/jimmunol.2400089}, url = {https://doi.org/10.4049/jimmunol.2400089}, author = {Udeshi, Namrata D and Xu, Charles and Jiang, Zuzhi and Gao, Shihong Max and Yin, Qian and Luo, Wei and Carr, Steven A and Davis, Mark M and Li, Jiefu} } @article {69251, title = {The cell-type-specific spatial organization of the anterior thalamic nuclei of the mouse brain.}, journal = {Cell Reports}, volume = {43}, year = {2024}, month = {2024 Feb 29}, pages = {113842}, abstract = {

Understanding the cell-type composition and spatial organization of brain regions is crucial for interpreting brain computation and function. In the thalamus, the anterior thalamic nuclei (ATN) are involved in a wide variety of functions, yet the cell-type composition of the ATN remains unmapped at a single-cell and spatial resolution. Combining single-cell RNA sequencing, spatial transcriptomics, and multiplexed fluorescent in situ hybridization, we identify three discrete excitatory cell-type clusters that correspond to the known nuclei of the ATN and uncover marker genes, molecular pathways, and putative functions of these cell types. We further illustrate graded spatial variation along the dorsomedial-ventrolateral axis for all individual nuclei of the ATN and additionally demonstrate that the anteroventral nucleus exhibits spatially covarying protein products and long-range inputs. Collectively, our study reveals discrete and continuous cell-type organizational principles of the ATN, which will help to guide and interpret experiments on ATN computation and function.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2024.113842}, author = {Kapustina, Margarita and Zhang, Angela A and Tsai, Jennifer Y J and Bristow, Brianna N and Kraus, Larissa and Sullivan, Kaitlin E and Erwin, Sarah R and Wang, Lihua and Stach, Tara R and Clements, Jody and Lemire, Andrew L and Cembrowski, Mark S} } @article {69546, title = {Chemical Induction of Longevity-Promoting Colanic Acid in the Host{\textquoteright}s Microbiota}, journal = {bioRxiv}, year = {2024}, month = {2024 Jul 23}, abstract = {

Microbiota-derived metabolites have emerged as key regulators of longevity. The metabolic activity of the gut microbiota, influenced by dietary components and ingested chemical compounds, profoundly impacts host fitness. While the benefits of dietary prebiotics are well-known, chemically targeting the gut microbiota to enhance host fitness remains largely unexplored. Here, we report a novel chemical approach to induce a pro-longevity bacterial metabolite in the host gut. We discovered that specific Escherichia coli strains overproduce colanic acids (CAs) when exposed to a low dose of cephaloridine, leading to an increased lifespan in host Caenorhabditis elegans. In the mouse gut, oral administration of low-dose cephaloridine induces the transcription of the capsular biosynthesis operon responsible for CA biosynthesis in commensal E. coli, which overcomes the inhibition of CA biosynthesis above 30 degrees C and enables its induction directly from the microbiota. Importantly, low-dose cephaloridine induces CA independently of its antibiotic properties through a previously unknown mechanism mediated by the membrane-bound histidine kinase ZraS. Our work lays the foundation for microbiota-based therapeutics through the chemical modulation of bacterial metabolism and reveals the promising potential of bacteria-targeting drugs in promoting host longevity.

}, doi = {10.1101/2024.07.23.604802}, url = {https://www.doi.org/10.1101/2024.07.23.604802}, author = {Hu, Guo and Cooke, Matthew Brandon and Wen, Alice X and Yu, Xin and Wang, Jin and Herman, Christophe and Wang, Meng Carla} } @article {69535, title = {Closing the Experiment-Modeling-Perturbation Loop in Whole-Brain Neuroscience.}, journal = {Neurosci Bull}, year = {2024}, month = {2024 Jul 16}, issn = {1995-8218}, doi = {10.1007/s12264-024-01253-8}, author = {Ahrens, Misha B} } @article {69548, title = {Cohesin prevents cross-domain gene coactivation.}, journal = {Nat Genet}, year = {2024}, month = {2024 Jul 24}, abstract = {

The contrast between the disruption of genome topology after cohesin loss and the lack of downstream gene expression changes instigates intense debates regarding the structure-function relationship between genome and gene regulation. Here, by analyzing transcriptome and chromatin accessibility at the single-cell level, we discover that, instead of dictating population-wide gene expression levels, cohesin supplies a general function to neutralize stochastic coexpression tendencies of cis-linked genes in single cells. Notably, cohesin loss induces widespread gene coactivation and chromatin co-opening tens of million bases apart in cis. Spatial genome and protein imaging reveals that cohesin prevents gene co-bursting along the chromosome and blocks spatial mixing of transcriptional hubs. Single-molecule imaging shows that cohesin confines the exploration of diverse enhancer and core promoter binding transcriptional regulators. Together, these results support that cohesin arranges nuclear topology to control gene coexpression in single cells.

}, issn = {1546-1718}, doi = {10.1038/s41588-024-01852-1}, url = {https://doi.org/10.1038/s41588-024-01852-1}, author = {Dong, Peng and Zhang, Shu and Gandin, Valentina and Xie, Liangqi and Wang, Lihua and Lemire, Andrew L and Li, Wenhong and Otsuna, Hideo and Kawase, Takashi and Lander, Arthur D and Chang, Howard Y and Liu, Zhe J} } @article {69489, title = {Comparative connectomics of the descending and ascending neurons of the Drosophila nervous system: stereotypy and sexual dimorphism}, journal = {bioRxiv}, year = {2024}, month = {2024 Jun 06}, abstract = {

In most complex nervous systems there is a clear anatomical separation between the nerve cord, which contains most of the final motor outputs necessary for behaviour, and the brain. In insects, the neck connective is both a physical and information bottleneck connecting the brain and the ventral nerve cord (VNC, spinal cord analogue) and comprises diverse populations of descending (DN), ascending (AN) and sensory ascending neurons, which are crucial for sensorimotor signalling and control.Integrating three separate EM datasets, we now provide a complete connectomic description of the ascending and descending neurons of the female nervous system of Drosophila and compare them with neurons of the male nerve cord. Proofread neuronal reconstructions have been matched across hemispheres, datasets and sexes. Crucially, we have also matched 51\% of DN cell types to light level data defining specific driver lines as well as classifying all ascending populations.We use these results to reveal the general architecture, tracts, neuropil innervation and connectivity of neck connective neurons. We observe connected chains of descending and ascending neurons spanning the neck, which may subserve motor sequences. We provide a complete description of sexually dimorphic DN and AN populations, with detailed analysis of circuits implicated in sex-related behaviours, including female ovipositor extrusion (DNp13), male courtship (DNa12/aSP22) and song production (AN hemilineage 08B). Our work represents the first EM-level circuit analyses spanning the entire central nervous system of an adult animal.

}, doi = {10.1101/2024.06.04.596633}, url = {https://www.biorxiv.org/content/early/2024/06/06/2024.06.04.596633}, author = {St{\"u}rner, Tomke and Brooks, Paul and Serratosa Capdevila, Laia and Morris, Billy J. and Javier, Alexandre and Fang, Siqi and Gkantia, Marina and Cachero, Sebastian and Beckett, Isabella R. and Champion, Andrew S. and Moitra, Ilina and Richards, Alana and Klemm, Finja and Kugel, Leonie and Namiki, Shigehiro and Cheong, Han S.J. and Kovalyak, Julie and Tenshaw, Emily and Parekh, Ruchi and Schlegel, Philipp and Phelps, Jasper S. and Mark, Brandon and Dorkenwald, Sven and Bates, Alexander S. and Matsliah, Arie and Yu, Szi-Chieh and McKellar, Claire E. and Sterling, Amy and Seung, Sebastian and Murthy, Mala and Tuthill, John and Lee, Wei-Chung A. and Card, Gwyneth M. and Costa, Marta and Jefferis, Gregory S.X.E. and Eichler, Katharina} } @article {69441, title = {Compartmentalized Cytoplasmic Flows Direct Protein Transport to the Cell{\textquoteright}s Leading Edge}, journal = {bioRxiv}, year = {2024}, month = {2024 May 14}, abstract = {

Inside the cell, proteins essential for signaling, morphogenesis, and migration navigate complex pathways, typically via vesicular trafficking or microtubule-driven mechanisms 1-3. However, the process by which soluble cytoskeletal monomers maneuver through the cytoplasm{\textquoteright}s ever-changing environment to reach their destinations without using these pathways remains unknown. 4-6 Here, we show that actin cytoskeletal treadmilling leads to the formation of a semi-permeable actin-myosin barrier, creating a specialized compartment separated from the rest of the cell body that directs proteins toward the cell edge by advection, diffusion facilitated by fluid flow. Contraction at this barrier generates a molecularly non-specific fluid flow that transports actin, actin-binding proteins, adhesion proteins, and even inert proteins forward. The local curvature of the barrier specifically targets these proteins toward protruding edges of the leading edge, sites of new filament growth, effectively coordinating protein distribution with cellular dynamics. Outside this compartment, diffusion remains the primary mode of protein transport, contrasting sharply with the directed advection within. This discovery reveals a novel protein transport mechanism that redefines the front of the cell as a pseudo-organelle, actively orchestrating protein mobilization for cellular front activities such as protrusion and adhesion. By elucidating a new model of protein dynamics at the cellular front, this work contributes a critical piece to the puzzle of how cells adapt their internal structures for targeted and rapid response to extracellular cues. The findings challenge the current understanding of intracellular transport, suggesting that cells possess highly specialized and previously unrecognized organizational strategies for managing protein distribution efficiently, providing a new framework for understanding the cellular architecture{\textquoteright}s role in rapid response and adaptation to environmental changes.

}, doi = {10.1101/2024.05.12.593794}, url = {https://www.biorxiv.org/content/early/2024/05/14/2024.05.12.593794}, author = {Galbraith, Catherine G and English, Brian P and Boehm, Ulrike and Galbraith, James A} } @article {68656, title = {Connectome-constrained networks predict neural activity across the fly visual system}, journal = {Nature}, year = {2024}, month = {2024 Sep 11}, abstract = {

We can now measure the connectivity of every neuron in a neural circuit, but we cannot measure other biological details, including the dynamical characteristics of each neuron. The degree to which measurements of connectivity alone can inform the understanding of neural computation is an open question. Here we show that with experimental measurements of only the connectivity of a biological neural network, we can predict the neural activity underlying a specified neural computation. We constructed a model neural network with the experimentally determined connectivity for 64 cell types in the motion pathways of the fruit fly optic lobe but with unknown parameters for the single-neuron and single-synapse properties. We then optimized the values of these unknown parameters using techniques from deep learning, to allow the model network to detect visual motion. Our mechanistic model makes detailed, experimentally testable predictions for each neuron in the connectome. We found that model predictions agreed with experimental measurements of neural activity across 26 studies. Our work demonstrates a strategy for generating detailed hypotheses about the mechanisms of neural circuit function from connectivity measurements. We show that this strategy is more likely to be successful when neurons are sparsely connected-a universally observed feature of biological neural networks across species and brain regions.

}, doi = {10.1038/s41586-024-07939-3}, url = {https://doi.org/10.1038/s41586-024-07939-3}, author = {Janne K. Lappalainen and Fabian D. Tschopp and Sridhama Prakhya and Mason McGill and Aljoscha Nern and Kazunori Shinomiya and Shin-ya Takemura and Eyal Gruntman and Jakob H. Macke and Srinivas C. Turaga} } @article {69373, title = {Connectome-driven neural inventory of a complete visual system}, journal = {Nature}, year = {2024}, month = {2025 Mar 26}, abstract = {

Vision provides animals with detailed information about their surroundings, conveying diverse features such as color, form, and movement across the visual scene. Computing these parallel spatial features requires a large and diverse network of neurons, such that in animals as distant as flies and humans, visual regions comprise half the brain{\textquoteright}s volume. These visual brain regions often reveal remarkable structure-function relationships, with neurons organized along spatial maps with shapes that directly relate to their roles in visual processing. To unravel the stunning diversity of a complex visual system, a careful mapping of the neural architecture matched to tools for targeted exploration of that circuitry is essential. Here, we report a new connectome of the right optic lobe from a male Drosophila central nervous system FIB-SEM volume and a comprehensive inventory of the fly{\textquoteright}s visual neurons. We developed a computational framework to quantify the anatomy of visual neurons, establishing a basis for interpreting how their shapes relate to spatial vision. By integrating this analysis with connectivity information, neurotransmitter identity, and expert curation, we classified the 53,000 neurons into 727 types, about half of which are systematically described and named for the first time. Finally, we share an extensive collection of split-GAL4 lines matched to our neuron type catalog. Together, this comprehensive set of tools and data unlock new possibilities for systematic investigations of vision in Drosophila, a foundation for a deeper understanding of sensory processing.

}, doi = {10.1038/s41586-025-08746-0}, url = {https://doi.org/10.1038/s41586-025-08746-0}, author = {Aljoscha Nern and Frank Loesche and Shin-ya Takemura and Laura E Burnett and Marisa Dreher and Eyal Gruntman and Judith Hoeller and Gary B Huang and Michal Januszewski and Nathan C Klapoetke and Sanna Koskela and Kit D Longden and Zhiyuan Lu and Stephan Preibisch and Wei Qiu and Edward M Rogers and Pavithraa Seenivasan and Arthur Zhao and John Bogovic and Brandon S Canino and Jody Clements and Michael Cook and Samantha Finley-May and Miriam A Flynn and Imran Hameed and Kenneth J Hayworth and Gary Patrick Hopkins and Philip M Hubbard and William T Katz and Julie Kovalyak and Shirley A Lauchie and Meghan Leonard and Alanna Lohff and Charli A Maldonado and Caroline Mooney and Nneoma Okeoma and Donald J Olbris and Christopher Ordish and Tyler Paterson and Emily M Phillips and Tobias Pietzsch and Jennifer Rivas Salinas and Patricia K Rivlin and Ashley L Scott and Louis A Scuderi and Satoko Takemura and Iris Talebi and Alexander Thomson and Eric T Trautman and Lowell Umayam and Claire Walsh and John J Walsh and C Shan Xu and Emily A Yakal and Tansy Yang and Ting Zhao and Jan Funke and Reed George and Harald F Hess and Gregory S X E Jefferis and Christopher Knecht and Wyatt Korff and Stephen M Plaza and Sandro Romani and Stephan Saalfeld and Louis K Scheffer and Stuart Berg and Gerald M Rubin and Michael B Reiser} } @article {69403, title = {Connectomic Analysis of Mitochondria in the Central Brain of Drosophila}, journal = {bioRxiv}, year = {2024}, month = {2024 Apr 25}, abstract = {

Mitochondria are an integral part of the metabolism of a neuron. EM images of fly brain volumes, taken for connectomics, contain mitochondria as well as the cells and synapses that have already been reported. Here, from the Drosophila hemibrain dataset, we extract, classify, and measure approximately 6 million mitochondria among roughly 21 thousand neurons of more than 5500 cell types. Each mitochondrion is classified by its appearance - dark and dense, light and sparse, or intermediate - and the location, orientation, and size (in voxels) are annotated. These mitochondria are added to our publicly available data portal, and each synapse is linked to its closest mitochondrion. Using this data, we show quantitative evidence that mitochodrial trafficing extends to the smallest dimensions in neurons. The most basic characteristics of mitochondria - volume, distance from synapses, and color - vary considerably between cell types, and between neurons with different neurotransmitters. We find that polyadic synapses with more post-synaptic densities (PSDs) have closer and larger mitochondria on the pre-synaptic side, but smaller and more distant mitochondria on the PSD side. We note that this relationship breaks down for synapses with only one PSD, suggesting a different role for such synapses.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2024.04.21.590464}, url = {https://www.biorxiv.org/content/early/2024/04/25/2024.04.21.590464}, author = {Patricia K Rivlin and Michal Januszewski and Kit D Longden and Erika Neace and Louis K Scheffer and Christopher Ordish and Jody Clements and Elliott Phillips and Natalie Smith and Satoko Takemura and Lowell Umayam and Claire Walsh and Emily A Yakal and Stephen M Plaza and Stuart Berg} } @article {69138, title = {Connectomic reconstruction predicts visual features used for navigation.}, journal = {Nature}, volume = {634}, year = {2024}, month = {2024 Oct 02}, pages = {181-190}, abstract = {

Many animals use visual information to navigate, but how such information is encoded and integrated by the navigation system remains incompletely understood. In Drosophila melanogaster, EPG neurons in the central complex compute the heading direction by integrating visual input from ER neurons, which are part of the anterior visual pathway (AVP). Here we densely reconstruct all neurons in the AVP using electron-microscopy data. The AVP comprises four neuropils, sequentially linked by three major classes of neurons: MeTu neurons, which connect the medulla in the optic lobe to the small unit of the anterior optic tubercle (AOTUsu) in the central brain; TuBu neurons, which connect the AOTUsu to the bulb neuropil; and ER neurons, which connect the bulb to the EPG neurons. On the basis of morphologies, connectivity between neural classes and the locations of synapses, we identify distinct information channels that originate from four types of MeTu neurons, and we further divide these into ten subtypes according to the presynaptic connections in the medulla and the postsynaptic connections in the AOTUsu. Using the connectivity of the entire AVP and the dendritic fields of the MeTu neurons in the optic lobes, we infer potential visual features and the visual area from which any ER neuron receives input. We confirm some of these predictions physiologically. These results provide a strong foundation for understanding how distinct sensory features can be extracted and transformed across multiple processing stages to construct higher-order cognitive representations.

}, doi = {10.1038/s41586-024-07967-z}, url = {https://doi.org/10.1038/s41586-024-07967-z}, author = {Garner, Dustin and Kind, Emil and Yuet Ha Lai, Jennifer and Nern, Aljoscha and Zhao, Arthur and Houghton, Lucy and Sancer, Gizem and Wolff, Tanya and Rubin, Gerald M and Wernet, Mathias F and Kim, Sung Soo} } @article {69663, title = {A consensus definition for deep layer 6 excitatory neurons in mouse neocortex}, journal = {bioRxiv}, year = {2024}, month = {2024 Nov 05}, abstract = {

To understand neocortical function, we must first define its cell types. Recent studies indicate that neurons in the deepest cortical layer play roles in mediating thalamocortical interactions and modulating brain state and are implicated in neuropsychiatric disease. However, understanding the functions of deep layer 6 (L6b) neurons has been hampered by the lack of agreed upon definitions for these cell types. We compared commonly used methods for defining L6b neurons, including molecular, transcriptional and morphological approaches as well as transgenic mouse lines, and identified a core population of L6b neurons. This population does not innervate sensory thalamus, unlike layer 6 corticothalamic neurons (L6CThNs) in more superficial layer 6. Rather, single L6b neurons project ipsilaterally between cortical areas. Although L6b neurons undergo early developmental changes, we found that their intrinsic electrophysiological properties were stable after the first postnatal week. Our results provide a consensus definition for L6b neurons, enabling comparisons across studies.

}, doi = {10.1101/2024.11.04.621933}, url = {https://doi.org/10.1101/2024.11.04.621933}, author = {Kim, Su-Jeong and Babola, Travis A. and Lee, Kihwan and Matney, Chanel J. and Spiegel, Alina C. and Liew, Michael H. and Schulteis, Eva M. and Coye, Austin E. and Proskurin, Mikhail and Kang, Hyunwook and Kim, Julia A. and Chevee, Maxime and Lee, Kiwoong and Kanold, Patrick O. and Goff, Loyal A. and Kim, Juhyun and Brown, Solange P} } @article {69348, title = {Convolutional Neural Network Transformer (CNNT) for Fluorescence Microscopy image Denoising with Improved Generalization and Fast Adaptation}, journal = {arXiv}, year = {2024}, month = {2024 Apr 6}, abstract = {

Deep neural networks have been applied to improve the image quality of fluorescence microscopy imaging. Previous methods are based on convolutional neural networks (CNNs) which generally require more time-consuming training of separate models for each new imaging experiment, impairing the applicability and generalization. Once the model is trained (typically with tens to hundreds of image pairs) it can then be used to enhance new images that are like the training data. In this study, we proposed a novel imaging-transformer based model, Convolutional Neural Network Transformer (CNNT), to outperform the CNN networks for image denoising. In our scheme we have trained a single CNNT based backbone model from pairwise high-low SNR images for one type of fluorescence microscope (instance structured illumination, iSim). Fast adaption to new applications was achieved by fine-tuning the backbone on only 5-10 sample pairs per new experiment. Results show the CNNT backbone and fine-tuning scheme significantly reduces the training time and improves the image quality, outperformed training separate models using CNN approaches such as - RCAN and Noise2Fast. Here we show three examples of the efficacy of this approach on denoising wide-field, two-photon and confocal fluorescence data. In the confocal experiment, which is a 5 by 5 tiled acquisition, the fine-tuned CNNT model reduces the scan time form one hour to eight minutes, with improved quality.

}, author = {Azaan Rehman and Alexander Zhovmer and Ryo Sato and Yosuke Mukoyama and Jiji Chen and Alberto Rissone and Rosa Puertollano and Harshad Vishwasrao and Hari Shroff and Christian A. Combs and Hui Xue} } @article {69558, title = {Convolutional neural network transformer (CNNT) for fluorescence microscopy image denoising with improved generalization and fast adaptation.}, journal = {Sci Rep}, volume = {14}, year = {2024}, month = {2024 Aug 06}, pages = {18184}, abstract = {

Deep neural networks can improve the quality of fluorescence microscopy images. Previous methods, based on Convolutional Neural Networks (CNNs), require time-consuming training of individual models for each experiment, impairing their applicability and generalization. In this study, we propose a novel imaging-transformer based model, Convolutional Neural Network Transformer (CNNT), that outperforms CNN based networks for image denoising. We train a general CNNT based backbone model from pairwise high-low Signal-to-Noise Ratio (SNR) image volumes, gathered from a single type of fluorescence microscope, an instant Structured Illumination Microscope. Fast adaptation to new microscopes is achieved by fine-tuning the backbone on only 5-10 image volume pairs per new experiment. Results show that the CNNT backbone and fine-tuning scheme significantly reduces training time and improves image quality, outperforming models trained using only CNNs such as 3D-RCAN and Noise2Fast. We show three examples of efficacy of this approach in wide-field, two-photon, and confocal fluorescence microscopy.

}, issn = {2045-2322}, doi = {10.1038/s41598-024-68918-2}, url = {https://doi.org/10.1038/s41598-024-68918-2}, author = {Rehman, Azaan and Zhovmer, Alexander and Sato, Ryo and Mukouyama, Yoh-Suke and Chen, Jiji and Rissone, Alberto and Puertollano, Rosa and Liu, Jiamin and Vishwasrao, Harshad D and Shroff, Hari and Combs, Christian A and Xue, Hui} } @article {69588, title = {Coordinated cross-brain activity during accumulation of sensory evidence and decision commitment}, journal = {bioRxiv}, year = {2024}, month = {2024 Aug 25}, abstract = {

Cognition is produced by the continuous interactions between many regions across the brain, but has typically been studied one brain region at a time. How signals in different regions coordinate to achieve a single coherent action remains unclear. Here, we address this question by characterizing the simultaneous interactions between up to 20 brain regions across the brain (10 targeted regions per hemisphere), of rats performing the {\textquotedblleft}Poisson Clicks{\textquotedblright} task, a decision-making task that demands the gradual accumulation of momentary evidence. Using 8 Neuropixels probes in each animal, we recorded simultaneously in prefrontal cortex, striatum, motor cortex, hippocampus, amygdala, and thalamus. To assess decision-related interactions between regions, we quantified correlations of each region{\textquoteright}s {\textquotedblleft}decision variable{\textquotedblright}: moment-to-moment co-fluctuations along the axis in neural state space that best predicts the upcoming choice. This revealed a network of strongly correlated brain regions that include the dorsomedial frontal cortex (dmFC), anterior dorsal striatum (ADS), and primary motor cortex (M1), whose decision variables also led the rest of the brain. If coordinated activity within this subnetwork reflects an ongoing evidence accumulation process, these correlations should cease at the time of decision commitment. We therefore compared correlations before versus after {\textquotedblleft}nTc{\textquotedblright}, a recently reported estimator for the time of internal decision commitment. We found that correlations in the decision variables between different brain regions decayed to near-zero after nTc. Additionally, we found that choice-predictive activity steadily increased over time before nTc, but abruptly stopped growing at nTc, consistent with an evidence accumulation process that has stopped evolving at that time. Assessing nTc from the activity of individual regions revealed that nTc could be reliably detected earlier in M1 than other regions. These results show that evidence accumulation involves coordination within a network of frontal cortical and striatal regions, and suggests that termination of this process may initiate in M1.

}, doi = {10.1101/2024.08.21.609044}, url = {https://www.doi.org/10.1101/2024.08.21.609044}, author = {Bondy, Adrian G. and Charlton, Julie A. and Luo, Thomas Zhihao and Kopec, Charles D. and Stagnaro, Wynne M. and Venditto, Sarah Jo C. and Lynch, Laura and Janarthanan, Sanjeev and Oline, Stefan N. and Harris, Timothy D. and Brody, Carlos D.} } @article {69286, title = {Coordinated head direction representations in mouse anterodorsal thalamic nucleus and retrosplenial cortex.}, journal = {Elife}, volume = {13}, year = {2024}, month = {2024 Mar 12}, abstract = {

The sense of direction is critical for survival in changing environments and relies on flexibly integrating self-motion signals with external sensory cues. While the anatomical substrates involved in head direction (HD) coding are well known, the mechanisms by which visual information updates HD representations remain poorly understood. Retrosplenial cortex (RSC) plays a key role in forming coherent representations of space in mammals and it encodes a variety of navigational variables, including HD. Here, we use simultaneous two-area tetrode recording to show that RSC HD representation is nearly synchronous with that of the anterodorsal nucleus of thalamus (ADn), the obligatory thalamic relay of HD to cortex, during rotation of a prominent visual cue. Moreover, coordination of HD representations in the two regions is maintained during darkness. We further show that anatomical and functional connectivity are consistent with a strong feedforward drive of HD information from ADn to RSC, with anatomically restricted corticothalamic feedback. Together, our results indicate a concerted global HD reference update across cortex and thalamus.

}, keywords = {Animals, Anterior Thalamic Nuclei, Cerebral Cortex, Cues, Gyrus Cinguli, Mammals, Mice, Rotation}, issn = {2050-084X}, doi = {10.7554/eLife.82952}, author = {van der Goes, Marie-Sophie H and Voigts, Jakob and Newman, Jonathan P and Toloza, Enrique H S and Brown, Norma J and Murugan, Pranav and Harnett, Mark T} } @article {69351, title = {COPII with ALG2 and ESCRTs control lysosome-dependent microautophagy of ER exit sites.}, journal = {Dev Cell}, year = {2024}, month = {2024 Apr 06}, abstract = {

Endoplasmic reticulum exit sites (ERESs) are tubular outgrowths of endoplasmic reticulum that serve as the earliest station for protein sorting and export into the secretory pathway. How these structures respond to different cellular conditions remains unclear. Here, we report that ERESs undergo lysosome-dependent microautophagy when Ca\ is released by lysosomes in response to nutrient stressors such as mTOR inhibition or amino acid starvation in mammalian cells. Targeting and uptake of ERESs into lysosomes were observed\ by\ super-resolution live-cell imaging and focus ion beam scanning electron microscopy (FIB-SEM). The mechanism\ was ESCRT dependent and required\ ubiquitinated SEC31, ALG2, and ALIX, with a knockout of ALG2 or function-blocking mutations of ALIX preventing engulfment of ERESs by lysosomes. In\ vitro, reconstitution of the pathway was possible using lysosomal lipid-mimicking giant unilamellar vesicles and purified recombinant components. Together, these findings demonstrate a pathway of lysosome-dependent ERES microautophagy mediated by COPII, ALG2, and ESCRTS induced by nutrient stress.

}, issn = {1878-1551}, doi = {10.1016/j.devcel.2024.03.027}, author = {Liao, Ya-Cheng and Pang, Song and Li, Wei-Ping and Shtengel, Gleb and Choi, Heejun and Schaefer, Kathy and Xu, C Shan and Lippincott-Schwartz, Jennifer} } @article {69089, title = {Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment.}, journal = {Nat. Commun.}, year = {2024}, month = {2024 May 16}, abstract = {

In the nucleus, biological processes are driven by proteins that diffuse through and bind to a meshwork of nucleic acid polymers. To better understand this interplay, we present an imaging platform to simultaneously visualize single protein dynamics together with the local chromatin environment in live cells. Together with super-resolution imaging, new fluorescent probes, and biophysical modeling, we demonstrate that nucleosomes display differential diffusion and packing arrangements as chromatin density increases whereas the viscoelastic properties and accessibility of the interchromatin space remain constant. Perturbing nuclear functions impacts nucleosome diffusive properties in a manner that is dependent both on local chromatin density and on relative location within the nucleus. Our results support a model wherein transcription locally stabilizes nucleosomes while simultaneously allowing for the free exchange of nuclear proteins. Additionally, they reveal that nuclear heterogeneity arises from both active and passive processes and highlight the need to account for different organizational principles when modeling different chromatin environments.

}, doi = {10.1038/s41467-024-48562-0}, author = {Daugird, Timothy A and Shi, Yu and Holland, Katie L and Rostamian, Hosein and Liu, Zhe and Lavis, Luke D and Rodriguez, Joseph and Strahl, Brian D and Legant, Wesley R} } @article {69442, title = {Coumarin as a general switching auxiliary to prepare photochromic and spontaneously blinking fluorophores}, journal = {bioRxiv}, year = {2024}, month = {2024 May 12}, abstract = {

Single-molecule localization microscopy (SMLM) uses activatable or switchable fluorophores to create non-diffraction limited maps of molecular location in biological samples. Despite the utility of this imaging technique, the portfolio of appropriate labels for SMLM remains limited. Here, we describe a general strategy for the construction of {\textquotedblleft}glitter bomb{\textquotedblright} labels by simply combining rhodamine and coumarin dyes though an amide bond. Condensation of the ortho-carboxyl group on the pendant phenyl ring of rhodamine dyes with a 7-aminocoumarin yields photochromic or spontaneously blinking fluorophores depending on the parent rhodamine structure. We apply this strategy to prepare labels useful super-resolution experiments in fixed cells using different attachment techniques. This general glitter bomb strategy should lead to improved labels for SMLM, ultimately enabling the creation of detailed molecular maps in biological samples.

}, doi = {10.1101/2024.05.12.593749}, url = {https://www.biorxiv.org/content/early/2024/05/12/2024.05.12.593749}, author = {Jradi, Fadi M. and English, Brian P. and Brown, Timothy A. and Aaron, Jesse and Khuon, Satya and Galbraith, James A. and Galbraith, Catherine G. and Lavis, Luke D.} } @article {69527, title = {CRISPR-array-mediated imaging of non-repetitive and multiplex genomic loci in living cells.}, journal = {Nat Methods}, year = {2024}, month = {2024 Jul 04}, abstract = {

Dynamic imaging of genomic loci is key for understanding gene regulation, but methods for imaging genomes, in particular non-repetitive DNAs, are limited. We developed CRISPRdelight, a DNA-labeling system based on endonuclease-deficient CRISPR-Cas12a (dCas12a), with an engineered CRISPR array to track DNA location and motion. CRISPRdelight enables robust imaging of all examined 12 non-repetitive genomic loci in different cell lines. We revealed the confined movement of the CCAT1 locus (chr8q24) at the nuclear periphery for repressed expression and active motion in the interior nucleus for transcription. We uncovered the selective repositioning of HSP gene loci to nuclear speckles, including a remarkable relocation of HSPH1 (chr13q12) for elevated transcription during stresses. Combining CRISPR-dCas12a and RNA aptamers allowed multiplex imaging of four types of satellite DNA loci with a single array, revealing their spatial proximity to the nucleolus-associated domain. CRISPRdelight is a user-friendly and robust system for imaging and tracking genomic dynamics and regulation.

}, issn = {1548-7105}, doi = {10.1038/s41592-024-02333-3}, url = {https://www.doi.org/10.1038/s41592-024-02333-3}, author = {Yang, Liang-Zhong and Min, Yi-Hui and Liu, Yu-Xin and Gao, Bao-Qing and Liu, Xiao-Qi and Huang, Youkui and Wang, Haifeng and Yang, Li and Liu, Zhe J and Chen, Ling-Ling} } @article {69328, title = {Cryo-electron tomographic investigation of native hippocampal glutamatergic synapses}, journal = {eLife}, year = {2024}, month = {2024 Nov 11}, abstract = {

Chemical synapses are the major sites of communication between neurons in the nervous system and mediate either excitatory or inhibitory signaling. At excitatory synapses, glutamate is the primary neurotransmitter and upon release from presynaptic vesicles, is detected by postsynaptic glutamate receptors, which include ionotropic AMPA and NMDA receptors. Here, we have developed methods to identify glutamatergic synapses in brain tissue slices, label AMPA receptors with small gold nanoparticles (AuNPs), and prepare lamella for cryo-electron tomography studies. The targeted imaging of glutamatergic synapses in the lamella is facilitated by fluorescent pre- and postsynaptic signatures, and the subsequent tomograms allow for the identification of key features of chemical synapses, including synaptic vesicles, the synaptic cleft, and AuNP-labeled AMPA receptors. These methods pave the way for imaging brain regions at high resolution, using unstained, unfixed samples preserved under near-native conditions.

}, doi = {10.7554/eLife.98458}, url = {https://doi.org/10.7554/eLife.98458}, author = {Aya Matsui and Catherine Spangler and Johannes Elferich and Momoko Shiozaki and Nikki Jean and Xiaowei Zhao and Maozhen Qin and Haining Zhong and Zhiheng Yu and Eric Gouaux} } @article {69224, title = {CSPP1 stabilizes microtubules by capping both plus and minus ends.}, journal = {Journal of Molecular Cell Biology}, year = {2024}, month = {2024 Feb 22}, abstract = {

Although the dynamic instability of microtubules (MTs) is fundamental to many cellular functions, quiescent MTs with unattached free distal ends are commonly present and play important roles in various events to power cellular dynamics. However, how these free MT tips are stabilized remains poorly understood. Here, we report that centrosome and spindle pole protein 1 (CSPP1) caps and stabilizes both plus and minus ends of static MTs. Real-time imaging of laser-ablated MTs in live cells showed deposition of CSPP1 at the newly generated MT ends, whose dynamic instability was concomitantly suppressed. Consistently, MT ends in CSPP1-overexpressing cells were hyper-stabilized, while those in CSPP1-depleted cells were much more dynamic. This CSPP1-elicited stabilization of MTs was demonstrated to be achieved by suppressing intrinsic MT catastrophe and restricting the polymerization. Importantly, CSPP1-bound MTs were resistant to MCAK-mediated depolymerization. These findings delineate a previously uncharacterized CSPP1 activity that integrates MT end capping to orchestrate quiescent MTs.

}, issn = {1759-4685}, doi = {10.1093/jmcb/mjae007}, author = {Wang, Zhikai and Wang, Wenwen and Liu, Shuaiyu and Yang, Fengrui and Liu, Xu and Hua, Shasha and Zhu, Lijuan and Xu, Aoqing and Hill, Donald L and Wang, Dongmei and Jiang, Kai and Lippincott-Schwartz, Jennifer and Liu, Xing and Yao, Xuebiao} } @article {69140, title = {Cutting through stress.}, journal = {Nature Metabolism}, year = {2024}, month = {2024 Jan 02}, issn = {2522-5812}, doi = {10.1038/s42255-023-00946-0}, author = {Jasper, Luis A and Wang, Meng C} } @article {69568, title = {DaCapo: a modular deep learning framework for scalable 3D image segmentation}, journal = {arXiv}, year = {2024}, month = {2024 Aug 05}, abstract = {

DaCapo is a specialized deep learning library tailored to expedite the training and application of existing machine learning approaches on large, near-isotropic image data. In this correspondence, we introduce DaCapo{\textquoteright}s unique features optimized for this specific domain, highlighting its modular structure, efficient experiment management tools, and scalable deployment capabilities. We discuss its potential to improve access to large-scale, isotropic image segmentation and invite the community to explore and contribute to this open-source initiative.

}, doi = {10.48550/arXiv.2408.02834}, url = {https://doi.org/10.48550/arXiv.2408.02834}, author = {Patton, William and Jeff L Rhoades and Zouinkhi, Marwan and Ackerman, David G and Malin-Mayor, Caroline and Adjavon, Diane and Heinrich, Larissa and Bennett, Davis and Zubov, Yurii and Team, CellMap Project and Weigel, Aubrey and Funke, Jan} } @article {69602, title = {Data Release: High-Resolution Imaging and Segmentation of P7 Mouse Tissue Microarchitecture Using FIB-SEM and Machine Learning}, journal = {bioRxiv}, year = {2024}, month = {2024 Sep 07}, abstract = {

This report presents a comprehensive data release exploring the tissue microarchitecture of P7 aged mice using Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) combined with machine learning-based segmentations of nuclei. The study includes high-resolution 3D volumes and nucleus segmentations for seven vital tissues{\textemdash}pancreas, liver, kidney, heart, thymus, hippocampus, and skin{\textemdash}from a single mouse. The detailed datasets are openly accessible on OpenOrganelle.org, providing a valuable resource for the scientific community to support further research and collaboration.

}, doi = {10.1101/2024.09.05.611438}, url = {https://www.doi.org/10.1101/2024.09.05.611438}, author = {Ackerman, David and Avetissian, Emma and Bleck, Christopher K. E. and Bogovic, John A. and Innerberger, Michael and Korff, Wyatt and Li, Wei-Ping and Lu, Zhiyuan and Petruncio, Alyson and Preibisch, Stephan and Qiu, Wei and Jeff L Rhoades and Saalfeld, Stephan and Silva, Malan and Trautman, Eric T. and Vorimo, Rebecca and Weigel, Aubrey and Yu, Zhiheng and Zubov, Yurii and ,} } @article {69706, title = {Days-old zebrafish rapidly learn to recognize threatening agents through noradrenergic and forebrain circuits.}, journal = {Curr Biol}, year = {2024}, month = {2024 Dec 19}, abstract = {

Animals need to rapidly learn to recognize and avoid predators. This ability may be especially important for young animals due to their increased vulnerability. It is unknown whether, and how, nascent vertebrates are capable of such rapid learning. Here, we used a robotic predator-prey interaction assay to show that 1\ week after fertilization-a developmental stage where they have approximately 1\% the number of neurons of adults-zebrafish larvae rapidly and robustly learn to recognize a stationary object as a threat after the object pursues the fish for \~{}1\ min. Larvae continue to avoid the threatening object after it stops moving and can learn to distinguish threatening from non-threatening objects of a different color. Whole-brain functional imaging revealed the multi-timescale activity of noradrenergic neurons and forebrain circuits that encoded the threat. Chemogenetic ablation of those populations prevented the learning. Thus, a noradrenergic and forebrain multiregional network underlies the ability of young vertebrates to rapidly learn to recognize potential predators within their first week of life.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2024.11.057}, author = {Zocchi, Dhruv and Nguyen, Millen and Marquez-Legorreta, Emmanuel and Siwanowicz, Igor and Singh, Chanpreet and Prober, David A and Hillman, Elizabeth M C and Ahrens, Misha B} } @article {69567, title = {Decomposing heterogeneous dynamical systems with graph neural networks}, journal = {arXiv}, year = {2024}, month = {2024 Jul 27}, abstract = {

Natural physical, chemical, and biological dynamical systems are often complex, with heterogeneous components interacting in diverse ways. We show that graph neural networks can be designed to jointly learn the interaction rules and the structure of the heterogeneity from data alone. The learned latent structure and dynamics can be used to virtually decompose the complex system which is necessary to parameterize and infer the underlying governing equations. We tested the approach with simulation experiments of moving particles and vector fields that interact with each other. While our current aim is to better understand and validate the approach with simulated data, we anticipate it to become a generally applicable tool to uncover the governing rules underlying complex dynamics observed in nature.

}, doi = {10.48550/arXiv.2407.19160}, url = {https://doi.org/10.48550/arXiv.2407.19160}, author = {Allier, C{\'e}dric and Schneider, Magdalena C and Innerberger, Michael and Heinrich, Larissa and Bogovic, John A and Saalfeld, Stephan} } @article {69256, title = {Dendritic voltage imaging maps the biophysical basis of plateau potentials in the hippocampus}, journal = {bioRxiv}, year = {2024}, month = {2024 Mar 7}, abstract = {

Dendrites on neurons integrate synaptic inputs to determine spike timing. Dendrites also convey back-propagating action potentials (bAPs) which interact with synaptic inputs to produce plateau potentials and to mediate synaptic plasticity. The biophysical rules which govern the timing, spatial structures, and ionic character of dendritic excitations are not well understood. We developed molecular, optical, and computational tools to map sub-millisecond voltage dynamics throughout the dendritic trees of CA1 pyramidal neurons under diverse optogenetic and synaptic stimulus patterns, in acute brain slices. We observed history-dependent bAP propagation in distal dendrites, driven by locally generated Na+ spikes (dSpikes). Dendritic depolarization creates a transient window for dSpike propagation, opened by A-type KV channel inactivation, and closed by slow NaV inactivation. Collisions of dSpikes with synaptic inputs triggered calcium channel and N-methyl-D-aspartate receptor (NMDAR)-dependent plateau potentials, with accompanying complex spikes at the soma. This hierarchical ion channel network acts as a spike-rate accelerometer, providing an intuitive picture of how dendritic excitations shape associative plasticity rules.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2023.06.02.543490}, url = {https://www.biorxiv.org/content/early/2024/03/07/2023.06.02.543490}, author = {Pojeong Park and J. David Wong-Campos and Daniel Itkis and Byung Hun Lee and Yitong Qi and Hunter C. Davis and Jonathan B. Grimm and Sarah E. Plutkis and Luke Lavis and Adam Ezra Cohen} } @article {68919, title = {The density of regulatory information is a major determinant of evolutionary constraint on non-coding DNA in Drosophila}, journal = {Molecular Biology and Evolution}, volume = {41}, year = {2024}, month = {2024 Feb 01}, pages = {msae004}, abstract = {

The density and distribution of regulatory information in non-coding DNA of eukaryotic genomes is largely unknown. Evolutionary analyses have estimated that \~{}60\% of nucleotides in intergenic regions of the\ D. melanogaster\ genome is functionally relevant. This estimate is difficult to reconcile with the commonly accepted idea that enhancers are compact regulatory elements that generally encompass less than 1 kilobase of DNA. Here, we approached this issue through a functional dissection of the regulatory region of the gene\ shavenbaby\ (svb). Most of the \~{}90 kilobases of this large regulatory region is highly conserved in the genus\ Drosophila, though characterized enhancers occupy a small fraction of this region. By analyzing the regulation of\ svb\ in different contexts of\ Drosophila\ development, we found that the regulatory architecture that drives\ svb\ expression in the abdominal pupal epidermis is organized in a dramatically different way than the information that drives\ svb\ expression in the embryonic epidermis. While in the embryonic epidermis\ svb\ is activated by compact and dispersed enhancers,\ svb\ expression in the pupal epidermis is driven by large regions with enhancer activity, which occupy a great portion of the\ svb cis-regulatory DNA. We observed that other developmental genes also display a dense distribution of putative regulatory elements in their regulatory regions. Furthermore, we found that a large percentage of conserved non-coding DNA of the\ Drosophila\ genome is contained within putative regulatory DNA. These results suggest that part of the evolutionary constraint on non-coding DNA of\ Drosophila\ is explained by the density of regulatory information.

}, doi = {10.1093/molbev/msae004}, url = {https://doi.org/10.1093/molbev/msae004}, author = {Gonzalo Sabar{\'\i}s and Daniela M. Ort{\'\i}z and Ian Laiker and Ignacio Mayansky and Sujay Naik and Giacomo Cavalli and David L. Stern and Ella Preger-Ben Noon and Nicol{\'a}s Frankel} } @article {69317, title = {Detecting abnormal cell behaviors from dry mass time series}, journal = {Scientific Reports}, volume = {14}, year = {2024}, month = {2024 Mar 20}, abstract = {

The prediction of pathological changes on single cell behaviour is a challenging task for deep learning models. Indeed, in self-supervised learning methods, no prior labels are used for the training and all of the information for event predictions are extracted from the data themselves. We present here a novel self-supervised learning model for the detection of anomalies in a given cell population, StArDusTS. Cells are monitored over time, and analysed to extract time-series of dry mass values. We assessed its performances on different cell lines, showing a precision of 96\% in the automatic detection of anomalies. Additionally, anomaly detection was also associated with cell measurement errors inherent to the acquisition or analysis pipelines, leading to an improvement of the upstream methods for feature extraction. Our results pave the way to novel architectures for the continuous monitoring of cell cultures in applied research or bioproduction applications, and for the prediction of pathological cellular changes.

}, doi = {10.1038/s41598-024-57684-w}, url = {https://www.nature.com/articles/s41598-024-57684-whttps://www.nature.com/articles/s41598-024-57684-w.pdfhttps://www.nature.com/articles/s41598-024-57684-w.pdfhttps://www.nature.com/articles/s41598-024-57684-w}, author = {Bailly, Romain and Malfante, Marielle and Allier, C{\'e}dric and Paviolo, Chiara and Ghenim, Lamya and Padmanabhan, Kiran and Bardin, Sabine and Mars, J{\'e}r{\^o}me} } @article {69327, title = {Development of a First-in-Class RIPK1 Degrader to Enhance Antitumor Immunity}, journal = {Nat Commun}, volume = {15}, year = {2024}, month = {2024 Dec 16}, pages = {10683}, abstract = {

The scaffolding function of receptor interacting protein kinase 1 (RIPK1) confers intrinsic and extrinsic resistance to immune checkpoint blockades (ICBs) and emerges as a promising target for improving cancer immunotherapies. To address the challenge posed by a poorly defined binding pocket within the intermediate domain of RIPK1, here we harness proteolysis targeting chimera (PROTAC) technology to develop a RIPK1 degrader, LD4172. LD4172 exhibits potent and selective RIPK1 degradation both in vitro and in vivo. Degradation of RIPK1 by LD4172 triggers immunogenic cell death, enhances tumor-infiltrating lymphocyte responses, and sensitizes tumors to anti-PD1 therapy in female C57BL/6J mice. This work reports a RIPK1 degrader that serves as a chemical probe for investigating the scaffolding functions of RIPK1 and as a potential therapeutic agent to enhance tumor responses to ICBs therapy.

}, doi = {10.1038/s41467-024-55006-2}, url = {https://doi.org/10.1038/s41467-024-55006-2}, author = {Xin Yu and Dong Lu and Xiaoli Qi and Hanfeng Lin and Bryan L. Holloman and Feng Jin and Longyong Xu and Lang Ding and Weiyi Peng and Meng C. Wang and Xi Chen and Jin Wang} } @article {69693, title = {Development of a novel methodology for ascertaining scientific opinion and extent of agreement.}, journal = {PLoS One}, volume = {19}, year = {2024}, month = {2024 Dec 06}, pages = {e0313541}, abstract = {

We take up the challenge of developing an international network with capacity to survey the world{\textquoteright}s scientists on an ongoing basis, providing rich datasets regarding the opinions of scientists and scientific sub-communities, both at a time and also over time. The novel methodology employed sees local coordinators, at each institution in the network, sending survey invitation emails internally to scientists at their home institution. The emails link to a {\textquoteright}10 second survey{\textquoteright}, where the participant is presented with a single statement to consider, and a standard five-point Likert scale. In June 2023, a group of 30 philosophers and social scientists invited 20,085 scientists across 30 institutions in 12 countries to participate, gathering 6,807 responses to the statement Science has put it beyond reasonable doubt that COVID-19 is caused by a virus. The study demonstrates that it is possible to establish a global network to quickly ascertain scientific opinion on a large international scale, with high response rate, low opt-out rate, and in a way that allows for significant (perhaps indefinite) repeatability. Measuring scientific opinion in this new way would be a valuable complement to currently available approaches, potentially informing policy decisions and public understanding across diverse fields.

}, keywords = {COVID-19, Humans, Public Opinion, SARS-CoV-2, Science, Surveys and Questionnaires}, issn = {1932-6203}, doi = {10.1371/journal.pone.0313541}, author = {Vickers, Peter and Adamo, Ludovica and Alfano, Mark and Clark, Cory and Cresto, Eleonora and Cui, He and Dang, Haixin and Dells{\'e}n, Finnur and Dupin, Nathalie and Gradowski, Laura and Graf, Simon and Guevara, Aline and Hallap, Mark and Hamilton, Jesse and Hardey, Mariann and Helm, Paula and Landrum, Asheley and Levy, Neil and Machery, Edouard and Mills, Sarah and Muller, Se{\'a}n and Sheppard, Joanne and N K, Shinod and Slater, Matthew and Stegenga, Jacob and Strandin, Henning and Stuart, Michael T and Sweet, David and Tasdan, Ufuk and Taylor, Henry and Towler, Owen and Tulodziecki, Dana and Tworek, Heidi and Wallbank, Rebecca and Wiltsche, Harald and Mitchell Finnigan, Samantha} } @article {68794, title = {Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak-Keller-Segel chemotaxis model}, journal = {Proceedings of the National Academy of Sciences}, year = {2024}, month = {2024 Jan 09}, abstract = {

Chemotactic bacteria not only navigate chemical gradients, but also shape their environments by consuming and secreting attractants. Investigating how these processes influence the dynamics of bacterial populations has been challenging because of a lack of experimental methods for measuring spatial profiles of chemoattractants in real time. Here, we use a fluorescent sensor for aspartate to directly measure bacterially generated chemoattractant gradients during collective migration. Our measurements show that the standard Patlak-Keller-Segel model for collective chemotactic bacterial migration breaks down at high cell densities. To address this, we propose modifications to the model that consider the impact of cell density on bacterial chemotaxis and attractant consumption. With these changes, the model explains our experimental data across all cell densities, offering new insight into chemotactic dynamics. Our findings highlight the significance of considering cell density effects on bacterial behavior, and the potential for fluorescent metabolite sensors to shed light on the complex emergent dynamics of bacterial communities.

}, doi = {10.1073/pnas.230925112}, url = {https://doi.org/10.1073/pnas.230925112}, author = {Trung V. Phan and Henry H. Mattingly and Lam Vo and Jonathan S. Marvin and Loren L. Looger and Thierry Emonet} } @article {69710, title = {Discovery of neuronal cell types by pairing whole cell reconstructions with RNA expression profiles}, journal = {bioRxiv}, year = {2024}, month = {12/2024}, abstract = {

Effective classification of neuronal cell types requires both molecular and morphological descriptors to be collected in situ at single cell resolution. However, current spatial transcriptomics techniques are not compatible with imaging workflows that successfully reconstruct the morphology of complete axonal projections. Here, we introduce a new methodology that combines tissue clearing, submicron whole-brain two photon imaging, and Expansion-Assisted Iterative Fluorescence In Situ Hybridization (EASI-FISH) to assign molecular identities to fully reconstructed neurons in the mouse brain, which we call morphoFISH. We used morphoFISH to molecularly identify a previously unknown population of cingulate neurons projecting ipsilaterally to the dorsal striatum and contralaterally to higher-order thalamus. By pairing whole-brain morphometry, improved techniques for nucleic acid preservation and spatial gene expression, morphoFISH offers a quantitative solution for discovery of multimodal cell types and complements existing techniques for characterization of increasingly fine-grained cellular heterogeneity in brain circuits.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2024.12.30.630829}, url = {https://www.biorxiv.org/content/early/2024/12/31/2024.12.30.630829}, author = {The MouseLight Project Team and Ferreira, Tiago A. and Eddison, Mark and Copeland, Monique and Lay, Mary and Tenshaw, Emily and Weldon, Monet and Schauder, David and Olbris, Donald J. and Rokicki, Konrad and Spruston, Nelson and Tillberg, Paul W. and Korff, Wyatt and Dudman, Joshua T.} } @article {69701, title = {Distinct roles of ascorbic acid in extracellular vesicles and free form: Implications for metabolism and oxidative stress in presymptomatic Huntington{\textquoteright}s disease.}, journal = {Free Radic Biol Med}, volume = {227}, year = {2024}, month = {2024 Dec 09}, pages = {521-535}, abstract = {

Huntington{\textquoteright}s disease (HD) is a neurodegenerative disorder caused by a CAG trinucleotide repeat expansion in the first exon of the huntingtin gene. The huntingtin protein (Htt) is ubiquitously expressed and localized in several organelles, including endosomes, where it plays an essential role in intracellular trafficking. Presymptomatic HD is associated with a failure in energy metabolism and oxidative stress. Ascorbic acid is a potent antioxidant that plays a key role in modulating neuronal metabolism and is highly concentrated in the brain. During synaptic activity, neurons take up ascorbic acid released by glial cells; however, this process is disrupted in HD. In this study, we aim to elucidate the molecular and cellular mechanisms underlying this dysfunction. Using an electrophysiological approach in presymptomatic YAC128 HD slices, we observed decreased ascorbic acid flux from astrocytes to neurons, which altered neuronal metabolic substrate preferences. Ascorbic acid efflux and recycling were also decreased in cultured astrocytes from YAC128 HD mice. We confirmed our findings using GFAP-HD160Q, an HD mice model expressing mutant N-terminal Htt mainly in astrocytes. For the first time, we demonstrated that ascorbic acid is released from astrocytes via extracellular vesicles (EVs). Decreased number of particles and exosomal markers were observed in EV fractions from cultured YAC128 HD astrocytes and Htt-KD cells. We observed reduced number of multivesicular bodies (MVBs) in YAC128 HD striatum via electron microscopy, suggesting mutant Htt alters MVB biogenesis. EVs containing ascorbic acid effectively reduced reactive oxygen species, whereas "free" ascorbic acid played a role in modulating neuronal metabolic substrate preferences. These findings suggest that the early redox imbalance observed in HD arises from a reduced release of ascorbic acid-containing EVs by astrocytes. Meanwhile, a decrease in "free" ascorbic acid likely contributes to presymptomatic metabolic impairment.

}, issn = {1873-4596}, doi = {10.1016/j.freeradbiomed.2024.12.001}, url = {https://doi.org/10.1016/j.freeradbiomed.2024.12.001}, author = {Beltr{\'a}n, Felipe A and Torres-D{\'\i}az L, Leandro and Troncoso-Escudero, Paulina and Villalobos-Gonz{\'a}lez, Juan and Mayorga-Weber, Gonzalo and Lara, Marcelo and Covarrubias-Pinto, Adriana and Valdivia, Sharin and Vicencio, Isidora and Papic, Eduardo and Paredes-Mart{\'\i}nez, Carolina and Silva-Janu{\`a}rio, Mara E and Rojas, Alejandro and daSilva, Luis L P and Court, Felipe and Rosas-Arellano, Abraham and B{\'a}tiz, Luis Federico and Rojas, Patricio and Rivera, Francisco J and Castro, Maite A} } @article {69173, title = {Distributed fMRI dynamics predict distinct EEG rhythms across sleep and wakefulness.}, journal = {bioRxiv}, year = {2024}, month = {2024 Jan 30}, abstract = {

The brain exhibits rich oscillatory dynamics that vary across tasks and states, such as the EEG oscillations that define sleep. These oscillations play critical roles in cognition and arousal, but the brainwide mechanisms underlying them are not yet described. Using simultaneous EEG and fast fMRI in subjects drifting between sleep and wakefulness, we developed a machine learning approach to investigate which brainwide fMRI dynamics predict alpha (8-12 Hz) and delta (1-4 Hz) rhythms. We predicted moment-by-moment EEG power from fMRI activity in held-out subjects, and found that information about alpha power was represented by a remarkably small set of regions, segregated in two distinct networks linked to arousal and visual systems. Conversely, delta rhythms were diffusely represented on a large spatial scale across the cortex. These results identify distributed networks that predict delta and alpha rhythms, and establish a computational framework for investigating fMRI brainwide dynamics underlying EEG oscillations.

}, doi = {10.1101/2024.01.29.577429}, url = {https://doi.org/10.1101/2024.01.29.577429}, author = {Leandro P. L. Jacob and Sydney M. Bailes and Stephanie D. Williams and Carsen Stringer and Laura D. Lewis} } @article {69318, title = {Diversification of small RNA pathways underlies germline RNA interference incompetence in wild Caenorhabditis elegans strains.}, journal = {Genetics}, volume = {226}, year = {2024}, month = {2024 Jan 3}, abstract = {

The discovery that experimental delivery of dsRNA can induce gene silencing at target genes revolutionized genetics research, by both uncovering essential biological processes and creating new tools for developmental geneticists. However, the efficacy of exogenous RNA interference (RNAi) varies dramatically within the Caenorhabditis elegans natural population, raising questions about our understanding of RNAi in the lab relative to its activity and significance in nature. Here, we investigate why some wild strains fail to mount a robust RNAi response to germline targets. We observe diversity in mechanism: in some strains, the response is stochastic, either on or off among individuals, while in others, the response is consistent but delayed. Increased activity of the Argonaute PPW-1, which is required for germline RNAi in the laboratory strain N2, rescues the response in some strains but dampens it further in others. Among wild strains, genes known to mediate RNAi exhibited very high expression variation relative to other genes in the genome as well as allelic divergence and strain-specific instances of pseudogenization at the sequence level. Our results demonstrate functional diversification in the small RNA pathways in C. elegans and suggest that RNAi processes are evolving rapidly and dynamically in nature.

}, keywords = {Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Germ Cells, Humans, RNA Interference, RNA, Double-Stranded, RNA, Small Interfering}, issn = {1943-2631}, doi = {10.1093/genetics/iyad191}, author = {Chou, Han Ting and Valencia, Francisco and Alexander, Jacqueline C and Bell, Avery Davis and Deb, Diptodip and Pollard, Daniel A and Paaby, Annalise B} } @article {69633, title = {A Drosophila computational brain model reveals sensorimotor processing.}, journal = {Nature}, volume = {634}, year = {2024}, month = {2024 Oct 02}, pages = {210-219}, abstract = {

The recent assembly of the adult Drosophila melanogaster central brain connectome, containing more than 125,000 neurons and 50 million synaptic connections, provides a template for examining sensory processing throughout the brain. Here we create a leaky integrate-and-fire computational model of the entire Drosophila brain, on the basis of neural connectivity and neurotransmitter identity, to study circuit properties of feeding and grooming behaviours. We show that activation of sugar-sensing or water-sensing gustatory neurons in the computational model accurately predicts neurons that respond to tastes and are required for feeding initiation. In addition, using the model to activate neurons in the feeding region of the Drosophila brain predicts those that elicit motor neuron firing-a testable hypothesis that we validate by optogenetic activation and behavioural studies. Activating different classes of gustatory neurons in the model makes accurate predictions of how several taste modalities interact, providing circuit-level insight into aversive and appetitive taste processing. Additionally, we applied this model to mechanosensory circuits and found that computational activation of mechanosensory neurons predicts activation of a small set of neurons comprising the antennal grooming circuit, and accurately describes the circuit response upon activation of different mechanosensory subtypes. Our results demonstrate that modelling brain circuits using only synapse-level connectivity and predicted neurotransmitter identity generates experimentally testable hypotheses and can describe complete sensorimotor transformations.

}, keywords = {Animals, Brain, Computer Simulation, Connectome, Drosophila melanogaster, Feeding Behavior, Female, Grooming, Male, Models, Neurological, Motor Neurons, Optogenetics, Synapses, Taste}, issn = {1476-4687}, doi = {10.1038/s41586-024-07763-9}, url = {https://doi.org/10.1038/s41586-024-07763-9}, author = {Shiu, Philip K and Sterne, Gabriella R and Spiller, Nico and Franconville, Romain and Sandoval, Andrea and Zhou, Joie and Simha, Neha and Kang, Chan Hyuk and Yu, Seongbong and Kim, Jinseop S and Dorkenwald, Sven and Matsliah, Arie and Schlegel, Philipp and Yu, Szi-Chieh and McKellar, Claire E and Sterling, Amy and Costa, Marta and Eichler, Katharina and Bates, Alexander Shakeel and Eckstein, Nils and Funke, Jan and Jefferis, Gregory S X E and Murthy, Mala and Bidaye, Salil S and Hampel, Stefanie and Seeds, Andrew M and Scott, Kristin} } @article {68830, title = {Dynamic 1D Search and Processive Nucleosome Translocations by RSC and ISW2 Chromatin Remodelers}, journal = {eLife}, year = {2024}, month = {2024 Mar 18}, abstract = {

Eukaryotic gene expression is linked to chromatin structure and nucleosome positioning by ATP-dependent chromatin remodelers that establish and maintain nucleosome-depleted regions (NDRs) near transcription start sites. Conserved yeast RSC and ISW2 remodelers exert antagonistic effects on nucleosomes flanking NDRs, but the temporal dynamics of remodeler search, engagement, and directional nucleosome mobilization for promoter accessibility are unknown. Using optical tweezers and two-color single-particle imaging, we investigated the Brownian diffusion of RSC and ISW2 on free DNA and sparse nucleosome arrays. RSC and ISW2 rapidly scan DNA by one-dimensional hopping and sliding, respectively, with dynamic collisions between remodelers followed by recoil or apparent co-diffusion. Static nucleosomes block remodeler diffusion resulting in remodeler recoil or sequestration. Remarkably, both RSC and ISW2 use ATP hydrolysis to translocate mono-nucleosomes processively at ~30 bp/s on extended linear DNA under tension. Processivity and opposing push-pull directionalities of nucleosome translocation shown by RSC and ISW2 shape the distinctive landscape of promoter chromatin.

}, doi = {10.7554/eLife.91433}, url = {https://doi.org/10.7554/eLife.91433}, author = {Jee Min Kim and Claudia C. Carcamo and Sina Jazani and Zepei Xie and Xinyu A. Feng and Matthew Poyton and Katie L. Holland and Jonathan B. Grimm and Luke D. Lavis and Taekjip Ha and Carl Wu} } @article {69516, title = {Dynamic assemblies of parvalbumin interneurons in brain oscillations.}, journal = {Neuron}, year = {2024}, month = {2024 Jun 02}, abstract = {

Brain oscillations are crucial for perception, memory, and behavior. Parvalbumin-expressing (PV) interneurons are critical for these oscillations, but their population dynamics remain unclear. Using voltage imaging, we simultaneously recorded membrane potentials in up to 26 PV interneurons in\ vivo during hippocampal ripple oscillations in mice. We found that PV cells generate ripple-frequency rhythms by forming highly dynamic cell assemblies. These assemblies exhibit rapid and significant changes from cycle to cycle, varying greatly in both size and membership. Importantly, this variability is not just random spiking failures of individual neurons. Rather, the activities of other PV cells contain significant information about whether a PV cell spikes or not in a given cycle. This coordination persists without network oscillations, and it exists in subthreshold potentials even when the cells are not spiking. Dynamic assemblies of interneurons may provide a new mechanism to modulate postsynaptic dynamics and impact cognitive functions flexibly and rapidly.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2024.05.015}, author = {Huang, Yi-Chieh and Chen, Hui-Ching and Lin, Yu-Ting and Lin, Szu-Ting and Zheng, Qinsi and Abdelfattah, Ahmed S and Lavis, Luke D and Schreiter, Eric R and Lin, Bei-Jung and Chen, Tsai-Wen} } @article {69692, title = {Elevated IL-22 as a result of stress-induced gut leakage suppresses septal neuron activation to ameliorate anxiety-like behavior.}, journal = {Immunity}, year = {2024}, month = {2024 Dec 04}, pages = {S1074-7613(24)00523-5}, abstract = {

Psychological stress and its sequelae pose a major challenge to public health. Immune activation is conventionally thought to aggravate stress-related mental diseases such as anxiety disorders and depression. Here, we sought to identify potentially beneficial consequences of immune activation in response to stress. We showed that stress led to increased interleukin (IL)-22 production in the intestine as a result of stress-induced gut leakage. IL-22 was both necessary and sufficient to attenuate stress-induced anxiety behaviors in mice. More specifically, IL-22 gained access to the septal area of the brain and directly suppressed neuron activation. Furthermore, human patients with clinical depression displayed reduced IL-22 levels, and exogenous IL-22 treatment ameliorated depressive-like behavior elicited by chronic stress in mice. Our study thus identifies a gut-brain axis in response to stress, whereby IL-22 reduces neuronal activation and concomitant anxiety behavior, suggesting that early immune activation can provide protection against psychological stress.

}, issn = {1097-4180}, doi = {10.1016/j.immuni.2024.11.008}, author = {Xia, Mengyu and Lu, Junmei and Lan, Jiabin and Teng, Teng and Shiao, Rani and Sun, Hongbin and Jin, Zheyu and Liu, Xueer and Wang, Jie and Wu, Hongyan and Wang, Changchun and Yi, Han and Qi, Qingqing and Li, Jixi and Schneeberger, Marc and Shen, Wei and Lu, Boxun and Chen, Lei and Ilanges, Anoj and Zhou, Xinyu and Yu, Xiaofei} } @article {69543, title = {Elucidating and Optimizing the Photochemical Mechanism of Coumarin-Caged Tertiary Amines.}, journal = {J Am Chem Soc}, year = {2024}, month = {2024 Jul 18}, abstract = {

Photoactivatable or "caged" pharmacological agents combine the high spatiotemporal specificity of light application with the molecular specificity of drugs. A key factor in all optopharmacology experiments is the mechanism of uncaging, which dictates the photochemical quantum yield and determines the byproducts produced by the light-driven chemical reaction. In previous work, we demonstrated that coumarin-based photolabile groups could be used to cage tertiary amine drugs as quaternary ammonium salts. Although stable, water-soluble, and useful for experiments in brain tissue, these first-generation compounds exhibit relatively low uncaging quantum yield (Φ \< 1\%) and release the toxic byproduct formaldehyde upon photolysis. Here, we elucidate the photochemical mechanisms of coumarin-caged tertiary amines and then optimize the major pathway using chemical modification. We discovered that the combination of 3,3-dicarboxyazetidine and bromine substituents shift the mechanism of release to heterolysis, eliminating the formaldehyde byproduct and giving photolabile tertiary amine drugs with Φ \> 20\%-a 35-fold increase in uncaging efficiency. This new "ABC" cage allows synthesis of improved photoactivatable derivatives of escitalopram and nicotine along with a novel caged agonist of the oxytocin receptor.

}, issn = {1520-5126}, doi = {10.1021/jacs.4c03092}, author = {Banala, Sambashiva and Jin, Xiao-Tao and Dilan, Tanya L and Sheu, Shu-Hsien and Clapham, David E and Drenan, Ryan M and Lavis, Luke D} } @article {69544, title = {Encoding of cerebellar dentate neuronal activity during visual attention in rhesus macaques}, journal = {bioRxiv}, year = {2024}, month = {2024 Jul 20}, abstract = {

The role of cerebellum in controlling eye movements is well established, but its contribution to more complex forms of visual behavior has remained elusive. To study cerebellar activity during visual attention we recorded extracellular activity of dentate nucleus (DN) neurons in two non-human primates (NHPs). NHPs were trained to read the direction indicated by a peripheral visual stimulus while maintaining fixation at the center, and report the direction of the cue by performing a saccadic eye movement into the same direction following a delay. We found that single unit DN neurons modulated spiking activity over the entire time-course of the task, and that their activity often bridged temporally separated intra-trial events, yet in a heterogeneous manner. To better understand the heterogeneous relationship between task structure, behavioral performance and neural dynamics, we constructed a behavioral, an encoding and a decoding model. Both NHPs showed different behavioral strategies, which influenced the performance. Activity of the DN neurons reflected the unique strategies, with the direction of the visual stimulus frequently being encoded long before an upcoming saccade. Retrograde labeling of the recording location indicated that these neurons receive predominantly inputs from Purkinje cells in the lateral cerebellum as well as neurons of the principal olive and medial pons, all regions known to connect with neurons in the prefrontal cortex contributing to planning of saccades. Together, our results highlight that DN neurons can dynamically modulate their activity during a visual attention task, comprising not only sensorimotor but also cognitive attentional components.

}, doi = {10.1101/2024.07.18.604119}, url = {https://www.doi.org/10.1101/2024.07.18.604119}, author = {Flierman, Nico A. and Koay, Sue Ann and van Hoogstraten, Willem S. and Ruigrok, Tom J.H. and Roelfsema, Pieter R. and Badura, Aleksandra and De Zeeuw, Chris I.} } @article {69225, title = {An engineered biosensor enables dynamic aspartate measurements in living cells.}, journal = {Elife}, volume = {12}, year = {2024}, month = {2024 Feb 23}, abstract = {

Intracellular levels of the amino acid aspartate are responsive to changes in metabolism in mammalian cells and can correspondingly alter cell function, highlighting the need for robust tools to measure aspartate abundance. However, comprehensive understanding of aspartate metabolism has been limited by the throughput, cost, and static nature of the mass spectrometry (MS)-based measurements that are typically employed to measure aspartate levels. To address these issues, we have developed a green fluorescent protein (GFP)-based sensor of aspartate (jAspSnFR3), where the fluorescence intensity corresponds to aspartate concentration. As a purified protein, the sensor has a 20-fold increase in fluorescence upon aspartate saturation, with dose-dependent fluorescence changes covering a physiologically relevant aspartate concentration range and no significant off target binding. Expressed in mammalian cell lines, sensor intensity correlated with aspartate levels measured by MS and could resolve temporal changes in intracellular aspartate from genetic, pharmacological, and nutritional manipulations. These data demonstrate the utility of jAspSnFR3 and highlight the opportunities it provides for temporally resolved and high-throughput applications of variables that affect aspartate levels.

}, keywords = {Animals, Aspartic Acid, Biosensing Techniques, Cell Line, Green Fluorescent Proteins, Mammals}, issn = {2050-084X}, doi = {10.7554/eLife.90024}, author = {Davidsen, Kristian and Marvin, Jonathan S and Aggarwal, Abhi and Brown, Timothy A and Sullivan, Lucas B} } @article {69145, title = {Epigenetic priming of embryonic lineages in the mammalian epiblast}, journal = {bioRxiv}, year = {2024}, month = {2024 Jan 11}, abstract = {

Understanding the diversification of mammalian cell lineages is an essential to embryonic development, organ regeneration and tissue engineering. Shortly after implantation in the uterus, the pluripotent cells of the mammalian epiblast generate the three germ layers: ectoderm, mesoderm and endoderm1. Although clonal analyses suggest early specification of epiblast cells towards particular cell lineages2{\textendash}4, single-cell transcriptomes do not identify lineage-specific markers in the epiblast5{\textendash}11\ and thus, the molecular regulation of such specification remains unknow. Here, we studied the epigenetic landscape of single epiblast cells, which revealed lineage priming towards endoderm, ectoderm or mesoderm. Unexpectedly, epiblast cells with mesodermal priming show a strong signature for the endothelial/endocardial fate, suggesting early specification of this lineage aside from other mesoderm. Through clonal analysis and live imaging, we show that endothelial precursors show early lineage divergence from the rest of mesodermal derivatives. In particular, cardiomyocytes and endocardial cells show limited lineage relationship, despite being temporally and spatially co-recruited during gastrulation. Furthermore, analysing the live tracks of single cells through unsupervised classification of cell migratory activity, we found early behavioral divergence of endothelial precursors shortly after the onset of mesoderm migration towards the cardiogenic area. These results provide a new model for the phenotypically silent specification of mammalian cell lineages in pluripotent cells of the epiblast and modify current knowledge on the sequence and timing of cardiovascular lineages diversification.

}, doi = {10.1101/2024.01.11.575188}, url = {https://doi.org/10.1101/2024.01.11.575188}, author = {Miquel Sendra and Katie McDole and Daniel Jimenez-Carretero and Juan de Dios Hourcade and Susana Temi{\~n}o and L{\'e}o Guignard and Philipp J Keller and F{\'a}tima S{\'a}nchez-Cabo and Jorge N. Dom{\'\i}nguez and Miguel Torres} } @article {69218, title = {Epigenetic repression of cFos supports sequential formation of distinct spatial memories.}, journal = {bioRxiv}, year = {2024}, month = {2024 Feb 21}, abstract = {

Expression of the immediate early gene cFos modifies the epigenetic landscape of activated neurons with downstream effects on synaptic plasticity. The production of cFos is inhibited by a long-lived isoform of another Fos family gene, ΔFosB. It has been speculated that this negative feedback mechanism may be critical for protecting episodic memories from being overwritten by new information. Here, we investigate the influence of ΔFosB inhibition on cFos expression and memory. Hippocampal neurons in slice culture produce more cFos on the first day of stimulation compared to identical stimulation on the following day. This downregulation affects all hippocampal subfields and requires histone deacetylation. Overexpression of ΔFosB in individual pyramidal neurons effectively suppresses cFos, indicating that accumulation of ΔFosB is the causal mechanism. Water maze training of mice over several days leads to accumulation of ΔFosB in granule cells of the dentate gyrus, but not in CA3 and CA1. Because the dentate gyrus is thought to support pattern separation and cognitive flexibility, we hypothesized that inhibiting the expression of ΔFosB would affect reversal learning, i.e., the ability to successively learn new platform locations in the water maze. The results indicate that pharmacological HDAC inhibition, which prevents cFos repression, impairs reversal learning, while learning and memory of the initial platform location remain unaffected. Our study supports the hypothesis that epigenetic mechanisms tightly regulate cFos expression in individual granule cells to orchestrate the formation of time-stamped memories.

}, doi = {10.1101/2024.02.16.580703}, url = {https://doi.org/10.1101/2024.02.16.580703}, author = {Andreas Franzelin and Paul J. Lamothe-Molina and Christine E. Gee and Andrey Formozov and Eric R Schreiter and Fabio Morellini and Thomas Glenn Oertner} } @article {69319, title = {Evaluation of the Cytosolic Uptake of HaloTag Using a pH-Sensitive Dye}, journal = {ACS Chemical Biology}, year = {2024}, month = {2024 Mar 25}, abstract = {

The efficient cytosolic delivery of proteins is critical for advancing novel therapeutic strategies. Current delivery methods are severely limited by endosomal entrapment, and detection methods lack sophistication in tracking the fate of delivered protein cargo. HaloTag, a commonly used protein in chemical biology and a challenging delivery target, is an exceptional model system for understanding and exploiting cellular delivery. Here, we employed a combinatorial strategy to direct HaloTag to the cytosol. We established the use of Virginia Orange, a pH-sensitive fluorophore, and Janelia Fluor 585, a similar but pH-agnostic fluorophore, in a fluorogenic assay to ascertain protein localization within human cells. Using this assay, we investigated HaloTag delivery upon modification with cell-penetrating peptides, carboxyl group esterification, and cotreatment with an endosomolytic agent. We found efficacious cytosolic entry with two distinct delivery methods. This study expands the toolkit for detecting the cytosolic access of proteins and highlights that multiple intracellular delivery strategies can be used synergistically to effect cytosolic access. Moreover, HaloTag is poised to serve as a platform for the delivery of varied cargo into human cells.

}, issn = {1554-8929}, doi = {10.1021/acschembio.3c0071310.1021/acschembio.3c00713.s001}, url = {https://pubs.acs.org/doi/10.1021/acschembio.3c00713https://pubs.acs.org/doi/pdf/10.1021/acschembio.3c00713https://pubs.acs.org/doi/pdf/10.1021/acschembio.3c00713https://pubs.acs.org/doi/suppl/10.1021/acschembio.3c00713/suppl_file/cb3c00713_si_001.pdf}, author = {Giancola, JoLynn B. and Grimm, Jonathan B. and Jun, Joomyung V. and Petri, Yana D. and Lavis, Luke D. and Raines, Ronald T.} } @article {69397, title = {Expansion of in vitro Toxoplasma gondii cysts using enzymatically enhanced ultrastructure expansion microscopy}, journal = {mSphere}, volume = {e0032224}, year = {2024}, month = {2024 Aug 27}, abstract = {

Expansion microscopy (ExM) is an innovative approach to achieve super-resolution images without using super-resolution microscopes, based on the physical expansion of the sample. The advent of ExM has unlocked the detail of super-resolution images for a broader scientific circle, lowering the cost and entry skill requirements for the field. One of its branches, ultrastructure expansion microscopy (U-ExM), has become popular among research groups studying apicomplexan parasites, including the acute stage of Toxoplasma gondii infection. Here, we show that the chronic cyst-forming stage of Toxoplasma, however, resists U-ExM expansion, impeding precise protein localization. We then solve the in vitro cyst{\textquoteright}s resistance to denaturation required for successful U-ExM. As the cyst{\textquoteright}s main structural protein CST1 contains a mucin domain, we added an enzymatic digestion step using the pan-mucinase StcE prior to the expansion protocol. This allowed full expansion of the cysts in fibroblasts and primary neuronal cell culture without disrupting immunofluorescence analysis of parasite proteins. Using StcE-enhanced U-ExM, we clarified the localization of the GRA2 protein, which is important for establishing a normal cyst, observing GRA2 granules spanning across the CST1 cyst wall. The StcE-U-ExM protocol allows accurate pinpointing of proteins in the bradyzoite cyst, which will greatly facilitate investigation of the underlying biology of cyst formation and its vulnerabilities.

}, doi = {10.1128/msphere.00322-24}, url = {https://www.doi.org/10.1128/msphere.00322-24}, author = {Bondarenko, Kseniia and Limoge, Floriane and Pedram, Kayvon and Gissot, Mathieu and Young, Joanna C.} } @article {69154, title = {Failure to mate enhances investment in behaviors that may promote mating reward and impairs the ability to cope with stressors via a subpopulation of Neuropeptide F receptor neurons.}, journal = {PLoS Genetics}, volume = {20}, year = {2024}, month = {2024 Jan 18}, pages = {e1011054}, abstract = {

Living in dynamic environments such as the social domain, where interaction with others determines the reproductive success of individuals, requires the ability to recognize opportunities to obtain natural rewards and cope with challenges that are associated with achieving them. As such, actions that promote survival and reproduction are reinforced by the brain reward system, whereas coping with the challenges associated with obtaining these rewards is mediated by stress-response pathways, the activation of which can impair health and shorten lifespan. While much research has been devoted to understanding mechanisms underlying the way by which natural rewards are processed by the reward system, less attention has been given to the consequences of failure to obtain a desirable reward. As a model system to study the impact of failure to obtain a natural reward, we used the well-established courtship suppression paradigm in Drosophila melanogaster as means to induce repeated failures to obtain sexual reward in male flies. We discovered that beyond the known reduction in courtship actions caused by interaction with non-receptive females, repeated failures to mate induce a stress response characterized by persistent motivation to obtain the sexual reward, reduced male-male social interaction, and enhanced aggression. This frustrative-like state caused by the conflict between high motivation to obtain sexual reward and the inability to fulfill their mating drive impairs the capacity of rejected males to tolerate stressors such as starvation and oxidative stress. We further show that sensitivity to starvation and enhanced social arousal is mediated by the disinhibition of a small population of neurons that express receptors for the fly homologue of neuropeptide Y. Our findings demonstrate for the first time the existence of social stress in flies and offers a framework to study mechanisms underlying the crosstalk between reward, stress, and reproduction in a simple nervous system that is highly amenable to genetic manipulation.

}, keywords = {Animals, Drosophila melanogaster, Female, Humans, Male, Neurons, Neuropeptides, Reproduction, Reward, Sexual Behavior, Animal}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1011054}, author = {Ryvkin, Julia and Omesi, Liora and Kim, Yong-Kyu and Levi, Mali and Pozeilov, Hadar and Barak-Buchris, Lital and Agranovich, Bella and Abramovich, Ifat and Gottlieb, Eyal and Jacob, Avi and N{\"a}ssel, Dick R and Heberlein, Ulrike and Shohat-Ophir, Galit} } @article {69649, title = {FITM2 deficiency results in ER lipid accumulation, ER stress, and reduced apolipoprotein B lipidation and VLDL triglyceride secretion in vitro and in mouse liver.}, journal = {Mol Metab}, year = {2024}, month = {2024 Oct 18}, pages = {102048}, abstract = {

OBJECTIVES: Triglycerides (TGs) associate with apolipoprotein B100 (apoB100) to form very low density lipoproteins (VLDLs) in the liver. The repertoire of factors that facilitate this association is incompletely understood. FITM2, an integral endoplasmic reticulum (ER) protein, was originally discovered as a factor participating in cytosolic lipid droplet (LD) biogenesis in tissues that do not form VLDL. We hypothesized that in the liver, in addition to promoting cytosolic LD formation, FITM2 would also transfer TG from its site of synthesis in the ER membrane to nascent VLDL particles within the ER lumen.

METHODS: Experiments were conducted using a rat hepatic cell line (McArdle-RH7777, or McA cells), an established model of mammalian lipoprotein metabolism, and mice. FITM2 expression was reduced using siRNA in cells and by liver specific cre-recombinase mediated deletion of the Fitm2 gene in mice. Effects of FITM2 deficiency on VLDL assembly and secretion in\ vitro and in\ vivo were measured by multiple methods, including density gradient ultracentrifugation, chromatography, mass spectrometry, stimulated Raman scattering (SRS) microscopy, sub-cellular fractionation, immunoprecipitation, immunofluorescence, and electron microscopy.

MAIN FINDINGS: 1) FITM2-deficient hepatic cells in\ vitro and in\ vivo secrete TG-depleted VLDL particles, but the number of particles is unchanged compared to controls; 2) FITM2 deficiency in mice on a high fat diet (HFD) results in decreased plasma TG levels. The number of apoB100-containing lipoproteins remains similar, but shift from VLDL to low density lipoprotein (LDL) density; 3) Both in\ vitro and in\ vivo, when TG synthesis is stimulated and FITM2 is deficient, TG accumulates in the ER, and despite its availability this pool is unable to fully lipidate apoB100 particles; 4) FITM2 deficiency disrupts ER morphology and results in ER stress.

PRINCIPAL CONCLUSIONS: The results suggest that FITM2 contributes to VLDL lipidation, especially when newly synthesized hepatic TG is in abundance. In addition to its fundamental importance in VLDL assembly, the results also suggest that under dysmetabolic conditions, FITM2 may be an important factor in the partitioning of TG between cytosolic LDs and VLDL particles.

}, issn = {2212-8778}, doi = {10.1016/j.molmet.2024.102048}, url = {https://doi.org/10.1016/j.molmet.2024.102048}, author = {Wang, Haizhen and Nikain, Cyrus and Fortounas, Konstantinos I and Amengual, Jaime and Tufanli, Ozlem and La Forest, Maxwell and Yu, Yong and Wang, Meng C and Watts, Russell and Lehner, Richard and Qiu, Yunping and Cai, Min and Kurland, Irwin J and Goldberg, Ira J and Rajan, Sujith and Hussain, M Mahmood and Brodsky, Jeffrey L and Fisher, Edward A} } @article {69223, title = {Fluorescence complementation-based FRET imaging reveals centromere assembly dynamics.}, journal = {Molecular Biology of the Cell}, year = {2024}, month = {2024 Feb 21}, pages = {mbcE23090379}, abstract = {

Visualization of specific molecules and their assembly in real time and space is essential to delineate how cellular dynamics and signaling circuit are orchestrated during cell division cycle. Our recent studies reveal structural insights into human centromere-kinetochore core CCAN complex. Here we introduce a method for optically imaging trimeric and tetrameric protein interactions at nanometer spatial resolution in live cells using fluorescence complementation-based F{\"o}rster resonance energy transfer (FC-FRET). Complementary fluorescent protein molecules were first used to visualize dimerization followed by FRET measurements. Using FC- FRET, we visualized centromere CENP-SXTW tetramer assembly dynamics in live cells, and dimeric interactions between CENP-TW dimer and kinetochore protein Spc24/25 dimer in dividing cells. We further delineated the interactions of monomeric CENP-T with Spc24/25 dimer in dividing cells. Surprisingly, our analyses revealed critical role of CDK1 kinase activity in the initial recruitment of Spc24/25 by CENP-T. However, interactions between CENP-T and Spc24/25 during chromosome segregation is independent of CDK1. Thus, FC-FRET provides a unique approach to delineate spatiotemporal dynamics of trimerized and tetramerized proteins at nanometer scale and establishes a platform to report the precise regulation of multimeric protein interactions in space and time in live cells.

}, issn = {1939-4586}, doi = {10.1091/mbc.E23-09-0379}, author = {Dou, Zhen and Liu, Ran and Gui, Ping and Fu, Chuanhai and Lippincott-Schwartz, Jennifer and Yao, Xuebiao and Liu, Xing} } @article {69108, title = {A fluorogenic complementation tool kit for interrogating lipid droplet-organelle interaction}, journal = {J. Cell Biol.}, volume = {223}, year = {2024}, month = {2024 Jul 01}, pages = {e202311126}, abstract = {

Contact sites between lipid droplets and other organelles are essential for cellular lipid and energy homeostasis upon metabolic demands. Detection of these contact sites at the nanometer scale over time in living cells is challenging. We developed a tool kit for detecting contact sites based on fluorogen-activated bimolecular complementation at CONtact sites, FABCON, using a reversible, low-affinity split fluorescent protein, splitFAST. FABCON labels contact sites with minimal perturbation to organelle interaction. Via FABCON, we quantitatively demonstrated that endoplasmic reticulum (ER)- and mitochondria (mito)-lipid droplet contact sites are dynamic foci in distinct metabolic conditions, such as during lipid droplet biogenesis and consumption. An automated analysis pipeline further classified individual contact sites into distinct subgroups based on size, likely reflecting differential regulation and function. Moreover, FABCON is generalizable to visualize a repertoire of organelle contact sites including ER-mito. Altogether, FABCON reveals insights into the dynamic regulation of lipid droplet-organelle contact sites and generates new hypotheses for further mechanistical interrogation during metabolic regulation.

}, doi = {10.1083/jcb.202311126 }, url = {https://doi.org/10.1083/jcb.202311126 }, author = {Xiao Li and Rico Gamuyao and Ming-Lun Wu and Woo Jung Cho and Nathan B. Kurtz and Sharon V. King and R.A. Petersen and Daniel R. Stabley and Caleb Lindow and Leslie Climer and Abbas Shirinifard and Francesca Ferrara and Robert E. Throm and Camenzind G. Robinson and Alex Carisey and Alison G. Tebo and Chi-Lun Chang} } @article {69658, title = {The Fly Disco: Hardware and software for optogenetics and fine-grained fly behavior analysis}, journal = {bioRxiv}, year = {2024}, month = {2024 Nov 04}, abstract = {

In the fruit fly, Drosophila melanogaster, connectome data and genetic tools provide a unique opportunity to study complex behaviors including navigation, mating, aggression, and grooming in an organism with a tractable nervous system of 140,000 neurons. Here we present the Fly Disco, a flexible system for high quality video collection, optogenetic manipulation, and fine-grained behavioral analysis of freely walking and socializing fruit fly groups. The data collection hardware and software automates the collection of videos synced to programmable optogenetic stimuli. Key pipeline features include behavioral analysis based on trajectories of 21 keypoints and optogenetic-specific summary statistics and data visualization. We created the multifly dataset for pose estimation that includes 9701 examples enriched in complex behaviors. All hardware designs, software, and the multifly dataset are freely available.

}, doi = {10.1101/2024.11.04.621948}, url = {https://doi.org/10.1101/2024.11.04.621948}, author = {Robie, Alice A and Taylor, Adam L and Schretter, Catherine E and Kabra, Mayank and Branson, Kristin} } @article {69320, title = {Focal adhesions contain three specialized actin nanoscale layers}, journal = {Nature Communications}, volume = {15}, year = {2024}, month = {2024 Mar 21}, abstract = {

Focal adhesions (FAs) connect inner workings of cell to the extracellular matrix to control cell adhesion, migration and mechanosensing. Previous studies demonstrated that FAs contain three vertical layers, which connect extracellular matrix to the cytoskeleton. By using super-resolution iPALM microscopy, we identify two additional nanoscale layers within FAs, specified by actin filaments bound to tropomyosin isoforms Tpm1.6 and Tpm3.2. The Tpm1.6-actin filaments, beneath the previously identified α-actinin cross-linked actin filaments, appear critical for adhesion maturation and controlled cell motility, whereas the adjacent Tpm3.2-actin filament layer beneath seems to facilitate adhesion disassembly. Mechanistically, Tpm3.2 stabilizes ACF-7/MACF1 and KANK-family proteins at adhesions, and hence targets microtubule plus-ends to FAs to catalyse their disassembly. Tpm3.2 depletion leads to disorganized microtubule network, abnormally stable FAs, and defects in tail retraction during migration. Thus, FAs are composed of distinct actin filament layers, and each may have specific roles in coupling adhesions to the cytoskeleton, or in controlling adhesion dynamics.

}, doi = {10.1038/s41467-024-46868-7}, url = {https://www.nature.com/articles/s41467-024-46868-7https://www.nature.com/articles/s41467-024-46868-7.pdfhttps://www.nature.com/articles/s41467-024-46868-7.pdfhttps://www.nature.com/articles/s41467-024-46868-7}, author = {Kumari, Reena and Ven, Katharina and Chastney, Megan and Kokate, Shrikant B. and Per{\"a}nen, Johan and Aaron, Jesse and Kogan, Konstantin and Almeida-Souza, Leonardo and Kremneva, Elena and Poincloux, Renaud and Chew, Teng-Leong and Gunning, Peter W. and Ivaska, Johanna and Lappalainen, Pekka} } @article {69461, title = {Four-dimensional quantitative analysis of cell plate development in Arabidopsis using lattice light sheet microscopy identifies robust transition points between growth phases}, journal = {J Exp Bot}, volume = {75}, year = {2024}, month = {2024 May 20}, pages = {2829-2847}, abstract = {

Cell plate formation during cytokinesis entails multiple stages occurring concurrently and requiring orchestrated vesicle delivery, membrane remodelling, and timely deposition of polysaccharides, such as callose. Understanding such a dynamic process requires dissection in time and space; this has been a major hurdle in studying cytokinesis. Using lattice light sheet microscopy (LLSM), we studied cell plate development in four dimensions, through the behavior of yellow fluorescent protein (YFP)-tagged cytokinesis-specific GTPase RABA2a vesicles. We monitored the entire duration of cell plate development, from its first emergence, with the aid of YFP-RABA2a, in both the presence and absence of cytokinetic callose. By developing a robust cytokinetic vesicle volume analysis pipeline, we identified distinct behavioral patterns, allowing the identification of three easily trackable cell plate developmental phases. Notably, the phase transition between phase I and phase II is striking, indicating a switch from membrane accumulation to the recycling of excess membrane material. We interrogated the role of callose using pharmacological inhibition with LLSM and electron microscopy. Loss of callose inhibited the phase transitions, establishing the critical role and timing of the polysaccharide deposition in cell plate expansion and maturation. This study exemplifies the power of combining LLSM with quantitative analysis to decode and untangle such a complex process.

}, keywords = {Arabidopsis, Cytokinesis, Glucans, Microscopy}, issn = {1460-2431}, doi = {10.1093/jxb/erae091}, author = {Sinclair, Rosalie and Wang, Minmin and Jawaid, Muhammad Zaki and Longkumer, Toshisangba and Aaron, Jesse and Rossetti, Blair and Wait, Eric and McDonald, Kent and Cox, Daniel and Heddleston, John and Wilkop, Thomas and Drakakaki, Georgia} } @article {69252, title = {Four-dimensional quantitative analysis of cell plate development using lattice light sheet microscopy identifies robust transition points between growth phases.}, journal = {Journal of Experimental Botany}, year = {2024}, month = {2024 Mar 4}, abstract = {

Cell plate formation during cytokinesis entails multiple stages occurring concurrently and requiring orchestrated vesicle delivery, membrane remodeling, and timely polysaccharide deposition, such as callose. Understanding such a dynamic process requires dissection in time and space; this has been a major hurdle in studying cytokinesis. Using lattice light sheet microscopy (LLSM) we studied cell plate development in four dimensions, through the behavior of the cytokinesis specific GTPase YFP-RABA2a vesicles. We monitored the entire length of cell plate development, from its first emergence, with the aid of YFP-RABA2a, both in the presence and absence of cytokinetic callose. By developing a robust cytokinetic vesicle volume analysis pipeline, we identified distinct behavioral patterns, allowing the identification of three easily trackable, cell plate developmental phases. Notably, the phase transition between phase I and phase II is striking, indicating a switch from membrane accumulation to the recycling of excess membrane material. We interrogated the role of callose using pharmacological inhibition with LLSM and electron microscopy. Loss of callose inhibited the phase transitions, establishing the critical role and timing of the polysaccharide deposition in cell plate expansion and maturation. This study exemplifies the power of combining LLSM with quantitative analysis to decode and untangle such a complex process.

}, issn = {1460-2431}, doi = {10.1093/jxb/erae091}, author = {Sinclair, Rosalie and Wang, Minmin and Jawaid, Muhammad Zaki and Longkumer, Toshisangba and Aaron, Jesse and Rossetti, Blair and Wait, Eric and McDonald, Kent and Cox, Daniel and Heddleston, John and Wilkop, Thomas and Drakakaki, Georgia} } @article {69660, title = {From the fly connectome to exact ring attractor dynamics}, journal = {bioRxiv}, year = {2024}, month = {2024 Nov 01}, abstract = {

A cognitive compass enabling spatial navigation requires neural representation of heading direction (HD), yet the neural circuit architecture enabling this representation remains unclear. While various network models have been proposed to explain HD systems, these models rely on simplified circuit architectures that are incompatible with empirical observations from connectomes. Here we construct a novel network model for the fruit fly HD system that satisfies both connectome-derived architectural constraints and the functional requirement of continuous heading representation. We characterize an ensemble of continuous attractor networks where compass neurons providing local mutual excitation are coupled to inhibitory neurons. We discover a new mechanism where continuous heading representation emerges from combining symmetric and anti-symmetric activity patterns. Our analysis reveals three distinct realizations of these networks that all match observed compass neuron activity but differ in their predictions for inhibitory neuron activation patterns. Further, we found that deviations from these realizations can be compensated by cell-type-specific rescaling of synaptic weights, which could be potentially achieved through neuromodulation. This framework can be extended to incorporate the complete fly central complex connectome and could reveal principles of neural circuits representing other continuous quantities, such as spatial location, across insects and vertebrates.

}, doi = {10.1101/2024.11.01.621596}, url = {https://doi.org/10.1101/2024.11.01.621596}, author = {Biswas, Tirthabir and Stanoev, Angel and Romani, Sandro and Fitzgerald, James E.} } @article {69678, title = {Genomes of two invasive Adelges species (hemlock woolly adelgid and pineapple gall adelgid) enable characterization of nicotinic acetylcholine receptors}, journal = {bioRxiv}, year = {2024}, month = {2024 Nov 26}, abstract = {

Two invasive hemipteran adelgids cause widespread damage to North American conifers. Adelges tsugae (the hemlock woolly adelgid) has decimated Tsuga canadensis and Tsuga caroliniana (the Eastern and Carolina hemlocks, respectively). A. tsugae was introduced from East Asia and reproduces parthenogenetically in North America, where it can kill trees rapidly. A. abietis, introduced from Europe, makes pineapple galls on several North American spruce species, and weakens trees, increasing their susceptibility to other stresses. Broad-spectrum insecticides that are often used to control adelgid populations can have off-target impacts on beneficial insects and the development of more selective chemical treatments could improve control methods and minimize ecological damage. Whole genome sequencing was performed on both species to aid in development of targeted pest control solutions and improve species conservation. The assembled A. tsugae and A. abietis genomes are 231.71 Mbp and 290.39 Mbp, respectively, each consisting of nine chromosomes and both genomes are over 96\% complete based on BUSCO assessment. Genome annotation identified 11,424 and 14,118 protein-coding genes in A. tsugae and A. abietis, respectively. Comparative analysis across 29 Hemipteran species and 14 arthropod outgroups identified 31,666 putative gene families. Gene family expansions in A. abietis included ABC transporters and carboxypeptidases involved in carbohydrate metabolism, while both species showed contractions in core histone families and oxidoreductase pathways. Gene family expansions in A. tsugae highlighted families associated with the regulation of cell differentiation and development (survival motor protein, SMN; juvenile hormone acid methyltransferase JHAMT) as well as those that may be involved in the suppression of plant immunity (clip domain serine protease-D, CLIPD; Endoplasmic reticulum aminopeptidase 1, ERAP1). Among the analyzed gene families, Nicotinic acetylcholine receptors (nAChRs) maintained consistent copy numbers and structural features across species, a finding particularly relevant given their role as targets for current forestry management insecticides. Detailed phylogenetic analysis of nAChR subunits across adelgids and other ecologically important insects revealed remarkable conservation in both sequence composition and predicted structural features, providing crucial insights for the development of more selective pest control strategies.

}, doi = {10.1101/2024.11.21.624573}, url = {https://doi.org/10.1101/2024.11.21.624573}, author = {Glendening, A M and Stephens, Cole and Vuruputoor, Vidya S and Stern, David L and Hogenhout, Saskia A and Mathers, Thomas C and Chaganti, Tesko and Pauloski, Nicole and Cernak, Tim A and Wegrzyn, Jill L and Fetter, Karl C} } @article {69661, title = {GESIAP3.0: Sensor-based Image Analysis Program for Transmission Visualization In Vivo}, journal = {bioRxiv}, year = {2024}, month = {2024 Oct 31}, abstract = {

Synaptic transmission mediated by various neurotransmitters influences a wide range of behaviors. However, understanding how neuromodulatory transmitters encode diverse behaviors and affect their functions remains challenging. Here, we introduce GESIAP3.0, an advanced, third-generation image analysis program based on genetically encoded sensors. This tool enables precise quantitative analysis of transmission in both awake, freely moving animals and immobilized subjects. GESIAP3.0 incorporates movement correction algorithms that effectively eliminate image displacement in behaving animals while optimizing synaptic information extraction and simplifying computations on commodity computers. Quantitative analysis of cholinergic, dopaminergic, and serotonergic transmission, corrected for tissue movement, revealed synaptic properties consistent with measurements from ex vivo wide-field and in vivo two-photon imaging under stable conditions. This validates the applicability of GESIAP3.0 for analyzing synaptic properties of neuromodulatory transmission in behaving animals.

}, doi = {10.1101/2024.10.28.620522}, url = {https://doi.org/10.1101/2024.10.28.620522}, author = {Zhu, Roger E. and Diao, Xintong and Liu, Xiaoyu and Ru, Qin and Wu, Zenan and Zhang, Ziyuan and Looger, Loren L. and Zhu, Jiazhu} } @article {69659, title = {A global dopaminergic learning rate enables adaptive foraging across many options}, journal = {bioRxiv}, year = {2024}, month = {2024 Nov 05}, abstract = {

In natural environments, animals must efficiently allocate their choices across multiple concurrently available resources when foraging, a complex decision-making process not fully captured by existing models. To understand how rodents learn to navigate this challenge we developed a novel paradigm in which untrained, water-restricted mice were free to sample from six options rewarded at a range of deterministic intervals and positioned around the walls of a large ( 2m) arena. Mice exhibited rapid learning, matching their choices to integrated reward ratios across six options within the first session. A reinforcement learning model with separate states for staying or leaving an option and a dynamic, global learning rate was able to accurately reproduce mouse learning and decision-making. Fiber photometry recordings revealed that dopamine in the nucleus accumbens core (NAcC), but not dorsomedial striatum (DMS), more closely reflected the global learning rate than local error-based updating. Altogether, our results provide insight into the neural substrate of a learning algorithm that allows mice to rapidly exploit multiple options when foraging in large spatial environments.

}, doi = {10.1101/2024.11.04.621923}, url = {https://doi.org/10.1101/2024.11.04.621923}, author = {Grima, Laura L and Guo, Yipei and Narayan, Lakshmi and Hermundstad, Ann M and Dudman, Joshua T} } @article {69680, title = {Global Neuron Shape Reasoning with Point Affinity Transformers}, journal = {bioRxiv}, year = {2024}, month = {2024 Nov 24}, abstract = {

Connectomics is a subfield of neuroscience that aims to map the brain{\textquoteright}s intricate wiring diagram. Accurate neuron segmentation from microscopy volumes is essential for automating connectome reconstruction. However, current state-of-the-art algorithms use image-based convolutional neural networks that are limited to local neuron shape context. Thus, we introduce a new framework that reasons over global neuron shape with a novel point affinity transformer. Our framework embeds a (multi-)neuron point cloud into a fixed-length feature set from which we can decode any point pair affinities, enabling clustering neuron point clouds for automatic proofreading. We also show that the learned feature set can easily be mapped to a contrastive embedding space that enables neuron type classification using a simple KNN classifier. Our approach excels in two demanding connectomics tasks: proofreading segmentation errors and classifying neuron types. Evaluated on three benchmark datasets derived from state-of-the-art connectomes, our method outperforms point transformers, graph neural networks, and unsupervised clustering baselines.

}, doi = {10.1101/2024.11.24.625067}, url = {https://doi.org/10.1101/2024.11.24.625067}, author = {Troidl, Jakob and Knittel, Johannes and Li, Wanhua and Zhan, Fangneng and Pfister, Hanspeter and Turaga, Srinivas} } @article {69254, title = {Haploidy-linked cell proliferation defects limit larval growth in Zebrafish}, journal = {Open Biol.}, volume = {14}, year = {2024}, month = {2024 Oct 09}, pages = {240126}, abstract = {

Haploid larvae in non-mammalian vertebrates are lethal, with characteristic organ growth retardation collectively called {\textquoteright}haploid syndrome{\textquoteright}. In contrast to mammals, whose haploid intolerance is attributed to imprinting misregulation, the cellular principle of haploidy-linked defects in non-mammalian vertebrates remains unknown. Here, we investigated cellular defects that disrupt the ontogeny of gynogenetic haploid zebrafish larvae. Unlike diploid control larvae, haploid larvae manifested unscheduled cell death at the organogenesis stage, attributed to haploidy-linked p53 upregulation. Moreover, we found that haploid larvae specifically suffered the gradual aggravation of mitotic spindle monopolarization during 1-3 days post-fertilization, causing spindle assembly checkpoint-mediated mitotic arrest throughout the entire body. High-resolution imaging revealed that this mitotic defect accompanied the haploidy-linked centrosome loss occurring concomitantly with the gradual decrease in larval cell size. Either resolution of mitotic arrest or depletion of p53 partially improved organ growth in haploid larvae. Based on these results, we propose that haploidy-linked mitotic defects and cell death are parts of critical cellular causes shared among vertebrates that limit the larval growth in the haploid state, contributing to an evolutionary constraint on allowable ploidy status in the vertebrate life cycle.

}, doi = {10.1098/rsob.240126}, url = {https://doi.org/10.1098/rsob.240126}, author = {Kan Yaguchi and Daiki Saito and Triveni Menon and Akira Matsura and Takeomi Mizutani and Tomoya Kotani and Sreelaja Nair and Ryota Uehara} } @article {69250, title = {High-Performance Genetically Encoded Green Fluorescent Biosensors for Intracellular l-Lactate.}, journal = {ACS Central Science}, volume = {10}, year = {2024}, month = {2024 Feb 28}, pages = {402-416}, abstract = {

l-Lactate is a monocarboxylate produced during the process of cellular glycolysis and has long generally been considered a waste product. However, studies in recent decades have provided new perspectives on the physiological roles of l-lactate as a major energy substrate and a signaling molecule. To enable further investigations of the physiological roles of l-lactate, we have developed a series of high-performance (Δ/ = 15 to 30 ), intensiometric, genetically encoded green fluorescent protein (GFP)-based intracellular l-lactate biosensors with a range of affinities. We evaluated these biosensors in cultured cells and demonstrated their application in an preparation of brain tissue. Using these biosensors, we were able to detect glycolytic oscillations, which we analyzed and mathematically modeled.

}, issn = {2374-7943}, doi = {10.1021/acscentsci.3c01250}, author = {Hario, Saaya and Le, Giang N T and Sugimoto, Hikaru and Takahashi-Yamashiro, Kei and Nishinami, Suguru and Toda, Hirofumi and Li, Selene and Marvin, Jonathan S and Kuroda, Shinya and Drobizhev, Mikhail and Terai, Takuya and Nasu, Yusuke and Campbell, Robert E} } @article {69578, title = {A high-throughput microfabricated platform for rapid quantification of metastatic potential.}, journal = {Sci Adv}, volume = {10}, year = {2024}, month = {2024 Aug 16}, pages = {eadk0015}, abstract = {

Assays that measure morphology, proliferation, motility, deformability, and migration are used to study the invasiveness of cancer cells. However, native invasive potential of cells may be hidden from these contextual metrics because they depend on culture conditions. We created a micropatterned chip that mimics the native environmental conditions, quantifies the invasive potential of tumor cells, and improves our understanding of the malignancy signatures. Unlike conventional assays, which rely on indirect measurements of metastatic potential, our method uses three-dimensional microchannels to measure the basal native invasiveness without chemoattractants or microfluidics. No change in cell death or proliferation is observed on our chips. Using six cancer cell lines, we show that our system is more sensitive than other motility-based assays, measures of nuclear deformability, or cell morphometrics. In addition to quantifying metastatic potential, our platform can distinguish between motility and invasiveness, help study molecular mechanisms of invasion, and screen for targeted therapeutics.

}, keywords = {Cell Line, Tumor, Cell Movement, Cell Proliferation, High-Throughput Screening Assays, Humans, Lab-On-A-Chip Devices, Microtechnology, Neoplasm Invasiveness, Neoplasm Metastasis, Neoplasms}, issn = {2375-2548}, doi = {10.1126/sciadv.adk0015}, url = {https://doi.org/10.1126/sciadv.adk0015}, author = {Bhattacharya, Smiti and Ettela, Abora and Haydak, Jonathan and Hobson, Chad M and Stern, Alan and Yoo, Miran and Chew, Teng-Leong and Gusella, G Luca and Gallagher, Emily J and Hone, James C and Azeloglu, Evren U} } @article {69383, title = {Hippocampal cholecystokinin-expressing interneurons regulate temporal coding and contextual learning}, journal = {Neuron}, year = {2024}, month = {2024 Apr 17}, abstract = {

Cholecystokinin-expressing interneurons (CCKIs) are hypothesized to shape pyramidal cell-firing patterns and regulate network oscillations and related network state transitions. To directly probe their role in the CA1 region, we silenced their activity using optogenetic and chemogenetic tools in mice. Opto-tagged CCKIs revealed a heterogeneous population, and their optogenetic silencing triggered wide disinhibitory network changes affecting both pyramidal cells and other interneurons. CCKI silencing enhanced pyramidal cell burst firing and altered the temporal coding of place cells: theta phase precession was disrupted, whereas sequence reactivation was enhanced. Chemogenetic CCKI silencing did not alter the acquisition of spatial reference memories on the Morris water maze but enhanced the recall of contextual fear memories and enabled selective recall when similar environments were tested. This work suggests the key involvement of CCKIs in the control of place-cell temporal coding and the formation of contextual memories.

}, issn = {08966273}, doi = {10.1016/j.neuron.2024.03.019}, url = {https://doi.org/10.1016/j.neuron.2024.03.019}, author = {Rangel Guerrero, D{\'a}maris K. and Balueva, Kira and Barayeu, Uladzislau and Baracskay, Peter and Gridchyn, Igor and Nardin, Michele and Roth, Chiara Nina and Wulff, Peer and Csicsvari, Jozsef} } @article {69040, title = {hkb is required for DIP-α expression and target recognition in the Drosophila neuromuscular circuit}, journal = {Communications Biology}, volume = {7}, year = {2024}, month = {2024 Apr 27}, abstract = {

Our nervous system contains billions of neurons that form precise connections with each other through interactions between cell surface proteins (CSPs). In Drosophila, the Dpr and DIP immunoglobulin protein subfamilies form homophilic or heterophilic interactions to instruct synaptic connectivity, synaptic growth and cell survival. However, the upstream regulation and downstream signaling mechanisms of Dprs and DIPs are not clear. In the Drosophila larval neuromuscular system,\ DIP-α\ is expressed in the dorsal and ventral type-Is motor neurons (MNs). We conducted an F1 dominant modifier genetic screen to identify regulators of Dprs and DIPs. We found that the transcription factor,\ huckebein\ (hkb), genetically interacts with\ DIP-α\ and is important for target recognition specifically in the dorsal Is MN, but not the ventral Is MN. Loss of\ hkb\ led to complete removal of\ DIP-α\ expression. We then confirmed that this specificity is through the dorsal Is MN specific transcription factor,\ even-skipped\ (eve), which acts downstream of\ hkb. Genetic interaction between\ hkb\ and\ eve\ revealed that they act in the same pathway to regulate dorsal Is MN connectivity. Our study provides insight into the transcriptional regulation of\ DIP-α\ and suggests that distinct regulatory mechanisms exist for the same CSP in different neurons.

}, doi = {10.1038/s42003-024-06184-8}, url = {https://doi.org/10.1038/s42003-024-06184-8}, author = {Robert A Carrillo and Yupu Wang and Rio Salazar and Luciano Simonetta and Violet Sorrentino and Terrence J Gatton and Bill Wu and Christopher G Vecsey} } @article {68279, title = {Homeodomain proteins hierarchically specify neuronal diversity and synaptic connectivity}, journal = {eLife}, year = {2024}, month = {2024 Jan 05}, abstract = {

The brain generates diverse neuron types which express unique homeodomain transcription factors (TFs) and assemble into precise neural circuits. Yet a mechanistic framework is lacking for how homeodomain TFs specify both neuronal fate and synaptic connectivity. We use\ Drosophila\ lamina neurons (L1-L5) to show the homeodomain TF Brain-specific homeobox (Bsh) is initiated in lamina precursor cells (LPCs) where it specifies L4/L5 fate and suppresses homeodomain TF Zfh1 to prevent L1/L3 fate. Subsequently, Bsh activates the homeodomain TF Apterous (Ap) in L4 in a feedforward loop to express the synapse recognition molecule DIP-β, in part by Bsh direct binding a\ DIP-β\ intron. Thus, homeodomain TFs function hierarchically: primary homeodomain TF (Bsh) first specifies neuronal fate, and subsequently acts with secondary homeodomain TF (Ap) to activate DIP-β, thereby generating precise synaptic connectivity. We speculate that hierarchical homeodomain TF function may represent a general principle for coordinating neuronal fate specification and circuit assembly.

}, doi = {10.7554/eLife.90133}, url = {https://doi.org/10.7554/eLife.90133}, author = {Chundi Xu and Tyler B. Ramos and Ed M. Rogers and Michael B. Reiser and Chris Q. Doe} } @article {68831, title = {Host ZCCHC3 blocks HIV-1 infection and production by a dual mechanism}, journal = {iScience}, year = {2024}, month = {05/2024}, abstract = {

Most mammalian cells prevent viral infection and proliferation by expressing various restriction factors and sensors that activate the immune system. While anti-human immunodeficiency virus type 1 (HIV-1) host restriction factors have been identified, most of them are antagonized by viral proteins. This has severely hindered their development in anti-HIV-1 therapy. Here, we describe CCHC-type zinc-finger-containing protein 3 (ZCCHC3) as a novel anti-HIV-1 factor that is not antagonized by viral proteins. ZCCHC3 suppresses production of HIV-1 and other retroviruses. We show that ZCCHC3 acts by binding to Gag nucleocapsid protein via zinc-finger motifs. This prevents interaction between the Gag nucleocapsid protein and viral genome and results in production of genome-deficient virions. ZCCHC3 also binds to the long terminal repeat on the viral genome via the middle-folded domain, sequestering the viral genome to P-bodies, which leads to decreased viral replication and production. Such a dual antiviral mechanism is distinct from that of any other known host restriction factors. Therefore, ZCCHC3 is a novel potential target in anti-HIV-1 therapy.

}, doi = {10.1101/2023.06.14.544911}, url = {https://doi.org/10.1101/2023.06.14.544911}, author = {Binbin Yi and Yuri L Tanaka and Hidetaka Kosako and Erika P Butlertanaka and Prabuddha Sengupta and Jennifer Lippincott-Schwartz and Akatsuki Saito and Shige H. Yoshimura} } @article {69518, title = {Hot-Distance: Combining One-Hot and Signed Distance Embeddings for Segmentation}, journal = {arXiv}, year = {2024}, month = {2024 Jun 25}, pages = {2406.17936}, abstract = {

Machine learning models are only as good as the data to which they are fit. As such, it is always preferable to use as much data as possible in training models. What data can be used for fitting a model depends a lot on the formulation of the task. We introduce Hot-Distance, a novel segmentation target that incorporates the strength of signed boundary distance prediction with the flexibility of one-hot encoding, to increase the amount of usable training data for segmentation of subcellular structures in focused ion beam scanning electron microscopy (FIB-SEM).

}, doi = {10.48550/arXiv.2406.17936}, url = {https://doi.org/10.48550/arXiv.2406.17936}, author = {Marwan Zouinkhi and Jeff L Rhoades and Aubrey V. Weigel} } @article {68589, title = {How microscopic epistasis and clonal interference shape the fitness trajectory in a spin glass model of microbial long-term evolution}, journal = {eLife}, year = {2024}, month = {2024 Feb 20}, abstract = {

The adaptive dynamics of evolving microbial populations takes place on a complex fitness landscape generated by epistatic interactions. The population generically consists of multiple competing strains, a phenomenon known as clonal interference. Microscopic epistasis and clonal interference are central aspects of evolution in microbes, but their combined effects on the functional form of the population{\textquoteright}s mean fitness are poorly understood. Here, we develop a computational method that resolves the full microscopic complexity of an evolving population subject to a standard serial dilution protocol. We find that stronger microscopic epistasis gives rise to fitness trajectories with slower growth independent of the number of competing strains, which we quantify with power-law fits and understand mechanistically via a random walk model that neglects dynamical correlations between genes. We show that clonal interference leads to fitness trajectories with faster growth (in functional form) without microscopic epistasis, but has a negligible effect when epistasis is sufficiently strong, indicating that the role of clonal interference depends intimately on the underlying fitness landscape.

}, doi = {10.7554/eLife.87895}, url = {https://doi.org/10.7554/eLife.87895}, author = {Nicholas M. Boffi and Yipei Guo and Chris H. Rycroft and Ariel Amir} } @article {69730, title = {How short peptides can disassemble ultra-stable tau fibrils extracted from Alzheimer{\textquoteright}s disease brain by a strain-relief mechanism}, journal = {Alzheimer{\textquoteright}s \& Dementia}, volume = {20}, year = {2024}, month = {01/2025}, abstract = {

Background

Reducing fibrous aggregates of protein tau is a possible strategy for halting progression of Alzheimer{\textquoteright}s disease (AD). Previously we found that in vitro the D-peptide D-TLKIVWC fragments tau fibrils from AD brains (AD-tau) into benign segments, whereas its six-residue analog D-TLKIVW cannot. However, the underlying fragmentation mechanism remains unknown, preventing the further development of this type of drug candidate for AD.

Method

To understand the necessity of the cysteine residue of D-TLKIVWC in fragmenting AD-tau, we designed a series of peptides of sequence D-TLKIVWX varying only at the seventh residue, X. To better understand the fragmentation process of AD-tau, we conducted a time-course dot blot and EM experiment. We determined the structures of D-TLKIVWX amyloid-like fibrils by atomic force microscopy and cryo-electron microscopy. We studied the complexes of D-TLKIVWX (X = I, S, R) with AD-tau by cryo-electron microscopy and confirmed the binding site between D-TLKIVWX and Tau through NMR.

Result

These D-TLKIVWX candidates showed various efficacies in fragmenting AD-tau in vitro, in which X = Ile was the best performer. From electron microscopy, we discovered that D-TLKIVWX peptides form amyloid-like fibrils themselves, and from atomic force microscopy we learned that these fibrils have a right-handed helical twist, in contrast to the left-handed helical twist of AD-tau. From cryo-EM we learned that D-TLKIVWX protofilaments bind to tau fibrils of opposing twist.

Conclusion

We find that the amyloid-like, fibril-forming property of D-TLKIVWX contributes to the fragmentation of AD-tau fibrils. We propose the strain-relief mechanism of fragmentation and believe the fragmentation of AD-tau fibrils is driven by the release of torsion in D-TLKIVWX protofilaments.

}, issn = {1552-5260}, doi = {10.1002/alz.085001}, url = {https://alz-journals.onlinelibrary.wiley.com/toc/15525279/20/S6}, author = {Hou, Ke and Ge, Peng and Sawaya, Michael R and Dolinsky, Joshua L. and Yang, Yuan and Jiang, Yi Xiao and Lutter, Liisa and Boyer, David and Cheng, Xinyi and Pi, Justin and Zhang, Jeffrey and Lu, Jiahui and Yang, Shixin and Yu, Zhiheng and Feigon, Juli and Eisenberg, David S.} } @article {69456, title = {Hue selectivity from recurrent circuitry in Drosophila}, journal = {Nat Neurosci}, year = {2024}, month = {2024 May 16}, abstract = {

In the perception of color, wavelengths of light reflected off objects are transformed into the derived quantities of brightness, saturation and hue. Neurons responding selectively to hue have been reported in primate cortex, but it is unknown how their narrow tuning in color space is produced by upstream circuit mechanisms. We report the discovery of neurons in the Drosophila optic lobe with hue-selective properties, which enables circuit-level analysis of color processing. From our analysis of an electron microscopy volume of a whole Drosophila brain, we construct a connectomics-constrained circuit model that accounts for this hue selectivity. Our model predicts that recurrent connections in the circuit are critical for generating hue selectivity. Experiments using genetic manipulations to perturb recurrence in adult flies confirm this prediction. Our findings reveal a circuit basis for hue selectivity in color vision.

}, issn = {1546-1726}, doi = {10.1038/s41593-024-01640-4}, author = {Christenson, Matthias P and Sanz Diez, Alvaro and Heath, Sarah L and Saavedra-Weisenhaus, Maia and Adachi, Atsuko and Nern, Aljoscha and Abbott, L F and Behnia, Rudy} } @article {68969, title = {iATPSnFR2: a high dynamic range fluorescent sensor for monitoring intracellular ATP}, journal = {Proc Natl Acad Sci U S A}, year = {2024}, month = {2024 May 21}, abstract = {

We developed a significantly improved genetically encoded quantitative adenosine triphosphate (ATP) sensor to provide real-time dynamics of ATP levels in subcellular compartments. iATPSnFR2 is a variant of iATPSnFR1, a previously developed sensor that has circularly permuted super-folder GFP inserted between the ATP-binding helices of the\ ε-subunit of a bacterial F0-F1\ ATPase. Optimizing the linkers joining the two domains resulted in a \~{} 5-6 fold improvement in the dynamic range compared to the previous generation sensor, with excellent discrimination against other analytes and affinity variants varying from 4 μM to 500 μM. A chimeric version of this sensor fused to either the HaloTag protein or a suitably spectrally separated fluorescent protein, provides a ratiometric readout allowing comparisons of ATP across cellular regions. Subcellular targeting of the sensor to nerve terminals reveals previously uncharacterized single synapse metabolic signatures, while targeting to the mitochondrial matrix allowed direct quantitative probing of oxidative phosphorylation dynamics.

}, doi = {10.1073/pnas.2314604121 }, author = {Jonathan S. Marvin and Alexandros C. Kokotos and Mukesh Kumar and Camila Pulido and Ariana N. Tkachuk and Jocelyn Shuxin Yao and Timothy A. Brown and Timothy A. Ryan} } @article {69708, title = {An Image Processing Tool for Automated Quantification of Bacterial Burdens in Zebrafish Larvae.}, journal = {Zebrafish}, year = {2024}, month = {12/2024}, abstract = {

Zebrafish larvae are used to model the pathogenesis of multiple bacteria. This transparent model offers the unique advantage of allowing quantification of fluorescent bacterial burdens (fluorescent pixel counts [FPC]) by facile microscopical methods, replacing enumeration of bacteria using time-intensive plating of lysates on bacteriological media. Accurate FPC measurements require laborious manual image processing to mark the outside borders of the animals so as to delineate the bacteria inside the animals from those in the culture medium that they are in. Here, we have developed an automated ImageJ/Fiji-based macro that accurately detects the outside borders of -infected larvae.

}, issn = {1557-8542}, doi = {10.1089/zeb.2024.0170}, author = {Yamaguchi, Naoya and Otsuna, Hideo and Eisenberg-Bord, Michal and Ramakrishnan, Lalita} } @article {69576, title = {An Image Processing Tool for Automated Quantification of Bacterial Burdens in Zebrafish Larvae}, journal = {bioRxiv}, year = {2024}, month = {2024 Aug 19}, abstract = {

Zebrafish larvae are used to model the pathogenesis of multiple bacteria. This transparent model offers the unique advantage of allowing quantification of fluorescent bacterial burdens (fluorescent pixel counts: FPC) in vivo by facile microscopical methods, replacing enumeration of bacteria using time-intensive plating of lysates on bacteriological media. Accurate FPC measurements require laborious manual image processing to mark the outside borders of the animals so as to delineate the bacteria inside the animals from those in the culture medium that they are in. Here, we have developed an automated ImageJ/Fiji-based macro that accurately detect the outside borders of Mycobacterium marinum-infected larvae.

}, doi = {10.1101/2024.08.16.608298}, url = {hhtps://doi.org/10.1101/2024.08.16.608298}, author = {Yamaguchi, Naoya and Otsuna, Hideo and Eisenberg-Bord, Michal and Ramakrishnan, Lalita} } @article {69142, title = {Image processing tools for petabyte-scale light sheet microscopy data.}, journal = {Nat. Methods}, year = {2024}, month = {2024 Oct 17}, abstract = {

Light sheet microscopy is a powerful technique for high-speed three-dimensional imaging of subcellular dynamics and large biological specimens. However, it often generates datasets ranging from hundreds of gigabytes to petabytes in size for a single experiment. Conventional computational tools process such images far slower than the time to acquire them and often fail outright due to memory limitations. To address these challenges, we present PetaKit5D, a scalable software solution for efficient petabyte-scale light sheet image processing. This software incorporates a suite of commonly used processing tools that are optimized for memory and performance. Notable advancements include rapid image readers and writers, fast and memory-efficient geometric transformations, high-performance Richardson-Lucy deconvolution and scalable Zarr-based stitching. These features outperform state-of-the-art methods by over one order of magnitude, enabling the processing of petabyte-scale image data at the full teravoxel rates of modern imaging cameras. The software opens new avenues for biological discoveries through large-scale imaging experiments.

}, doi = {10.1038/s41592-024-02475-4}, url = {https://doi.org/10.1038/s41592-024-02475-4}, author = {Xiongtao Ruan and Matthew Mueller and Gaoxiang Liu and Frederik G{\"o}rlitz and Tian-Ming Fu and Daniel E. Milkie and Joshua Lillvis and Alison Killilea and Eric Betzig and Srigokul Upadhyayula} } @article {69440, title = {Imaging the extracellular matrix in live tissues and organisms with a glycan-binding fluorophore}, journal = {bioRxiv}, year = {2024}, month = {2024 May 10}, abstract = {

All multicellular systems produce and dynamically regulate extracellular matrices (ECM) that play important roles in both biochemical and mechanical signaling. Though the spatial arrangement of these extracellular assemblies is critical to their biological functions, visualization of ECM structure is challenging, in part because the biomolecules that compose the ECM are difficult to fluorescently label individually and collectively. Here, we present a cell-impermeable small molecule fluorophore, termed Rhobo6, that turns on and red shifts upon reversible binding to glycans. Given that most ECM components are densely glycosylated, the dye enables wash-free visualization of ECM, in systems ranging from in vitro substrates to in vivo mouse mammary tumors. Relative to existing techniques, Rhobo6 provides a broad substrate profile, superior tissue penetration, nonperturbative labeling, and negligible photobleaching. This work establishes a straightforward method for imaging the distribution of ECM in live tissues and organisms, lowering barriers for investigation of extracellular biology.

}, doi = {10.1101/2024.05.09.593460}, url = {https://www.biorxiv.org/content/early/2024/05/10/2024.05.09.593460}, author = {Fiore, Antonio and Yu, Guoqiang and Northey, Jason J. and Patel, Ronak and Ravenscroft, Thomas A. and Ikegami, Richard and Kolkman, Wiert and Kumar, Pratik and Grimm, Jonathan B. and Dilan, Tanya L. and Ruetten, Virginia M.S. and Ahrens, Misha B. and Shroff, Hari and Lavis, Luke D. and Wang, Shaohe and Weaver, Valerie M. and Pedram, Kayvon} } @article {69215, title = {Integrating across behaviors and timescales to understand the neural control of movement.}, journal = {Current Opinion in Neurobiology}, volume = {85}, year = {2024}, month = {2024 Feb 13}, pages = {102843}, abstract = {

The nervous system evolved to enable navigation throughout the environment in the pursuit of resources. Evolutionarily newer structures allowed increasingly complex adaptations but necessarily added redundancy. A dominant view of movement neuroscientists is that there is a one-to-one mapping between brain region and function. However, recent experimental data is hard to reconcile with the most conservative interpretation of this framework, suggesting a degree of functional redundancy during the performance of well-learned, constrained behaviors. This apparent redundancy likely stems from the bidirectional interactions between the various cortical and subcortical structures involved in motor control. We posit that these bidirectional connections enable flexible interactions across structures that change depending upon behavioral demands, such as during acquisition, execution or adaptation of a skill. Observing the system across both multiple actions and behavioral timescales can help isolate the functional contributions of individual structures, leading to an integrated understanding of the neural control of movement.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2024.102843}, author = {Gmaz, Jimmie M and Keller, Jason A and Dudman, Joshua T and Gallego, Juan A} } @article {69609, title = {Integration of estimated regional gene expression with neuroimaging and clinical phenotypes at biobank scale.}, journal = {PLoS Biol}, volume = {22}, year = {2024}, month = {2024 Sep 13}, pages = {e3002782}, abstract = {

An understanding of human brain individuality requires the integration of data on brain organization across people and brain regions, molecular and systems scales, as well as healthy and clinical states. Here, we help advance this understanding by leveraging methods from computational genomics to integrate large-scale genomic, transcriptomic, neuroimaging, and electronic-health record data sets. We estimated genetically regulated gene expression (gr-expression) of 18,647 genes, across 10 cortical and subcortical regions of 45,549 people from the UK Biobank. First, we showed that patterns of estimated gr-expression reflect known genetic-ancestry relationships, regional identities, as well as inter-regional correlation structure of directly assayed gene expression. Second, we performed transcriptome-wide association studies (TWAS) to discover 1,065 associations between individual variation in gr-expression and gray-matter volumes across people and brain regions. We benchmarked these associations against results from genome-wide association studies (GWAS) of the same sample and found hundreds of novel associations relative to these GWAS. Third, we integrated our results with clinical associations of gr-expression from the Vanderbilt Biobank. This integration allowed us to link genes, via gr-expression, to neuroimaging and clinical phenotypes. Fourth, we identified associations of polygenic gr-expression with structural and functional MRI phenotypes in the Human Connectome Project (HCP), a small neuroimaging-genomic data set with high-quality functional imaging data. Finally, we showed that estimates of gr-expression and magnitudes of TWAS were generally replicable and that the p-values of TWAS were replicable in large samples. Collectively, our results provide a powerful new resource for integrating gr-expression with population genetics of brain organization and disease.

}, issn = {1545-7885}, doi = {10.1371/journal.pbio.3002782}, url = {https://doi.org/10.1371/journal.pbio.3002782}, author = {Hoang, Nhung and Sardaripour, Neda and Ramey, Grace D and Schilling, Kurt and Liao, Emily and Chen, Yiting and Park, Jee Hyun and Bledsoe, Xavier and Landman, Bennett A and Gamazon, Eric R and Benton, Mary Lauren and Capra, John A and Rubinov, Mikail} } @article {69141, title = {Interactive simulation and visualization of point spread functions in single molecule imaging.}, journal = {Optics Communications}, year = {2024}, month = {2024 Mar 20}, abstract = {

The point spread function (PSF) is fundamental to any type of microscopy, most importantly so for single-molecule localization techniques, where the exact PSF shape is crucial for precise molecule localization at the nanoscale. Optical aberrations and fixed fluorophore dipoles often result in non-isotropic and distorted PSFs, impairing and biasing conventional fitting approaches. Further, PSF shapes are deliberately modified in PSF engineering approaches for providing improved sensitivity, e.g., for 3D localization or determination of dipole orientation. As this can lead to highly complex PSF shapes, a tool for visualizing expected PSFs would facilitate the interpretation of obtained data and the design of experimental approaches. To this end, we introduce a comprehensive and accessible computer application that allows for the simulation of realistic PSFs based on the full vectorial PSF model. Our tool incorporates a wide range of microscope and fluorophore parameters, including orientationally constrained fluorophores, as well as custom aberrations, transmission and phase masks, thus enabling an accurate representation of various imaging conditions. An additional feature is the simulation of crowded molecular environments with overlapping PSFs. Further, our app directly provides the Cram{\'e}r{\textendash}Rao bound for assessing the best achievable localization precision under given conditions. Finally, our software allows for the fitting of custom aberrations directly from experimental data, as well as the generation of a large dataset with randomized simulation parameters, effectively bridging the gap between simulated and experimental scenarios, and enhancing experimental design and result validation.

}, doi = {10.1016/j.optcom.2024.130463}, url = {https://www.sciencedirect.com/science/article/pii/S0030401824002001?via\%3Dihub}, author = {Magdalena C. Schneider and Fabian Hinterer and Alexander Jesacher and Gerhard J. Sch{\"u}tz} } @article {69420, title = {An interphase actin wave promotes mitochondrial content mixing and organelle homeostasis.}, journal = {Nat Commun}, volume = {15}, year = {2024}, month = {2024 May 07}, pages = {3793}, abstract = {

Across the cell cycle, mitochondrial dynamics are regulated by a cycling wave of actin polymerization/depolymerization. In metaphase, this wave induces actin comet tails on mitochondria that propel these organelles to drive spatial mixing, resulting in their equitable inheritance by daughter cells. In contrast, during interphase the cycling actin wave promotes localized mitochondrial fission. Here, we identify the F-actin nucleator/elongator FMNL1 as a positive regulator of the wave. FMNL1-depleted cells exhibit decreased mitochondrial polarization, decreased mitochondrial oxygen consumption, and increased production of reactive oxygen species. Accompanying these changes is a loss of hetero-fusion of wave-fragmented mitochondria. Thus, we propose that the interphase actin wave maintains mitochondrial homeostasis by promoting mitochondrial content mixing. Finally, we investigate the mechanistic basis for the observation that the wave drives mitochondrial motility in metaphase but mitochondrial fission in interphase. Our data indicate that when the force of actin polymerization is resisted by mitochondrial tethering to microtubules, as in interphase, fission results.

}, keywords = {Actins, Animals, Formins, Hela Cells, Homeostasis, Humans, Interphase, Microtubules, Mitochondria, Mitochondrial Dynamics, Mitochondrial Proteins, Reactive Oxygen Species}, issn = {2041-1723}, doi = {10.1038/s41467-024-48189-1}, author = {Coscia, Stephen M and Moore, Andrew S and Thompson, Cameron P and Tirrito, Christian F and Ostap, E Michael and Holzbaur, Erika L F} } @article {69643, title = {IRE1α silences dsRNA to prevent taxane-induced pyroptosis in triple-negative breast cancer.}, journal = {Cell}, year = {2024}, month = {2024 Oct 14}, abstract = {

Chemotherapy is often combined with immune checkpoint inhibitor (ICIs) to enhance immunotherapy responses. Despite the approval of chemo-immunotherapy in multiple human cancers, many immunologically cold tumors remain unresponsive. The mechanisms determining the immunogenicity of chemotherapy are elusive. Here, we identify the ER stress sensor IRE1α as a critical checkpoint that restricts the immunostimulatory effects of taxane chemotherapy and prevents the innate immune recognition of immunologically cold triple-negative breast cancer (TNBC). IRE1α RNase silences taxane-induced double-stranded RNA (dsRNA) through regulated IRE1-dependent decay (RIDD) to prevent NLRP3 inflammasome-dependent pyroptosis. Inhibition of IRE1α in Trp53 TNBC allows taxane to induce extensive dsRNAs that are sensed by ZBP1, which in turn activates NLRP3-GSDMD-mediated pyroptosis. Consequently, IRE1α RNase inhibitor plus taxane converts PD-L1-negative, ICI-unresponsive TNBC tumors into PD-L1 immunogenic tumors that are hyper-sensitive to ICI. We reveal IRE1α as a cancer cell defense mechanism that prevents taxane-induced danger signal accumulation and pyroptotic cell death.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2024.09.032}, url = {https://doi.org/10.1016/j.cell.2024.09.032}, author = {Xu, Longyong and Peng, Fanglue and Luo, Qin and Ding, Yao and Yuan, Fei and Zheng, Liting and He, Wei and Zhang, Sophie S and Fu, Xin and Liu, Jin and Mutlu, Ayse Sena and Wang, Shuyue and Nehring, Ralf Bernd and Li, Xingyu and Tang, Qianzi and Li, Catherine and Lv, Xiangdong and Dobrolecki, Lacey E and Zhang, Weijie and Han, Dong and Zhao, Na and Jaehnig, Eric and Wang, Jingyi and Wu, Weiche and Graham, Davis A and Li, Yumei and Chen, Rui and Peng, Weiyi and Chen, Yiwen and Catic, Andre and Zhang, Zhibin and Zhang, Bing and Mustoe, Anthony M and Koong, Albert C and Miles, George and Lewis, Michael T and Wang, Meng C and Rosenberg, Susan M and O{\textquoteright}Malley, Bert W and Westbrook, Thomas F and Xu, Han and Zhang, Xiang H-F and Osborne, C Kent and Li, Jin Billy and Ellis, Matthew J and Rimawi, Mothaffar F and Rosen, Jeffrey M and Chen, Xi} } @article {69483, title = {It only takes seconds for a human monoclonal autoantibody to inhibit N-methyl-D-aspartate receptors}, journal = {bioRxiv}, year = {2024}, month = {2024 Jun 01}, abstract = {

Transfer of autoantibodies targeting ionotropic N-methyl-D-aspartate receptors in autoimmune encephalitis patients into mice leads to typical disease signs. Long-term effects of the pathogenic antibodies consist of immunoglobulin G-induced crosslinking and receptor internalization. We focused on the direct and immediate impact of a specific pathogenic patient-derived monoclonal autoantibody (immunoglobulin G $\#$003-102) on receptor function.We performed cell-attached recordings in cells transfected with the GluN1 and GluN2A subunit of the N-methyl-D-aspartate receptor. Immunoglobulin G $\#$003-102 binds to the amino-terminal domain of the glycine-binding GluN1 subunit. It reduced simultaneous receptor openings significantly compared to controls at both low and high glutamate and glycine concentrations. Closer examination of our data in 50-second to 2-second intervals revealed, that Immunoglobulin G $\#$003-102 rapidly decreases the number of open receptors. However, antigen-binding fragments of immunoglobulin G $\#$003-102 did not reduce the receptor openings.In conclusion, patient-derived immunoglobulin G $\#$003-102 inhibits N-methyl-D-aspartate receptors rapidly and directly before receptor internalization occurs and the entire immunoglobulin G is necessary for this acute inhibitory effect. This suggests an application of the antigen-binding fragment-like constructs of $\#$003-102 as a potential new treatment strategy for shielding the pathogenic epitopes on the N-methyl-D-aspartate receptors.

}, doi = {10.1101/2024.05.28.595700}, url = {https://www.biorxiv.org/content/early/2024/06/01/2024.05.28.595700}, author = {Yang, Shang and Heckmann, Johanna and Taha, Abdulla and Gao, Shiqiang and Steinke, Stephan and Hust, Michael and Pr{\"u}{\ss}, Harald and Furukawa, Hiro and Geis, Christian and Heckmann, Manfred and Yu-Strzelczyk, Jing} } @article {69525, title = {iTome Volumetric Serial Sectioning Apparatus for TEM}, journal = {bioRxiv}, year = {2024}, month = {2024 Jul 07}, abstract = {

An automated ultra-microtome capable of sectioning thousands of ultrathin sections onto standard TEM slot grids was developed and used to section: a complete Drosophila melanogaster first-instar larva, three sections per grid, into 4,866 34-nm-thick sections with a cutting and pickup success rate of 99.74\%; 30 microns of mouse cortex measuring roughly 400 um x 2000 um at 40 nm per slice; and a full adult Drosophila brain and ventral nerve column into 9,300 sections with a pickup success rate of 99.95\%. The apparatus uses optical interferometers to monitor a reference distance between the cutting knife and multiple sample blocks. Cut sections are picked up from the knife-boat water surface while they are still anchored to the cutting knife. Blocks without embedded tissue are used to displace tissue-containing sections away from the knife edge so that the tissue regions end up in the grid slot instead of on the grid rim.

}, doi = {10.1101/2024.07.02.601671}, url = {https://doi.org/10.1101/2024.07.02.601671 }, author = {Peale, David R. and Hess, Harald and Lee, P. R. and Cardona, Albert and Bock, Davi D. and Schneider-Mizell, Casey and Fetter, Richard D. and Lee, Wei-Ping and Robinson, Camenzind G. and Iyer, Nirmala and Managan, Claire} } @article {69703, title = {Ketamine induces plasticity in a norepinephrine-astroglial circuit to promote behavioral perseverance.}, journal = {Neuron}, year = {2024}, month = {2024 Dec 16}, pages = {1-15}, abstract = {

Transient exposure to ketamine can trigger lasting changes in behavior and mood. We found that brief ketamine exposure causes long-term suppression of futility-induced passivity in larval zebrafish, reversing the "giving-up" response that normally occurs when swimming fails to cause forward movement. Whole-brain imaging revealed that ketamine hyperactivates the norepinephrine-astroglia circuit responsible for passivity. After ketamine washout, this circuit exhibits hyposensitivity to futility, leading to long-term increased perseverance. Pharmacological, chemogenetic, and optogenetic manipulations show that norepinephrine and astrocytes are necessary and sufficient for ketamine{\textquoteright}s long-term perseverance-enhancing aftereffects. In\ vivo calcium imaging revealed that astrocytes in adult mouse cortex are similarly activated during futility in the tail suspension test and that acute ketamine exposure also induces astrocyte hyperactivation. The cross-species conservation of ketamine{\textquoteright}s modulation of noradrenergic-astroglial circuits and evidence that plasticity in this pathway can alter the behavioral response to futility hold promise for identifying new strategies to treat affective disorders.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2024.11.011}, url = {https://doi.org/10.1016/j.neuron.2024.11.011}, author = {Duque, Marc and Chen, Alex B and Hsu, Eric and Narayan, Sujatha and Rymbek, Altyn and Begum, Shahinoor and Saher, Gesine and Cohen, Adam E and Olson, David E and Li, Yulong and Prober, David A and Bergles, Dwight E and Fishman, Mark C and Engert, Florian and Ahrens, Misha B} } @article {69444, title = {The kinase ZYG-1 phosphorylates the cartwheel protein SAS-5 to drive centriole assembly in C. elegans}, journal = {EMBO Rep}, year = {2024}, month = {2024 May 14}, abstract = {

Centrioles organize centrosomes, the cell{\textquoteright}s primary microtubule-organizing centers (MTOCs). Centrioles double in number each cell cycle, and mis-regulation of this process is linked to diseases such as cancer and microcephaly. In C. elegans, centriole assembly is controlled by the Plk4 related-kinase ZYG-1, which recruits the SAS-5-SAS-6 complex. While the kinase activity of ZYG-1 is required for centriole assembly, how it functions has not been established. Here we report that ZYG-1 physically interacts with and phosphorylates SAS-5 on 17 conserved serine and threonine residues in vitro. Mutational scanning reveals that serine 10 and serines 331/338/340 are indispensable for proper centriole assembly. Embryos expressing SAS-5 exhibit centriole assembly failure, while those expressing SAS-5 possess extra centrioles. We show that in the absence of serine 10 phosphorylation, the SAS-5-SAS-6 complex is recruited to centrioles, but is not stably incorporated, possibly due to a failure to coordinately recruit the microtubule-binding protein SAS-4. Our work defines the critical role of phosphorylation during centriole assembly and reveals that ZYG-1 might play a role in preventing the formation of excess centrioles.

}, issn = {1469-3178}, doi = {10.1038/s44319-024-00157-y}, author = {Sankaralingam, Prabhu and Wang, Shaohe and Liu, Yan and Oegema, Karen F and O{\textquoteright}Connell, Kevin F} } @article {69168, title = {KMT2 family of H3K4 methyltransferases: enzymatic activity-dependent and -independent functions.}, journal = {Journal of Molecular Biology}, year = {2024}, month = {2024 Jan 22}, pages = {168453}, abstract = {

Histone-lysine N-methyltransferase 2 (KMT2) methyltransferases play critical roles in gene regulation, cell differentiation, animal development, and human diseases. KMT2 biological roles are often attributed to their methyltransferase activities on lysine 4 of histone H3 (H3K4). However, recent data indicate that KMT2 proteins also possess non-enzymatic functions. In this review, we discuss the current understanding of KMT2 family, with a focus on their enzymatic activity-dependent and -independent functions. Six mammalian KMT2 proteins of three subgroups, KMT2A/B (MLL1/2), KMT2C/D (MLL3/4), and KMT2F/G (SETD1A/B or SET1A/B), have shared and distinct protein domains, catalytic substrates, genomic localizations, and associated complex subunits. Recent studies have revealed the central role of KMT2C/D in enhancer regulation, differentiation, and development and have highlighted KMT2C/D enzymatic activity-dependent and independent roles in mouse embryonic development and cell differentiation. Catalytic dependent and independent roles for KMT2A/B and KMT2F/G in gene regulation, differentiation, and development are less understood. Finally, we provide our perspectives and lay out future research directions that may help advance the investigation on enzymatic activity-dependent and -independent biological roles and working mechanisms of KMT2 methyltransferases.

}, issn = {1089-8638}, doi = {10.1016/j.jmb.2024.168453}, author = {Van, Hieu T and Xie, Guojia and Dong, Peng and Liu, Zhe and Ge, Kai} } @article {69526, title = {LarvaTagger: Manual and automatic tagging of drosophila larval behaviour.}, journal = {Bioinformatics}, year = {2024}, month = {2024 Jul 05}, abstract = {

MOTIVATION: As more behavioural assays are carried out in large-scale experiments on Drosophila larvae, the definitions of the archetypal actions of a larva are regularly refined. In addition, video recording and tracking technologies constantly evolve. Consequently, automatic tagging tools for Drosophila larval behaviour must be retrained to learn new representations from new data. However, existing tools cannot transfer knowledge from large amounts of previously accumulated data.We introduce LarvaTagger, a piece of software that combines a pre-trained deep neural network, providing a continuous latent representation of larva actions for stereotypical behaviour identification, with a graphical user interface to manually tag the behaviour and train new automatic taggers with the updated ground truth.

RESULTS: We reproduced results from an automatic tagger with high accuracy, and we demonstrated that pre-training on large databases accelerates the training of a new tagger, achieving similar prediction accuracy using less data.

AVAILABILITY: All the code is free and open source. Docker images are also available. See gitlab.pasteur.fr/nyx/LarvaTagger.jl.

SUPPLEMENTARY INFORMATION: Supplementary material is available at Bioinformatics online.

}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btae441}, author = {Laurent, Francois and Blanc, Alexandre and May, Lilly and G{\'a}ndara, Lautaro and Cocanougher, Benjamin T and Jones, Benjamin M W and Hague, Peter and Barre, Chloe and Vestergaard, Christian L and Crocker, Justin and Zlatic, Marta and Jovanic, Tihana and Masson, Jean-Baptiste} } @article {69528, title = {Lattice light sheet microscopy reveals 4D force propagation dynamics and leading-edge behaviors in an embryonic epithelium in Drosophila.}, journal = {Curr Biol}, year = {2024}, month = {2024 Jun 27}, abstract = {

How pulsed contractile dynamics drive the remodeling of cell and tissue topologies in epithelial sheets has been a key question in development and disease. Due to constraints in imaging and analysis technologies, studies that have described the in\ vivo mechanisms underlying changes in cell and neighbor relationships have largely been confined to analyses of planar apical regions. Thus, how the volumetric nature of epithelial cells affects force propagation and remodeling of the cell surface in three dimensions, including especially the apical-basal axis, is unclear. Here, we perform lattice light sheet microscopy (LLSM)-based analysis to determine how far and fast forces propagate across different apical-basal layers, as well as where topological changes initiate from in a columnar epithelium. These datasets are highly time- and depth-resolved and reveal that topology-changing forces are spatially entangled, with contractile force generation occurring across the observed apical-basal axis in a pulsed fashion, while the conservation of cell volumes constrains instantaneous cell deformations. Leading layer behaviors occur opportunistically in response to favorable phasic conditions, with lagging layers "zippering" to catch up as new contractile pulses propel further changes in cell topologies. These results argue against specific zones of topological initiation and demonstrate the importance of systematic 4D-based analysis in understanding how forces and deformations in cell dimensions propagate in a three-dimensional environment.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2024.06.017}, url = {https://www.doi.org/10.1016/j.cub.2024.06.017}, author = {Vanderleest, Timothy E and Xie, Yi and Budhathoki, Rashmi and Linvill, Katie and Hobson, Chad and Heddleston, John and Loerke, Dinah and Blankenship, J Todd} } @article {69372, title = {Leptin Activated Hypothalamic BNC2 Neurons Acutely Suppress Food Intake}, journal = {bioRxiv}, year = {2024}, month = {12 Apr 2024}, abstract = {

Leptin is an adipose tissue hormone that maintains homeostatic control of adipose tissue mass by regulating the activity of specific neural populations controlling appetite and metabolism1. Leptin regulates food intake by inhibiting orexigenic agouti-related protein (AGRP) neurons and activating anorexigenic pro-opiomelanocortin (POMC) neurons2. However, while AGRP neurons regulate food intake on a rapid time scale, acute activation of POMC neurons has only a minimal effect3{\textendash}5. This has raised the possibility that there is a heretofore unidentified leptin-regulated neural population that suppresses appetite on a rapid time scale. Here, we report the discovery of a novel population of leptin-target neurons expressing basonuclin 2 (Bnc2) that acutely suppress appetite by directly inhibiting AGRP neurons. Opposite to the effect of AGRP activation, BNC2 neuronal activation elicited a place preference indicative of positive valence in hungry but not fed mice. The activity of BNC2 neurons is finely tuned by leptin, sensory food cues, and nutritional status. Finally, deleting leptin receptors in BNC2 neurons caused marked hyperphagia and obesity, similar to that observed in a leptin receptor knockout in AGRP neurons. These data indicate that BNC2-expressing neurons are a key component of the neural circuit that maintains energy balance, thus filling an important gap in our understanding of the regulation of food intake and leptin action.

}, doi = {10.1101/2024.01.25.577315}, url = {https://www.biorxiv.org/content/early/2024/04/12/2024.01.25.577315}, author = {Han L. Tan and Luping Yin and Yuqi Tan and Jessica Ivanov and Kaja Plucinska and Anoj Ilanges and Brian R. Herb and Putianqi Wang and Christin Kosse and Paul Cohen and Dayu Lin and Jeffrey M. Friedman} } @article {69226, title = {Live-cell imaging powered by computation.}, journal = {Nature Reviews Molecular Cell Biology}, year = {2024}, month = {2024 Feb 20}, abstract = {

The proliferation of microscopy methods for live-cell imaging offers many new possibilities for users but can also be challenging to navigate. The prevailing challenge in live-cell fluorescence microscopy is capturing intra-cellular dynamics while preserving cell viability. Computational methods can help to address this challenge and are now shifting the boundaries of what is possible to capture in living systems. In this Review, we discuss these computational methods focusing on artificial intelligence-based approaches that can be layered on top of commonly used existing microscopies as well as hybrid methods that integrate computation and microscope hardware. We specifically discuss how computational approaches can improve the signal-to-noise ratio, spatial resolution, temporal resolution and multi-colour capacity of live-cell imaging.

}, issn = {1471-0080}, doi = {10.1038/s41580-024-00702-6}, author = {Shroff, Hari and Testa, Ilaria and Jug, Florian and Manley, Suliana} } @article {69401, title = {Machine learning reveals the control mechanics of an insect wing hinge}, journal = {Nature}, volume = {628}, year = {2024}, month = {2024 Apr 17}, pages = {795-803}, abstract = {

Insects constitute the most species-rich radiation of metazoa, a success that is due to the evolution of active flight. Unlike pterosaurs, birds and bats, the wings of insects did not evolve from legs, but are novel structures that are attached to the body via a biomechanically complex hinge that transforms tiny, high-frequency oscillations of specialized power muscles into the sweeping back-and-forth motion of the wings. The hinge consists of a system of tiny, hardened structures called sclerites that are interconnected to one another via flexible joints and regulated by the activity of specialized control muscles. Here we imaged the activity of these muscles in a fly using a genetically encoded calcium indicator, while simultaneously tracking the three-dimensional motion of the wings with high-speed cameras. Using machine learning, we created a convolutional neural network that accurately predicts wing motion from the activity of the steering muscles, and an encoder-decoder that predicts the role of the individual sclerites on wing motion. By replaying patterns of wing motion on a dynamically scaled robotic fly, we quantified the effects of steering muscle activity on aerodynamic forces. A physics-based simulation incorporating our hinge model generates flight manoeuvres that are remarkably similar to those of free-flying flies. This integrative, multi-disciplinary approach reveals the mechanical control logic of the insect wing hinge, arguably among the most sophisticated and evolutionarily important skeletal structures in the natural world.

}, keywords = {Animals, Biomechanical Phenomena, Calcium, Drosophila melanogaster, Female, Flight, Animal, Machine Learning, Movement, Muscles, Neural Networks, Computer, Robotics, Wings, Animal}, issn = {1476-4687}, doi = {10.1038/s41586-024-07293-4}, author = {Melis, Johan M and Siwanowicz, Igor and Dickinson, Michael H} } @article {68956, title = {Magnetic voluntary head-fixation in transgenic rats enables lifetime imaging of hippocampal neurons}, journal = {Nat. Commun.}, year = {2024}, month = {2024 May 16}, abstract = {

The precise neural mechanisms within the brain that contribute to the remarkable lifetime persistence of memory remain unknown. Existing techniques to record neurons in animals are either unsuitable for longitudinal recording from the same cells or make it difficult for animals to express their full naturalistic behavioral repertoire. We present a magnetic voluntary head-fixation system that provides stable optical access to the brain during complex behavior. Compared to previous systems that used mechanical restraint, there are no moving parts and animals can engage and disengage entirely at will. This system is failsafe, easy for animals to use and reliable enough to allow long-term experiments to be routinely performed. Together with a novel two-photon fluorescence collection scheme that increases two-photon signal and a transgenic rat line that stably expresses the calcium sensor GCaMP6f in dorsal CA1, we are able to track and record activity from the same hippocampal neurons, during behavior, over a large fraction of animals{\textquoteright} lives.

}, doi = {10.1038/s41467-024-48505-9}, author = {P. D. Rich and S. Y. Thiberge and B. B. Scott and C. Guo and D. G. Tervo and C. D. Brody and A. Y. Karpova and N. D. Daw and D. W. Tank} } @article {69632, title = {Maintaining and updating accurate internal representations of continuous variables with a handful of neurons.}, journal = {Nat Neurosci}, year = {2024}, month = {2024 Oct 03}, abstract = {

Many animals rely on persistent internal representations of continuous variables for working memory, navigation, and motor control. Existing theories typically assume that large networks of neurons are required to maintain such representations accurately; networks with few neurons are thought to generate discrete representations. However, analysis of two-photon calcium imaging data from tethered flies walking in darkness suggests that their small head-direction system can maintain a surprisingly continuous and accurate representation. We thus ask whether it is possible for a small network to generate a continuous, rather than discrete, representation of such a variable. We show analytically that even very small networks can be tuned to maintain continuous internal representations, but this comes at the cost of sensitivity to noise and variations in tuning. This work expands the computational repertoire of small networks, and raises the possibility that larger networks could represent more and higher-dimensional variables than previously thought.

}, issn = {1546-1726}, doi = {10.1038/s41593-024-01766-5}, url = {https://10.1038/s41593-024-01766-5}, author = {Noorman, Marcella and Hulse, Brad K and Jayaraman, Vivek and Romani, Sandro and Hermundstad, Ann M} } @article {69171, title = {Mapping of multiple neurotransmitter receptor subtypes and distinct protein complexes to the connectome.}, journal = {Neuron}, year = {2024}, month = {2024 Jan 24}, abstract = {

Neurons express various combinations of neurotransmitter receptor (NR) subunits and receive inputs from multiple neuron types expressing different neurotransmitters. Localizing NR subunits to specific synaptic inputs has been challenging. Here, we use epitope-tagged endogenous NR subunits, expansion light-sheet microscopy, and electron microscopy (EM) connectomics to molecularly characterize synapses in Drosophila. We show that in directionally selective motion-sensitive neurons, different multiple NRs elaborated a highly stereotyped molecular topography with NR localized to specific domains receiving cell-type-specific inputs. Developmental studies suggested that NRs or complexes of them with other membrane proteins determine patterns of synaptic inputs. In support of this model, we identify a transmembrane protein selectively associated with a subset of spatially restricted synapses and demonstrate its requirement for synapse formation through genetic analysis. We propose that mechanisms that regulate the precise spatial distribution of NRs provide a molecular cartography specifying the patterns of synaptic connections onto dendrites.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2023.12.014}, author = {Sanfilippo, Piero and Kim, Alexander J and Bhukel, Anuradha and Yoo, Juyoun and Mirshahidi, Pegah S and Pandey, Vijaya and Bevir, Harry and Yuen, Ashley and Mirshahidi, Parmis S and Guo, Peiyi and Li, Hong-Sheng and Wohlschlegel, James A and Aso, Yoshinori and Zipursky, S Lawrence} } @article {69550, title = {A Markovian dynamics for Caenorhabditis elegans behavior across scales}, journal = {Proceedings of the National Academy of Sciences}, volume = {121}, year = {2024}, month = {2024 Jul 01}, pages = {e2318805121}, abstract = {

Complex phenotypes, such as an animal{\textquoteright}s behavior, generally depend on an overwhelming number of processes that span a vast range of scales. While there is no reason that behavioral dynamics permit simple models, by subsuming inherent nonlinearities and memory into maximally predictive microstates, we find one for Caenorhabditis elegans foraging. The resulting {\textquotedblleft}Markov worm{\textquotedblright} is effectively indistinguishable from real worm motion across a range of timescales, and we can decompose our model dynamics both to recover and reveal behavioral states. Finally, we connect postures to trajectories, illuminating how worms explore the environment in different behavioral states. How do we capture the breadth of behavior in animal movement, from rapid body twitches to aging? Using high-resolution videos of the nematode worm Caenorhabditis elegans, we show that a single dynamics connects posture-scale fluctuations with trajectory diffusion and longer-lived behavioral states. We take short posture sequences as an instantaneous behavioral measure, fixing the sequence length for maximal prediction. Within the space of posture sequences, we construct a fine-scale, maximum entropy partition so that transitions among microstates define a high-fidelity Markov model, which we also use as a means of principled coarse-graining. We translate these dynamics into movement using resistive force theory, capturing the statistical properties of foraging trajectories. Predictive across scales, we leverage the longest-lived eigenvectors of the inferred Markov chain to perform a top{\textendash}down subdivision of the worm{\textquoteright}s foraging behavior, revealing both {\textquotedblleft}runs-and-pirouettes{\textquotedblright} as well as previously uncharacterized finer-scale behaviors. We use our model to investigate the relevance of these fine-scale behaviors for foraging success, recovering a trade-off between local and global search strategies.

}, doi = {10.1073/pnas.2318805121}, url = {https://doi.org/10.1073/pnas.2318805121}, author = {Antonio C. Costa and Tosif Ahamed and David Jordan and Greg J. Stephens} } @article {69247, title = {MarShie: a clearing protocol for 3D analysis of single cells throughout the bone marrow at subcellular resolution.}, journal = {Nature Communincations}, volume = {15}, year = {2024}, month = {2024 Feb 26}, pages = {1764}, abstract = {

Analyzing immune cell interactions in the bone marrow is vital for understanding hematopoiesis and bone homeostasis. Three-dimensional analysis of the complete, intact bone marrow within the cortex of whole long bones remains a challenge, especially at subcellular resolution. We present a method that stabilizes the marrow and provides subcellular resolution of fluorescent signals throughout the murine femur, enabling identification and spatial characterization of hematopoietic and stromal cell subsets. By combining a pre-processing algorithm for stripe artifact removal with a machine-learning approach, we demonstrate reliable cell segmentation down to the deepest bone marrow regions. This reveals age-related changes in the marrow. It highlights the interaction between CXCR1 cells and the vascular system in homeostasis, in contrast to other myeloid cell types, and reveals their spatial characteristics after injury. The broad applicability of this method will contribute to a better understanding of bone marrow biology.

}, keywords = {Animals, Bone Marrow, Bone Marrow Cells, Hematopoiesis, Hematopoietic Stem Cells, Mice, Stromal Cells}, issn = {2041-1723}, doi = {10.1038/s41467-024-45827-6}, author = {Mertens, Till Fabian and Liebheit, Alina Tabea and Ehl, Johanna and K{\"o}hler, Ralf and Rakhymzhan, Asylkhan and Woehler, Andrew and Katth{\"a}n, Lukas and Ebel, Gernot and Liublin, Wjatscheslaw and Kasapi, Ana and Triantafyllopoulou, Antigoni and Schulz, Tim Julius and Niesner, Raluca Aura and Hauser, Anja Erika} } @article {69170, title = {Mechanical stretch regulates macropinocytosis in Hydra vulgaris.}, journal = {Molecular Biology of the Cell}, year = {2024}, month = {2024 Jan 24}, pages = {mbcE22020065}, abstract = {

Cells rely on a diverse array of engulfment processes to sense, exploit, and adapt to their environments. Among these, macropinocytosis enables indiscriminate and rapid uptake of large volumes of fluid and membrane, rendering it a highly versatile engulfment strategy. Much of the molecular machinery required for macropinocytosis has been well established, yet how this process is regulated in the context of organs and organisms remains poorly understood. Here, we report the discovery of extensive macropinocytosis in the outer epithelium of the cnidarian . Exploiting {\textquoteright}s relatively simple body plan, we developed approaches to visualize macropinocytosis over extended periods of time, revealing constitutive engulfment across the entire body axis. We show that the direct application of planar stretch leads to calcium influx and the inhibition of macropinocytosis. Finally, we establish a role for stretch-activated channels in inhibiting this process. Together, our approaches provide a platform for the mechanistic dissection of constitutive macropinocytosis in physiological contexts and highlight a potential role for macropinocytosis in responding to cell surface tension. [Media: see text] [Media: see text] [Media: see text] [Media: see text].

}, issn = {1939-4586}, doi = {10.1091/mbc.E22-02-0065}, author = {Skokan, Taylor D and Hobmayer, Bert and McKinley, Kara L and Vale, Ronald D} } @article {68793, title = {Mechanisms of memory-supporting neuronal dynamics in hippocampal area CA3}, journal = {Cell}, volume = {S0092-8674}, year = {2024}, month = {2024 Oct 17}, pages = {01141-3}, abstract = {

Hippocampal CA3 is central to memory formation and retrieval. Although various network mechanisms have been proposed, direct evidence is lacking. Using intracellular Vm recordings and optogenetic manipulations in behaving mice, we found that CA3 place-field activity is produced by a symmetric form of behavioral timescale synaptic plasticity (BTSP) at recurrent synapses among CA3 pyramidal neurons but not at synapses from the dentate gyrus (DG). Additional manipulations revealed that excitatory input from the entorhinal cortex (EC) but not the DG was required to update place cell activity based on the animal{\textquoteright}s movement. These data were captured by a computational model that used BTSP and an external updating input to produce attractor dynamics under online learning conditions. Theoretical analyses further highlight the superior memory storage capacity of such networks, especially when dealing with correlated input patterns. This evidence elucidates the cellular and circuit mechanisms of learning and memory formation in the hippocampus.

}, doi = {10.1016/j.cell.2024.09.041}, url = {https://doi.org/10.1016/j.cell.2024.09.041}, author = {Yiding Li and John J. Briguglio and Sandro Romani and Jeffrey C. Magee} } @article {69484, title = {Mechanosensory representation of wing deformations}, journal = {bioRxiv}, year = {2024}, month = {2024 Jun 02}, abstract = {

Efficient representation of structural deformations is crucial for monitoring the instantaneous state of biological structures. Insects{\textquoteright} ability to encode wing deformations during flight demonstrates a general morphological computing principle applicable across sensory systems in nature as well as engineered systems. To characterize how relevant features are encoded, we measured and modelled displacement and strain across dragonfly wing surfaces in tethered and free flight. Functional interpretations were supported by neuroanatomical maps, and ablation and perturbation experiments. We find that signal redundancy is reduced by non-random sensor distributions and that morphology limits the stimulus space such that sensory systems can monitor natural states with few sensors. Deviations from the natural states are detected by a flexible population of additional sensors with many distinguishable activation patterns.

}, doi = {10.1101/2024.06.02.596338}, url = {https://www.biorxiv.org/content/early/2024/06/02/2024.06.02.596338}, author = {Yarger, Alexandra M and Maeda, Masateru and Siwanowicz, Igor and Kajiyama, Haruhiro and Walker, Simon M and Bomphrey, Richard J and Lin, Huai-Ti} } @article {69545, title = {Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells}, journal = {Nat. Struct. Mol. Biol.}, year = {2024}, month = {2024 Oct 04}, abstract = {

Pioneer transcription factors (PTFs) possess the unique capability to access closed chromatin regions and initiate cell fate changes, yet the underlying mechanisms remain elusive. Here, we characterized the single-molecule dynamics of PTFs targeting chromatin in living cells, revealing a notable {\textquoteright}confined target search{\textquoteright} mechanism. PTFs such as FOXA1, FOXA2, SOX2, OCT4 and KLF4 sampled chromatin more frequently than non-PTF MYC, alternating between fast free diffusion in the nucleus and slower confined diffusion within mesoscale zones. Super-resolved microscopy showed closed chromatin organized as mesoscale nucleosome-dense domains, confining FOXA2 diffusion locally and enriching its binding. We pinpointed specific histone-interacting disordered regions, distinct from DNA-binding domains, crucial for confined target search kinetics and pioneer activity within closed chromatin. Fusion to other factors enhanced pioneer activity. Kinetic simulations suggested that transient confinement could increase target association rate by shortening search time and binding repeatedly. Our findings illuminate how PTFs recognize and exploit closed chromatin organization to access targets, revealing a pivotal aspect of gene regulation.

}, doi = {10.1038/s41594-024-01385-5}, url = {https://www.doi.org/10.1038/s41594-024-01385-5}, author = {Wang, Zuhui and Wang, Bo and Niu, Di and Yin, Chao and Bi, Ying and Cattoglio, Claudia and Loh, Kyle M and Lavis, Luke D and Ge, Hao and Deng, Wulan} } @article {69400, title = {Mitochondrially-associated actin waves maintain organelle homeostasis and equitable inheritance.}, journal = {Curr Opin Cell Biol}, volume = {88}, year = {2024}, month = {2024 Apr 30}, pages = {102364}, abstract = {

First identified in dividing cells as revolving clusters of actin filaments, these are now understood as mitochondrially-associated actin waves that are active throughout the cell cycle. These waves are formed from the polymerization of actin onto a subset of mitochondria. Within minutes, this F-actin depolymerizes while newly formed actin filaments assemble onto neighboring mitochondria. In interphase, actin waves locally fragment the mitochondrial network, enhancing mitochondrial content mixing to maintain organelle homeostasis. In dividing cells actin waves spatially mix mitochondria in the mother cell to ensure equitable partitioning of these organelles between daughter cells. Progress has been made in understanding the consequences of actin cycling as well as the underlying molecular mechanisms, but many questions remain, and here we review these elements. Also, we draw parallels between mitochondrially-associated actin cycling and cortical actin waves. These dynamic systems highlight the remarkable plasticity of the actin cytoskeleton.

}, issn = {1879-0410}, doi = {10.1016/j.ceb.2024.102364}, author = {Coscia, Stephen M and Moore, Andrew S and Wong, Yvette C and Holzbaur, Erika L F} } @article {69622, title = {A modular chemigenetic calcium indicator for multiplexed in vivo functional imaging.}, journal = {Nat Methods}, year = {2024}, month = {2024 Sep 20}, abstract = {

Genetically encoded fluorescent calcium indicators allow cellular-resolution recording of physiology. However, bright, genetically targetable indicators that can be multiplexed with existing tools in vivo are needed for simultaneous imaging of multiple signals. Here we describe WHaloCaMP, a modular chemigenetic calcium indicator built from bright dye-ligands and protein sensor domains. Fluorescence change in WHaloCaMP results from reversible quenching of the bound dye via a strategically placed tryptophan. WHaloCaMP is compatible with rhodamine dye-ligands that fluoresce from green to near-infrared, including several that efficiently label the brain in animals. When bound to a near-infrared dye-ligand, WHaloCaMP shows a 7{\texttimes} increase in fluorescence intensity and a 2.1-ns increase in fluorescence lifetime upon calcium binding. We use WHaloCaMP1a to image Ca responses in vivo in flies and mice, to perform three-color multiplexed functional imaging of hundreds of neurons and astrocytes in zebrafish larvae and to quantify Ca concentration using fluorescence lifetime imaging microscopy (FLIM).

}, issn = {1548-7105}, doi = {10.1038/s41592-024-02411-6}, url = {https://doi.org/10.1038/s41592-024-02411-6}, author = {Farrants, Helen and Shuai, Yichun and Lemon, William C and Monroy Hernandez, Christian and Zhang, Deng and Yang, Shang and Patel, Ronak and Qiao, Guanda and Frei, Michelle S and Plutkis, Sarah E and Grimm, Jonathan B and Hanson, Timothy L and Tomaska, Filip and Turner, Glenn C and Stringer, Carsen and Keller, Philipp J and Beyene, Abraham G and Chen, Yao and Liang, Yajie and Lavis, Luke D and Schreiter, Eric R} } @article {69534, title = {Molecular and cellular mechanisms of teneurin signaling in synaptic partner matching.}, journal = {Cell}, year = {2024}, month = {2024 Jul 03}, abstract = {

In developing brains, axons exhibit remarkable precision in selecting synaptic partners among many non-partner cells. Evolutionarily conserved teneurins are transmembrane proteins that instruct synaptic partner matching. However, how intracellular signaling pathways execute teneurins{\textquoteright} functions is unclear. Here, we use in situ proximity labeling to obtain the intracellular interactome of a teneurin (Ten-m) in the Drosophila brain. Genetic interaction studies using quantitative partner matching assays in both olfactory receptor neurons (ORNs) and projection neurons (PNs) reveal a common pathway: Ten-m binds to and negatively regulates a RhoGAP, thus activating the Rac1 small GTPases to promote synaptic partner matching. Developmental analyses with single-axon resolution identify the cellular mechanism of synaptic partner matching: Ten-m signaling promotes local F-actin levels and stabilizes ORN axon branches that contact partner PN dendrites. Combining spatial proteomics and high-resolution phenotypic analyses, this study advanced our understanding of both cellular and molecular mechanisms of synaptic partner matching.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2024.06.022}, author = {Xu, Chuanyun and Li, Zhuoran and Lyu, Cheng and Hu, Yixin and McLaughlin, Colleen N and Wong, Kenneth Kin Lam and Xie, Qijing and Luginbuhl, David J and Li, Hongjie and Udeshi, Namrata D and Svinkina, Tanya and Mani, D R and Han, Shuo and Li, Tongchao and Li, Yang and Guajardo, Ricardo and Ting, Alice Y and Carr, Steven A and Li, Jiefu and Luo, Liqun} } @article {69615, title = {A molecular switch for stress-induced activation of retrograde mitochondrial transport}, journal = {bioRxiv}, year = {2024}, month = {2024 Sep 14}, abstract = {

The cellular distribution of mitochondria in response to stress and local energy needs is governed by the relative activities of kinesin and dynein. The mechanism for switching between these two opposite polarity microtubule motors remains unknown. Here, we coupled a novel cellular synthetic cargo transport assay with AlphaFold2-guided mutagenesis to identify a regulatory helix in the mitochondrial adaptor protein (TRAK) that mediates switching between kinesin- and dynein-driven transport. Differences in the helix sequence explain why two near-identical TRAK isoforms transport mitochondria in predominantly opposite directions. Phosphorylation of the regulatory helix by stress-activated kinases causes the activation of dynein and dissociation of kinesin. Our results reveal a molecular mechanism for coordinating the directional transport of mitochondria in response to intracellular signals.

}, doi = {10.1101/2024.09.13.612963}, url = {https://doi.org/10.1101/2024.09.13.612963}, author = {Gladkova, Christina and Paez-Segala, Maria G. and Grant, William P. and Myers, Samuel A. and Wang, Yuxiao and Vale, Ronald D.} } @article {69321, title = {More than just {\textquoteright}added value{\textquoteright}: The perils of not establishing shared core facilities in resource-constrained communities.}, journal = {J Microsc}, year = {2024}, month = {2024 Feb 20}, abstract = {

The accelerating pace of technological advancements necessitates specialised expertise and cutting-edge instruments to maintain competitive research in life sciences. Core facilities - collaborative laboratories equipped with state-of-the-art tools and staffed by expert personnel - are vital resources that support diverse scientific endeavours. However, their adoption in lower-income communities has been comparatively stagnant due to both financial and cultural challenges. This paper explores the perils of not supporting core facilities on national research enterprises, underscoring the need for balanced investments in discovery science and crucial infrastructure support. We explore the implications from the perspectives of funders, university leaders and lab heads. We advocate for a paradigm shift to recognise these facilities as essential components of national research efforts. Core facilities are positioned not as optional but as strategic investments that can catalyse breakthroughs, particularly in environments with limited resources.

}, issn = {1365-2818}, doi = {10.1111/jmi.13277}, author = {Rahmoon, Mai A and Hobson, Chad M and Aaron, Jesse S and Balasubramanian, Harikrushnan and Chew, Teng-Leong} } @article {69219, title = {More than just {\textquoteright}added value{\textquoteright}: The perils of not establishing shared core facilities in resource-constrained communities.}, journal = {Journal of Microscopy}, year = {2024}, month = {2024 Feb 20}, abstract = {

The accelerating pace of technological advancements necessitates specialised expertise and cutting-edge instruments to maintain competitive research in life sciences. Core facilities - collaborative laboratories equipped with state-of-the-art tools and staffed by expert personnel - are vital resources that support diverse scientific endeavours. However, their adoption in lower-income communities has been comparatively stagnant due to both financial and cultural challenges. This paper explores the perils of not supporting core facilities on national research enterprises, underscoring the need for balanced investments in discovery science and crucial infrastructure support. We explore the implications from the perspectives of funders, university leaders and lab heads. We advocate for a paradigm shift to recognise these facilities as essential components of national research efforts. Core facilities are positioned not as optional but as strategic investments that can catalyse breakthroughs, particularly in environments with limited resources.

}, issn = {1365-2818}, doi = {10.1111/jmi.13277}, author = {Rahmoon, Mai A and Hobson, Chad M and Aaron, Jesse S and Balasubramanian, Harikrushnan and Chew, Teng-Leong} } @article {69169, title = {Motion of VAPB molecules reveals ER-mitochondria contact site subdomains.}, journal = {Nature}, volume = {626}, year = {2024}, month = {2024 Jan 24}, pages = {169-176}, abstract = {

To coordinate cellular physiology, eukaryotic cells rely on the rapid exchange of molecules at specialized organelle-organelle contact sites. Endoplasmic reticulum-mitochondrial contact sites (ERMCSs) are particularly vital communication hubs, playing key roles in the exchange of signalling molecules, lipids and metabolites. ERMCSs are maintained by interactions between complementary tethering molecules on the surface of each organelle. However, due to the extreme sensitivity of these membrane interfaces to experimental perturbation, a clear understanding of their nanoscale organization and regulation is still lacking. Here we combine three-dimensional electron microscopy with high-speed molecular tracking of a model organelle tether, Vesicle-associated membrane protein (VAMP)-associated protein B (VAPB), to map the structure and diffusion landscape of ERMCSs. We uncovered dynamic subdomains within VAPB contact sites that correlate with ER membrane curvature and undergo rapid remodelling. We show that VAPB molecules enter and leave ERMCSs within seconds, despite the contact site itself remaining stable over much longer time scales. This metastability allows ERMCSs to remodel with changes in the physiological environment to accommodate metabolic needs of the cell. An amyotrophic lateral sclerosis-associated mutation in VAPB perturbs these subdomains, likely impairing their remodelling capacity and resulting in impaired interorganelle communication. These results establish high-speed single-molecule imaging as a new tool for mapping the structure of contact site interfaces and reveal that the diffusion landscape of VAPB at contact sites is a crucial component of ERMCS homeostasis.

}, keywords = {Amyotrophic Lateral Sclerosis, Endoplasmic Reticulum, Humans, Mitochondria, Mitochondrial Membranes, Signal Transduction, Vesicular Transport Proteins}, issn = {1476-4687}, doi = {10.1038/s41586-023-06956-y}, author = {Obara, Christopher J and Nixon-Abell, Jonathon and Moore, Andrew S and Riccio, Federica and Hoffman, David P and Shtengel, Gleb and Xu, C Shan and Schaefer, Kathy and Pasolli, H Amalia and Masson, Jean-Baptiste and Hess, Harald F and Calderon, Christopher P and Blackstone, Craig and Lippincott-Schwartz, Jennifer} } @article {69301, title = {Motor neurons generate pose-targeted movements via proprioceptive sculpting.}, journal = {Nature}, year = {2024}, month = {2024 Mar 20}, abstract = {

Motor neurons are the final common pathway through which the brain controls movement of the body, forming the basic elements from which all movement is composed. Yet how a single motor neuron contributes to control during natural movement remains unclear. Here we anatomically and functionally characterize the individual roles of the motor neurons that control head movement in the fly, Drosophila melanogaster. Counterintuitively, we find that activity in a single motor neuron rotates the head in different directions, depending on the starting posture of the head, such that the head converges towards a pose determined by the identity of the stimulated motor neuron. A feedback model predicts that this convergent behaviour results from motor neuron drive interacting with proprioceptive feedback. We identify and genetically suppress a single class of proprioceptive neuron that changes the motor neuron-induced convergence as predicted by the feedback model. These data suggest a framework for how the brain controls movements: instead of directly generating movement in a given direction by activating a fixed set of motor neurons, the brain controls movements by adding bias to a continuing proprioceptive-motor loop.

}, issn = {1476-4687}, doi = {10.1038/s41586-024-07222-5}, author = {Gorko, Benjamin and Siwanowicz, Igor and Close, Kari and Christoforou, Christina and Hibbard, Karen L and Kabra, Mayank and Lee, Allen and Park, Jin-Yong and Li, Si Ying and Chen, Alex B and Namiki, Shigehiro and Chen, Chenghao and Tuthill, John C and Bock, Davi D and Rouault, Herv{\'e} and Branson, Kristin and Ihrke, Gudrun and Huston, Stephen J} } @article {68936, title = {Multi-day neuron tracking in high-density electrophysiology recordings using earth mover{\textquoteright}s distance}, journal = {eLife}, year = {2024}, month = {2024-07-10}, abstract = {

Accurate tracking of the same neurons across multiple days is crucial for studying changes in neuronal activity during learning and adaptation. Advances in high-density extracellular electrophysiology recording probes, such as Neuropixels, provide a promising avenue to accomplish this goal. Identifying the same neurons in multiple recordings is, however, complicated by non-rigid movement of the tissue relative to the recording sites (drift) and loss of signal from some neurons. Here, we propose a neuron tracking method that can identify the same cells independent of firing statistics, that are used by most existing methods. Our method is based on between-day non-rigid alignment of spike-sorted clusters. We verified the same cell identity in mice using measured visual receptive fields. This method succeeds on datasets separated from 1 to 47 days, with an 84\% average recovery rate.

}, doi = {10.7554/eLife.92495.3}, url = {https://doi.org/10.7554/eLife.92495.3}, author = {Augustine Xiaoran Yuan and Jennifer Colonell and Anna Lebedeva and Adam Charles and Timothy Harris} } @article {69559, title = {Nanoscale volumetric fluorescence imaging via photochemical sectioning}, journal = {bioRxiv}, year = {2024}, month = {2024 Aug 05}, abstract = {

Optical nanoscopy of intact biological specimens has been transformed by recent advancements in hydrogel-based tissue clearing and expansion, enabling the imaging of cellular and subcellular structures with molecular contrast. However, existing high-resolution fluorescence microscopes have limited imaging depth, which prevents the study of whole-mount specimens without physical sectioning. To address this challenge, we developed {\textquotedblleft}photochemical sectioning,{\textquotedblright} a spatially precise, light-based sample sectioning process. By combining photochemical sectioning with volumetric lattice light-sheet imaging and petabyte-scale computation, we imaged and reconstructed axons and myelination sheaths across entire mouse olfactory bulbs at nanoscale resolution. An olfactory-bulb-wide analysis of myelinated and unmyelinated axons revealed distinctive patterns of axon degeneration and de-/dysmyelination in the neurodegenerative mouse, highlighting the potential for peta- to exabyte-scale super-resolution studies using this approach.

}, doi = {10.1101/2024.08.01.605857}, url = {https://doi.org/10.1101/2024.08.01.605857}, author = {Wang, Wei and Ruan, Xiongtao and Liu, Gaoxiang and Milkie, Daniel E. and Li, Wenping and Betzig, Eric and Upadhyayula, Srigokul and Gao, Ruixuan} } @article {69511, title = {Near-infrared nanosensors enable optical imaging of oxytocin with selectivity over vasopressin in acute mouse brain slices.}, journal = {Proc Natl Acad Sci U S A}, volume = {121}, year = {2024}, month = {2024 Jun 25}, pages = {e2314795121}, abstract = {

Oxytocin plays a critical role in regulating social behaviors, yet our understanding of its function in both neurological health and disease remains incomplete. Real-time oxytocin imaging probes with spatiotemporal resolution relevant to its endogenous signaling are required to fully elucidate oxytocin{\textquoteright}s role in the brain. Herein, we describe a near-infrared oxytocin nanosensor (nIROXT), a synthetic probe capable of imaging oxytocin in the brain without interference from its structural analogue, vasopressin. nIROXT leverages the inherent tissue-transparent fluorescence of single-walled carbon nanotubes (SWCNT) and the molecular recognition capacity of an oxytocin receptor peptide fragment to selectively and reversibly image oxytocin. We employ these nanosensors to monitor electrically stimulated oxytocin release in brain tissue, revealing oxytocin release sites with a median size of 3 {\textmu}m in the paraventricular nucleus of C57BL/6 mice, which putatively represents the spatial diffusion of oxytocin from its point of release. These data demonstrate that covalent SWCNT constructs, such as nIROXT, are powerful optical tools that can be leveraged to measure neuropeptide release in brain tissue.

}, keywords = {Animals, Brain, Male, Mice, Mice, Inbred C57BL, Nanotubes, Carbon, Optical Imaging, Oxytocin, Receptors, Oxytocin, Spectroscopy, Near-Infrared, Vasopressins}, issn = {1091-6490}, doi = {10.1073/pnas.2314795121}, author = {Mun, Jaewan and Navarro, Nicole and Jeong, Sanghwa and Ouassil, Nicholas and Leem, Esther and Beyene, Abraham G and Landry, Markita P} } @article {69510, title = {Neocortical inhibitory imbalance predicts successful sensory detection.}, journal = {Cell Rep}, volume = {43}, year = {2024}, month = {2024 Jun 20}, pages = {114233}, abstract = {

Perceptual success depends on fast-spiking, parvalbumin-positive interneurons (FS/PVs). However, competing theories of optimal rate and correlation in pyramidal (PYR) firing make opposing predictions regarding the underlying FS/PV dynamics. We addressed this with population calcium imaging of FS/PVs and putative PYR neurons during threshold detection. In primary somatosensory and visual neocortex, a distinct PYR subset shows increased rate and spike-count correlations on detected trials ("hits"), while most show no rate change and decreased correlations. A larger fraction of FS/PVs predicts hits with either rate increases or decreases. Using computational modeling, we found that inhibitory imbalance, created by excitatory "feedback" and interactions between FS/PV pools, can account for the data. Rate-decreasing FS/PVs increase rate and correlation in a PYR subset, while rate-increasing FS/PVs reduce correlations and offset enhanced excitation in PYR neurons. These findings indicate that selection of informative PYR ensembles, through transient inhibitory imbalance, is a common motif of optimal neocortical processing.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2024.114233}, author = {Deister, Christopher A and Moore, Alexander I and Voigts, Jakob and Bechek, Sophia and Lichtin, Rebecca and Brown, Tyler C and Moore, Christopher I} } @article {69008, title = {Nested neural circuits generate distinct acoustic signals during Drosophila courtship}, journal = {Current Biology}, volume = {34}, year = {2024}, month = {2024 Feb 26}, pages = {808-24}, abstract = {

Many motor control systems generate multiple movements using a common set of muscles. How are premotor circuits able to flexibly generate diverse movement patterns? Here, we characterize the neuronal circuits that drive the distinct courtship songs of\ Drosophila melanogaster. Male flies vibrate their wings towards females to produce two different song modes {\textendash} pulse and sine song {\textendash} which signal species identity and male quality. Using cell-type specific genetic reagents and the connectome, we provide a cellular and synaptic map of the circuits in the male ventral nerve cord that generate these songs and examine how activating or inhibiting each cell type within these circuits affects the song. Our data reveal that the song circuit is organized into two nested feed-forward pathways, with extensive reciprocal and feed-back connections. The larger network produces pulse song, the more complex and ancestral song form. A subset of this network produces sine song, the simpler and more recent form. Such nested organization may be a common feature of motor control circuits in which evolution has layered increasing flexibility on to a basic movement pattern.

}, doi = {10.1016/j.cub.2024.01.015}, url = {https://doi.org/10.1016/j.cub.2024.01.015}, author = {Joshua L. Lillvis and Kaiyu Wang and Hiroshi M. Shiozaki and Min Xu and David L. Stern and Barry J. Dickson} } @article {68921, title = {Network statistics of the whole-brain connectome of Drosophila}, journal = {Nature}, volume = {634}, year = {2024}, month = {2024 Oct 02}, pages = {153{\textendash}165}, abstract = {

Brains comprise complex networks of neurons and connections, similar to the nodes and edges of artificial networks. Network analysis applied to the wiring diagrams of brains can offer insights into how they support computations and regulate the flow of\ information underlying perception and behaviour. The completion of the first whole-brain connectome of an adult fly, containing over 130,000 neurons and millions of synaptic connections, offers an opportunity to analyse the statistical properties and topological features of a complete brain. Here we computed the prevalence of two- and three-node motifs, examined their strengths, related this information to both neurotransmitter composition and cell type annotations, and compared these metrics with wiring diagrams of other animals. We found that the network of the fly brain displays rich-club organization, with a large population (30\% of the connectome) of highly connected neurons. We identified subsets of rich-club neurons that may serve as integrators or broadcasters of signals. Finally, we examined subnetworks based on 78 anatomically defined brain regions or neuropils. These data products are shared within the FlyWire Codex (https://codex.flywire.ai) and should serve as a foundation for models and experiments exploring the relationship between neural activity and anatomical structure.

}, doi = {10.1038/s41586-024-07968-y}, url = {https://doi.org/10.1038/s41586-024-07968-y}, author = {Albert Lin and Runzhe Yang and Sven Dorkenwald and Arie Matsliah and Amy R. Sterling and Philipp Schlegel and Szi-chieh Yu and Claire E. McKellar and Marta Costa and Katharina Eichler and Alexander Shakeel Bates and Nils Eckstein and Jan Funke and Gregory S.X.E. Jefferis and Mala Murthy} } @article {68710, title = {A neural basis of choking under pressure}, journal = {Neuron}, year = {2024}, month = {2024 Sep 07}, abstract = {

Incentives tend to drive improvements in performance. But when incentives get too high, we can "choke under pressure" and underperform right when it matters most. What neural processes might lead to choking under pressure? We studied rhesus monkeys performing a challenging reaching task in which they underperformed when an unusually large "jackpot" reward was at stake, and we sought a neural mechanism that might result in that underperformance. We found that increases in reward drive neural activity during movement preparation into, and then past, a zone of optimal performance. We conclude that neural signals of reward and motor preparation interact in the motor cortex (MC) in a manner that can explain why we choke under pressure.

}, doi = {10.1016/j.neuron.2024.08.012}, url = {https://doi.org/10.1016/j.neuron.2024.08.012}, author = {Adam L. Smoulder and Patrick J. Marino and Emily R. Oby and Sam E. Snyder and Hiroo Miyata and Nick P. Pavlovsky and William E. Bishop and Byron M. Yu and Steven M. Chase and Aaron P. Batista} } @article {69172, title = {A neural circuit architecture for rapid learning in goal-directed navigation}, journal = {Neuron}, volume = {112}, year = {2024}, month = {2024 May 23}, pages = {2581-2599.e23}, abstract = {

Anchoring goals to spatial representations enables flexible navigation but is challenging in novel environments when both representations must be acquired simultaneously. We propose a framework for how Drosophila uses internal representations of head direction (HD) to build goal representations upon selective thermal reinforcement. We show that flies use stochastically generated fixations and directed saccades to express heading preferences in an operant visual learning paradigm and that HD neurons are required to modify these preferences based on reinforcement. We used a symmetric visual setting to expose how flies{\textquoteright} HD and goal representations co-evolve and how the reliability of these interacting representations impacts behavior. Finally, we describe how rapid learning of new goal headings may rest on a behavioral policy whose parameters are flexible but whose form is genetically encoded in circuit architecture. Such evolutionarily structured architectures, which enable rapidly adaptive behavior driven by internal representations, may be relevant across species.

}, doi = {https://doi.org/10.1016/j.neuron.2024.04.036}, url = {https://doi.org/10.1016/j.neuron.2024.04.036}, author = {Chuntao Dan and Brad K. Hulse and Ramya Kappagantula and Vivek Jayaraman and Ann M. Hermundstad} } @article {69542, title = {Neural circuit basis of placebo pain relief.}, journal = {Nature}, year = {2024}, month = {2024 Jul 24}, abstract = {

Placebo effects are striking demonstrations of mind-body interactions . During pain perception, in the absence of any treatment, an expectation of pain relief can reduce the experience of pain, a phenomenon known as placebo analgesia . However, despite the strength of placebo effects and their impact on everyday human experience and failure of clinical trials for new therapeutics , the neural circuit basis of placebo effects has remained elusive. Here, we show that analgesia from the expectation of pain relief is mediated by rostral anterior cingulate cortex (rACC) neurons that project to the pontine nucleus (rACC{\textrightarrow}Pn), a pre-cerebellar nucleus with no established function in pain. We created a behavioral assay that generates placebo-like anticipatory pain relief in mice. In vivo calcium imaging of neural activity and electrophysiological recordings in brain slices showed that expectations of pain relief boost the activity of rACC{\textrightarrow}Pn neurons and potentiate neurotransmission in this pathway. Transcriptomic studies of Pn neurons revealed an abundance of opioid receptors, further suggesting a role in pain modulation. Inhibition of the rACC{\textrightarrow}Pn pathway disrupted placebo analgesia and decreased pain thresholds, whereas activation elicited analgesia in the absence of placebo conditioning. Finally, Purkinje cells exhibited activity patterns resembling those of rACC{\textrightarrow}Pn neurons during pain relief expectation, providing cellular-level evidence of a role for the cerebellum in cognitive pain modulation. These findings open the possibility of targeting this prefrontal cortico-ponto-cerebellar pathway with drugs or neurostimulation to treat pain.

}, issn = {1476-4687}, doi = {10.1038/s41586-024-07816-z}, author = {Chen, Chong and Niehaus, Jesse K and Dinc, Fatih and Huang, Karen L and Barnette, Alexander L and Tassou, Adrien and Shuster, S Andrew and Wang, Lihua and Lemire, Andrew and Menon, Vilas and Ritola, Kimberly and Hantman, Adam and Zeng, Hongkui and Schnitzer, Mark J and Scherrer, Gr{\'e}gory} } @article {69438, title = {Neural Control of Naturalistic Behavior Choices}, journal = {Annu Rev Neurosci}, year = {2024}, month = {2024 May 09}, abstract = {

In the natural world, animals make decisions on an ongoing basis, continuously selecting which action to undertake next. In the lab, however, the neural bases of decision processes have mostly been studied using artificial trial structures. New experimental tools based on the genetic toolkit of model organisms now make it experimentally feasible to monitor and manipulate neural activity in small subsets of neurons during naturalistic behaviors. We thus propose a new approach to investigating decision processes, termed reverse neuroethology. In this approach, experimenters select animal models based on experimental accessibility and then utilize cutting-edge tools such as connectomes and genetically encoded reagents to analyze the flow of information through an animal{\textquoteright}s nervous system during naturalistic choice behaviors. We describe how the reverse neuroethology strategy has been applied to understand the neural underpinnings of innate, rapid decision making, with a focus on defensive behavioral choices in the vinegar fly Drosophila melanogaster.

}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-111020-094019}, author = {Asinof, Samuel K and Card, Gwyneth M} } @article {69045, title = {Neural-circuit basis of song preference learning in fruit flies}, journal = {iScience}, volume = {27}, year = {2024}, month = {2024 Jul 19}, abstract = {

As observed in human language learning and song learning in birds, the fruit fly Drosophila melanogaster changes its auditory behaviors according to prior sound experiences. This phenomenon, known as song preference learning in flies, requires GABAergic input to pC1 neurons in the brain, with these neurons playing a key role in mating behavior. The neural circuit basis of this GABAergic input, however, is not known. Here, we find that GABAergic neurons expressing the sex-determination gene doublesex are necessary for song preference learning. In the brain, only four doublesex-expressing GABAergic neurons exist per hemibrain, identified as pCd-2 neurons. pCd-2 neurons directly, and in many cases mutually, connect with pC1 neurons, suggesting the existence of reciprocal circuits between them. Moreover, GABAergic and dopaminergic inputs to doublesex-expressing GABAergic neurons are necessary for song preference learning. Together, this study provides a neural circuit model that underlies experience-dependent auditory plasticity at a single-cell resolution.

}, doi = {10.1016/j.isci.2024.110266}, url = {https://doi.org/10.1016/j.isci.2024.110266}, author = {Keisuke Imoto and Yuki Ishikawa and Yoshinori Aso and Jan Funke and Ryoya Tanaka and Azusa Kamikouchi} } @article {68889, title = {Neuronal wiring diagram of an adult brain.}, journal = {Nature}, volume = {634}, year = {2024}, month = {2024 Oct 02}, pages = {124-138}, abstract = {

Connections between neurons can be mapped by acquiring and analysing electron microscopic brain images. In recent years, this approach has been applied to chunks of brains to reconstruct local connectivity maps that are highly informative, but nevertheless inadequate for understanding brain function more globally. Here we present a neuronal wiring diagram of a whole brain containing 5 {\texttimes} 107 chemical synapses between 139,255 neurons reconstructed from an adult female Drosophila melanogaster. The resource also incorporates annotations of cell classes and types, nerves, hemilineages and predictions of neurotransmitter identities. Data products are available for download, programmatic access and interactive browsing and have been made interoperable with other fly data resources. We derive a projectome-a map of projections between regions-from the connectome and report on tracing of synaptic pathways and the analysis of information flow from inputs (sensory and ascending neurons) to outputs (motor, endocrine and descending neurons) across both hemispheres and between the central brain and the optic lobes. Tracing from a subset of photoreceptors to descending motor pathways illustrates how structure can uncover putative circuit mechanisms underlying sensorimotor behaviours. The technologies and open ecosystem reported here set the stage for future large-scale connectome projects in other species.

}, doi = {10.1038/s41586-024-07558-y}, url = {https://doi.org/10.1038/s41586-024-07558-y}, author = {Dorkenwald, Sven and Matsliah, Arie and Sterling, Amy R and Schlegel, Philipp and Yu, Szi-Chieh and McKellar, Claire E and Lin, Albert and Costa, Marta and Eichler, Katharina and Yin, Yijie and Silversmith, Will and Schneider-Mizell, Casey and Jordan, Chris S and Brittain, Derrick and Halageri, Akhilesh and Kuehner, Kai and Ogedengbe, Oluwaseun and Morey, Ryan and Gager, Jay and Kruk, Krzysztof and Perlman, Eric and Yang, Runzhe and Deutsch, David and Bland, Doug and Sorek, Marissa and Lu, Ran and Macrina, Thomas and Lee, Kisuk and Bae, J Alexander and Mu, Shang and Nehoran, Barak and Mitchell, Eric and Popovych, Sergiy and Wu, Jingpeng and Jia, Zhen and Castro, Manuel and Kemnitz, Nico and Ih, Dodam and Bates, Alexander Shakeel and Eckstein, Nils and Funke, Jan and Collman, Forrest and Bock, Davi D and Jefferis, Gregory S X E and Seung, H Sebastian and Murthy, Mala} } @article {68258, title = {NeuronBridge: an intuitive web application for neuronal morphology search across large data sets}, journal = {BMC Bioinformatics}, volume = {25}, year = {2024}, month = {2024 Mar 15}, pages = {114}, abstract = {

Background

Neuroscience research in\ Drosophila\ is benefiting from large-scale connectomics efforts using electron microscopy (EM) to reveal all the neurons in a brain and their connections. To exploit this knowledge base, researchers relate a connectome{\textquoteright}s structure to neuronal function, often by studying individual neuron cell types. Vast libraries of fly driver lines expressing fluorescent reporter genes in sets of neurons have been created and imaged using confocal light microscopy (LM), enabling the targeting of neurons for experimentation. However, creating a fly line for driving gene expression within a single neuron found in an EM connectome remains a challenge, as it typically requires identifying a pair of driver lines where only the neuron of interest is expressed in both. This task and other emerging scientific workflows require finding similar neurons across large data sets imaged using different modalities.

Results

Here, we present NeuronBridge, a web application for easily and rapidly finding putative morphological matches between large data sets of neurons imaged using different modalities. We describe the functionality and construction of the NeuronBridge service, including its user-friendly graphical user interface (GUI), extensible data model, serverless cloud architecture, and massively parallel image search engine.

Conclusions

NeuronBridge fills a critical gap in the\ Drosophila\ research workflow and is used by hundreds of neuroscience researchers around the world. We offer our software code, open APIs, and processed data sets for integration and reuse, and provide the application as a service at\ http://neuronbridge.janelia.org.

}, doi = {10.1186/s12859-024-05732-7}, url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-024-05732-7}, author = {Jody Clements and Cristian Goina and Philip M. Hubbard and Takashi Kawase and Donald J. Olbris and Hideo Otsuna and Robert Svirskas and Konrad Rokicki} } @article {69439, title = {Neurotransmitter classification from electron microscopy images at synaptic sites in Drosophila melanogaster}, journal = {Cell}, volume = {187}, year = {2024}, month = {2024 May 09}, pages = {2574-2594.e23}, abstract = {

High-resolution electron microscopy of nervous systems has enabled the reconstruction of synaptic connectomes. However, we do not know the synaptic sign for each connection (i.e., whether a connection is excitatory or inhibitory), which is implied by the released transmitter. We demonstrate that artificial neural networks can predict transmitter types for presynapses from electron micrographs: a network trained to predict six transmitters (acetylcholine, glutamate, GABA, serotonin, dopamine, octopamine) achieves an accuracy of 87\% for individual synapses, 94\% for neurons, and 91\% for known cell types across a D.\ melanogaster whole brain. We visualize the ultrastructural features used for prediction, discovering subtle but significant differences between transmitter phenotypes. We also analyze transmitter distributions across the brain and find that neurons that develop together largely express only one fast-acting transmitter (acetylcholine, glutamate, or GABA). We hope that our publicly available predictions act as an accelerant for neuroscientific hypothesis generation for the fly.

}, keywords = {Animals, Brain, Connectome, Drosophila melanogaster, gamma-Aminobutyric Acid, Microscopy, Electron, Neural Networks, Computer, Neurons, Neurotransmitter Agents, Synapses}, issn = {1097-4172}, doi = {10.1016/j.cell.2024.03.016}, author = {Eckstein, Nils and Bates, Alexander Shakeel and Champion, Andrew and Du, Michelle and Yin, Yijie and Schlegel, Philipp and Lu, Alicia Kun-Yang and Rymer, Thomson and Finley-May, Samantha and Paterson, Tyler and Parekh, Ruchi and Dorkenwald, Sven and Matsliah, Arie and Yu, Szi-Chieh and McKellar, Claire and Sterling, Amy and Eichler, Katharina and Costa, Marta and Seung, Sebastian and Murthy, Mala and Hartenstein, Volker and Jefferis, Gregory S X E and Funke, Jan} } @article {68839, title = {New genetic tools for mushroom body output neurons in~Drosophila}, journal = {eLife}, year = {2024}, month = {2024 Jan 24}, abstract = {

How memories of past events influence behavior is a key question in neuroscience. The major associative learning center in\ Drosophila, the Mushroom Body (MB), communicates to the rest of the brain through Mushroom Body Output Neurons (MBONs). While 21 MBON cell types have their dendrites confined to small compartments of the MB lobes, analysis of EM connectomes revealed the presence of an additional 14 MBON cell types that are atypical in having dendritic input both within the MB lobes and in adjacent brain regions. Genetic reagents for manipulating atypical MBONs and experimental data on their functions has been lacking. In this report we describe new cell-type-specific GAL4 drivers for many MBONs, including the majority of atypical MBONs. Using these genetic reagents, we conducted optogenetic activation screening to examine their ability to drive behaviors and learning. These reagents provide important new tools for the study of complex behaviors in\ Drosophila.

}, doi = {10.7554/eLife.90523}, url = {https://doi.org/10.7554/eLife.90523}, author = {Rubin, Gerald M and Aso, Yoshinori} } @article {69635, title = {New Statistical Metric for Robust Target Detection in Cryo-EM Using 2DTM}, journal = {bioRxiv}, year = {2024}, month = {2024 Oct 03}, abstract = {

2D template matching (2DTM) can be used to detect molecules and their assemblies in cellular cryo-EM images with high positional and orientational accuracy. While 2DTM successfully detects spherical targets such as large ribosomal subunits, challenges remain in detecting smaller and more aspherical targets in various environments. In this work, a novel 2DTM metric, referred to as the 2DTM p-value, is developed to extend the 2DTM framework to more complex applications. The 2DTM p-value combines information from two previously used 2DTM metrics, namely the 2DTM signal-to-noise ratio (SNR) and z-score, which are derived from the cross-correlation coefficient between the target and the template. The 2DTM p-value demonstrates robust detection accuracies under various imaging and sample conditions and outperforms the 2DTM SNR and z-score alone. Specifically, the 2DTM p-value improves the detection of aspherical targets such as a modified artificial tubulin patch particle (500 kDa) and a much smaller clathrin monomer (193 kDa) in simulated data. It also accurately recovers mature 60S ribosomes in yeast lamellae samples, even under conditions of increased Gaussian noise. The new metric will enable the detection of a wider variety of targets in both purified and cellular samples through 2DTM.

}, doi = {10.1101/2024.10.01.616095}, url = {https://doi.org/10.1101/2024.10.01.616095}, author = {Zhang, Kexin and Cossio, Pilar and Rangan, Aaditya and Lucas, Bronwyn and Grigorieff, Nikolaus} } @article {69402, title = {NMDAR-mediated activation of pannexin1 channels contributes to the detonator properties of hippocampal mossy fiber synapses.}, journal = {iScience}, volume = {27}, year = {2024}, month = {2024 Apr 06}, pages = {109681}, abstract = {

Pannexins are large-pore ion channels expressed throughout the mammalian brain that participate in various neuropathologies; however, their physiological roles remain obscure. Here, we report that pannexin1 channels (Panx1) can be synaptically activated under physiological recording conditions in rodent acute hippocampal slices. Specifically, NMDA receptor (NMDAR)-mediated responses at the mossy fiber to CA3 pyramidal cell synapse were followed by a slow postsynaptic inward current that could activate CA3 pyramidal cells but was absent in Panx1 knockout mice. Immunoelectron microscopy revealed that Panx1 was localized near the postsynaptic density. Further, Panx1-mediated currents were potentiated by metabotropic receptors and bidirectionally modulated by burst-timing-dependent plasticity of NMDAR-mediated transmission. Lastly, Panx1 channels were preferentially recruited when NMDAR activation enters a supralinear regime, resulting in temporally delayed burst-firing. Thus, Panx1 can contribute to synaptic amplification and broadening the temporal associativity window for co-activated pyramidal cells, thereby supporting the auto-associative functions of the CA3 region.

}, issn = {2589-0042}, doi = {10.1016/j.isci.2024.109681}, author = {Rangel-Sandoval, Cinthia and Soula, Marisol and Li, Wei-Ping and Castillo, Pablo E and Hunt, David L} } @article {69471, title = {Norepinephrine changes behavioral state via astroglial purinergic signaling}, journal = {Science}, year = {2024}, month = {2025 May 15}, abstract = {

Both neurons and glia communicate through diffusible neuromodulators; however, how neuron-glial interactions in such neuromodulatory networks influence circuit computation and behavior is unclear. During futility-induced behavioral transitions in the larval zebrafish, the neuromodulator norepinephrine (NE) drives fast excitation and delayed inhibition of behavior and circuit activity. We found that astroglial purinergic signaling implements the inhibitory arm of this motif. In larval zebrafish, NE triggers astroglial release of adenosine triphosphate (ATP), extracellular conversion of ATP into adenosine, and behavioral suppression through activation of hindbrain neuronal adenosine receptors. Our results suggest a computational and behavioral role for an evolutionarily conserved astroglial purinergic signaling axis in NE-mediated behavioral and brain state transitions and position astroglia as important effectors in neuromodulatory signaling.

Preprint:\ https://www.biorxiv.org/content/early/2024/05/23/2024.05.23.595576

}, doi = {10.1126/science.adq5233}, url = {https://www.science.org/stoken/author-tokens/ST-2654/full}, author = {Chen, Alex B. and Duque, Marc and Wang, Vickie M. and Dhanasekar, Mahalakshmi and Mi, Xuelong and Rymbek, Altyn and Tocquer, Loeva and Narayan, Sujatha and Prober, David and Yu, Guoqiang and Wyart, Claire and Engert, Florian and Ahrens, Misha B.} } @article {69675, title = {A novel rhodopsin-based voltage indicator for simultaneous two-photon optical recording with GCaMP in vivo}, journal = {bioRxiv}, year = {2024}, month = {2024 Nov 15}, abstract = {

Genetically encoded voltage indicators (GEVIs) allow optical recording of membrane potential from targeted cells in vivo. However, red GEVIs that are compatible with two-photon microscopy and that can be multiplexed in vivo with green reporters like GCaMP, are currently lacking. To address this gap, we explored diverse rhodopsin proteins as GEVIs and engineered a novel GEVI, 2Photron, based on a rhodopsin from the green algae Klebsormidium nitens. 2Photron, combined with two photon ultrafast local volume excitation (ULoVE), enabled multiplexed readout of spiking and subthreshold voltage simultaneously with GCaMP calcium signals in visual cortical neurons of awake, behaving mice. These recordings revealed the cell-specific relationship of spiking and subthreshold voltage dynamics with GCaMP responses, highlighting the challenges of extracting underlying spike trains from calcium imaging.

}, doi = {10.1101/2024.11.15.623698}, url = {https://doi.org/10.1101/2024.11.15.623698}, author = {Villette, Vincent and Yang, Shang and Valenti, Rosario and Macklin, John J. and Bradley, Jonathan and Mathieu, Benjamin and Lombardini, Alberto and Podgorski, Kaspar and Dieudonn{\'e}, St{\'e}phane and Schreiter, Eric R. and Abdelfattah, Ahmed S.} } @article {69010, title = {Olfactory sensory neuron population expansions influence projection neuron adaptation and enhance odour tracking}, journal = {Nat Commun}, volume = {15}, year = {2024}, month = {2024 Aug 15}, pages = {7041}, abstract = {

The evolutionary expansion of sensory neuron populations detecting important environmental cues is widespread, but functionally enigmatic. We investigated this phenomenon through comparison of homologous olfactory pathways of Drosophila melanogaster and its close relative Drosophila sechellia, an extreme specialist for Morinda citrifolia noni fruit. D. sechellia has evolved species-specific expansions in select, noni-detecting olfactory sensory neuron (OSN) populations, through multigenic changes. Activation and inhibition of defined proportions of neurons demonstrate that OSN number increases contribute to stronger, more persistent, noni-odour tracking behaviour. These expansions result in increased synaptic connections of sensory neurons with their projection neuron (PN) partners, which are conserved in number between species. Surprisingly, having more OSNs does not lead to greater odour-evoked PN sensitivity or reliability. Rather, pathways with increased sensory pooling exhibit reduced PN adaptation, likely through weakened lateral inhibition. Our work reveals an unexpected functional impact of sensory neuron population expansions to explain ecologically-relevant, species-specific behaviour.

}, doi = {10.1038/s41467-024-50808-w}, url = {https://doi.org/10.1038/s41467-024-50808-w}, author = {Suguru Takagi and Liliane Abuin and S. David Stupski and J. Roman Arguello and Lucia Prieto-Godino and David L. Stern and Steeve Cruchet and Raquel {\'A}lvarez-Oca{\~n}a and Carl F. R. Wienecke and Floris van Breugel and Thomas O. Auer and Richard Benton} } @article {69669, title = {ONIX: a unified open-source platform for multimodal neural recording and perturbation during naturalistic behavior.}, journal = {Nat Methods}, year = {2024}, month = {2024 Nov 11}, abstract = {

Behavioral neuroscience faces two conflicting demands: long-duration recordings from large neural populations and unimpeded animal behavior. To meet this challenge we developed ONIX, an open-source data acquisition system with high data throughput (2 GB s) and low closed-loop latencies (\<1 ms) that uses a 0.3-mm thin tether to minimize behavioral impact. Head position and rotation are tracked in three dimensions and used to drive active commutation without torque measurements. ONIX can acquire data from combinations of passive electrodes, Neuropixels probes, head-mounted microscopes, cameras, three-dimensional trackers and other data sources. We performed uninterrupted, long (~7 h) neural recordings in mice as they traversed complex three-dimensional terrain, and multiday sleep-tracking recordings (~55 h). ONIX enabled exploration with similar mobility as nonimplanted animals, in contrast to conventional tethered systems, which have restricted movement. By combining long recordings with full mobility, our technology will enable progress on questions that require high-quality neural recordings during ethologically grounded behaviors.

}, issn = {1548-7105}, doi = {10.1038/s41592-024-02521-1}, url = {https://doi.org/10.1038/s41592-024-02521-1}, author = {Newman, Jonathan P and Zhang, Jie and Cuevas-L{\'o}pez, Aar{\'o}n and Miller, Nicholas J and Honda, Takato and van der Goes, Marie-Sophie H and Leighton, Alexandra H and Carvalho, Filipe and Lopes, Gon{\c c}alo and Lakunina, Anna and Siegle, Joshua H and Harnett, Mark T and Wilson, Matthew A and Voigts, Jakob} } @article {69399, title = {Optimization in Visual Motion Estimation.}, journal = {Annu Rev Vis Sci}, year = {2024}, month = {2024 Apr 25}, abstract = {

Sighted animals use visual signals to discern directional motion in their environment. Motion is not directly detected by visual neurons, and it must instead be computed from light signals that vary over space and time. This makes visual motion estimation a near universal neural computation, and decades of research have revealed much about the algorithms and mechanisms that generate directional signals. The idea that sensory systems are optimized for performance in natural environments has deeply impacted this research. In this article, we review the many ways that optimization has been used to quantitatively model visual motion estimation and reveal its underlying principles. We emphasize that no single optimization theory has dominated the literature. Instead, researchers have adeptly incorporated different computational demands and biological constraints that are pertinent to the specific brain system and animal model under study. The successes and failures of the resulting optimization models have thereby provided insights into how computational demands and biological constraints together shape neural computation.

}, issn = {2374-4650}, doi = {10.1146/annurev-vision-101623-025432}, author = {Clark, Damon A and Fitzgerald, James E} } @article {68531, title = {Organelle proteomic profiling reveals lysosomal heterogeneity in association with longevity}, journal = {eLife}, year = {2024}, month = {2024 Jan 19}, abstract = {

Lysosomes are active sites to integrate cellular metabolism and signal transduction. A collection of proteins enriched at lysosomes mediate these metabolic and signaling functions. Both lysosomal metabolism and lysosomal signaling have been linked with longevity regulation; however, how lysosomes adjust their protein composition to accommodate this regulation remains unclear. Using large-scale proteomic profiling, we systemically profiled lysosome- enriched proteomes in association with different longevity mechanisms. We further discovered the lysosomal recruitment of AMPK and nucleoporin proteins and their requirements for longevity in response to increased lysosomal lipolysis. Through comparative proteomic analyses of lysosomes from different tissues and labeled with different markers, we discovered lysosomal heterogeneity across tissues as well as the specific enrichment of the Ragulator complex on Cystinosin positive lysosomes. Together, this work uncovers lysosomal proteome heterogeneity at different levels and provides resources for understanding the contribution of lysosomal proteome dynamics in modulating signal transduction, organelle crosstalk and organism longevity.

}, doi = {10.7554/eLife.85214}, url = {https://doi.org/10.7554/eLife.85214}, author = {Yong Yu and Shihong M. Gao and Youchen Guan and Pei-Wen Hu and Qinghao Zhang and Jiaming Liu and Bentian Jing and Qian Zhao and David M Sabatini and Monther Abu-Remaileh and Sung Yun Jung and Meng C. Wang} } @article {69229, title = {Organization of an ascending circuit that conveys flight motor state in Drosophila.}, journal = {Current Biology}, year = {2024}, month = {2024 Feb 13}, abstract = {

Natural behaviors are a coordinated symphony of motor acts that drive reafferent (self-induced) sensory activation. Individual sensors cannot disambiguate exafferent (externally induced) from reafferent sources. Nevertheless, animals readily differentiate between these sources of sensory signals to carry out adaptive behaviors through corollary discharge circuits (CDCs), which provide predictive motor signals from motor pathways to sensory processing and other motor pathways. Yet, how CDCs comprehensively integrate into the nervous system remains unexplored. Here, we use connectomics, neuroanatomical, physiological, and behavioral approaches to resolve the network architecture of two pairs of ascending histaminergic neurons (AHNs) in Drosophila, which function as a predictive CDC in other insects. Both AHN pairs receive input primarily from a partially overlapping population of descending neurons, especially from DNg02, which controls wing motor output. Using Ca imaging and behavioral recordings, we show that AHN activation is correlated to flight behavior and precedes wing motion. Optogenetic activation of DNg02 is sufficient to activate AHNs, indicating that AHNs are activated by descending commands in advance of behavior and not as a consequence of sensory input. Downstream, each AHN pair targets predominantly non-overlapping networks, including those that process visual, auditory, and mechanosensory information, as well as networks controlling wing, haltere, and leg sensorimotor control. These results support the conclusion that the AHNs provide a predictive motor signal about wing motor state to mostly non-overlapping sensory and motor networks. Future work will determine how AHN signaling is driven by other descending neurons and interpreted by AHN downstream targets to maintain adaptive sensorimotor performance.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2024.01.071}, author = {Cheong, Han S J and Boone, Kaitlyn N and Bennett, Marryn M and Salman, Farzaan and Ralston, Jacob D and Hatch, Kaleb and Allen, Raven F and Phelps, Alec M and Cook, Andrew P and Phelps, Jasper S and Erginkaya, Mert and Lee, Wei-Chung A and Card, Gwyneth M and Daly, Kevin C and Dacks, Andrew M} } @article {69325, title = {Patch-walking: Coordinated multi-pipette patch clamp for efficiently finding synaptic connections}, journal = {eLife}, volume = {13}, year = {2024}, month = {2024 Nov 18}, pages = {RP97399}, abstract = {

Significant technical challenges exist when measuring synaptic connections between neurons in living brain tissue. The patch clamping technique, when used to probe for synaptic connections, is manually laborious and time-consuming. To improve its efficiency, we pursued another approach: instead of retracting all patch clamping electrodes after each recording attempt, we cleaned just one of them and reused it to obtain another recording while maintaining the others. With one new patch clamp recording attempt, many new connections can be probed. By placing one pipette in front of the others in this way, one can {\textquoteright}walk{\textquoteright} across the mouse brain slice, termed {\textquoteright}patch-walking.{\textquoteright} We performed 136 patch clamp attempts for two pipettes, achieving 71 successful whole cell recordings (52.2\%). Of these, we probed 29 pairs (i.e. 58 bidirectional probed connections) averaging 91 μm intersomatic distance, finding three connections. Patch-walking yields 80-92\% more probed connections, for experiments with 10-100 cells than the traditional synaptic connection searching method.

}, doi = {10.7554/elife.97399}, url = {https://doi.org/10.7554/elife.97399}, author = {Mighten C. Yip and Mercedes M. Gonzalez and Colby F. Lewallen and Corey R. Landry and Ilya Kolb and Bo Yang and William M. Stoy and Ming-fai Fong and Matthew JM Rowan and Edward S. Boyden and Craig R. Forest} } @article {69704, title = {Periodic ER-plasma membrane junctions support long-range Ca signal integration in dendrites.}, journal = {Cell}, year = {2024}, month = {2024 Dec 18}, abstract = {

Neuronal dendrites must relay synaptic inputs over long distances, but the mechanisms by which activity-evoked intracellular signals propagate over macroscopic distances remain unclear. Here, we discovered a system of periodically arranged endoplasmic reticulum-plasma membrane (ER-PM) junctions tiling the plasma membrane of dendrites at \~{}1\ μm intervals, interlinked by a meshwork of ER tubules patterned in a ladder-like array. Populated with Junctophilin-linked plasma membrane voltage-gated Ca channels and ER Ca-release channels (ryanodine receptors), ER-PM junctions are hubs for ER-PM crosstalk, fine-tuning of Ca homeostasis, and local activation of the Ca/calmodulin-dependent protein kinase II. Local spine stimulation activates the Ca modulatory machinery, facilitating signal transmission and ryanodine-receptor-dependent Ca release at ER-PM junctions over 20\ μm away. Thus, interconnected ER-PM junctions support signal propagation and Ca release from the spine-adjacent ER. The capacity of this subcellular architecture to modify both local and distant membrane-proximal biochemistry potentially contributes to dendritic computations.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2024.11.029}, author = {Benedetti, Lorena and Fan, Ruolin and Weigel, Aubrey V and Moore, Andrew S and Houlihan, Patrick R and Kittisopikul, Mark and Park, Grace and Petruncio, Alyson and Hubbard, Philip M and Pang, Song and Xu, C Shan and Hess, Harald F and Saalfeld, Stephan and Rangaraju, Vidhya and Clapham, David E and De Camilli, Pietro and Ryan, Timothy A and Lippincott-Schwartz, Jennifer} } @article {69705, title = {Permanent cilia loss during cerebellar granule cell neurogenesis involves withdrawal of cilia maintenance and centriole capping.}, journal = {Proc Natl Acad Sci U S A}, volume = {121}, year = {2024}, month = {2024 Dec 24}, pages = {e2408083121}, abstract = {

Brain neurons utilize the primary cilium as a privileged compartment to detect and respond to extracellular ligands such as Sonic hedgehog (SHH). However, cilia in cerebellar granule cell (GC) neurons disassemble during differentiation through ultrastructurally unique intermediates, a process we refer to as cilia deconstruction. In addition, mature neurons do not reciliate despite having docked centrioles. Here, we identify molecular changes that accompany cilia deconstruction and centriole docking in GC neurons. We used single cell transcriptomic and immunocytological analyses to compare the transcript levels and subcellular localization of proteins between progenitor, differentiating, and mature GCs. Differentiating GCs lacked transcripts for key activators of premitotic cilia resorption, indicating that cilia disassembly in differentiating cells is distinct from premitotic cilia resorption. Instead, during differentiation, transcripts of many genes required for cilia maintenance-specifically those encoding components of intraflagellar transport, pericentrosomal material, and centriolar satellites-decreased. The abundance of several corresponding proteins in and around cilia and centrosomes also decreased. These changes coincided with downregulation of SHH signaling prior to differentiation, even in a mutant with excessive SHH activation. Finally, mother centrioles in maturing granule neurons recruited the cap complex protein, CEP97. These data suggest that a global, developmentally programmed decrease in cilium maintenance in differentiating GCs mediates cilia deconstruction, while capping of docked mother centrioles prevents cilia regrowth and dysregulated SHH signaling. Our study provides mechanistic insights expanding our understanding of permanent cilia loss in multiple tissue-specific contexts.

}, keywords = {Animals, Cell Differentiation, Centrioles, Cerebellum, Cilia, Hedgehog Proteins, Mice, Neurogenesis, Neurons, Signal Transduction}, issn = {1091-6490}, doi = {10.1073/pnas.2408083121}, author = {Constable, Sandii and Ott, Carolyn M and Lemire, Andrew L and White, Kevin and Xun, Yu and Lim, Amin and Lippincott-Schwartz, Jennifer and Mukhopadhyay, Saikat} } @article {69136, title = {Permanent deconstruction of intracellular primary cilia in differentiating granule cell neurons.}, journal = {J Cell Biol.}, volume = {223}, year = {2024}, month = {2024 Aug 13}, pages = {e202404038}, abstract = {

Primary cilia on granule cell neuron progenitors in the developing cerebellum detect sonic hedgehog to facilitate proliferation. Following differentiation, cerebellar granule cells become the most abundant neuronal cell type in the brain. While granule cell cilia are essential during early developmental stages, they become infrequent upon maturation. Here, we provide nanoscopic resolution of cilia in situ using large-scale electron microscopy volumes and immunostaining of mouse cerebella. In many granule cells, we found intracellular cilia, concealed from the external environment. Cilia were disassembled in differentiating granule cell neurons-in a process we call cilia deconstruction-distinct from premitotic cilia resorption in proliferating progenitors. In differentiating granule cells, cilia deconstruction involved unique disassembly intermediates, and, as maturation progressed, mother centriolar docking at the plasma membrane. Unlike ciliated neurons in other brain regions, our results show the deconstruction of concealed cilia in differentiating granule cells, which might prevent mitogenic hedgehog responsiveness. Ciliary deconstruction could be paradigmatic of cilia removal during differentiation in other tissues.

}, doi = {10.1016/j.cub.2024.07.036}, url = {https://doi.org/10.1016/j.cub.2024.07.036 }, author = {Ott, Carolyn M and Constable, Sandii and Nguyen, Tri M and White, Kevin and Lee, Wei-Chung Allen and Lippincott-Schwartz, Jennifer and Mukhopadhyay, Saikat} } @article {69139, title = {Petascale pipeline for precise alignment of images from serial section electron microscopy.}, journal = {Nature Communications}, volume = {15}, year = {2024}, month = {2024 Jan 04}, pages = {289}, abstract = {

The reconstruction of neural circuits from serial section electron microscopy (ssEM) images is being accelerated by automatic image segmentation methods. Segmentation accuracy is often limited by the preceding step of aligning 2D section images to create a 3D image stack. Precise and robust alignment in the presence of image artifacts is challenging, especially as datasets are attaining the petascale. We present a computational pipeline for aligning ssEM images with several key elements. Self-supervised convolutional nets are trained via metric learning to encode and align image pairs, and they are used to initialize iterative fine-tuning of alignment. A procedure called vector voting increases robustness to image artifacts or missing image data. For speedup the series is divided into blocks that are distributed to computational workers for alignment. The blocks are aligned to each other by composing transformations with decay, which achieves a global alignment without resorting to a time-consuming global optimization. We apply our pipeline to a whole fly brain dataset, and show improved accuracy relative to prior state of the art. We also demonstrate that our pipeline scales to a cubic millimeter of mouse visual cortex. Our pipeline is publicly available through two open source Python packages.

}, keywords = {Animals, Brain, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Mice, Microscopy, Electron}, issn = {2041-1723}, doi = {10.1038/s41467-023-44354-0}, author = {Popovych, Sergiy and Macrina, Thomas and Kemnitz, Nico and Castro, Manuel and Nehoran, Barak and Jia, Zhen and Bae, J Alexander and Mitchell, Eric and Mu, Shang and Trautman, Eric T and Saalfeld, Stephan and Li, Kai and Seung, H Sebastian} } @article {69128, title = {Phase diversity-based wavefront sensing for fluorescence microscopy.}, journal = {Optica}, volume = {11}, year = {2024}, month = {2024 Jun 10}, pages = {806-820}, abstract = {

Fluorescence microscopy is an invaluable tool in biology, yet its performance is compromised when the wavefront of light is distorted due to optical imperfections or the refractile nature of the sample. Such optical aberrations can dramatically lower the information content of images by degrading image contrast, resolution, and signal. Adaptive optics (AO) methods can sense and subsequently cancel the aberrated wavefront, but are too complex, inefficient, slow, or expensive for routine adoption by most labs. Here we introduce a rapid, sensitive, and robust wavefront sensing scheme based on phase diversity, a method successfully deployed in astronomy but underused in microscopy. Our method enables accurate wavefront sensing to less than λ/35 root mean square (RMS) error with few measurements, and AO with no additional hardware besides a corrective element. After validating the method with simulations, we demonstrate calibration of a deformable mirror \> 100-fold faster than comparable methods (corresponding to wavefront sensing on the ~100 ms scale), and sensing and subsequent correction of severe aberrations (RMS wavefront distortion exceeding λ/2), restoring diffraction-limited imaging on extended biological samples.

}, doi = {10.1364/OPTICA.518559}, url = {https://doi.org/10.1364/OPTICA.518559}, author = {Johnson, Courtney and Guo, Min and Schneider, Magdalena C and Su, Yijun and Khuon, Satya and Reiser, Nikolaj and Wu, Yicong and Riviere, Patrick La and Shroff, Hari} } @article {69472, title = {The physical and cellular mechanism of structural color change in zebrafish.}, journal = {Proc Natl Acad Sci U S A}, volume = {121}, year = {2024}, month = {2024 Jun 04}, pages = {e2308531121}, abstract = {

Many animals exhibit remarkable colors that are produced by the constructive interference of light reflected from arrays of intracellular guanine crystals. These animals can fine-tune their crystal-based structural colors to communicate with each other, regulate body temperature, and create camouflage. While it is known that these changes in color are caused by changes in the angle of the crystal arrays relative to incident light, the cellular machinery that drives color change is not understood. Here, using a combination of 3D focused ion beam scanning electron microscopy (FIB-SEM), micro-focused X-ray diffraction, superresolution fluorescence light microscopy, and pharmacological perturbations, we characterized the dynamics and 3D cellular reorganization of crystal arrays within zebrafish iridophores during norepinephrine (NE)-induced color change. We found that color change results from a coordinated 20{\textdegree} tilting of the intracellular crystals, which alters both crystal packing and the angle at which impinging light hits the crystals. Importantly, addition of the dynein inhibitor dynapyrazole-a completely blocked this NE-induced red shift by hindering crystal dynamics upon NE addition. FIB-SEM and microtubule organizing center (MTOC) mapping showed that microtubules arise from two MTOCs located near the poles of the iridophore and run parallel to, and in between, individual crystals. This suggests that dynein drives crystal angle change in response to NE by binding to the limiting membrane surrounding individual crystals and walking toward microtubule minus ends. Finally, we found that intracellular cAMP regulates the color change process. Together, our results provide mechanistic insight into the cellular machinery that drives structural color change.

}, keywords = {Animals, Color, Microscopy, Electron, Scanning, Norepinephrine, Pigmentation, Zebrafish, Zebrafish Proteins}, issn = {1091-6490}, doi = {10.1073/pnas.2308531121}, author = {Gur, Dvir and Moore, Andrew S and Deis, Rachael and Song, Pang and Wu, Xufeng and Pinkas, Iddo and Deo, Claire and Iyer, Nirmala and Hess, Harald F and Hammer, John A and Lippincott-Schwartz, Jennifer} } @article {69579, title = {Plasticity-induced actin polymerization in the dendritic shaft regulates intracellular AMPA receptor trafficking.}, journal = {Elife}, volume = {13}, year = {2024}, month = {2024 Aug 15}, abstract = {

AMPA-type receptors (AMPARs) are rapidly inserted into synapses undergoing plasticity to increase synaptic transmission, but it is not fully understood if and how AMPAR-containing vesicles are selectively trafficked to these synapses. Here, we developed a strategy to label AMPAR GluA1 subunits expressed from their endogenous loci in cultured rat hippocampal neurons and characterized the motion of GluA1-containing vesicles using single-particle tracking and mathematical modeling. We find that GluA1-containing vesicles are confined and concentrated near sites of stimulation-induced structural plasticity. We show that confinement is mediated by actin polymerization, which hinders the active transport of GluA1-containing vesicles along the length of the dendritic shaft by modulating the rheological properties of the cytoplasm. Actin polymerization also facilitates myosin-mediated transport of GluA1-containing vesicles to exocytic sites. We conclude that neurons utilize F-actin to increase vesicular GluA1 reservoirs and promote exocytosis proximal to the sites of synaptic activity.

}, keywords = {Actins, Animals, Cells, Cultured, Dendrites, Exocytosis, Hippocampus, Neuronal Plasticity, Neurons, Polymerization, Protein Transport, Rats, Receptors, AMPA}, issn = {2050-084X}, doi = {10.7554/eLife.80622}, url = {https://doi.org/10.7554/eLife.80622}, author = {Wong, Victor C and Houlihan, Patrick R and Liu, Hui and Walpita, Deepika and DeSantis, Michael C and Liu, Zhe and O{\textquoteright}Shea, Erin K} } @article {69149, title = {Prediction of Cellular Identities from Trajectory and Cell Fate Information}, journal = {arXiv}, year = {2024}, month = {2024 Jan 11}, abstract = {

Determining cell identities in imaging sequences is an important yet challenging task. The conventional method for cell identification is via cell tracking, which is complex and can be time-consuming. In this study, we propose an innovative approach to cell identification during early C. elegans embryogenesis using machine learning. We employed random forest, MLP, and LSTM models, and tested cell classification accuracy on 3D time-lapse confocal datasets spanning the first 4 hours of embryogenesis. By leveraging a small number of spatial-temporal features of individual cells, including cell trajectory and cell fate information, our models achieve an accuracy of over 90\%, even with limited data. We also determine the most important feature contributions and can interpret these features in the context of biological knowledge. Our research demonstrates the success of predicting cell identities in 4D imaging sequences directly from simple spatio-temporal features.

}, doi = {10.48550/arXiv.2401.06182}, url = {https://doi.org/10.48550/arXiv.2401.06182}, author = {Baiyang Dai and Jiamin Yang and Hari Shroff and Patrick La Riviere} } @article {69689, title = {Quantitative Attributions with Counterfactuals}, journal = {bioRxiv}, year = {2024}, month = {2024 Dec 02}, abstract = {

We address the problem of explaining the decision process of deep neural network classifiers on images, which is of particular importance in biomedical datasets where class-relevant differences are not always obvious to a human observer. Our proposed solution, termed quantitative attribution with counterfactuals (QuAC), generates visual explanations that highlight class-relevant differences by attributing the classifier decision to changes of visual features in small parts of an image. To that end, we train a separate network to generate counterfactual images (i.e., to translate images between different classes). We then find the most important differences using novel discriminative attribution methods. Crucially, QuAC allows scoring of the attribution and thus provides a measure to quantify and compare the fidelity of a visual explanation. We demonstrate the suitability and limitations of QuAC on two datasets: (1) a synthetic dataset with known class differences, representing different levels of protein aggregation in cells and (2) an electron microscopy dataset of D. melanogaster synapses with different neurotransmitters, where QuAC reveals so far unknown visual differences. We further discuss how QuAC can be used to interrogate mispredictions to shed light on unexpected inter-class similarities and intra-class differences.

}, doi = {10.1101/2024.11.26.625505}, url = {https://doi.org/10.1101/2024.11.26.625505}, author = {Adjavon, Diane-Yayra and Eckstein, Nils and Bates, Alexander S. and Jefferis, Gregory S.X.E. and Funke, Jan} } @article {69688, title = {Quantitative Spatial Analysis of Chromatin Biomolecular Condensates using Cryo-Electron Tomography}, journal = {bioRxiv}, year = {2024}, month = {2024 Dec 02}, abstract = {

Phase separation is an important mechanism to generate certain biomolecular condensates and organize the cell interior. Condensate formation and function remain incompletely understood due to difficulties in visualizing the condensate interior at high resolution. Here we analyzed the structure of biochemically reconstituted chromatin condensates through cryo-electron tomography. We found that traditional blotting methods of sample preparation were inadequate, and high-pressure freezing plus focused ion beam milling was essential to maintain condensate integrity. To identify densely packed molecules within the condensate, we integrated deep learning-based segmentation with novel context-aware template matching. Our approaches were developed on chromatin condensates, and were also effective on condensed regions of in situ native chromatin. Using these methods, we determined the average structure of nucleosomes to 6.1 and 12 {\r A} resolution in reconstituted and native systems, respectively, and found that nucleosomes have a nearly random orientation distribution in both cases. Our methods should be applicable to diverse biochemically reconstituted biomolecular condensates and to some condensates in cells.

}, doi = {10.1101/2024.12.01.626131}, url = {https://doi.org/10.1101/2024.12.01.626131}, author = {Zhou, Huabin and Hutchings, Joshua and Shiozaki, Momoko and Zhao, Xiaowei and Doolittle, Lynda K. and Yang, Shixin and Yan, Rui and Jean, Nikki and Riggi, Margot and Yu, Zhiheng and Villa, Elizabeth and Rosen, Michael K.} } @article {69285, title = {RAL-1 signaling regulates lipid composition in .}, journal = {MicroPubl Biol}, volume = {2024}, year = {2024}, month = {2024 Feb 21}, abstract = {

Signaling by the Ral small GTPase is poorly understood . animals with constitutively activated RAL-1 or deficient for the inhibitory RalGAP, HGAP-1 /2, display pale intestines. Staining with Oil Red O detected decreased intestinal lipids in the deletion mutant relative to the wild type. Constitutively activated RAL-1 decreased lipid detected by stimulated Raman scattering (SRS) microscopy, a label-free method of detecting lipid by laser excitation and detection. A signaling-deficient missense mutant for RAL-1 also displayed reduced lipid staining via SRS. We conclude that RAL-1 signaling regulates lipid homeostasis, biosynthesis or storage in live animals.

}, issn = {2578-9430}, doi = {10.17912/micropub.biology.001054}, author = {Wu, You and Lee, Minjung and Mutlu, A Sena and Wang, Meng and Reiner, David J} } @article {69655, title = {Rapid Whole-Organ Characterization via Quantitative Light-Sheet Microscopy}, journal = {Laser \& Photonics Reviews}, year = {2024}, month = {2024 Oct 22}, pages = {2401177}, abstract = {

Whole-organ imaging and characterization at a submicron level provide abundant information on development and diseases while remaining a big challenge, especially in the context of time load. Herein, a quantitative light-sheet microscopy platform that enabled highly time-efficient assessments of fibrous structures within the intact cleared tissue is developed. Dual-view inverted selective plane illumination microscopy (diSPIM), followed by improved registration and deconvolution, led to submicron isotropic imaging of mouse upper genital tract with one hundred-fold speed-ups than previous efforts. Further, optical metrics quantifying 3D local density and structural complexity of targets based on parallel and vectorized convolution in both spatial and frequency domains are developed. Collectively, ≈400{\textendash}2000 fold increases in time efficiency counting for imaging, postprocessing, and quantitative characterization compared to the traditional method is gained. Using this platform, automatic identification of medulla and cortex within the mouse ovary at over 90\% overlap with manual selection by anatomy experts is achieved. Additionally, heterogeneous distributions of immune cells in the mouse ovary and fallopian tube, offering a unique perspective for understanding the immune microenvironment are discovered. This work paves the way for future whole-organ study, and exhibits potential with promise for offering mechanistic insights into physiological and pathological alterations of biological tissues.

}, keywords = {immune microenvironment, light-sheet microscopy, quantitative characterization, whole-organ imaging}, doi = {10.1002/lpor.202401177}, url = {https://doi.org/10.1002/lpor.202401177}, author = {Chen, Lingmei and Su, Yijun and Qian, Shuhao and Zhou, Lingxi and Han, Tao and Wang, Chuncheng and Jiang, Rushan and Ding, Zhihua and Guo, Min and Liu, Zhiyi} } @article {69217, title = {A ratiometric ER calcium sensor for quantitative comparisons across cell types and subcellular regions.}, journal = {bioRxiv}, year = {2024}, month = {2024 Feb 16}, abstract = {

The endoplasmic reticulum (ER) is an important regulator of Ca2+\ in cells and dysregulation of ER calcium homeostasis can lead to numerous pathologies. Understanding how various pharmacological and genetic perturbations of ER Ca2+\ homeostasis impacts cellular physiology would likely be facilitated by more quantitative measurements of ER Ca2+\ levels that allow easier comparisons across conditions. Here, we developed a ratiometric version of our original ER-GCaMP probe that allows for more quantitative comparisons of the concentration of Ca2+\ in the ER across cell types and sub-cellular compartments. Using this approach we show that the resting concentration of ER Ca2+ in primary dissociated neurons is substantially lower than that in measured in embryonic fibroblasts.

}, doi = {10.1101/2024.02.15.580492}, url = {https://doi.org/10.1101/2024.02.15.580492}, author = {Ryan J. Farrell and Kirsten G. Bredvik and Michael B. Hoppa and S. Thomas Hennigan and Timothy A. Brown and Timothy A. Ryan} } @article {69404, title = {Recognising the importance and impact of Imaging Scientists: Global guidelines for establishing career paths within core facilities}, journal = {J Microsc}, year = {2024}, month = {2024 May 01}, abstract = {

In the dynamic landscape of scientific research, imaging core facilities are vital hubs propelling collaboration and innovation at the technology development and dissemination frontier. Here, we present a collaborative effort led by Global BioImaging (GBI), introducing international recommendations geared towards elevating the careers of Imaging Scientists in core facilities. Despite the critical role of Imaging Scientists in modern research ecosystems, challenges persist in recognising their value, aligning performance metrics and providing avenues for career progression and job security. The challenges encompass a mismatch between classic academic career paths and service-oriented roles, resulting in a lack of understanding regarding the value and impact of Imaging Scientists and core facilities and how to evaluate them properly. They further include challenges around sustainability, dedicated training opportunities and the recruitment and retention of talent. Structured across these interrelated sections, the recommendations within this publication aim to propose globally applicable solutions to navigate these challenges. These recommendations apply equally to colleagues working in other core facilities and research institutions through which access to technologies is facilitated and supported. This publication emphasises the pivotal role of Imaging Scientists in advancing research programs and presents a blueprint for fostering their career progression within institutions all around the world.

}, issn = {1365-2818}, doi = {10.1111/jmi.13307}, author = {Wright, Graham D and Thompson, Kerry A and Reis, Yara and Bischof, Johanna and Hockberger, Philip Edward and Itano, Michelle S and Yen, Lisa and Adelodun, Stephen Taiye and Bialy, Nikki and Brown, Claire M and Chaabane, Linda and Chew, Teng-Leong and Chitty, Andrew I and Cordeli{\`e}res, Fabrice P and De Niz, Mariana and Ellenberg, Jan and Engelbrecht, Lize and Fabian-Morales, Eunice and Fazeli, Elnaz and Fernandez-Rodriguez, Julia and Ferrando-May, Elisa and Fletcher, Georgina and Galloway, Graham John and Guerrero, Adan and Guimar{\~a}es, Jander Matos and Jacobs, Caron A and Jayasinghe, Sachintha and Kable, Eleanor and Kitten, Gregory T and Komoto, Shinya and Ma, Xiaoxiao and Marques, J{\'e}ssica Ara{\'u}jo and Millis, Bryan A and Miranda, Kildare and JohnO{\textquoteright}Toole, Peter and Olatunji, Sunday Yinka and Paina, Federica and Pollak, Cora Noemi and Prats, Clara and Pylv{\"a}n{\"a}inen, Joanna W and Rahmoon, Mai Atef and Reiche, Michael A and Riches, James Douglas and Rossi, Andres Hugo and Salamero, Jean and Thiriet, Caroline and Terjung, Stefan and Vasconcelos, Aldenora Dos Santos and Keppler, Antje} } @article {69248, title = {Recommendations for accelerating open preprint peer review to improve the culture of science}, journal = {PLOS Biology}, volume = {22}, year = {2024}, month = {2024 Feb 29}, pages = {e3002502}, abstract = {

Peer review is an important part of the scientific process, but traditional peer review at journals is coming under increased scrutiny for its inefficiency and lack of transparency. As preprints become more widely used and accepted, they raise the possibility of rethinking the peer-review process. Preprints are enabling new forms of peer review that have the potential to be more thorough, inclusive, and collegial than traditional journal peer review, and to thus fundamentally shift the culture of peer review toward constructive collaboration. In this Consensus View, we make a call to action to stakeholders in the community to accelerate the growing momentum of preprint sharing and provide recommendations to empower researchers to provide open and constructive peer review for preprints.

}, doi = {10.1371/journal.pbio.300250210.1371/journal.pbio.3002502.g001}, url = {https://dx.plos.org/10.1371/journal.pbio.3002502https://dx.plos.org/10.1371/journal.pbio.3002502https://dx.plos.org/10.1371/journal.pbio.3002502.g001}, author = {Avissar-Whiting, Michele and Belliard, Fr{\'e}d{\'e}rique and Bertozzi, Stefano M. and Brand, Amy and Brown, Katherine and Cl{\'e}ment-Stoneham, G{\'e}raldine and Dawson, Stephanie and Dey, Gautam and Ecer, Daniel and Edmunds, Scott C. and Farley, Ashley and Fischer, Tara D. and Franko, Maryrose and Fraser, James S. and Funk, Kathryn and Ganier, Clarisse and Harrison, Melissa and Hatch, Anna and Hazlett, Haley and Hindle, Samantha and Hook, Daniel W. and Hurst, Phil and Kamoun, Sophien and Kiley, Robert and Lacy, Michael M. and LaFlamme, Marcel and Lawrence, Rebecca and Lemberger, Thomas and Leptin, Maria and Lumb, Elliott and MacCallum, Catriona J. and Marcum, Christopher Steven and Marinello, Gabriele and Mendon{\c c}a, Alex and Monaco, Sara and Neves, Kleber and Pattinson, Damian and Polka, Jessica K. and Puebla, Iratxe and Rittman, Martyn and Royle, Stephen J. and Saderi, Daniela and Sever, Richard and Shearer, Kathleen and Spiro, John E. and Stern, Bodo and Taraborelli, Dario and Vale, Ron and Vasquez, Claudia G. and Waltman, Ludo and Watt, Fiona M. and Weinberg, Zara Y. and Williams, Mark} } @article {69231, title = {Recording physiological history of cells with chemical labeling.}, journal = {Science}, volume = {383}, year = {2024}, month = {2024 Feb 23}, pages = {890-897}, abstract = {

Recordings of the physiological history of cells provide insights into biological processes, yet obtaining such recordings is a challenge. To address this, we introduce a method to record transient cellular events for later analysis. We designed proteins that become labeled in the presence of both a specific cellular activity and a fluorescent substrate. The recording period is set by the presence of the substrate, whereas the cellular activity controls the degree of the labeling. The use of distinguishable substrates enabled the recording of successive periods of activity. We recorded protein-protein interactions, G protein-coupled receptor activation, and increases in intracellular calcium. Recordings of elevated calcium levels allowed selections of cells from heterogeneous populations for transcriptomic analysis and tracking of neuronal activities in flies and zebrafish.

}, keywords = {Animals, Calcium, Cell Physiological Phenomena, Cells, Coloring Agents, Gene Expression Profiling, Protein Interaction Domains and Motifs, Staining and Labeling, Zebrafish}, issn = {1095-9203}, doi = {10.1126/science.adg0812}, author = {Huppertz, Magnus-Carsten and Wilhelm, Jonas and Grenier, Vincent and Schneider, Martin W and Falt, Tjalda and Porzberg, Nicola and Hausmann, David and Hoffmann, Dirk C and Hai, Ling and Tarnawski, Miroslaw and Pino, Gabriela and Slanchev, Krasimir and Kolb, Ilya and Acuna, Claudio and Fenk, Lisa M and Baier, Herwig and Hiblot, Julien and Johnsson, Kai} } @article {69517, title = {Resolution in super-resolution microscopy - definition, trade-offs and perspectives.}, journal = {Nat Rev Mol Cell Biol}, year = {2024}, month = {2024 Jul 01}, abstract = {

Super-resolution microscopy (SRM) is gaining popularity in biosciences; however, claims about optical resolution are contested and often misleading. In this Viewpoint, experts share their views on resolution and common trade-offs, such as labelling and post-processing, aiming to clarify them for biologists and facilitate deeper understanding and best use of SRM.

}, issn = {1471-0080}, doi = {10.1038/s41580-024-00755-7}, author = {Prakash, Kirti and Baddeley, David and Eggeling, Christian and Fiolka, Reto and Heintzmann, Rainer and Manley, Suliana and Radenovic, Aleksandra and Smith, Carlas and Shroff, Hari and Schermelleh, Lothar} } @book {69492, title = {Salivary gland developmental mechanics}, series = {Current Topics in Developmental Biology}, year = {2024}, publisher = {Elsevier}, organization = {Elsevier}, abstract = {

The salivary gland undergoes branching morphogenesis to elaborate into a tree-like structure with numerous saliva-secreting acinar units, all joined by a hierarchical ductal system. The expansive epithelial surface generated by branching morphogenesis serves as the structural basis for the efficient production and delivery of saliva. Here, we elucidate the process of salivary gland morphogenesis, emphasizing the role of mechanics. Structurally, the developing salivary gland is characterized by a stratified epithelium tightly encased by the basement membrane, which is in turn surrounded by a mesenchyme consisting of a dense network of interstitial matrix and mesenchymal cells. Diverse cell types and extracellular matrices bestow this developing organ with organized, yet spatially varied mechanical properties. For instance, the surface epithelial sheet of the bud is highly fluidic due to its high cell motility and weak cell-cell adhesion, rendering it highly pliable. In contrast, the inner core of the bud is more rigid, characterized by reduced cell motility and strong cell-cell adhesion, which likely provide structural support for the tissue. The interactions between the surface epithelial sheet and the inner core give rise to budding morphogenesis. Furthermore, the basement membrane and the mesenchyme offer mechanical constraints that could play a pivotal role in determining the higher-order architecture of a fully mature salivary gland.

}, issn = {00702153}, doi = {10.1016/bs.ctdb.2024.05.002}, url = {https://doi.org/10.1016/bs.ctdb.2024.05.002}, author = {Morales, E. Angelo and Wang, Shaohe} } @article {69425, title = {Salivary Gland Tissue Recombination Can Modify Cell Fate}, journal = {J Dent Res}, year = {2024}, month = {2024 May 07}, pages = {220345241247484}, abstract = {

Although mesenchyme is essential for inducing the epithelium of ectodermal organs, its precise role in organ-specific epithelial fate determination remains poorly understood. To elucidate the roles of tissue interactions in cellular differentiation, we performed single-cell RNA sequencing and imaging analyses on recombined tissues, where mesenchyme and epithelium were switched ex vivo between two types of embryonic mouse salivary glands: the parotid gland (a serous gland) and the submandibular gland (a predominantly mucous gland). We found partial induction of molecules that define gland-specific acinar and myoepithelial cells in recombined salivary epithelium. The parotid epithelium recombined with submandibular mesenchyme began to express mucous acinar genes not intrinsic to the parotid gland. While myoepithelial cells do not normally line parotid acini, newly induced myoepithelial cells densely populated recombined parotid acini. However, mucous acinar and myoepithelial markers continued to be expressed in submandibular epithelial cells recombined with parotid mesenchyme. Consequently, some epithelial cells appeared to be plastic, such that their fate could still be modified in response to mesenchymal signaling, whereas other epithelial cells appeared to be already committed to a specific fate. We also discovered evidence for bidirectional induction: transcriptional changes were observed not only in the epithelium but also in the mesenchyme after heterotypic tissue recombination. For example, parotid epithelium induced the expression of muscle-related genes in submandibular fibroblasts that began to mimic parotid fibroblast gene expression. These studies provide the first comprehensive unbiased molecular characterization of tissue recombination approaches exploring the regulation of cell fate.

}, issn = {1544-0591}, doi = {10.1177/00220345241247484}, author = {Sekiguchi, R and Martin, D and Doyle, A D and Wang, S and Yamada, K M} } @article {69473, title = {SciJava Ops: An Improved Algorithms Framework for Fiji and Beyond}, journal = {Front. Bioinform.}, volume = {4}, year = {2024}, month = {2024 Sep 26}, abstract = {

Decades of iteration on scientific imaging hardware and software has yielded an explosion in not only the size, complexity, and heterogeneity of image datasets but also in the tooling used to analyze this data. This wealth of image analysis tools, spanning different programming languages, frameworks, and data structures, is itself a problem for data analysts who must adapt to new technologies and integrate established routines to solve increasingly complex problems. While many {\textquotedblleft}bridge{\textquotedblright} layers exist to unify pairs of popular tools, there exists a need for a general solution to unify new and existing toolkits. The SciJava Ops library presented here addresses this need through two novel principles. Algorithm implementations are declared as plugins called Ops, providing a uniform interface regardless of the toolkit they came from. Users express their needs declaratively to the Op environment, which can then find and adapt available Ops on demand. By using these principles instead of direct function calls, users can write streamlined workflows while avoiding the translation boilerplate of bridge layers. Developers can easily extend SciJava Ops to introduce new libraries and more efficient, specialized algorithm implementations, even immediately benefitting existing workflows. We provide several use cases showing both user and developer benefits, as well as benchmarking data to quantify the negligible impact on overall analysis performance. We have initially deployed SciJava Ops on the Fiji platform, however it would be suitable for integration with additional analysis platforms in the future.

}, doi = {10.3389/fbinf.2024.1435733}, url = {https://doi.org/10.3389/fbinf.2024.1435733 }, author = {Gabriel J. Selzer and Curtis T. Rueden and Mark C. Hiner and Edward L. Evans III and David Kolb and Marcel Wiedenmann and Christian Birkhold and Tim-Oliver Buchholz and Stefan Helfrich and Brian Northan and Alison Walter and Johannes Schindelin and Tobias Pietzsch and Stephan Saalfeld and Michael R. Berthold and Kevin W. Eliceiri} } @article {69253, title = {Sensory neuron population expansion enhances odor tracking without sensitizing projection neurons}, journal = {bioRxiv}, year = {2024}, month = {2024 Feb 28}, abstract = {

The evolutionary expansion of sensory neuron populations detecting important environmental cues is widespread, but functionally enigmatic. We investigated this phenomenon through comparison of homologous neural pathways of Drosophila melanogaster and its close relative Drosophila sechellia, an extreme specialist for Morinda citrifolia noni fruit. D. sechellia has evolved species-specific expansions in select, noni-detecting olfactory sensory neuron (OSN) populations, through multigenic changes. Activation and inhibition of defined proportions of neurons demonstrate that OSN population increases contribute to stronger, more persistent, noni-odor tracking behavior. These sensory neuron expansions result in increased synaptic connections with their projection neuron (PN) partners, which are conserved in number between species. Surprisingly, having more OSNs does not lead to greater odor-evoked PN sensitivity or reliability. Rather, pathways with increased sensory pooling exhibit reduced PN adaptation, likely through weakened lateral inhibition. Our work reveals an unexpected functional impact of sensory neuron expansions to explain ecologically-relevant, species-specific behavior.

}, doi = {10.1101/2023.09.15.556782}, url = {https://www.biorxiv.org/content/early/2024/02/28/2023.09.15.556782}, author = {Suguru Takagi and Gizem Sancer and Liliane Abuin and S. David Stupski and J. Roman Arguello and Lucia L. Prieto-Godino and David L. Stern and Steeve Cruchet and Raquel {\'A}lvarez-Oca{\~n}a and Carl F. R. Wienecke and Floris van Breugel and James M. Jeanne and Thomas O. Auer and Richard Benton} } @article {69227, title = {A series of spontaneously blinking dyes for super-resolution microscopy}, journal = {bioRxiv}, year = {2024}, month = {2024 Feb 24}, abstract = {

Spontaneously blinking fluorophores permit the detection and localization of individual molecules without reducing buffers or caging groups, thus simplifying single-molecule localization microscopy (SMLM). The intrinsic blinking properties of such dyes are dictated by molecular structure and modulated by environment, which can limit utility. We report a series of tuned spontaneously blinking dyes with duty cycles that span two orders of magnitude, allowing facile SMLM in cells and dense biomolecular structures.

}, doi = {10.1101/2024.02.23.581625}, url = {https://www.biorxiv.org/content/early/2024/02/24/2024.02.23.581625}, author = {Katie L. Holland and Sarah E. Plutkis and Timothy A. Daugird and Abhishek Sau and Jonathan B. Grimm and Brian P. English and Qinsi Zheng and Sandeep Dave and Fariha Rahman and Liangqi Xie and Peng Dong and Ariana N. Tkachuk and Timothy A. Brown and Robert H. Singer and Zhe Liu and Catherine G. Galbraith and Siegfried M. Musser and Wesley R. Legant and Luke D. Lavis} } @article {69608, title = {Serotonergic modulation of swallowing in a complete fly vagus nerve connectome.}, journal = {Curr Biol}, year = {2024}, month = {2024 Sep 05}, abstract = {

How the body interacts with the brain to perform vital life functions, such as feeding, is a fundamental issue in physiology and neuroscience. Here, we use a whole-animal scanning transmission electron microscopy volume of Drosophila to map the neuronal circuits that connect the entire enteric nervous system to the brain via the insect vagus nerve at synaptic resolution. We identify a gut-brain feedback loop in which Piezo-expressing mechanosensory neurons in the esophagus convey food passage information to a cluster of six serotonergic neurons in the brain. Together with information on food value, these central serotonergic neurons enhance the activity of serotonin receptor 7-expressing motor neurons that drive swallowing. This elemental circuit architecture includes an axo-axonic synaptic connection from the glutamatergic motor neurons innervating the esophageal muscles onto the mechanosensory neurons that signal to the serotonergic neurons. Our analysis elucidates a neuromodulatory sensory-motor system in which ongoing motor activity is strengthened through serotonin upon completion of a biologically meaningful action, and it may represent an ancient form of motor learning.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2024.08.025}, url = {https://doi.org/10.1016/j.cub.2024.08.025}, author = {Schoofs, Andreas and Miroschnikow, Anton and Schlegel, Philipp and Zinke, Ingo and Schneider-Mizell, Casey M and Cardona, Albert and Pankratz, Michael J} } @article {68655, title = {Smart Lattice Light Sheet Microscopy for imaging rare and complex cellular events}, journal = {Nature Methods}, volume = {21}, year = {2024}, month = {2024 Feb 01}, pages = {301-310}, abstract = {

Light sheet microscopes enable rapid, high-resolution imaging of biological specimens; however, biological processes span a variety of spatiotemporal scales. Moreover, long-term phenotypes are often instigated by rare or fleeting biological events that are difficult to capture with a single imaging modality and constant imaging parameters. To overcome this limitation, we present smartLLSM, a microscope that incorporates AI-based instrument control to autonomously switch between epifluorescent inverted imaging and lattice light sheet microscopy. We apply this technology to two major scenarios. First, we demonstrate that the instrument provides population-level statistics of cell cycle states across thousands of cells on a coverslip. Second, we show that by using real-time image feedback to switch between imaging modes, the instrument autonomously captures multicolor 3D datasets or 4D time-lapse movies of dividing cells at rates that dramatically exceed human capabilities. Quantitative image analysis on high-content + high-throughput datasets reveal kinetochore and chromosome dynamics in dividing cells and determine the effects of drug perturbation on cells in specific mitotic stages. This new methodology enables efficient detection of rare events within a heterogeneous cell population and records these processes with high spatiotemporal 4D imaging over statistically significant replicates.

}, doi = {10.1038/s41592-023-02126-0}, url = {https://doi.org/10.1038/s41592-023-02126-0}, author = {Yu Shi and Jimmy S. Tabet and Daniel E. Milkie and Timothy A. Daugird and Chelsea Q. Yang and Andrea Giovannucci and Wesley R. Legant} } @article {69296, title = {Social state gates vision using three circuit mechanisms in Drosophila}, journal = {Nature}, year = {2024}, month = {2024 Nov 20}, abstract = {

Animals are often bombarded with visual information and must prioritize specific visual features based on their current needs. The neuronal circuits that detect and relay visual features have been well studied. Much less is known about how an animal adjusts its visual attention as its goals or environmental conditions change. During social behaviours, flies need to focus on nearby flies. Here we study how the flow of visual information is altered when female Drosophila enter an aggressive state. From the connectome, we identify three state-dependent circuit motifs poised to modify the response of an aggressive female to fly-sized visual objects: convergence of excitatory inputs from neurons conveying select visual features and internal state; dendritic disinhibition of select visual feature detectors; and a switch that toggles between two visual feature detectors. Using cell-type-specific genetic tools, together with behavioural and neurophysiological analyses, we show that each of these circuit motifs is used during female aggression. We reveal that features of this same switch operate in male Drosophila during courtship pursuit, suggesting that disparate social behaviours may share circuit mechanisms. Our study provides a compelling example of using the connectome to infer circuit mechanisms that underlie dynamic processing of sensory signals.

}, doi = {10.1038/s41586-024-08255-6}, url = {https://doi.org/10.1038/s41586-024-08255-6}, author = {Catherine E. Schretter and Tom Hindmarsh Sten and Nathan Klapoetke and Mei Shao and Aljoscha Nern and Marisa Dreher and Daniel Bushey and Alice A. Robie and Adam L. Taylor and Kristin M. Branson and Adriane Otopalik and Vanessa Ruta and Gerald M. Rubin} } @article {69146, title = {Song Torrent: A modular, open-source 96-chamber audio and video recording apparatus with optogenetic activation and inactivation capabilities for Drosophila}, journal = {bioRxiv}, year = {2024}, month = {2024 Jan 10}, abstract = {

Background

Results

Implications

}, doi = {10.1101/2024.01.09.574712}, url = {https://doi.org/10.1101/2024.01.09.574712}, author = {Steve Sawtelle and Lakshmi Narayan and Yun Ding and Elizabeth Kim and Emily L. Behrman and Joshua L. Lillvis and Takashi Kawase and David L. Stern} } @article {69443, title = {Spatial mapping of hepatic ER and mitochondria architecture reveals zonated remodeling in fasting and obesity}, journal = {Nat Commun}, volume = {15}, year = {2024}, month = {2024 May 10}, pages = {3982}, abstract = {

The hepatocytes within the liver present an immense capacity to adapt to changes in nutrient availability. Here, by using high resolution volume electron microscopy, we map how hepatic subcellular spatial organization is regulated during nutritional fluctuations and as a function of liver zonation. We identify that fasting leads to remodeling of endoplasmic reticulum (ER) architecture in hepatocytes, characterized by the induction of single rough ER sheet around the mitochondria, which becomes larger and flatter. These alterations are enriched in periportal and mid-lobular hepatocytes but not in pericentral hepatocytes. Gain- and loss-of-function in vivo models demonstrate that the Ribosome receptor binding protein1 (RRBP1) is required to enable fasting-induced ER sheet-mitochondria interactions and to regulate hepatic fatty acid oxidation. Endogenous RRBP1 is enriched around periportal and mid-lobular regions of the liver. In obesity, ER-mitochondria interactions are distinct and fasting fails to induce rough ER sheet-mitochondrion interactions. These findings illustrate the importance of a regulated molecular architecture for hepatocyte metabolic flexibility.

}, keywords = {Animals, Endoplasmic Reticulum, Fasting, Fatty Acids, Hepatocytes, Humans, Liver, Male, Mice, Mice, Inbred C57BL, Mitochondria, Mitochondria, Liver, Obesity, Oxidation-Reduction, Ribosomal Proteins}, issn = {2041-1723}, doi = {10.1038/s41467-024-48272-7}, author = {Parlakg{\"u}l, G{\"u}ne{\c s} and Pang, Song and Artico, Leonardo L and Min, Nina and Cagampan, Erika and Villa, Reyna and Goncalves, Renata L S and Lee, Grace Yankun and Xu, C Shan and Hotam{\i}{\c s}l{\i}gil, G{\"o}khan S and Arruda, Ana Paula} } @article {69694, title = {Spatial single-cell Organellomics reveals nutrient dependent hepatocyte heterogeneity and predicts pathophysiological status in vivo}, journal = {bioRxiv}, year = {2024}, month = {2024 Dec 08}, abstract = {

Cellular heterogeneity within complex tissues and organs is essential to coordinate biological processes across biological scales. The effect of local cues and tissue microenvironments on cell heterogeneity has been mainly studied at the transcriptional level. However, it is within the subcellular scale - the organelles - that lays the machinery to conduct most metabolic reactions and maintain cells alive, ensuring proper tissue function. How changes in subcellular organization under different microenvironments define the functional diversity of cells within organs remains largely unexplored. Here we determine how organelles adapt to different microenvironments using the mouse liver as model system, in combination with computational approaches and machine-learning. To understand organelle adaptation in response to changing nutritional conditions, we analyzed 3D fluorescent microscopy volumes of liver samples labeled to simultaneously visualize mitochondria, peroxisomes, and lipid droplets from mice subjected to different diets: a control diet, a high-fat diet, and a control diet plus fasting. A Cellpose based pipeline was implemented for cell and organelle segmentation, which allowed us to measure 100 different organelle metrics and helped us define subcellular architectures in liver samples at the single cell level. Our results showed that hepatocytes display distinct subcellular architectures within different regions of the liver-close to the central vein, in the middle region, and near the portal vein- and across the various diet groups, thus reflecting their adaptation to specific nutritional inputs. Principal component analysis and clustering of hepatocytes based on organelle signatures revealed 12 different hepatocyte categories within the different experimental groups, highlighting a reduction in hepatocyte heterogeneity under nutritional perturbations. Finally, using single cell organelle signatures exclusively, we generated machine learning models that were able to predict with high accuracy different hepatocyte categories, diet groups, and the stages of MASLD. Our results demonstrate how organelle signatures can be used as hallmarks to define hepatocyte heterogeneity and their adaptation to different nutritional conditions. In the future, our strategy, which combines subcellular resolution imaging of liver volumes and machine learning, could help establish protocols to better define and predict liver disease progression.

}, doi = {10.1101/2024.12.06.627285}, url = {https://doi.org/10.1101/2024.12.06.627285}, author = {Hillsley, Alexander and Adhikari, Raghabendra and Johnson, Alana Dowdell and Espinosa-Medina, Isabel and Funke, Jan and Feliciano, Daniel} } @article {69352, title = {Spike sorting with Kilosort4}, journal = {Nat Methods}, year = {2024}, month = {2024 Apr 08}, abstract = {

Spike sorting is the computational process of extracting the firing times of single neurons from recordings of local electrical fields. This is an important but hard problem in neuroscience, made complicated by the nonstationarity of the recordings and the dense overlap in electrical fields between nearby neurons. To address the spike-sorting problem, we have been openly developing the Kilosort framework. Here we describe the various algorithmic steps introduced in different versions of Kilosort. We also report the development of Kilosort4, a version with substantially improved performance due to clustering algorithms inspired by graph-based approaches. To test the performance of Kilosort, we developed a realistic simulation framework that uses densely sampled electrical fields from real experiments to generate nonstationary spike waveforms and realistic noise. We found that nearly all versions of Kilosort outperformed other algorithms on a variety of simulated conditions and that Kilosort4 performed best in all cases, correctly identifying even neurons with low amplitudes and small spatial extents in high drift conditions.

}, issn = {1548-7105}, doi = {10.1038/s41592-024-02232-7}, author = {Pachitariu, Marius and Sridhar, Shashwat and Pennington, Jacob and Stringer, Carsen} } @article {69329, title = {A split-GAL4 driver line resource for Drosophila CNS cell types}, journal = {bioRxiv}, year = {2024}, month = {2024 Jan 10}, abstract = {

Techniques that enable precise manipulations of subsets of neurons in the fly central nervous system have greatly facilitated our understanding of the neural basis of behavior. Split-GAL4 driver lines allow specific targeting of cell types in Drosophila melanogaster and other species. We describe here a collection of 3060 lines targeting a range of cell types in the adult Drosophila central nervous system and 1373 lines characterized in third-instar larvae. These tools enable functional, transcriptomic, and proteomic studies based on precise anatomical targeting. NeuronBridge and other search tools relate light microscopy images of these split-GAL4 lines to connectomes reconstructed from electron microscopy images. The collections are the result of screening over 77,000 split hemidriver combinations. In addition to images and fly stocks for these well-characterized lines, we make available 300,000 new 3D images of other split-GAL4 lines.

}, doi = {10.1101/2024.01.09.574419}, url = {https://www.biorxiv.org/content/early/2024/04/01/2024.01.09.574419}, author = {Geoffrey W Meissner and Allison Vannan and Jennifer Jeter and Kari Close and Gina M DePasquale and Zachary Dorman and Kaitlyn Forster and Jaye Anne Beringer and Theresa V Gibney and Joanna H Hausenfluck and Yisheng He and Kristin Henderson and Lauren Johnson and Rebecca M Johnston and Gudrun Ihrke and Nirmala Iyer and Rachel Lazarus and Kelley Lee and Hsing-Hsi Li and Hua-Peng Liaw and Brian Melton and Scott Miller and Reeham Motaher and Alexandra Novak and Omotara Ogundeyi and Alyson Petruncio and Jacquelyn Price and Sophia Protopapas and Susana Tae and Jennifer Taylor and Rebecca Vorimo and Brianna Yarbrough and Kevin Xiankun Zeng and Christopher T Zugates and Heather Dionne and Claire Angstadt and Kelly Ashley and Amanda Cavallaro and Tam Dang and Guillermo A Gonzalez III and Karen L Hibbard and Cuizhen Huang and Jui-Chun Kao and Todd Laverty and Monti Mercer and Brenda Perez and Scarlett Pitts and Danielle Ruiz and Viruthika Vallanadu and Grace Zhiyu Zheng and Cristian Goina and Hideo Otsuna and Konrad Rokicki and Robert R Svirskas and Han SJ Cheong and Michael-John Dolan and Erica Ehrhardt and Kai Feng and Basel El Galfi and Jens Goldammer and Stephen J Huston and Nan Hu and Masayoshi Ito and Claire McKellar and Ryo Minegishi and Shigehiro Namiki and Aljoscha Nern and Catherine E Schretter and Gabriella R Sterne and Lalanti Venkatasubramanian and Kaiyu Wang and Tanya Wolff and Ming Wu and Reed George and Oz Malkesman and Yoshinori Aso and Gwyneth M Card and Barry J Dickson and Wyatt Korff and Kei Ito and James W Truman and Marta Zlatic and Gerald M Rubin and FlyLight Project Team} } @article {69287, title = {Spot Spine, a freely available ImageJ plugin for 3D detection and morphological analysis of dendritic spines}, journal = {F1000Research}, volume = {13}, year = {2024}, month = {2024 Mar 11}, abstract = {

Background

Dendritic spines are tiny protrusions found along the dendrites of neurons, and their number is a measure of the density of synaptic connections. Altered density and morphology is observed in several pathologies, and spine formation as well as morphological changes correlate with learning and memory. The detection of spines in microscopy images and the analysis of their morphology is therefore a prerequisite for many studies. We have developed a new open-source, freely available, plugin for ImageJ/FIJI, called Spot Spine, that allows detection and morphological measurements of spines in three dimensional images.

Method

Local maxima are detected in spine heads, and the intensity distribution around the local maximum is computed to perform the segmentation of each spine head. Spine necks are then traced from the spine head to the dendrite. Several parameters can be set to optimize detection and segmentation, and manual correction gives further control over the result of the process.

Results

The plugin allows the analysis of images of dendrites obtained with various labeling and imaging methods. Quantitative measurements are retrieved including spine head volume and surface, and neck length.

Conclusion

The plugin and instructions for use are available at https://imagej.net/plugins/spot-spine.

}, doi = {10.12688/f1000research.146327.1}, author = {Gilles, JF and Mailly, P and Ferreira, T and Boudier, T and Heck, N} } @article {69419, title = {Statistical signature of subtle behavioural changes in large-scale behavioural assays}, journal = {bioRxiv}, year = {2024}, month = {2024 May 5}, abstract = {

The central nervous system can generate various behaviours, including motor responses, which we can observe through video recordings. Recent advancements in genetics, automated behavioural acquisition at scale, and machine learning enable us to link behaviours to their underlying neural mechanisms causally. Moreover, in some animals, such as the Drosophila larva, this mapping is possible at unprecedented scales of millions of animals and single neurons, allowing us to identify the neural circuits generating particular behaviours.These high-throughput screening efforts are invaluable, linking the activation or suppression of specific neurons to behavioural patterns in millions of animals. This provides a rich dataset to explore how diverse nervous system responses can be to the same stimuli. However, challenges remain in identifying subtle behaviours from these large datasets, including immediate and delayed responses to neural activation or suppression, and understanding these behaviours on a large scale. We introduce several statistically robust methods for analyzing behavioural data in response to these challenges: 1) A generative physical model that regularizes the inference of larval shapes across the entire dataset. 2) An unsupervised kernel-based method for statistical testing in learned behavioural spaces aimed at detecting subtle deviations in behaviour. 3) A generative model for larval behavioural sequences, providing a benchmark for identifying complex behavioural changes. 4) A comprehensive analysis technique using suffix trees to categorize genetic lines into clusters based on common action sequences. We showcase these methodologies through a behavioural screen focused on responses to an air puff, analyzing data from 280,716 larvae across 568 genetic lines.Author Summary There is a significant gap in understanding between the architecture of neural circuits and the mechanisms of action selection and behaviour generation.Drosophila larvae have emerged as an ideal platform for simultaneously probing behaviour and the underlying neuronal computation [1]. Modern genetic tools allow efficient activation or silencing of individual and small groups of neurons. Combining these techniques with standardized stimuli over thousands of individuals makes it possible to relate neurons to behaviour causally. However, extracting these relationships from massive and noisy recordings requires the development of new statistically robust approaches. We introduce a suite of statistical methods that utilize individual behavioural data and the overarching structure of the behavioural screen to deduce subtle behavioural changes from raw data. Given our study{\textquoteright}s extensive number of larvae, addressing and preempting potential challenges in body shape recognition is critical for enhancing behaviour detection. To this end, we have adopted a physics-informed inference model. Our first group of techniques enables robust statistical analysis within a learned continuous behaviour latent space, facilitating the detection of subtle behavioural shifts relative to reference genetic lines. A second array of methods probes for subtle variations in action sequences by comparing them to a bespoke generative model. Together, these strategies have enabled us to construct representations of behavioural patterns specific to a lineage and identify a roster of {\textquotedblright}hit{\textquotedblright} neurons with the potential to influence behaviour subtly.

}, doi = {10.1101/2024.05.03.591825}, url = {https://www.biorxiv.org/content/early/2024/05/05/2024.05.03.591825}, author = {Alexandre Blanc and Fran{\c c}ois Laurent and Alex Barbier{\textendash}Chebbah and Benjamin T. Cocanougher and Benjamin M.W. Jones and Peter Hague and Marta Zlatic and Rayan Chikhi and Christian L. Vestergaard and Tihana Jovanic and Jean-Baptiste Masson and Chlo{\'e} Barr{\'e}} } @article {69502, title = {Steering From the Rear: Coordination of Central Pattern Generators Underlying Navigation by Ascending Interneurons}, journal = {bioRxiv}, year = {2024}, month = {2024 Jun 17}, abstract = {

Understanding how animals coordinate movements to achieve goals is a fundamental pursuit in neuroscience. Here we explore how neurons that reside in posterior lower-order regions of a locomotor system and project to anterior higher-order regions influence steering and navigation. We characterized the anatomy and functional role of a population of ascending interneurons in the ventral nerve cord of Drosophila larvae. Through electron microscopy reconstructions and light microscopy, we determined that the cholinergic 19f cells receive input primarily from premotor interneurons and synapse upon a diverse array of postsynaptic targets within the anterior segments including other 19f cells. Calcium imaging of 19f activity in isolated CNS preparations in relation to motor neurons revealed that 19f neurons are recruited into most larval motor programmes. 19f activity lags behind motor neuron activity and as a population, the cells encode spatio-temporal patterns of locomotor activity in the larval CNS. Optogenetic manipulations of 19f cell activity in isolated CNS preparations revealed that they coordinate the activity of central pattern generators underlying exploratory headsweeps and forward locomotion in a context and location specific manner. In behaving animals, activating 19f cells suppressed exploratory headsweeps and slowed forward locomotion, while inhibition of 19f activity potentiated headsweeps, slowing forward movement. Inhibiting activity in 19f cells ultimately affected the ability of larvae to remain in the vicinity of an odor source during an olfactory navigation task. Overall, our findings provide insights into how ascending interneurons monitor motor activity and shape interactions amongst rhythm generators underlying complex navigational tasks.

}, doi = {10.1101/2024.06.17.598162}, url = {https://www.biorxiv.org/content/early/2024/06/17/2024.06.17.598162}, author = {Jonaitis, Julius and Hibbard, Karen L and Layte, Kaity McCafferty and Hiramoto, Atsuki and Cardona, Albert and Truman, James W and Nose, Akinao and Zwart, Maarten F and Pulver, Stefan R} } @article {69687, title = {Structural dynamics of human ribosomes in situ reconstructed by exhaustive high-resolution template matching.}, journal = {Mol Cell}, year = {2024}, month = {2024 Nov 25}, abstract = {

Protein synthesis is central to life and requires the ribosome, which catalyzes the stepwise addition of amino acids to a polypeptide chain by undergoing a sequence of structural transformations. Here, we employed high-resolution template matching (HRTM) on cryoelectron microscopy (cryo-EM) images of directly cryofixed living cells to obtain a set of ribosomal configurations covering the entire elongation cycle, with each configuration occurring at its native abundance. HRTM{\textquoteright}s position and orientation precision and ability to detect small targets (\~{}300\ kDa) made it possible to order these configurations along the reaction coordinate and to reconstruct molecular features of any configuration along the elongation cycle. Visualizing the cycle{\textquoteright}s structural dynamics by combining a sequence of \>40 reconstructions into a 3D movie readily revealed component and ligand movements, some of them surprising, such as spring-like intramolecular motion, providing clues about the molecular mechanisms involved in some still mysterious steps during chain elongation.

}, issn = {1097-4164}, doi = {10.1016/j.molcel.2024.11.003}, author = {Rickgauer, J Peter and Choi, Heejun and Moore, Andrew S and Denk, Winfried and Lippincott-Schwartz, Jennifer} } @article {69109, title = {Structure, interaction, and nervous connectivity of beta cell primary cilia}, journal = {Nat Commun}, volume = {15}, year = {2024}, month = {2024 Oct 24}, pages = {9168}, abstract = {

Primary cilia are sensory organelles present in many cell types, partaking in various signaling processes. Primary cilia of pancreatic beta cells play pivotal roles in paracrine signaling and their dysfunction is linked to diabetes. Yet, the structural basis for their functions is unclear. We present three-dimensional reconstructions of beta cell primary cilia by electron and expansion microscopy. These cilia are spatially confined within deep ciliary pockets or narrow spaces between cells, lack motility components and display an unstructured axoneme organization. Furthermore, we observe a plethora of beta cell cilia-cilia and cilia-cell interactions with other islet and non-islet cells. Most remarkably, we have identified and characterized axo-ciliary synapses between beta cell cilia and the cholinergic islet innervation. These findings highlight the beta cell cilia{\textquoteright}s role in islet connectivity, pointing at their function in integrating islet intrinsic and extrinsic signals and contribute to understanding their significance in health and diabetes.

}, doi = {10.1038/s41467-024-53348-5}, url = {https://doi.org/10.1038/s41467-024-53348-5}, author = {Andreas M{\"u}ller and Nikolai Klena and Song Pang and Leticia Elizabeth Galicia Garcia and Davud Sulaymankhil and Oleksandra Topcheva and Monika Seliskar and Hassan Mziaut and Eyke Sch{\"o}niger and Daniela Friedland and Nicole Kipke and Susanne Kretschmar and Carla M{\"u}nster and J{\"u}rgen Weitz and Marius Distler and Thomas Kurth and Deborah Schmidt and Harald F. Hess and C. Shan Xu and Gaia Pigino and Michele Solimena} } @article {69611, title = {Sub-threshold neuronal activity and the dynamical regime of cerebral cortex.}, journal = {Nat Commun}, volume = {15}, year = {2024}, month = {2024 Sep 11}, pages = {7958}, abstract = {

Cortical neurons exhibit temporally irregular spiking patterns and heterogeneous firing rates. These features arise in model circuits operating in a {\textquoteright}fluctuation-driven regime{\textquoteright}, in which fluctuations in membrane potentials emerge from the network dynamics. However, it is still debated whether the cortex operates in such a regime. We evaluated the fluctuation-driven hypothesis by analyzing spiking and sub-threshold membrane potentials of neurons in the frontal cortex of mice performing a decision-making task. We showed that while standard fluctuation-driven models successfully account for spiking statistics, they fall short in capturing the heterogeneity in sub-threshold activity. This limitation is an inevitable outcome of bombarding single-compartment neurons with a large number of pre-synaptic inputs, thereby clamping the voltage of all neurons to more or less the same average voltage. To address this, we effectively incorporated dendritic morphology into the standard models. Inclusion of dendritic morphology in the neuronal models increased neuronal selectivity and reduced error trials, suggesting a functional role for dendrites during decision-making. Our work suggests that, during decision-making, cortical neurons in high-order cortical areas operate in a fluctuation-driven regime.

}, keywords = {Action Potentials, Animals, Cerebral Cortex, Decision Making, Dendrites, Frontal Lobe, Male, Membrane Potentials, Mice, Mice, Inbred C57BL, Models, Neurological, Neurons}, issn = {2041-1723}, doi = {10.1038/s41467-024-51390-x}, url = {https://doi.org/10.1038/s41467-024-51390-x}, author = {Amsalem, Oren and Inagaki, Hidehiko and Yu, Jianing and Svoboda, Karel and Darshan, Ran} } @article {69612, title = {Synaptic Specializations at Dopamine Release Sites Orchestrate Efficient and Precise Neuromodulatory Signaling}, journal = {bioRxiv}, year = {2024}, month = {2024 Sep 16}, abstract = {

Dopamine is a key chemical neuromodulator that plays vital roles in various brain functions. Traditionally, neuromodulators like dopamine are believed to be released in a diffuse manner and are not commonly associated with synaptic structures where pre- and postsynaptic processes are closely aligned. Our findings challenge this conventional view. Using single-bouton optical measurements of dopamine release, we discovered that dopamine is predominantly released from varicosities that are juxtaposed against the processes of their target neurons. Dopamine axons specifically target neurons expressing dopamine receptors, forming synapses to release dopamine. Interestingly, varicosities that were not directly apposed to dopamine receptor-expressing processes or associated with neurons lacking dopamine receptors did not release dopamine, regardless of their vesicle content. The ultrastructure of dopamine release sites share common features of classical synapses. We further show that the dopamine released at these contact sites induces a precise, dopamine-gated biochemical response in the target processes. Our results indicate that dopamine release sites share key characteristics of conventional synapses that enable relatively precise and efficient neuromodulation of their targets.

}, doi = {10.1101/2024.09.16.613338}, url = {https://doi.org/10.1101/2024.09.16.613338}, author = {Bulumulla, Chandima and Walpita, Deepika and Iyer, Nirmala and Eddison, Mark and Patel, Ronak and Alcor, Damien and Ackerman, David and Beyene, Abraham G} } @article {69698, title = {Temporal BMP4 effects on mouse embryonic and extraembryonic developmentAbstract}, journal = {Nature}, volume = {634}, year = {2024}, month = {09-2024}, pages = {652 - 661}, abstract = {

The developing placenta, which in mice originates through the extraembryonic ectoderm (ExE), is essential for mammalian embryonic development. Yet unbiased characterization of the differentiation dynamics\ of the ExE and its interactions with the embryo proper remains incomplete. Here we develop a temporal single-cell model of mouse gastrulation that maps continuous and parallel differentiation in embryonic and extraembryonic lineages. This is matched with a three-way perturbation approach to target signalling from the embryo proper, the ExE alone, or both. We show that ExE specification involves early spatial and transcriptional bifurcation of uncommitted ectoplacental cone cells and chorion progenitors. Early BMP4 signalling from chorion progenitors is required for proper differentiation of uncommitted ectoplacental cone cells and later for their specification towards trophoblast giant cells. We also find biphasic regulation by BMP4 in the embryo. The early ExE-originating BMP4 signal is necessary for proper mesoendoderm bifurcation and for\ allantois and primordial germ cell specification. However, commencing at embryonic day 7.5, embryo-derived BMP4 restricts the primordial germ cell pool size by favouring differentiation of their extraembryonic mesoderm precursors towards an allantois fate. ExE and embryonic tissues are therefore entangled in time, space and signalling axes, highlighting the importance of their integrated understanding and modelling in vivo and in vitro.

}, issn = {0028-0836}, doi = {10.1038/s41586-024-07937-5}, url = {https://www.nature.com/articles/s41586-024-07937-5https://www.nature.com/articles/s41586-024-07937-5.pdfhttps://www.nature.com/articles/s41586-024-07937-5.pdfhttps://www.nature.com/articles/s41586-024-07937-5}, author = {Hadas, Ron and Rubinstein, Hernan and Mittnenzweig, Markus and Mayshar, Yoav and Ben-Yair, Raz and Cheng, Saifeng and Aguilera-Castrejon, Alejandro and Reines, Netta and Orenbuch, Ayelet-Hashahar and Lifshitz, Aviezer and Chen, Dong-Yuan and Elowitz, Michael B. and Zernicka-Goetz, Magdalena and Hanna, Jacob H. and Tanay, Amos and Stelzer, Yonatan} } @article {69589, title = {A theory of rapid behavioral inferences under the pressure of time}, journal = {PRX Life}, volume = {4}, year = {2024}, month = {2026 Mar 05}, abstract = {

To survive, animals must be able to quickly infer the state of their surroundings. For example, to successfully escape an approaching predator, prey must quickly estimate the direction of approach from incoming sensory stimuli and guide their behavior accordingly. Such rapid inferences are particularly challenging because the animal has only a brief window of time to gather sensory stimuli, and yet the accuracy of inference is critical for survival. Due to evolutionary pressures, nervous systems have likely evolved effective computational strategies that enable accurate inferences under strong time limitations. Traditionally, the relationship between the speed and accuracy of inference has been described by the {\textquotedblleft}speed-accuracy tradeoff{\textquotedblright} (SAT), which quantifies how the average performance of an ideal observer improves as the observer has more time to collect incoming stimuli. While this trial-averaged description can reasonably account for individual inferences made over long timescales, it does not capture individual inferences on short timescales, when trial-to-trial variability gives rise to diverse patterns of error dynamics. We show that an ideal observer can exploit this single-trial structure by adaptively tracking the dynamics of its belief about the state of the environment, which enables it to speed its own inferences and more reliably track its own error, but also causes it to violate the SAT. We show that these features can be used to improve overall performance during rapid escape. The resulting behavior qualitatively reproduces features of escape behavior in the fruit fly\ Drosophila melanogaster, whose escapes have presumably been highly optimized by natural selection.

Preprint:\ https://www.doi.org/10.1101/2024.08.26.609738

}, doi = {10.1103/8m59-vf2m}, url = { https://doi.org/10.1103/8m59-vf2m}, author = {Hermundstad, Ann M and M{\l}ynarski, Wiktor F} } @article {69282, title = {Three-dimensional spatio-angular fluorescence microscopy with a polarized dual-view inverted selective-plane illumination microscope (pol-diSPIM)}, journal = {bioRxiv}, year = {2024}, month = {2024 Mar 12}, abstract = {

Polarized fluorescence microscopy is a valuable tool for measuring molecular orientations, but techniques for recovering three-dimensional orientations and positions of fluorescent ensembles are limited. We report a polarized dual-view light-sheet system for determining the three-dimensional orientations and diffraction-limited positions of ensembles of fluorescent dipoles that label biological structures, and we share a set of visualization, histogram, and profiling tools for interpreting these positions and orientations. We model our samples, their excitation, and their detection using coarse-grained representations we call orientation distribution functions (ODFs). We apply ODFs to create physics-informed models of image formation with spatio-angular point-spread and transfer functions. We use theory and experiment to conclude that light-sheet tilting is a necessary part of our design for recovering all three-dimensional orientations. We use our system to extend known two-dimensional results to three dimensions in FM1-43-labelled giant unilamellar vesicles, fast-scarlet-labelled cellulose in xylem cells, and phalloidin-labelled actin in U2OS cells. Additionally, we observe phalloidin-labelled actin in mouse fibroblasts grown on grids of labelled nanowires and identify correlations between local actin alignment and global cell-scale orientation, indicating cellular coordination across length scales.Competing Interest StatementH.S., A.K., S.M., P.L.R., R.O., Y.W., and T.C. hold US Patent $\#$11428632.

}, doi = {10.1101/2024.03.09.584243}, url = {https://www.biorxiv.org/content/early/2024/03/12/2024.03.09.584243}, author = {Talon Chandler and Min Guo and Yijun Su and Jiji Chen and Yicong Wu and Junyu Liu and Atharva Agashe and Robert S. Fischer and Shalin B. Mehta and Abhishek Kumar and Tobias I. Baskin and Valentin Jamouille and Huafeng Liu and Vinay Swaminathan and Amrinder Nain and Rudolf Oldenbourg and Patrick La Riviere and Hari Shroff} } @article {69674, title = {Tracking fructose 1,6-bisphosphate dynamics in liver cancer cells using a fluorescent biosensor}, journal = {iScience}, volume = {27}, year = {2024}, month = {2024 Nov 20}, pages = {111336}, abstract = {

Summary HYlight is a genetically encoded fluorescent biosensor that ratiometrically monitors fructose 1,6-bisphosphate (FBP), a key glycolytic metabolite. Given the role of glucose in liver cancer metabolism, we expressed HYlight in human liver cancer cells and primary mouse hepatocytes. Through in\ vitro, in silico, and in cellulo experiments, we showed HYlight{\textquoteright}s ability to monitor FBP changes linked to glycolysis, not gluconeogenesis. HYlight{\textquoteright}s affinity for FBP was \~{}1\ μM and stable within physiological pH range. HYlight demonstrated weak binding to dihydroxyacetone phosphate, and its ratiometric response was influenced by both ionic strength and phosphate. Therefore, simulating cytosolic conditions in\ vitro was necessary to establish a reliable correlation between HYlight{\textquoteright}s cellular responses and FBP concentrations. FBP concentrations were found to be in the lower micromolar range, far lower than previous millimolar estimates. Altogether, this biosensor approach offers real-time monitoring of FBP concentrations at single-cell resolution, making it an invaluable tool for the understanding of cancer metabolism.

}, keywords = {biochemistry methods, cancer, metabolomics}, issn = {2589-0042}, doi = {https://doi.org/10.1016/j.isci.2024.111336}, url = {https://www.sciencedirect.com/science/article/pii/S2589004224025616}, author = {Israel P{\'e}rez-Ch{\'a}vez and John N. Koberstein and Julia Malo Pueyo and Eduardo H. Gilglioni and Didier Vertommen and Nicolas Baeyens and Daria Ezerina and Esteban N. Gurzov and Joris Messens} } @article {69349, title = {Transformers do not outperform Cellpose}, journal = {bioRxiv}, year = {2024}, month = {2024 Apr 7}, abstract = {

In a recent publication, Ma et al [1] claim that a transformer-based cellular segmentation method called Mediar [2] {\textemdash} which won a Neurips challenge {\textemdash} outperforms Cellpose [3] (0.897 vs 0.543 median F1 score). Here we show that this result was obtained by artificially impairing Cellpose in multiple ways. When we removed these impairments, Cellpose outperformed Mediar (0.861 vs 0.826 median F1 score on the updated test set). To further investigate the performance of transformers for cellular segmentation, we replaced the Cellpose backbone with a transformer. The transformer-Cellpose model also did not outperform the standard Cellpose (0.848 median F1 test score). Our results suggest that transformers do not advance the state-of-the-art in cellular segmentation.

}, doi = {10.1101/2024.04.06.587952}, url = {https://www.biorxiv.org/content/early/2024/04/07/2024.04.06.587952}, author = {Carsen Stringer and Marius Pachitariu} } @article {69144, title = {Transforming chemigenetic bimolecular fluorescence complementation systems into chemical dimerizers using chemistry.}, journal = {bioRxiv}, year = {2024}, month = {2024 Jan 01}, abstract = {

Chemigenetic tags are versatile labels for fluorescence microscopy that combine some of the advantages of genetically encoded tags with small molecule fluorophores. The Fluorescence Activating and absorbance Shifting Tags (FASTs) bind a series of highly fluorogenic and cell-permeable chromophores. Furthermore, FASTs can be used in complementation-based systems for detecting or inducing protein-protein interactions, depending on the exact FAST protein variant chosen. In this study, we systematically explore substitution patterns on FAST fluorogens and generate a series of fluorogens that bind to FAST variants, thereby activating their fluorescence. This effort led to the discovery of a novel fluorogen with superior properties, as well as a fluorogen that transforms splitFAST systems into a fluorogenic dimerizer, eliminating the need for additional protein engineering.

}, doi = {10.1101/2023.12.30.573644}, url = {https://doi.org/10.1101/2023.12.30.573644}, author = {Pratik Kumar and Alina Gutu and Amelia Waring and Timothy A. Brown and Luke D. Lavis and Alison G. Tebo} } @article {69491, title = {Transport and Organization of Individual Vimentin Filaments Within Dense Networks Revealed by Single Particle Tracking and 3D FIB-SEM}, journal = {bioRxiv}, year = {2024}, month = {2024 Jun 10}, abstract = {

Vimentin intermediate filaments (VIFs) form complex, tight-packed networks; due to this density, traditional ensemble labeling and imaging approaches cannot accurately discern single filament behavior. To address this, we introduce a sparse vimentin-SunTag labeling strategy to unambiguously visualize individual filament dynamics. This technique confirmed known long-range dynein and kinesin transport of peripheral VIFs and uncovered extensive bidirectional VIF motion within the perinuclear vimentin network, a region we had thought too densely bundled to permit such motility. To examine the nanoscale organization of perinuclear vimentin, we acquired high-resolution electron microscopy volumes of a vitreously frozen cell and reconstructed VIFs and microtubules within a 50 um3 window. Of 583 VIFs identified, most were integrated into long, semi-coherent bundles that fluctuated in width and filament packing density. Unexpectedly, VIFs displayed minimal local co-alignment with microtubules, save for sporadic cross-over sites that we predict facilitate cytoskeletal crosstalk. Overall, this work demonstrates single VIF dynamics and organization in the cellular milieu for the first time.

}, doi = {10.1101/2024.06.10.598346}, url = {https://www.biorxiv.org/content/early/2024/06/10/2024.06.10.598346}, author = {Renganathan, Bhuvanasundar and Moore, Andrew S. and Yeo, Wei-Hong and Petruncio, Alyson and Ackerman, David and Wiegel, Aubrey and CellMap Team and Pasolli, H. Amalia and Xu, C. Shan and Hess, Harald F and Serpinskaya, Anna S. and Zhang, Hao F. and Lippincott-Schwartz, Jennifer and Gelfand, Vladimir I.} } @article {69673, title = {TUDCA modulates drug bioavailability to regulate resistance to acute ER stress in Saccharomyces cerevisiae}, journal = {Mol Biol Cell}, year = {2024}, month = {2024 Dec 11}, pages = {mbcE24040147}, abstract = {

Cells counter accumulation of misfolded secretory proteins in the endoplasmic reticulum (ER) through activation of the Unfolded Protein Response (UPR). Small molecules termed chemical chaperones can promote protein folding to alleviate ER stress. The bile acid tauroursodeoxycholic acid (TUDCA), has been described as a chemical chaperone. While promising in models of protein folding diseases, TUDCA{\textquoteright}s mechanism of action remains unclear. Here, we found TUDCA can rescue growth of yeast treated with the ER stressor tunicamycin (Tm), even in the absence of a functional UPR. In contrast, TUDCA failed to rescue growth on other ER stressors. Nor could TUDCA attenuate chronic UPR associated with specific gene deletions or over-expression of a misfolded mutant secretory protein. Neither pretreatment with or delayed addition of TUDCA conferred protection against Tm. Importantly, attenuation of Tm-induced toxicity required TUDCA{\textquoteright}s critical micelle forming concentration, suggesting a mechanism where TUDCA directly sequesters drugs. Indeed, in several assays, TUDCA treated cells closely resembled cells treated with lower doses of Tm. In addition, we found TUDCA can inhibit dyes from labeling intracellular compartments. Thus, our study challenges the model of TUDCA as a chemical chaperone and suggests that TUDCA decreases drug bioavailability, allowing cells to adapt to ER stress.

}, doi = {10.1091/mbc.E24-04-0147}, url = {https://doi.org/10.1091/mbc.E24-04-0147}, author = {Chadwick, Sarah R. and Stack-Couture, Samuel and Berg, Matthew D. and Gregorio, Sonja Di and Lung, Bryan and Genereaux, Julie and Moir, Robyn D. and Brandl, Christopher J. and Willis, Ian M. and Snapp, Erik L. and Lajoie, Patrick} } @article {69662, title = {Type IV pili-associated secretion of a biofilm matrix protein from Clostridium perfringens that forms intermolecular isopeptide bonds}, journal = {bioRxiv}, year = {2024}, month = {2024 Nov 04}, abstract = {

Clostridium perfringens is a Gram-positive anaerobic spore-forming bacterial pathogen of humans and animals. C. perfringens also produces type IV pili (T4P) and has two complete sets of T4P-associated genes, one of which has been shown to produce surface pili needed for cell adherence. One hypothesis about the role of the other set of T4P genes is that they could comprise a system analogous to the type II secretion systems (TTSS) found in Gram-negative bacteria, which is used to export folded proteins from the periplasm through the outer membrane to the extracellular environment. Gram-positive bacteria have a similar secretion barrier in the thick peptidoglycan (PG) layer, which blocks secretion of folded proteins \>25 kD. To determine if the T4P-associated genes comprise a Gram-positive TTSS, the secretome of mutants lacking type IV pilins were examined and a single protein, a von Willebrand A domain containing protein BsaC (CPE0517) was identified as being dependent on PilA3 for secretion. BsaC is in an operon with a signal peptidase and two putative biofilm matrix proteins with homology to Bacillus subtilis TasA. One of these proteins, BsaA, was shown by another group to produce high mol wt oligomers. We analyzed BsaA monomer interactions with de novo modeling, which projected that the monomers formed isopeptide bonds as part of a donor strand exchange process. Mutations in residues predicted to form the isopeptide bonds led to loss of oligomerization, supporting the predicted bond formation process. Phylogenetic analysis showed the BsaA family of proteins are widespread among bacteria and archaea but only a subset are predicted to form isopeptide bonds.

}, doi = {10.1101/2024.11.04.621531}, url = {https://doi.org/10.1101/2024.11.04.621531}, author = {Kivimaki, Sarah E. and Dempsey, Samantha and Tani, Julia M. and Camper, Colette and Hicklin, Ian K. and Blaby-Haas, Crysten E. and Brown, Anne M and Melville, Stephen} } @article {69350, title = {Ultra-high density electrodes improve detection, yield, and cell type identification in neuronal recordings}, journal = {bioRxiv}, year = {2024}, month = {2024 Apr 10}, abstract = {

To understand the neural basis of behavior, it is essential to sensitively and accurately measure neural activity at single neuron and single spike resolution. Extracellular electrophysiology delivers this, but it has biases in the neurons it detects and it imperfectly resolves their action potentials. To minimize these limitations, we developed a silicon probe with much smaller and denser recording sites than previous designs, called Neuropixels Ultra (NP Ultra). This device samples neuronal activity at ultra-high spatial density ( 10 times higher than previous probes) with low noise levels, while trading off recording span. NP Ultra is effectively an implantable voltage-sensing camera that captures a planar image of a neuron{\textquoteright}s electrical field. We use a spike sorting algorithm optimized for these probes to demonstrate that the yield of visually-responsive neurons in recordings from mouse visual cortex improves up to 3-fold. We show that NP Ultra can record from small neuronal structures including axons and dendrites. Recordings across multiple brain regions and four species revealed a subset of extracellular action potentials with unexpectedly small spatial spread and axon-like features. We share a large-scale dataset of these brain-wide recordings in mice as a resource for studies of neuronal biophysics. Finally, using ground-truth identification of three major inhibitory cortical cell types, we found that these cell types were discriminable with approximately 75\% success, a significant improvement over lower-resolution recordings. NP Ultra improves spike sorting performance, detection of subcellular compartments, and cell type classification to enable more powerful dissection of neural circuit activity during behavior.

}, doi = {10.1101/2023.08.23.554527}, url = {https://www.biorxiv.org/content/early/2024/04/10/2023.08.23.554527}, author = {Zhiwen Ye and Andrew M Shelton and Jordan R Shaker and Julien M Boussard and Jennifer Colonell and Daniel Birman and Sahar Manavi and Susu Chen and Charlie Windolf and Cole Hurwitz and Tomoyuki Namima and Frederico Pedraja and Shahaf Weiss and Bogdan Raducanu and Torbj{\o}rn Ness and Xiaoxuan Jia and Giulia Mastroberardino and L. Federico Rossi and Matteo Carandini and Michael Hausser and Gaute T Einevoll and Gilles Laurent and Nathaniel B Sawtell and Wyeth Bair and Anitha Pasupathy and Carolina Mora-Lopez and Barun Dutta and Liam Paninski and Joshua H Siegle and Christof Koch and Shawn R Olsen and Timothy D Harris and Nicholas A Steinmetz} } @article {69459, title = {Ultrastructural differences impact cilia shape and external exposure across cell classes in the visual cortex}, journal = {Curr Biol}, year = {2024}, month = {2024 May 13}, abstract = {

A primary cilium is a membrane-bound extension from the cell surface that contains receptors for perceiving and transmitting signals that modulate cell state and activity. Primary cilia in the brain are less accessible than cilia on cultured cells or epithelial tissues because in the brain they protrude into a deep, dense network of glial and neuronal processes. Here, we investigated cilia frequency, internal structure, shape, and position in large, high-resolution transmission electron microscopy volumes of mouse primary visual cortex. Cilia extended from the cell bodies of nearly all excitatory and inhibitory neurons, astrocytes, and oligodendrocyte precursor cells (OPCs) but were absent from oligodendrocytes and microglia. Ultrastructural comparisons revealed that the base of the cilium and the microtubule organization differed between neurons and glia. Investigating cilia-proximal features revealed that many cilia were directly adjacent to synapses, suggesting that cilia are poised to encounter locally released signaling molecules. Our analysis indicated that synapse proximity is likely due to random encounters in the neuropil, with no evidence that cilia modulate synapse activity as would be expected in tetrapartite synapses. The observed cell class differences in proximity to synapses were largely due to differences in external cilia length. Many key structural features that differed between neuronal and glial cilia influenced both cilium placement and shape and, thus, exposure to processes and synapses outside the cilium. Together, the ultrastructure both within and around neuronal and glial cilia suggest differences in cilia formation and function across cell types in the brain.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2024.04.043}, author = {Ott, Carolyn M and Torres, Russel and Kuan, Tung-Sheng and Kuan, Aaron and Buchanan, JoAnn and Elabbady, Leila and Seshamani, Sharmishtaa and Bodor, Agnes L and Collman, Forrest and Bock, Davi D and Lee, Wei Chung and da Costa, Nuno Ma{\c c}arico and Lippincott-Schwartz, Jennifer} } @inbook {69316, title = {Visualization of Glutamatergic Neurotransmission in Diverse Model Organisms with Genetically Encoded Indicators}, booktitle = {New Technologies for Glutamate Interaction: Neurons and Glia}, volume = {2780}, number = {Neuromethods}, year = {2024}, pages = {3{\textendash}34}, publisher = {Humana}, organization = {Humana}, address = {New York, NY}, abstract = {

Glutamate is the principal excitatory neurotransmitter, and occasionally subserves inhibitory roles, in the vertebrate nervous system. Glutamatergic synapses are dense in the vertebrate brain, at \textasciitilde1/μm3. Glutamate is released from and onto diverse components of the nervous system, including neurons, glia, and other cells. Methods for glutamate detection are critically important for understanding the function of synapses and neural circuits in normal physiology, development, and disease. Here we describe the development, optimization, and deployment of genetically encoded fluorescent glutamate indicators. We review the theoretical considerations governing glutamate sensor properties from first principles of synapse biology, microscopy, and protein structure-function relationships. We provide case studies of the state-of-the-art iGluSnFR glutamate sensor, encompassing design and optimization, mechanism of action, in vivo imaging, data analysis, and future directions. We include detailed protocols for iGluSnFR imaging in common preparations (bacteria, cell culture, and brain slices) and model organisms (worm, fly, fish, rodent).

}, isbn = {978-1-0716-3742-5}, doi = {10.1007/978-1-0716-3742-5_1}, url = {https://doi.org/10.1007/978-1-0716-3742-5_1}, author = {Aggarwal, Abhi and Chan, Joyce and Waring, Amelia K. and Negrean, Adrian and Marvin, Jonathan S. and Podgorski, Kaspar and Looger, Loren L.}, editor = {Kukley, Maria} } @article {69679, title = {Whole-body simulation of realistic fruit fly locomotion with deep reinforcement learning}, journal = {bioRxiv}, year = {2024}, month = {2024 Nov 22}, abstract = {

The body of an animal influences how the nervous system produces behavior. Therefore, detailed modeling of the neural control of sensorimotor behavior requires a detailed model of the body. Here we contribute an anatomically-detailed biomechanical whole-body model of the fruit fly Drosophila melanogaster in the MuJoCo physics engine. Our model is general-purpose, enabling the simulation of diverse fly behaviors, both on land and in the air. We demonstrate the generality of our model by simulating realistic locomotion, both flight and walking. To support these behaviors, we have extended MuJoCo with phenomenological models of fluid forces and adhesion forces. Through data-driven end-to-end reinforcement learning, we demonstrate that these advances enable the training of neural network controllers capable of realistic locomotion along complex trajectories based on high-level steering control signals. We demonstrate the use of visual sensors and the re-use of a pre-trained general-purpose flight controller by training the model to perform visually guided flight tasks. Our project is an open-source platform for modeling neural control of sensorimotor behavior in an embodied context.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2024.03.11.584515}, url = {https://www.biorxiv.org/content/early/2024/11/22/2024.03.11.584515}, author = {Vaxenburg, Roman and Siwanowicz, Igor and Merel, Josh and Robie, Alice A. and Morrow, Carmen and Novati, Guido and Stefanidi, Zinovia and Both, Gert-Jan and Card, Gwyneth M. and Reiser, Michael B. and Botvinick, Matthew M. and Branson, Kristin M. and Tassa, Yuval and Turaga, Srinivas C.} } @article {69634, title = {Why do we have so many excitatory neurons?}, journal = {bioRxiv}, year = {2024}, month = {2024 Oct 05}, abstract = {

Approximately four in five neurons are excitatory. This is true across functional regions and species. Why do we have so many excitatory neurons? Little is known. Here we provide a normative answer to this question. We designed a task-agnostic, learning-independent and experiment-testable measurement of functional complexity, which quantifies the network{\textquoteright}s ability to solve complex problems. Using the larval Drosophila whole-brain electron microscopy connectome, we discovered the optimal Excitatory-Inhibitory (E-I) ratio that maximizes the functional complexity: 75-81\% percentage of neurons are excitatory. This number is consistent with the true distribution observed via scRNA-seq. We found that the abundance of excitatory neurons confers an advantage in functional complexity, but only when inhibitory neurons are highly connected. In contrast, when the E-I identities are sampled uniformly (not dependent on connectivity), the optimal E-I ratio falls around equal population size, and its overall achieved functional complexity is sub-optimal. Our functional complexity measurement offers a normative explanation for the over-abundance of excitatory neurons in the brain. We anticipate that this approach will further uncover the functional significance of various neural network structures.

}, doi = {10.1101/2024.09.24.614724}, url = {https://doi.org/10.1101/2024.09.24.614724}, author = {Wang, Qingyang and Cardona, Albert and Zlatic, Marta and Vogelstein, Joshua T. and Priebe, Carey E.} } @article {69667, title = {Wireless recordings from dragonfly target detecting neurons during prey interception flight}, journal = {bioRxiv}, year = {2024}, month = {2024 Nov 13}, abstract = {

Target interception is a complex sensorimotor behavior which requires fine tuning of the sensory system and its strategic coordination with the motor system. Despite various theories about how interception is achieved, its neural implementation remains unknown. We have previously shown that hunting dragonflies employ a balance of reactive and predictive control to intercept prey, using sophisticated model driven predictions to account for expected prey and self-motion. Here we explore the neural substrate of this interception system by investigating a well-known class of target-selective descending neurons (TSDNs). These cells have long been speculated to underlie interception steering but have never been studied in a behaving dragonfly. We combined detailed neuroanatomy, high-precision kinematics data and state-of-the-art neural telemetry to measure TSDN activity during flight. We found that TSDNs are exquisitely tuned to prey angular size and speed at ethological distances, and that they synapse directly onto neck and wing motoneurons in an unusual manner. However, we found that TSDNs were only weakly active during flight and are thus unlikely to provide the primary steering signal. Instead, they appear to drive the foveating head movements that stabilize prey on the eye before and likely throughout the interception flight. We suggest the TSDN population implements the reactive portion of the interception steering control system, coordinating head and wing movements to compensate for unexpected prey motion.

}, doi = {10.1101/2024.11.12.622977}, url = {https://doi.org/10.1101/2024.11.12.622977}, author = {Lin, Huai-Ti and Siwanowicz, Igor and Leonardo, Anthony} } @article {69421, title = {YAP condensates are highly organized hubs}, journal = {iScience}, year = {2024}, month = {2024 May 07}, pages = {109927}, abstract = {

YAP/TEAD signaling is essential for organismal development, cell proliferation, and cancer progression. As a transcriptional coactivator, how YAP activates its downstream target genes is incompletely understood. YAP forms biomolecular condensates in response to hyperosmotic stress, concentrating transcription-related factors to activate downstream target genes. However, whether YAP forms condensates under other signals, how YAP condensates organize and function, and how YAP condensates activate transcription in general are unknown. Here, we report that endogenous YAP forms sub-micron scale condensates in response to Hippo pathway regulation and actin cytoskeletal tension. YAP condensates are stabilized by the transcription factor TEAD1, and recruit BRD4, a coactivator that is enriched at active enhancers. Using single-particle tracking, we found that YAP condensates slowed YAP diffusion within condensate boundaries, a possible mechanism for promoting YAP target search. These results reveal that YAP condensate formation is a highly regulated process that is critical for YAP/TEAD target gene expression.

}, issn = {2589-0042}, doi = {https://doi.org/10.1016/j.isci.2024.109927}, url = {https://www.sciencedirect.com/science/article/pii/S2589004224011490}, author = {Siyuan Hao and Ye Jin Lee and Nadav Benhamou Goldfajn and Eduardo Flores and Jindayi Liang and Hannah Fuehrer and Justin Demmerle and Jennifer Lippincott-Schwartz and Zhe Liu and Shahar Sukenik and Danfeng Cai} } @article {68698, title = {3D architecture and a bi-cellular mechanism of touch detection in mechanosensory corpuscle}, journal = {Science Advances}, volume = {9}, year = {2023}, month = {2023 Sep 15}, pages = {eadi4147}, abstract = {

Mechanosensory corpuscles detect transient touch and vibratory signals in the skin of vertebrates, enabling navigation, foraging, and precise manipulation of objects1. The corpuscle core comprises a terminal neurite of a mechanoreceptor afferent, the only known touch-sensing element within corpuscles, surrounded by terminal Schwann cells called lamellar cells (LCs)2{\textendash}4. However, the precise corpuscular ultrastructure, and the role of LCs in touch detection are unknown. Here we used enhanced focused ion beam scanning electron microscopy and electron tomography to reveal the three-dimensional architecture of avian Meissner (Grandry) corpuscle5. We show that corpuscles contain a stack of LCs innervated by two afferents, which form large-area contacts with LCs. LCs form tether-like connections with the afferent membrane and contain dense core vesicles which release their content onto the afferent. Furthermore, by performing simultaneous electrophysiological recordings from both cell types, we show that mechanosensitive LCs use calcium influx to trigger action potential firing in the afferent and thus serve as physiological touch sensors in the skin. Our findings suggest a bi-cellular mechanism of touch detection, which comprises the afferent and LCs, likely enables corpuscles to encode the nuances of tactile stimuli.

}, doi = {10.1126/sciadv.adi4147}, url = {https://doi.org/10.1126/sciadv.adi4147}, author = {Yury A. Nikolaev and Luke H. Ziolkowski and Song Pang and Wei-Ping Li and Viktor V. Feketa and C. Shan Xu and Elena O. Gracheva and Sviatoslav N. Bagriantsev} } @article {68519, title = {ACC neural ensemble dynamics are structured by strategy prevalence}, journal = {eLife}, year = {2023}, month = {2023 Nov 22}, abstract = {

Medial frontal cortical areas are thought to play a critical role in the brain{\textquoteright}s ability to flexibly deploy strategies that are effective in complex settings. Still, the specific circuit computations that underpin this foundational aspect of intelligence remain unclear. Here, by examining neural ensemble activity in rats that sample different strategies in a self-guided search for latent task structure, we demonstrate a robust tracking of individual strategy prevalence in the anterior cingulate cortex (ACC), especially in an area homologous to primate area 32D. Prevalence encoding in the ACC is wide-scale, independent of reward delivery, and persists through a substantial ensemble reorganization that tags ACC representations with contextual content. Our findings argue that ACC ensemble dynamics is structured by a summary statistic of recent behavioral choices, raising the possibility that ACC plays a role in estimating - through statistical learning - which actions promote the occurrence of events in the environment.

}, doi = {10.7554/eLife.84897}, url = {https://doi.org/10.7554/eLife.84897}, author = {Mikhail Proskurin and Maxim Manakov and Alla Y. Karpova} } @article {68967, title = {All-optical reporting of chloride ion driving force in the nervous system}, journal = {bioRxiv}, year = {2023}, month = {2023 Sep 01}, abstract = {

Ionic driving forces provide the net electromotive force for ion movement across membranes and are therefore a fundamental property of all cells. In the nervous system, chloride driving force (DFCl) determines inhibitory signaling, as fast synaptic inhibition is mediated by chloride-permeable GABAA\ and glycine receptors. Here we present a new tool for all-Optical Reporting of CHloride Ion Driving force (ORCHID). We demonstrate ORCHID{\textquoteright}s ability to provide accurate, high-throughput measurements of resting and dynamic DFCl\ from genetically targeted cell types over a range of timescales. ORCHID confirms theoretical predictions about the biophysical mechanisms that establish DFCl, reveals novel differences in DFCl\ between neurons and astrocytes under different network conditions, and affords the first\ in vivo\ measurements of intact DFCl\ in mouse cortical neurons. This work extends our understanding of chloride homeostasis and inhibitory synaptic transmission and establishes a precedent for utilizing all-optical methods to assess ionic driving force.

}, doi = {10.1101/2023.08.30.555464}, url = {https://doi.org/10.1101/2023.08.30.555464}, author = {Joshua S. Selfe and Teresa J. S. Steyn and Eran F. Shorer and Richard J. Burman and Kira M. D{\"u}sterwald and Ahmed S. Abdelfattah and Eric R. Schreiter and Sarah E. Newey and Colin J. Akerman and Joseph V. Raimondo} } @article {69090, title = {All-optical reporting of inhibitory receptor driving force in the nervous system.}, journal = {bioRxiv}, year = {2023}, month = {2023 Nov 20}, abstract = {

Ionic driving forces provide the net electromotive force for ion movement across receptors, channels, and transporters, and are a fundamental property of all cells. In the brain for example, fast synaptic inhibition is mediated by chloride permeable GABAA receptors, and single-cell intracellular recordings have been the only method for estimating driving forces across these receptors (DFGABAA). Here we present a new tool for quantifying inhibitory receptor driving force named ORCHID: all-Optical Reporting of CHloride Ion Driving force. We demonstrate ORCHID{\textquoteright}s ability to provide accurate, high-throughput measurements of resting and dynamic DFGABAA from genetically targeted cell types over multiple timescales. ORCHID confirms theoretical predictions about the biophysical mechanisms that establish DFGABAA, reveals novel differences in DFGABAA between neurons and astrocytes, and affords the first\ in vivo\ measurements of intact DFGABAA. This work extends our understanding of inhibitory synaptic transmission and establishes a precedent for all-optical methods to assess ionic driving forces.

}, doi = {10.1101/2023.08.30.555464}, url = {https://doi.org/10.1101/2023.08.30.555464}, author = {Joshua S. Selfe and Teresa J. S. Steyn and Eran F. Shorer and Richard J. Burman and Kira M. D{\"u}sterwald and Ahmed S. Abdelfattah and Eric R. Schreiter and Sarah E. Newey and Colin J. Akerman and Joseph V. Raimondo} } @article {69137, title = {Anatomically distributed neural representations of instincts in the hypothalamus.}, journal = {bioRxiv}, year = {2023}, month = {2023 Dec 07}, abstract = {

Artificial activation of anatomically localized, genetically defined hypothalamic neuron populations is known to trigger distinct innate behaviors, suggesting a hypothalamic nucleus-centered organization of behavior control. To assess whether the encoding of behavior is similarly anatomically confined, we performed simultaneous neuron recordings across twenty hypothalamic regions in freely moving animals. Here we show that distinct but anatomically distributed neuron ensembles encode the social and fear behavior classes, primarily through mixed selectivity. While behavior class-encoding ensembles were spatially distributed, individual ensembles exhibited strong localization bias. Encoding models identified that behavior actions, but not motion-related variables, explained a large fraction of hypothalamic neuron activity variance. These results identify unexpected complexity in the hypothalamic encoding of instincts and provide a foundation for understanding the role of distributed neural representations in the expression of behaviors driven by hardwired circuits.

}, doi = {10.1101/2023.11.21.568163}, url = {https://doi.org/10.1101/2023.11.21.568163}, author = {Stagkourakis, Stefanos and Spigolon, Giada and Marks, Markus and Feyder, Michael and Kim, Joseph and Perona, Pietro and Pachitariu, Marius and Anderson, David J} } @article {68807, title = {Architecture and dynamics of a desmosome-endoplasmic reticulum complex.}, journal = {Nature Cell Biology}, volume = {25}, year = {2023}, month = {2023 Jun 16}, pages = {823-835}, abstract = {

The endoplasmic reticulum (ER) forms a dynamic network that contacts other cellular membranes to regulate stress responses, calcium signalling and lipid transfer. Here, using high-resolution volume electron microscopy, we find that the ER forms a previously unknown association with keratin intermediate filaments and desmosomal cell-cell junctions. Peripheral ER assembles into mirror image-like arrangements at desmosomes and exhibits nanometre proximity to keratin filaments and the desmosome cytoplasmic plaque. ER tubules exhibit stable associations with desmosomes, and perturbation of desmosomes or keratin filaments alters ER organization, mobility and expression of ER stress transcripts. These findings indicate that desmosomes and the keratin cytoskeleton regulate the distribution, function and dynamics of the ER network. Overall, this study reveals a previously unknown subcellular architecture defined by the structural integration of ER tubules with an epithelial intercellular junction.

}, keywords = {Cytoskeleton, Desmosomes, Endoplasmic Reticulum, Intermediate Filaments, Keratins}, issn = {1476-4679}, doi = {10.1038/s41556-023-01154-4}, author = {Bharathan, Navaneetha Krishnan and Giang, William and Hoffman, Coryn L and Aaron, Jesse S and Khuon, Satya and Chew, Teng-Leong and Preibisch, Stephan and Trautman, Eric T and Heinrich, Larissa and Bogovic, John and Bennett, Davis and Ackerman, David and Park, Woohyun and Petruncio, Alyson and Weigel, Aubrey V and Saalfeld, Stephan and Wayne Vogl, A and Stahley, Sara N and Kowalczyk, Andrew P} } @article {67907, title = {Ascending neurons convey behavioral state to integrative sensory and action selection centers in the brain}, journal = {Nature Neuroscience}, year = {2023}, month = {2023 Mar 31}, abstract = {

Knowledge of one{\textquoteright}s own behavioral state{\textemdash}whether one is walking, grooming, or resting{\textemdash}is critical for contextualizing sensory cues including interpreting visual motion and tracking odor sources. Additionally, awareness of one{\textquoteright}s own posture is important to avoid initiating destabilizing or physically impossible actions. Ascending neurons (ANs), interneurons in the vertebrate spinal cord or insect ventral nerve cord (VNC) that project to the brain, may provide such high-fidelity behavioral state signals. However, little is known about what ANs encode and where they convey signals in any brain. To address this gap, we performed a large-scale functional screen of AN movement encoding, brain targeting, and motor system patterning in the adult fly,\ Drosophila melanogaster. Using a new library of AN sparse driver lines, we measured the functional properties of 247 genetically-identifiable ANs by performing two-photon microscopy recordings of neural activity in tethered, behaving flies. Quantitative, deep network-based neural and behavioral analyses revealed that ANs nearly exclusively encode high-level behaviors{\textemdash}primarily walking as well as resting and grooming{\textemdash}rather than low-level joint or limb movements. ANs that convey self-motion{\textemdash}resting, walking, and responses to gust-like puff stimuli{\textemdash}project to the brain{\textquoteright}s anterior ventrolateral protocerebrum (AVLP), a multimodal, integrative sensory hub, while those that encode discrete actions{\textemdash}eye grooming, turning, and proboscis extension{\textemdash}project to the brain{\textquoteright}s gnathal ganglion (GNG), a locus for action selection. The structure and polarity of AN projections within the VNC are predictive of their functional encoding and imply that ANs participate in motor computations while also relaying state signals to the brain. Illustrative of this are ANs that temporally integrate proboscis extensions over tens-of-seconds, likely through recurrent interconnectivity. Thus, in line with long-held theoretical predictions, ascending populations convey high-level behavioral state signals almost exclusively to brain regions implicated in sensory feature contextualization and action selection.

}, doi = {10.1038/s41593-023-01281-z}, author = {Chin-Lin Chen and Florian Aymanns and Ryo Minegishi and Victor D. V. Matsuda and Nicolas Talabot and Semih G{\"u}nel and Barry J. Dickson and Pavan Ramdya} } @article {68587, title = {Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations.}, journal = {Nature Biotechnology}, volume = {41}, year = {2023}, month = {2023 Jan 01}, pages = {44-49}, abstract = {

We present a method to automatically identify and track nuclei in time-lapse microscopy recordings of entire developing embryos. The method combines deep learning and global optimization. On a mouse dataset, it reconstructs 75.8\% of cell lineages spanning 1 h, as compared to 31.8\% for the competing method. Our approach improves understanding of where and when cell fate decisions are made in developing embryos, tissues, and organs.

}, keywords = {Animals, Blastocyst, Cell Lineage, Embryo, Mammalian, Mice, Microscopy}, issn = {1546-1696}, doi = {10.1038/s41587-022-01427-7}, author = {Malin-Mayor, Caroline and Hirsch, Peter and Guignard, Leo and McDole, Katie and Wan, Yinan and Lemon, William C and Kainmueller, Dagmar and Keller, Philipp J and Preibisch, Stephan and Funke, Jan} } @article {68787, title = {Autophagy receptor NDP52 alters DNA conformation to modulate RNA polymerase II transcription.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 May 18}, pages = {2855}, abstract = {

NDP52 is an autophagy receptor involved in the recognition and degradation of invading pathogens and damaged organelles. Although NDP52 was first identified in the nucleus and is expressed throughout the cell, to date, there is no clear nuclear functions for NDP52. Here, we use a multidisciplinary approach to characterise the biochemical properties and nuclear roles of NDP52. We find that NDP52 clusters with RNA Polymerase II (RNAPII) at transcription initiation sites and that its overexpression promotes the formation of additional transcriptional clusters. We also show that depletion of NDP52 impacts overall gene expression levels in two model mammalian cells, and that transcription inhibition affects the spatial organisation and molecular dynamics of NDP52 in the nucleus. This directly links NDP52 to a role in RNAPII-dependent transcription. Furthermore, we also show that NDP52 binds specifically and with high affinity to double-stranded DNA (dsDNA) and that this interaction leads to changes in DNA structure in vitro. This, together with our proteomics data indicating enrichment for interactions with nucleosome remodelling proteins and DNA structure regulators, suggests a possible function for NDP52 in chromatin regulation. Overall, here we uncover nuclear roles for NDP52 in gene expression and DNA structure regulation.

}, keywords = {Animals, Autophagy, DNA, Mammals, Nuclear Proteins, Nucleic Acid Conformation, RNA Polymerase II}, issn = {2041-1723}, doi = {10.1038/s41467-023-38572-9}, author = {Dos Santos, {\'A}lia and Rollins, Daniel E and Hari-Gupta, Yukti and McArthur, Hannah and Du, Mingxue and Ru, Sabrina Yong Zi and Pidlisna, Kseniia and Stranger, Ane and Lorgat, Faeeza and Lambert, Danielle and Brown, Ian and Howland, Kevin and Aaron, Jesse and Wang, Lin and Ellis, Peter J I and Chew, Teng-Leong and Martin-Fernandez, Marisa and Pyne, Alice L B and Toseland, Christopher P} } @article {68565, title = {Behavioral state-dependent modulation of insulin-producing cells in Drosophila.}, journal = {Current Biology}, volume = {33}, year = {2023}, month = {2023 Feb 06}, pages = {449}, abstract = {

Insulin signaling plays a pivotal role in metabolic control and aging, and insulin accordingly is a key factor in several human diseases. Despite this importance, the in\ vivo activity dynamics of insulin-producing cells (IPCs) are poorly understood. Here, we characterized the effects of locomotion on the activity of IPCs in Drosophila. Using in\ vivo electrophysiology and calcium imaging, we found that IPCs were strongly inhibited during walking and flight and that their activity rebounded and overshot after cessation of locomotion. Moreover, IPC activity changed rapidly during behavioral transitions, revealing that IPCs are modulated on fast timescales in behaving animals. Optogenetic activation of locomotor networks ex\ vivo, in the absence of actual locomotion or changes in hemolymph sugar levels, was sufficient to inhibit IPCs. This demonstrates that the behavioral state-dependent inhibition of IPCs is actively controlled by neuronal pathways and is independent of changes in glucose concentration. By contrast, the overshoot in IPC activity after locomotion was absent ex\ vivo and after starvation, indicating that it was not purely driven by feedforward signals but additionally required feedback derived from changes in hemolymph sugar concentration. We hypothesize that IPC inhibition during locomotion supports mobilization of fuel stores during metabolically demanding behaviors, while the rebound in IPC activity after locomotion contributes to replenishing muscle glycogen stores. In addition, the rapid dynamics of IPC modulation support a potential role of insulin in the state-dependent modulation of sensorimotor processing.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2022.12.005}, author = {Liessem, Sander and Held, Martina and Bisen, Rituja S and Haberkern, Hannah and Lacin, Haluk and Bockem{\"u}hl, Till and Ache, Jan M} } @article {68714, title = {The big warp: Registration of disparate retinal imaging modalities and an example overlay of ultrawide-field photos and en-face OCTA images.}, journal = {PLoS One}, volume = {18}, year = {2023}, month = {2023 Apr 25}, pages = {e0284905}, abstract = {

PURPOSE: To develop an algorithm and scripts to combine disparate multimodal imaging modalities and show its use by overlaying en-face optical coherence tomography angiography (OCTA) images and Optos ultra-widefield (UWF) retinal images using the Fiji (ImageJ) plugin BigWarp.

METHODS: Optos UWF images and Heidelberg en-face OCTA images were collected from various patients as part of their routine care. En-face OCTA images were generated and ten (10) images at varying retinal depths were exported. The Fiji plugin BigWarp was used to transform the Optos UWF image onto the en-face OCTA image using matching reference points in the retinal vasculature surrounding the macula. The images were then overlayed and stacked to create a series of ten combined Optos UWF and en-face OCTA images of increasing retinal depths. The first algorithm was modified to include two scripts that automatically aligned all the en-face OCTA images.

RESULTS: The Optos UWF image could easily be transformed to the en-face OCTA images using BigWarp with common vessel branch point landmarks in the vasculature. The resulting warped Optos image was then successfully superimposed onto the ten Optos UWF images. The scripts more easily allowed for automatic overlay of the images.

CONCLUSIONS: Optos UWF images can be successfully superimposed onto en-face OCTA images using freely available software that has been applied to ocular use. This synthesis of multimodal imaging may increase their potential diagnostic value. Script A is publicly available at https://doi.org/10.6084/m9.figshare.16879591.v1 and Script B is available at https://doi.org/10.6084/m9.figshare.17330048.

}, keywords = {Fluorescein Angiography, Fundus Oculi, Humans, Retina, Retinal Vessels, Tomography, Optical Coherence}, issn = {1932-6203}, doi = {10.1371/journal.pone.0284905}, author = {Thuma, Tobin B T and Bogovic, John A and Gunton, Kammi B and Jimenez, Hiram and Negreiros, Bernardo and Pulido, Jose S} } @article {68709, title = {BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets.}, journal = {Nature Methods}, volume = {20}, year = {2023}, month = {2023 Jun 01}, abstract = {

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

}, issn = {1548-7105}, doi = {10.1038/s41592-023-01848-5}, author = {Manubens-Gil, Linus and Zhou, Zhi and Chen, Hanbo and Ramanathan, Arvind and Liu, Xiaoxiao and Liu, Yufeng and Bria, Alessandro and Gillette, Todd and Ruan, Zongcai and Yang, Jian and Radojevi{\'c}, Miroslav and Zhao, Ting and Cheng, Li and Qu, Lei and Liu, Siqi and Bouchard, Kristofer E and Gu, Lin and Cai, Weidong and Ji, Shuiwang and Roysam, Badrinath and Wang, Ching-Wei and Yu, Hongchuan and Sironi, Amos and Iascone, Daniel Maxim and Zhou, Jie and Bas, Erhan and Conde-Sousa, Eduardo and Aguiar, Paulo and Li, Xiang and Li, Yujie and Nanda, Sumit and Wang, Yuan and Muresan, Leila and Fua, Pascal and Ye, Bing and He, Hai-Yan and Staiger, Jochen F and Peter, Manuel and Cox, Daniel N and Simonneau, Michel and Oberlaender, Marcel and Jefferis, Gregory and Ito, Kei and Gonzalez-Bellido, Paloma and Kim, Jinhyun and Rubel, Edwin and Cline, Hollis T and Zeng, Hongkui and Nern, Aljoscha and Chiang, Ann-Shyn and Yao, Jianhua and Roskams, Jane and Livesey, Rick and Stevens, Janine and Liu, Tianming and Dang, Chinh and Guo, Yike and Zhong, Ning and Tourassi, Georgia and Hill, Sean and Hawrylycz, Michael and Koch, Christof and Meijering, Erik and Ascoli, Giorgio A and Peng, Hanchuan} } @article {68933, title = {Biomechanical origins of proprioceptor feature selectivity and topographic maps in the Drosophila leg.}, journal = {Neuron}, year = {2023}, month = {2023 Aug 04}, abstract = {

Our ability to sense and move our bodies relies on proprioceptors, sensory neurons that detect mechanical forces within the body. Different subtypes of proprioceptors detect different kinematic features, such as joint position, movement, and vibration, but the mechanisms that underlie proprioceptor feature selectivity remain poorly understood. Using single-nucleus RNA sequencing (RNA-seq), we found that proprioceptor subtypes in the Drosophila leg lack differential expression of mechanosensitive ion channels. However, anatomical reconstruction of the proprioceptors and connected tendons revealed major biomechanical differences between subtypes. We built a model of the proprioceptors and tendons that identified a biomechanical mechanism for joint angle selectivity and predicted the existence of a topographic map of joint angle, which we confirmed using calcium imaging. Our findings suggest that biomechanical specialization is a key determinant of proprioceptor feature selectivity in Drosophila. More broadly, the discovery of proprioceptive maps reveals common organizational principles between proprioception and other topographically organized sensory systems.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2023.07.009}, author = {Mamiya, Akira and Sustar, Anne and Siwanowicz, Igor and Qi, Yanyan and Lu, Tzu-Chiao and Gurung, Pralaksha and Chen, Chenghao and Phelps, Jasper S and Kuan, Aaron T and Pacureanu, Alexandra and Lee, Wei-Chung Allen and Li, Hongjie and Mhatre, Natasha and Tuthill, John C} } @article {68964, title = {Brain wiring determinants uncovered by integrating connectomes and transcriptomes.}, journal = {Current Biology}, volume = {33}, year = {2023}, month = {2023 Aug 23}, pages = {3998-3998}, abstract = {

Advances in brain connectomics have demonstrated the extraordinary complexity of neural circuits. Developing neurons encounter the axons and dendrites of many different neuron types and form synapses with only a subset of them. During circuit assembly, neurons express cell-type-specific repertoires comprising many cell adhesion molecules (CAMs) that can mediate interactions between developing neurites. Many CAM families have been shown to contribute to brain wiring in different ways. It has been challenging, however, to identify receptor-ligand pairs directly matching neurons with their synaptic targets. Here, we integrated the synapse-level connectome of the neural circuit with the developmental expression patterns and binding specificities of CAMs on pre- and postsynaptic neurons in the Drosophila visual system. To overcome the complexity of neural circuits, we focus on pairs of genetically related neurons that make differential wiring choices. In the motion detection circuit, closely related subtypes of T4/T5 neurons choose between alternative synaptic targets in adjacent layers of neuropil. This choice correlates with the matching expression in synaptic partners of different receptor-ligand pairs of the Beat and Side families of CAMs. Genetic analysis demonstrated that presynaptic Side-II and postsynaptic Beat-VI restrict synaptic partners to the same layer. Removal of this receptor-ligand pair disrupts layers and leads to inappropriate targeting of presynaptic sites and postsynaptic dendrites. We propose that different Side/Beat receptor-ligand pairs collaborate with other recognition molecules to determine wiring specificities in the fly brain. Combining transcriptomes, connectomes, and protein interactome maps allow unbiased identification of determinants of brain wiring.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2023.08.020}, author = {Yoo, Juyoun and Dombrovski, Mark and Mirshahidi, Parmis and Nern, Aljoscha and LoCascio, Samuel A and Zipursky, S Lawrence and Kurmangaliyev, Yerbol Z} } @article {68647, title = {Brain-wide neural activity underlying memory-guided movement}, journal = {bioRxiv}, year = {2023}, month = {2023 Mar 02}, abstract = {

Behavior requires neural activity across the brain, but most experiments probe neurons in a single area at a time. Here we used multiple Neuropixels probes to record neural activity simultaneously in brain-wide circuits, in mice performing a memory-guided directional licking task. We targeted brain areas that form multi-regional loops with anterior lateral motor cortex (ALM), a key circuit node mediating the behavior. Neurons encoding sensory stimuli, choice, and actions were distributed across the brain. However, in addition to ALM, coding of choice was concentrated in subcortical areas receiving input from ALM, in an ALM-dependent manner. Choice signals were first detected in ALM and the midbrain, followed by the thalamus, and other brain areas. At the time of movement initiation, choice-selective activity collapsed across the brain, followed by new activity patterns driving specific actions. Our experiments provide the foundation for neural circuit models of decision-making and movement initiation.

}, doi = {10.1101/2023.03.01.530520}, url = {https://doi.org/10.1101/2023.03.01.530520}, author = {Susu Chen and Yi Liu and Ziyue Wang and Jennifer Colonell and Liu D. Liu and Han Hou and Nai-Wen Tien and Tim Wang and Timothy Harris and Shaul Druckmann and Nuo Li and Karel Svoboda} } @article {68808, title = {Cell type-specific contributions to a persistent aggressive internal state in female Drosophila}, journal = {bioRxiv}, year = {2023}, month = {2023 Jun 07}, abstract = {

Persistent internal states are important for maintaining survival-promoting behaviors, such as aggression. In female\ Drosophila melanogaster, we have previously shown that individually activating either aIPg or pC1d cell types can induce aggression. Here we investigate further the individual roles of these cholinergic, sexually dimorphic cell types, and the reciprocal connections between them, in generating a persistent aggressive internal state. We find that a brief 30-second optogenetic stimulation of aIPg neurons was sufficient to promote an aggressive internal state lasting at least 10 minutes, whereas similar stimulation of pC1d neurons did not. While we previously showed that stimulation of pC1e alone does not evoke aggression, persistent behavior could be promoted through simultaneous stimulation of pC1d and pC1e, suggesting an unexpected synergy of these cell types in establishing a persistent aggressive state. Neither aIPg nor pC1d show persistent neuronal activity themselves, implying that the persistent internal state is maintained by other mechanisms. Moreover, inactivation of pC1d did not significantly reduce aIPg-evoked persistent aggression arguing that the aggressive state did not depend on pC1d-aIPg recurrent connectivity. Our results suggest the need for alternative models to explain persistent female aggression.

}, doi = {10.1101/2023.06.07.543722}, url = {https://doi.org/10.1101/2023.06.07.543722}, author = {Hui Chiu and Alice A. Robie and Kristin M. Branson and Tanvi Vippa and Samantha Epstein and Gerald M. Rubin and David J. Anderson and Catherine E. Schretter} } @article {68931, title = {Cell-type-specific plasticity shapes neocortical dynamics for motor learning}, journal = {bioRxiv}, year = {2023}, month = {2023 Aug 14}, abstract = {

Neocortical spiking dynamics control aspects of behavior, yet how these dynamics emerge during motor learning remains elusive. Activity-dependent synaptic plasticity is likely a key mechanism, as it reconfigures network architectures that govern neural dynamics. Here, we examined how the mouse premotor cortex acquires its well-characterized neural dynamics that control movement timing, specifically lick timing. To probe the role of synaptic plasticity, we have genetically manipulated proteins essential for major forms of synaptic plasticity, Ca2+/calmodulin-dependent protein kinase II (CaMKII) and Cofilin, in a region and cell-type-specific manner. Transient inactivation of CaMKII in the premotor cortex blocked learning of new lick timing without affecting the execution of learned action or ongoing spiking activity. Furthermore, among the major glutamatergic neurons in the premotor cortex, CaMKII and Cofilin activity in pyramidal tract (PT) neurons, but not intratelencephalic (IT) neurons, is necessary for learning. High-density electrophysiology in the premotor cortex uncovered that neural dynamics anticipating licks are progressively shaped during learning, which explains the change in lick timing. Such reconfiguration in behaviorally relevant dynamics is impeded by CaMKII manipulation in PT neurons. Altogether, the activity of plasticity-related proteins in PT neurons plays a central role in sculpting neocortical dynamics to learn new behavior.

}, doi = {10.1101/2023.08.09.552699}, url = {https://doi.org/10.1101/2023.08.09.552699}, author = {Shouvik Majumder and Koichi Hirokawa and Zidan Yang and Ronald Paletzki and Charles R. Gerfen and Lorenzo Fontolan and Sandro Romani and Anant Jain and Ryohei Yasuda and Hidehiko K. Inagaki} } @article {68627, title = {The challenges and opportunities of open-access microscopy facilities.}, journal = {Journal of Microscopy}, year = {2023}, month = {2023 Feb 13}, abstract = {

Microscopy core facilities are increasingly utilized research resources, but they are generally only available to users within the host institution. Such localized access misses an opportunity to facilitate research across a broader user base. Here, we present the model of an open-access microscopy facility, using the Advanced Imaging Center (AIC) at Howard Hughes Medical Institute Janelia Research Campus as an example. The AIC has pioneered a model whereby advanced microscopy technologies and expertise are made accessible to researchers on a global scale. We detail our experiences in addressing the considerable challenges associated with this model for those who may be interested in launching an open-access imaging facility. Importantly, we focus on how this model can empower researchers, particularly those from resource-constrained settings. This article is protected by copyright. All rights reserved.

}, issn = {1365-2818}, doi = {10.1111/jmi.13176}, author = {Cartwright, Heather N and Hobson, Chad M and Chew, Teng-Leong and Reiche, Michael A and Aaron, Jesse S} } @article {68257, title = {Characterization, Comparison, and Optimization of Lattice Light Sheets}, journal = {Science Advances}, year = {2023}, month = {2023 Mar 31}, abstract = {

Lattice light sheet microscopy excels at the non-invasive imaging of three-dimensional (3D) dynamic processes at high spatiotemporal resolution within cells and developing embryos. Recently, several papers have called into question the performance of lattice light sheets relative to the Gaussian sheets most common in light sheet microscopy. Here we undertake a comprehensive theoretical and experimental analysis of various forms of light sheet microscopy which both demonstrates and explains why lattice light sheets provide significant improvements in resolution and photobleaching reduction. The analysis provides a procedure to select the correct light sheet for a desired experiment and specifies the processing that maximizes the use of all fluorescence generated within the light sheet excitation envelope for optimal resolution while minimizing image artifacts and photodamage. Development of a new type of {\textquotedblleft}harmonic balanced{\textquotedblright} lattice light sheet is shown to improve performance at all spatial frequencies within its 3D resolution limits and maintains this performance over lengthened propagation distances allowing for expanded fields of view.

}, doi = {10.1126/sciadv.ade6623}, url = {https://doi.org/10.1126/sciadv.ade6623}, author = {Gaoxiang Liu and Xiongtao Ruan and Daniel E. Milkie and Frederik G{\"o}rlitz and Matthew Mueller and Wilmene Hercule and Alison Kililea and Eric Betzig and Srigokul Upadhyayula} } @article {69041, title = {Ciliary localization of a light-activated neuronal GPCR shapes behavior.}, journal = {Proceedings of the National Academy of Sciences of the USA}, volume = {120}, year = {2023}, month = {2023 Oct 16}, pages = {e2311131120}, abstract = {

Many neurons in the central nervous system produce a single primary cilium that serves as a specialized signaling organelle. Several neuromodulatory G-protein-coupled receptors (GPCRs) localize to primary cilia in neurons, although it is not understood how GPCR signaling from the cilium impacts circuit function and behavior. We find that the vertebrate ancient long opsin A (VALopA), a G-coupled GPCR extraretinal opsin, targets to cilia of zebrafish spinal neurons. In the developing 1-d-old zebrafish, brief light activation of VALopA in neurons of the central pattern generator circuit for locomotion leads to sustained inhibition of coiling, the earliest form of locomotion. We find that a related extraretinal opsin, VALopB, is also G-coupled, but is not targeted to cilia. Light-induced activation of VALopB also suppresses coiling, but with faster kinetics. We identify the ciliary targeting domains of VALopA. Retargeting of both opsins shows that the locomotory response is prolonged and amplified when signaling occurs in the cilium. We propose that ciliary localization provides a mechanism for enhancing GPCR signaling in central neurons.

}, issn = {1091-6490}, doi = {10.1073/pnas.2311131120}, author = {Winans, Amy M and Friedmann, Drew and Stanley, Cherise and Xiao, Tong and Liu, Tsung-Li and Chang, Christopher J and Isacoff, Ehud Y} } @article {68974, title = {Combinatorial circuit dynamics orchestrate flexible motor patterns in Drosophila.}, journal = {bioRxiv}, year = {2023}, month = {2023 Sep 07}, abstract = {

Motor systems flexibly implement diverse motor programs to pattern behavioral sequences, yet their neural underpinnings remain unclear. Here, we investigated the neural circuit mechanisms of flexible courtship behavior in\ Drosophila. Courting males alternately produce two types of courtship song. By recording calcium signals in the ventral nerve cord (VNC) in behaving flies, we found that different songs are produced by activating overlapping neural populations with distinct motor functions in a combinatorial manner. Recordings from the brain suggest that song is driven by two descending pathways {\textendash} one defines when to sing and the other specifies what song to sing. Connectomic analysis reveals that these {\textquotedblleft}when{\textquotedblright} and {\textquotedblleft}what{\textquotedblright} descending pathways provide structured input to VNC neurons with different motor functions. These results suggest that dynamic changes in the activation patterns of descending pathways drive different combinations of motor modules, thereby flexibly switching between different motor actions.

}, doi = {10.1101/2022.12.14.520499}, url = {https://doi.org/10.1101/2022.12.14.520499}, author = {Hiroshi M. Shiozaki and Kaiyu Wang and Joshua L. Lillvis and Min Xu and Barry J. Dickson and David L. Stern} } @article {68805, title = {Comparative connectomics and escape behavior in larvae of closely related Drosophila species.}, journal = {Current Biology}, year = {2023}, month = {2023 May 31}, abstract = {

Evolution has generated an enormous variety of morphological, physiological, and behavioral traits in animals. How do behaviors evolve in different directions in species equipped with similar neurons and molecular components? Here we adopted a comparative approach to investigate the similarities and differences of escape behaviors in response to noxious stimuli and their underlying neural circuits between closely related drosophilid species. Drosophilids show a wide range of escape behaviors in response to noxious cues, including escape crawling, stopping, head casting, and rolling. Here we find that D.\ santomea, compared with its close relative D.\ melanogaster, shows a higher probability of rolling in response to noxious stimulation. To assess whether this behavioral difference could be attributed to differences in neural circuitry, we\ generated focused ion beam-scanning electron microscope volumes of the ventral nerve cord of D.\ santomea to reconstruct the downstream partners of mdIV, a nociceptive sensory neuron in D.\ melanogaster. Along with partner interneurons of mdVI (including Basin-2, a multisensory integration neuron necessary for rolling) previously identified in D.\ melanogaster, we identified two additional partners of mdVI in D.\ santomea. Finally, we showed that joint activation of one of the partners (Basin-1) and a common partner (Basin-2) in D.\ melanogaster increased rolling probability, suggesting that the high rolling probability in D.\ santomea is mediated by the additional activation of Basin-1 by mdIV. These results provide a plausible mechanistic explanation for how closely related species exhibit quantitative differences in the likelihood of expressing the same behavior.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2023.05.043}, author = {Zhu, Jiayi and Boivin, Jean-Christophe and Pang, Song and Xu, C Shan and Lu, Zhiyuan and Saalfeld, Stephan and Hess, Harald F and Ohyama, Tomoko} } @article {69018, title = {Complete human day 14 post-implantation embryo models from na{\"\i}ve ES cells}, journal = {Nature}, year = {2023}, month = {09/2023}, abstract = {

The ability to study human post-implantation development remains limited due to ethical and technical challenges associated with intrauterine development after implantation1. Embryo-like models with spatially organized morphogenesis of all defining embryonic and extra-embryonic tissues of the post-implantation human conceptus (i.e., embryonic disk, bilaminar disk, yolk- and chorionic sacs, surrounding trophoblasts) remain lacking2. Mouse na{\"\i}ve embryonic stem cells (ESCs) have recently been shown to give rise to embryonic and extra-embryonic stem cells capable of self-assembling into post-gastrulation mouse Structured Stem cell-based Embryo Models with spatially organized morphogenesis (SEMs)3. Here, we extend these findings to humans, while using only genetically unmodified human na{\"\i}ve ESCs (in HENSM conditions)4. Such human fully integrated SEMs recapitulate the organization of nearly all known lineages and compartments of post-implantation human embryos including epiblast, hypoblast, extra-embryonic mesoderm, and trophoblast surrounding the latter layers. These human complete SEMs demonstrated developmental growth dynamics that resemble key hallmarks of post-implantation stage embryogenesis up to 13-14 days post-fertilization (dpf) (Carnegie stage 6a). This includes embryonic disk and bilaminar disk formation, epiblast lumenogenesis, polarized amniogenesis, anterior-posterior symmetry breaking, PGC specification, polarized yolk sac with visceral and parietal endoderm, extra-embryonic mesoderm expansion that defines a chorionic cavity and a connecting stalk, a trophoblast surrounding compartment demonstrating syncytium and lacunae formation. This SEM platform may enable the experimental interrogation of previously inaccessible windows of human early post-implantation up to peri-gastrulation development.

}, issn = {0028-0836}, doi = {10.1038/s41586-023-06604-5}, url = {https://www.nature.com/articles/s41586-023-06604-5https://www.nature.com/articles/s41586-023-06604-5.pdfhttps://www.nature.com/articles/s41586-023-06604-5.pdfhttps://www.nature.com/articles/s41586-023-06604-5}, author = {Oldak, Bernardo and Wildschutz, Emilie and Bondarenko, Vladyslav and Comar, Mehmet-Yunus and Zhao, Cheng and Aguilera-Castrejon, Alejandro and Tarazi, Shadi and Viukov, Sergey and Pham, Thi Xuan Ai and Ashouokhi, Shahd and Lokshtanov, Dmitry and Roncato, Francesco and Ariel, Eitan and Rose, Max and Livnat, Nir and Shani, Tom and Joubran, Carine and Cohen, Roni and Addadi, Yoseph and Chemla, Muriel and Kedmi, Merav and Keren-Shaul, Hadas and Pasque, Vincent and Petropoulos, Sophie and Lanner, Fredrik and Novershtern, Noa and Hanna, Jacob H.} } @article {69022, title = {A complete reconstruction of the early visual system of an adult insect.}, journal = {Current Biology}, volume = {33}, year = {2023}, month = {2023 Nov 06}, pages = {4611-4623}, abstract = {

For most model organisms in neuroscience, research into visual processing in the brain is difficult because of a lack of high-resolution maps that capture complex neuronal circuitry. The microinsect Megaphragma viggianii, because of its small size and non-trivial behavior, provides a unique opportunity for tractable whole-organism connectomics. We image its whole head using serial electron microscopy. We reconstruct its compound eye and analyze the optical properties of the ommatidia as well as the connectome of the first visual neuropil-the lamina. Compared with the fruit fly and the honeybee, Megaphragma visual system is highly simplified: it has 29 ommatidia per eye and 6 lamina neuron types. We report features that are both stereotypical among most ommatidia and specialized to some. By identifying the "barebones" circuits critical for flying insects, our results will facilitate constructing computational models of visual processing in insects.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2023.09.021}, author = {Chua, Nicholas J and Makarova, Anastasia A and Gunn, Pat and Villani, Sonia and Cohen, Ben and Thasin, Myisha and Wu, Jingpeng and Shefter, Deena and Pang, Song and Xu, C Shan and Hess, Harald F and Polilov, Alexey A and Chklovskii, Dmitri B} } @article {69039, title = {A comprehensive neuroanatomical survey of the Drosophila Lobula Plate Tangential Neurons with predictions for their optic flow sensitivity.}, journal = {bioRxiv}, year = {2023}, month = {2023 Oct 17}, abstract = {

Flying insects exhibit remarkable navigational abilities controlled by their compact nervous systems. Optic flow, the pattern of changes in the visual scene induced by locomotion, is a crucial sensory cue for robust self-motion estimation, especially during rapid flight. Neurons that respond to specific, large-field optic flow patterns have been studied for decades, primarily in large flies, such as houseflies, blowflies, and hover flies. The best-known optic-flow sensitive neurons are the large tangential cells of the dipteran lobula plate, whose visual-motion responses, and to a lesser extent, their morphology, have been explored using single-neuron neurophysiology. Most of these studies have focused on the large, Horizontal and Vertical System neurons, yet the lobula plate houses a much larger set of {\textquoteright}optic-flow{\textquoteright} sensitive neurons, many of which have been challenging to unambiguously identify or to reliably target for functional studies. Here we report the comprehensive reconstruction and identification of the Lobula Plate Tangential Neurons in an Electron Microscopy (EM) volume of a whole Drosophila brain. This catalog of 58 LPT neurons (per brain hemisphere) contains many neurons that are described here for the first time and provides a basis for systematic investigation of the circuitry linking self-motion to locomotion control. Leveraging computational anatomy methods, we estimated the visual motion receptive fields of these neurons and compared their tuning to the visual consequence of body rotations and translational movements. We also matched these neurons, in most cases on a one-for-one basis, to stochastically labeled cells in genetic driver lines, to the mirror-symmetric neurons in the same EM brain volume, and to neurons in an additional EM data set. Using cell matches across data sets, we analyzed the integration of optic flow patterns by neurons downstream of the LPTs and find that most central brain neurons establish sharper selectivity for global optic flow patterns than their input neurons. Furthermore, we found that self-motion information extracted from optic flow is processed in distinct regions of the central brain, pointing to diverse foci for the generation of visual behaviors.

}, doi = {10.1101/2023.10.16.562634}, url = {https://doi.org/10.1101/2023.10.16.562634}, author = {Arthur Zhao and Aljoscha Nern and Sanna Koskela and Marisa Dreher and Mert Erginkaya and Connor W Laughland and Henrique DF Ludwig and Alex G Thomson and Judith Hoeller and Ruchi Parekh and Sandro Romani and Davi D Bock and Eugenia Chiappe and Michael B Reiser} } @article {69038, title = {A comprehensive strategy to strengthen bioimaging in Africa through the Africa Microscopy Initiative.}, journal = {Nature Cell Biology}, volume = {25}, year = {2023}, month = {2023 Oct 19}, pages = {1387-1393}, issn = {1476-4679}, doi = {10.1038/s41556-023-01221-w}, author = {Reiche, Michael Anton and Jacobs, Caron Adrienne and Aaron, Jesse Scott and Mizrahi, Valerie and Warner, Digby Francis and Chew, Teng-Leong} } @article {69036, title = {Conjoint specification of action by neocortex and striatum.}, journal = {bioRxiv}, year = {2023}, month = {2023 Oct 05}, abstract = {

The interplay between two major forebrain structures - cortex and subcortical striatum - is critical for flexible, goal-directed action. Traditionally, it has been proposed that striatum is critical for selecting what type of action is initiated while the primary motor cortex is involved in the online control of movement execution. Recent data indicates that striatum may also be critical for specifying movement execution. These alternatives have been difficult to reconcile because when comparing very distinct actions, as in the vast majority of work to date, they make essentially indistinguishable predictions. Here, we develop quantitative models to reveal a somewhat paradoxical insight: only comparing neural activity during similar actions makes strongly distinguishing predictions. We thus developed a novel reach-to-pull task in which mice reliably selected between two similar, but distinct reach targets and pull forces. Simultaneous cortical and subcortical recordings were uniquely consistent with a model in which cortex and striatum jointly specify flexible parameters of action during movement execution.

}, doi = {10.1101/2023.10.04.560957}, url = {https://doi.org/10.1101/2023.10.04.560957}, author = {Junchol Park and Peter Polidoro and Catia Fortunato and Jon Arnold and Brett Mensh and Juan A. Gallego and Joshua T. Dudman} } @article {69104, title = {Connectivity underlying motor cortex activity during naturalistic goal-directed behavior.}, journal = {bioRxiv}, year = {2023}, month = {2023 Nov 26}, abstract = {

Neural representations of information are shaped by local network interactions. Previous studies linking neural coding and cortical connectivity focused on stimulus selectivity in the sensory cortex\ 1{\textendash}4. Here we study neural activity in the motor cortex during naturalistic behavior in which mice gathered rewards with multidirectional tongue reaching. This behavior does not require training and thus allowed us to probe neural coding and connectivity in motor cortex before its activity is shaped by learning a specific task. Neurons typically responded during and after reaching movements and exhibited conjunctive tuning to target location and reward outcome. We used an all-optical\ 5,4,6,7\ method for large-scale causal functional connectivity mapping\ in vivo. Mapping connectivity between \> 20,000,000 excitatory neuronal pairs revealed fine-scale columnar architecture in layer 2/3 of the motor cortex. Neurons displayed local (\< 100 {\textmu}m) like-to-like connectivity according to target-location tuning, and inhibition over longer spatial scales. Connectivity patterns comprised a continuum, with abundant weakly connected neurons and sparse strongly connected neurons that function as network hubs. Hub neurons were weakly tuned to target-location and reward-outcome but strongly influenced neighboring neurons. This network of neurons, encoding location and outcome of movements to different motor goals, may be a general substrate for rapid learning of complex, goal-directed behaviors.

}, doi = {10.1101/2023.11.25.568673}, url = {https://doi.org/10.1101/2023.11.25.568673}, author = {Arseny Finkelstein and Kayvon Daie and M{\'a}rton R{\'o}zsa and Ran Darshan and Karel Svoboda} } @article {68800, title = {A Connectome of the Male Drosophila Ventral Nerve Cord}, journal = {bioRxiv}, year = {2023}, month = {2023 Jun 06}, abstract = {

Animal behavior is principally expressed through neural control of muscles. Therefore understanding how the brain controls behavior requires mapping neuronal circuits all the way to motor neurons. We have previously established technology to collect large-volume electron microscopy data sets of neural tissue and fully reconstruct the morphology of the neurons and their chemical synaptic connections throughout the volume. Using these tools we generated a dense wiring diagram, or connectome, for a large portion of the\ Drosophila\ central brain. However, in most animals, including the fly, the majority of motor neurons are located outside the brain in a neural center closer to the body, i.e. the mammalian spinal cord or insect ventral nerve cord (VNC). In this paper, we extend our effort to map full neural circuits for behavior by generating a connectome of the VNC of a male fly.

}, doi = {10.1101/2023.06.05.543757}, url = {https://doi.org/10.1101/2023.06.05.543757}, author = {Shin-ya Takemura and Kenneth J Hayworth and Gary B Huang and Michal Januszewski and Zhiyuan Lu and Elizabeth C Marin and Stephan Preibisch and C Shan Xu and John Bogovic and Andrew S Champion and Han S J Cheong and Marta Costa and Katharina Eichler and William Katz and Christopher Knecht and Feng Li and Billy J Morris and Christopher Ordish and Patricia K Rivlin and Philipp Schlegel and Kazunori Shinomiya and Tomke Sturner and Ting Zhao and Griffin Badalamente and Dennis Bailey and Paul Brooks and Brandon S Canino and Jody Clements and Michael Cook and Octave Duclos and Christopher R Dunne and Kelli Fairbanks and Siqi Fang and Samantha Finley-May and Audrey Francis and Reed George and Marina Gkantia and Kyle Harrington and Gary Patrick Hopkins and Joseph Hsu and Philip M Hubbard and Alexandre Javier and Dagmar Kainmueller and Wyatt Korff and Julie Kovalyak and Dominik Krzeminski and Shirley A Lauchie and Alanna Lohff and Charli Maldonado and Emily A Manley and Caroline Mooney and Erika Neace and Matthew Nichols and Omotara Ogundeyi and Nneoma Okeoma and Tyler Paterson and Elliott Phillips and Emily M Phillips and Caitlin Ribeiro and Sean M Ryan and Jon Thomson Rymer and Anne K Scott and Ashley L Scott and David Shepherd and Aya Shinomiya and Claire Smith and Alia Suleiman and Satoko Takemura and Iris Talebi and Imaan F M Tamimi and Eric T Trautman and Lowell Umayam and John J Walsh and Tansy Yang and Gerald M Rubin and Louis K Scheffer and Jan Funke and Stephan Saalfeld and Harald F Hess and Stephen M Plaza and Gwyneth M Card and Gregory S X E Jefferis and Stuart Berg} } @article {68835, title = {The contribution of inflammatory astrocytes to BBB impairments in a brain-chip model of Parkinson{\textquoteright}s disease.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 Jun 20}, pages = {3651}, abstract = {

Astrocyte dysfunction has previously been linked to multiple neurodegenerative disorders including Parkinson{\textquoteright}s disease (PD). Among their many roles, astrocytes are mediators of the brain immune response, and astrocyte reactivity is a pathological feature of PD. They are also involved in the formation and maintenance of the blood-brain barrier (BBB), but barrier integrity is compromised in people with PD. This study focuses on an unexplored area of PD pathogenesis by characterizing the interplay between astrocytes, inflammation and BBB integrity, and by combining patient-derived induced pluripotent stem cells with microfluidic technologies to generate a 3D human BBB\ chip. Here we report that astrocytes derived from female donors harboring the PD-related LRRK2 G2019S mutation are pro-inflammatory and fail to support the formation of a functional capillary in vitro. We show that inhibition of MEK1/2 signaling attenuates the inflammatory profile of mutant astrocytes and rescues BBB formation, providing insights into mechanisms regulating barrier integrity in PD. Lastly, we confirm that vascular changes are also observed in the human\ postmortem substantia nigra of both males and females with PD.

}, keywords = {Astrocytes, Blood-Brain Barrier, Brain, Female, Humans, Male, Parkinson Disease, Substantia Nigra}, issn = {2041-1723}, doi = {10.1038/s41467-023-39038-8}, author = {de Rus Jacquet, A and Alpaugh, M and Denis, H L and Tancredi, J L and Boutin, M and Decaestecker, J and Beauparlant, C and Herrmann, L and Saint-Pierre, M and Parent, M and Droit, A and Breton, S and Cicchetti, F} } @article {68657, title = {Cristae formation is a mechanical buckling event controlled by the inner membrane lipidome}, journal = {bioRxiv}, year = {2023}, month = {2023 Mar 15}, abstract = {

The inner mitochondrial membrane (IMM) is the site of bulk ATP generation in cells and has a broadly conserved lipid composition enriched in unsaturated phospholipids and cardiolipin (CL). While proteins that shape the IMM and its characteristic cristae membranes (CM) have been defined, specific mechanisms by which mitochondrial lipids dictate its structure and function have yet to be elucidated. Here we combine experimental lipidome dissection with multi-scale modeling to investigate how lipid interactions shape CM morphology and ATP generation. When modulating fatty acid unsaturation in engineered yeast strains, we observed that loss of di-unsaturated phospholipids (PLs) led to a breakpoint in IMM topology and respiratory capacity. We found that PL unsaturation modulates the organization of ATP synthases that shape cristae ridges. Based on molecular modeling of mitochondrial-specific membrane adaptations, we hypothesized that conical lipids like CL buffer against the effects of saturation on the IMM. In cells, we discovered that loss of CL collapses the IMM at intermediate levels of PL saturation, an effect that is independent of ATP synthase oligomerization. To explain this interaction, we employed a continuum modeling approach, finding that lipid and protein-mediated curvatures are predicted to act in concert to form curved membranes in the IMM. The model highlighted a snapthrough instability in cristae tubule formation, which could drive IMM collapse upon small changes in composition. The interaction between CL and di-unsaturated PLs suggests that growth conditions that alter the fatty acid pool, such as oxygen availability, could define CL function. While loss of CL only has a minimal phenotype under standard laboratory conditions, we show that its synthesis is essential under microaerobic conditions that better mimic natural yeast fermentation. Lipid and protein-mediated mechanisms of curvature generation can thus act together to support mitochondrial architecture under changing environments.

}, doi = {10.1101/2023.03.13.532310}, url = {https://doi.org/10.1101/2023.03.13.532310}, author = {Kailash Venkatraman and Christopher T Lee and Guadalupe C. Garcia and Arijit Mahapatra and Guy Perkins and Keun-Young Kim and Hilda Amalia Pasolli and Sebastien Phan and Jennifer Lippincott-Schwartz and Mark Ellisman and Padmini Rangamani and Itay Budin} } @article {68467, title = {De novo protein identification in mammalian sperm using high-resolution in situ cryo-electron tomography}, journal = {Cell}, volume = {186}, year = {2023}, month = {2023 Nov 09}, pages = {5041-5053.e19}, abstract = {

Understanding molecular mechanisms of cellular pathways requires knowledge of the identities of participating proteins, their cellular localization and their 3D structures. Contemporary workflows typically require multiple techniques to identify target proteins, track their localization using fluorescence microscopy, followed by\ in vitro\ structure determination. To identify mammal-specific sperm proteins and understand their functions, we developed a visual proteomics workflow to directly address these challenges. Our\ in situ\ cryo-electron tomography and subtomogram averaging provided 6.0 {\r A} resolution reconstructions of axonemal microtubules and their associated proteins. The well-resolved secondary and tertiary structures allowed us to computationally match, in an unbiased manner, novel densities in our 3D reconstruction maps with 21,615 AlphaFold2-predicted protein models of the mouse proteome. We identified Tektin 5, CCDC105 and SPACA9 as novel microtubule inner proteins that form an extensive network crosslinking the lumen of microtubule and existing proteins. Additional biochemical and mass spectrometry analyses helped validate potential candidates. The novel axonemal sperm structures identified by this approach form an extensive interaction network within the lumen of microtubules, suggesting they have a role in the mechanical and elastic properties of the microtubule filaments required for the vigorous beating motions of flagella.

}, doi = {10.1016/j.cell.2023.09.017}, url = {https://doi.org/10.1016/j.cell.2023.09.017}, author = {Zhen Chen and Momoko Shiozaki and Kelsey M. Haas and Shumei Zhao and Caiying Guo and Benjamin J. Polacco and Zhiheng Yu and Nevan J. Krogan and Robyn M. Kaake and Ronald D. Vale and David A. Agard} } @article {69093, title = {Decoding life{\textquoteright}s inner workings: advances in quantitative bioimaging.}, journal = {Open Biology}, volume = {13}, year = {2023}, month = {2023 Nov 29}, pages = {230329}, abstract = {

This special feature of , titled {\textquoteright}Advances in Quantitative Bioimaging{\textquoteright}, proposes an overview of the latest advancements in quantitative bioimaging techniques and their wide-ranging applications. The articles cover various topics, including modern imaging methods that enable visualization on a nanoscale, such as super-resolution microscopy and single-particle analysis. These techniques offer unparalleled insights into complex molecular structures and dynamic cellular processes , such as mapping nuclear pore proteins or tracking single histone deposition events throughout the cell cycle. The articles presented in this edition showcase cutting-edge quantitative imaging techniques coupled with advanced computational analysis capable of precisely measuring biological structures and processes. Examples range from correlating calcium release events to underlying protein organization in heart cells to pioneering tools for categorizing changes in microglia morphology under various conditions. This editorial highlights how these advancements are revolutionizing our understanding of living systems, while acknowledging challenges that must be addressed to fully exploit the potential of these emerging technologies, such as improving molecular probes, algorithms and correlation protocols.

}, keywords = {Algorithms, Microscopy, Fluorescence, Molecular Structure}, issn = {2046-2441}, doi = {10.1098/rsob.230329}, author = {Henriques, Ricardo and Leterrier, Christophe and Weigel, Aubrey} } @article {69111, title = {Different spectral sensitivities of ON- and OFF-motion pathways enhance the detection of approaching color objects in Drosophila.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 Nov 24}, pages = {7693}, abstract = {

Color and motion are used by many species to identify salient objects. They are processed largely independently, but color contributes to motion processing in humans, for example, enabling moving colored objects to be detected when their luminance matches the background. Here, we demonstrate an unexpected, additional contribution of color to motion vision in Drosophila. We show that behavioral ON-motion responses are more sensitive to UV than for OFF-motion, and we identify cellular pathways connecting UV-sensitive R7 photoreceptors to ON and OFF-motion-sensitive T4 and T5 cells, using neurogenetics and calcium imaging. Remarkably, this contribution of color circuitry to motion vision enhances the detection of approaching UV discs, but not green discs with the same chromatic contrast, and we show how this could generalize for systems with ON- and OFF-motion pathways. Our results provide a computational and circuit basis for how color enhances motion vision to favor the detection of saliently colored objects.

}, keywords = {Animals, Drosophila, Humans, Motion Perception, Photoreceptor Cells, Vision, Ocular}, issn = {2041-1723}, doi = {10.1038/s41467-023-43566-8}, author = {Longden, Kit D and Rogers, Edward M and Nern, Aljoscha and Dionne, Heather and Reiser, Michael B} } @article {69092, title = {Different spectral sensitivities of ON- and OFF-motion pathways enhance the detection of approaching color objects in Drosophila.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 Nov 24}, pages = {7693}, abstract = {

Color and motion are used by many species to identify salient objects. They are processed largely independently, but color contributes to motion processing in humans, for example, enabling moving colored objects to be detected when their luminance matches the background. Here, we demonstrate an unexpected, additional contribution of color to motion vision in Drosophila. We show that behavioral ON-motion responses are more sensitive to UV than for OFF-motion, and we identify cellular pathways connecting UV-sensitive R7 photoreceptors to ON and OFF-motion-sensitive T4 and T5 cells, using neurogenetics and calcium imaging. Remarkably, this contribution of color circuitry to motion vision enhances the detection of approaching UV discs, but not green discs with the same chromatic contrast, and we show how this could generalize for systems with ON- and OFF-motion pathways. Our results provide a computational and circuit basis for how color enhances motion vision to favor the detection of saliently colored objects.

}, keywords = {Animals, Drosophila, Humans, Motion Perception, Photoreceptor Cells, Vision, Ocular}, issn = {2041-1723}, doi = {10.1038/s41467-023-43566-8}, author = {Longden, Kit D and Rogers, Edward M and Nern, Aljoscha and Dionne, Heather and Reiser, Michael B} } @article {68664, title = {Differential Encoding of Trace and Delay Fear Memory in the Entorhinal Cortex.}, journal = {Experimental Neurobiology}, volume = {32}, year = {2023}, month = {2023 Feb 28}, pages = {20-30}, abstract = {

Trace fear conditioning is characterized by a stimulus-free trace interval (TI) between the conditioned stimulus (CS) and the unconditioned stimulus (US), which requires an array of brain structures to support the formation and storage of associative memory. The entorhinal cortex (EC) has been proposed to provide essential neural code for resolving temporal discontinuity in conjunction with the hippocampus. However, how the CS and TI are encoded at the neuronal level in the EC is not clear. In Exp. 1, we tested the effect of bilateral pre-training electrolytic lesions of EC on trace vs. delay fear conditioning using rats as subjects. We found that the lesions impaired the acquisition of trace but not delay fear conditioning confirming that EC is a critical brain area for trace fear memory formation. In Exp. 2, single-unit activities from EC were recorded during the pre-training baseline and post-training retention sessions following trace or delay conditioning. The recording results showed that a significant proportion of the EC neurons modulated their firing during TI after the trace conditioning, but not after the delay fear conditioning. Further analysis revealed that the majority of modulated units decreased the firing rate during the TI or the CS. Taken together, these results suggest that EC critically contributes to trace fear conditioning by modulating neuronal activity during the TI to facilitate the association between the CS and US across a temporal gap.

}, issn = {1226-2560}, doi = {10.5607/en22042}, author = {Kong, Mi-Seon and Kim, Namsoo and Jo, Kyeong Im and Kim, Sung-Phil and Choi, June-Seek} } @article {67959, title = {Dimensionality reduction of calcium-imaged neuronal population activity}, journal = {Nature Computational Science}, year = {2023}, month = {2023 Jan 01}, abstract = {

Calcium imaging has been widely adopted for its ability to record from large neuronal populations. To summarize the time course of neural activity, dimensionality reduction methods, which have been applied extensively to population spiking activity, may be particularly useful. However, it is unclear if the dimensionality reduction methods applied to spiking activity are appropriate for calcium imaging. We thus carried out a systematic study of design choices based on standard dimensionality reduction methods. We also developed a novel method to perform deconvolution and dimensionality reduction simultaneously (termed CILDS). CILDS most accurately recovered the single-trial, low-dimensional time courses from calcium imaging that would have been recovered from spiking activity. CILDS also outperformed the other methods on calcium imaging recordings from larval zebrafish and mice. More broadly, this study represents a foundation for summarizing calcium imaging recordings of large neuronal populations using dimensionality reduction in diverse experimental settings.

}, doi = {10.1038/s43588-022-00390-2}, url = {https://doi.org/10.1038/s43588-022-00390-2}, author = {Tze Hui Koh and William E. Bishop and Takashi Kawashima and Brian B. Jeon and Ranjani Srinivasan and Sandra J. Kuhlman and Misha B. Ahrens and Steven M. Chase and Byron M. Yu} } @article {68954, title = {Direct observation of the conformational states of PIEZO1.}, journal = {Nature}, volume = {620}, year = {2023}, month = {2023 Aug 31}, pages = {1117-1125}, abstract = {

PIEZOs are mechanosensitive ion channels that convert force into chemoelectric signals and have essential roles in diverse physiological settings. In vitro studies have proposed that PIEZO channels transduce mechanical force through the deformation of extensive blades of transmembrane domains emanating from a central ion-conducting pore. However, little is known about how these channels interact with their native environment and which molecular movements underlie activation. Here we directly observe the conformational dynamics of the blades of individual PIEZO1 molecules in a cell using nanoscopic fluorescence imaging. Compared with previous structural models of PIEZO1, we show that the blades are significantly expanded at rest by the bending stress exerted by the plasma membrane. The degree of expansion varies dramatically along the length of the blade, where decreased binding strength between subdomains can explain increased flexibility of the distal blade. Using chemical and mechanical modulators of PIEZO1, we show that blade expansion and channel activation are correlated. Our findings begin to uncover how PIEZO1 is activated in a native environment. More generally, as we reliably detect conformational shifts of single nanometres from populations of channels, we expect that this approach will serve as a framework for the structural analysis of membrane proteins through nanoscopic imaging.

}, issn = {1476-4687}, doi = {10.1038/s41586-023-06427-4}, author = {Mulhall, Eric M and Gharpure, Anant and Lee, Rachel M and Dubin, Adrienne E and Aaron, Jesse S and Marshall, Kara L and Spencer, Kathryn R and Reiche, Michael A and Henderson, Scott C and Chew, Teng-Leong and Patapoutian, Ardem} } @article {68959, title = {Dissecting Cell Plate Development During Plant Cytokinesis.}, journal = {Microscopy and Microanalysis}, volume = {29}, year = {2023}, month = {2023 Jul 22}, pages = {865}, keywords = {Cytokinesis}, issn = {1435-8115}, doi = {10.1093/micmic/ozad067.428}, author = {Sinclair, Rosalie and Cox, Daniel and Heddleston, John and Aaron, Jesse and Wait, Eric and Wilkop, Thomas and Drakakaki, Georgia} } @article {68634, title = {Distinct mobility patterns of BRCA2 molecules at DNA damage sites}, journal = {Nucleic Acids Res.}, year = {2023}, month = {2024 Jul 02}, pages = {gkae559}, abstract = {

BRCA2 is an essential tumor suppressor protein involved in promoting faithful repair of DNA lesions. The activity of BRCA2 needs to be tuned precisely to be active when and where it is needed. Here, we quantified the spatio-temporal dynamics of BRCA2 in living cells using aberration-corrected multifocal microscopy (acMFM). Using multicolor imaging to identify DNA damage sites, we were able to quantify its dynamic motion patterns in the nucleus and at DNA damage sites. While a large fraction of BRCA2 molecules localized near DNA damage sites appear immobile, an additional fraction of molecules exhibits subdiffusive motion, providing a potential mechanism to retain an increased number of molecules at DNA lesions. Super-resolution microscopy revealed inhomogeneous localization of BRCA2 relative to other DNA repair factors at sites of DNA damage. This suggests the presence of multiple nanoscale compartments in the chromatin surrounding the DNA lesion, which could play an important role in the contribution of BRCA2 to the regulation of the repair process.

}, doi = {10.1093/nar/gkae559 }, url = {https://doi.org/10.1093/nar/gkae559 }, author = {Maarten W. Paul and Jesse Aaron and Eric Wait and Romano M. van Genderen and Ihor Smal and Teng-Leong Chew and Roland Kanaar and Claire Wyman} } @article {69091, title = {Distributed representations of innate behaviors in the hypothalamus do not predict specialized functional centers.}, journal = {bioRxiv}, year = {2023}, month = {2023 Nov 21}, abstract = {

Survival behaviors are orchestrated by hardwired circuits located in deep subcortical brain regions, most prominently the hypothalamus. Artificial activation of spatially localized, genetically defined hypothalamic cell populations is known to trigger distinct behaviors, suggesting a nucleus-centered organization of behavioral control. However, no study has investigated the hypothalamic representation of innate behaviors using unbiased, large-scale single neuron recordings. Here, using custom silicon probes, we performed recordings across the rostro-caudal extent of the medial hypothalamus in freely moving animals engaged in a diverse array of social and predator defense ({\textquotedblleft}fear{\textquotedblright}) behaviors. Nucleus-averaged activity revealed spatially distributed generic {\textquotedblleft}ignition signals{\textquotedblright} that occurred at the onset of each behavior, and did not identify sparse, nucleus-specific behavioral representations. Single-unit analysis revealed that social and fear behavior classes are encoded by activity in distinct sets of spatially distributed neuronal ensembles spanning the entire hypothalamic rostro-caudal axis. Individual ensemble membership, however, was drawn from neurons in 3-4 adjacent nuclei. Mixed selectivity was identified as the most prevalent mode of behavior representation by individual hypothalamic neurons. Encoding models indicated that a significant fraction of the variance in single neuron activity is explained by behavior. This work reveals that innate behaviors are encoded in the hypothalamus by activity in spatially distributed neural ensembles that each span multiple neighboring nuclei, complementing the prevailing view of hypothalamic behavioral control by single nucleus-restricted cell types derived from perturbational studies.

}, doi = {10.1101/2023.11.21.568163}, url = {https://doi.org/10.1101/2023.11.21.568163}, author = {Stefanos Stagkourakis and Giada Spigolon and Markus Marks and Michael Feyder and Joseph Kim and Pietro Perona and Marius Pachitariu and David J. Anderson} } @article {68786, title = {Distributing task-related neural activity across a cortical network through task-independent connections.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 May 18}, pages = {2851}, abstract = {

Task-related neural activity is widespread across populations of neurons during goal-directed behaviors. However, little is known about the synaptic reorganization and circuit mechanisms that lead to broad activity changes. Here we trained a subset of neurons in a spiking network with strong synaptic interactions to reproduce the activity of neurons in the motor cortex during a decision-making task. Task-related activity, resembling the neural data, emerged across the network, even in the untrained neurons. Analysis of trained networks showed that strong untrained synapses, which were independent of the task and determined the dynamical state of the network, mediated the spread of task-related activity. Optogenetic perturbations suggest that the motor cortex is strongly-coupled, supporting the applicability of the mechanism to cortical networks. Our results reveal a cortical mechanism that facilitates distributed representations of task-variables by spreading the activity from a subset of plastic neurons to the entire network through task-independent strong synapses.

}, keywords = {Action Potentials, Models, Neurological, Neurons, Synapses}, issn = {2041-1723}, doi = {10.1038/s41467-023-38529-y}, author = {Kim, Christopher M and Finkelstein, Arseny and Chow, Carson C and Svoboda, Karel and Darshan, Ran} } @article {68632, title = {DNA-initiated epigenetic cascades driven by C9orf72 hexanucleotide repeat.}, journal = {Neuron}, volume = {111}, year = {2023}, month = {2023 Apr 19}, pages = {1205-21}, abstract = {

The C9orf72 hexanucleotide repeat expansion (HRE) is the most frequent genetic cause of the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here, we describe the pathogenic cascades that are initiated by the C9orf72 HRE DNA. The HRE DNA binds to its protein partner DAXX and promotes its liquid-liquid phase separation, which is capable of reorganizing genomic structures. An HRE-dependent nuclear accumulation of DAXX drives chromatin remodeling and epigenetic changes such as histone hypermethylation and hypoacetylation in patient cells. While regulating global gene expression, DAXX plays a key role in the suppression of basal and stress-inducible expression of C9orf72 via chromatin remodeling and epigenetic modifications of the promoter of the major C9orf72 transcript. Downregulation of DAXX or rebalancing the epigenetic modifications mitigates the stress-induced sensitivity of C9orf72-patient-derived motor neurons. These studies reveal a C9orf72 HRE DNA-dependent regulatory mechanism for both local and genomic architectural changes in the relevant diseases.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2023.01.022}, author = {Liu, Yang and Huang, Zhiyuan and Liu, Honghe and Ji, Zhicheng and Arora, Amit and Cai, Danfeng and Wang, Hongjin and Liu, Mingming and Simko, Eric A J and Zhang, Yanjun and Periz, Goran and Liu, Zhe and Wang, Jiou} } @article {69007, title = {Driver lines for studying associative learning in Drosophila}, journal = {bioRxiv}, year = {2023}, month = {2023 Sep 16}, abstract = {

The mushroom body (MB) is the center for associative learning in insects. In Drosophila, intersectional split-GAL4 drivers and electron microscopy (EM) connectomes have laid the foundation for precise interrogation of the MB neural circuits. However, many cell types upstream and downstream of the MB remained to be investigated due to lack of driver lines. Here we describe a new collection of over 800 split-GAL4 and split-LexA drivers that cover approximately 300 cell types, including sugar sensory neurons, putative nociceptive ascending neurons, olfactory and thermo-/hygro-sensory projection neurons, interneurons connected with the MB-extrinsic neurons, and various other cell types. We characterized activation phenotypes for a subset of these lines and identified the sugar sensory neuron line most suitable for reward substitution. Leveraging the thousands of confocal microscopy images associated with the collection, we analyzed neuronal morphological stereotypy and discovered that one set of mushroom body output neurons, MBON08/MBON09, exhibits striking individuality and asymmetry across animals. In conjunction with the EM connectome maps, the driver lines reported here offer a powerful resource for functional dissection of neural circuits for associative learning in adult Drosophila.

}, doi = {https://doi.org/10.7554/elife.94168.4}, url = {https://doi.org/10.7554/elife.94168.4 }, author = {Yichun Shuai and Megan Sammons and Gabriella Sterne and Karen Hibbard and He Yang and Ching-Po Yang and Claire Managan and Igor Siwanowicz and Tzumin Lee and Gerald M. Rubin and Glenn Turner and Yoshinori Aso} } @article {68654, title = {Drosophila antennae are dispensable for gravity orientation}, journal = {bioRxiv}, year = {2023}, month = {2023 Mar 10}, abstract = {

The nearly constant downward force of gravity has powerfully shaped the behaviors of many organisms [1]. Walking flies readily orient against gravity in a behavior termed negative gravitaxis. In\ Drosophila\ this behavior is studied by observing the position of flies in vials [2{\textendash}4] or simple mazes [5{\textendash}9]. These assays have been used to conduct forward-genetic screens [5,\ 6,\ 8] and as simple tests of locomotion deficits [10{\textendash}12]. Despite this long history of investigation, the sensory basis of gravitaxis is largely unknown [1]. Recent studies have implicated the antennae as a major mechanosensory input [3,\ 4], but many details remain unclear. Fly orientation behavior is expected to depend on the direction and amplitude of the gravitational pull, but little is known about the sensitivity of flies to these features of the environment. Here we directly measure the gravity-dependent orientation behavior of flies walking on an adjustable tilted platform, that is inspired by previous insect studies [13{\textendash}16]. In this arena, flies can freely orient with respect to gravity. Our findings indicate that flies are exquisitely sensitive to the direction of gravity{\textquoteright}s pull. Surprisingly, this orientation behavior does not require antennal mechanosensory input, suggesting that other sensory structures must be involved.

}, doi = {10.1101/2023.03.08.531317}, url = {https://doi.org/10.1101/2023.03.08.531317}, author = {Nikolay Kladt and Michael B. Reiser} } @article {68932, title = {Dynamics of cortical contrast adaptation predict perception of signals in noise.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 Aug 09}, pages = {4817}, abstract = {

Neurons throughout the sensory pathway adapt their responses depending on the statistical structure of the sensory environment. Contrast gain control is a form of adaptation in the auditory cortex, but it is unclear whether the dynamics of gain control reflect efficient adaptation, and whether they shape behavioral perception. Here, we trained mice to detect a target presented in background noise shortly after a change in the contrast of the background. The observed changes in cortical gain and behavioral detection followed the dynamics of a normative model of efficient contrast gain control; specifically, target detection and sensitivity improved slowly in low contrast, but degraded rapidly in high contrast. Auditory cortex was required for this task, and cortical responses were not only similarly affected by contrast but predicted variability in behavioral performance. Combined, our results demonstrate that dynamic gain adaptation supports efficient coding in auditory cortex and predicts the perception of sounds in noise.

}, keywords = {Acoustic Stimulation, Adaptation, Physiological, Animals, Auditory Cortex, Auditory Perception, Mice, Noise, Sound}, issn = {2041-1723}, doi = {10.1038/s41467-023-40477-6}, author = {Angeloni, Christopher F and M{\l}ynarski, Wiktor and Piasini, Eugenio and Williams, Aaron M and Wood, Katherine C and Garami, Linda and Hermundstad, Ann M and Geffen, Maria N} } @article {69054, title = {Effects of stochastic coding on olfactory discrimination in flies and mice.}, journal = {PLoS Biology}, volume = {21}, year = {2023}, month = {2023 Oct 31}, pages = {e3002206}, abstract = {

Sparse coding can improve discrimination of sensory stimuli by reducing overlap between their representations. Two factors, however, can offset sparse coding{\textquoteright}s benefits: similar sensory stimuli have significant overlap and responses vary across trials. To elucidate the effects of these 2 factors, we analyzed odor responses in the fly and mouse olfactory regions implicated in learning and discrimination-the mushroom body (MB) and the piriform cortex (PCx). We found that neuronal responses fall along a continuum from extremely reliable across trials to extremely variable or stochastic. Computationally, we show that the observed variability arises from noise within central circuits rather than sensory noise. We propose this coding scheme to be advantageous for coarse- and fine-odor discrimination. More reliable cells enable quick discrimination between dissimilar odors. For similar odors, however, these cells overlap and do not provide distinguishing information. By contrast, more unreliable cells are decorrelated for similar odors, providing distinguishing information, though these benefits only accrue with extended training with more trials. Overall, we have uncovered a conserved, stochastic coding scheme in vertebrates and invertebrates, and we identify a candidate mechanism, based on variability in a winner-take-all (WTA) inhibitory circuit, that improves discrimination with training.

}, keywords = {Animals, Diptera, Learning, Mice, Odorants, Olfactory Pathways, Olfactory Perception, Smell}, issn = {1545-7885}, doi = {10.1371/journal.pbio.3002206}, author = {Srinivasan, Shyam and Daste, Simon and Modi, Mehrab N and Turner, Glenn C and Fleischmann, Alexander and Navlakha, Saket} } @article {68806, title = {Environmental dynamics shape perceptual decision bias.}, journal = {PLoS Computational Biology}, volume = {19}, year = {2023}, month = {2023 Jun 08}, pages = {e1011104}, abstract = {

To interpret the sensory environment, the brain combines ambiguous sensory measurements with knowledge that reflects context-specific prior experience. But environmental contexts can change abruptly and unpredictably, resulting in uncertainty about the current context. Here we address two questions: how should context-specific prior knowledge optimally guide the interpretation of sensory stimuli in changing environments, and do human decision-making strategies resemble this optimum? We probe these questions with a task in which subjects report the orientation of ambiguous visual stimuli that were drawn from three dynamically switching distributions, representing different environmental contexts. We derive predictions for an ideal Bayesian observer that leverages knowledge about the statistical structure of the task to maximize decision accuracy, including knowledge about the dynamics of the environment. We show that its decisions are biased by the dynamically changing task context. The magnitude of this decision bias depends on the observer{\textquoteright}s continually evolving belief about the current context. The model therefore not only predicts that decision bias will grow as the context is indicated more reliably, but also as the stability of the environment increases, and as the number of trials since the last context switch grows. Analysis of human choice data validates all three predictions, suggesting that the brain leverages knowledge of the statistical structure of environmental change when interpreting ambiguous sensory signals.

}, keywords = {Bayes Theorem, Bias, Brain, Decision Making, Humans, Uncertainty}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1011104}, author = {Charlton, Julie A and M{\l}ynarski, Wiktor F and Bai, Yoon H and Hermundstad, Ann M and Goris, Robbe L T} } @article {69021, title = {Extracellular glutamate and GABA transients at the transition from interictal spiking to seizures.}, journal = {Brain}, year = {2023}, month = {2023 Oct 03}, abstract = {

Focal epilepsy is associated with intermittent brief population discharges (interictal spikes), which resemble sentinel spikes that often occur at the onset of seizures. Why interictal spikes self-terminate whilst seizures persist and propagate is incompletely understood. We used fluorescent glutamate and GABA sensors in an awake rodent model of neocortical seizures to resolve the spatiotemporal evolution of both neurotransmitters in the extracellular space. Interictal spikes were accompanied by brief glutamate transients which were maximal at the initiation site and rapidly propagated centrifugally. GABA transients lasted longer than glutamate transients and were maximal \~{}1.5 mm from the focus where they propagated centripetally. Prior to seizure initiation GABA transients were attenuated, whilst glutamate transients increased, consistent with a progressive failure of local inhibitory restraint. As seizures increased in frequency, there was a gradual increase in the spatial extent of spike-associated glutamate transients associated with interictal spikes. Neurotransmitter imaging thus reveals a progressive collapse of an annulus of feed-forward GABA release, allowing seizures to escape from local inhibitory restraint.

}, issn = {1460-2156}, doi = {10.1093/brain/awad336}, author = {Shimoda, Yoshiteru and Leite, Marco and Graham, Robert T and Marvin, Jonathan S and Hasseman, Jeremy and Kolb, Ilya and Looger, Loren L and Magloire, Vincent and Kullmann, Dimitri M} } @article {68715, title = {Extracellular matrix assembly stress initiates Drosophila central nervous system morphogenesis.}, journal = {Developmental Cell}, year = {2023}, month = {2023 Apr 17}, abstract = {

Forces controlling tissue morphogenesis are attributed to cellular-driven activities, and any role for extracellular matrix (ECM) is assumed to be passive. However, all polymer networks, including ECM, can develop autonomous stresses during their assembly. Here, we examine the morphogenetic function of an ECM before reaching homeostatic equilibrium by analyzing de novo ECM assembly during Drosophila ventral nerve cord (VNC) condensation. Asymmetric VNC shortening and a rapid decrease in surface area correlate with the exponential assembly of collagen IV (Col4) surrounding the tissue. Concomitantly, a transient developmentally induced Col4 gradient leads to coherent long-range flow of ECM, which equilibrates the Col4 network. Finite element analysis and perturbation of Col4 network formation through the generation of dominant Col4 mutations that affect assembly reveal that VNC morphodynamics is partially driven by a sudden increase in ECM-driven surface tension. These data suggest that ECM assembly stress and associated network instabilities can actively participate in tissue morphogenesis.

}, issn = {1878-1551}, doi = {10.1016/j.devcel.2023.03.019}, author = {Serna-Morales, Eduardo and S{\'a}nchez-S{\'a}nchez, Besaiz J and Marcotti, Stefania and Nichols, Angus and Bhargava, Anushka and Dragu, Anca and Hirvonen, Liisa M and Diaz-de-la-Loza, Maria-Del-Carmen and Mink, Matyas and Cox, Susan and Rayfield, Emily and Lee, Rachel M and Hobson, Chad M and Chew, Teng-Leong and Stramer, Brian M} } @article {68784, title = {Extracellular matrix assembly stress initiates Drosophila central nervous system morphogenesis.}, journal = {Developmental Cell}, volume = {58}, year = {2023}, month = {2023 May 22}, pages = {825-835.e6}, abstract = {

Forces controlling tissue morphogenesis are attributed to cellular-driven activities, and any role for extracellular matrix (ECM) is assumed to be passive. However, all polymer networks, including ECM, can develop autonomous stresses during their assembly. Here, we examine the morphogenetic function of an ECM before reaching homeostatic equilibrium by analyzing de novo ECM assembly during Drosophila ventral nerve cord (VNC) condensation. Asymmetric VNC shortening and a rapid decrease in surface area correlate with the exponential assembly of collagen IV (Col4) surrounding the tissue. Concomitantly, a transient developmentally induced Col4 gradient leads to coherent long-range flow of ECM, which equilibrates the Col4 network. Finite element analysis and perturbation of Col4 network formation through the generation of dominant Col4 mutations that affect assembly reveal that VNC morphodynamics is partially driven by a sudden increase in ECM-driven surface tension. These data suggest that ECM assembly stress and associated network instabilities can actively participate in tissue morphogenesis.

}, keywords = {Animals, Central Nervous System, Drosophila, Extracellular Matrix, Morphogenesis}, issn = {1878-1551}, doi = {10.1016/j.devcel.2023.03.019}, author = {Serna-Morales, Eduardo and S{\'a}nchez-S{\'a}nchez, Besaiz J and Marcotti, Stefania and Nichols, Angus and Bhargava, Anushka and Dragu, Anca and Hirvonen, Liisa M and Diaz-de-la-Loza, Maria-Del-Carmen and Mink, Matyas and Cox, Susan and Rayfield, Emily and Lee, Rachel M and Hobson, Chad M and Chew, Teng-Leong and Stramer, Brian M} } @article {68465, title = {Facemap: a framework for modeling neural activity based on orofacial tracking}, journal = {Nature Neuroscience}, year = {2023}, month = {2023 Nov 20}, abstract = {

Recent studies in mice have shown that orofacial behaviors drive a large fraction of neural activity across the brain. To understand the nature and function of these signals, we need better computational models to characterize the behaviors and relate them to neural activity. Here we developed Facemap, a framework consisting of a keypoint tracking algorithm and a deep neural network encoder for predicting neural activity. We used the Facemap keypoints as input for the deep neural network to predict the activity of \~{}50,000 simultaneously-recorded neurons and in visual cortex we doubled the amount of explained variance compared to previous methods. Our keypoint tracking algorithm was more accurate than existing pose estimation tools, while the inference speed was several times faster, making it a powerful tool for closed-loop behavioral experiments. The Facemap tracker was easy to adapt to data from new labs, requiring as few as 10 annotated frames for near-optimal performance. We used Facemap to find that the neuronal activity clusters which were highly driven by behaviors were more spatially spread-out across cortex. We also found that the deep keypoint features inferred by the model had time-asymmetrical state dynamics that were not apparent in the raw keypoint data. In summary, Facemap provides a stepping stone towards understanding the function of the brainwide neural signals and their relation to behavior.

}, doi = {10.1038/s41593-023-01490-6}, url = {https://doi.org/10.1038/s41593-023-01490-6}, author = {Atika Syeda and Lin Zhong and Renee Tung and Will Long and Marius Pachitariu and Carsen Stringer} } @article {68665, title = {Fast and sensitive GCaMP calcium indicators for imaging neural populations.}, journal = {Nature}, year = {2023}, month = {2023 Mar 15}, abstract = {

Calcium imaging with protein-based indicators is widely used to follow neural activity in intact nervous systems, but current protein sensors report neural activity at timescales much slower than electrical signalling and are limited by trade-offs between sensitivity and kinetics. Here we used large-scale screening and structure-guided mutagenesis to develop and optimize several fast and sensitive GCaMP-type indicators. The resulting {\textquoteright}jGCaMP8{\textquoteright} sensors, based on the calcium-binding protein calmodulin and a fragment of endothelial nitric oxide synthase, have ultra-fast kinetics (half-rise times of 2 ms) and the highest sensitivity for neural activity reported for a protein-based calcium sensor. jGCaMP8 sensors will allow tracking of large populations of neurons on timescales relevant to neural computation.

}, issn = {1476-4687}, doi = {10.1038/s41586-023-05828-9}, author = {Zhang, Yan and Rozsa, Marton and Liang, Yajie and Bushey, Daniel and Wei, Ziqiang and Zheng, Jihong and Reep, Daniel and Broussard, Gerard Joey and Tsang, Arthur and Tsegaye, Getahun and Narayan, Sujatha and Obara, Christopher J and Lim, Jing-Xuan and Patel, Ronak and Zhang, Rongwei and Ahrens, Misha B and Turner, Glenn C and Wang, Samuel S-H and Korff, Wyatt L and Schreiter, Eric R and Svoboda, Karel and Hasseman, Jeremy P and Kolb, Ilya and Looger, Loren L} } @article {68630, title = {Fast and sensitive GCaMP calcium indicators for neuronal imaging.}, journal = {The Journal of Physiology}, year = {2023}, month = {2023 Feb 22}, abstract = {

We review the principles of development and deployment of genetically encoded calcium indicators (GECIs) for the detection of neural activity. Our focus is on the popular GCaMP family of green GECIs, culminating in the recent release of the jGCaMP8 sensors, with dramatically improved kinetics relative to previous generations. We summarize the properties of GECIs in multiple color channels (blue, cyan, green, yellow, red, far-red) and highlight areas for further improvement. With their low-millisecond rise-times, the jGCaMP8 indicators allow new classes of experiments following neural activity in timeframes approaching the underlying computations. Abstract legend: GCaMP calcium sensors are widely used to report neuronal activity via fluorescence readout. This article is protected by copyright. All rights reserved.

}, issn = {1469-7793}, doi = {10.1113/JP283832}, author = {Zhang, Yan and Looger, Loren L} } @article {68628, title = {Finding the right type of cell.}, journal = {eLife}, volume = {12}, year = {2023}, month = {2023 Feb 16}, abstract = {

A new method allows researchers to automatically assign cells into different cell types and tissues, a step which is critical for understanding complex organisms.

}, issn = {2050-084X}, doi = {10.7554/eLife.86172}, author = {Scheffer, Louis K} } @article {68973, title = {FIOLA: an accelerated pipeline for fluorescence imaging online analysis.}, journal = {Nature Methods}, volume = {20}, year = {2023}, month = {2023 Sep 01}, pages = {1417-1425}, abstract = {

Optical microscopy methods such as calcium and voltage imaging enable fast activity readout of large neuronal populations using light. However, the lack of corresponding advances in online algorithms has slowed progress in retrieving information about neural activity during or shortly after an experiment. This gap not only prevents the execution of real-time closed-loop experiments, but also hampers fast experiment-analysis-theory turnover for high-throughput imaging modalities. Reliable extraction of neural activity from fluorescence imaging frames at speeds compatible with indicator dynamics and imaging modalities poses a challenge. We therefore developed FIOLA, a framework for fluorescence imaging online analysis that extracts neuronal activity from calcium and voltage imaging movies at speeds one order of magnitude faster than state-of-the-art methods. FIOLA exploits algorithms optimized for parallel processing on GPUs and CPUs. We demonstrate reliable and scalable performance of FIOLA on both simulated and real calcium and voltage imaging datasets. Finally, we present an online experimental scenario to provide guidance in setting FIOLA parameters and to highlight the trade-offs of our approach.

}, keywords = {Algorithms, Calcium, Microscopy, Optical Imaging}, issn = {1548-7105}, doi = {10.1038/s41592-023-01964-2}, author = {Cai, Changjia and Dong, Cynthia and Friedrich, Johannes and Rozsa, Marton and Pnevmatikakis, Eftychios A and Giovannucci, Andrea} } @article {68790, title = {Flexible specificity of memory in Drosophila depends on a comparison between choices}, journal = {eLife}, year = {2023}, month = {2023 Jun 15}, abstract = {

Memory guides behavior across widely varying environments and must therefore be both sufficiently specific and general. A memory too specific will be useless in even a slightly different environment, while an overly general memory may lead to suboptimal choices. Animals successfully learn to both distinguish between very similar stimuli and generalize across cues. Rather than forming memories that strike a balance between specificity and generality,\ Drosophila\ can flexibly categorize a given stimulus into different groups depending on the options available. We asked how this flexibility manifests itself in the well-characterized learning and memory pathways of the fruit fly. We show that flexible categorization in neuronal activity as well as behavior depends on the order and identity of the perceived stimuli. Our results identify the neural correlates of flexible stimulus-categorization in the fruit fly.

}, doi = {10.7554/eLife.80923}, url = {https://doi.org/10.7554/eLife.80923}, author = {Mehrab N Modi and Adithya Rajagopalan and Herv{\'e} Rouault and Yoshinori Aso and Glenn C Turner} } @article {68521, title = {From primordial clocks to circadian oscillators}, journal = {Nature}, year = {2023}, month = {2023 Apr 01}, abstract = {

Circadian rhythms play an essential role in many biological processes and surprisingly only three prokaryotic proteins are required to constitute a true post-translational circadian oscillator. The evolutionary history of the three Kai proteins indicates that KaiC is the oldest member and central component of the clock, with subsequent additions of KaiB and KaiA to regulate its phosphorylation state for time synchronization. The canonical KaiABC system in cyanobacteria is well understood, but little is known about more ancient systems that possess just KaiBC, except for reports that they might exhibit a basic, hourglass-like timekeeping mechanism. Here, we investigate the primordial circadian clock in\ Rhodobacter sphaeroides\ (RS) that contains only KaiBC to elucidate its inner workings despite the missing KaiA. Using a combination X-ray crystallography and cryo-EM we find a novel dodecameric fold for KaiCRS\ where two hexamers are held together by a coiled-coil bundle of 12 helices. This interaction is formed by the C-terminal extension of KaiCRS\ and serves as an ancient regulatory moiety later superseded by KaiA. A coiled-coil register shift between daytime- and nighttime-conformations is connected to the phosphorylation sites through a long-range allosteric network that spans over 160 {\r A}. Our kinetic data identify the difference in ATP-to-ADP ratio between day and night as the environmental cue that drives the clock and further unravels mechanistic details that shed light on the evolution of self-sustained oscillators.

}, doi = {10.1038/s41586-023-05836-9}, url = {https://doi.org/10.1038/s41586-023-05836-9}, author = {Warintra Pitsawong and Ricardo A. P. P{\'a}dua and Timothy Grant and Marc Hoemberger and Renee Otten and Niels Bradshaw and Nikolaus Grigorieff and Dorothee Kern} } @article {68588, title = {Functional specialization and structured representations for space and time in prefrontal cortex}, journal = {bioRxiv}, year = {2023}, month = {2023 Jan 18}, abstract = {

Individual neurons in prefrontal cortex {\textendash} a key brain area involved in cognitive functions {\textendash} are selective for variables such as space or time, as well as more cognitive aspects of tasks, such as learned categories. Many neurons exhibit mixed selectivity, that is, they show selectivity for multiple variables. A fundamental question is whether neurons are functionally specialized for particular variables and how selectivity for different variables intersects across the population. Here, we analyzed neural correlates of space and time in rats performing a navigational task with two behaviorally important categories {\textendash} starts and goals. Using simultaneous recordings of many medial prefrontal cortex (mPFC) neurons during behavior, we found that population codes for elapsed time were invariant to different locations within categories, and subsets of neurons had functional preferences for time or space across categories. Thus, mPFC exhibits structured selectivity, which may facilitate complex behaviors by efficiently generating informative representations of multiple variables.

}, doi = {10.1101/2023.01.16.524214}, url = {https://doi.org/10.1101/2023.01.16.524214}, author = {Claudia B{\"o}hm and Albert K. Lee} } @article {68960, title = {Functionalization and higher-order organization of liposomes with DNA nanostructures.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 Aug 29}, pages = {5256}, abstract = {

Small unilamellar vesicles (SUVs) are indispensable model membranes, organelle mimics, and drug and vaccine carriers. However, the lack of robust techniques to functionalize or organize preformed SUVs limits their applications. Here we use DNA nanostructures to coat, cluster, and pattern sub-100-nm liposomes, generating distance-controlled vesicle networks, strings and dimers, among other configurations. The DNA coating also enables attachment of proteins to liposomes, and temporal control of membrane fusion driven by SNARE protein complexes. Such a convenient and versatile method of engineering premade vesicles both structurally and functionally is highly relevant to bottom-up biology and targeted delivery.

}, keywords = {Blister, DNA, Engineering, Humans, Liposomes, Nanostructures, Polymers}, issn = {2041-1723}, doi = {10.1038/s41467-023-41013-2}, author = {Zhang, Zhao and Feng, Zhaomeng and Zhao, Xiaowei and Jean, Dominique and Yu, Zhiheng and Chapman, Edwin R} } @article {68676, title = {Fundamental law underlying predictive remapping}, journal = {Physical Review Research}, volume = {5}, year = {2023}, month = {2023 Mar 29}, abstract = {

Predictive remapping (PRE ){\textemdash}the ability of cells in retinotopic brain structures to transiently exhibit spatiotemporal shifts beyond the spatial extent of their classical anatomical receptive fields{\textemdash}has been proposed as a primary mechanism that stabilizes an organism{\textquoteright}s percept of the visual world around the time of a saccadic eye movement. Despite the well-documented effects of PRE , a biologically plausible mathematical framework that specifies a fundamental law and the functional neural architecture that actively mediates this ubiquitous phenomenon does not exist. We introduce the Newtonian model of PRE , where each modular component of PRE manifests as three temporally overlapping forces: centripetal ( fC ), convergent ( fP ), and translational ( fT ), that perturb retinotopic cells from their equilibrium extent. The resultant and transient influences of these forces fC + fP + fT gives rise to a neuronal force field that governs the spatiotemporal dynamics of PRE . This neuronal force field fundamentally obeys an inverse-distance law PRE ∝ 1 r1.6 , akin to Newton{\textquoteright}s law of universal gravitation [I. Newton, Newton{\textquoteright}s Principia: The Mathematical Principles of Natural Philosophy (Geo. P. Putnam, New-York, 1850)] and activates retinotopic elastic fields elϕ{\textquoteright}s. We posit that elϕ{\textquoteright}s are transient functional neural structures that are self-generated by visual systems during active vision and approximate the sloppiness (or degrees of spatial freedom) within which receptive fields are allowed to shift, while ensuring that retinotopic organization does not collapse. The predictions of this general model are borne out by the spatiotemporal changes in visual sensitivity to probe stimuli in human subjects around the time of an eye movement and qualitatively match neural sensitivity signatures associated with predictive shifts in the receptive fields of cells in premotor and higher-order retinotopic brain structures. The introduction of this general model opens the search for possible biophysical implementations and provides experimentalists with a simple, elegant, yet powerful mathematical framework they can now use to generate experimentally testable predictions across a range of biological systems.

}, doi = {10.1103/PhysRevResearch.5.013214}, url = {https://link.aps.org/doi/10.1103/PhysRevResearch.5.013214}, author = {Adeyefa-Olasupo, Ifedayo-Emmanuel} } @article {68772, title = {Glutamate indicators with improved activation kinetics and localization for imaging synaptic transmission.}, journal = {Nature Methods}, volume = {20}, year = {2023}, month = {2023 Jun 01}, abstract = {

The fluorescent glutamate indicator iGluSnFR enables imaging of neurotransmission with genetic and molecular specificity. However, existing iGluSnFR variants exhibit low in vivo signal-to-noise ratios, saturating activation kinetics and exclusion from postsynaptic densities. Using a multiassay screen in bacteria, soluble protein and cultured neurons, we generated variants with improved signal-to-noise ratios and kinetics. We developed surface display constructs that improve iGluSnFR{\textquoteright}s nanoscopic localization to postsynapses. The resulting indicator iGluSnFR3 exhibits rapid nonsaturating activation kinetics and reports synaptic glutamate release with decreased saturation and increased specificity versus extrasynaptic signals in cultured neurons. Simultaneous imaging and electrophysiology at individual boutons in mouse visual cortex showed that iGluSnFR3 transients report single action potentials with high specificity. In vibrissal sensory cortex layer 4, we used iGluSnFR3 to characterize distinct patterns of touch-evoked feedforward input from thalamocortical boutons and both feedforward and recurrent input onto L4 cortical neuron dendritic spines.

}, issn = {1548-7105}, doi = {10.1038/s41592-023-01863-6}, author = {Aggarwal, Abhi and Liu, Rui and Chen, Yang and Ralowicz, Amelia J and Bergerson, Samuel J and Tomaska, Filip and Mohar, Boaz and Hanson, Timothy L and Hasseman, Jeremy P and Reep, Daniel and Tsegaye, Getahun and Yao, Pantong and Ji, Xiang and Kloos, Marinus and Walpita, Deepika and Patel, Ronak and Mohr, Manuel A and Tillberg, Paul W and Looger, Loren L and Marvin, Jonathan S and Hoppa, Michael B and Konnerth, Arthur and Kleinfeld, David and Schreiter, Eric R and Podgorski, Kaspar} } @article {68595, title = {Hacking brain development to test models of sensory coding}, journal = {bioRxiv}, year = {2023}, month = {2023 Jan 26}, abstract = {

Animals can discriminate myriad sensory stimuli but can also generalize from learned experience. You can probably distinguish the favorite teas of your colleagues while still recognizing that all tea pales in comparison to coffee. Tradeoffs between detection, discrimination, and generalization are inherent at every layer of sensory processing. During development, specific quantitative parameters are wired into perceptual circuits and set the playing field on which plasticity mechanisms play out. A primary goal of systems neuroscience is to understand how material properties of a circuit define the logical operations{\textemdash} computations--that it makes, and what good these computations are for survival. A cardinal method in biology{\textemdash}and the mechanism of evolution--is to change a unit or variable within a system and ask how this affects organismal function. Here, we make use of our knowledge of developmental wiring mechanisms to modify hard-wired circuit parameters in the\ Drosophila melanogaster\ mushroom body and assess the functional and behavioral consequences. By altering the number of expansion layer neurons (Kenyon cells) and their dendritic complexity, we find that input number, but not cell number, tunes odor selectivity. Simple odor discrimination performance is maintained when Kenyon cell number is reduced and augmented by Kenyon cell expansion.

}, doi = {10.1101/2023.01.25.525425}, url = {https://doi.org/10.1101/2023.01.25.525425}, author = {Maria Ahmed and Adithya E. Rajagopalan and Yijie Pan and Ye Li and Donnell L. Williams and Erik A. Pedersen and Manav Thakral and Angelica Previero and Kari C. Close and Christina P. Christoforou and Dawen Cai and Glenn C. Turner and Josephine Clowney} } @article {68008, title = {Hierarchical architecture of dopaminergic circuits enables second-order conditioning in Drosophila}, journal = {eLife}, year = {2023}, month = {2023 Jan 24}, abstract = {

Dopaminergic neurons with distinct projection patterns and physiological properties compose memory subsystems in a brain. However, it is poorly understood whether or how they interact during complex learning. Here, we identify a feedforward circuit formed between dopamine subsystems and show that it is essential for second-order conditioning, an ethologically important form of higher-order associative learning. The\ Drosophila\ mushroom body comprises a series of dopaminergic compartments, each of which exhibits distinct memory dynamics. We find that a slow and stable memory compartment can serve as an effective {\textquotedblleft}teacher{\textquotedblright} by instructing other faster and transient memory compartments via a single key interneuron, which we identify by connectome analysis and neurotransmitter prediction. This excitatory interneuron acquires enhanced response to reward-predicting odor after first-order conditioning and, upon activation, evokes dopamine release in the {\textquotedblleft}student{\textquotedblright} compartments. These hierarchical connections between dopamine subsystems explain distinct properties of first- and second-order memory long known by behavioral psychologists.

}, doi = {10.7554/eLife.79042}, url = {https://doi.org/10.7554/eLife.79042}, author = {Daichi Yamada and Daniel Bushey and Li Feng and Karen Hibbard and Megan Sammons and Jan Funke and Ashok Litwin-Kumar and Toshihide Hige and Yoshinori Aso} } @article {69076, title = {High-fidelity 3D live-cell nanoscopy through data-driven enhanced super-resolution radial fluctuation.}, journal = {Nature Methods}, year = {2023}, month = {2023 Nov 13}, abstract = {

Live-cell super-resolution microscopy enables the imaging of biological structure dynamics below the diffraction limit. Here we present enhanced super-resolution radial fluctuations (eSRRF), substantially improving image fidelity and resolution compared to the original SRRF method. eSRRF incorporates automated parameter optimization based on the data itself, giving insight into the trade-off between resolution and fidelity. We demonstrate eSRRF across a range of imaging modalities and biological systems. Notably, we extend eSRRF to three dimensions by combining it with multifocus microscopy. This realizes live-cell volumetric super-resolution imaging with an acquisition speed of ~1 volume per second. eSRRF provides an accessible super-resolution approach, maximizing information extraction across varied experimental conditions while minimizing artifacts. Its optimal parameter prediction strategy is generalizable, moving toward unbiased and optimized analyses in super-resolution microscopy.

}, issn = {1548-7105}, doi = {10.1038/s41592-023-02057-w}, author = {Laine, Romain F and Heil, Hannah S and Coelho, Simao and Nixon-Abell, Jonathon and Jimenez, Ang{\'e}lique and Wiesner, Theresa and Mart{\'\i}nez, Dami{\'a}n and Galgani, Tommaso and R{\'e}gnier, Louise and Stubb, Aki and Follain, Gautier and Webster, Samantha and Goyette, Jesse and Dauphin, Aurelien and Salles, Audrey and Culley, Si{\^a}n and Jacquemet, Guillaume and Hajj, Bassam and Leterrier, Christophe and Henriques, Ricardo} } @article {68560, title = {Hippocampal spatial representations exhibit a hyperbolic geometry that expands with experience.}, journal = {Nature Neuroscience}, volume = {26}, year = {2023}, month = {2023 Jan 01}, pages = {131-139}, abstract = {

Daily experience suggests that we perceive distances near us linearly. However, the actual geometry of spatial representation in the brain is unknown. Here we report that neurons in the CA1 region of rat hippocampus that mediate spatial perception represent space according to a non-linear hyperbolic geometry. This geometry uses an exponential scale and yields greater positional information than a linear scale. We found that the size of the representation matches the optimal predictions for the number of CA1 neurons. The representations also dynamically expanded proportional to the logarithm of time that the animal spent exploring the environment, in correspondence with the maximal mutual information that can be received. The dynamic changes tracked even small variations due to changes in the running speed of the animal. These results demonstrate how neural circuits achieve efficient representations using dynamic hyperbolic geometry.

}, keywords = {Animals, Brain, CA1 Region, Hippocampal, Hippocampus, Neurons, Rats, Space Perception}, issn = {1546-1726}, doi = {10.1038/s41593-022-01212-4}, author = {Zhang, Huanqiu and Rich, P Dylan and Lee, Albert K and Sharpee, Tatyana O} } @article {68957, title = {Hydrophobic interactions dominate the recognition of a KRAS G12V neoantigen.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 Aug 21}, pages = {5063}, abstract = {

Specificity remains a major challenge to current therapeutic strategies for cancer. Mutation associated neoantigens (MANAs) are products of genetic alterations, making them highly specific therapeutic targets. MANAs are HLA-presented (pHLA) peptides derived from intracellular mutant proteins that are otherwise inaccessible to antibody-based therapeutics. Here, we describe the cryo-EM structure of an antibody-MANA pHLA complex. Specifically, we determine a TCR mimic (TCRm) antibody bound to its MANA target, the KRAS peptide presented by HLA-A*03:01. Hydrophobic residues appear to account for the specificity of the mutant G12V residue. We also determine the structure of the wild-type G12 peptide bound to HLA-A*03:01, using X-ray crystallography. Based on these structures, we perform screens to validate the key residues required for peptide specificity. These experiments led us to a model for discrimination between the mutant and the wild-type peptides presented on HLA-A*03:01 based exclusively on hydrophobic interactions.

}, keywords = {Antibodies, HLA-A Antigens, Hydrophobic and Hydrophilic Interactions, Proto-Oncogene Proteins p21(ras), Recognition, Psychology}, issn = {2041-1723}, doi = {10.1038/s41467-023-40821-w}, author = {Wright, Katharine M and DiNapoli, Sarah R and Miller, Michelle S and Aitana Azurmendi, P and Zhao, Xiaowei and Yu, Zhiheng and Chakrabarti, Mayukh and Shi, WuXian and Douglass, Jacqueline and Hwang, Michael S and Hsiue, Emily Han-Chung and Mog, Brian J and Pearlman, Alexander H and Paul, Suman and Konig, Maximilian F and Pardoll, Drew M and Bettegowda, Chetan and Papadopoulos, Nickolas and Kinzler, Kenneth W and Vogelstein, Bert and Zhou, Shibin and Gabelli, Sandra B} } @article {68697, title = {Identifying determinants of synaptic specificity by integrating connectomes and transcriptomes}, journal = {bioRxiv}, year = {2023}, month = {2023 Apr 04}, abstract = {

How do developing neurons select their synaptic partners? To identify molecules matching synaptic partners, we integrated the synapse-level connectome of neural circuits with the developmental expression patterns and binding specificities of cell adhesion molecules (CAMs) on pre- and postsynaptic neurons. We focused on parallel synaptic pathways in the Drosophila visual system, in which closely related neurons form synapses onto closely related target neurons. We show that the choice of synaptic partners correlates with the matching expression of receptor-ligand pairs of Beat and Side proteins of the immunoglobulin superfamily (IgSF) CAMs. Genetic analysis demonstrates that these proteins determine the choice between alternative synaptic targets. Combining transcriptomes, connectomes, and protein interactome maps provides a framework to uncover the molecular logic of synaptic connectivity.

}, doi = {10.1101/2023.04.03.534791}, url = {https://doi.org/10.1101/2023.04.03.534791}, author = {Juyoun Yoo and Mark Dombrovski and Parmis Mirshahidi and Aljoscha Nern and Samuel A. LoCascio and S. Lawrence Zipursky and Yerbol Z. Kurmangaliyev} } @article {69055, title = {Imagining the future of optical microscopy: everything, everywhere, all at once.}, journal = {Communications Biology}, volume = {6}, year = {2023}, month = {2023 Oct 28}, pages = {1096}, abstract = {

The optical microscope has revolutionized biology since at least the 17 Century. Since then, it has progressed from a largely observational tool to a powerful bioanalytical platform. However, realizing its full potential to study live specimens is hindered by a daunting array of technical challenges. Here, we delve into the current state of live imaging to explore the barriers that must be overcome and the possibilities that lie ahead. We venture to envision a future where we can visualize and study everything, everywhere, all at once - from the intricate inner workings of a single cell to the dynamic interplay across entire organisms, and a world where scientists could access the necessary microscopy technologies anywhere.

}, keywords = {Microscopy}, issn = {2399-3642}, doi = {10.1038/s42003-023-05468-9}, author = {Balasubramanian, Harikrushnan and Hobson, Chad M and Chew, Teng-Leong and Aaron, Jesse S} } @article {68562, title = {In situ cryo-electron tomography reveals the asymmetric architecture of mammalian sperm axonemes.}, journal = {Nature Structural \& Molecular Biology}, volume = {30}, year = {2023}, month = {2023 Mar 01}, pages = {360-9}, abstract = {

The flagella of mammalian sperm display non-planar, asymmetric beating, in contrast to the planar, symmetric beating of flagella from sea urchin sperm and unicellular organisms. The molecular basis of this difference is unclear. Here, we perform in situ cryo-electron tomography of mouse and human sperm, providing the highest-resolution structural information to date. Our subtomogram averages reveal mammalian sperm-specific protein complexes within the microtubules, the radial spokes and nexin-dynein regulatory complexes. The locations and structures of these complexes suggest potential roles in enhancing the mechanical strength of mammalian sperm axonemes and regulating dynein-based axonemal bending. Intriguingly, we find that each of the nine outer microtubule doublets is decorated with a distinct combination of sperm-specific complexes. We propose that this asymmetric distribution of proteins differentially regulates the sliding of each microtubule doublet and may underlie the asymmetric beating of mammalian sperm.

}, issn = {1545-9985}, doi = {10.1038/s41594-022-00861-0}, author = {Chen, Zhen and Greenan, Garrett A and Shiozaki, Momoko and Liu, Yanxin and Skinner, Will M and Zhao, Xiaowei and Zhao, Shumei and Yan, Rui and Yu, Zhiheng and Lishko, Polina V and Agard, David A and Vale, Ronald D} } @article {68837, title = {Input density tunes Kenyon cell sensory responses in the Drosophila mushroom body.}, journal = {Current Biology}, year = {2023}, month = {2023 Jun 20}, abstract = {

The ability to discriminate sensory stimuli with overlapping features is thought to arise in brain structures called expansion layers, where neurons carrying information about sensory features make combinatorial connections onto a much larger set of cells. For 50 years, expansion coding has been a prime topic of theoretical neuroscience, which seeks to explain how quantitative parameters of the expansion circuit influence sensory sensitivity, discrimination, and generalization. Here, we investigate the developmental events that produce the quantitative parameters of the arthropod expansion layer, called the mushroom body. Using Drosophila melanogaster as a model, we employ genetic and chemical tools to engineer changes to circuit development. These allow us to produce living animals with hypothesis-driven variations on natural expansion layer wiring parameters. We then test the functional and behavioral consequences. By altering the number of expansion layer neurons (Kenyon cells) and their dendritic complexity, we find that input density, but not cell number, tunes neuronal odor selectivity. Simple odor discrimination behavior is maintained when the Kenyon cell number is reduced and augmented by Kenyon cell number expansion. Animals with increased input density to each Kenyon cell show increased overlap in Kenyon cell odor responses and become worse at odor discrimination tasks.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2023.05.064}, author = {Ahmed, Maria and Rajagopalan, Adithya E and Pan, Yijie and Li, Ye and Williams, Donnell L and Pedersen, Erik A and Thakral, Manav and Previero, Angelica and Close, Kari C and Christoforou, Christina P and Cai, Dawen and Turner, Glenn C and Clowney, E Josephine} } @article {68886, title = {Input density tunes Kenyon cell sensory responses in the Drosophila mushroom body.}, journal = {Current Biology}, volume = {33}, year = {2023}, month = {2023 Jul 10}, pages = {2742-2760.e12}, abstract = {

The ability to discriminate sensory stimuli with overlapping features is thought to arise in brain structures called expansion layers, where neurons carrying information about sensory features make combinatorial connections onto a much larger set of cells. For 50 years, expansion coding has been a prime topic of theoretical neuroscience, which seeks to explain how quantitative parameters of the expansion circuit influence sensory sensitivity, discrimination, and generalization. Here, we investigate the developmental events that produce the quantitative parameters of the arthropod expansion layer, called the mushroom body. Using Drosophila melanogaster as a model, we employ genetic and chemical tools to engineer changes to circuit development. These allow us to produce living animals with hypothesis-driven variations on natural expansion layer wiring parameters. We then test the functional and behavioral consequences. By altering the number of expansion layer neurons (Kenyon cells) and their dendritic complexity, we find that input density, but not cell number, tunes neuronal odor selectivity. Simple odor discrimination behavior is maintained when the Kenyon cell number is reduced and augmented by Kenyon cell number expansion. Animals with increased input density to each Kenyon cell show increased overlap in Kenyon cell odor responses and become worse at odor discrimination tasks.

}, keywords = {Animals, Drosophila, Drosophila melanogaster, Drosophila Proteins, Mushroom Bodies, Neurons, Odorants}, issn = {1879-0445}, doi = {10.1016/j.cub.2023.05.064}, author = {Ahmed, Maria and Rajagopalan, Adithya E and Pan, Yijie and Li, Ye and Williams, Donnell L and Pedersen, Erik A and Thakral, Manav and Previero, Angelica and Close, Kari C and Christoforou, Christina P and Cai, Dawen and Turner, Glenn C and Clowney, E Josephine} } @article {68934, title = {Investigating the composition and recruitment of the mycobacterial ImuA{\textquoteright}-ImuB-DnaE2 mutasome.}, journal = {eLife}, volume = {12}, year = {2023}, month = {2023 Aug 02}, abstract = {

A DNA damage-inducible mutagenic gene cassette has been implicated in the emergence of drug resistance in during anti-tuberculosis (TB) chemotherapy. However, the molecular composition and operation of the encoded {\textquoteright}mycobacterial mutasome{\textquoteright} - minimally comprising DnaE2 polymerase and ImuA{\textquoteright} and ImuB accessory proteins - remain elusive. Following exposure of mycobacteria to DNA damaging agents, we observe that DnaE2 and ImuB co-localize with the DNA polymerase III β subunit (β clamp) in distinct intracellular foci. Notably, genetic inactivation of the mutasome in an mutant containing a disrupted β clamp-binding motif abolishes ImuB-β clamp focus formation, a phenotype recapitulated pharmacologically by treating bacilli with griselimycin and in biochemical assays in which this β clamp-binding antibiotic collapses pre-formed ImuB-β clamp complexes. These observations establish the essentiality of the ImuB-β clamp interaction for mutagenic DNA repair in mycobacteria, identifying the mutasome as target for adjunctive therapeutics designed to protect anti-TB drugs against emerging resistance.

}, keywords = {Antitubercular Agents, Bacterial Proteins, DNA Repair, Mutagenesis, Mycobacterium tuberculosis}, issn = {2050-084X}, doi = {10.7554/eLife.75628}, author = {Gessner, Sophia and Martin, Zela Alexandria-Mae and Reiche, Michael A and Santos, Joana A and Dinkele, Ryan and Ramudzuli, Atondaho and Dhar, Neeraj and de Wet, Timothy J and Anoosheh, Saber and Lang, Dirk M and Aaron, Jesse and Chew, Teng-Leong and Herrmann, Jennifer and M{\"u}ller, Rolf and McKinney, John D and Woodgate, Roger and Mizrahi, Valerie and Venclovas, {\v C}eslovas and Lamers, Meindert H and Warner, Digby F} } @article {68832, title = {The Janelia Atalanta plasmids provide a simple and efficient CRISPR/Cas9-mediated homology directed repair platform for Drosophila}, journal = {bioRxiv}, year = {2023}, month = {2023 Jun 17}, abstract = {

Homology-directed repair (HDR) is a powerful tool for modifying genomes in precise ways to address many biological questions. Use of Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR)-Cas9 induced targeted DNA double-strand breakage has substantially simplified use of homology-directed repair to introduce specific perturbations in\ Drosophila, but existing platforms for CRISPR-Cas9-mediated HDR in\ Drosophila\ involve multiple cloning steps and have low efficiency. To simplify cloning of HDR plasmids, we designed a new plasmid platform, the Janelia Atalanta (pJAT) series, that exploits recent advances in dsDNA synthesis to facilitate Gateway cloning of gRNA sequences and homology arms in one step. Surprisingly, the pJAT plasmids yielded considerably higher HDR efficiency (approximately 25\%) than we have observed with other approaches. pJAT plasmids work in multiple\ Drosophila\ species and exhibited such high efficiency that previously impossible experiments in\ Drosophila, such as driving targeted chromosomal inversions, were made possible. We provide pJAT plasmids for a range of commonly performed experiments including targeted insertional mutagenesis, insertion of phiC31-mediated attP landing sites, generation of strains carrying a germ-line source of Cas9, and induction of chromosomal rearrangements. We also provide {\textquotedblleft}empty{\textquotedblright} pJAT plasmids with multiple cloning sites to simplify construction of plasmids with new functionality. The pJAT platform is generic and may facilitate improved efficiency CRISPR-Cas9 HDR in a wide range of model and non-model organisms.

}, doi = {10.1101/2023.06.17.545412}, url = {https://doi.org/10.1101/2023.06.17.545412}, author = {David L. Stern and Elizabeth Kim and Emily L. Behrman} } @article {69126, title = {Ketamine modulates a norepinephrine-astroglial circuit to persistently suppress futility-induced passivity.}, journal = {bioRxiv}, year = {2023}, month = {2023 Dec 29}, abstract = {

Mood-altering compounds hold promise for the treatment of many psychiatric disorders, such as depression, but connecting their molecular, circuit, and behavioral effects has been challenging. Here we find that, analogous to effects in rodent learned helplessness models, ketamine pre-exposure persistently suppresses futility-induced passivity in larval zebrafish. While antidepressants are thought to primarily act on neurons, brain-wide imaging in behaving zebrafish showed that ketamine elevates intracellular calcium in astroglia for many minutes, followed by persistent calcium downregulation post-washout. Calcium elevation depends on astroglial α1-adrenergic receptors and is required for suppression of passivity. Chemo-/optogenetic perturbations of noradrenergic neurons and astroglia demonstrate that the aftereffects of glial calcium elevation are sufficient to suppress passivity by inhibiting neuronal-astroglial integration of behavioral futility. Imaging in mouse cortex reveals that ketamine elevates astroglial calcium through conserved pathways, suggesting that ketamine exerts its behavioral effects by persistently modulating evolutionarily ancient neuromodulatory systems spanning neurons and astroglia.

}, doi = {10.1101/2022.12.29.522099}, url = {https://doi.org/10.1101/2022.12.29.522099}, author = {Marc Duque and Alex B. Chen and Eric Hsu and Sujatha Narayan and Altyn Rymbek and Shahinoor Begum and Gesine Saher and Adam E. Cohen and David E. Olson and David A. Prober and Dwight E. Bergles and Mark C. Fishman and Florian Engert and Misha B. Ahrens} } @article {69053, title = {Lactate biosensors for spectrally and spatially multiplexed fluorescence imaging.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 Oct 27}, pages = {6598}, abstract = {

L-Lactate is increasingly appreciated as a key metabolite and signaling molecule in mammals. However, investigations of the inter- and intra-cellular dynamics of L-lactate are currently hampered by the limited selection and performance of L-lactate-specific genetically encoded biosensors. Here we now report a spectrally and functionally orthogonal pair of high-performance genetically encoded biosensors: a green fluorescent extracellular L-lactate biosensor, designated eLACCO2.1, and a red fluorescent intracellular L-lactate biosensor, designated R-iLACCO1. eLACCO2.1 exhibits excellent membrane localization and robust fluorescence response. To the best of our knowledge, R-iLACCO1 and its affinity variants exhibit larger fluorescence responses than any previously reported intracellular L-lactate biosensor. We demonstrate spectrally and spatially multiplexed imaging of L-lactate dynamics by coexpression of eLACCO2.1 and R-iLACCO1 in cultured cells, and in vivo imaging of extracellular and intracellular L-lactate dynamics in mice.

}, keywords = {Animals, Biosensing Techniques, Cells, Cultured, Fluorescence Resonance Energy Transfer, Lactic Acid, Mammals, Mice, Optical Imaging}, issn = {2041-1723}, doi = {10.1038/s41467-023-42230-5}, author = {Nasu, Yusuke and Aggarwal, Abhi and Le, Giang N T and Vo, Camilla Trang and Kambe, Yuki and Wang, Xinxing and Beinlich, Felix R M and Lee, Ashley Bomin and Ram, Tina R and Wang, Fangying and Gorzo, Kelsea A and Kamijo, Yuki and Boisvert, Marc and Nishinami, Suguru and Kawamura, Genki and Ozawa, Takeaki and Toda, Hirofumi and Gordon, Grant R and Ge, Shaoyu and Hirase, Hajime and Nedergaard, Maiken and Paquet, Marie-Eve and Drobizhev, Mikhail and Podgorski, Kaspar and Campbell, Robert E} } @article {68607, title = {Large-scale brain-wide neural recording in nonhuman primates}, journal = {bioRxiv}, year = {2023}, month = {2023 Feb 04}, abstract = {

High-density, integrated silicon electrodes have begun to transform systems neuroscience, by enabling large-scale neural population recordings with single cell resolution. Existing technologies, however, have provided limited functionality in nonhuman primate species such as macaques, which offer close models of human cognition and behavior. Here, we report the design, fabrication, and performance of Neuropixels 1.0-NHP, a high channel count linear electrode array designed to enable large-scale simultaneous recording in superficial and deep structures within the macaque or other large animal brain. These devices were fabricated in two versions: 4416 electrodes along a 45 mm shank, and 2496 along a 25 mm shank. For both versions, users can programmably select 384 channels, enabling simultaneous multi-area recording with a single probe. We demonstrate recording from over 3000 single neurons within a session, and simultaneous recordings from over 1000 neurons using multiple probes. This technology represents a significant increase in recording access and scalability relative to existing technologies, and enables new classes of experiments involving fine-grained electrophysiological characterization of brain areas, functional connectivity between cells, and simultaneous brain-wide recording at scale.

}, doi = {10.1101/2023.02.01.526664}, url = {https://doi.org/10.1101/2023.02.01.526664}, author = {Eric M. Trautmann and Janis K. Hesse and Gabriel M. Stine and Ruobing Xia and Shude Zhu and Daniel J. O{\textquoteright}Shea and Bill Karsh and Jennifer Colonell and Frank F. Lanfranchi and Saurabh Vyas and Andrew Zimnik and Natalie A. Steinmann and Daniel A. Wagenaar and Alexandru Andrei and Carolina Mora Lopez and John O{\textquoteright}Callaghan and Jan Putzeys and Bogdan C. Raducanu and Marleen Welkenhuysen and Mark Churchland and Tirin Moore and Michael Shadlen and Krishna Shenoy and Doris Tsao and Barundeb Dutta and Timothy Harris} } @article {68774, title = {A leaky integrate-and-fire computational model based on the connectome of the entire adult Drosophila brain reveals insights into sensorimotor processing}, journal = {bioRxiv}, year = {2023}, month = {2023 May 02}, abstract = {

The forthcoming assembly of the adult\ Drosophila melanogaster\ central brain connectome, containing over 125,000 neurons and 50 million synaptic connections, provides a template for examining sensory processing throughout the brain. Here, we create a leaky integrate-and-fire computational model of the entire\ Drosophila\ brain, based on neural connectivity and neurotransmitter identity, to study circuit properties of feeding and grooming behaviors. We show that activation of sugar-sensing or water-sensing gustatory neurons in the computational model accurately predicts neurons that respond to tastes and are required for feeding initiation. Computational activation of neurons in the feeding region of the\ Drosophila\ brain predicts those that elicit motor neuron firing, a testable hypothesis that we validate by optogenetic activation and behavioral studies. Moreover, computational activation of different classes of gustatory neurons makes accurate predictions of how multiple taste modalities interact, providing circuit-level insight into aversive and appetitive taste processing. Our computational model predicts that the sugar and water pathways form a partially shared appetitive feeding initiation pathway, which our calcium imaging and behavioral experiments confirm. Additionally, we applied this model to mechanosensory circuits and found that computational activation of mechanosensory neurons predicts activation of a small set of neurons comprising the antennal grooming circuit that do not overlap with gustatory circuits, and accurately describes the circuit response upon activation of different mechanosensory subtypes. Our results demonstrate that modeling brain circuits purely from connectivity and predicted neurotransmitter identity generates experimentally testable hypotheses and can accurately describe complete sensorimotor transformations.

}, doi = {10.1101/2023.05.02.539144}, url = {https://doi.org/10.1101/2023.05.02.539144}, author = {Philip K. Shiu and Gabriella R. Sterne and Nico Spiller and Romain Franconville and Andrea Sandoval and Joie Zhou and Neha Simha and Chan Hyuk Kang and Seongbong Yu and Jinseop S. Kim and Sven Dorkenwald and Arie Matsliah and Philipp Schlegel and Szi-chieh Yu and Claire E. McKellar and Amy Sterling and Marta Costa and Katharina Eichler and Gregory S.X.E. Jefferis and Mala Murthy and Alexander Shakeel Bates and Nils Eckstein and Jan Funke and Salil S. Bidaye and Stefanie Hampel and Andrew M. Seeds and Kristin Scott} } @article {68771, title = {Lipid flipping in the omega-3 fatty-acid transporter.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 May 08}, pages = {2571}, abstract = {

Mfsd2a is the transporter for docosahexaenoic acid (DHA), an omega-3 fatty acid, across the blood brain barrier (BBB). Defects in Mfsd2a are linked to ailments from behavioral and motor dysfunctions to microcephaly. Mfsd2a transports long-chain unsaturated fatty-acids, including DHA and α-linolenic acid (ALA), that are attached to the zwitterionic lysophosphatidylcholine (LPC) headgroup. Even with the recently determined structures of Mfsd2a, the molecular details of how this transporter performs the energetically unfavorable task of translocating and flipping lysolipids across the lipid bilayer remains unclear. Here, we report five single-particle cryo-EM structures of Danio rerio Mfsd2a (drMfsd2a): in the inward-open conformation in the ligand-free state and displaying lipid-like densities modeled as ALA-LPC at four distinct\ positions. These Mfsd2a snapshots detail the flipping mechanism for lipid-LPC from outer to inner membrane leaflet and release for membrane integration on the cytoplasmic side. These results also map Mfsd2a mutants that disrupt lipid-LPC transport and are associated with disease.

}, keywords = {Biological Transport, Blood-Brain Barrier, Docosahexaenoic Acids, Fatty Acids, Omega-3, Lysophosphatidylcholines, Membrane Transport Proteins, Symporters}, issn = {2041-1723}, doi = {10.1038/s41467-023-37702-7}, author = {Nguyen, Chi and Lei, Hsiang-Ting and Lai, Louis Tung Faat and Gallenito, Marc J and Mu, Xuelang and Matthies, Doreen and Gonen, Tamir} } @article {68564, title = {Local shape descriptors for neuron segmentation.}, journal = {Nature Methods}, volume = {20}, year = {2023}, month = {2023 Feb 01}, pages = {295-303}, abstract = {

We present an auxiliary learning task for the problem of neuron segmentation in electron microscopy volumes. The auxiliary task consists of the prediction of local shape descriptors (LSDs), which we combine with conventional voxel-wise direct neighbor affinities for neuron boundary detection. The shape descriptors capture local statistics about the neuron to be segmented, such as diameter, elongation, and direction. On a study comparing several existing methods across various specimen, imaging techniques, and resolutions, auxiliary learning of LSDs consistently increases segmentation accuracy of affinity-based methods over a range of metrics. Furthermore, the addition of LSDs promotes affinity-based segmentation methods to be on par with the current state of the art for neuron segmentation (flood-filling networks), while being two orders of magnitudes more efficient-a critical requirement for the processing of future petabyte-sized datasets.

}, issn = {1548-7105}, doi = {10.1038/s41592-022-01711-z}, author = {Sheridan, Arlo and Nguyen, Tri M and Deb, Diptodip and Lee, Wei-Chung Allen and Saalfeld, Stephan and Turaga, Srinivas C and Manor, Uri and Funke, Jan} } @article {68922, title = {Localization of fixed dipoles at high precision by accounting for sample drift during illumination}, journal = {Applied Physics Letters}, volume = {123}, year = {2023}, month = {2023 Jul 13}, abstract = {

Single molecule localization microscopy relies on the precise quantification of the position of single dye emitters in a sample. This precision is improved by the number of photons that can be detected from each molecule. Particularly recording at cryogenic temperatures dramatically reduces photobleaching and would, hence, in principle, allow the user to massively increase the illumination time to several seconds. The downside of long illuminations, however, would be image blur due to inevitable jitter or drift occurring during the illuminations, which deteriorates the localization precision. In this paper, we theoretically demonstrate that a parallel recording of the fiducial marker beads together with a fitting approach accounting for the full drift trajectory allows for largely eliminating drift effects for drift magnitudes of several hundred nanometers per frame. We showcase the method for linear and diffusional drift as well as oscillations, assuming fixed dipole orientations during each illumination.

}, issn = {0003-6951}, doi = {10.1063/5.0137834}, url = {https://doi.org/10.1063/5.0137834}, author = {Hinterer, Fabian and Schneider, Magdalena C. and Hubmer, Simon and L{\'o}pez-Mart{\'\i}nez, Montserrat and Ramlau, Ronny and Sch{\"u}tz, Gerhard J.} } @article {69009, title = {Low-latency extracellular spike assignment for high-density electrodes at single-neuron resolution}, journal = {bioRxiv}, year = {2023}, month = {2023 Sep 15}, abstract = {

Real-time neural signal processing is essential for brain-machine interfaces and closed-loop neuronal perturbations. However, most existing applications sacrifice cell-specific identity and temporal spiking information for speed. We developed a hybrid hardware-software system that utilizes a Field Programmable Gate Array (FPGA) chip to acquire and process data in parallel, enabling individual spikes from many simultaneously recorded neurons to be assigned single-neuron identities with 1-millisecond latency. The FPGA assigns labels, validated with ground-truth data, by comparing multichannel spike waveforms from tetrode or silicon probe recordings to a spike-sorted model generated offline in software. This platform allowed us to rapidly inactivate a region in vivo based on spikes from an upstream neuron before these spikes could excite the downstream region. Furthermore, we could decode animal location within 3 ms using data from a population of individual hippocampal neurons. These results demonstrate our system{\textquoteright}s suitability for a broad spectrum of research and clinical applications.

}, doi = {10.1101/2023.09.14.557854}, url = {https://doi.org/10.1101/2023.09.14.557854}, author = {Chongxi Lai and Dohoung Kim and Brian Lustig and Shinsuke Tanaka and Brian Barbarits and Lakshmi Narayan and Jennifer Colonell and Ole Paulsen and Albert K. Lee and Timothy D. Harris} } @article {68935, title = {Lysosomal release of amino acids at ER three-way junctions regulates transmembrane and secretory protein mRNA translation.}, journal = {bioRxiv}, year = {2023}, month = {2023 Aug 03}, abstract = {

One-third of the mammalian proteome is comprised of transmembrane and secretory proteins that are synthesized on endoplasmic reticulum (ER). Here, we investigate the spatial distribution and regulation of mRNAs encoding these membrane and secretory proteins (termed "secretome" mRNAs) through live cell, single molecule tracking to directly monitor the position and translation states of secretome mRNAs on ER and their relationship to other organelles. Notably, translation of secretome mRNAs occurred preferentially near lysosomes on ER marked by the ER junction-associated protein, Lunapark. Knockdown of Lunapark reduced the extent of secretome mRNA translation without affecting translation of other mRNAs. Less secretome mRNA translation also occurred when lysosome function was perturbed by raising lysosomal pH or inhibiting lysosomal proteases. Secretome mRNA translation near lysosomes was enhanced during amino acid deprivation. Addition of the integrated stress response inhibitor, ISRIB, reversed the translation inhibition seen in Lunapark knockdown cells, implying an eIF2 dependency. Altogether, these findings uncover a novel coordination between ER and lysosomes, in which local release of amino acids and other factors from ER-associated lysosomes patterns and regulates translation of mRNAs encoding secretory and membrane proteins.

}, doi = {10.1101/2023.08.01.551382}, author = {Choi, Heejun and Liao, Ya-Cheng and Yoon, Young J and Grimm, Jonathan and Lavis, Luke D and Singer, Robert H and Lippincott-Schwartz, Jennifer} } @article {68791, title = {Mapping memories: pulse-chase labeling reveals AMPA receptor dynamics during memory formation.}, journal = {bioRxiv}, year = {2023}, month = {2023 May 29}, abstract = {

A tool to map changes in synaptic strength during a defined time window could provide powerful insights into the mechanisms governing learning and memory. We developed a technique, Extracellular Protein Surface Labeling in Neurons (EPSILON), to map α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) insertion\ in vivo\ by pulse-chase labeling of surface AMPARs with membrane-impermeable dyes. This approach allows for single-synapse resolution maps of plasticity in genetically targeted neurons during memory formation. We investigated the relationship between synapse-level and cell-level memory encodings by mapping synaptic plasticity and cFos expression in hippocampal CA1 pyramidal cells upon contextual fear conditioning (CFC). We observed a strong correlation between synaptic plasticity and cFos expression, suggesting a synaptic mechanism for the association of cFos expression with memory engrams. The EPSILON technique is a useful tool for mapping synaptic plasticity and may be extended to investigate trafficking of other transmembrane proteins.

}, doi = {10.1101/2023.05.26.541296}, url = {https://doi.org/10.1101/2023.05.26.541296}, author = {Doyeon Kim and Pojeong Park and Xiuyuan Li and J. David Wong Campos and He Tian and Eric M. Moult and Jonathan B. Grimm and Luke Lavis and Adam E. Cohen} } @article {68700, title = {Mental navigation and telekinesis with a hippocampal map-based brain-machine interface}, journal = {bioRxiv}, year = {2023}, month = {2023 Apr 10}, abstract = {

The hippocampus is critical for recollecting and imagining experiences. This is believed to involve voluntarily drawing from hippocampal memory representations of people, events, and places, including the hippocampus{\textquoteright} map-like representations of familiar environments. However, whether the representations in such {\textquotedblleft}cognitive maps{\textquotedblright} can be volitionally and selectively accessed is unknown. We developed a brain-machine interface to test if rats could control their hippocampal activity in a flexible, goal-directed, model-based manner. We show that rats can efficiently navigate or direct objects to arbitrary goal locations within a virtual reality arena solely by activating and sustaining appropriate hippocampal representations of remote places. This should provide insight into the mechanisms underlying episodic memory recall, mental simulation/planning, and imagination, and open up possibilities for high-level neural prosthetics utilizing hippocampal representations.

}, doi = {10.1101/2023.04.07.536077}, url = {https://doi.org/10.1101/2023.04.07.536077}, author = {Chongxi Lai and Shinsuke Tanaka and Timothy D. Harris and Albert K. Lee} } @article {68586, title = {Mesolimbic dopamine adapts the rate of learning from action.}, journal = {Nature}, year = {2023}, month = {2023 Jan 18}, abstract = {

Recent success in training artificial agents and robots derives from a combination of direct learning of behavioural policies and indirect learning through value functions. Policy learning and value learning use distinct algorithms that optimize behavioural performance and reward prediction, respectively. In animals, behavioural learning and the role of mesolimbic dopamine signalling have been extensively evaluated with respect to reward prediction; however, so far there has been little consideration of how direct policy learning might inform our understanding. Here we used a comprehensive dataset of orofacial and body movements to understand how behavioural policies evolved as naive, head-restrained mice learned a trace conditioning paradigm. Individual differences in initial dopaminergic reward responses correlated with the emergence of learned behavioural policy, but not the emergence of putative value encoding for a predictive cue. Likewise, physiologically calibrated manipulations of mesolimbic dopamine produced several effects inconsistent with value learning but predicted by a neural-network-based model that used dopamine signals to set an adaptive rate, not an error signal, for behavioural policy learning. This work provides strong evidence that phasic dopamine activity can regulate direct learning of behavioural policies, expanding the explanatory power of reinforcement learning models for animal learning.

}, issn = {1476-4687}, doi = {10.1038/s41586-022-05614-z}, author = {Coddington, Luke T and Lindo, Sarah E and Dudman, Joshua T} } @article {68773, title = {Meta-learning in head fixed mice navigating in virtual reality: A Behavioral Analysis}, journal = {bioRxiv}, year = {2023}, month = {2023 May 02}, abstract = {

Animals can learn general task structures and use them to solve new problems with novel sensory specifics. This capacity of {\textquoteleft}learning to learn{\textquoteright}, or meta-learning, is difficult to achieve in artificial systems, and the mechanisms by which it is achieved in animals are unknown. As a step toward enabling mechanistic studies, we developed a behavioral paradigm that demonstrates meta-learning in head-fixed mice. We trained mice to perform a two-alternative forced-choice task in virtual reality (VR), and successively changed the visual cues that signaled reward location. Mice showed increased learning speed in both cue generalization and serial reversal tasks. During reversal learning, behavior exhibited sharp transitions, with the transition occurring earlier in each successive reversal. Analysis of motor patterns revealed that animals utilized similar motor programs to execute the same actions in response to different cues but modified the motor programs during reversal learning. Our study demonstrates that mice can perform meta-learning tasks in VR, thus opening up opportunities for future mechanistic studies.

}, doi = {10.1101/2023.05.01.538936}, url = {https://doi.org/10.1101/2023.05.01.538936}, author = {Xinyu Zhao and Rachel Gattoni and Andrea Kozlosky and Angela Jacobs and Colin Morrow and Sarah Lindo and Nelson Spruston} } @article {68149, title = {Metamorphosis of memory circuits in Drosophila reveal a strategy for evolving a larval brain.}, journal = {eLife}, year = {2023}, month = {2023 Jan 25}, abstract = {

Insects like\ Drosophila\ produce a second brain adapted to the form and behavior of a larva. Neurons for both larval and adult brains are produced by the same stem cells (neuroblasts) but the larva possesses only the earliest born neurons produced from each. To understand how a functional larval brain is made from this reduced set of neurons, we examined the origins and metamorphic fates of the neurons of the larval and adult mushroom body circuits. The adult mushroom body core is built sequentially of γ Kenyon cells, that form a medial lobe, followed by α{\textquoteright}β{\textquoteright}, and αβ Kenyon cells that form additional medial lobes and two vertical lobes. Extrinsic input (MBINs) and output (MBONs) neurons divide this core into computational compartments. The larval mushroom body contains only γ neurons. Its medial lobe compartments are roughly homologous to those of the adult and same MBONs are used for both. The larval vertical lobe, however, is an analogous {\textquotedblleft}facsimile{\textquotedblright} that uses a larval-specific branch on the γ neurons to make up for the missing α{\textquoteright}β{\textquoteright}, and αβ neurons. The extrinsic cells for the facsimile are early-born neurons that trans-differentiate to serve a mushroom body function in the larva and then shift to other brain circuits in the adult. These findings are discussed in the context of the evolution of a larval brain in insects with complete metamorphosis.

}, doi = {10.7554/eLife.80594}, url = {https://doi.org/110.7554/eLife.80594}, author = {James W. Truman and Jacquelyn Price and Rosa L. Miyares and Tzumin Lee} } @article {68836, title = {Method To Diversify Cyanine Chromophore Functionality Enables Improved Biomolecule Tracking and Intracellular Imaging.}, journal = {Journal of the American Chemical Society}, volume = {145}, year = {2023}, month = {2023 Jun 27}, pages = {14647{\textendash}14659}, abstract = {

Heptamethine indocyanines are invaluable probes for near-infrared (NIR) imaging. Despite broad use, there are only a few synthetic methods to assemble these molecules, and each has significant limitations. Here, we report the use of pyridinium benzoxazole (PyBox) salts as heptamethine indocyanine precursors. This method is high yielding, simple to implement, and provides access to previously unknown chromophore functionality. We applied this method to create molecules to address two outstanding objectives in NIR fluorescence imaging. First, we used an iterative approach to develop molecules for protein-targeted tumor imaging. When compared to common NIR fluorophores, the optimized probe increases the tumor specificity of monoclonal antibody (mAb) and nanobody conjugates. Second, we developed cyclizing heptamethine indocyanines with the goal of improving cellular uptake and fluorogenic properties. By modifying both the electrophilic and nucleophilic components, we demonstrate that the solvent sensitivity of the ring-open/ring-closed equilibrium can be modified over a wide range. We then show that a chloroalkane derivative of a compound with tuned cyclization properties undergoes particularly efficient no-wash live cell imaging using organelle-targeted HaloTag self-labeling proteins. Overall, the chemistry reported here broadens the scope of accessible chromophore functionality, and, in turn, enables the discovery of NIR probes with promising properties for advanced imaging applications.

}, issn = {1520-5126}, doi = {10.1021/jacs.3c01765}, author = {Usama, Syed Muhammad and Marker, Sierra C and Li, Dong-Hao and Caldwell, Donald R and Stroet, Marcus and Patel, Nimit L and Tebo, Alison G and Hernot, Sophie and Kalen, Joseph D and Schnermann, Martin} } @article {69103, title = {Mitochondrial GTP metabolism controls reproductive aging in C.~elegans.}, journal = {Developmental Cell}, volume = {58}, year = {2023}, month = {2023 Dec 04}, pages = {2718-2731.e7}, abstract = {

Healthy mitochondria are critical for reproduction. During aging, both reproductive fitness and mitochondrial homeostasis decline. Mitochondrial metabolism and dynamics are key factors in supporting mitochondrial homeostasis. However, how they are coupled to control reproductive health remains unclear. We report that mitochondrial GTP (mtGTP) metabolism acts through mitochondrial dynamics factors to regulate reproductive aging. We discovered that germline-only inactivation of GTP- but not ATP-specific succinyl-CoA synthetase (SCS) promotes reproductive longevity in Caenorhabditis elegans. We further identified an age-associated increase in mitochondrial clustering surrounding oocyte nuclei, which is attenuated by GTP-specific SCS inactivation. Germline-only induction of mitochondrial fission factors sufficiently promotes mitochondrial dispersion and reproductive longevity. Moreover, we discovered that bacterial inputs affect mtGTP levels and dynamics factors to modulate reproductive aging. These results demonstrate the significance of mtGTP metabolism in regulating oocyte mitochondrial homeostasis and reproductive longevity and identify mitochondrial fission induction as an effective strategy to improve reproductive health.

}, keywords = {Aging, Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Guanosine Triphosphate, Longevity, Mitochondria, Mitochondrial Dynamics, Reproduction}, issn = {1878-1551}, doi = {10.1016/j.devcel.2023.08.019}, author = {Lee, Yi-Tang and Savini, Marzia and Chen, Tao and Yang, Jin and Zhao, Qian and Ding, Lang and Gao, Shihong Max and Senturk, Mumine and Sowa, Jessica N and Wang, Jue D and Wang, Meng C} } @article {68998, title = {Mitochondrial GTP metabolism controls reproductive aging in C.~elegans.}, journal = {Developmental Cell}, year = {2023}, month = {2023 Sep 07}, abstract = {

Healthy mitochondria are critical for reproduction. During aging, both reproductive fitness and mitochondrial homeostasis decline. Mitochondrial metabolism and dynamics are key factors in supporting mitochondrial homeostasis. However, how they are coupled to control reproductive health remains unclear. We report that mitochondrial GTP (mtGTP) metabolism acts through mitochondrial dynamics factors to regulate reproductive aging. We discovered that germline-only inactivation of GTP- but not ATP-specific succinyl-CoA synthetase (SCS) promotes reproductive longevity in Caenorhabditis elegans. We further identified an age-associated increase in mitochondrial clustering surrounding oocyte nuclei, which is attenuated by GTP-specific SCS inactivation. Germline-only induction of mitochondrial fission factors sufficiently promotes mitochondrial dispersion and reproductive longevity. Moreover, we discovered that bacterial inputs affect mtGTP levels and dynamics factors to modulate reproductive aging. These results demonstrate the significance of mtGTP metabolism in regulating oocyte mitochondrial homeostasis and reproductive longevity and identify mitochondrial fission induction as an effective strategy to improve reproductive health.

}, issn = {1878-1551}, doi = {10.1016/j.devcel.2023.08.019}, author = {Lee, Yi-Tang and Savini, Marzia and Chen, Tao and Yang, Jin and Zhao, Qian and Ding, Lang and Gao, Shihong Max and Senturk, Mumine and Sowa, Jessica N and Wang, Jue D and Wang, Meng C} } @article {68696, title = {Mitochondrial GTP Metabolism Regulates Reproductive Aging}, journal = {bioRxiv}, year = {2023}, month = {2023 Apr 03}, abstract = {

Healthy mitochondria are critical for reproduction. During aging, both reproductive fitness and mitochondrial homeostasis decline. Mitochondrial metabolism and dynamics are key factors in supporting mitochondrial homeostasis. However, how they are coupled to control reproductive health remains unclear. We report that mitochondrial GTP metabolism acts through mitochondrial dynamics factors to regulate reproductive aging. We discovered that germline-only inactivation of GTP- but not ATP-specific succinyl-CoA synthetase (SCS), promotes reproductive longevity in\ Caenorhabditis elegans.\ We further revealed an age-associated increase in mitochondrial clustering surrounding oocyte nuclei, which is attenuated by the GTP-specific SCS inactivation. Germline-only induction of mitochondrial fission factors sufficiently promotes mitochondrial dispersion and reproductive longevity. Moreover, we discovered that bacterial inputs affect mitochondrial GTP and dynamics factors to modulate reproductive aging. These results demonstrate the significance of mitochondrial GTP metabolism in regulating oocyte mitochondrial homeostasis and reproductive longevity and reveal mitochondrial fission induction as an effective strategy to improve reproductive health.

}, doi = {10.1101/2023.04.02.535296}, url = {https://doi.org/10.1101/2023.04.02.535296}, author = {Yi-Tang Lee and Marzia Savini and Tao Chen and Jin Yang and Qian Zhao and Lang Ding and Shihong Max Gao and Mumine Senturk and Jessica Sowa and Jue D. Wang and Meng C. Wang} } @article {69127, title = {Model-Based Inference of Synaptic Plasticity Rules}, journal = {bioRxiv}, year = {2023}, month = {2023 Dec 12}, abstract = {

Understanding learning through synaptic plasticity rules in the brain is a grand challenge for neuroscience. Here we introduce a novel computational framework for inferring plasticity rules from experimental data on neural activity trajectories and behavioral learning dynamics. Our methodology parameterizes the plasticity function to provide theoretical interpretability and facilitate gradient-based optimization. For instance, we use Taylor series expansions or multilayer perceptrons to approximate plasticity rules, and we adjust their parameters via gradient descent over entire trajectories to closely match observed neural activity and behavioral data. Notably, our approach can learn intricate rules that induce long nonlinear time-dependencies, such as those incorporating postsynaptic activity and current synaptic weights. We validate our method through simulations, accurately recovering established rules, like Oja{\textquoteright}s, as well as more complex hypothetical rules incorporating reward-modulated terms. We assess the resilience of our technique to noise and, as a tangible application, apply it to behavioral data from\ Drosophila\ during a probabilistic reward-learning experiment. Remarkably, we identify an active forgetting component of reward learning in flies that enhances the predictive accuracy of previous models. Overall, our modeling framework provides an exciting new avenue to elucidate the computational principles governing synaptic plasticity and learning in the brain.

}, doi = {10.1101/2023.12.11.571103}, url = {https://doi.org/10.1101/2023.12.11.571103}, author = {Yash Mehta and Danil Tyulmankov and Adithya E. Rajagopalan and Glenn C. Turner and James E. Fitzgerald and Jan Funke} } @article {68783, title = {Modulation of calcium signaling {\textquotedblleft}on demand{\textquotedblright} to decipher the molecular mechanisms responsible for primary aldosteronism}, journal = {Archives of Cardiovascular Diseases Supplements}, volume = {15}, year = {2023}, month = {2023 May 01}, pages = {188}, abstract = {

Primary aldosteronism\ (PA) is the most frequent form of secondary hypertension. Over the past two decades, major advances have been made in our understanding of the disease with the identification of germline or somatic mutations in ion channels and pumps. These mutations enhance\ calcium signaling, the main trigger of\ aldosterone\ biosynthesis.

}, issn = {18786480}, doi = {10.1016/j.acvdsp.2023.03.021}, url = {https://doi.org/10.1016/j.acvdsp.2023.03.021}, author = {Fedlaoui, Bakhta and Cosentino, Teresa and Al Sayed, Zeina R. and Fernandes-Rosa, Fabio L. and Hulot, Jean-S{\'e}bastien and Magnus, Chris and Sternson, Scott M. and Travers-Allard, Simon and Baron, St{\'e}phanie and Giscos-Douriez, Isabelle and Zennaro, Maria Christina and Boulkroun, Sheerazed} } @article {68469, title = {Multimodal mapping of cell types and projections in the central nucleus of the amygdala}, journal = {eLife}, year = {2023}, month = {2023 Jan 20}, abstract = {

The central nucleus of the amygdala (CEA) is a brain region that integrates external and internal sensory information and executes innate and adaptive behaviors through distinct output pathways. Despite its complex functions, the diversity of molecularly defined neuronal types in the CEA and their contributions to major axonal projection targets have not been examined systematically. Here, we performed single-cell RNA-sequencing (scRNA-Seq) to classify molecularly defined cell types in the CEA and identified marker-genes to map the location of these neuronal types using\ expansion\ assisted iterative fluorescence in\ situ\ hybridization (EASI-FISH). We developed new methods to integrate EASI-FISH with 5-plex retrograde axonal labeling to determine the spatial, morphological, and connectivity properties of \~{}30,000 molecularly defined CEA neurons. Our study revealed spatio-molecular organization of the CEA, with medial and lateral CEA associated with distinct cell families. We also found a long-range axon projection network from the CEA, where target regions receive inputs from multiple molecularly defined cell types. Axon collateralization was found primarily among projections to hindbrain targets, which are distinct from forebrain projections. This resource reports marker-gene combinations for molecularly defined cell types and axon-projection types, which will be useful for selective interrogation of these neuronal populations to study their contributions to the diverse functions of the CEA.

}, doi = {10.7554/eLife.84262}, url = {https://doi.org/10.7554/eLife.84262}, author = {Yuhan Wang and Sabine Krabbe and Mark Eddison and Fredrick E. Henry and Greg Fleishman and Andrew L. Lemire and Lihua Wang and Wyatt Korff and Paul W. Tillberg and Andreas L{\"u}thi and Scott M. Sternson} } @article {68965, title = {Multiscale head anatomy of Megaphragma (Hymenoptera: Trichogrammatidae).}, journal = {Arthropod Structure and Development}, volume = {76}, year = {2023}, month = {2023 Sep 01}, pages = {101299}, abstract = {

Methods of three-dimensional electron microscopy have been actively developed recently and open up great opportunities for morphological work. This approach is especially useful for studying microinsects, since it is possible to obtain complete series of high-resolution sections of a whole insect. Studies on the genus Megaphragma are especially important, since the unique phenomenon of lysis of most of the neuron nuclei was discovered in species of this genus. In this study we reveal the anatomical structure of the head of Megaphragma viggianii at all levels from organs to subcellular structures. Despite the miniature size of the body, most of the organ systems of M.\ viggianii retain the structural plan and complexity of organization at all levels. The set of muscles and the well-developed stomatogastric nervous system of this species correspond to those of larger insects, and there is also a well-developed tracheal system in the head of this species. Reconstructions of the head of M.\ viggianii at the cellular and subcellular levels were obtained, and of volumetric data were analyzed. A total of 689 nucleated cells of the head were reconstructed. The ultrastructure of M.\ viggianii is surprisingly complex, and the evolutionary benefits of such complexity are probably among the factors limiting the further miniaturization of parasitoid wasps.

}, issn = {1873-5495}, doi = {10.1016/j.asd.2023.101299}, author = {Desyatirkina, Inna A and Makarova, Anastasia A and Pang, Song and Xu, C Shan and Hess, Harald and Polilov, Alexey A} } @article {69058, title = {Nanometer-scale views of visual cortex reveal anatomical features of primary cilia poised to detect synaptic spillover}, journal = {bioRxiv}, year = {2023}, month = {2023 Nov 01}, abstract = {

A primary cilium is a thin membrane-bound extension off a cell surface that contains receptors for perceiving and transmitting signals that modulate cell state and activity. While many cell types have a primary cilium, little is known about primary cilia in the brain, where they are less accessible than cilia on cultured cells or epithelial tissues and protrude from cell bodies into a deep, dense network of glial and neuronal processes. Here, we investigated cilia frequency, internal structure, shape, and position in large, high-resolution transmission electron microscopy volumes of mouse primary visual cortex. Cilia extended from the cell bodies of nearly all excitatory and inhibitory neurons, astrocytes, and oligodendrocyte precursor cells (OPCs), but were absent from oligodendrocytes and microglia. Structural comparisons revealed that the membrane structure at the base of the cilium and the microtubule organization differed between neurons and glia. OPC cilia were distinct in that they were the shortest and contained pervasive internal vesicles only occasionally observed in neuron and astrocyte cilia. Investigating cilia-proximal features revealed that many cilia were directly adjacent to synapses, suggesting cilia are well poised to encounter locally released signaling molecules. The internal anatomy, including microtubule changes and centriole location, defined key structural features including cilium placement and shape. Together, the anatomical insights both within and around neuron and glia cilia provide new insights into cilia formation and function across cell types in the brain.

}, doi = {10.1101/2023.10.31.564838}, url = {https://doi.org/10.1101/2023.10.31.564838}, author = {Carolyn M Ott and Russel Torres and Tung-Sheng Kuan and Aaron T Kuan and JoAnn Buchanan and Leila Elabbady and Sharmishtaa Seshamani and Agnes L Bodor and Forrest C Collman and Davi D Bock and Wei-Chung Allen Lee and Nuno Macarico da Costa and Jennifer Lippincott-Schwartz} } @article {68785, title = {Nanoparticle-based targeting of microglia improves the neural regeneration enhancing effects of immunosuppression in the zebrafish retina.}, journal = {Communications Biology}, volume = {6}, year = {2023}, month = {2023 May 18}, pages = {534}, abstract = {

Retinal M{\"u}ller glia function as injury-induced stem-like cells in zebrafish but not mammals. However, insights gleaned from zebrafish have been applied to stimulate nascent regenerative responses in the mammalian retina. For instance, microglia/macrophages regulate M{\"u}ller glia stem cell activity in the chick, zebrafish, and mouse. We previously showed that post-injury immunosuppression by the glucocorticoid dexamethasone accelerated retinal regeneration kinetics in zebrafish. Similarly, microglia ablation enhances regenerative outcomes in the mouse retina. Targeted immunomodulation of microglia reactivity may therefore enhance the regenerative potential of M{\"u}ller glia for therapeutic purposes. Here, we investigated potential mechanisms by which post-injury dexamethasone accelerates retinal regeneration kinetics, and the effects of dendrimer-based targeting of dexamethasone to reactive microglia. Intravital time-lapse imaging revealed that post-injury dexamethasone inhibited microglia reactivity. The dendrimer-conjugated formulation: (1) decreased dexamethasone-associated systemic toxicity, (2) targeted dexamethasone to reactive microglia, and (3) improved the regeneration enhancing effects of immunosuppression by increasing stem/progenitor proliferation rates. Lastly, we show that the gene rnf2 is required for the enhanced regeneration effect of D-Dex. These data support the use of dendrimer-based targeting of reactive immune cells to reduce toxicity and enhance the regeneration promoting effects of immunosuppressants in the retina.

}, keywords = {Animals, Dendrimers, Dexamethasone, Immunosuppression Therapy, Mammals, Mice, Microglia, Retina, Zebrafish}, issn = {2399-3642}, doi = {10.1038/s42003-023-04898-9}, author = {Emmerich, Kevin and White, David T and Kambhampati, Siva P and Casado, Grace L and Fu, Tian-Ming and Chunawala, Zeeshaan and Sahoo, Arpan and Nimmagadda, Saumya and Krishnan, Nimisha and Saxena, Meera T and Walker, Steven L and Betzig, Eric and Kannan, Rangaramanujam M and Mumm, Jeff S} } @article {69057, title = {Nanoscale imaging reveals the mechanisms of ER-to-Golgi transport via a dynamic tubular-vesicular network}, journal = {bioRxiv}, year = {2023}, month = {2023 Oct 27}, abstract = {

The endoplasmic reticulum (ER) and the Golgi apparatus are the first sorting stations along the secretory pathway of mammalian cells and have a crucial role in protein quality control and cellular homeostasis. While machinery components mediating ER-to-Golgi transport have been mapped, it is unclear how exchange between the two closely juxtaposed organelles is coordinated in living cells. Here, using gene editing to tag machinery components, live-cell confocal and stimulated emission depletion (STED) super-resolution microscopy, we show that ER-to-Golgi transport occurs via a dynamic network of tubules positive for the small GTPase ARF4. swCOPI machinery is tightly associated to this network and moves with tubular-vesicular structures. Strikingly, the ARF4 network appears to be continuous with the ER and ARF4 tubules remodel around static ER exit sites (ERES) defined by COPII machinery. We were further able to dissect the steps of ER-to-Golgi transport with functional trafficking assays. A wave of cargo released from the ER percolates through peripheral and Golgi-tethered ARF4 structures before filling the cis-Golgi. Perturbation via acute degradation of ARF4 shows an active regulatory role for the GTPase and COPI in anterograde transport. Our data supports a model in which anterograde ER-to-Golgi transport occurs via an ARF4 tubular-vesicular network directly connecting the ER and Golgi-associated pre-cisternae.

}, doi = {10.1101/2023.10.27.563951}, url = {https://doi.org/10.1101/2023.10.27.563951}, author = {Luis Wong-Dilworth and Gresy Bregu and Steffen Restel and Carmen Rodilla-Ramirez and Svenja Ebeling and Shelly Harel and Paula Leupold and Jonathan Grimm and Luke D. Lavis and Jessica Angulo-Capel and Felix Campelo and Francesca Bottanelli} } @article {68966, title = {The Neural Basis of Drosophila Courtship Song}, journal = {bioRxiv}, year = {2023}, month = {2023 Sep 01}, abstract = {

Animal sounds are produced by patterned vibrations of specific organs, but the neural circuits that drive these vibrations are not well defined in any animal. Here we provide a functional and synaptic map of most of the neurons in the\ Drosophila\ male ventral nerve cord (the analog of the vertebrate spinal cord) that drive complex, patterned song during courtship. Male\ Drosophila\ vibrate their wings toward females during courtship to produce two distinct song modes {\textendash} pulse and sine song {\textendash} with characteristic features that signal species identity and male quality. We identified song-producing neural circuits by optogenetically activating and inhibiting identified cell types in the ventral nerve cord (VNC) and by tracing their patterns of synaptic connectivity in the male VNC connectome. The core song circuit consists of at least eight cell types organized into overlapping circuits, where all neurons are required for pulse song and a subset are required for sine song. The pulse and sine circuits each include a feed-forward pathway from brain descending neurons to wing motor neurons, with extensive reciprocal and feed-back connections. We also identify specific neurons that shape the individual features of each song mode. These results reveal commonalities amongst diverse animals in the neural mechanisms that generate diverse motor patterns from a single set of muscles.

}, doi = {10.1101/2023.08.30.555537}, url = {https://doi.org/10.1101/2023.08.30.555537}, author = {Joshua L. Lillvis and Kaiyu Wang and Hiroshi M. Shiozaki and Min Xu and David L. Stern and Barry J. Dickson} } @article {68571, title = {Neural circuit mechanisms for transforming learned olfactory valences into wind-oriented movement}, journal = {eLife}, year = {2023}, month = {2023 Sep 18}, abstract = {

How memories are used by the brain to guide future action is poorly understood. In olfactory associative learning in Drosophila, multiple compartments of the mushroom body act in parallel to assign valence to a stimulus. Here, we show that appetitive memories stored in different compartments induce different levels of upwind locomotion. Using a photoactivation screen of a new collection of split-GAL4 drivers and EM connectomics, we identified a cluster of neurons postsynaptic to the mushroom body output neurons (MBONs) that can trigger robust upwind steering. These UpWind Neurons (UpWiNs) integrate inhibitory and excitatory synaptic inputs from MBONs of appetitive and aversive memory compartments, respectively. After training, disinhibition from the appetitive-memory MBONs enhances the response of UpWiNs to reward-predicting odors. Blocking UpWiNs impaired appetitive memory and reduced upwind locomotion during retrieval. Photoactivation of UpWiNs also increased the chance of returning to a location where activation was initiated, suggesting an additional role in olfactory navigation. Thus, our results provide insight into how learned abstract valences are gradually transformed into concrete memory-driven actions through divergent and convergent networks, a neuronal architecture that is commonly found in the vertebrate and invertebrate brains.

}, doi = {10.7554/eLife.85756}, url = {https://doi.org/10.7554/eLife.85756}, author = {Yoshinori Aso and Daichi Yamada and Daniel Bushey and Karen Hibbard and Megan Sammons and Hideo Otsuna and Yichun Shuai and Toshihide Hige} } @article {68918, title = {Nonlinear manifolds underlie neural population activity during behaviour.}, journal = {bioRxiv}, year = {2023}, month = {2023 Jul 21}, abstract = {

There is rich variety in the activity of single neurons recorded during behaviour. Yet, these diverse single neuron responses can be well described by relatively few patterns of neural co-modulation. The study of such low-dimensional structure of neural population activity has provided important insights into how the brain generates behaviour. Virtually all of these studies have used linear dimensionality reduction techniques to estimate these population-wide co-modulation patterns, constraining them to a flat "neural manifold". Here, we hypothesised that since neurons have nonlinear responses and make thousands of distributed and recurrent connections that likely amplify such nonlinearities, neural manifolds should be intrinsically nonlinear. Combining neural population recordings from monkey motor cortex, mouse motor cortex, mouse striatum, and human motor cortex, we show that: 1) neural manifolds are intrinsically nonlinear; 2) the degree of their nonlinearity varies across architecturally distinct brain regions; and 3) manifold nonlinearity becomes more evident during complex tasks that require more varied activity patterns. Simulations using recurrent neural network models confirmed the proposed relationship between circuit connectivity and manifold nonlinearity, including the differences across architecturally distinct regions. Thus, neural manifolds underlying the generation of behaviour are inherently nonlinear, and properly accounting for such nonlinearities will be critical as neuroscientists move towards studying numerous brain regions involved in increasingly complex and naturalistic behaviours.

}, doi = {10.1101/2023.07.18.549575}, url = {https://doi.org/10.1101/2023.07.18.549575}, author = {Fortunato, C{\'a}tia and Bennasar-V{\'a}zquez, Jorge and Park, Junchol and Chang, Joanna C and Miller, Lee E and Dudman, Joshua T and Perich, Matthew G and Gallego, Juan A} } @article {68635, title = {OME-Zarr: a cloud-optimized bioimaging file format with international community support.}, journal = {Histochemistry and Cell Biology}, volume = {160}, year = {2023}, month = {2023 Feb 25}, pages = {223-251}, abstract = {

A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the format itself {\textendash} OME-Zarr {\textendash} along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain {\textemdash} the file format that underlies so many personal, institutional, and global data management and analysis tasks.

}, doi = {10.1007/s00418-023-02209-1}, url = {https://doi.org/10.1007/s00418-023-02209-1}, author = {Josh Moore and Daniela Basurto-Lozada and S{\'e}bastien Besson and John Bogovic and Eva M. Brown and Jean-Marie Burel and Gustavo de Medeiros and Erin E. Diel and David Gault and Satrajit S. Ghosh and Ilan Gold and Yaroslav O. Halchenko and Matthew Hartley and Dave Horsfall and Mark S. Keller and Mark Kittisopikul and Gabor Kovacs and Ayb{\"u}ke K{\"u}pc{\"u} Yolda{\c s} and Albane le Tournoulx de la Villegeorges and Tong Li and Prisca Liberali and Melissa Linkert and Dominik Lindner and Joel L{\"u}thi and Jeremy Maitin-Shepard and Trevor Manz and Matthew McCormick and Khaled Mohamed and William Moore and Bugra {\"O}zdemir and Constantin Pape and Lucas Pelkmans and Martin Prete and Tobias Pietzsch and Stephan Preibisch and Norman Rzepka and David R. Stirling and Jonathan Striebel and Christian Tischer and Daniel Toloudis and Petr Walczysko and Alan M. Watson and Frances Wong and Kevin A. Yamauchi and Omer Bayraktar and Muzlifah Haniffa and Stephan Saalfeld and Jason R. Swedlow} } @article {69042, title = {Optimized Red-Absorbing Dyes for Imaging and Sensing}, journal = {Journal of the American Chemical Society}, year = {2023}, month = {2023 Oct 16}, abstract = {

Rhodamine dyes are excellent scaffolds for developing a broad range of fluorescent probes. A key property of rhodamines is their equilibrium between a colorless lactone and fluorescent zwitterion. Tuning the lactone{\textendash}zwitterion equilibrium constant (KL{\textendash}Z) can optimize dye properties for specific biological applications. Here, we use known and novel organic chemistry to prepare a comprehensive collection of rhodamine dyes to elucidate the structure{\textendash}activity relationships that govern\ KL{\textendash}Z. We discovered that the auxochrome substituent strongly affects the lactone{\textendash}zwitterion equilibrium, providing a roadmap for the rational design of improved rhodamine dyes. Electron-donating auxochromes, such as julolidine, work in tandem with fluorinated pendant phenyl rings to yield bright, red-shifted fluorophores for live-cell single-particle tracking (SPT) and multicolor imaging. The\ N-aryl auxochrome combined with fluorination yields red-shifted F{\"o}rster resonance energy transfer (FRET) quencher dyes useful for creating a new semisynthetic indicator to sense cAMP using fluorescence lifetime imaging microscopy (FLIM). Together, this work expands the synthetic methods available for rhodamine synthesis, generates new reagents for advanced fluorescence imaging experiments, and describes structure{\textendash}activity relationships that will guide the design of future probes.

}, issn = {0002-7863}, doi = {10.1021/jacs.3c0527310.1021/jacs.3c05273}, url = {https://pubs.acs.org/doi/10.1021/jacs.3c05273}, author = {Grimm, Jonathan B. and Tkachuk, Ariana N. and Patel, Ronak and Hennigan, S. Thomas and Gutu, Alina and Dong, Peng and Gandin, Valentina and Osowski, Anastasia M. and Holland, Katie L. and Liu, Zhe J. and Brown, Timothy A. and Lavis, Luke D.} } @article {68828, title = {Organization of an Ascending Circuit that Conveys Flight Motor State}, journal = {bioRxiv}, year = {2023}, month = {2023 Jun 09}, abstract = {

Natural behaviors are a coordinated symphony of motor acts which drive self-induced or reafferent sensory activation. Single sensors only signal presence and magnitude of a sensory cue; they cannot disambiguate exafferent (externally-induced) from reafferent sources. Nevertheless, animals readily differentiate between these sources of sensory signals to make appropriate decisions and initiate adaptive behavioral outcomes. This is mediated by predictive motor signaling mechanisms, which emanate from motor control pathways to sensory processing pathways, but how predictive motor signaling circuits function at the cellular and synaptic level is poorly understood. We use a variety of techniques, including connectomics from both male and female electron microscopy volumes, transcriptomics, neuroanatomical, physiological and behavioral approaches to resolve the network architecture of two pairs of ascending histaminergic neurons (AHNs), which putatively provide predictive motor signals to several sensory and motor neuropil. Both AHN pairs receive input primarily from an overlapping population of descending neurons, many of which drive wing motor output. The two AHN pairs target almost exclusively non-overlapping downstream neural networks including those that process visual, auditory and mechanosensory information as well as networks coordinating wing, haltere, and leg motor output. These results support the conclusion that the AHN pairs multi-task, integrating a large amount of common input, then tile their output in the brain, providing predictive motor signals to non-overlapping sensory networks affecting motor control both directly and indirectly.

}, doi = {10.1101/2023.06.07.544074}, url = {https://doi.org/10.1101/2023.06.07.544074}, author = {Han S. J. Cheong and Kaitlyn N. Boone and Marryn M. Bennett and Farzaan Salman and Jacob D. Ralston and Kaleb Hatch and Raven F. Allen and Alec M. Phelps and Andrew P. Cook and Jasper S. Phelps and Mert Erginkaya and Wei-Chung A. Lee and Gwyneth M. Card and Kevin C. Daly and Andrew M. Dacks} } @article {67789, title = {Organizing memories for generalization in complementary learning systems.}, journal = {Nature Neuroscience}, volume = {26}, year = {2023}, month = {2023 Aug 01}, pages = {1438-1448}, abstract = {

Our ability to remember the past is essential for guiding our future behavior. Psychological and neurobiological features of declarative memories are known to transform over time in a process known as systems consolidation. While many theories have sought to explain the time-varying role of hippocampal and neocortical brain areas, the computational principles that govern these transformations remain unclear. Here we propose a theory of systems consolidation in which hippocampal-cortical interactions serve to optimize generalizations that guide future adaptive behavior. We use mathematical analysis of neural network models to characterize fundamental performance tradeoffs in systems consolidation, revealing that memory components should be organized according to their predictability. The theory shows that multiple interacting memory systems can outperform just one, normatively unifying diverse experimental observations and making novel experimental predictions. Our results suggest that the psychological taxonomy and neurobiological organization of declarative memories reflect a system optimized for behaving well in an uncertain future.

}, doi = {10.1038/s41593-023-01382-9}, url = {https://doi.org/10.1038/s41593-023-01382-9}, author = {Weinan Sun and Madhu Advani and Nelson Spruston and Andrew Saxe and James E. Fitzgerald} } @article {68675, title = {Origin of wiring specificity in an olfactory map revealed by neuron type-specific, time-lapse imaging of dendrite targeting.}, journal = {eLife}, volume = {12}, year = {2023}, month = {2023 Mar 28}, abstract = {

How does wiring specificity of neural maps emerge during development? Formation of the adult olfactory glomerular map begins with patterning of projection neuron (PN) dendrites at the early pupal stage. To better understand the origin of wiring specificity of this map, we created genetic tools to systematically characterize dendrite patterning across development at PN type-specific resolution. We find that PNs use lineage and birth order combinatorially to build the initial dendritic map. Specifically, birth order directs dendrite targeting in rotating and binary manners for PNs of the anterodorsal and lateral lineages, respectively. Two-photon- and adaptive optical lattice light-sheet microscope-based time-lapse imaging reveals that PN dendrites initiate active targeting with direction-dependent branch stabilization on the timescale of seconds. Moreover, PNs that are used in both the larval and adult olfactory circuits prune their larval-specific dendrites and re-extend new dendrites simultaneously to facilitate timely olfactory map organization. Our work highlights the power and necessity of type-specific neuronal access and time-lapse imaging in identifying wiring mechanisms that underlie complex patterns of functional neural maps.

}, issn = {2050-084X}, doi = {10.7554/eLife.85521}, author = {Wong, Kenneth Kin Lam and Li, Tongchao and Fu, Tian-Ming and Liu, Gaoxiang and Lyu, Cheng and Kohani, Sayeh and Xie, Qijing and Luginbuhl, David J and Upadhyayula, Srigokul and Betzig, Eric and Luo, Liqun} } @article {68631, title = {Phase separation of Hippo signalling complexes.}, journal = {EMBO Journal}, volume = {42}, year = {2023}, month = {2023 Feb 20}, pages = {e112863}, abstract = {

The Hippo pathway was originally discovered to control tissue growth in Drosophila and includes the Hippo kinase (Hpo; MST1/2 in mammals), scaffold protein Salvador (Sav; SAV1 in mammals) and the Warts kinase (Wts; LATS1/2 in mammals). The Hpo kinase is activated by binding to Crumbs-Expanded (Crb-Ex) and/or Merlin-Kibra (Mer-Kib) proteins at the apical domain of epithelial cells. Here we show that activation of Hpo also involves the formation of supramolecular complexes with properties of a biomolecular condensate, including concentration dependence and\ sensitivity to starvation, macromolecular crowding, or 1,6-hexanediol treatment. Overexpressing Ex or Kib induces formation of micron-scale Hpo condensates in the cytoplasm, rather than at the apical membrane. Several Hippo pathway components contain unstructured low-complexity domains and purified Hpo-Sav complexes undergo phase separation in\ vitro. Formation of Hpo condensates is conserved in human cells. We propose that apical Hpo kinase activation occurs in phase separated "signalosomes" induced by clustering of upstream pathway components.

}, issn = {1460-2075}, doi = {10.15252/embj.2022112863}, author = {Bonello, Teresa T and Cai, Danfeng and Fletcher, Georgina C and Wiengartner, Kyler and Pengilly, Victoria and Lange, Kimberly S and Liu, Zhe and Lippincott-Schwartz, Jennifer and Kavran, Jennifer M and Thompson, Barry J} } @article {68917, title = {Pinpoint: trajectory planning for multi-probe electrophysiology and injections in an interactive web-based 3D environment}, journal = {bioRxiv}, year = {2023}, month = {2023 Jul 15}, abstract = {

Targeting deep brain structures during electrophysiology and injections requires intensive training and expertise. Even with experience, researchers often can{\textquoteright}t be certain that a probe is placed precisely in a target location and this complexity scales with the number of simultaneous probes used in an experiment. Here, we present Pinpoint, open-source software that allows for interactive exploration of stereotaxic insertion plans. Once an insertion plan is created, Pinpoint allows users to save these online and share them with collaborators. 3D modeling tools allow users to explore their insertions alongside rig and implant hardware and ensure plans are physically possible. Probes in Pinpoint can be linked to electronic micro-manipulators allowing real-time visualization of current brain region targets alongside neural data. In addition, Pinpoint can control manipulators to automate and parallelize the insertion process. Compared to previously available software, Pinpoint{\textquoteright}s easy access through web browsers, extensive features, and real-time experiment integration enable more efficient and reproducible recordings.

}, doi = {10.1101/2023.07.14.548952}, url = {https://doi.org/10.1101/2023.07.14.548952}, author = {Daniel Birman and Kenneth J. Yang and Steven J. West and Bill Karsh and Yoni Browning and the International Brain Laboratory and Joshua H. Siegle and Nicholas A. Steinmetz} } @article {68770, title = {The power of peer networking for improving STEM faculty job applications: a successful pilot programme.}, journal = {Proceedings. Biological Sciences}, volume = {290}, year = {2023}, month = {2023 Apr 26}, pages = {20230124}, abstract = {

To attain a faculty position, postdoctoral fellows submit job applications that require considerable time and effort to produce. Although mentors and colleagues review these applications, postdocs rarely receive iterative feedback from reviewers with the breadth of expertise typically found on an academic search committee. To address this gap, we describe an international peer-reviewing programme for postdocs across disciplines to receive reciprocal, iterative feedback on faculty applications. A participant survey revealed that nearly all participants would recommend the programme to others. Furthermore, our programme was more likely to attract postdocs who struggled to find mentoring, possibly because of their identity as a woman or member of an underrepresented population in STEM or because they changed fields. Between 2018 and 2021, our programme provided nearly 150 early career academics with a diverse and supportive community of peer mentors during the difficult search for a faculty position and continues to do so today. As the transition from postdoc to faculty represents the largest {\textquoteright}leak{\textquoteright} in the academic pipeline, implementation of similar programmes by universities or professional societies would provide psycho-social support necessary to prevent attrition of individuals from underrepresented populations as well as increase the chances of success for early career academics in their search for independence.

}, keywords = {Faculty, Female, Humans, Mentoring, Mentors, Peer Group, Pilot Projects}, issn = {1471-2954}, doi = {10.1098/rspb.2023.0124}, author = {Guardia, Carlos M and Kane, Erin and Tebo, Alison G and Sanders, Anna A W M and Kaya, Devrim and Grogan, Kathleen E} } @article {68708, title = {Predictive and robust gene selection for spatial transcriptomics.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 Apr 12}, pages = {2091}, abstract = {

A prominent trend in single-cell transcriptomics is providing spatial context alongside a characterization of each cell{\textquoteright}s molecular state. This typically requires targeting an a priori selection of genes, often covering less than 1\% of the genome, and a key question is how to optimally determine the small gene panel. We address this challenge by introducing a flexible deep learning framework, PERSIST, to identify informative gene targets for spatial transcriptomics studies by leveraging reference scRNA-seq data. Using datasets spanning different brain regions, species, and scRNA-seq technologies, we show that PERSIST reliably identifies panels that provide more accurate prediction of the genome-wide expression profile, thereby capturing more information with fewer genes. PERSIST can be adapted to specific biological goals, and we demonstrate that PERSIST{\textquoteright}s binarization of gene expression levels enables models trained on scRNA-seq data to generalize with to spatial transcriptomics data, despite the complex shift between these technologies.

}, keywords = {Gene Expression Profiling, Sequence Analysis, RNA, Single-Cell Analysis, Transcriptome}, issn = {2041-1723}, doi = {10.1038/s41467-023-37392-1}, author = {Covert, Ian and Gala, Rohan and Wang, Tim and Svoboda, Karel and S{\"u}mb{\"u}l, Uygar and Lee, Su-In} } @article {69075, title = {Preserved neural dynamics across animals performing similar behaviour.}, journal = {Nature}, year = {2023}, month = {2023 Nov 08}, abstract = {

Animals of the same species exhibit similar behaviours that are advantageously adapted to their body and environment. These behaviours are shaped at the species level by selection pressures over evolutionary timescales. Yet, it remains unclear how these common behavioural adaptations emerge from the idiosyncratic neural circuitry of each individual. The overall organization of neural circuits is preserved across individuals because of their common evolutionarily specified developmental programme. Such organization at the circuit level may constrain neural activity, leading to low-dimensional latent dynamics across the neural population. Accordingly, here we suggested that the shared circuit-level constraints within a species would lead to suitably preserved latent dynamics across individuals. We analysed recordings of neural populations from monkey and mouse motor cortex to demonstrate that neural dynamics in individuals from the same species are surprisingly preserved when they perform similar behaviour. Neural population dynamics were also preserved when animals consciously planned future movements without overt behaviour and enabled the decoding of planned and ongoing movement across different individuals. Furthermore, we found that preserved neural dynamics extend beyond cortical regions to the dorsal striatum, an evolutionarily older structure. Finally, we used neural network models to demonstrate that behavioural similarity is necessary but not sufficient for this preservation. We posit that these emergent dynamics result from evolutionary constraints on brain development and thus reflect fundamental properties of the neural basis of behaviour.

}, issn = {1476-4687}, doi = {10.1038/s41586-023-06714-0}, author = {Safaie, Mostafa and Chang, Joanna C and Park, Junchol and Miller, Lee E and Dudman, Joshua T and Perich, Matthew G and Gallego, Juan A} } @article {69011, title = {Quantitative Profiling of Lysosomal pH Heterogeneity using Fluorescence Lifetime Imaging Microscopy}, journal = {bioRxiv}, year = {2023}, month = {2023 Sep 26}, abstract = {

Lysosomes play crucial roles in maintaining cellular homeostasis and promoting organism fitness. The pH of lysosomes is a crucial parameter for their proper function, and it is dynamically influenced by both intracellular and environmental factors. Here, we present a method based on fluorescence lifetime imaging microscopy (FLIM) for quantitatively analyzing lysosomal pH profiles in diverse types of primary mammalian cells and in different tissues of the live organism Caenorhabditis elegans. This FLIM-based method exhibits high sensitivity in resolving subtle pH differences, thereby revealing the heterogeneity of the lysosomal population within a cell and between cell types. The method enables rapid measurement of lysosomal pH changes in response to various environmental stimuli. Furthermore, the FLIM measurement of pH-sensitive dyes circumvents the need for transgenic reporters and mitigates potential confounding factors associated with varying dye concentrations or excitation light intensity. This FLIM approach offers absolute quantification of lysosomal pH and highlights the significance of lysosomal pH heterogeneity and dynamics, providing a valuable tool for studying lysosomal functions and their regulation in various physiological and pathological contexts.

}, doi = {10.1101/2023.09.25.559395}, url = {https://doi.org/10.1101/2023.09.25.559395}, author = {Dinghuan Deng and Youchen Guan and Baiping Wang and Hui Zheng and Ayse Sena Mutlu and Meng Carla Wang} } @article {68920, title = {Rastermap: a discovery method for neural population recordings}, journal = {Nat. Neurosci.}, year = {2023}, month = {2024 Oct 16}, abstract = {

Neurophysiology has long progressed through exploratory experiments and chance discoveries. Anecdotes abound of researchers listening to spikes in real time and noticing patterns of activity related to ongoing stimuli or behaviors. With the advent of large-scale recordings, such close observation of data has become difficult. To find patterns in large-scale neural data, we developed {\textquoteright}Rastermap{\textquoteright}, a visualization method that displays neurons as a raster plot after sorting them along a one-dimensional axis based on their activity patterns. We benchmarked Rastermap on realistic simulations and then used it to explore recordings of tens of thousands of neurons from mouse cortex during spontaneous, stimulus-evoked and task-evoked epochs. We also applied Rastermap to whole-brain zebrafish recordings; to wide-field imaging data; to electrophysiological recordings in rat hippocampus, monkey frontal cortex and various cortical and subcortical regions in mice; and to artificial neural networks. Finally, we illustrate high-dimensional scenarios where Rastermap and similar algorithms cannot be used effectively.

}, doi = {10.1038/s41593-024-01783-4}, url = {https://doi.org/10.1038/s41593-024-01783-4}, author = {Carsen Stringer and Lin Zhong and Atika Syeda and Fengtong Du and Marius Pachitariu} } @article {68915, title = {Rational Engineering of an Improved Genetically Encoded pH Sensor Based on Superecliptic pHluorin.}, journal = {ACS Sensors}, volume = {8}, year = {2023}, month = {2023 Aug 25}, pages = {3014-3022}, abstract = {

Genetically encoded pH sensors based on fluorescent proteins are valuable tools for the imaging of cellular events that are associated with pH changes, such as exocytosis and endocytosis. Superecliptic pHluorin (SEP) is a pH-sensitive green fluorescent protein (GFP) variant widely used for such applications. Here, we report the rational design, development, structure, and applications of Lime, an improved SEP variant with higher fluorescence brightness and greater pH sensitivity. The X-ray crystal structure of Lime supports the mechanistic rationale that guided the introduction of beneficial mutations. Lime provides substantial improvements relative to SEP for imaging of endocytosis and exocytosis. Furthermore, Lime and its variants are advantageous for a broader range of applications including the detection of synaptic release and neuronal voltage changes.

}, issn = {2379-3694}, doi = {10.1021/acssensors.3c00484}, author = {Shen, Yi and Wen, Yurong and Sposini, Silvia and Vishwanath, Anjali Amrapali and Abdelfattah, Ahmed S and Schreiter, Eric R and Lemieux, M Joanne and de Juan-Sanz, Jaime and Perrais, David and Campbell, Robert E} } @article {68385, title = {Rationalized deep learning super-resolution microscopy for sustained live imaging of rapid subcellular processes.}, journal = {Nature Biotechnology}, volume = {41}, year = {2023}, month = {2023 Mar 01}, pages = {367-77}, abstract = {

The goal when imaging bioprocesses with optical microscopy is to acquire the most spatiotemporal information with the least invasiveness. Deep neural networks have substantially improved optical microscopy, including image super-resolution and restoration, but still have substantial potential for artifacts. In this study, we developed rationalized deep learning (rDL) for structured illumination microscopy and lattice light sheet microscopy (LLSM) by incorporating prior knowledge of illumination patterns and, thereby, rationally guiding the network to denoise raw images. Here we demonstrate that rDL structured illumination microscopy eliminates spectral bias-induced resolution degradation and reduces model uncertainty by five-fold, improving the super-resolution information by more than ten-fold over other computational approaches. Moreover, rDL applied to LLSM enables self-supervised training by using the spatial or temporal continuity of noisy data itself, yielding results similar to those of supervised methods. We demonstrate the utility of rDL by imaging the rapid kinetics of motile cilia, nucleolar protein condensation during light-sensitive mitosis and long-term interactions between membranous and membrane-less organelles.

}, issn = {1546-1696}, doi = {10.1038/s41587-022-01471-3}, author = {Qiao, Chang and Li, Di and Liu, Yong and Zhang, Siwei and Liu, Kan and Liu, Chong and Guo, Yuting and Jiang, Tao and Fang, Chuyu and Li, Nan and Zeng, Yunmin and He, Kangmin and Zhu, Xueliang and Lippincott-Schwartz, Jennifer and Dai, Qionghai and Li, Dong} } @article {68795, title = {Rejuvenating old fluorophores with new chemistry.}, journal = {Current Opinions in Chemical Biology}, volume = {75}, year = {2023}, month = {2023 Jun 01}, pages = {102335}, abstract = {

The field of organic chemistry began with 19th century scientists identifying and then expanding upon synthetic dye molecules for textiles. In the 20th century, dye chemistry continued with the aim of developing photographic sensitizers and laser dyes. Now, in the 21st century, the rapid evolution of biological imaging techniques provides a new driving force for dye chemistry. Of the extant collection of synthetic fluorescent dyes for biological imaging, two classes reign supreme: rhodamines and cyanines. Here, we provide an overview of recent examples where modern chemistry is used to build these old-but-venerable classes of optically responsive molecules. These new synthetic methods access new fluorophores, which then enable sophisticated imaging experiments leading to new biological insights.

}, issn = {1879-0402}, doi = {10.1016/j.cbpa.2023.102335}, author = {Schnermann, Martin J and Lavis, Luke D} } @article {68537, title = {Reward expectations direct learning and drive operant matching in Drosophila}, journal = {Proceedings of the National Academy of Sciences of the U.S.A.}, volume = {120}, year = {2023}, month = {2023 Sep 26}, pages = {e2221415120}, abstract = {

Foraging animals must use decision-making strategies that dynamically adapt to the changing availability of rewards in the environment. A wide diversity of animals do this by distributing their choices in proportion to the rewards received from each option, Herrnstein{\textquoteright}s operant matching law. Theoretical work suggests an elegant mechanistic explanation for this ubiquitous behavior, as operant matching follows automatically from simple synaptic plasticity rules acting within behaviorally relevant neural circuits. However, no past work has mapped operant matching onto plasticity mechanisms in the brain, leaving the biological relevance of the theory unclear. Here we discovered operant matching in\ Drosophila\ and showed that it requires synaptic plasticity that acts in the mushroom body and incorporates the expectation of reward. We began by developing a novel behavioral paradigm to measure choices from individual flies as they learn to associate odor cues with probabilistic rewards. We then built a model of the fly mushroom body to explain each fly{\textquoteright}s sequential choice behavior using a family of biologically-realistic synaptic plasticity rules. As predicted by past theoretical work, we found that synaptic plasticity rules could explain fly matching behavior by incorporating stimulus expectations, reward expectations, or both. However, by optogenetically bypassing the representation of reward expectation, we abolished matching behavior and showed that the plasticity rule must specifically incorporate reward expectations. Altogether, these results reveal the first synaptic level mechanisms of operant matching and provide compelling evidence for the role of reward expectation signals in the fly brain.

}, doi = {10.1073/pnas.2221415120}, url = {https://doi.org/10.1073/pnas.2221415120}, author = {Adithya E. Rajagopalan and Ran Darshan and Karen L. Hibbard and James E. Fitzgerald and Glenn C. Turner} } @article {68885, title = {A rise-to-threshold process for a relative-value decision.}, journal = {Nature}, volume = {619}, year = {2023}, month = {2023 Jul 05}, pages = {563-571}, abstract = {

Whereas progress has been made in the identification of neural signals related to rapid, cued decisions, less is known about how brains guide and terminate more ethologically relevant decisions in which an animal{\textquoteright}s own behaviour governs the options experienced over minutes. Drosophila search for many seconds to minutes for egg-laying sites with high relative value and have neurons, called oviDNs, whose activity fulfills necessity and sufficiency criteria for initiating the egg-deposition motor programme. Here we show that oviDNs express a calcium signal that (1) dips when an egg is internally prepared (ovulated), (2) drifts up and down over seconds to minutes-in a manner influenced by the relative value of substrates-as a fly determines whether to lay an egg and (3) reaches a consistent peak level just before the abdomen bend for egg deposition. This signal is apparent in the cell bodies of oviDNs in the brain and it probably reflects a behaviourally relevant rise-to-threshold process in the ventral nerve cord, where the synaptic terminals of oviDNs are located and where their output can influence behaviour. We provide perturbational evidence that the egg-deposition motor programme is initiated once this process hits a threshold and that subthreshold variation in this process regulates the time spent considering options and, ultimately, the choice taken. Finally, we identify a small recurrent circuit that feeds into oviDNs and show that activity in each of its constituent cell types is required for laying an egg. These results argue that a rise-to-threshold process regulates a relative-value, self-paced decision and provide initial insight into the underlying circuit mechanism for building this process.

}, issn = {1476-4687}, doi = {10.1038/s41586-023-06271-6}, author = {Vijayan, Vikram and Wang, Fei and Wang, Kaiyu and Chakravorty, Arun and Adachi, Atsuko and Akhlaghpour, Hessameddin and Dickson, Barry J and Maimon, Gaby} } @article {69012, title = {A rotational velocity estimate constructed through visuomotor competition updates the fly{\textquoteright}s neural compass}, journal = {bioRxiv}, year = {2023}, month = {2023 Sep 26}, abstract = {

Navigating animals continuously integrate velocity signals to update internal representations of their directional heading and spatial location in the environment. How neural circuits combine sensory and motor information to construct these velocity estimates and how these self-motion signals, in turn, update internal representations that support navigational computations are not well understood. Recent work in Drosophila has identified a neural circuit that performs angular path integration to compute the fly{\textquoteright}s head direction, but the nature of the velocity signal is unknown. Here we identify a pair of neurons necessary for angular path integration that encode the fly{\textquoteright}s rotational velocity with high accuracy using both visual optic flow and motor information. This estimate of rotational velocity does not rely on a moment-to-moment integration of sensory and motor information. Rather, when visual and motor signals are congruent, these neurons prioritize motor information over visual information, and when the two signals are in conflict, reciprocal inhibition selects either the motor or visual signal. Together, our results suggest that flies update their head direction representation by constructing an estimate of rotational velocity that relies primarily on motor information and only incorporates optic flow signals in specific sensorimotor contexts, such as when the motor signal is absent.

}, doi = {10.1101/2023.09.25.559373}, url = {https://doi.org/10.1101/2023.09.25.559373}, author = {Brad K Hulse and Angel Stanoev and Daniel B Turner-Evans and Johannes Seelig and Vivek Jayaraman} } @article {68316, title = {The SARS-CoV-2 accessory protein Orf3a is not an ion channel, but does interact with trafficking proteins}, journal = {eLife}, year = {2023}, month = {2023 Jan 25}, abstract = {

The severe acute respiratory syndrome associated coronavirus 2 (SARS-CoV-2) and SARS-CoV-1 accessory protein Orf3a colocalizes with markers of the plasma membrane, endocytic pathway, and Golgi apparatus. Some reports have led to annotation of both Orf3a proteins as a viroporin. Here we show that neither SARS-CoV-2 nor SARS-CoV-1 form functional ion conducting pores and that the conductances measured are common contaminants in overexpression and with high levels of protein in reconstitution studies. Cryo-EM structures of both SARS-CoV-2 and SARS-CoV-1 Orf3a display a narrow constriction and the presence of a basic aqueous vestibule, which would not favor cation permeation. We observe enrichment of the late endosomal marker Rab7 upon SARS-CoV-2 Orf3a overexpression, and co-immunoprecipitation with VPS39. Interestingly, SARS-CoV-1 Orf3a does not cause the same cellular phenotype as SARS-CoV-2 Orf3a and does not interact with VPS39. To explain this difference, we find that a divergent, unstructured loop of SARS-CoV-2 Orf3a facilitates its binding with VPS39, a HOPS complex tethering protein involved in late endosome and autophagosome fusion with lysosomes. We suggest that the added loop enhances SARS-CoV-2 Orf3a ability to co-opt host cellular trafficking mechanisms for viral exit or host immune evasion.

}, doi = {10.7554/eLife.84477}, url = {https://doi.org/10.7554/eLife.84477}, author = {Alexandria N. Miller and Patrick R. Houlihan and Ella Matamala and Deny Cabezas-Bratesco and Gi Young Lee and Ben Cristofori-Armstrong and Tanya L. Dilan and Silvia Sanchez-Martinez and Doreen Matthies and Rui Yan and Zhiheng Yu and Dejian Ren and Sebastian E. Brauchi and David E. Clapham} } @article {68466, title = {A scalable implementation of the recursive least-squares algorithm for training spiking neural networks}, journal = {Frontiers in Neuroinformatics}, year = {2023}, month = {2023 Jun 27}, abstract = {

Training spiking recurrent neural networks on neuronal recordings or behavioral tasks has become a prominent tool to study computations in the brain. With an increasing size and complexity of neural recordings, there is a need for fast algorithms that can scale to large datasets. We present optimized CPU and GPU implementations of the recursive least-squares algorithm in spiking neural networks. The GPU implementation allows training networks to reproduce neural activity of an order of millions neurons at order of magnitude times faster than the CPU implementation. We demonstrate this by applying our algorithm to reproduce the activity of\ \>\ 66, 000 recorded neurons of a mouse performing a decision-making task. The fast implementation enables efficient training of large-scale spiking models, thus allowing for\ in-silico\ study of the dynamics and connectivity underlying multi-area computations.

}, doi = {10.3389/fninf.2023.1099510}, url = {https://doi.org/10.3389/fninf.2023.1099510}, author = {Benjamin J. Arthur and Christopher M. Kim and Susu Chen and Stephan Preibisch and Ran Darshan} } @article {68629, title = {A searchable image resource of Drosophila GAL4-driver expression patterns with single neuron resolution.}, journal = {eLife}, volume = {12}, year = {2023}, month = {2023 Feb 23}, abstract = {

Precise, repeatable genetic access to specific neurons via GAL4/UAS and related methods is a key advantage of Drosophila neuroscience. Neuronal targeting is typically documented using light microscopy of full GAL4 expression patterns, which generally lack the single-cell resolution required for reliable cell type identification. Here we use stochastic GAL4 labeling with the MultiColor FlpOut approach to generate cellular resolution confocal images at large scale. We are releasing aligned images of 74,000 such adult central nervous systems. An anticipated use of this resource is to bridge the gap between neurons identified by electron or light microscopy. Identifying individual neurons that make up each GAL4 expression pattern improves the prediction of split-GAL4 combinations targeting particular neurons. To this end we have made the images searchable on the NeuronBridge website. We demonstrate the potential of NeuronBridge to rapidly and effectively identify neuron matches based on morphology across imaging modalities and datasets.

}, issn = {2050-084X}, doi = {10.7554/eLife.80660}, author = {Meissner, Geoffrey Wilson and Nern, Aljoscha and Dorman, Zachary and Depasquale, Gina M and Forster, Kaitlyn and Gibney, Theresa and Hausenfluck, Joanna H and He, Yisheng and Iyer, Nirmala A and Jeter, Jennifer and Johnson, Lauren and Johnston, Rebecca M and Lee, Kelley and Melton, Brian and Yarbrough, Brianna and Zugates, Christopher T and Clements, Jody and Goina, Cristian and Otsuna, Hideo and Rokicki, Konrad and Svirskas, Robert R and Aso, Yoshinori and Card, Gwyneth M and Dickson, Barry J and Ehrhardt, Erica and Goldammer, Jens and Ito, Masayoshi and Kainmueller, Dagmar and Korff, Wyatt and Mais, Lisa and minegishi, ryo and Namiki, Shigehiro and Rubin, Gerald M and Sterne, Gabriella R and Wolff, Tanya and Malkesman, Oz} } @article {68646, title = {Selective Serotonin Reuptake Inhibitors within Cells: Temporal Resolution in Cytoplasm, Endoplasmic Reticulum, and Membrane.}, journal = {Journal of Neuroscience}, year = {2023}, month = {2023 Mar 02}, abstract = {

Selective serotonin reuptake inhibitors (SSRIs) are the most prescribed treatment for individuals experiencing major depressive disorder (MDD). The therapeutic mechanisms that take place before, during, or after SSRIs bind the serotonin transporter (SERT) are poorly understood, partially because no studies exist of the cellular and subcellular pharmacokinetic properties of SSRIs in living cells. We studied escitalopram and fluoxetine using new intensity-based drug-sensing fluorescent reporters ("iDrugSnFRs") targeted to the plasma membrane (PM), cytoplasm, or endoplasmic reticulum (ER) of cultured neurons and mammalian cell lines. We also employed chemical detection of drug within cells and phospholipid membranes. The drugs attain equilibrium in neuronal cytoplasm and ER, at approximately the same concentration as the externally applied solution, with time constants of a few s (escitalopram) or 200-300 s (fluoxetine). Simultaneously, the drugs accumulate within lipid membranes by >= 18-fold (escitalopram) or 180-fold (fluoxetine), and possibly by much larger factors. Both drugs leave cytoplasm, lumen, and membranes just as quickly during washout. We synthesized membrane-impermeant quaternary amine derivatives of the two SSRIs. The quaternary derivatives are substantially excluded from membrane, cytoplasm, and ER for \> 2.4 h. They inhibit SERT transport-associated currents 6- or 11-fold less potently than the SSRIs (escitalopram or fluoxetine derivative, respectively), providing useful probes for distinguishing compartmentalized SSRI effects. Although our measurements are orders of magnitude faster than the "therapeutic lag" of SSRIs, these data suggest that SSRI-SERT interactions within organelles or membranes may play roles during either the therapeutic effects or the "antidepressant discontinuation syndrome".Selective serotonin reuptake inhibitors stabilize mood in several disorders. In general, these drugs bind to the serotonin (5-hydroxytryptamine) transporter (SERT), which clears serotonin from CNS and peripheral tissues. SERT ligands are effective and relatively safe; primary care practitioners often prescribe them. However, they have several side effects and require 2 to 6 weeks of continuous administration until they act effectively. How they work remains perplexing, contrasting with earlier assumptions that the therapeutic mechanism involves SERT inhibition followed by increased extracellular serotonin levels. This study establishes that two SERT ligands, fluoxetine and escitalopram, enter neurons within minutes, while simultaneously accumulating in many membranes. Such knowledge will motivate future research, hopefully revealing where and how SERT ligands "engage" their therapeutic target(s).

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.1519-22.2022}, author = {Nichols, Aaron L and Blumenfeld, Zack and Luebbert, Laura and Knox, Hailey J and Muthusamy, Anand K and Marvin, Jonathan S and Kim, Charlene H and Grant, Stephen N and Walton, David P and Cohen, Bruce N and Hammar, Rebekkah and Looger, Loren and Artursson, Per and Dougherty, Dennis A and Lester, Henry A} } @article {68690, title = {Sensitivity optimization of a rhodopsin-based fluorescent voltage indicator}, journal = {Neuron}, volume = {111}, year = {2023}, month = {2023 May 17}, pages = {1547-1563}, abstract = {

The ability to optically image cellular transmembrane voltages at millisecond-timescale resolutions can offer unprecedented insight into the function of living brains in behaving animals. Here, we present a\ point mutation\ that increases the sensitivity of Ace2 opsin-based voltage indicators. We use the mutation to develop Voltron2, an improved chemigeneic voltage indicator that has a 65\% higher sensitivity to single APs and 3-fold higher sensitivity to subthreshold potentials than Voltron. Voltron2 retained the sub-millisecond kinetics and photostability of its predecessor, although with lower baseline fluorescence. In multiple\ in\ vitro\ and\ in\ vivo\ comparisons with its predecessor across multiple species, we found Voltron2 to be more sensitive to APs and subthreshold fluctuations. Finally, we used Voltron2 to study and evaluate the possible mechanisms of\ interneuron\ synchronization in the mouse hippocampus. Overall, we have discovered a generalizable mutation that significantly increases the sensitivity of Ace2 rhodopsin-based sensors, improving their voltage reporting capability.

}, issn = {08966273}, doi = {10.1016/j.neuron.2023.03.009}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0896627323002052}, author = {Abdelfattah, Ahmed S. and Zheng, Jihong and Singh, Amrita and Huang, Yi-Chieh and Reep, Daniel and Tsegaye, Getahun and Tsang, Arthur and Arthur, Benjamin J. and Rehorova, Monika and Olson, Carl V.L. and Shuai, Yichun and Zhang, Lixia and Fu, Tian-Ming and Milkie, Daniel E. and Moya, Maria V. and Weber, Timothy D. and Lemire, Andrew L. and Baker, Christopher A. and Falco, Natalie and Zheng, Qinsi and Grimm, Jonathan B. and Yip, Mighten C. and Walpita, Deepika and Chase, Martin and Campagnola, Luke and Murphy, Gabe J. and Wong, Allan M. and Forest, Craig R. and Mertz, Jerome and Economo, Michael N. and Turner, Glenn C. and Koyama, Minoru and Lin, Bei-Jung and Betzig, Eric and Novak, Ondrej and Lavis, Luke D. and Svoboda, Karel and Korff, Wyatt and Chen, Tsai-Wen and Schreiter, Eric R. and Hasseman, Jeremy P. and Kolb, Ilya} } @article {68695, title = {Sequence and Structural Motifs Controlling the Broad Substrate Specificity of the Mycobacterial Hormone-Sensitive Lipase LipN}, journal = {ACS Omega}, volume = {8}, year = {2023}, month = {2023 Mar 30}, pages = {13252 - 13264}, abstract = {

Mycobacterium tuberculosis\ has a complex life cycle transitioning between active and dormant growth states depending on environmental conditions. LipN (Rv2970c) is a conserved mycobacterial serine hydrolase with regulated catalytic activity at the interface between active and dormant growth conditions. LipN also catalyzes the xenobiotic degradation of a tertiary ester substrate and contains multiple conserved motifs connected with the ability to catalyze the hydrolysis of difficult tertiary ester substrates. Herein, we expanded a library of fluorogenic ester substrates to include more tertiary and constrained esters and screened 33 fluorogenic substrates for activation by LipN, identifying its unique substrate signature. LipN preferred short, unbranched ester substrates, but had its second highest activity against a heteroaromatic five-membered oxazole ester. Oxazole esters are present in multiple mycobacterial serine hydrolase inhibitors but have not been tested widely as ester substrates. Combined structural modeling, kinetic measurements, and substitutional analysis of LipN showcased a fairly rigid binding pocket preorganized for catalysis of short ester substrates. Substitution of diverse amino acids across the binding pocket significantly impacted the folded stability and catalytic activity of LipN with two conserved motifs (HGGGW and GDSAG) playing interconnected, multidimensional roles in regulating its substrate specificity. Together this detailed substrate specificity profile of LipN illustrates the complex interplay between structure and function in mycobacterial hormone-sensitive lipase homologues and indicates oxazole esters as promising inhibitor and substrate scaffolds for mycobacterial hydrolases.

}, issn = {2470-1343}, doi = {10.1021/acsomega.3c0053410.1021/acsomega.3c00534.s001}, url = {https://pubs.acs.org/doi/10.1021/acsomega.3c00534}, author = {Schemenauer, Daniel E. and Pool, Emily H. and Raynor, Stephanie N. and Ruiz, Gabriela P. and Goehring, Leah M. and Koelper, Andrew J. and Wilson, Madeleine A. and Durand, Anthony J. and Kourtoglou, Elexi C. and Larsen, Erik M. and Lavis, Luke D. and Esteb, John J. and Hoops, Geoffrey C. and Johnson, R. Jeremy} } @article {68717, title = {Simultaneous photoactivation and high-speed structural tracking reveal diffusion-dominated motion in the endoplasmic reticulum}, journal = {bioRxiv}, year = {2023}, month = {2023 Apr 25}, abstract = {

The endoplasmic reticulum (ER) is a structurally complex, membrane-enclosed compartment that stretches from the nuclear envelope to the extreme periphery of eukaryotic cells. The organelle is crucial for numerous distinct cellular processes, but how these processes are spatially regulated within the structure is unclear. Traditional imaging-based approaches to understanding protein dynamics within the organelle are limited by the convoluted structure and rapid movement of molecular components. Here, we introduce a combinatorial imaging and machine learning-assisted image analysis approach to track the motion of photoactivated proteins within the ER of live cells. We find that simultaneous knowledge of the underlying ER structure is required to accurately analyze fluorescently-tagged protein redistribution, and after appropriate structural calibration we see all proteins assayed show signatures of Brownian diffusion-dominated motion over micron spatial scales. Remarkably, we find that in some cells the ER structure can be explored in a highly asymmetric manner, likely as a result of uneven connectivity within the organelle. This remains true independently of the size, topology, or folding state of the fluorescently-tagged molecules, suggesting a potential role for ER connectivity in driving spatially regulated biology in eukaryotes.

}, doi = {10.1101/2023.04.23.537908}, url = {https://doi.org/10.1101/2023.04.23.537908}, author = {Matteo Dora and Christopher J. Obara and Tim Abel and Jennifer Lippincott-Schwarz and David Holcman} } @article {68838, title = {Small-field visual projection neurons detect translational optic flow and support walking control}, journal = {bioRxiv}, year = {2023}, month = {2023 Jun 22}, abstract = {

Animals rely on visual motion for navigating the world, and research in flies has clarified how neural circuits extract information from moving visual scenes. However, the major pathways connecting these patterns of optic flow to behavior remain poorly understood. Using a high-throughput quantitative assay of visually guided behaviors and genetic neuronal silencing, we discovered a region in\ Drosophila{\textquoteright}s protocerebrum critical for visual motion following. We used neuronal silencing, calcium imaging, and optogenetics to identify a single cell type, LPC1, that innervates this region, detects translational optic flow, and plays a key role in regulating forward walking. Moreover, the population of LPC1s can estimate the travelling direction, such as when gaze direction diverges from body heading. By linking specific cell types and their visual computations to specific behaviors, our findings establish a foundation for understanding how the nervous system uses vision to guide navigation.

}, doi = {10.1101/2023.06.21.546024}, url = {https://doi.org/10.1101/2023.06.21.546024}, author = {Mathew D. Isaacson and Jessica L. M. Eliason and Aljoscha Nern and Edward M. Rogers and Gus K. Lott and Tanya Tabachnik and William J. Rowell and Austin W. Edwards and Wyatt L. Korff and Gerald M. Rubin and Kristin Branson and Michael B. Reiser} } @article {68666, title = {Social association predicts immunological similarity in rewilded mice}, journal = {bioRxiv}, year = {2023}, month = {2023 Mar 16}, abstract = {

Environmental influences on immune phenotypes are well-documented, but our understanding of which elements of the environment affect immune systems, and how, remains vague. Behaviors, including socializing with others, are central to an individual{\textquoteright}s interaction with its environment. We tracked behavior of rewilded laboratory mice of three inbred strains in outdoor enclosures and examined contributions of behavior, including social associations, to immune phenotypes. We found that the more associated two individuals were, the more similar their immune phenotypes were. Social association was particularly predictive of similar memory T and B cell profiles and was more influential than sibling relationships or worm infection status. These results highlight the importance of social networks for immune phenotype and reveal important immunological correlates of social life.

}, doi = {10.1101/2023.03.15.532825}, url = {https://doi.org/10.1101/2023.03.15.532825}, author = {A. E. Downie and O. Oyesola and R. S. Barre and Q. Caudron and Y.-H. Chen and E. J. Dennis and R. Garnier and K. Kiwanuka and A. Menezes and D. J. Navarrete and O. Mondrag{\'o}n-Palomino and J. B. Saunders and C. K. Tokita and K. Zaldana and K. Cadwell and P. Loke and A. L. Graham} } @article {68578, title = {Solving the spike sorting problem with Kilosort}, journal = {bioRxiv}, year = {2023}, month = {2023 Jan 07}, abstract = {

Spike sorting is the computational process of extracting the firing times of single neurons from recordings of local electrical fields. This is an important but hard problem in neuroscience, complicated by the non-stationarity of the recordings and the dense overlap in electrical fields between nearby neurons. To solve the spike sorting problem, we have continuously developed over the past eight years a framework known as Kilosort. This paper describes the various algorithmic steps introduced in different versions of Kilosort. We also report the development of Kilosort4, a new version with substantially improved performance due to new clustering algorithms inspired by graph-based approaches. To test the performance of Kilosort, we developed a realistic simulation framework which uses densely sampled electrical fields from real experiments to generate non-stationary spike waveforms and realistic noise. We find that nearly all versions of Kilosort outperform other algorithms on a variety of simulated conditions, and Kilosort4 performs best in all cases, correctly identifying even neurons with low amplitudes and small spatial extents in high drift conditions.

}, doi = {10.1101/2023.01.07.523036}, url = {https://doi.org/10.1101/2023.01.07.523036}, author = {Marius Pachitariu and Shashwat Sridhar and Carsen Stringer} } @article {69125, title = {Spatiotemporal-social association predicts immunological similarity in rewilded mice.}, journal = {Science Advances}, volume = {9}, year = {2023}, month = {2023 Dec 22}, pages = {eadh8310}, abstract = {

Environmental influences on immune phenotypes are well-documented, but our understanding of which elements of the environment affect immune systems, and how, remains vague. Behaviors, including socializing with others, are central to an individual{\textquoteright}s interaction with its environment. We therefore tracked behavior of rewilded laboratory mice of three inbred strains in outdoor enclosures and examined contributions of behavior, including associations measured from spatiotemporal co-occurrences, to immune phenotypes. We found extensive variation in individual and social behavior among and within mouse strains upon rewilding. In addition, we found that the more associated two individuals were, the more similar their immune phenotypes were. Spatiotemporal association was particularly predictive of similar memory T and B cell profiles and was more influential than sibling relationships or shared infection status. These results highlight the importance of shared spatiotemporal activity patterns and/or social networks for immune phenotype and suggest potential immunological correlates of social life.

}, keywords = {Animals, Immune System, Mice, Phenotype, Social Behavior}, issn = {2375-2548}, doi = {10.1126/sciadv.adh8310}, author = {Downie, Alexander E and Oyesola, Oyebola and Barre, Ramya S and Caudron, Quentin and Chen, Ying-Han and Dennis, Emily J and Garnier, Romain and Kiwanuka, Kasalina and Menezes, Arthur and Navarrete, Daniel J and Mondrag{\'o}n-Palomino, Octavio and Saunders, Jesse B and Tokita, Christopher K and Zaldana, Kimberly and Cadwell, Ken and Loke, P{\textquoteright}ng and Graham, Andrea L} } @article {68633, title = {Specialized actin nanoscale layers control focal adhesion turnover}, journal = {bioRxiv}, year = {2023}, month = {2023 Feb 15}, abstract = {

Focal adhesions (FAs) connect inner workings of the cell to the extracellular matrix to control cell adhesion, migration, and mechanosensing1,2. Previous studies demonstrated that FAs contain three vertical layers, which connect extracellular matrix to the cytoskeleton3,4,5. However, cellular processes rely on precisely-regulated FA turnover, but the molecular machineries that control FA assembly and disassembly have remained elusive. By using super-resolution iPALM microscopy, we identified two unprecedented nanoscale layers within FAs, specified by actin filaments bound to tropomyosin isoforms Tpm1.6 and Tpm3.2. The Tpm1.6-actin filaments beneath the previously identified {\textquoteleft}actin-regulatory layer{\textquoteright} are critical for adhesion maturation and controlled cell motility, whereas the Tpm3.2-actin filament layer towards the bottom of FA facilitates adhesion disassembly. Mechanistically, Tpm3.2 stabilizes KANK-family proteins at adhesions, and hence targets microtubule plus-ends to FAs to catalyse their disassembly. Loss of Tpm3.2 leads to disorganized microtubule network, abnormally stable FAs, and defects in tail retraction during cell migration. Thus, FAs are composed of at least three distinct actin filament layers, each having specific roles in coupling of adhesion to the cytoskeleton, or in controlling adhesion dynamics. In a broader context, these findings demonstrate how distinct actin filament populations can co-exist and perform specific functions within a defined cellular compartment.

}, doi = {10.1101/2023.02.15.528622}, url = {https://doi.org/10.1101/2023.02.15.528622}, author = {Reena Kumari and Katharina Ven and Megan Chastney and Johan Per{\"a}nen and Jesse Aaron and Leonardo Almeida-Souza and Elena Kremneva and Renaud Poincloux and Teng-Leong Chew and Peter W. Gunning and Johanna Ivaska and Pekka Lappalainen} } @article {68930, title = {Stimulus edges induce orientation tuning in superior colliculus.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 Aug 08}, pages = {4756}, abstract = {

Orientation columns exist in the primary visual cortex (V1) of cat and primates but not mouse. Intriguingly, some recent studies reported the presence of orientation and direction columns in the mouse superficial superior colliculus (sSC), while others reported a lack of columnar organization therein. Using in vivo calcium imaging of sSC in the awake mouse brain, we found that the presence of columns is highly stimulus dependent. Specifically, we observed orientation and direction columns formed by sSC neurons retinotopically mapped to the edge of grating stimuli. For both excitatory and inhibitory neurons in sSC, orientation selectivity can be induced by the edge with their preferred orientation perpendicular to the edge orientation. Furthermore, we found that this edge-induced orientation selectivity is associated with saliency encoding. These findings indicate that the tuning properties of sSC neurons are not fixed by circuit architecture but rather dependent on the spatiotemporal properties of the stimulus.

}, keywords = {Animals, Calcium, Neurons, Photic Stimulation, Superior Colliculi, Visual Cortex}, issn = {2041-1723}, doi = {10.1038/s41467-023-40444-1}, author = {Liang, Yajie and Lu, Rongwen and Borges, Katharine and Ji, Na} } @article {68888, title = {Stochastic coding: a conserved feature of odor representations and its implications for odor discrimination}, journal = {bioRxiv}, year = {2023}, month = {2023 Jun 29}, abstract = {

Sparse coding is thought to improve discrimination of sensory stimuli by reducing overlap between their representations. Two factors, however, can offset sparse coding{\textquoteright}s advantages. Similar sensory stimuli have significant overlap, and responses vary across trials. To elucidate the effect of these two factors, we analyzed odor responses in the fly and mouse olfactory regions implicated in learning and discrimination --- the Mushroom Body (MB) and the Piriform Cortex (PCx). In both species, we show that neuronal responses fall along a continuum from extremely reliable across trials to extremely variable or stochastic. Computationally, we show that the range of observed variability arises from probabilistic synapses in inhibitory feedback connections within central circuits rather than sensory noise, as is traditionally assumed. We propose this coding scheme to be advantageous for coarse- and fine-odor discrimination. More reliable cells enable quick discrimination between dissimilar odors. For similar odors, however, these cells overlap, and do not provide distinguishing information. By contrast, more unreliable cells are decorrelated for similar odors, providing distinguishing information, though this requires extended training with more trials. Overall, we have uncovered a stochastic coding scheme that is conserved in vertebrates and invertebrates, and we identify a candidate mechanism, based on variability in a winner-take-all inhibitory circuit, that improves discrimination with training.

}, doi = {10.1101/2023.06.27.546757}, url = {https://doi.org/10.1101/2023.06.27.546757}, author = {Shyam Srinivasan and Simon Daste and Mehrab Modi and Glenn Turner and Alexander Fleischmann and Saket Navlakha} } @article {68798, title = {Structural Diversity within the Endoplasmic Reticulum-From the Microscale to the Nanoscale.}, journal = {Cold Spring Harbor Perspectives in Biology}, volume = {15}, year = {2023}, month = {2023 Jun 01}, abstract = {

The endoplasmic reticulum (ER) is a continuous, highly dynamic membrane compartment that is crucial for numerous basic cellular functions. The ER stretches from the nuclear envelope to the outer periphery of all living eukaryotic cells. This ubiquitous organelle shows remarkable structural complexity, adopting a range of shapes, curvatures, and length scales. Canonically, the ER is thought to be composed of two simple membrane elements: sheets and tubules. However, recent advances in superresolution light microscopy and three-dimensional electron microscopy have revealed an astounding diversity of nanoscale ER structures, greatly expanding our view of ER organization. In this review, we describe these diverse ER structures, focusing on what is known of their regulation and associated functions in mammalian cells.

}, keywords = {Animals, Endoplasmic Reticulum, Mammals, Microscopy, Electron, Nuclear Envelope}, issn = {1943-0264}, doi = {10.1101/cshperspect.a041259}, author = {Obara, Christopher J and Moore, Andrew S and Lippincott-Schwartz, Jennifer} } @article {68517, title = {Structured cerebellar connectivity supports resilient pattern separation.}, journal = {Nature}, volume = {613}, year = {2023}, month = {2023 Jan 01}, pages = {543-549}, abstract = {

The cerebellum is thought to help\ detect and correct errors between intended and executed commands and is critical for social behaviours, cognition and emotion. Computations for motor control must be performed quickly to correct errors in real time and should be sensitive to small differences between patterns for fine error correction while being resilient to noise. Influential theories of cerebellar information processing have largely assumed random network connectivity, which increases the encoding capacity of the network{\textquoteright}s first layer. However, maximizing encoding capacity reduces the resilience to noise. To understand how neuronal circuits address this fundamental trade-off, we mapped the feedforward connectivity in the mouse cerebellar cortex using automated large-scale transmission electron microscopy and convolutional neural network-based image segmentation. We found that both the input and output layers of the circuit exhibit redundant and selective connectivity motifs, which contrast with prevailing models. Numerical simulations suggest that these redundant, non-random connectivity motifs increase the resilience to noise at a negligible cost to the overall encoding capacity. This work reveals how neuronal network structure can support a trade-off between encoding capacity and redundancy, unveiling principles of biological network architecture with implications for the design of artificial neural networks.

}, issn = {1476-4687}, doi = {10.1038/s41586-022-05471-w}, author = {Nguyen, Tri M and Thomas, Logan A and Jeff L Rhoades and Ricchi, Ilaria and Yuan, Xintong Cindy and Sheridan, Arlo and Hildebrand, David G C and Funke, Jan and Regehr, Wade G and Lee, Wei-Chung Allen} } @article {68566, title = {Synaptic gradients transform object location to action.}, journal = {Nature}, volume = {613}, year = {2023}, month = {2023 Jan 04}, pages = {534-42}, abstract = {

To survive, animals must convert sensory information into appropriate behaviours. Vision is a common sense for locating ethologically relevant stimuli and guiding motor responses. How circuitry converts object location in retinal coordinates to movement direction in body coordinates remains largely unknown. Here we show through behaviour, physiology, anatomy and connectomics in Drosophila that visuomotor transformation occurs by conversion of topographic maps formed by the dendrites of feature-detecting visual projection neurons (VPNs) into synaptic weight gradients of VPN outputs onto central brain neurons. We demonstrate how this gradient motif transforms the anteroposterior location of a visual looming stimulus into the fly{\textquoteright}s directional escape. Specifically, we discover that two neurons postsynaptic to a looming-responsive VPN type promote opposite takeoff directions. Opposite synaptic weight gradients onto these neurons from looming VPNs in different visual field regions convert localized looming threats into correctly oriented escapes. For a second looming-responsive VPN type, we demonstrate graded responses along the dorsoventral axis. We show that this synaptic gradient motif generalizes across all 20 primary VPN cell types and most often arises without VPN axon topography. Synaptic gradients may thus be a general mechanism for conveying spatial features of sensory information into directed motor outputs.

}, issn = {1476-4687}, doi = {10.1038/s41586-022-05562-8}, author = {Dombrovski, Mark and Peek, Martin Y and Park, Jin-Yong and Vaccari, Andrea and Sumathipala, Marissa and Morrow, Carmen and Breads, Patrick and Zhao, Arthur and Kurmangaliyev, Yerbol Z and Sanfilippo, Piero and Rehan, Aadil and Polsky, Jason and Alghailani, Shada and Tenshaw, Emily and Namiki, Shigehiro and Zipursky, S Lawrence and Card, Gwyneth M} } @article {68801, title = {Systematic annotation of a complete adult male Drosophila nerve cord connectome reveals principles of functional organisation}, journal = {bioRxiv}, year = {2023}, month = {2023 Jun 06}, abstract = {

Our companion paper (Takemura et al., 2023) introduces the first completely proofread connectome of the nerve cord of an animal that can walk or fly. The base connectome consists of neuronal morphologies and the connections between them. However, in order to efficiently navigate and understand this connectome, it is crucial to have a system of annotations that systematically categorises and names neurons, linking them to the existing literature. In this paper we describe the comprehensive annotation of the VNC connectome, first by a system of hierarchical coarse annotations, then by grouping left-right and serially homologous neurons and eventually by defining systematic cell types for the intrinsic interneurons and sensory neurons of the VNC; descending and motor neurons are typed in (Cheong et al., 2023). We assign a sensory modality to over 5000 sensory neurons, cluster them by connectivity, and identify serially homologous cell types and a layered organisation likely corresponding to peripheral topography. We identify the developmental neuroblast of origin of the large majority of VNC neurons and confirm that (in most cases) all secondary neurons of each hemilineage express a single neurotransmitter. Neuroblast hemilineages are serially repeated along the segments of the nerve cord and generally exhibit consistent hemilineage-to-hemilineage connectivity across neuromeres, supporting the idea that hemilineages are a major organisational feature of the VNC. We also find that more than a third of individual neurons belong to serially homologous cell types, which were crucial for identifying motor neurons and sensory neurons across leg neuropils. Categorising interneurons by their neuropil innervation patterns provides an additional organisation axis. Over half of the intrinsic neurons of the VNC appear dedicated to the legs, with the majority restricted to single leg neuropils; in contrast, inhibitory interneurons connecting different leg neuropils, especially those crossing the midline, appear rarer than anticipated by standard models of locomotor circuitry. Our annotations are being released as part of the neuprint.janelia.org web application and also serve as the basis of programmatic analysis of the connectome through dedicated tools that we describe in this paper.

}, doi = {10.1101/2023.06.05.543407}, url = {https://doi.org/10.1101/2023.06.05.543407}, author = {Elizabeth C Marin and Billy J Morris and Tomke Stuerner and Andrew S Champion and Dominik Krzeminski and Griffin Badalamente and Marina Gkantia and Imaan F M Tamimi and Siqi Fang and Sung Soo Moon and Han S J Cheong and Feng Li and Philipp Schlegel and Stuart Berg and FlyEM Project Team and Gwyneth M Card and Marta Costa and David Shepherd and Gregory S X E Jefferis} } @article {68606, title = {TEMPO enables sequential genetic labeling and manipulation of vertebrate cell lineages.}, journal = {Neuron}, volume = {111}, year = {2023}, month = {2023 Feb 01}, pages = {345-361.e10}, abstract = {

During development, regulatory factors appear in a precise order to determine cell fates over time. Consequently, to investigate complex tissue development, it is necessary to visualize and manipulate cell lineages with temporal control. Current strategies for tracing vertebrate cell lineages lack genetic access to sequentially produced cells. Here, we present TEMPO (Temporal Encoding and Manipulation in a Predefined Order), an imaging-readable genetic tool allowing differential labeling and manipulation of consecutive cell generations in vertebrates. TEMPO is based on CRISPR and powered by a cascade of gRNAs that drive orderly activation and inactivation of reporters and/or effectors. Using TEMPO to visualize zebrafish and mouse neurogenesis, we recapitulated birth-order-dependent neuronal fates. Temporally manipulating cell-cycle regulators in mouse cortex progenitors altered the proportion and distribution of neurons and glia, revealing the effects of temporal gene perturbation on serial cell fates. Thus, TEMPO enables sequential manipulation of molecular factors, crucial to study cell-type specification.

}, keywords = {Animals, Cell Differentiation, Cell Lineage, Gene Expression Regulation, Developmental, Mice, Neurogenesis, Neuroglia, Neurons, Zebrafish}, issn = {1097-4199}, doi = {10.1016/j.neuron.2022.10.035}, author = {Espinosa-Medina, Isabel and Feliciano, Daniel and Belmonte-Mateos, Carla and Linda Miyares, Rosa and Garcia-Marques, Jorge and Foster, Benjamin and Lindo, Sarah and Pujades, Cristina and Koyama, Minoru and Lee, Tzumin} } @article {68884, title = {Ten-fold Robust Expansion Microscopy.}, journal = {Bio-Protocol}, volume = {13}, year = {2023}, month = {2023 Jun 20}, pages = {e4698}, abstract = {

Expansion microscopy (ExM) is a powerful technique to overcome the diffraction limit of light microscopy that can be applied in both tissues and cells. In ExM, samples are embedded in a swellable polymer gel to physically expand the sample and isotropically increase resolution in x, y, and z. By systematic exploration of the ExM recipe space, we developed a novel ExM method termed Ten-fold Robust Expansion Microscopy (TREx) that, as the original ExM method, requires no specialized equipment or procedures. TREx enables ten-fold expansion of both thick mouse brain tissue sections and cultured human cells, can be handled easily, and enables high-resolution subcellular imaging with a single expansion step. Furthermore, TREx can provide ultrastructural context to subcellular protein localization by combining antibody-stained samples with off-the-shelf small molecule stains for both total protein and membranes.

}, issn = {2331-8325}, doi = {10.21769/BioProtoc.4698}, author = {Damstra, Hugo G J and Mohar, Boaz and Eddison, Mark and Akhmanova, Anna and Kapitein, Lukas C and Tillberg, Paul W} } @article {69077, title = {Tensor formalism for predicting synaptic connections with ensemble modeling or optimization.}, journal = {arXiv}, year = {2023}, month = {2023 Oct 31}, abstract = {

Theoretical neuroscientists often try to understand how the structure of a neural network relates to its function by focusing on structural features that would either follow from optimization or occur consistently across possible implementations. Both optimization theories and ensemble modeling approaches have repeatedly proven their worth, and it would simplify theory building considerably if predictions from both theory types could be derived and tested simultaneously. Here we show how tensor formalism from theoretical physics can be used to unify and solve many optimization and ensemble modeling approaches to predicting synaptic connectivity from neuronal responses. We specifically focus on analyzing the solution space of synaptic weights that allow a thresholdlinear neural network to respond in a prescribed way to a limited number of input conditions. For optimization purposes, we compute the synaptic weight vector that minimizes an arbitrary quadratic loss function. For ensemble modeling, we identify synaptic weight features that occur consistently across all solutions bounded by an arbitrary quadratic function. We derive a common solution to this suite of nonlinear problems by showing how each of them reduces to an equivalent linear problem that can be solved analytically. Although identifying the equivalent linear problem is nontrivial, our tensor formalism provides an elegant geometrical perspective that allows us to solve the problem numerically. The final algorithm is applicable to a wide range of interesting neuroscience problems, and the associated geometric insights may carry over to other scientific problems that require constrained optimization.

}, doi = {10.48550/arXiv.2310.20309}, url = {https://doi.org/10.48550/arXiv.2310.20309}, author = {Tirthabir Biswas and Tianzhi Lambus Li and James E. Fitzgerald} } @article {68999, title = {Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions.}, journal = {Cell Reports}, volume = {42}, year = {2023}, month = {2023 Aug 24}, pages = {113015}, abstract = {

The execution of cognitive functions requires coordinated circuit activity across different brain areas that involves the associated firing of neuronal assemblies. Here, we tested the circuit mechanism behind assembly interactions between the hippocampus and the medial prefrontal cortex (mPFC) of adult rats by recording neuronal populations during a rule-switching task. We identified functionally coupled CA1-mPFC cells that synchronized their activity beyond that expected from common spatial coding or oscillatory firing. When such cell pairs fired together, the mPFC cell strongly phase locked to CA1 theta oscillations and maintained consistent theta firing phases, independent of the theta timing of their CA1 counterpart. These functionally connected CA1-mPFC cells formed interconnected assemblies. While firing together with their CA1 assembly partners, mPFC cells fired along specific theta sequences. Our results suggest that upregulated theta oscillatory firing of mPFC cells can signal transient interactions with specific CA1 assemblies, thus enabling distributed computations.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2023.113015}, author = {Nardin, Michele and Kaefer, Karola and Stella, Federico and Csicsvari, Jozsef} } @article {68667, title = {Three-dimensional reconstructions of mechanosensory end organs suggest a unifying mechanism underlying dynamic, light touch}, journal = {Neuron}, year = {2023}, month = {2023 Oct 18}, abstract = {

Specialized mechanosensory end organs within mammalian skin{\textemdash}hair follicle-associated lanceolate complexes, Meissner corpuscles, and Pacinian corpuscles{\textemdash}enable our perception of light, dynamic touch1. In each of these end organs, fast-conducting mechanically sensitive neurons, called Aβ low-threshold mechanoreceptors (Aβ LTMRs), associate with resident glial cells, known as terminal Schwann cells (TSCs) or lamellar cells, to form complex axon ending structures. Lanceolate-forming and corpuscle-innervating Aβ LTMRs share a low threshold for mechanical activation, a rapidly adapting (RA) response to force indentation, and high sensitivity to dynamic stimuli1{\textendash}6. How mechanical stimuli lead to activation of the requisite mechanotransduction channel Piezo27{\textendash}15\ and Aβ RA-LTMR excitation across the morphologically dissimilar mechanosensory end organ structures is not understood. Here, we report the precise subcellular distribution of Piezo2 and high-resolution, isotropic 3D reconstructions of all three end organs formed by Aβ RA-LTMRs determined by large volume enhanced Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) imaging. We found that within each end organ, Piezo2 is enriched along the sensory axon membrane and is minimally or not expressed in TSCs and lamellar cells. We also observed a large number of small cytoplasmic protrusions enriched along the Aβ RA-LTMR axon terminals associated with hair follicles, Meissner corpuscles, and Pacinian corpuscles. These axon protrusions reside within close proximity to axonal Piezo2, occasionally contain the channel, and often form adherens junctions with nearby non-neuronal cells. Our findings support a unified model for Aβ RA-LTMR activation in which axon protrusions anchor Aβ RA-LTMR axon terminals to specialized end organ cells, enabling mechanical stimuli to stretch the axon in hundreds to thousands of sites across an individual end organ and leading to activation of proximal Piezo2 channels and excitation of the neuron.

}, doi = {10.1016/j.neuron.2023.08.023}, url = {https://doi.org/10.1016/j.neuron.2023.08.023}, author = {Annie Handler and Qiyu Zhang and Song Pang and Tri M. Nguyen and Michael Iskols and Michael Nolan-Tamariz and Stuart Cattel and Rebecca Plumb and Brianna Sanchez and Karyl Ashjian and Aria Shotland and Bartianna Brown and Madiha Kabeer and Josef Turecek and Genelle Rankin and Wangchu Xiang and Elisa C. Pavarino and Nusrat Africawala and Celine Santiago and Wei-Chung Allen Lee and C. Shan Xu and David D. Ginty} } @article {68674, title = {Time-resolved correlation of distributed brain activity tracks E-I balance and accounts for diverse scale-free phenomena.}, journal = {Cell Reports}, volume = {42}, year = {2023}, month = {2023 Mar 24}, pages = {112254}, abstract = {

Much of systems neuroscience posits the functional importance of brain activity patterns that lack natural scales of sizes, durations, or frequencies. The field has developed prominent, and sometimes competing, explanations for the nature of this scale-free activity. Here, we reconcile these explanations across species and modalities. First, we link estimates of excitation-inhibition (E-I) balance with time-resolved correlation of distributed brain activity. Second, we develop an unbiased method for sampling time series constrained by this time-resolved correlation. Third, we use this method to show that estimates of E-I balance account for diverse scale-free phenomena without need to attribute additional function or importance to these phenomena. Collectively, our results simplify existing explanations of scale-free brain activity and provide stringent tests on future theories that seek to transcend these explanations.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2023.112254}, author = {Nanda, Aditya and Johnson, Graham W and Mu, Yu and Ahrens, Misha B and Chang, Catie and Englot, Dario J and Breakspear, Michael and Rubinov, Mikail} } @article {68561, title = {Time-tagged ticker tapes for intracellular recordings.}, journal = {Nature Biotechnology}, volume = {41}, year = {2023}, month = {2023 May 01}, pages = {631-9}, abstract = {

Recording transcriptional histories of a cell would enable deeper understanding of cellular developmental trajectories and responses to external perturbations. Here we describe an engineered protein fiber that incorporates diverse fluorescent marks during its growth to store a ticker tape-like history. An embedded HaloTag reporter incorporates user-supplied dyes, leading to colored stripes that map the growth of each individual fiber to wall clock time. A co-expressed eGFP tag driven by a promoter of interest records a history of transcriptional activation. High-resolution multi-spectral imaging on fixed samples reads the cellular histories, and interpolation of eGFP marks relative to HaloTag timestamps provides accurate absolute timing. We demonstrate recordings of doxycycline-induced transcription in HEK cells and cFos promoter activation in cultured neurons, with a single-cell absolute accuracy of 30-40 minutes over a 12-hour recording. The protein-based ticker tape design we present here could be generalized to achieve massively parallel single-cell recordings of diverse physiological modalities.

}, issn = {1546-1696}, doi = {10.1038/s41587-022-01524-7}, author = {Lin, Dingchang and Li, Xiuyuan and Moult, Eric and Park, Pojeong and Tang, Benjamin and Shen, Hao and Grimm, Jonathan B and Falco, Natalie and Jia, Bill Z and Baker, David and Lavis, Luke D and Cohen, Adam E} } @article {68827, title = {Tissue Morphogenesis Through Dynamic Cell and Matrix Interactions.}, journal = {Annual Reviews Cell Developmental Biology}, year = {2023}, month = {2023 Jun 14}, abstract = {

Multicellular organisms generate tissues of diverse shapes and functions from cells and extracellular matrices. Their adhesion molecules mediate cell-cell and cell-matrix interactions, which not only play crucial roles in maintaining tissue integrity but also serve as key regulators of tissue morphogenesis. Cells constantly probe their environment to make decisions: They integrate chemical and mechanical information from the environment via diffusible ligand- or adhesion-based signaling to decide whether to release specific signaling molecules or enzymes, to divide or differentiate, to move away or stay, or even whether to live or die. These decisions in turn modify their environment, including the chemical nature and mechanical properties of the extracellular matrix. Tissue morphology is the physical manifestation of the remodeling of cells and matrices by their historical biochemical and biophysical landscapes. We review our understanding of matrix and adhesion molecules in tissue morphogenesis, with an emphasis on key physical interactions that drive morphogenesis. Expected final online publication date for the , Volume 39 is October 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

}, issn = {1530-8995}, doi = {10.1146/annurev-cellbio-020223-031019}, author = {Wu, Di and Yamada, Kenneth M and Wang, Shaohe} } @article {68788, title = {Tissue-specific transcriptome analyses in Drosophila provide novel insights into the mode of action of the insecticide spinosad and the function of its target, nAChRα6.}, journal = {Pest Management Science}, year = {2023}, month = {2023 May 29}, abstract = {

BACKGROUND: The insecticides spinosad and imidacloprid are neurotoxins with distinct modes of action. Both target nicotinic acetylcholine receptors (nAChRs), albeit different subunits. Spinosad is an allosteric modulator, that upon binding initiates endocytosis of its target, nAChRα6. Imidacloprid binding triggers excessive neuronal ion influx. Despite these differences, low-dose effects converge downstream in the precipitation of oxidative stress and neurodegeneration.

RESULTS: Using RNA-Seq, we compared the transcriptional signatures of spinosad and imidacloprid, at low-dose exposures. Both insecticides cause upregulation of Glutathione S-transferase and Cytochrome P450 genes in the brain and downregulation in the fat body, whereas reduced expression of immune-related genes is observed in both tissues. Spinosad shows unique impacts on genes involved in lysosomal function, protein folding, and reproduction. Co-expression analyses revealed little to no correlation between genes affected by spinosad and nAChRα6 expressing neurons, but a positive correlation with glial cell markers. We also detected and experimentally confirmed nAChRα6 expression in fat body cells and male germline cells. This led us to uncover lysosomal dysfunction in the fat body following spinosad exposure, and a fitness cost in spinosad-resistant (nAChRα6 null) males - oxidative stress in testes, and reduced fertility.

CONCLUSION: Spinosad and imidacloprid share transcriptional perturbations in immunity-, energy homeostasis-, and oxidative stress-related genes. Low doses of other neurotoxic insecticides should be investigated for similar impacts. While target-site spinosad resistance mutation has evolved in the field, this may have a fitness cost. Our findings demonstrate the power of tissue-specific transcriptomics approach and the use of single-cell transcriptome data. This article is protected by copyright. All rights reserved.

}, issn = {1526-4998}, doi = {10.1002/ps.7585}, author = {Martelli, Felipe and Ravenscroft, Thomas A and Hutchison, William and Batterham, Philip} } @article {68897, title = {Toward scalable reuse of vEM data: OME-Zarr to the rescue.}, journal = {Methods in Cell Biology}, volume = {177}, year = {2023}, month = {2023 Jul 20}, pages = {359-387}, abstract = {

The growing size of EM volumes is a significant barrier to findable, accessible, interoperable, and reusable (FAIR) sharing. Storage, sharing, visualization and processing are challenging for large datasets. Here we discuss a recent development toward the standardized storage of volume electron microscopy (vEM) data which addresses many of the issues that researchers face. The OME-Zarr format splits data into more manageable, performant chunks enabling streaming-based access, and unifies important metadata such as multiresolution pyramid descriptions. The file format is designed for centralized and remote storage (e.g., cloud storage or file system) and is therefore ideal for sharing large data. By coalescing on a common, community-wide format, these benefits will expand as ever more data is made available to the scientific community.

}, keywords = {Information Storage and Retrieval, Volume Electron Microscopy}, issn = {0091-679X}, doi = {10.1016/bs.mcb.2023.01.016}, author = {Rzepka, Norman and Bogovic, John A and Moore, Joshua A} } @article {68958, title = {Towards Generalizable Organelle Segmentation in Volume Electron Microscopy.}, journal = {Microscopy and Microanalysis}, volume = {29}, year = {2023}, month = {2023 Jul 22}, pages = {975}, keywords = {Organelles, Volume Electron Microscopy}, issn = {1435-8115}, doi = {10.1093/micmic/ozad067.487}, author = {Heinrich, Larissa and Patton, Will and Bennett, Davis and Ackerman, David and Park, Grace and Bogovic, John A and Eckstein, Nils and Petruncio, Alyson and Clements, Jody and Pang, Song and Shan Xu, C and Funke, Jan and Korff, Wyatt and Hess, Harald and Lippincott-Schwartz, Jennifer and Saalfeld, Stephan and Weigel, Aubrey} } @article {68809, title = {Transforming descending input into behavior: The organization of premotor circuits in the Drosophila Male Adult Nerve Cord connectome}, journal = {bioRxiv}, year = {2023}, month = {2023 Jun 07}, abstract = {

In most animals, a relatively small number of descending neurons (DNs) connect higher brain centers in the animal{\textquoteright}s head to motor neurons (MNs) in the nerve cord of the animal{\textquoteright}s body that effect movement of the limbs. To understand how brain signals generate behavior, it is critical to understand how these descending pathways are organized onto the body MNs. In the fly, Drosophila melanogaster, MNs controlling muscles in the leg, wing, and other motor systems reside in a ventral nerve cord (VNC), analogous to the mammalian spinal cord. In companion papers, we introduced a densely-reconstructed connectome of the Drosophila Male Adult Nerve Cord (MANC,\ Takemura et al., 2023), including cell type and developmental lineage annotation (Marin et al., 2023), which provides complete VNC connectivity at synaptic resolution. Here, we present a first look at the organization of the VNC networks connecting DNs to MNs based on this new connectome information. We proofread and curated all DNs and MNs to ensure accuracy and reliability, then systematically matched DN axon terminals and MN dendrites with light microscopy data to link their VNC morphology with their brain inputs or muscle targets. We report both broad organizational patterns of the entire network and fine-scale analysis of selected circuits of interest. We discover that direct DN-MN connections are infrequent and identify communities of intrinsic neurons linked to control of different motor systems, including putative ventral circuits for walking, dorsal circuits for flight steering and power generation, and intermediate circuits in the lower tectulum for coordinated action of wings and legs. Our analysis generates hypotheses for future functional experiments and, together with the MANC connectome, empowers others to investigate these and other circuits of the Drosophila ventral nerve cord in richer mechanistic detail.

}, doi = {10.1101/2023.06.07.543976}, url = {https://doi.org/10.1101/2023.06.07.543976}, author = {H. S. J. Cheong and K. Eichler and T. Stuerner and S. K. Asinof and A. S. Champion and E. C. Marin and T. B. Oram and M. Sumathipala and L. Venkatasubramanian and S. Namiki and I. Siwanowicz and M. Costa and S. Berg and Janelia FlyEM Project Team and G. S. X. E. Jefferis and G. M. Card} } @article {68968, title = {Ultra-high density electrodes improve detection, yield, and cell type specificity of brain recordings.}, journal = {bioRxiv}, year = {2023}, month = {2023 Aug 25}, abstract = {

To study the neural basis of behavior, we require methods to sensitively and accurately measure neural activity at single neuron and single spike resolution. Extracellular electrophysiology is a principal method for achieving this, but it has biases in the neurons it detects and it imperfectly resolves their action potentials. To overcome these limitations, we developed a silicon probe with significantly smaller and denser recording sites than previous designs, called Neuropixels Ultra (NP Ultra). This device measures neuronal activity at ultra-high densities (\>1300 sites per mm, 10 times higher than previous probes), with 6 {\textmu}m center-to-center spacing and low noise. This device effectively comprises an implantable voltage-sensing camera that captures a planar image of a neuron{\textquoteright}s electrical field. We introduce a new spike sorting algorithm optimized for these probes and use it to find that the yield of visually-responsive neurons in recordings from mouse visual cortex improves \~{}3-fold. Recordings across multiple brain regions and four species revealed a subset of unexpectedly small extracellular action potentials not previously reported. Further experiments determined that, in visual cortex, these do not correspond to major subclasses of interneurons and instead likely reflect recordings from axons. Finally, using ground-truth identification of cortical inhibitory cell types with optotagging, we found that cell type was discriminable with approximately 75\% success among three types, a significant improvement over lower-resolution recordings. NP Ultra improves spike sorting performance, sampling bias, and cell type classification.

}, doi = {10.1101/2023.08.23.554527}, author = {Ye, Zhiwen and Shelton, Andrew M and Shaker, Jordan R and Boussard, Julien and Colonell, Jennifer and Manavi, Sahar and Chen, Susu and Windolf, Charlie and Hurwitz, Cole and Namima, Tomoyuki and Pedraja, Federico and Weiss, Shahaf and Raducanu, Bogdan and Ness, Torbj{\o}rn V and Einevoll, Gaute T and Laurent, Gilles and Sawtell, Nathaniel B and Bair, Wyeth and Pasupathy, Anitha and Mora Lopez, Carolina and Dutta, Barun and Paninski, Liam and Siegle, Joshua H and Koch, Christof and Olsen, Shawn R and Harris, Timothy D and Steinmetz, Nicholas A} } @conference {69206, title = {Unsupervised Learning of Object-Centric Embeddings for Cell Instance Segmentation in Microscopy Images}, booktitle = {2023 IEEE/CVF International Conference on Computer Vision (ICCV)}, year = {2023}, month = {2023 Oct 01}, publisher = {IEEE}, organization = {IEEE}, address = {Paris, France}, abstract = {

Segmentation of objects in microscopy images is required for many biomedical applications. We introduce object-centric embeddings (OCEs), which embed image patches such that the spatial offsets between patches cropped from the same object are preserved. Those learnt embeddings can be used to delineate individual objects and thus obtain instance segmentations. Here, we show theoretically that, under assumptions commonly found in microscopy images, OCEs can be learnt through a self-supervised task that predicts the spatial offset between image patches. Together, this forms an unsupervised cell instance segmentation method which we evaluate on nine diverse large-scale microscopy datasets. Segmentations obtained with our method lead to substantially improved results, compared to state-of-the-art baselines on six out of nine datasets, and perform on par on the remaining three datasets. If ground-truth annotations are available, our method serves as an excellent starting point for supervised training, reducing the required amount of ground-truth needed by one order of magnitude, thus substantially increasing the practical applicability of our method. Source code is available at github.com/funkelab/cellulus.

}, doi = {10.1109/ICCV51070.2023.01944}, url = {https://ieeexplore.ieee.org/document/10377649/}, author = {Wolf, Steffen and Lalit, Manan and McDole, Katie and Funke, Jan} } @article {69074, title = {Vagal sensory neurons mediate the Bezold-Jarisch reflex and induce syncope.}, journal = {Nature}, volume = {623}, year = {2023}, month = {2023 Nov 01}, pages = {387-396}, abstract = {

Visceral sensory pathways mediate homeostatic reflexes, the dysfunction of which leads to many neurological disorders. The Bezold-Jarisch reflex (BJR), first described in 1867, is a cardioinhibitory reflex that is speculated to be mediated by vagal sensory neurons (VSNs) that also triggers syncope. However, the molecular identity, anatomical organization, physiological characteristics and behavioural influence of cardiac VSNs remain mostly unknown. Here we leveraged single-cell RNA-sequencing data and HYBRiD tissue clearing to show that VSNs that express neuropeptide Y receptor Y2 (NPY2R) predominately connect the heart ventricular wall to the area postrema. Optogenetic activation of NPY2R VSNs elicits the classic triad of BJR responses-hypotension, bradycardia and suppressed respiration-and causes an animal to faint. Photostimulation during high-resolution echocardiography and laser Doppler flowmetry with behavioural observation revealed a range of phenotypes reflected in clinical syncope, including reduced cardiac output, cerebral hypoperfusion, pupil dilation and eye-roll. Large-scale Neuropixels brain recordings and machine-learning-based modelling showed that this manipulation causes the suppression of activity across a large distributed neuronal population that is not explained by changes in spontaneous behavioural movements. Additionally, bidirectional manipulation of the periventricular zone had a push-pull effect, with inhibition leading to longer syncope periods and activation inducing arousal. Finally, ablating NPY2R VSNs specifically abolished the BJR. Combined, these results demonstrate a genetically defined cardiac reflex that recapitulates characteristics of human syncope at physiological, behavioural and neural network levels.

}, keywords = {Area Postrema, Bradycardia, Cardiac Output, Low, Echocardiography, Heart, Heart Rate, Humans, Hypotension, Laser-Doppler Flowmetry, Nerve Net, Reflex, Sensory Receptor Cells, Single-Cell Gene Expression Analysis, Syncope, vagus nerve}, issn = {1476-4687}, doi = {10.1038/s41586-023-06680-7}, author = {Lovelace, Jonathan W and Ma, Jingrui and Yadav, Saurabh and Chhabria, Karishma and Shen, Hanbing and Pang, Zhengyuan and Qi, Tianbo and Sehgal, Ruchi and Zhang, Yunxiao and Bali, Tushar and Vaissiere, Thomas and Tan, Shawn and Liu, Yuejia and Rumbaugh, Gavin and Ye, Li and Kleinfeld, David and Stringer, Carsen and Augustine, Vineet} } @article {69073, title = {Volitional activation of remote place representations with a hippocampal brain-machine interface.}, journal = {Science}, volume = {382}, year = {2023}, month = {2023 Nov 03}, pages = {566-573}, abstract = {

The hippocampus is critical for recollecting and imagining experiences. This is believed to involve voluntarily drawing from hippocampal memory representations of people, events, and places, including maplike representations of familiar environments. However, whether representations in such "cognitive maps" can be volitionally accessed is unknown. We developed a brain-machine interface to test whether rats can do so by controlling their hippocampal activity in a flexible, goal-directed, and model-based manner. We found that rats can efficiently navigate or direct objects to arbitrary goal locations within a virtual reality arena solely by activating and sustaining appropriate hippocampal representations of remote places. This provides insight into the mechanisms underlying episodic memory recall, mental simulation and planning, and imagination and opens up possibilities for high-level neural prosthetics that use hippocampal representations.

}, keywords = {Animals, Brain-Computer Interfaces, Hippocampus, Humans, Imagination, Memory, Episodic, Mental Recall, Rats}, issn = {1095-9203}, doi = {10.1126/science.adh5206}, author = {Lai, Chongxi and Tanaka, Shinsuke and Harris, Timothy D and Lee, Albert K} } @article {68792, title = {Voltage dynamics of dendritic integration and back-propagation in vivo}, journal = {bioRxiv}, year = {2023}, month = {2023 May 26}, abstract = {

Neurons integrate synaptic inputs within their dendrites and produce spiking outputs, which then propagate down the axon and back into the dendrites where they contribute to plasticity. Mapping the voltage dynamics in dendritic arbors of live animals is crucial for understanding neuronal computation and plasticity rules. Here we combine patterned channelrhodopsin activation with dual-plane structured illumination voltage imaging, for simultaneous perturbation and monitoring of dendritic and somatic voltage in Layer 2/3 pyramidal neurons in anesthetized and awake mice. We examined the integration of synaptic inputs and compared the dynamics of optogenetically evoked, spontaneous, and sensory-evoked back-propagating action potentials (bAPs). Our measurements revealed a broadly shared membrane voltage throughout the dendritic arbor, and few signatures of electrical compartmentalization among synaptic inputs. However, we observed spike rate acceleration-dependent propagation of bAPs into distal dendrites. We propose that this dendritic filtering of bAPs may play a critical role in activity-dependent plasticity.

}, doi = {10.1101/2023.05.25.542363}, url = {https://doi.org/10.1101/2023.05.25.542363}, author = {J. David Wong-Campos and Pojeong Park and Hunter Davis and Yitong Qi and He Tian and Daniel G. Itkis and Doyeon Kim and Sarah E. Plutkis and Luke Lavis and Adam E. Cohen} } @article {68104, title = {Volume-transmitted GABA waves pace epileptiform rhythms in the hippocampal network}, journal = {Current Biology}, volume = {33}, year = {2023}, month = {2023 Apr 10}, pages = {1249}, abstract = {

Mechanisms that entrain and drive rhythmic epileptiform discharges remain debated. Traditionally, this quest has been focusing on interneuronal networks driven by GABAergic connections that activate synaptic or extrasynaptic receptors. However, synchronised interneuronal discharges could also trigger a transient elevation of extracellular GABA across the tissue volume, thus raising tonic GABAA\ receptor conductance (Gtonic) in multiple cells. Here, we use patch-clamp GABA {\textquoteleft}sniffer{\textquoteright} and optical GABA sensor to show that periodic epileptiform discharges are preceded by region-wide, rising waves of extracellular GABA. Neural network simulations that incorporate volume-transmitted GABA signals point to mechanistic principles underpinning this relationship. We validate this hypothesis using simultaneous patch-clamp recordings from multiple nerve cells, selective optogenetic stimulation of fast-spiking interneurons. Critically, we manipulate GABA uptake to suppress extracellular GABA waves but not synaptic GABAergic transmission, which shows a clear effect on rhythm generation. Our findings thus unveil a key role of extrasynaptic, volume-transmitted GABA actions in pacing regenerative rhythmic activity in brain networks.

}, doi = {10.1016/j.cub.2023.02.051}, url = {https://doi.org/10.1016/j.cub.2023.02.051}, author = {Vincent Magloire and Leonid P. Savtchenko and Sergyi Sylantyev and Thomas P. Jensen and Nicholas Cole and Jonathan S. Marvin and Loren L. Looger and Dimitri M. Kullmann and Matthew C. Walker and Ivan Pavlov and Dmitri A. Rusakov} } @article {67946, title = {2,7-Diaminobenzopyrylium Dyes Are Live-Cell Mitochondrial Stains2,7-Diaminobenzopyrylium Dyes Are Live-Cell Mitochondrial Stains}, journal = {ACS Bio \& Med Chem Au}, volume = {2}, year = {2022}, month = {2022 Jun 15}, pages = {307-12}, abstract = {

Small-molecule fluorescent stains enable the imaging of cellular structures without the need for genetic manipulation. Here, we introduce 2,7-diaminobenzopyrylium (DAB) dyes as live-cell mitochondrial stains excited with violet light. This amalgam of the coumarin and rhodamine fluorophore structures yields dyes with high photostability and tunable spectral properties.

}, issn = {2694-2437}, doi = {10.1021/acsbiomedchemau.1c00068}, url = {https://pubs.acs.org/doi/10.1021/acsbiomedchemau.1c00068}, author = {Banala, Sambashiva and Tkachuk, Ariana N. and Patel, Ronak and Kumar, Pratik and Brown, Timothy A. and Lavis, Luke D.} } @article {68513, title = {The 3D ultrastructure of the chordotonal organs in the antenna of a microwasp remains complex although simplified.}, journal = {Scientific Reports}, volume = {12}, year = {2022}, month = {2022 Nov 23}, pages = {20172}, abstract = {

Insect antennae are astonishingly versatile and have multiple sensory modalities. Audition, detection of airflow, and graviception are combined in the antennal chordotonal organs. The miniaturization of these complex multisensory organs has never been investigated. Here we present a comprehensive study of the structure and scaling of the antennal chordotonal organs of the extremely miniaturized parasitoid wasp Megaphragma viggianii based on 3D electron microscopy. Johnston{\textquoteright}s organ of M. viggianii consists of 19 amphinematic scolopidia (95 cells); the central organ consists of five scolopidia (20 cells). Plesiomorphic composition includes one accessory cell per scolopidium, but in M. viggianii this ratio is only 0.3. Scolopale rods in Johnston{\textquoteright}s organ have a unique structure. Allometric analyses demonstrate the effects of scaling on the antennal chordotonal organs in insects. Our results not only shed light on the universal principles of miniaturization of sense organs, but also provide context for future interpretation of the M. viggianii connectome.

}, keywords = {Animals, Arthropod Antennae, Insecta, Mechanoreceptors, Microscopy, Electron, Sense Organs}, issn = {2045-2322}, doi = {10.1038/s41598-022-24390-4}, author = {Diakova, Anna V and Makarova, Anastasia A and Pang, Song and Xu, C Shan and Hess, Harald and Polilov, Alexey A} } @article {68115, title = {Accurate angular integration with only a handful of neurons.}, journal = {bioRxiv}, year = {2022}, month = {2022 May 25}, abstract = {

To flexibly navigate, many animals rely on internal spatial representations that persist when the animal is standing still in darkness, and update accurately by integrating the animal{\textquoteright}s movements in the absence of localizing sensory cues. Theories of mammalian head direction cells have proposed that these dynamics can be realized in a special class of networks that maintain a localized bump of activity via structured recurrent connectivity, and that shift this bump of activity via angular velocity input. Although there are many different variants of these so-called ring attractor networks, they all rely on large numbers of neurons to generate representations that persist in the absence of input and accurately integrate angular velocity input. Surprisingly, in the fly,\ Drosophila melanogaster, a head direction representation is maintained by a much smaller number of neurons whose dynamics and connectivity resemble those of a ring attractor network. These findings challenge our understanding of ring attractors and their putative implementation in neural circuits. Here, we analyzed failures of angular velocity integration that emerge in small attractor networks with only a few computational units. Motivated by the peak performance of the fly head direction system in darkness, we mathematically derived conditions under which small networks, even with as few as 4 neurons, achieve the performance of much larger networks. The resulting description reveals that by appropriately tuning the network connectivity, the network can maintain persistent representations over the continuum of head directions, and it can accurately integrate angular velocity inputs. We then analytically determined how performance degrades as the connectivity deviates from this optimally-tuned setting, and we find a trade-off between network size and the tuning precision needed to achieve persistence and accurate integration. This work shows how even small networks can accurately track an animal{\textquoteright}s movements to guide navigation, and it informs our understanding of the functional capabilities of discrete systems more broadly.

}, doi = {10.1101/2022.05.23.493052}, url = {https://doi.org/10.1101/2022.05.23.493052}, author = {Marcella Noorman and Brad K Hulse and Vivek Jayaraman and Sandro Romani and Ann M Hermundstad} } @article {68045, title = {Actin nano-architecture of phagocytic podosomes}, journal = {Nature Communications}, volume = {13}, year = {2022}, month = {2022 Jul 27}, pages = {4363}, abstract = {

Podosomes are actin-enriched adhesion structures important for multiple cellular processes, including migration, bone remodeling, and phagocytosis. Here, we characterized the structure and organization of phagocytic podosomes using interferometric photoactivated localization microscopy (iPALM), a super-resolution microscopy technique capable of 15-20 nm resolution, together with structured illumination microscopy (SIM) and localization-based superresolution microscopy. Phagocytic podosomes were observed during frustrated phagocytosis, a model in which cells attempt to engulf micro-patterned IgG antibodies. For circular patterns, this resulted in regular arrays of podosomes with well-defined geometry. Using persistent homology, we developed a pipeline for semi-automatic identification and measurement of podosome features. These studies revealed an "hourglass" shape of the podosome actin core, a protruding "knob" at the bottom of the core, and two actin networks extending from the core. Additionally, the distributions of paxillin, talin, myosin II, α-actinin, cortactin, and microtubules relative to actin were characterized.

}, doi = {10.1101/2022.05.04.490675}, author = {J. Cody Herron and Shiqiong Hu and Takashi Watanabe and Ana T. Nogueira and Bei Liu and Megan Kern and Jesse Aaron and Aaron Taylor and Michael Pablo and Teng-Leong Chew and Timothy C. Elston and Klaus M. Hahn} } @article {68023, title = {Allosteric interactions prime androgen receptor dimerization and activation.}, journal = {Molecular Cell}, volume = {82}, year = {2022}, month = {2022 Jun 02}, pages = {2021-31}, abstract = {

The androgen receptor (AR) is a nuclear receptor that governs gene expression programs required for prostate development and male phenotype maintenance. Advanced prostate cancers display AR hyperactivation and transcriptome expansion, in part, through AR amplification and interaction with oncoprotein cofactors. Despite its biological importance, how AR domains and cofactors cooperate to bind DNA has remained elusive. Using single-particle cryo-electron microscopy, we isolated three conformations of AR bound to DNA, showing that AR forms a non-obligate dimer, with the buried dimer interface utilized by ancestral steroid receptors repurposed to facilitate cooperative DNA binding. We identify novel allosteric surfaces which are compromised in androgen insensitivity syndrome and reinforced by AR{\textquoteright}s oncoprotein cofactor, ERG, and by DNA-binding motifs. Finally, we present evidence that this plastic dimer interface may have been adopted for transactivation at the expense of DNA binding. Our work highlights how fine-tuning AR{\textquoteright}s cooperative interactions translate to consequences in development and disease.

}, issn = {1097-4164}, doi = {10.1016/j.molcel.2022.03.035}, author = {Wasmuth, Elizabeth V and Broeck, Arnaud Vanden and LaClair, Justin R and Hoover, Elizabeth A and Lawrence, Kayla E and Paknejad, Navid and Pappas, Kyrie and Matthies, Doreen and Wang, Biran and Feng, Weiran and Watson, Philip A and Zinder, John C and Karthaus, Wouter R and de la Cruz, M Jason and Hite, Richard K and Manova-Todorova, Katia and Yu, Zhiheng and Weintraub, Susan T and Klinge, Sebastian and Sawyers, Charles L} } @article {68193, title = {Architecture and dynamics of a novel desmosome-endoplasmic reticulum organelle}, journal = {bioRxiv}, year = {2022}, month = {2022 Jul 08}, abstract = {

The endoplasmic reticulum (ER) forms a dynamic network that contacts other cellular membranes to regulate stress responses, calcium signaling, and lipid transfer. Using high-resolution volume electron microscopy, we find that the ER forms a previously unknown association with keratin intermediate filaments and desmosomal cell-cell junctions. Peripheral ER assembles into mirror image-like arrangements at desmosomes and exhibits nanometer proximity to keratin filaments and the desmosome cytoplasmic plaque. ER tubules exhibit stable associations with desmosomes, and perturbation of desmosomes or keratin filaments alters ER organization and mobility. These findings indicate that desmosomes and the keratin cytoskeleton pattern the distribution of the ER network. Overall, this study reveals a previously unknown subcellular architecture defined by the structural integration of ER tubules with an epithelial intercellular junction.

}, doi = {10.1101/2022.07.07.499185}, url = {https://doi.org/10.1101/2022.07.07.499185}, author = {Navaneetha Krishnan Bharathan and William Giang and Jesse S. Aaron and Satya Khuon and Teng-Leong Chew and Stephan Preibisch and Eric T. Trautman and Larissa Heinrich and John Bogovic and Davis Bennett and David Ackerman and Woohyun Park and Alyson Petruncio and Aubrey V. Weigel and Stephan Saalfeld and COSEM Project Team and A. Wayne Vogl and Sara N. Stahley and Andrew P. Kowalczyk} } @article {68313, title = {Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations.}, journal = {Nature Biotechnology}, year = {2022}, month = {2022 Sep 05}, abstract = {

We present a method to automatically identify and track nuclei in time-lapse microscopy recordings of entire developing embryos. The method combines deep learning and global optimization. On a mouse dataset, it reconstructs 75.8\% of cell lineages spanning 1 h, as compared to 31.8\% for the competing method. Our approach improves understanding of where and when cell fate decisions are made in developing embryos, tissues, and organs.

}, issn = {1546-1696}, doi = {10.1038/s41587-022-01427-7}, author = {Malin-Mayor, Caroline and Hirsch, Peter and Guignard, Leo and McDole, Katie and Wan, Yinan and Lemon, William C and Kainmueller, Dagmar and Keller, Philipp J and Preibisch, Stephan and Funke, Jan} } @article {69715, title = {Best practice standards for circular RNA research}, journal = {Nature Methods}, volume = {19}, year = {2022}, month = {05/2022}, pages = {1208 - 1220}, abstract = {

Circular RNAs (circRNAs) are formed in all domains of life and via different mechanisms. There has been an explosion in the number of circRNA papers in recent years; however, as a relatively young field, circRNA biology has an urgent need for common experimental standards for isolating, analyzing, expressing and depleting circRNAs. Here we propose a set of guidelines for circRNA studies based on the authors{\textquoteright} experience. This Perspective will specifically address the major class of circRNAs in Eukarya that are generated by a spliceosome-catalyzed back-splicing event. We hope that the implementation of best practice principles for circRNA research will help move the field forward and allow a better functional understanding of this fascinating group of RNAs.

}, issn = {1548-7091}, doi = {10.1038/s41592-022-01487-2}, url = {https://www.nature.com/articles/s41592-022-01487-2https://www.nature.com/articles/s41592-022-01487-2.pdfhttps://www.nature.com/articles/s41592-022-01487-2.pdfhttps://www.nature.com/articles/s41592-022-01487-2}, author = {Nielsen, Anne F. and Bindereif, Albrecht and Bozzoni, Irene and Hanan, Mor and Hansen, Thomas B. and Irimia, Manuel and Kadener, Sebastian and Kristensen, Lasse S. and Legnini, Ivano and Morlando, Mariangela and Jarlstad Olesen, Morten T. and Pasterkamp, R. Jeroen and Preibisch, Stephan and Rajewsky, Nikolaus and Suenkel, Christin and Kjems, J{\o}rgen} } @article {68165, title = {Binding partners regulate unfolding of myosin VI to activate the molecular motor.}, journal = {The Biochemical Journal}, volume = {479}, year = {2022}, month = {2022 Jul 15}, pages = {1409-1428}, abstract = {

Myosin VI is the only minus-end actin motor and is coupled to various cellular processes ranging from endocytosis to transcription. This multi-potent nature is achieved through alternative isoform splicing and interactions with a network of binding partners. There is a complex interplay between isoforms and binding partners to regulate myosin VI. Here, we have compared the regulation of two myosin VI splice isoforms by two different binding partners. By combining biochemical and single-molecule approaches, we propose that myosin VI regulation follows a generic mechanism, independently of the spliced isoform and the binding partner involved. We describe how myosin VI adopts an autoinhibited backfolded state which is released by binding partners. This unfolding activates the motor, enhances actin binding and can subsequently trigger dimerization. We have further expanded our study by using single molecule imaging to investigate the impact of binding partners upon myosin VI molecular organisation and dynamics.

}, issn = {1470-8728}, doi = {10.1042/BCJ20220025}, author = {Dos Santos, {\'A}lia and Fili, Natalia and Hari-Gupta, Yukti and Gough, Rosemarie E and Wang, Lin and Martin-Fernandez, Marisa and Arron, Jesse and Wait, Eric and Chew, Teng Leong and Toseland, Chris} } @article {68274, title = {Biomechanical origins of proprioceptive maps in the Drosophila leg}, journal = {bioRxiv}, year = {2022}, month = {2022 Aug 09}, abstract = {

Proprioception, the sense of body position and movement, is essential for effective motor control. Because proprioceptive sensory neurons are embedded in complex and dynamic tissues, it has been challenging to understand how they sense and encode mechanical stimuli. Here, we find that proprioceptor neurons in the\ Drosophila\ femur are organized into functional groups that are biomechanically specialized to detect features of tibia joint kinematics. The dendrites of position and vibration-tuned proprioceptors receive distinct mechanical signals via the\ arculum, an elegant mechanical structure that decomposes movement of the tibia joint into orthogonal components. The cell bodies of position-tuned proprioceptors form a\ goniotopic\ map of joint angle, whereas the dendrites of vibration-tuned proprioceptors form a\ tonotopic\ map of tibia vibration frequency. Our findings reveal biomechanical mechanisms that underlie proprioceptor feature selectivity and identify common organizational principles between proprioception and other topographically organized sensory systems.

}, doi = {10.1101/2022.08.08.503192}, url = {https://doi.org/10.1101/2022.08.08.503192}, author = {Akira Mamiya and Pralaksha Gurung and Igor Siwanowicz and Anne Sustar and Chenghao Chen and Jasper S. Phelps and Aaron T. Kuan and Alexandra Pacureanu and Wei-Chung Allen Lee and Natasha Mhatre and John C. Tuthill} } @article {68252, title = {Brain structure and synaptic protein expression alterations after antidepressant treatment in a Wistar-Kyoto rat model of depression.}, journal = {Journal of Affective Disorders}, volume = {314}, year = {2022}, month = {2022 Jul 22}, pages = {293-302}, abstract = {

BACKGROUND: Structural MRI has demonstrated brain alterations in depression pathology and antidepressants treatment. While synaptic plasticity has been previously proposed as the potential underlying mechanism of MRI findings at a cellular and molecular scale, there is still insufficient evidence to link the MRI findings and synaptic plasticity mechanisms in depression pathology.

METHODS: In this study, a Wistar-Kyoto (WKY) depression rat model was treated with antidepressants (citalopram or Jie-Yu Pills) and tested in a series of behavioral tests and a 7.0 MRI scanner. We then measured dendritic spine density within altered brain regions. We also examined expression of synaptic marker proteins (PSD-95 and SYP).

RESULTS: WKY rats exhibited depression-like behaviors in the sucrose preference test (SPT) and forced swim test (FST), and anxiety-like behaviors in the open field test (OFT). Both antidepressants reversed behavioral changes in SPT and OFT but not in FST. We found a correlation between SPT performance and brain volumes as detected by MRI. All structural changes were consistent with alterations of the corpus callosum (white matter), dendritic spine density, as well as PSD95 and SYP expression at different levels. Two antidepressants similarly reversed these macro- and micro-changes.

LIMITATIONS: The single dose of antidepressants was the major limitation of this study. Further studies should focus on the white matter microstructure changes and myelin-related protein alterations, in addition to comparing the effects of ketamine.

CONCLUSION: Translational evidence links structural MRI changes and synaptic plasticity alterations, which promote our understanding of SPT mechanisms and antidepressant response in WKY rats.

}, issn = {1573-2517}, doi = {10.1016/j.jad.2022.07.037}, author = {Li, Qi and Gao, Yao and Li, Hong and Liu, Hongmei and Wang, Dan and Pan, Weixing and Liu, Sha and Xu, Yong} } @article {67828, title = {A brainstem integrator for self-localization and positional homeostasis}, journal = {Cell}, volume = {185}, year = {2022}, month = {2022 Dec 22}, pages = {5011-5027.e20}, abstract = {

To accurately track self-location, animals need to integrate their movements through space. In amniotes, representations of self-location have been found in regions such as the hippocampus. It is unknown whether more ancient brain regions contain such representations and by which pathways they may drive locomotion. Fish displaced by water currents must prevent uncontrolled drift to potentially dangerous areas. We found that larval zebrafish track such movements and can later swim back to their earlier location. Whole-brain functional imaging revealed the circuit enabling this process of positional homeostasis. Position-encoding brainstem neurons integrate optic flow, then bias future swimming to correct for past displacements by modulating inferior olive and cerebellar activity. Manipulation of position-encoding or olivary neurons abolished positional homeostasis or evoked behavior as if animals had experienced positional shifts. These results reveal a multiregional hindbrain circuit in vertebrates for optic flow integration, memory of self-location, and its neural pathway to behavior.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2021.11.26.468907}, url = {https://www.biorxiv.org/content/early/2021/11/27/2021.11.26.468907}, author = {Yang, En and Zwart, Maarten F. and Rubinov, Mikail and James, Benjamin and Wei, Ziqiang and Narayan, Sujatha and Vladimirov, Nikita and Mensh, Brett D. and Fitzgerald, James E. and Ahrens, Misha B.} } @article {68503, title = {Brain-wide measurement of protein turnover with high spatial and temporal resolution}, journal = {bioRxiv}, year = {2022}, month = {2022 Nov 13}, abstract = {

Cells regulate function by synthesizing and degrading proteins. This turnover ranges from minutes to weeks, as it varies across proteins, cellular compartments, cell types, and tissues. Current methods for tracking protein turnover lack the spatial and temporal resolution needed to investigate these processes, especially in the intact brain, which presents unique challenges. We describe a pulse-chase method (DELTA) for measuring protein turnover with high spatial and temporal resolution throughout the body, including the brain. DELTA relies on rapid covalent capture by HaloTag of fluorophores that were optimized for bioavailability\ in vivo. The nuclear protein MeCP2 showed brain region- and cell type-specific turnover. The synaptic protein PSD95 was destabilized in specific brain regions by behavioral enrichment. A novel variant of expansion microscopy further facilitated turnover measurements at individual synapses. DELTA enables studies of adaptive and maladaptive plasticity in brain-wide neural circuits.

}, doi = {10.1101/2022.11.12.516226}, url = {https://doi.org/10.1101/2022.11.12.516226}, author = {Boaz Mohar and Jonathan B. Grimm and Ronak Patel and Timothy A. Brown and Paul Tillberg and Luke D. Lavis and Nelson Spruston and Karel Svoboda} } @article {68011, title = {BRD2 compartmentalizes the accessible genome.}, journal = {Nature Genetics}, volume = {54}, year = {2022}, month = {2022 Apr 11}, pages = {481-491}, abstract = {

Mammalian chromosomes are organized into megabase-sized compartments that are further subdivided into topologically associating domains (TADs). While the formation of TADs is dependent on cohesin, the mechanism behind compartmentalization remains enigmatic. Here, we show that the bromodomain and extraterminal (BET) family scaffold protein BRD2 promotes spatial mixing and compartmentalization of active chromatin after cohesin loss. This activity is independent of transcription but requires BRD2 to recognize acetylated targets through its double bromodomain and interact with binding partners with its low-complexity domain. Notably, genome compartmentalization mediated by BRD2 is antagonized on the one hand by cohesin and on the other hand by the BET homolog protein BRD4, both of which inhibit BRD2 binding to chromatin. Polymer simulation of our data supports a BRD2-cohesin interplay model of nuclear topology, in which genome compartmentalization results from a competition between loop extrusion and chromatin-state-specific affinity interactions.

}, keywords = {Animals, Cell Cycle Proteins, Chromatin, Chromosomes, Mammals, Nuclear Proteins, Protein Binding, Protein Domains, Transcription Factors}, issn = {1546-1718}, doi = {10.1038/s41588-022-01044-9}, author = {Xie, Liangqi and Dong, Peng and Qi, Yifeng and Hsieh, Tsung-Han S and English, Brian P and Jung, Seolkyoung and Chen, Xingqi and De Marzio, Margherita and Casellas, Rafael and Chang, Howard Y and Zhang, Bin and Tjian, Robert and Liu, Zhe} } @article {67992, title = {Bromodomains regulate dynamic targeting of the PBAF chromatin remodeling complex to chromatin hubs.}, journal = {Biophysical Journal}, volume = {121}, year = {2022}, month = {2022 May 3}, pages = {1738-1752}, abstract = {

Chromatin remodelers actively target arrays of acetylated nucleosomes at select enhancers and promoters to facilitate or shut down the repeated recruitment of RNA Pol II during transcriptional bursting. It is poorly understood how chromatin remodelers such as PBAF dynamically target different chromatin states inside a live cell. Our live-cell single molecule fluorescence microscopy study reveals chromatin hubs throughout the nucleus where PBAF rapidly cycles on and off the genome. Deletion of PBAF{\textquoteright}s bromodomains impairs targeting and stable engagement of chromatin in hubs. Dual color imaging reveals that PBAF targets both euchromatic and heterochromatic hubs with distinct genome binding kinetic profiles that mimic chromatin stability. Removal of PBAF{\textquoteright}s bromodomains stabilizes H3.3 binding within chromatin indicating that bromodomains may play a direct role in remodeling of the nucleosome. Our data suggests that PBAF{\textquoteright}s dynamic bromodomain mediated engagement of a nucleosome may reflect the chromatin remodeling potential of differentially bound chromatin states.

}, issn = {1542-0086}, doi = {10.1016/j.bpj.2022.03.027}, author = {Kenworthy, Charles A and Haque, Nayem and Liou, Shu-Hao and Chandris, Panagiotis and Wong, Vincent and Dziuba, Patrycja and Lavis, Luke D and Liu, Wei-Li and Singer, Robert H and Coleman, Robert A} } @article {68462, title = {Cap-dependent translation initiation monitored in living cells.}, journal = {Nature Communications}, volume = {13}, year = {2022}, month = {2022 Nov 02}, pages = {6558}, abstract = {

mRNA translation is tightly regulated to preserve cellular homeostasis. Despite extensive biochemical, genetic, and structural studies, a detailed understanding of mRNA translation regulation is lacking. Imaging methodologies able to resolve the binding dynamics of translation factors at single-cell and single-mRNA resolution were necessary to fully elucidate regulation of this paramount process. Here live-cell spectroscopy and single-particle tracking were combined to interrogate the binding dynamics of endogenous initiation factors to the 5{\textquoteright}cap. The diffusion of initiation factors (IFs) changed markedly upon their association with mRNA. Quantifying their diffusion characteristics revealed the sequence of IFs assembly and disassembly in cell lines and the clustering of translation in neurons. This approach revealed translation regulation at high spatial and temporal resolution that can be applied to the formation of any endogenous complex that results in a measurable shift in diffusion.

}, keywords = {Peptide Chain Initiation, Translational, Peptide Initiation Factors, Protein Biosynthesis, RNA Caps, RNA, Messenger}, issn = {2041-1723}, doi = {10.1038/s41467-022-34052-8}, author = {Gandin, Valentina and English, Brian P and Freeman, Melanie and Leroux, Louis-Philippe and Preibisch, Stephan and Walpita, Deepika and Jaramillo, Maritza and Singer, Robert H} } @article {67846, title = {Caveat fluorophore: an insiders{\textquoteright} guide to small-molecule fluorescent labels.}, journal = {Nature Methods}, volume = {19}, year = {2022}, month = {2022 Feb 01}, pages = {149-58}, abstract = {

The last three decades have brought a revolution in fluorescence microscopy. The development of new microscopes, fluorescent labels and analysis techniques has pushed the frontiers of biological imaging forward, moving from fixed to live cells, from diffraction-limited to super-resolution imaging and from simple cell culture systems to experiments in vivo. The large and ever-evolving collection of tools can be daunting for biologists, who must invest substantial time and effort in adopting new technologies to answer their specific questions. This is particularly relevant when working with small-molecule fluorescent labels, where users must navigate the jargon, idiosyncrasies and caveats of chemistry. Here, we present an overview of chemical dyes used in biology and provide frank advice from a chemist{\textquoteright}s perspective.

}, issn = {1548-7105}, doi = {10.1038/s41592-021-01338-6}, author = {Grimm, Jonathan B and Lavis, Luke D} } @article {68464, title = {Cellpose 2.0: how to train your own model.}, journal = {Nature Methods}, volume = {19}, year = {2022}, month = {2022 Nov 07}, pages = {1634-41}, abstract = {

Pretrained neural network models for biological segmentation can provide good out-of-the-box results for many image types. However, such models do not allow users to adapt the segmentation style to their specific needs and can perform suboptimally for test images that are very different from the training images. Here we introduce Cellpose 2.0, a new package that includes an ensemble of diverse pretrained models as well as a human-in-the-loop pipeline for rapid prototyping of new custom models. We show that models pretrained on the Cellpose dataset can be fine-tuned with only 500-1,000 user-annotated regions of interest (ROI) to perform nearly as well as models trained on entire datasets with up to 200,000 ROI. A human-in-the-loop approach further reduced the required user annotation to 100-200 ROI, while maintaining high-quality segmentations. We provide software tools such as an annotation graphical user interface, a model zoo and a human-in-the-loop pipeline to facilitate the adoption of Cellpose 2.0.

}, issn = {1548-7105}, doi = {10.1038/s41592-022-01663-4}, author = {Pachitariu, Marius and Stringer, Carsen} } @article {68502, title = {Channel-independent function of UNC-9/Innexin in spatial arrangement of GABAergic synapses in .}, journal = {eLife}, volume = {11}, year = {2022}, month = {2022 Nov 15}, abstract = {

Precise synaptic connection of neurons with their targets is essential for the proper functioning of the nervous system. A plethora of signaling pathways act in concert to mediate the precise spatial arrangement of synaptic connections. Here we show a novel role for a gap junction protein in controlling tiled synaptic arrangement in the GABAergic motor neurons in , in which their axons and synapses overlap minimally with their neighboring neurons within the same class. We found that while EGL-20/Wnt controls axonal tiling, their presynaptic tiling is mediated by a gap junction protein UNC-9/Innexin, that is localized at the presynaptic tiling border between neighboring dorsal D-type GABAergic motor neurons. Strikingly, the gap junction channel activity of UNC-9 is dispensable for its function in controlling tiled presynaptic patterning. While gap junctions are crucial for the proper functioning of the nervous system as channels, our finding uncovered the novel channel-independent role of UNC-9 in synapse patterning.

}, keywords = {Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Connexins, Membrane Proteins, Motor Neurons, Synapses}, issn = {2050-084X}, doi = {10.7554/eLife.80555}, author = {Hendi, Ardalan and Niu, Long-Gang and Snow, Andrew William and Ikegami, Richard and Wang, Zhao-Wen and Mizumoto, Kota} } @article {67857, title = {Characterization of ultrapotent chemogenetic ligands for research applications in non-human primates}, journal = {bioRxiv}, year = {2022}, month = {2022 Jan 07}, abstract = {

Chemogenetics is a technique for obtaining selective pharmacological control over a cell population by expressing an engineered receptor that is selectively activated by an exogenously administered ligand. A promising approach for neuronal modulation involves the use of {\textquotedblleft}Pharmacologically Selective Actuator Modules{\textquotedblright} (PSAMs); these chemogenetic receptors are selectively activated by ultrapotent {\textquotedblleft}Pharmacologically Selective Effector Molecules{\textquotedblright} (uPSEMs). To extend the use of PSAM/PSEMs to studies in nonhuman primates it is necessary to thoroughly characterize the efficacy and safety of these tools. We describe the time course and brain penetrance in rhesus monkeys of two compounds with promising binding specificity and efficacy profiles in\ in vitro\ studies, uPSEM792 and uPSEM817, after systemic administration. Rhesus macaques received subcutaneous (s.c.) or intravenous (i.v.) administration of uPSEM817(0.064 mg/kg) or uPSEM792 (0.87 mg/kg) and plasma and CSF samples were collected over the course of 48 hours. Both compounds exhibited good brain penetrance, relatively slow washout and negligible conversion to potential metabolites - varenicline or hydroxyvarenicline. In addition, we found that neither of these uPSEMs significantly altered heart rate or sleep. Our results indicate that both compounds are suitable candidates for neuroscience studies using PSAMs in nonhuman primates.

}, doi = {10.1101/2022.01.06.475241}, url = {https://doi.org/10.1101/2022.01.06.475241}, author = {Jessica Raper and Mark A. G. Eldridge and Scott. M. Sternson and Jalene Y. Shim and Grace P. Fomani and Barry J. Richmond and Thomas Wichmann and Adriana Galvan} } @article {68411, title = {Characterization of Ultrapotent Chemogenetic Ligands for Research Applications in Nonhuman Primates.}, journal = {ACS Chemical Neuroscience}, volume = {13}, year = {2022}, month = {2022 Nov 02}, pages = {3118-3125}, abstract = {

Chemogenetics is a technique for obtaining selective pharmacological control over a cell population by expressing an engineered receptor that is selectively activated by an exogenously administered ligand. A promising approach for neuronal modulation involves the use of "Pharmacologically Selective Actuator Modules" (PSAMs); these chemogenetic receptors are selectively activated by ultrapotent "Pharmacologically Selective Effector Molecules" (uPSEMs). To extend the use of PSAM/PSEMs to studies in nonhuman primates, it is necessary to thoroughly characterize the efficacy and safety of these tools. We describe the time course and brain penetrance in rhesus monkeys of two compounds with promising binding specificity and efficacy profiles in studies, uPSEM792 and uPSEM817, after systemic administration. Rhesus monkeys received subcutaneous (s.c.) or intravenous (i.v.) administration of uPSEM817 (0.064 mg/kg) or uPSEM792 (0.87 mg/kg), and plasma and cerebrospinal fluid samples were collected over 48 h. Both compounds exhibited good brain penetrance, relatively slow washout, and negligible conversion to potential metabolites-varenicline or hydroxyvarenicline. In addition, we found that neither of these uPSEMs significantly altered the heart rate or sleep. Our results indicate that both compounds are suitable candidates for neuroscience studies using PSAMs in nonhuman primates.

}, keywords = {Animals, Brain, Ligands, Macaca mulatta, Neurons, Varenicline}, issn = {1948-7193}, doi = {10.1021/acschemneuro.2c00525}, author = {Raper, Jessica and Eldridge, Mark A G and Sternson, Scott M and Shim, Jalene Y and Fomani, Grace P and Richmond, Barry J and Wichmann, Thomas and Galvan, Adriana} } @article {68463, title = {Chemically stable fluorescent proteins for advanced microscopy.}, journal = {Nature Methods}, volume = {19}, year = {2022}, month = {2022 Nov 07}, pages = {1612-21}, abstract = {

We report the rational engineering of a remarkably stable yellow fluorescent protein (YFP), {\textquoteright}hyperfolder YFP{\textquoteright} (hfYFP), that withstands chaotropic conditions that denature most biological structures within seconds, including superfolder green fluorescent protein (GFP). hfYFP contains no cysteines, is chloride insensitive and tolerates aldehyde and osmium tetroxide fixation better than common fluorescent proteins, enabling its use in expansion and electron microscopies. We solved crystal structures of hfYFP (to 1.7-{\r A} resolution), a monomeric variant, monomeric hyperfolder YFP (1.6 {\r A}) and an mGreenLantern mutant (1.2 {\r A}), and then rationally engineered highly stable 405-nm-excitable GFPs, large Stokes shift (LSS) monomeric GFP (LSSmGFP) and LSSA12 from these structures. Lastly, we directly exploited the chemical stability of hfYFP and LSSmGFP by devising a fluorescence-assisted protein purification strategy enabling all steps of denaturing affinity chromatography to be visualized using ultraviolet or blue light. hfYFP and LSSmGFP represent a new generation of robustly stable fluorescent proteins developed for advanced biotechnological applications.

}, issn = {1548-7105}, doi = {10.1038/s41592-022-01660-7}, author = {Campbell, Benjamin C and Paez-Segala, Maria G and Looger, Loren L and Petsko, Gregory A and Liu, Ce Feng} } @article {68080, title = {Combining multiple fluorescence imaging techniques in biology: when one microscope is not enough.}, journal = {Molecular Biology of the Cell}, volume = {33}, year = {2022}, month = {2022 May 15}, pages = {tp1}, abstract = {

While fluorescence microscopy has proven to be an exceedingly useful tool in bioscience, it is difficult to offer simultaneous high resolution, fast speed, large volume, and good biocompatibility in a single imaging technique. Thus, when determining the image data required to quantitatively test a complex biological hypothesis, it often becomes evident that multiple imaging techniques are necessary. Recent years have seen an explosion in development of novel fluorescence microscopy techniques, each of which features a unique suite of capabilities. In this Technical Perspective, we highlight recent studies to illustrate the benefits, and often the necessity, of combining multiple fluorescence microscopy modalities. We provide guidance in choosing optimal technique combinations to effectively address a biological question. Ultimately, we aim to promote a more well-rounded approach in designing fluorescence microscopy experiments, leading to more robust quantitative insight.

}, keywords = {Biology, Microscopy, Fluorescence, Optical Imaging}, issn = {1939-4586}, doi = {10.1091/mbc.E21-10-0506}, author = {Hobson, Chad M and Aaron, Jesse S} } @article {67896, title = {The complexin C-terminal amphipathic helix stabilizes the fusion pore open state by sculpting membranes.}, journal = {Nature Structural \& Molecular Biology}, volume = {29}, year = {2022}, month = {2022 Feb 07}, pages = {97-107}, abstract = {

Neurotransmitter release is mediated by proteins that drive synaptic vesicle fusion with the presynaptic plasma membrane. While soluble N-ethylmaleimide sensitive factor attachment protein receptors (SNAREs) form the core of the fusion apparatus, additional proteins play key roles in the fusion pathway. Here, we report that the C-terminal amphipathic helix of the mammalian accessory protein, complexin (Cpx), exerts profound effects on membranes, including the formation of pores and the efficient budding and fission of vesicles. Using nanodisc-black lipid membrane electrophysiology, we demonstrate that the membrane remodeling activity of Cpx modulates the structure and stability of recombinant exocytic fusion pores. Cpx had particularly strong effects on pores formed by small numbers of SNAREs. Under these conditions, Cpx increased the current through individual pores 3.5-fold, and increased the open time fraction from roughly 0.1 to 1.0. We propose that the membrane sculpting activity of Cpx contributes to the phospholipid rearrangements that underlie fusion by stabilizing highly curved membrane fusion intermediates.

}, issn = {1545-9985}, doi = {10.1038/s41594-021-00716-0}, author = {Courtney, Kevin C and Wu, Lanxi and Mandal, Taraknath and Swift, Mark and Zhang, Zhao and Alaghemandi, Mohammad and Wu, Zhenyong and Bradberry, Mazdak M and Deo, Claire and Lavis, Luke D and Volkmann, Niels and Hanein, Dorit and Cui, Qiang and Bao, Huan and Chapman, Edwin R} } @article {68520, title = {The connectome of an insect brain}, journal = {bioRxiv}, year = {2022}, month = {2022 Nov 28}, abstract = {

Brains contain networks of interconnected neurons, so knowing the network architecture is essential for understanding brain function. We therefore mapped the synaptic-resolution connectome of an insect brain (Drosophila\ larva) with rich behavior, including learning, value-computation, and action-selection, comprising 3,013 neurons and 544,000 synapses. We characterized neuron-types, hubs, feedforward and feedback pathways, and cross-hemisphere and brain-nerve cord interactions. We found pervasive multisensory and interhemispheric integration, highly recurrent architecture, abundant feedback from descending neurons, and multiple novel circuit motifs. The brain{\textquoteright}s most recurrent circuits comprised the input and output neurons of the learning center. Some structural features, including multilayer shortcuts and nested recurrent loops, resembled powerful machine learning architectures. The identified brain architecture provides a basis for future experimental and theoretical studies of neural circuits.

}, doi = {10.1101/2022.11.28.516756}, url = {https://doi.org/10.1101/2022.11.28.516756}, author = {Michael Winding and Benjamin D. Pedigo and Christopher L. Barnes and Heather G. Patsolic and Youngser Park and Tom Kazimiers and Akira Fushiki and Ingrid V. Andrade and Avinash Khandelwal and Javier Valdes-Aleman and Feng Li and Nadine Randel and Elizabeth Barsotti and Ana Correia and Richard D. Fetter and Volker Hartenstein and Carey E. Priebe and Joshua T. Vogelstein and Albert Cardona and Marta Zlatic} } @conference {67973, title = {Connectome-constrained Latent Variable Model of Whole-Brain Neural Activity}, booktitle = {International Conference on Learning Representations}, year = {2022}, month = {09/2021}, abstract = {

The availability of both anatomical connectivity and brain-wide neural activity measurements in C. elegans make the worm a promising system for learning detailed, mechanistic models of an entire nervous system in a data-driven way. However, one faces several challenges when constructing such a model. We often do not have direct experimental access to important modeling details such as single-neuron dynamics and the signs and strengths of the synaptic connectivity. Further, neural activity can only be measured in a subset of neurons, often indirectly via calcium imaging, and significant trial-to-trial variability has been observed. To address these challenges, we introduce a connectome-constrained latent variable model (CC-LVM) of the unobserved voltage dynamics of the entire C. elegans nervous system and the observed calcium signals. We used the framework of variational autoencoders to fit parameters of the mechanistic simulation constituting the generative model of the LVM to calcium imaging observations. A variational approximate posterior distribution over latent voltage traces for all neurons is efficiently inferred using an inference network, and constrained by a prior distribution given by the biophysical simulation of neural dynamics. We applied this model to an experimental whole-brain dataset, and found that connectomic constraints enable our LVM to predict the activity of neurons whose activity were withheld significantly better than models unconstrained by a connectome. We explored models with different degrees of biophysical detail, and found that models with realistic conductance-based synapses provide markedly better predictions than current-based synapses for this system.

}, url = {https://openreview.net/forum?id=CJzi3dRlJE-}, author = {Lu Mi and Richard Xu and Sridhama Prakhya and Albert Lin and Nir Shavit and Aravinthan Samuel and Srinivas C Turaga} } @article {67966, title = {The Consistency of Gastropod Identified Neurons Distinguishes Intra-Individual Plasticity From Inter-Individual Variability in Neural Circuits.}, journal = {Frontiers in Behavioral Neuroscience}, volume = {16}, year = {2022}, month = {2022 Mar 03}, pages = {855235}, abstract = {

Gastropod mollusks are known for their large, individually identifiable neurons, which are amenable to long-term intracellular recordings that can be repeated from animal to animal. The constancy of individual neurons can help distinguish state-dependent or temporal variation within an individual from actual variability between individual animals. Investigations into the circuitry underlying rhythmic swimming movements of the gastropod species, and have uncovered intra- and inter-individual variability in synaptic connectivity and serotonergic neuromodulation. has a reliably evoked escape swim behavior that is produced by a central pattern generator (CPG) composed of a small number of identifiable neurons. There is apparent individual variability in some of the connections between neurons that is inconsequential for the production of the swim behavior under normal conditions, but determines whether that individual can swim following a neural lesion. Serotonergic neuromodulation of synaptic strength intrinsic to the CPG creates neural circuit plasticity within an individual and contributes to reorganization of the network during recovery from injury and during learning. In , variability over time in the modulatory actions of serotonin and in expression of serotonin receptor genes in an identified neuron directly reflects variation in swimming behavior. Tracking behavior and electrophysiology over hours to days was necessary to identify the functional consequences of these intra-individual, time-dependent variations. This work demonstrates the importance of unambiguous neuron identification, properly assessing the animal and network states, and tracking behavior and physiology over time to distinguish plasticity within the same animal at different times from variability across individual animals.

}, issn = {1662-5153}, doi = {10.3389/fnbeh.2022.855235}, author = {Tamvacakis, Arianna N and Lillvis, Joshua L and Sakurai, Akira and Katz, Paul S} } @article {67960, title = {Context-dependent control of behavior in Drosophila.}, journal = {Current Opinion in Neurobiology}, volume = {73}, year = {2022}, month = {2022 Mar 11}, pages = {102523}, abstract = {

The representation of contextual information peripheral to a salient stimulus is central to an animal{\textquoteright}s ability to correctly interpret and flexibly respond to that stimulus. While the computations and circuits underlying the context-dependent modulation of stimulus-response pairings have typically been studied in vertebrates, the genetic tractability, numeric simplification, and well-characterized connectivity patterns of the Drosophila melanogaster brain have facilitated circuit-level insights into contextual processing. Recent studies in flies reveal the neuronal mechanisms that create flexible context-dependent behavioral responses to sensory events in conditions of predation threat, feeding regulation, and social interaction.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2022.02.003}, author = {Oram, Tess B and Card, Gwyneth M} } @article {68044, title = {Cryo-EM structure of the EBV ribonucleotide reductase BORF2 and mechanism of APOBEC3B inhibition.}, journal = {Science Advances}, volume = {8}, year = {2022}, month = {2022 Apr 29}, pages = {eabm2827}, abstract = {

Viruses use a plethora of mechanisms to evade immune responses. A recent example is neutralization of the nuclear DNA cytosine deaminase APOBEC3B by the Epstein-Barr virus (EBV) ribonucleotide reductase subunit BORF2. Cryo-EM studies of APOBEC3B-BORF2 complexes reveal a large \>1000-{\r A} binding surface composed of multiple structural elements from each protein, which effectively blocks the APOBEC3B active site from accessing single-stranded DNA substrates. Evolutionary optimization is suggested by unique insertions in BORF2 absent from other ribonucleotide reductases and preferential binding to APOBEC3B relative to the highly related APOBEC3A and APOBEC3G enzymes. A molecular understanding of this pathogen-host interaction has potential to inform the development of drugs that block the interaction and liberate the natural antiviral activity of APOBEC3B. In addition, given a role for APOBEC3B in cancer mutagenesis, it may also be possible for information from the interaction to be used to develop DNA deaminase inhibitors.

}, issn = {2375-2548}, doi = {10.1126/sciadv.abm2827}, author = {Shaban, Nadine M and Yan, Rui and Shi, Ke and Moraes, Sofia N and Cheng, Adam Z and Carpenter, Michael A and McLellan, Jason S and Yu, Zhiheng and Harris, Reuben S} } @article {67990, title = {Cryo-EM structures of the human GATOR1-Rag-Ragulator complex reveal a spatial-constraint regulated GAP mechanism.}, journal = {Molecular Cell}, volume = {36}, year = {2022}, month = {2022 May 01}, abstract = {

mTORC1 controls cellular metabolic processes in response to nutrient availability. Amino acid signals are transmitted to mTORC1 through the Rag GTPases, which are localized on the lysosomal surface by the Ragulator complex. The Rag GTPases receive amino acid signals from multiple upstream regulators. One negative regulator, GATOR1, is a GTPase activating protein (GAP) for RagA. GATOR1 binds to the Rag GTPases via two modes: an inhibitory mode and a GAP mode. How these two binding interactions coordinate to process amino acid signals is unknown. Here, we resolved three cryo-EM structural models of the GATOR1-Rag-Ragulator complex, with the Rag-Ragulator subcomplex occupying the inhibitory site, the GAP site, and both binding sites simultaneously. When the Rag GTPases bind to GATOR1 at the GAP site, both Rag subunits contact GATOR1 to coordinate their nucleotide loading states. These results reveal a potential GAP mechanism of GATOR1 during the mTORC1 inactivation process.

}, issn = {1097-4164}, doi = {10.1016/j.molcel.2022.03.002}, author = {Egri, Shawn B and Ouch, Christna and Chou, Hui-Ting and Yu, Zhiheng and Song, Kangkang and Xu, Chen and Shen, Kuang} } @article {68593, title = {Desmosomal connectomics of all somatic muscles in an annelid larva.}, journal = {eLife}, volume = {11}, year = {2022}, month = {2022 Dec 20}, abstract = {

Cells form networks in animal tissues through synaptic, chemical, and adhesive links. Invertebrate muscle cells often connect to other cells through desmosomes, adhesive junctions anchored by intermediate filaments. To study desmosomal networks, we skeletonised 853 muscle cells and their desmosomal partners in volume electron microscopy data covering an entire larva of the annelid . Muscle cells adhere to each other, to epithelial, glial, ciliated, and bristle-producing cells and to the basal lamina, forming a desmosomal connectome of over 2000 cells. The aciculae - chitin rods that form an endoskeleton in the segmental appendages - are highly connected hubs in this network. This agrees with the many degrees of freedom of their movement, as revealed by video microscopy. Mapping motoneuron synapses to the desmosomal connectome allowed us to infer the extent of tissue influenced by motoneurons. Our work shows how cellular-level maps of synaptic and adherent force networks can elucidate body mechanics.

}, keywords = {Animals, Annelida, Connectome, Larva, Muscles, Polychaeta}, issn = {2050-084X}, doi = {10.7554/eLife.71231}, author = {Jasek, Sanja and Veraszt{\'o}, Csaba and Brodrick, Emelie and Shahidi, R{\'e}za and Kazimiers, Tom and Kerbl, Alexandra and J{\'e}kely, G{\'a}sp{\'a}r} } @article {68164, title = {Development of an adrenocortical cell model of calcium signaling modulation to decipher the molecular mechanisms responsible for primary aldosteronism}, journal = {Archives of Cardiovascular Diseases Supplements}, volume = {14}, year = {2022}, month = {2022 Jun 01}, pages = {160}, abstract = {

Primary aldosteronism (PA) is the most frequent form of secondary hypertension. The identification of germline or somatic mutations in different genes coding for ion channels and defines PA as a channelopathy. These mutations promote activation of calcium signaling, the main trigger for aldosterone biosynthesis.

}, doi = {10.1016/j.acvdsp.2022.04.153}, url = {https://doi.org/10.1016/j.acvdsp.2022.04.153}, author = {BakhtaFedlaoui and Teresa Cosentino and Zeina R. Al Sayed and Isabelle Giscos-Douriez and Fabio L. Fernandes-Rosa and Jean-S{\'e}bastienHulot and Chris Magnus and Scott M. Sternson and Maria Christina Zennaro and Sheerazed Boulkroun} } @article {67875, title = {[Dilemma and breakthrough of acupuncture-moxibustion department under the situation of rapid expansion of hospital].}, journal = {Zhongguo Zhen Jiu}, volume = {42}, year = {2022}, month = {2022 Jan 12}, pages = {8-12}, abstract = {

Under the situation of the rapid expansion of hospital, the dilemma of acupuncture-moxibustion department, as well as the relevant solutions are explored. The main reasons for the shrinking situation of the service in acupuncture-moxibustion department include: the disease-based department division trends to divert many diseases suitably treated in acupuncture-moxibustion department; the environment pursuing economic benefits restricts the development of acupuncture-moxibustion therapy characterized by "simple and low-cost operation". There are three important approaches for breaking through the dilemma of acupuncture and moxibustion therapy. First, modifying the traditional service mode as waiting for patients in acupuncture-moxibustion department and promoting acupuncture and moxibustion technology to be adopted in other departments rather than limited only in acupuncture-moxibustion department. Second, increasing the charges of acupuncture and moxibustion technology rationally. Third, positioning accurately the role of acupuncture and moxibustion technology in health services based on its own characteristics and advantages and promoting it in community medical institutions. All of these solutions require the guidance of supporting policies.

}, keywords = {Acupuncture, Acupuncture Therapy, Hospitals, Humans, Moxibustion}, issn = {0255-2930}, doi = {10.13703/j.0255-2930.20201121-0002}, author = {Chen, Shao-Zong and Pan, Wei-Xing and Jing, Xiang-Hong and Fang, Jian-Qiao} } @article {68146, title = {Direct Observation of Compartment-Specific Localization and Dynamics of Voltage-Gated Sodium Channels.}, journal = {Journal of Neuroscience}, year = {2022}, month = {2022 Jun 06}, abstract = {

Brain enriched voltage-gated sodium channel (VGSC) Na1.2 and Na1.6 are critical for electrical signaling in the central nervous system. Previous studies have extensively characterized cell-type specific expression and electrophysiological properties of these two VGSCs and how their differences contribute to fine-tuning of neuronal excitability. However, due to lack of reliable labeling and imaging methods, the sub-cellular localization and dynamics of these homologous Na1.2 and Na1.6 channels remain understudied. To overcome this challenge, we combined genome editing, super-resolution and live-cell single molecule imaging to probe subcellular composition, relative abundances and trafficking dynamics of Na1.2 and Na1.6 in cultured mouse and rat neurons and in male and female mouse brain. We discovered a previously uncharacterized trafficking pathway that targets Na1.2 to the distal axon of unmyelinated neurons. This pathway utilizes distinct signals residing in the intracellular loop 1 (ICL1) between transmembrane domain I and II to suppress the retention of Na1.2 in the axon initial segment (AIS) and facilitate its membrane loading at the distal axon. As mouse pyramidal neurons undergo myelination, Na1.2 is gradually excluded from the distal axon as Na1.6 becomes the dominant VGSC in the axon initial segment and nodes of Ranvier. In addition, we revealed exquisite developmental regulation of Na1.2 and Na1.6 localizations in the axon initial segment and dendrites, clarifying the molecular identity of sodium channels in these subcellular compartments. Together, these results unveiled compartment-specific localizations and trafficking mechanisms for VGSCs, which could be regulated separately to modulate membrane excitability in the brain.Direct observation of endogenous voltage-gated sodium channels reveals a previously uncharacterized distal axon targeting mechanism and the molecular identity of sodium channels in distinct subcellular compartments.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0086-22.2022}, author = {Liu, Hui and Wang, Hong-Gang and Pitt, Geoffrey S and Liu, Zhe J} } @article {68296, title = {Disorder and the Neural Representation of Complex Odors.}, journal = {Frontiers in Computational Neuroscience}, volume = {16}, year = {2022}, month = {2022 Aug 08}, pages = {917786}, abstract = {

Animals smelling in the real world use a small number of receptors to sense a vast number of natural molecular mixtures, and proceed to learn arbitrary associations between odors and valences. Here, we propose how the architecture of olfactory circuits leverages disorder, diffuse sensing and redundancy in representation to meet these immense complementary challenges. First, the diffuse and disordered binding of receptors to many molecules compresses a vast but sparsely-structured odor space into a small receptor space, yielding an odor code that preserves similarity in a precise sense. Introducing any order/structure in the sensing degrades similarity preservation. Next, lateral interactions further reduce the correlation present in the low-dimensional receptor code. Finally, expansive disordered projections from the periphery to the central brain reconfigure the densely packed information into a high-dimensional representation, which contains multiple redundant subsets from which downstream neurons can learn flexible associations and valences. Moreover, introducing any order in the expansive projections degrades the ability to recall the learned associations in the presence of noise. We test our theory empirically using data from . Our theory suggests that the neural processing of sparse but high-dimensional olfactory information differs from the other senses in its fundamental use of disorder.

}, issn = {1662-5188}, doi = {10.3389/fncom.2022.917786}, author = {Krishnamurthy, Kamesh and Hermundstad, Ann M and Mora, Thierry and Walczak, Aleksandra M and Balasubramanian, Vijay} } @article {68166, title = {Distributing task-related neural activity across a cortical network through task-independent connections}, journal = {bioRxiv}, year = {2022}, month = {2022 Jun 18}, abstract = {

Task-related neural activity is widespread across populations of neurons during goal-directed behaviors. However, little is known about the synaptic reorganization and circuit mechanisms that lead to broad activity changes. Here we trained a limited subset of neurons in a spiking network with strong synaptic interactions to reproduce the activity of neurons in the motor cortex during a decision-making task. We found that task-related activity, resembling the neural data, emerged across the network, even in the untrained neurons. Analysis of trained networks showed that strong untrained synapses, which were independent of the task and determined the dynamical state of the network, mediated the spread of task-related activity. Optogenetic perturbations suggest that the motor cortex is strongly-coupled, supporting the applicability of the mechanism to cortical networks. Our results reveal a cortical mechanism that facilitates distributed representations of task-variables by spreading the activity from a subset of plastic neurons to the entire network through task-independent strong synapses.

}, doi = {10.1101/2022.06.17.496618}, url = {https://doi.org/10.1101/2022.06.17.496618}, author = {Christopher M. Kim and Arseny Finkelstein and Carson C. Chow and Karel Svoboda and Ran Darshan} } @article {68147, title = {Drosophila gustatory projections are segregated by taste modality and connectivity.}, journal = {eLife}, volume = {11}, year = {2022}, month = {2022 May 25}, abstract = {

Gustatory sensory neurons detect caloric and harmful compounds in potential food and convey this information to the brain to inform feeding decisions. To examine the signals that gustatory neurons transmit and receive, we reconstructed gustatory axons and their synaptic sites in the adult brain, utilizing a whole-brain electron microscopy volume. We reconstructed 87 gustatory projections from the proboscis labellum in the right hemisphere and 57 from the left, representing the majority of labellar gustatory axons. Gustatory neurons contain a nearly equal number of interspersed pre- and postsynaptic sites, with extensive synaptic connectivity among gustatory axons. Morphology- and connectivity-based clustering revealed six distinct groups, likely representing neurons recognizing different taste modalities. The vast majority of synaptic connections are between neurons of the same group. This study resolves the anatomy of labellar gustatory projections, reveals that gustatory projections are segregated based on taste modality, and uncovers synaptic connections that may alter the transmission of gustatory signals.

}, keywords = {Animals, Drosophila, Drosophila melanogaster, Drosophila Proteins, Sensory Receptor Cells, Taste}, issn = {2050-084X}, doi = {10.7554/eLife.78110}, author = {Engert, Stefanie and Sterne, Gabriella R and Bock, Davi D and Scott, Kristin} } @article {68750, title = {Efficient Gene Knockout in Salivary Gland Epithelial Explant Cultures}, journal = {Journal of Dental Research}, volume = {102}, year = {2022}, month = {11/2022}, pages = {197-206}, abstract = {

We have developed methods to achieve efficient CRISPR-Cas9{\textendash}mediated gene knockout in ex vivo mouse embryonic salivary epithelial explants. Salivary epithelial explants provide a valuable model for characterizing cell signaling, differentiation, and epithelial morphogenesis, but research has been limited by a paucity of efficient gene perturbation methods. Here, we demonstrate highly efficient gene perturbation by transient transduction of guide RNA{\textendash}expressing lentiviruses into Cas9-expressing salivary epithelial buds isolated from Cas9 transgenic mice. We first show that salivary epithelial explants can be cultured in low-concentration, nonsolidified Matrigel suspensions in 96-well plates, which greatly increases sample throughput compared to conventional cultures embedded in solidified Matrigel. We further show that salivary epithelial explants can grow and branch with FGF7 alone, while supplementing with insulin, transferrin, and selenium (ITS) enhances growth and branching. We then describe an efficient workflow to produce experiment-ready, high-titer lentiviruses within 1 wk after molecular cloning. To track transduced cells, we designed the lentiviral vector to coexpress a nuclear fluorescent reporter with the guide RNA. We routinely achieved 80\% transduction efficiency when antibiotic selection was used. Importantly, we detected robust loss of targeted protein products when testing 9 guide RNAs for 3 different genes. Moreover, targeting the β1 integrin gene (Itgb1) inhibited branching morphogenesis, which supports the importance of cell{\textendash}matrix adhesion in driving branching morphogenesis. In summary, we have established a lentivirus-based method that can efficiently perturb genes of interest in salivary epithelial explants, which will greatly facilitate studies of specific gene functions using this system.

}, doi = {10.1177/00220345221128201}, url = {https://doi.org/10.1177/00220345221128201}, author = {R. Sekiguchi and M.M. Mehlferber and K. Matsumoto and S. Wang} } @article {68984, title = {Embryo~model completes gastrulation to neurulation and organogenesis.}, journal = {Nature}, volume = {610}, year = {2022}, month = {10/2022}, pages = {143-153}, abstract = {

Embryonic stem (ES) cells can undergo many aspects of mammalian embryogenesis in vitro, but their developmental potential is substantially extended by interactions with extraembryonic stem cells, including trophoblast stem (TS) cells, extraembryonic endoderm stem (XEN) cells and inducible XEN (iXEN) cells. Here we assembled stem cell-derived embryos in vitro from mouse ES cells, TS cells and iXEN cells and showed that they recapitulate the development of whole natural mouse embryo in utero up to day 8.5 post-fertilization. Our embryo model displays headfolds with defined forebrain and midbrain regions and develops a beating heart-like structure, a trunk comprising a neural tube and somites, a tail bud containing neuromesodermal progenitors, a gut tube, and primordial germ cells. This complete embryo model develops within an extraembryonic yolk sac that initiates blood island development. Notably, we demonstrate that the neurulating embryo model assembled from Pax6-knockout ES cells aggregated with wild-type TS cells and iXEN cells recapitulates the ventral domain expansion of the neural tube that occurs in natural, ubiquitous Pax6-knockout embryos. Thus, these complete embryoids are a powerful in vitro model for dissecting the roles of diverse cell lineages and genes in development. Our results demonstrate the self-organization ability of ES cells and two types of extraembryonic stem cells to reconstitute mammalian development through and beyond gastrulation to neurulation and early organogenesis.

}, keywords = {Animals, Cell Lineage, Embryo, Mammalian, Embryonic Stem Cells, Endoderm, Gastrulation, Heart, Mesencephalon, Mice, Models, Biological, Neural Tube, Neurulation, Organogenesis, PAX6 Transcription Factor, Prosencephalon, Somites}, issn = {1476-4687}, doi = {10.1038/s41586-022-05246-3}, author = {Amadei, Gianluca and Handford, Charlotte E and Qiu, Chengxiang and De Jonghe, Joachim and Greenfeld, Hannah and Tran, Martin and Martin, Beth K and Chen, Dong-Yuan and Aguilera-Castrejon, Alejandro and Hanna, Jacob H and Elowitz, Michael B and Hollfelder, Florian and Shendure, Jay and Glover, David M and Zernicka-Goetz, Magdalena} } @article {67844, title = {ER proteins decipher the tubulin code to regulate organelle distribution.}, journal = {Nature}, volume = {601}, year = {2022}, month = {2022 Jan 01}, pages = {132-138}, abstract = {

Organelles move along differentially modified microtubules to establish and maintain their proper distributions and functions. However, how cells interpret these post-translational microtubule modification codes to selectively regulate organelle positioning remains largely unknown. The endoplasmic reticulum\ (ER) is an interconnected network of diverse morphologies that extends promiscuously throughout the cytoplasm, forming abundant contacts with other organelles. Dysregulation of endoplasmic reticulum morphology is tightly linked to neurologic disorders and cancer. Here we demonstrate that three membrane-bound endoplasmic reticulum proteins preferentially interact with different microtubule populations, with CLIMP63 binding centrosome microtubules, kinectin (KTN1) binding perinuclear polyglutamylated microtubules, and p180 binding glutamylated microtubules. Knockout of these proteins or manipulation of microtubule populations and glutamylation status results in marked changes in endoplasmic reticulum positioning, leading to similar redistributions of other organelles. During nutrient starvation, cells modulate CLIMP63 protein levels and p180-microtubule binding to bidirectionally move endoplasmic reticulum and lysosomes for proper autophagic responses.

}, issn = {1476-4687}, doi = {10.1038/s41586-021-04204-9}, author = {Zheng, Pengli and Obara, Christopher J and Szczesna, Ewa and Nixon-Abell, Jonathon and Mahalingan, Kishore K and Roll-Mecak, Antonina and Lippincott-Schwartz, Jennifer and Blackstone, Craig} } @article {68020, title = {ESCRT-mediated membrane repair protects tumor-derived cells against T cell attack.}, journal = {Science}, volume = {376}, year = {2022}, month = {2022 Apr 22}, pages = {377-382}, abstract = {

Cytotoxic T lymphocytes (CTLs) and natural killer cells kill virus-infected and tumor cells through the polarized release of perforin and granzymes. Perforin is a pore-forming toxin that creates a lesion in the plasma membrane of the target cell through which granzymes enter the cytosol and initiate apoptosis. Endosomal sorting complexes required for transport (ESCRT) proteins are involved in the repair of small membrane wounds. We found that ESCRT proteins were precisely recruited in target cells to sites of CTL engagement immediately after perforin release. Inhibition of ESCRT machinery in cancer-derived cells enhanced their susceptibility to CTL-mediated killing. Thus, repair of perforin pores by ESCRT machinery limits granzyme entry into the cytosol, potentially enabling target cells to resist cytolytic attack.

}, keywords = {Endosomal Sorting Complexes Required for Transport, Granzymes, Membrane Glycoproteins, Perforin, Pore Forming Cytotoxic Proteins, T-Lymphocytes, Cytotoxic}, issn = {1095-9203}, doi = {10.1126/science.abl3855}, author = {Ritter, Alex T and Shtengel, Gleb and Xu, C Shan and Weigel, Aubrey and Hoffman, David P and Freeman, Melanie and Iyer, Nirmala and Alivodej, Nensi and Ackerman, David and Voskoboinik, Ilia and Trapani, Joseph and Hess, Harald F and Mellman, Ira} } @article {68368, title = {The evolutionary dynamics of extrachromosomal DNA in human cancers.}, journal = {Nature Genetics}, year = {2022}, month = {2022 Sep 19}, abstract = {

Oncogene amplification on extrachromosomal DNA (ecDNA) is a common event, driving aggressive tumor growth, drug resistance and shorter survival. Currently, the impact of nonchromosomal oncogene inheritance-random identity by descent-is poorly understood. Also unclear is the impact of ecDNA on somatic variation and selection. Here integrating theoretical models of random segregation, unbiased image analysis, CRISPR-based ecDNA tagging with live-cell imaging and CRISPR-C, we demonstrate that random ecDNA inheritance results in extensive intratumoral ecDNA copy number heterogeneity and rapid adaptation to metabolic stress and targeted treatment. Observed ecDNAs benefit host cell survival or growth and can change within a single cell cycle. ecDNA inheritance can predict, a priori, some of the aggressive features of ecDNA-containing cancers. These properties are facilitated by the ability of ecDNA to rapidly adapt genomes in a way that is not possible through chromosomal oncogene amplification. These results show how the nonchromosomal random inheritance pattern of ecDNA contributes to poor outcomes for patients with cancer.

}, issn = {1546-1718}, doi = {10.1038/s41588-022-01177-x}, author = {Lange, Joshua T and Rose, John C and Chen, Celine Y and Pichugin, Yuriy and Xie, Liangqi and Tang, Jun and Hung, King L and Yost, Kathryn E and Shi, Quanming and Erb, Marcella L and Rajkumar, Utkrisht and Wu, Sihan and Taschner-Mandl, Sabine and Bernkopf, Marie and Swanton, Charles and Liu, Zhe and Huang, Weini and Chang, Howard Y and Bafna, Vineet and Henssen, Anton G and Werner, Benjamin and Mischel, Paul S} } @conference {68572, title = {Exact learning dynamics of deep linear networks with prior knowledge}, booktitle = {Neural Information Processing Systems}, year = {2022}, abstract = {

Learning in deep neural networks is known to depend critically on the knowledge embedded in the initial network weights. However, few theoretical results have precisely linked prior knowledge to learning dynamics. Here we derive exact solutions to the dynamics of learning with rich prior knowledge in deep linear networks by generalising Fukumizu{\textquoteright}s matrix Riccati solution \citep{fukumizu1998effect}. We obtain explicit expressions for the evolving network function, hidden representational similarity, and neural tangent kernel over training for a broad class of initialisations and tasks. The expressions reveal a class of task-independent initialisations that radically alter learning dynamics from slow non-linear dynamics to fast exponential trajectories while converging to a global optimum with identical representational similarity, dissociating learning trajectories from the structure of initial internal representations. We characterise how network weights dynamically align with task structure, rigorously justifying why previous solutions successfully described learning from small initial weights without incorporating their fine-scale structure. Finally, we discuss the implications of these findings for continual learning, reversal learning and learning of structured knowledge. Taken together, our results provide a mathematical toolkit for understanding the impact of prior knowledge on deep learning.

}, author = {Lukas Braun and Cl{\'e}mentine Domin{\'e} and James Fitzgerald and Andrew Saxe} } @article {68570, title = {Eye structure shapes neuron function in Drosophila motion vision}, journal = {bioRxiv}, year = {2022}, month = {2022 Dec 15}, abstract = {

Many animals rely on vision to navigate through their environment. The pattern of changes in the visual scene induced by self-motion is the\ optic flow1, which is first estimated in local patches by directionally selective (DS) neurons2{\textendash}4. But how should the arrays of DS neurons, each responsive to motion in a preferred direction at a specific retinal position, be organized to support robust decoding of optic flow by downstream circuits? Understanding this global organization is challenging because it requires mapping fine, local features of neurons across the animal{\textquoteright}s field of view3. In\ Drosophila, the asymmetric dendrites of the T4 and T5 DS neurons establish their preferred direction, making it possible to predict DS responses from anatomy4,5. Here we report that the preferred directions of fly DS neurons vary at different retinal positions and show that this spatial variation is established by the anatomy of the compound eye. To estimate the preferred directions across the visual field, we reconstructed hundreds of T4 neurons in a full brain EM volume6\ and discovered unexpectedly stereotypical dendritic arborizations that are independent of location. We then used whole-head μCT scans to map the viewing directions of all compound eye facets and found a non-uniform sampling of visual space that explains the spatial variation in preferred directions. Our findings show that the organization of preferred directions in the fly is largely determined by the compound eye, exposing an intimate and unexpected connection between the peripheral structure of the eye, functional properties of neurons deep in the brain, and the control of body movements.

}, doi = {10.1101/2022.12.14.520178}, url = {https://doi.org/10.1101/2022.12.14.520178}, author = {Arthur Zhao and Eyal Gruntman and Aljoscha Nern and Nirmala A. Iyer and Edward M. Rogers and Sanna Koskela and Igor Siwanowicz and Marisa Dreher and Miriam A. Flynn and Connor W. Laughland and Henrique D.F. Ludwig and Alex G. Thomson and Cullen P. Moran and Bruck Gezahegn and Davi D. Bock and Michael B. Reiser} } @article {68275, title = {Flexible control of behavioral variability mediated by an internal representation of head direction}, journal = {bioRxiv}, year = {2022}, month = {2022 Aug 19}, abstract = {

Internal representations are thought to support the generation of flexible, long-timescale behavioral patterns in both animals and artificial agents. Here, we present a novel conceptual framework for how\ Drosophila\ use their internal representation of head direction to maintain preferred headings in their surroundings, and how they learn to modify these preferences in the presence of selective thermal reinforcement. To develop the framework, we analyzed flies{\textquoteright} behavior in a classical operant visual learning paradigm and found that they use stochastically generated fixations and directed turns to express their heading preferences. Symmetries in the visual scene used in the paradigm allowed us to expose how flies{\textquoteright} probabilistic behavior in this setting is tethered to their head direction representation. We describe how flies{\textquoteright} ability to quickly adapt their behavior to the rules of their environment may rest on a behavioral policy whose parameters are flexible but whose form is genetically encoded in the structure of their circuits. Many of the mechanisms we outline may also be relevant for rapidly adaptive behavior driven by internal representations in other animals, including mammals.

}, doi = {10.1101/2021.08.18.456004}, url = {https://doi.org/10.1101/2021.08.18.456004}, author = {Chuntao Dan and Brad K. Hulse and Vivek Jayaraman and Ann M. Hermundstad} } @article {67848, title = {Fluorescence activation mechanism and imaging of drug permeation with new sensors for smoking-cessation ligands.}, journal = {eLife}, volume = {11}, year = {2022}, month = {2022 Jan 04}, abstract = {

Nicotinic partial agonists provide an accepted aid for smoking cessation and thus contribute to decreasing tobacco-related disease. Improved drugs constitute a continued area of study. However, there remains no reductionist method to examine the cellular and subcellular pharmacokinetic properties of these compounds in living cells. Here, we developed new intensity-based drug sensing fluorescent reporters ({\textquoteright}iDrugSnFRs{\textquoteright}) for the nicotinic partial agonists dianicline, cytisine, and two cytisine derivatives - 10-fluorocytisine and 9-bromo-10-ethylcytisine. We report the first atomic-scale structures of liganded periplasmic binding protein-based biosensors, accelerating development of iDrugSnFRs and also explaining the activation mechanism. The nicotinic iDrugSnFRs detect their drug partners in solution, as well as at the plasma membrane (PM) and in the endoplasmic reticulum (ER) of cell lines and mouse hippocampal neurons. At the PM, the speed of solution changes limits the growth and decay rates of the fluorescence response in almost all cases. In contrast, we found that rates of membrane crossing differ among these nicotinic drugs by \> 30 fold. The new nicotinic iDrugSnFRs provide insight into the real-time pharmacokinetic properties of nicotinic agonists and provide a methodology whereby iDrugSnFRs can inform both pharmaceutical neuroscience and addiction neuroscience.

}, issn = {2050-084X}, doi = {10.7554/eLife.74648}, author = {Nichols, Aaron L and Blumenfeld, Zack and Fan, ChengCheng and Luebbert, Laura and Blom, Annet Em and Cohen, Bruce N and Marvin, Jonathan S and Borden, Philip M and Kim, Charlene H and Muthusamy, Anand K and Shivange, Amol V and Knox, Hailey J and Campello, Hugo Rego and Wang, Jonathan H and Dougherty, Dennis A and Looger, Loren L and Gallagher, Timothy and Rees, Douglas C and Lester, Henry A} } @article {68558, title = {Fluorescence Screens for Identifying Central Nervous System-Acting Drug-Biosensor Pairs for Subcellular and Supracellular Pharmacokinetics.}, journal = {Bio-Protocol}, volume = {12}, year = {2022}, month = {2022 Nov 20}, abstract = {

Subcellular pharmacokinetic measurements have informed the study of central nervous system (CNS)-acting drug mechanisms. Recent investigations have been enhanced by the use of genetically encoded fluorescent biosensors for drugs of interest at the plasma membrane and in organelles. We describe screening and validation protocols for identifying hit pairs comprising a drug and biosensor, with each screen including 13-18 candidate biosensors and 44-84 candidate drugs. After a favorable hit pair is identified and validated via these protocols, the biosensor is then optimized, as described in other papers, for sensitivity and selectivity to the drug. We also show sample hit pair data that may lead to future intensity-based drug-sensing fluorescent reporters (iDrugSnFRs). These protocols will assist scientists to use fluorescence responses as criteria in identifying favorable fluorescent biosensor variants for CNS-acting drugs that presently have no corresponding biosensor partner. eLife (2022), DOI: 10.7554/eLife.74648 Graphical abstract.

}, issn = {2331-8325}, doi = {10.21769/BioProtoc.4551}, author = {Beatty, Zoe G and Muthusamy, Anand K and Unger, Elizabeth K and Dougherty, Dennis A and Tian, Lin and Looger, Loren L and Shivange, Amol V and Bera, Kallol and Lester, Henry A and Nichols, Aaron L} } @article {67863, title = {Fluorescent chemigenetic actuators and indicators for use in living animals.}, journal = {Current Opinion in Pharmacology}, volume = {62}, year = {2022}, month = {2022 Jan 15}, pages = {159-167}, abstract = {

Fluorescent indicators and actuators provide a means to optically observe and perturb dynamic events in living animals. Although chemistry and protein engineering have contributed many useful tools to observe and perturb cells, an emerging strategy is to use chemigenetics: systems in which a small molecule dye interacts with a genetically encoded protein domain. Here we review chemigenetic strategies that have been successfully employed in living animals as photosensitizers for photoablation experiments, fluorescent cell cycle indicators, and fluorescent indicators for studying dynamic biological signals. Although these strategies at times suffer from challenges, e.g. delivery of the small molecule and assembly of the chemigenetic unit in living animals, the advantages of using small molecules with high brightness, low photobleaching, no chromophore maturation time and expanded color palette, combined with the ability to genetically target them to specific cell types, make chemigenetic fluorescent actuators and indicators an attractive strategy for use in living animals.

}, issn = {1471-4973}, doi = {10.1016/j.coph.2021.12.007}, author = {Farrants, Helen and Tebo, Alison G} } @article {68422, title = {Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly.}, journal = {Science}, volume = {375}, year = {2022}, month = {03/2022}, pages = {eabk2432}, abstract = {

For more than 100 years, the fruit fly has been one of the most studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula , that includes 580,000 nuclei from 15 individually dissected sexed tissues as well as the entire head and body, annotated to \>250 distinct cell types. We provide an in-depth analysis of cell type-related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types between tissues, such as blood and muscle cells, reveals rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the community and serves as a reference to study genetic perturbations and disease models at single-cell resolution.

}, keywords = {Animals, Cell Nucleus, Databases, Genetic, Drosophila melanogaster, Drosophila Proteins, Female, Gene Expression Regulation, Gene Regulatory Networks, Genes, Insect, Male, RNA-Seq, Sex Characteristics, Single-Cell Analysis, Transcription Factors, Transcriptome}, issn = {1095-9203}, doi = {10.1126/science.abk2432}, author = {Li, Hongjie and Janssens, Jasper and De Waegeneer, Maxime and Kolluru, Sai Saroja and Davie, Kristofer and Gardeux, Vincent and Saelens, Wouter and David, Fabrice P A and Brbi{\'c}, Maria and Spanier, Katina and Leskovec, Jure and McLaughlin, Colleen N and Xie, Qijing and Jones, Robert C and Brueckner, Katja and Shim, Jiwon and Tattikota, Sudhir Gopal and Schnorrer, Frank and Rust, Katja and Nystul, Todd G and Carvalho-Santos, Zita and Ribeiro, Carlos and Pal, Soumitra and Mahadevaraju, Sharvani and Przytycka, Teresa M and Allen, Aaron M and Goodwin, Stephen F and Berry, Cameron W and Fuller, Margaret T and White-Cooper, Helen and Matunis, Erika L and DiNardo, Stephen and Galenza, Anthony and O{\textquoteright}Brien, Lucy Erin and Dow, Julian A T and Jasper, Heinrich and Oliver, Brian and Perrimon, Norbert and Deplancke, Bart and Quake, Stephen R and Luo, Liqun and Aerts, Stein and Agarwal, Devika and Ahmed-Braimah, Yasir and Arbeitman, Michelle and Ariss, Majd M and Augsburger, Jordan and Ayush, Kumar and Baker, Catherine C and Banisch, Torsten and Birker, Katja and Bodmer, Rolf and Bolival, Benjamin and Brantley, Susanna E and Brill, Julie A and Brown, Nora C and Buehner, Norene A and Cai, Xiaoyu Tracy and Cardoso-Figueiredo, Rita and Casares, Fernando and Chang, Amy and Clandinin, Thomas R and Crasta, Sheela and Desplan, Claude and Detweiler, Angela M and Dhakan, Darshan B and Don{\`a}, Erika and Engert, Stefanie and Floc{\textquoteright}hlay, Swann and George, Nancy and Gonz{\'a}lez-Segarra, Amanda J and Groves, Andrew K and Gumbin, Samantha and Guo, Yanmeng and Harris, Devon E and Heifetz, Yael and Holtz, Stephen L and Horns, Felix and Hudry, Bruno and Hung, Ruei-Jiun and Jan, Yuh Nung and Jaszczak, Jacob S and Jefferis, Gregory S X E and Karkanias, Jim and Karr, Timothy L and Katheder, Nadja Sandra and Kezos, James and Kim, Anna A and Kim, Seung K and Kockel, Lutz and Konstantinides, Nikolaos and Kornberg, Thomas B and Krause, Henry M and Labott, Andrew Thomas and Laturney, Meghan and Lehmann, Ruth and Leinwand, Sarah and Li, Jiefu and Li, Joshua Shing Shun and Li, Kai and Li, Ke and Li, Liying and Li, Tun and Litovchenko, Maria and Liu, Han-Hsuan and Liu, Yifang and Lu, Tzu-Chiao and Manning, Jonathan and Mase, Anjeli and Matera-Vatnick, Mikaela and Matias, Neuza Reis and McDonough-Goldstein, Caitlin E and McGeever, Aaron and McLachlan, Alex D and Moreno-Roman, Paola and Neff, Norma and Neville, Megan and Ngo, Sang and Nielsen, Tanja and O{\textquoteright}Brien, Caitlin E and Osumi-Sutherland, David and Ozel, Mehmet Neset and Papatheodorou, Irene and Petkovic, Maja and Pilgrim, Clare and Pisco, Angela Oliveira and Reisenman, Carolina and Sanders, Erin Nicole and Dos Santos, Gilberto and Scott, Kristin and Sherlekar, Aparna and Shiu, Philip and Sims, David and Sit, Rene V and Slaidina, Maija and Smith, Harold E and Sterne, Gabriella and Su, Yu-Han and Sutton, Daniel and Tamayo, Marco and Tan, Michelle and Tastekin, Ibrahim and Treiber, Christoph and Vacek, David and Vogler, Georg and Waddell, Scott and Wang, Wanpeng and Wilson, Rachel I and Wolfner, Mariana F and Wong, Yiu-Cheung E and Xie, Anthony and Xu, Jun and Yamamoto, Shinya and Yan, Jia and Yao, Zepeng and Yoda, Kazuki and Zhu, Ruijun and Zinzen, Robert P} } @conference {68678, title = {FourierNets enable the design of highly non-local optical encoders for computational imaging}, booktitle = {Advances in Neural Information Processing Systems}, year = {2022}, month = {10/2022}, abstract = {

Differentiable simulations of optical systems can be combined with deep learning-based reconstruction networks to enable high performance computational imaging via end-to-end (E2E) optimization of both the optical encoder and the deep decoder. This has enabled imaging applications such as 3D localization microscopy, depth estimation, and lensless photography via the optimization of local optical encoders. More challenging computational imaging applications, such as 3D snapshot microscopy which compresses 3D volumes into single 2D images, require a highly non-local optical encoder. We show that existing deep network decoders have a locality bias which prevents the optimization of such highly non-local optical encoders. We address this with a decoder based on a shallow neural network architecture using global kernel Fourier convolutional neural networks (FourierNets). We show that FourierNets surpass existing deep network based decoders at reconstructing photographs captured by the highly non-local DiffuserCam optical encoder. Further, we show that FourierNets enable E2E optimization of highly non-local optical encoders for 3D snapshot microscopy. By combining FourierNets with a large-scale multi-GPU differentiable optical simulation, we are able to optimize non-local optical encoders 170{\texttimes}\ to 7372{\texttimes}\ larger than prior state of the art, and demonstrate the potential for ROI-type specific optical encoding with a programmable microscope.

}, keywords = {Computer Vision and Pattern Recognition (cs.CV), electronic engineering, FOS: Computer and information sciences, FOS: Electrical engineering, Image and Video Processing (eess.IV), information engineering, Machine Learning (cs.LG)}, doi = {https://doi.org/10.48550/arXiv.2104.10611}, url = {https://openreview.net/forum?id=Kx1VCs1treH}, author = {Diptodip Deb and Zhenfei Jiao and Ruth R Sims and Alex Bo-Yuan Chen and Michael Broxton and Misha Ahrens and Kaspar Podgorski and Srinivas C Turaga}, editor = {Alice H. Oh and Alekh Agarwal and Danielle Belgrave and Kyunghyun Cho} } @article {67952, title = {A functionally ordered visual feature map in the Drosophila brain.}, journal = {Neuron}, volume = {110}, year = {2022}, month = {2022 May 18}, pages = {1700}, abstract = {

Topographic maps, the systematic spatial ordering of neurons by response tuning, are common across species. In Drosophila, the lobula columnar (LC) neuron types project from the optic lobe to the central brain, where each forms a glomerulus in a distinct position. However, the advantages of this glomerular arrangement are unclear. Here, we examine the functional and spatial relationships of 10 glomeruli using single-neuron calcium imaging. We discover novel detectors for objects smaller than the lens resolution (LC18) and for complex line motion (LC25). We find that glomeruli are spatially clustered by selectivity for looming versus drifting object motion and ordered by size tuning to form a topographic visual feature map. Furthermore, connectome analysis shows that downstream neurons integrate from sparse subsets of possible glomeruli combinations, which are biased for glomeruli encoding similar features. LC neurons are thus an explicit example of distinct feature detectors topographically organized to facilitate downstream circuit integration.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2022.02.013}, author = {Klapoetke, Nathan C and Nern, Aljoscha and Rogers, Edward M and Rubin, Gerald M and Reiser, Michael B and Card, Gwyneth M} } @article {68068, title = {Gene structure-based homology search identifies highly divergent putative effector gene family.}, journal = {Genome Biology and Evolution}, year = {2022}, month = {2022 May 09}, abstract = {

Homology of highly divergent genes often cannot be determined from sequence similarity alone. For example, we recently identified in the aphid Hormaphis cornu a family of rapidly evolving bicycle genes, which encode novel proteins implicated as plant gall effectors, and sequence similarity search methods yielded few putative bicycle homologs in other species. Coding sequence-independent features of genes, such as intron-exon boundaries, often evolve more slowly than coding sequences, however, and can provide complementary evidence for homology. We found that a linear logistic regression classifier using only structural features of bicycle genes identified many putative bicycle homologs in other species. Independent evidence from sequence features and intron locations supported homology assignments. To test the potential roles of bicycle genes in other aphids, we sequenced the genome of a second gall-forming aphid, Tetraneura nigriabdominalis, and found that many bicycle genes are strongly expressed in the salivary glands of the gall forming foundress. In addition, bicycle genes are strongly overexpressed in the salivary glands of a non-gall forming aphid, Acyrthosiphon pisum, and in the non-gall forming generations of Hormaphis cornu. These observations suggest that Bicycle proteins may be used by multiple aphid species to manipulate plants in diverse ways. Incorporation of gene structural features into sequence search algorithms may aid identification of deeply divergent homologs, especially of rapidly evolving genes involved in host-parasite interactions.

}, issn = {1759-6653}, doi = {10.1093/gbe/evac069}, author = {Stern, David L and Han, Clair} } @article {65808, title = {A geometric framework to predict structure from function in neural networks}, journal = {Physical Review Research}, volume = {4}, year = {2022}, month = {2022 Jun 29}, pages = {023255}, abstract = {

Neural computation in biological and artificial networks relies on nonlinear synaptic integration. The structural connectivity matrix of synaptic weights between neurons is a critical determinant of overall network function. However, quantitative links between neural network structure and function are complex and subtle. For example, many networks can give rise to similar functional responses, and the same network can function differently depending on context. Whether certain patterns of synaptic connectivity are required to generate specific network-level computations is largely unknown. Here we introduce a geometric framework for identifying synaptic connections required by steady-state responses in recurrent networks of rectified-linear neurons. Assuming that the number of specified response patterns does not exceed the number of input synapses, we analytically calculate all feedforward and recurrent connectivity matrices that can generate the specified responses from the network inputs. We then use this analytical characterization to rigorously analyze the solution space geometry and derive certainty conditions guaranteeing a non-zero synapse between neurons. Numerical simulations of feedforward and recurrent networks verify our analytical results. Our theoretical framework could be applied to neural activity data to make anatomical predictions that follow generally from the model architecture. It thus provides novel opportunities for discerning what model features are required to accurately relate neural network structure and function.

}, doi = {10.1103/PhysRevResearch.4.023255}, url = {https://doi.org/10.1103/PhysRevResearch.4.023255}, author = {Biswas, Tirthabir and Fitzgerald, James E} } @article {68414, title = {High-throughput automated methods for classical and operant conditioning of larvae.}, journal = {eLife}, volume = {11}, year = {2022}, month = {2022 Oct 28}, abstract = {

Learning which stimuli (classical conditioning) or which actions (operant conditioning) predict rewards or punishments can improve chances of survival. However, the circuit mechanisms that underlie distinct types of associative learning are still not fully understood. Automated, high-throughput paradigms for studying different types of associative learning, combined with manipulation of specific neurons in freely behaving animals, can help advance this field. The Drosophila melanogaster larva is a tractable model system for studying the circuit basis of behaviour, but many forms of associative learning have not yet been demonstrated in this animal. Here, we developed a high-throughput (i. e. multi-larva) training system that combines real-time behaviour detection of freely moving larvae with targeted opto- and thermogenetic stimulation of tracked animals. Both stimuli are controlled in either open- or closed-loop, and delivered with high temporal and spatial precision. Using this tracker, we show for the first time that Drosophila larvae can perform classical conditioning with no overlap between sensory stimuli (i. e. trace conditioning). We also demonstrate that larvae are capable of operant conditioning by inducing a bend direction preference through optogenetic activation of reward-encoding serotonergic neurons. Our results extend the known associative learning capacities of Drosophila larvae. Our automated training rig will facilitate the study of many different forms of associative learning and the identification of the neural circuits that underpin them.

}, issn = {2050-084X}, doi = {10.7554/eLife.70015}, author = {Croteau-Chonka, Elise C and Clayton, Michael S and Venkatasubramanian, Lalanti and Harris, Samuel N and Jones, Benjamin M W and Narayan, Lakshmi and Winding, Michael and Masson, Jean-Baptiste and Zlatic, Marta and Klein, Kristina T} } @article {68516, title = {Hippocampal representations of foraging trajectories depend upon spatial context.}, journal = {Nature Neuroscience}, volume = {25}, year = {2022}, month = {2022 Dec 02}, pages = {1693-1705}, abstract = {

Animals learn trajectories to rewards in both spatial, navigational contexts and relational, non-navigational contexts. Synchronous reactivation of hippocampal activity is thought to be critical for recall and evaluation of trajectories for learning. Do hippocampal representations differentially contribute to experience-dependent learning of trajectories across spatial and relational contexts? In this study, we trained mice to navigate to a hidden target in a physical arena or manipulate a joystick to a virtual target to collect delayed rewards. In a navigational context, calcium imaging in freely moving mice revealed that synchronous CA1 reactivation was retrospective and important for evaluation of prior navigational trajectories. In a non-navigational context, reactivation was prospective and important for initiation of joystick trajectories, even in the same animals trained in both contexts. Adaptation of trajectories to a new target was well-explained by a common learning algorithm in which hippocampal activity makes dissociable contributions to reinforcement learning computations depending upon spatial context.

}, keywords = {Animals, Hippocampus, Mental Recall, Mice, Prospective Studies, Retrospective Studies, Spatial Navigation}, issn = {1546-1726}, doi = {10.1038/s41593-022-01201-7}, author = {Jiang, Wan-Chen and Xu, Shengjin and Dudman, Joshua T} } @article {68067, title = {Hormone-controlled changes in the differentiation state of post-mitotic neurons.}, journal = {Current Biology}, volume = {32}, year = {2022}, month = {2022 May 23}, pages = {2341-2348}, abstract = {

While we think of neurons as having a fixed identity, many show spectacular plasticity. Metamorphosis drives massive changes in the fly brain; neurons that persist into adulthood often change in response to the steroid hormone ecdysone. Besides driving remodeling, ecdysone signaling can also alter the differentiation status of neurons. The three sequentially born subtypes of mushroom body (MB) Kenyon cells (γ, followed by α{\textquoteright}/β{\textquoteright}, and finally α/β) serve as a model of temporal fating. γ neurons are also used as a model of remodeling during metamorphosis. As γ neurons are the only functional Kenyon cells in the larval brain, they serve the function of all three adult subtypes. Correspondingly, larval γ neurons have a similar morphology to α{\textquoteright}/β{\textquoteright} and α/β neurons-their axons project dorsally and medially. During metamorphosis, γ neurons remodel to form a single medial projection. Both temporal fate changes and defects in remodeling therefore alter γ-neuron morphology in similar ways. Mamo, a broad-complex, tramtrack, and bric-{\`a}-brac/poxvirus and zinc finger (BTB/POZ)\ transcription factor critical for temporal specification of α{\textquoteright}/β{\textquoteright} neurons, was recently described as essential for γ remodeling. In a previous study, we noticed a change in the number of adult Kenyon cells expressing γ-specific markers when mamo was manipulated. These data implied a role for Mamo in γ-neuron fate specification, yet mamo is not expressed in γ neurons until pupariation, well past γ specification. This indicates that mamo has a later role in ensuring that γ neurons express the correct Kenyon cell subtype-specific genes in the adult brain.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2022.04.027}, author = {Lai, Yen-Wei and Miyares, Rosa L and Liu, Ling-Yu and Chu, Sao-Yu and Lee, Tzumin and Yu, Hung-Hsiang} } @article {68985, title = {Human primed and na{\"\i}ve PSCs are both able to differentiate into trophoblast stem cells.}, journal = {Stem Cell Reports}, volume = {17}, year = {2022}, month = {11/2022}, pages = {2484-2500}, abstract = {

The recent derivation of human trophoblast stem cells (TSCs) from placental cytotrophoblasts and blastocysts opened opportunities for studying the development and function of the human placenta. Recent reports have suggested that human na{\"\i}ve, but not primed, pluripotent stem cells (PSCs) retain an exclusive potential to generate TSCs. Here we report that, in the absence of WNT stimulation, transforming growth factor β (TGF-β) pathway inhibition leads to direct and robust conversion of primed human PSCs into TSCs. The resulting primed PSC-derived TSC lines exhibit self-renewal, can differentiate into the main trophoblast lineages, and present RNA and epigenetic profiles that are indistinguishable from recently established TSC lines derived from human placenta, blastocysts, or isogenic human na{\"\i}ve PSCs expanded under human enhanced na{\"\i}ve stem cell medium (HENSM) conditions. Activation of nuclear Yes-associated protein (YAP) signaling is sufficient for this conversion and necessary for human TSC maintenance. Our findings underscore a residual plasticity in primed human PSCs that allows their in\ vitro conversion into extra-embryonic trophoblast lineages.

}, keywords = {Blastocyst, Cell Differentiation, Female, Humans, Placenta, Pluripotent Stem Cells, Pregnancy, Trophoblasts}, issn = {2213-6711}, doi = {10.1016/j.stemcr.2022.09.008}, author = {Viukov, Sergey and Shani, Tom and Bayerl, Jonathan and Aguilera-Castrejon, Alejandro and Oldak, Bernardo and Sheban, Daoud and Tarazi, Shadi and Stelzer, Yonatan and Hanna, Jacob H and Novershtern, Noa} } @article {67931, title = {Identifying Inhibitors of -1 Programmed Ribosomal Frameshifting in a Broad Spectrum of Coronaviruses.}, journal = {Viruses}, volume = {14}, year = {2022}, month = {2022 Jan 18}, abstract = {

Recurrent outbreaks of novel zoonotic coronavirus (CoV) diseases in recent years have highlighted the importance of developing therapeutics with broad-spectrum activity against CoVs. Because all CoVs use -1 programmed ribosomal frameshifting (-1 PRF) to control expression of key viral proteins, the frameshift signal in viral mRNA that stimulates -1 PRF provides a promising potential target for such therapeutics. To test the viability of this strategy, we explored whether small-molecule inhibitors of -1 PRF in SARS-CoV-2 also inhibited -1 PRF in a range of bat CoVs-the most likely source of future zoonoses. Six inhibitors identified in new and previous screens against SARS-CoV-2 were evaluated against the frameshift signals from a panel of representative bat CoVs as well as MERS-CoV. Some drugs had strong activity against subsets of these CoV-derived frameshift signals, while having limited to no effect on -1 PRF caused by frameshift signals from other viruses used as negative controls. Notably, the serine protease inhibitor nafamostat suppressed -1 PRF significantly for multiple CoV-derived frameshift signals. These results suggest it is possible to find small-molecule ligands that inhibit -1 PRF specifically in a broad spectrum of CoVs, establishing frameshift signals as a viable target for developing pan-coronaviral therapeutics.

}, issn = {1999-4915}, doi = {10.3390/v14020177}, author = {Munshi, Sneha and Neupane, Krishna and Ileperuma, Sandaru M and Halma, Matthew T J and Kelly, Jamie A and Halpern, Clarissa F and Dinman, Jonathan D and Loerch, Sarah and Woodside, Michael T} } @article {67891, title = {Idiosyncratic learning performance in flies.}, journal = {Biology Letters}, volume = {18}, year = {2022}, month = {2022 Feb 01}, pages = {20210424}, abstract = {

Individuals vary in their innate behaviours, even when they have the same genome and have been reared in the same environment. The extent of individuality in plastic behaviours, like learning, is less well characterized. Also unknown is the extent to which intragenotypic differences in learning generalize: if an individual performs well in one assay, will it perform well in other assays? We investigated this using the fruit fly , an organism long-used to study the mechanistic basis of learning and memory. We found that isogenic flies, reared in identical laboratory conditions, and subject to classical conditioning that associated odorants with electric shock, exhibit clear individuality in their learning responses. Flies that performed well when an odour was paired with shock tended to perform well when the odour was paired with bitter taste or when other odours were paired with shock. Thus, individuality in learning performance appears to be prominent in isogenic animals reared identically, and individual differences in learning performance generalize across some aversive sensory modalities. Establishing these results in flies opens up the possibility of studying the genetic and neural circuit basis of individual differences in learning in a highly suitable model organism.

}, issn = {1744-957X}, doi = {10.1098/rsbl.2021.0424}, author = {Smith, Matthew A-Y and Honegger, Kyle S and Turner, Glenn and de Bivort, Benjamin} } @article {67858, title = {The importance of accounting for movement when relating neuronal activity to sensory and cognitive processes.}, journal = {Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {42}, year = {2022}, month = {2022 Feb 23}, pages = {1375-1382}, abstract = {

A surprising finding of recent studies in mouse is the dominance of widespread\ movement-related\ activity\ throughout the brain, including in early\ sensory\ areas. In awake subjects, failing to\ account\ for\ movement\ risks misattributing\ movement-related\ activity\ to other (e.g.,\ sensory\ or\ cognitive)\ processes. In this article, we 1) review task designs for separating task-related\ and\ movement-related\ activity, 2) review three {\textquoteright}case studies{\textquoteright} in which\ not\ considering\ movement\ would have resulted in critically different interpretations of\ neuronal\ function, and 3) discuss functional couplings that may prevent us from ever fully isolating\ sensory,\ motor, and\ cognitive-related\ activity. Our main thesis is that neural signals\ related\ to\ movement\ are ubiquitous, and therefore ought to be considered first and foremost when attempting to correlate\ neuronal\ activity\ with task-related\ processes.

}, doi = {10.1523/JNEUROSCI.1919-21.2021}, author = {Edward Zagha and Jeffrey C Erlich and Soohyun Lee and Gyorgy Lur and Daniel H O{\textquoteright}Connor and Nicholas A Steinmetz and Carsen Stringer and Hongdian Yang} } @article {68418, title = {In situ cell-type-specific cell-surface proteomic profiling in mice.}, journal = {Neuron}, year = {2022}, month = {10/2022}, abstract = {

Cell-surface proteins (CSPs) mediate intercellular communication throughout the lives of multicellular organisms. However, there are no generalizable methods for quantitative CSP profiling in specific cell types in vertebrate tissues. Here, we present in situ cell-surface proteome extraction by extracellular labeling (iPEEL), a proximity labeling method in mice that enables spatiotemporally precise labeling of cell-surface proteomes in a cell-type-specific environment in native tissues for discovery proteomics. Applying iPEEL to developing and mature cerebellar Purkinje cells revealed differential enrichment in CSPs with post-translational protein processing and synaptic functions in the developing and mature cell-surface proteomes, respectively. A proteome-instructed in\ vivo loss-of-function screen identified a critical, multifaceted role for Armh4 in Purkinje cell dendrite morphogenesis. Armh4 overexpression also disrupts dendrite morphogenesis; this effect requires its conserved cytoplasmic domain and is augmented by disrupting its endocytosis. Our results highlight the utility of CSP profiling in native mammalian tissues for identifying regulators of cell-surface signaling.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2022.09.025}, author = {Shuster, S Andrew and Li, Jiefu and Chon, URee and Sinantha-Hu, Miley C and Luginbuhl, David J and Udeshi, Namrata D and Carey, Dominique Kiki and Takeo, Yukari H and Xie, Qijing and Xu, Chuanyun and Mani, D R and Han, Shuo and Ting, Alice Y and Carr, Steven A and Luo, Liqun} } @article {68082, title = {In situ cryo-electron tomography reveals the asymmetric architecture of mammalian sperm axonemes}, journal = {bioRxiv}, year = {2022}, month = {2022 May 16}, abstract = {

The flagella of mammalian sperm display non-planar, asymmetric beating, in contrast to the planar, symmetric beating of flagella from sea urchin sperm and unicellular organisms. The molecular basis of this difference is unclear. Here, we perform\ in situ\ cryo-electron tomography of mouse and human sperm axonemes, providing the highest resolution structural information to date. Our subtomogram averages reveal mammalian sperm- specific protein complexes within the outer microtubule doublets, the radial spokes and nexin-dynein regulatory complexes. The locations and structures of these complexes suggest potential roles in enhancing the mechanical strength of mammalian sperm axonemes and regulating dynein-based axonemal bending. Intriguingly, we find that each of the nine outer microtubule doublets is decorated with a distinct combination of sperm- specific complexes. We propose that this asymmetric distribution of proteins differentially regulates the sliding of each microtubule doublet and may underlie the asymmetric beating of mammalian sperm.

}, doi = {10.1101/2022.05.15.492011}, url = {https://doi.org/10.1101/2022.05.15.492011}, author = {Zhen Chen and Garrett A. Greenan and Momoko Shiozaki and Yanxin Liu and Will M. Skinner and Xiaowei Zhao and Shumei Zhao and Rui Yan and Caiying Guo and Zhiheng Yu and Polina V. Lishko and David A. Agard and Ronald D. Vale} } @article {68010, title = {In situ single particle classification reveals distinct 60S maturation intermediates in cells.}, journal = {eLife}, year = {2022}, month = {2022 Aug 25}, abstract = {

Electron cryo-microscopy (cryo-EM) can generate high-resolution views of cells with faithful preservation of molecular structure.\ In situ\ cryo-EM, therefore, has enormous potential to reveal the atomic details of biological processes in their native context. However, in practice, the utility of\ in situ\ cryo-EM is limited by the difficulty of reliably locating and confidently identifying molecular targets (particles) and their conformational states in the crowded cellular environment. We recently showed that 2DTM, a fine-grained template-based search applied to cryo-EM micrographs, can localize particles in two-dimensional views of cells with high precision. Here we demonstrate that the signal-to-noise ratio (SNR) observed with 2DTM can be used to differentiate related complexes in focused ion beam (FIB)-milled cell sections. We apply this method in two contexts to locate and classify related intermediate states of 60S ribosome biogenesis in the\ Saccharomyces cerevisiae\ cell nucleus. In the first, we separate the nuclear pre-60S population from the cytoplasmic mature 60S population, using the subcellular localization to validate assignment. In the second, we show that relative 2DTM SNRs can be used to separate mixed populations of nuclear pre-60S that are not visually separable. We use a maximum likelihood approach to define the probability of each particle belonging to each class, thereby establishing a statistic to describe the confidence of our classification. Without the need to generate 3D reconstructions, 2DTM can be applied even when only a few target particles exist in a cell.

}, doi = {10.7554/eLife.79272}, url = {https://doi.org/10.7554/eLife.79272}, author = {Bronwyn A. Lucas and Kexin Zhang and Sarah Loerch and Nikolaus Grigorieff} } @article {68314, title = {In vivo visualization of nitrate dynamics using a genetically encoded biosensor}, journal = {Science Advances}, volume = {8}, year = {2022}, month = {2022 Oct 19}, abstract = {

Nitrate (NO3-) uptake and distribution are critical to plant life. Although the upstream regulation of nitrate uptake and downstream responses to nitrate in a variety of cells have been well-studied, it is still not possible to directly visualize the spatial and temporal distribution of nitrate with high resolution at the cellular level. Here, we report a nuclear-localized, genetically encoded biosensor, nlsNitraMeter3.0, for the quantitative visualization of nitrate distribution in\ Arabidopsis thaliana. The biosensor tracked the spatiotemporal distribution of nitrate along the primary root axis and disruptions by genetic mutation of transport (low nitrate uptake) and assimilation (high nitrate accumulation). The developed biosensor effectively monitors nitrate concentrations at cellular level in real time and spatiotemporal changes during the plant life cycle.

}, doi = {10.1126/sciadv.abq4915}, url = {https://doi.org/10.1126/sciadv.abq4915}, author = {Yen-Ning Chen and Heather Cartwright and Cheng-Hsun Ho} } @article {68556, title = {Inhibition of coronavirus HCoV-OC43 by targeting the eIF4F complex.}, journal = {Frontiers in Pharmacology}, volume = {13}, year = {2022}, month = {2022 Dec 01}, pages = {1029093}, abstract = {

The translation initiation complex 4F (eIF4F) is a rate-limiting factor in protein synthesis. Alterations in eIF4F activity are linked to several diseases, including cancer and infectious diseases. To this end, coronaviruses require eIF4F complex activity to produce proteins essential for their life cycle. Efforts to target coronaviruses by abrogating translation have been largely limited to repurposing existing eIF4F complex inhibitors. Here, we report the results of a high throughput screen to identify small molecules that disrupt eIF4F complex formation and inhibit coronavirus RNA and protein levels. Of 338,000 small molecules screened for inhibition of the eIF4F-driven, CAP-dependent translation, we identified SBI-1232 and two structurally related analogs, SBI-5844 and SBI-0498, that inhibit human coronavirus OC43 (HCoV-OC43; OC43) with minimal cell toxicity. Notably, gene expression changes after OC43 infection of Vero E6 or A549 cells were effectively reverted upon treatment with SBI-5844 or SBI-0498. Moreover, SBI-5844 or SBI-0498 treatment effectively impeded the eIF4F complex assembly, with concomitant inhibition of newly synthesized OC43 nucleocapsid protein and OC43 RNA and protein levels. Overall, we identify SBI-5844 and SBI-0498 as small molecules targeting the eIF4F complex that may limit coronavirus transcripts and proteins, thereby representing a basis for developing novel therapeutic modalities against coronaviruses.

}, issn = {1663-9812}, doi = {10.3389/fphar.2022.1029093}, author = {Feng, Yongmei and Grotegut, Stefan and Jovanovic, Predrag and Gandin, Valentina and Olson, Steven H and Murad, Rabi and Beall, Anne and Colayco, Sharon and De-Jesus, Paul and Chanda, Sumit and English, Brian P and Singer, Robert H and Jackson, Michael and Topisirovic, Ivan and Ronai, Ze{\textquoteright}ev A} } @article {67814, title = {Internal Models in Control, Bioengineering, and Neuroscience}, journal = {Annual Review of Control, Robotics, and Autonomous Systems}, volume = {5}, year = {2022}, month = {2021 Nov 29}, abstract = {

Internal models are nowadays customarily used in different domains of science and engineering to describe how living organisms or artificial computational units embed their acquired knowledge about recurring events taking place in the surrounding environment. This article reviews the internal model principle in control theory, bioengineering, and neuroscience, illustrating the fundamental concepts and theoretical developments of the few last decades of research.

}, issn = {2573-5144}, doi = {10.1146/control.2022.5.issue-110.1146/annurev-control-042920-102205}, url = {https://www.annualreviews.org/toc/control/5/1https://www.annualreviews.org/doi/10.1146/annurev-control-042920-102205https://www.annualreviews.org/doi/pdf/10.1146/annurev-control-042920-102205}, author = {Bin, Michelangelo and Huang, Jie and Isidori, Alberto and Marconi, Lorenzo and Mischiati, Matteo and Sontag, Eduardo} } @article {68293, title = {Isolation, cryo-laser scanning confocal microscope imaging and cryo-FIB milling of mouse glutamatergic synaptosomes.}, journal = {PLoS One}, volume = {17}, year = {2022}, month = {2022 Aug 12}, pages = {e0271799}, abstract = {

Ionotropic glutamate receptors (iGluRs) at postsynaptic terminals mediate the majority of fast excitatory neurotransmission in response to release of glutamate from the presynaptic terminal. Obtaining structural information on the molecular organization of iGluRs in their native environment, along with other signaling and scaffolding proteins in the postsynaptic density (PSD), and associated proteins on the presynaptic terminal, would enhance understanding of the molecular basis for excitatory synaptic transmission in normal and in disease states. Cryo-electron tomography (ET) studies of synaptosomes is one attractive vehicle by which to study iGluR-containing excitatory synapses. Here we describe a workflow for the preparation of glutamatergic synaptosomes for cryo-ET studies. We describe the utilization of fluorescent markers for the facile detection of the pre and postsynaptic terminals of glutamatergic synaptosomes using cryo-laser scanning confocal microscope (cryo-LSM). We further provide the details for preparation of lamellae, between ~100 to 200 nm thick, of glutamatergic synaptosomes using cryo-focused ion-beam (FIB) milling. We monitor the lamella preparation using a scanning electron microscope (SEM) and following lamella production, we identify regions for subsequent cryo-ET studies by confocal fluorescent imaging, exploiting the pre and postsynaptic fluorophores.

}, keywords = {Animals, Cryoelectron Microscopy, Electron Microscope Tomography, Lasers, Mice, Microscopy, Confocal, Synapses, Synaptosomes}, issn = {1932-6203}, doi = {10.1371/journal.pone.0271799}, author = {Gogoi, Prerana and Shiozaki, Momoko and Gouaux, Eric} } @article {68515, title = {Ketamine triggers a switch in excitatory neuronal activity across neocortex.}, journal = {Nature Neuroscience}, year = {2022}, month = {2022 Nov 24}, abstract = {

The brain can become transiently disconnected from the environment while maintaining vivid, internally generated experiences. This so-called {\textquoteright}dissociated state{\textquoteright} can occur in pathological conditions and under the influence of psychedelics or the anesthetic ketamine (KET). The cellular and circuit mechanisms producing the dissociative state remain poorly understood. We show in mice that KET causes spontaneously active neurons to become suppressed while previously silent neurons become spontaneously activated. This switch occurs in all cortical layers and different cortical regions, is induced by both systemic and cortical application of KET and is mediated by suppression of parvalbumin and somatostatin interneuron activity and inhibition of NMDA receptors and HCN channels. Combined, our results reveal two largely non-overlapping cortical neuronal populations-one engaged in wakefulness, the other contributing to the KET-induced brain state-and may lay the foundation for understanding how the brain might become disconnected from the surrounding environment while maintaining internal subjective experiences.

}, issn = {1546-1726}, doi = {10.1038/s41593-022-01203-5}, author = {Cichon, Joseph and Wasilczuk, Andrzej Z and Looger, Loren L and Contreras, Diego and Kelz, Max B and Proekt, Alex} } @article {68226, title = {Kinetic principles underlying pioneer function of GAGA transcription factor in live cells.}, journal = {Nature Structural and Molecular Biology}, volume = {29}, year = {2022}, month = {2022 Jul 01}, pages = {665-676}, abstract = {

How pioneer factors interface with chromatin to promote accessibility for transcription control is poorly understood in vivo. Here, we directly visualize chromatin association by the prototypical GAGA pioneer factor (GAF) in live Drosophila hemocytes. Single-particle tracking reveals that most GAF is chromatin bound, with a stable-binding fraction showing nucleosome-like confinement residing on chromatin for more than 2 min, far longer than the dynamic range of most transcription factors. These kinetic properties require the full complement of GAF{\textquoteright}s DNA-binding, multimerization and intrinsically disordered domains, and are autonomous from recruited chromatin remodelers NURF and PBAP, whose activities primarily benefit GAF{\textquoteright}s neighbors such as Heat Shock Factor. Evaluation of GAF kinetics together with its endogenous abundance indicates that, despite on-off dynamics, GAF constitutively and fully occupies major chromatin targets, thereby providing a temporal mechanism that sustains open chromatin for transcriptional responses to homeostatic, environmental and developmental signals.

}, keywords = {Animals, Chromatin, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Kinetics, Transcription Factors}, issn = {1545-9985}, doi = {10.1038/s41594-022-00800-z}, author = {Tang, Xiaona and Li, Taibo and Liu, Sheng and Wisniewski, Jan and Zheng, Qinsi and Rong, Yikang and Lavis, Luke D and Wu, Carl} } @article {68420, title = {KIRCD8 T cells suppress pathogenic T cells and are active in autoimmune diseases and COVID-19.}, journal = {Science}, volume = {376}, year = {2022}, month = {04/2022}, pages = {eabi9591}, abstract = {

In this work, we find that CD8 T cells expressing inhibitory killer cell immunoglobulin-like receptors (KIRs) are the human equivalent of Ly49CD8 regulatory T cells in mice and are increased in the blood and inflamed tissues of patients with a variety of autoimmune diseases. Moreover, these CD8 T cells efficiently eliminated pathogenic gliadin-specific CD4 T cells from the leukocytes of celiac disease patients in vitro. We also find elevated levels of KIRCD8 T cells, but not CD4 regulatory T cells, in COVID-19 patients, correlating with disease severity and vasculitis. Selective ablation of Ly49CD8 T cells in virus-infected mice led to autoimmunity after infection. Our results indicate that in both species, these regulatory CD8 T cells act specifically to suppress pathogenic T cells in autoimmune and infectious diseases.

}, keywords = {Animals, Autoimmune Diseases, CD8-Positive T-Lymphocytes, COVID-19, Humans, Mice, Receptors, KIR, T-Lymphocytes, Regulatory}, issn = {1095-9203}, doi = {10.1126/science.abi9591}, author = {Li, Jing and Zaslavsky, Maxim and Su, Yapeng and Guo, Jing and Sikora, Michael J and van Unen, Vincent and Christophersen, Asbj{\o}rn and Chiou, Shin-Heng and Chen, Liang and Li, Jiefu and Ji, Xuhuai and Wilhelmy, Julie and McSween, Alana M and Palanski, Brad A and Mallajosyula, Venkata Vamsee Aditya and Bracey, Nathan A and Dhondalay, Gopal Krishna R and Bhamidipati, Kartik and Pai, Joy and Kipp, Lucas B and Dunn, Jeffrey E and Hauser, Stephen L and Oksenberg, Jorge R and Satpathy, Ansuman T and Robinson, William H and Dekker, Cornelia L and Steinmetz, Lars M and Khosla, Chaitan and Utz, Paul J and Sollid, Ludvig M and Chien, Yueh-Hsiu and Heath, James R and Fernandez-Becker, Nielsen Q and Nadeau, Kari C and Saligrama, Naresha and Davis, Mark M} } @article {68366, title = {Learning of probabilistic punishment as a model of anxiety produces changes in action but not punisher encoding in the dmPFC and VTA.}, journal = {eLife}, volume = {11}, year = {2022}, month = {2022 Sep 14}, abstract = {

Previously, we developed a novel model for anxiety during motivated behavior by training rats to perform a task where actions executed to obtain a reward were probabilistically punished and observed that after learning, neuronal activity in the ventral tegmental area (VTA) and dorsomedial prefrontal cortex (dmPFC) represent the relationship between action and punishment risk (Park \& Moghaddam, 2017). Here we used male and female rats to expand on the previous work by focusing on neural changes in the dmPFC and VTA that were associated with the learning of probabilistic punishment, and anxiolytic treatment with diazepam after learning. We find that adaptive neural responses of dmPFC and VTA during the learning of anxiogenic contingencies are independent from the punisher experience and occur primarily during the peri-action and reward period. Our results also identify peri-action ramping of VTA neural calcium activity, and VTA-dmPFC correlated activity, as potential markers for the anxiolytic properties of diazepam.

}, issn = {2050-084X}, doi = {10.7554/eLife.78912}, author = {Jacobs, David S and Allen, Madeleine C and Park, Junchol and Moghaddam, Bita} } @article {67306, title = {Learning to represent continuous variables in heterogeneous neural networks}, journal = {Cell Reports}, volume = {39}, year = {2022}, month = {2022 Apr 05}, pages = {110612}, abstract = {

Manifold attractors are a key framework for understanding how continuous variables, such as position or head direction, are encoded in the brain. In this framework, the variable is represented along a continuum of persistent neuronal states which forms a manifold attactor. Neural networks with symmetric synaptic connectivity that can implement manifold attractors have become the dominant model in this framework. In addition to a symmetric connectome, these networks imply homogeneity of individual-neuron tuning curves and symmetry of the representational space; these features are largely inconsistent with neurobiological data. Here, we developed a theory for computations based on manifold attractors in trained neural networks and show how these manifolds can cope with diverse neuronal responses, imperfections in the geometry of the manifold and a high level of synaptic heterogeneity. In such heterogeneous trained networks, a continuous representational space emerges from a small set of stimuli used for training. Furthermore, we find that the network response to external inputs depends on the geometry of the representation and on the level of synaptic heterogeneity in an analytically tractable and interpretable way. Finally, we show that a too complex geometry of the neuronal representation impairs the attractiveness of the manifold and may lead to its destabilization. Our framework reveals that continuous features can be represented in the recurrent dynamics of heterogeneous networks without assuming unrealistic symmetry. It suggests that the representational space of putative manifold attractors in the brain dictates the dynamics in their vicinity.

}, doi = {10.1016/j.celrep.2022.110612}, url = {https://doi.org/10.1016/j.celrep.2022.110612}, author = {Ran Darshan and Alexander Rivkind} } @article {68471, title = {Leveraging the model-experiment loop: Examples from cellular slime mold chemotaxis.}, journal = {Exp Cell Res}, volume = {418}, year = {2022}, month = {09/2022}, pages = {113218}, abstract = {

Interplay between models and experimental data advances discovery and understanding in biology, particularly when models generate predictions that allow well-designed experiments to distinguish between alternative mechanisms. To illustrate how this feedback between models and experiments can lead to key insights into biological mechanisms, we explore three examples from cellular slime mold chemotaxis. These examples include studies that identified chemotaxis as the primary mechanism behind slime mold aggregation, discovered that cells likely measure chemoattractant gradients by sensing concentration differences across cell length, and tested the role of cell-associated chemoattractant degradation in shaping chemotactic fields. Although each study used a different model class appropriate to their hypotheses - qualitative, mathematical, or simulation-based - these examples all highlight the utility of modeling to formalize assumptions and generate testable predictions. A central element of this framework is the iterative use of models and experiments, specifically: matching experimental designs to the models, revising models based on mismatches with experimental data, and validating critical model assumptions and predictions with experiments. We advocate for continued use of this interplay between models and experiments to advance biological discovery.

}, keywords = {Chemotactic Factors, Chemotaxis, Computer Simulation, Dictyosteliida, Dictyostelium, Models, Biological}, issn = {1090-2422}, doi = {10.1016/j.yexcr.2022.113218}, author = {Zhu, Xinwen and Hager, Emily R and Huyan, Chuqiao and Sgro, Allyson E} } @article {68021, title = {Long-term imaging reveals behavioral plasticity during C. elegans dauer exit}, journal = {BMC Biology}, volume = {20}, year = {2022}, month = {2022 Dec 13}, pages = {277}, abstract = {

During their lifetime, animals must adapt their behavior to survive in changing environments. This ability requires the nervous system to adjust through dynamic expression of neurotransmitters and receptors but also through growth, spatial reorganization and connectivity while integrating external stimuli. For instance, despite having a fixed neuronal cell lineage, the nematode\ Caenorhabditis elegans{\textquoteright}\ nervous system remains plastic throughout its development. Here, we focus on a specific example of nervous system plasticity, the\ C. elegans\ dauer exit decision. Under unfavorable conditions, larvae will enter the non-feeding and non-reproductive dauer stage and adapt their behavior to cope with a new environment. Upon improved conditions, this stress resistant developmental stage is actively reversed to resume reproductive development. However, how different environmental stimuli regulate the exit decision mechanism and thereby drive the larva{\textquoteright}s behavioral change is unknown. To fill this gap, we developed a new open hardware method for long-term imaging (12h) of\ C. elegans\ larvae. We identified dauer-specific behavioral motifs and characterized the behavioral trajectory of dauer exit in different environments to identify key decision points. Combining long-term behavioral imaging with transcriptomics, we find that bacterial ingestion triggers a change in neuropeptide gene expression to establish post-dauer behavior. Taken together, we show how a developing nervous system can robustly integrate environmental changes, activate a developmental switch and adapt the organism{\textquoteright}s behavior to a new environment.

}, doi = {10.1186/s12915-022-01471-4}, url = {https://doi.org/10.1186/s12915-022-01471-4}, author = {Friedrich Preusser and Anika Neuschulz and Jan Philipp Junker and Nikolaus Rajewsky and Stephan Preibisch} } @article {68103, title = {Maintaining a stable head direction representation in naturalistic visual environments}, journal = {bioRxiv}, year = {2022}, month = {2022 May 18}, abstract = {

Many animals rely on a representation of head direction for flexible, goal-directed navigation. In insects, a compass-like head direction representation is maintained in a conserved brain region called the central complex. This head direction representation is updated by self-motion information and by tethering to sensory cues in the surroundings through a plasticity mechanism. However, under natural settings, some of these sensory cues may temporarily disappear{\textemdash}for example, when clouds hide the sun{\textemdash}and prominent landmarks at different distances from the insect may move across the animal{\textquoteright}s field of view during translation, creating potential conflicts for a neural compass. We used two-photon calcium imaging in head-fixed Drosophila behaving in virtual reality to monitor the fly{\textquoteright}s compass during navigation in immersive naturalistic environments with approachable local landmarks. We found that the fly{\textquoteright}s compass remains stable even in these settings by tethering to available global cues, likely preserving the animal{\textquoteright}s ability to perform compass-driven behaviors such as maintaining a constant heading.

}, doi = {10.1101/2022.05.17.492284}, url = {https://doi.org/10.1101/2022.05.17.492284}, author = {Hannah Haberkern and Shivam S Chitnis and Philip M Hubbard and Tobias Goulet and Ann M Hermundstad and Vivek Jayaraman} } @article {67964, title = {Many dissimilar protein domains switch between α-helix and β-sheet folds}, journal = {Nature Communications}, volume = {13}, year = {2022}, month = {2022 Jul01}, abstract = {

Hundreds of millions of structured proteins sustain life through chemical interactions and catalytic reactions1. Though dynamic, these proteins are assumed to be built upon fixed scaffolds of secondary structure, α-helices and β-sheets. Experimentally determined structures of over \>58,000 non-redundant proteins support this assumption, though it has recently been challenged by \~{}100 fold-switching proteins2. These {\textquotedblleft}metamorphic3{\textquotedblright} proteins, though ostensibly rare, raise the question of how many uncharacterized proteins have shapeshifting{\textendash}rather than fixed{\textendash}secondary structures. To address this question, we developed a comparative sequence-based approach that predicts fold-switching proteins from differences in secondary structure propensity. We applied this approach to the universally conserved NusG transcription factor family of \~{}15,000 proteins, one of which has a 50-residue regulatory subunit experimentally shown to switch between α-helical and β-sheet folds4. Our approach predicted that 25\% of the sequences in this family undergo similar α-helix ⇌ β-sheet transitions, a frequency two orders of magnitude larger than previously observed. Our predictions evade state-of-the-art computational methods but were confirmed experimentally by circular dichroism and nuclear magnetic resonance spectroscopy for all 10 assiduously chosen dissimilar variants. These results suggest that fold switching is a pervasive mechanism of transcriptional regulation in all kingdoms of life and imply that numerous uncharacterized proteins may also switch folds.

}, doi = {10.1101/2021.06.10.447921}, url = {https://doi.org/10.1101/2021.06.10.447921}, author = {Lauren L. Porter and Allen K. Kim and Swechha Rimal and Loren L. Looger and Ananya Majumdar and Brett D. Mensh and Mary Starich} } @article {68299, title = {Many sequence-diverse domains switch between alpha-helix and beta-sheet folds}, journal = {Biophysical Journal}, volume = {121}, year = {2022}, month = {2022 Feb 01}, pages = {156a}, abstract = {

The protein folding paradigm asserts that the three-dimensional structure of a protein is determined by its amino acid sequence. Here we show that a substantial population of proteins from the NusG superfamily of transcription factors do not adhere to this paradigm. Previous work demonstrated that one member of this superfamily has a regulatory domain that completely switches between α-helical and β-sheet folds, but the pervasiveness of this fold-switching mechanism is uncertain. To address this question, we developed a sequence-based predictor, which revealed that thousands of proteins from this superfamily switch folds. Circular dichroism and nuclear magnetic resonance spectroscopies of 10 sequence-diverse variants confirmed our predictions. By contrast, state-of-the-art methods based on the protein folding paradigm assume that related sequences adopt the same fold and thus predicted that the regulatory domains of all variants adopt only the β-sheet fold. Removal of this bias revealed that residue-residue contacts from both α-helical and β-sheet folds are conserved in a large subpopulation of fold-switching domains, poising them to assume disparate conformations. Our results suggest that fold switching is a pervasive mechanism of transcriptional regulation in all kingdoms of life and indicate that expanding the protein folding paradigm may reveal the involvement of fold-switching proteins in diverse biological processes.

}, issn = {00063495}, doi = {10.1016/j.bpj.2021.11.1945}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0006349521029209}, author = {Porter, Lauren L. and Kim, Allen and Looger, Loren and Majumdar, Ananya K. and Starich, Mary} } @article {68223, title = {Melding Synthetic Molecules and Genetically Encoded Proteins to Forge New Tools for Neuroscience.}, journal = {Annual Review Neuroscience}, volume = {45}, year = {2022}, month = {2022 Jul 08}, pages = {131-150}, abstract = {

Unraveling the complexity of the brain requires sophisticated methods to probe and perturb neurobiological processes with high spatiotemporal control. The field of chemical biology has produced general strategies to combine the molecular specificity of small-molecule tools with the cellular specificity of genetically encoded reagents. Here, we survey the application, refinement, and extension of these hybrid small-molecule:protein methods to problems in neuroscience, which yields powerful reagents to precisely measure and manipulate neural systems.

}, keywords = {Brain, Neurosciences}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-110520-030031}, author = {Kumar, Pratik and Lavis, Luke D} } @article {67929, title = {Melding Synthetic Molecules and Genetically Encoded Proteins to Forge New Tools for Neuroscience.}, journal = {Annual Review of Neuroscience}, year = {2022}, month = {2022 Feb 28}, abstract = {

Unraveling the complexity of the brain requires sophisticated methods to probe and perturb neurobiological processes with high spatiotemporal control. The field of chemical biology has produced general strategies to combine the molecular specificity of small-molecule tools with the cellular specificity of genetically encoded reagents. Here, we survey the application, refinement, and extension of these hybrid small-molecule:protein methods to problems in neuroscience, which yields powerful reagents to precisely measure and manipulate neural systems. Expected final online publication date for the , Volume 45 is July 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-110520-030031}, author = {Kumar, Pratik and Lavis, Luke D} } @article {67947, title = {Melding Synthetic Molecules and Genetically Encoded Proteins to Forge New Tools for Neuroscience.}, journal = {Annual Review Neuroscience}, year = {2022}, month = {2022 Feb 28}, abstract = {

Unraveling the complexity of the brain requires sophisticated methods to probe and perturb neurobiological processes with high spatiotemporal control. The field of chemical biology has produced general strategies to combine the molecular specificity of small-molecule tools with the cellular specificity of genetically encoded reagents. Here, we survey the application, refinement, and extension of these hybrid small-molecule:protein methods to problems in neuroscience, which yields powerful reagents to precisely measure and manipulate neural systems. Expected final online publication date for the , Volume 45 is July 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-110520-030031}, author = {Kumar, Pratik and Lavis, Luke D} } @article {68144, title = {Mesolimbic dopamine adapts the rate of learning from action.}, journal = {bioRxiv}, year = {2022}, month = {2022 May 31}, abstract = {

Recent success in training artificial agents and robots derives from a combination of direct learning of behavioral policies and indirect learning via value functions. Policy learning and value learning employ distinct algorithms that optimize behavioral performance and reward prediction, respectively. In animals, behavioral learning and the role of mesolimbic dopamine signaling have been extensively evaluated with respect to reward prediction; however, to date there has been little consideration of how direct policy learning might inform our understanding. Here we used a comprehensive dataset of orofacial and body movements to understand how behavioral policies evolve as naive, head-restrained mice learned a trace conditioning paradigm. Individual differences in initial dopaminergic reward responses correlated with the emergence of learned behavioral policy, but not the emergence of putative value encoding for a predictive cue. Likewise, physiologically-calibrated manipulations of mesolimbic dopamine produced multiple effects inconsistent with value learning but predicted by a neural network-based model that used dopamine signals to set an adaptive rate, not an error signal, for behavioral policy learning. This work provides strong evidence that phasic dopamine activity can regulate direct learning of behavioral policies, expanding the explanatory power of reinforcement learning models for animal learning.

}, doi = {10.1101/2021.05.31.446464}, url = {https://doi.org/10.1101/2021.05.31.446464}, author = {Luke T. Coddington and Sarah E. Lindo and Joshua T. Dudman} } @article {68472, title = {Microbial models of development: Inspiration for engineering self-assembled synthetic multicellularity.}, journal = {Semin Cell Dev Biol}, year = {2022}, month = {05/2022}, abstract = {

While the field of synthetic developmental biology has traditionally focused on the study of the rich developmental processes seen in metazoan systems, an attractive alternate source of inspiration comes from microbial developmental models. Microbes face unique lifestyle challenges when forming emergent multicellular collectives. As a result, the solutions they employ can inspire the design of novel multicellular systems. In this review, we dissect the strategies employed in multicellular development by two model microbial systems: the cellular slime mold Dictyostelium discoideum and the biofilm-forming bacterium Bacillus subtilis. Both microbes face similar challenges but often have different solutions, both from metazoan systems and from each other, to create emergent multicellularity. These challenges include assembling and sustaining a critical mass of participating individuals to support development, regulating entry into development, and assigning cell fates. The mechanisms these microbial systems exploit to robustly coordinate development under a wide range of conditions offer inspiration for a new toolbox of solutions to the synthetic development community. Additionally, recreating these phenomena synthetically offers a pathway to understanding the key principles underlying how these behaviors are be coordinated naturally.

}, issn = {1096-3634}, doi = {10.1016/j.semcdb.2022.04.014}, author = {Ricci-Tam, Chiara and Kuipa, Sophia and Kostman, Maya Peters and Aronson, Mark S and Sgro, Allyson E} } @article {67951, title = {A midbrain-thalamus-cortex circuit reorganizes cortical dynamics to initiate movement.}, journal = {Cell}, volume = {185}, year = {2022}, month = {2022 Mar 17}, pages = {1065}, abstract = {

Motor behaviors are often planned long before execution but only released after specific sensory events. Planning and execution are each associated with distinct patterns of motor cortex activity. Key questions are how these dynamic activity patterns are generated and how they relate to behavior. Here, we investigate the multi-regional neural circuits that link an auditory "Go cue" and the transition from planning to execution of directional licking. Ascending glutamatergic neurons in the midbrain reticular and pedunculopontine nuclei show short latency and phasic changes in spike rate that are selective for the Go cue. This signal is transmitted via the thalamus to the motor cortex, where it triggers a rapid reorganization of motor cortex state from planning-related activity to a motor command, which in turn drives appropriate movement. Our studies show how midbrain can control cortical dynamics via the thalamus for rapid and precise motor behavior.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2022.02.006}, author = {Inagaki, Hidehiko K and Chen, Susu and Ridder, Margreet C and Sah, Pankaj and Li, Nuo and Yang, Zidan and Hasanbegovic, Hana and Gao, Zhenyu and Gerfen, Charles R and Svoboda, Karel} } @article {68301, title = {Molecular cartography: charting the sea of molecular organization in live synapses with nanoscale precision}, journal = {Biophysical Journal}, volume = {121}, year = {2022}, month = {2022 Feb 01}, pages = {302a}, abstract = {

Understanding live-cell behavior in part requires high precision mapping of molecular species in 3-D dynamic environments. Approaches like single-molecule localization microscopy (SMLM) offer high promise for challenges posed by molecular cartography. Effectively, the precision of these approaches is dependent on the how many photons / second a fluorescent marker is capable of emitting. For this reason, many SRLM experiments are typically done using fluorescent organic dyes (such as Alexa Fluors) in reducing chemical environments which cause some organic dyes to stochastically cycle through dark states, allowing single-molecule localization (e.g. (d)STORM). The need to couple these dyes to antibodies and the harsh reducing conditions makes their application to live cell work problematic. To overcome these limitations, we made use of modifications to Janelia Fluor-based dyes which make them spontaneously cycle through dark states (blink) under physiological imaging conditions. The dyes are spectrally compatible with photo-activatable fluorescent proteins such as mEos and allow for simultaneous 2-color superresolution microscopy. When conjugated to a HaloTag, these artificial dyes can bind genetically encodable targets in live samples, allowing subsequent measurement in a live-cell environment. To correct for nanoscale chromatic aberrations we developed a new machine-learning based approach with reconstruction errors below achievable localization precisions. We show that these methods allow the reconstruction of live synapse surfaces and a variety of the associated molecular machineries with up to 50 nm accuracy in 3 dimensions.

}, issn = {00063495}, doi = {10.1016/j.bpj.2021.11.1246}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0006349521022219}, author = {Nelson, Andrew J. and Zheng, Qinsi and Lavis, Luke D. and Ryan, Timothy A.} } @article {68357, title = {Molecularly defined circuits for cardiovascular and cardiopulmonary control}, journal = {Nature}, volume = {606}, year = {2022}, month = {06/2022}, pages = {739 - 746}, abstract = {

The sympathetic and parasympathetic nervous systems regulate the activities of internal organs1, but the molecular and functional diversity of their constituent neurons and circuits remains largely unknown. Here we use retrograde neuronal tracing, single-cell RNA sequencing, optogenetics and physiological experiments to dissect the cardiac parasympathetic control circuit in mice. We show that cardiac-innervating neurons in the brainstem nucleus ambiguus (Amb) are comprised of two molecularly, anatomically and functionally distinct subtypes. The first, which we call ambiguus cardiovascular (ACV) neurons (approximately 35 neurons per Amb), define the classical cardiac parasympathetic circuit. They selectively innervate a subset of cardiac parasympathetic ganglion neurons and mediate the baroreceptor reflex, slowing heart rate and atrioventricular node conduction in response to increased blood pressure. The other, ambiguus cardiopulmonary (ACP) neurons (approximately 15 neurons per Amb) innervate cardiac ganglion neurons intermingled with and functionally indistinguishable from those innervated by ACV neurons. ACP neurons also innervate most or all lung parasympathetic ganglion neurons{\textemdash}clonal labelling shows that individual ACP neurons innervate both organs. ACP neurons mediate the dive reflex, the simultaneous bradycardia and bronchoconstriction that follows water immersion. Thus, parasympathetic control of the heart is organized into two parallel circuits, one that selectively controls cardiac function (ACV circuit) and another that coordinates cardiac and pulmonary function (ACP circuit). This new understanding of cardiac control has implications for treating cardiac and pulmonary diseases and for elucidating the control and coordination circuits of other organs.

}, issn = {0028-0836}, doi = {10.1038/s41586-022-04760-8}, url = {https://www.nature.com/articles/s41586-022-04760-8}, author = {Veerakumar, Avin and Yung, Andrea R. and Liu, Yin and Krasnow, Mark A.} } @article {68315, title = {Motion of single molecular tethers reveals dynamic subdomains at ER-mitochondria contact sites}, journal = {bioRxiv}, year = {2022}, month = {2022 Sep 03}, abstract = {

To coordinate cellular physiology, eukaryotic cells rely on the inter-organelle transfer of molecules at specialized organelle-organelle contact sites1,2. Endoplasmic reticulum-mitochondria contact sites (ERMCSs) are particularly vital communication hubs, playing key roles in the exchange of signaling molecules, lipids, and metabolites3. ERMCSs are maintained by interactions between complementary tethering molecules on the surface of each organelle4,5. However, due to the extreme sensitivity of these membrane interfaces to experimental perturbation6,7, a clear understanding of their nanoscale structure and regulation is still lacking. Here, we combine 3D electron microscopy with high-speed molecular tracking of a model organelle tether, VAPB, to map the structure and diffusion landscape of ERMCSs. From EM reconstructions, we identified subdomains within the contact site where ER membranes dramatically deform to match local mitochondrial curvature. In parallel live cell experiments, we observed that the VAPB tethers that mediate this interface were not immobile, but rather highly dynamic, entering and leaving the site in seconds. These subdomains enlarged during nutrient stress, indicating ERMCSs can readily remodel under different physiological conditions. An ALS-associated mutation in VAPB altered the normal fluidity of contact sites, likely perturbing effective communication across the contact site and preventing remodeling. These results establish high speed single molecule imaging as a new tool for mapping the structure of contact site interfaces and suggest that the diffusion landscape of VAPB is a crucial component of ERMCS homeostasis.

}, doi = {10.1101/2022.09.03.505525}, url = {https://doi.org/10.1101/2022.09.03.505525}, author = {Christopher J. Obara and Jonathon Nixon-Abell and Andrew S. Moore and Federica Riccio and David P. Hoffman and Gleb Shtengel and C. Shan Xu and Kathy Schaefer and H. Amalia Pasolli and Jean-Baptiste Masson and Harald F. Hess and Christopher P. Calderon and Craig Blackstone and Jennifer Lippincott-Schwartz} } @article {67962, title = {Motor cortical output for skilled forelimb movement is selectively distributed across projection neuron classes.}, journal = {Science Advances}, volume = {8}, year = {2022}, month = {2022 Mar 11}, pages = {eabj5167}, abstract = {

The interaction of descending neocortical outputs and subcortical premotor circuits is critical for shaping skilled movements. Two broad classes of motor cortical output projection neurons provide input to many subcortical motor areas: pyramidal tract (PT) neurons, which project throughout the neuraxis, and intratelencephalic (IT) neurons, which project within the cortex and subcortical striatum. It is unclear whether these classes are functionally in series or whether each class carries distinct components of descending motor control signals. Here, we combine large-scale neural recordings across all layers of motor cortex with cell type-specific perturbations to study cortically dependent mouse motor behaviors: kinematically variable manipulation of a joystick and a kinematically precise reach-to-grasp. We find that striatum-projecting IT neuron activity preferentially represents amplitude, whereas pons-projecting PT neurons preferentially represent the variable direction of forelimb movements. Thus, separable components of descending motor cortical commands are distributed across motor cortical projection cell classes.

}, issn = {2375-2548}, doi = {10.1126/sciadv.abj5167}, author = {Park, Junchol and Phillips, James W and Guo, Jian-Zhong and Martin, Kathleen A and Hantman, Adam W and Dudman, Joshua T} } @article {68194, title = {Multifunctional fluorophores for live-cell imaging and affinity capture of proteins}, journal = {bioRxiv}, year = {2022}, month = {2022 Jul 03}, abstract = {

The development of enzyme-based self-labeling tags allow the labeling of proteins in living cells with synthetic small-molecules. Use of a fluorophore-containing ligand enables the visualization of protein location inside cells using fluorescence microscopy. Alternatively, deployment of a biotin-containing ligand allows purification of tagged protein using affinity resins. Despite these various applications of self-labeling tags, most ligands serve a single purpose. Here, we describe self-labeling tag ligands that allow both visualization and subsequent capture of a protein. A key design principle is exploiting the chemical properties and size of a rhodamine fluorophore to optimize cell-permeability of the ligand and the capture efficiency of the biotin conjugate. This work generates useful {\textquotedblleft}multifunctional{\textquotedblright} fluorophores with generalizable design principles that will allow the construction of new tools for biology.

}, doi = {10.1101/2022.07.02.498544}, url = {https://doi.org/10.1101/2022.07.02.498544}, author = {Kumar, Pratik and Jason D. Vevea and Edwin R. Chapman and Luke D. Lavis} } @article {68413, title = {Muscles that move the retina augment compound eye vision in Drosophila.}, journal = {Nature}, year = {2022}, month = {2022 Oct 26}, abstract = {

Most animals have compound eyes, with tens to thousands of lenses attached rigidly to the exoskeleton. A natural assumption is that all of these species must resort to moving either their head or\ their body to actively change their visual input. However, classic anatomy has revealed that flies have muscles poised to move their retinas under the stable lenses of each compound eye. Here we show that Drosophila use their retinal muscles to smoothly track visual motion, which helps to stabilize the retinal image, and also to perform small saccades when viewing a stationary scene. We show that when the retina moves, visual receptive fields shift accordingly, and that even the smallest retinal saccades activate visual neurons. Using a head-fixed behavioural paradigm, we find that Drosophila perform binocular, vergence movements of their retinas-which could enhance depth perception-when crossing gaps, and impairing the physiology of retinal motor neurons alters gap-crossing trajectories during free behaviour. That flies evolved an ability to actuate their retinas suggests that moving the eye independently of the head is broadly paramount for animals. The similarities of smooth and saccadic movements of the Drosophila retina and the vertebrate eye highlight a notable example of convergent evolution.

}, issn = {1476-4687}, doi = {10.1038/s41586-022-05317-5}, author = {Fenk, Lisa M and Avritzer, Sofia C and Weisman, Jazz L and Nair, Aditya and Randt, Lucas D and Mohren, Thomas L and Siwanowicz, Igor and Maimon, Gaby} } @article {67963, title = {Myosin VI regulates the spatial organisation of mammalian transcription initiation.}, journal = {Nature Communications}, volume = {13}, year = {2022}, month = {2022 Mar 15}, pages = {1346}, abstract = {

During transcription, RNA Polymerase II (RNAPII) is spatially organised within the nucleus into clusters that correlate with transcription activity. While this is a hallmark of genome regulation in mammalian cells, the mechanisms concerning the assembly, organisation and stability remain unknown. Here, we have used combination of single molecule imaging and genomic approaches to explore the role of nuclear myosin VI (MVI) in the nanoscale organisation of RNAPII. We reveal that MVI in the nucleus acts as the molecular anchor that holds RNAPII in high density clusters. Perturbation of MVI leads to the disruption of RNAPII localisation, chromatin organisation and subsequently a decrease in gene expression. Overall, we uncover the fundamental role of MVI in the spatial regulation of gene expression.

}, issn = {2041-1723}, doi = {10.1038/s41467-022-28962-w}, author = {Hari-Gupta, Yukti and Fili, Natalia and Dos Santos, {\'A}lia and Cook, Alexander W and Gough, Rosemarie E and Reed, Hannah C W and Wang, Lin and Aaron, Jesse and Venit, Tomas and Wait, Eric and Grosse-Berkenbusch, Andreas and Gebhardt, J Christof M and Percipalle, Piergiorgio and Chew, Teng-Leong and Martin-Fernandez, Marisa and Toseland, Christopher P} } @article {67993, title = {A natural timeless polymorphism allowing circadian clock synchronization in "white nights".}, journal = {Nature Communications}, volume = {13}, year = {2022}, month = {2022 Mar 31}, pages = {1724}, abstract = {

Daily temporal organisation offers a fitness advantage and is determined by an interplay between environmental rhythms and circadian clocks. While light:dark cycles robustly synchronise circadian clocks, it is not clear how animals experiencing only weak environmental cues deal with this problem. Like humans, Drosophila originate in sub-Saharan Africa and spread North up to the polar circle, experiencing long summer days or even constant light (LL). LL disrupts clock function, due to constant activation of CRYPTOCHROME, which induces degradation of the clock protein TIMELESS (TIM), but temperature cycles are able to overcome these deleterious effects of LL. We show here that for this to occur a recently evolved natural timeless allele (ls-tim) is required, encoding the less light-sensitive L-TIM in addition to S-TIM, the only form encoded by the ancient s-tim allele. We show that only ls-tim flies can synchronise their behaviour to semi-natural conditions typical for Northern European summers, suggesting that this functional gain is driving the Northward ls-tim spread.

}, keywords = {Animals, Circadian Clocks, Circadian Rhythm, Drosophila, Drosophila Proteins, Light}, issn = {2041-1723}, doi = {10.1038/s41467-022-29293-6}, author = {Lamaze, Angelique and Chen, Chenghao and Leleux, Solene and Xu, Min and George, Rebekah and Stanewsky, Ralf} } @article {68272, title = {neuPrint: An open access tool for EM connectomics.}, journal = {Frontiers in Neuroinformatics}, volume = {16}, year = {2022}, month = {2022 Jul 20}, pages = {896292}, abstract = {

Due to advances in electron microscopy and deep learning, it is now practical to reconstruct a connectome, a description of neurons and the chemical synapses between them, for significant volumes of neural tissue. Smaller past reconstructions were primarily used by domain experts, could be handled by downloading data, and performance was not a serious problem. But new and much larger reconstructions upend these assumptions. These networks now contain tens of thousands of neurons and tens of millions of connections, with yet larger reconstructions pending, and are of interest to a large community of non-specialists. Allowing other scientists to make use of this data needs more than publication-it requires new tools that are publicly available, easy to use, and efficiently handle large data. We introduce neuPrint to address these data analysis challenges. Neuprint contains two major components-a web interface and programmer APIs. The web interface is designed to allow any scientist worldwide, using only a browser, to quickly ask and answer typical biological queries about a connectome. The neuPrint APIs allow more computer-savvy scientists to make more complex or higher volume queries. NeuPrint also provides features for assessing reconstruction quality. Internally, neuPrint organizes connectome data as a graph stored in a neo4j database. This gives high performance for typical queries, provides access though a public and well documented query language Cypher, and will extend well to future larger connectomics databases. Our experience is also an experiment in open science. We find a significant fraction of the readers of the article proceed to examine the data directly. In our case preprints worked exactly as intended, with data inquiries and PDF downloads starting immediately after pre-print publication, and little affected by formal publication later. From this we deduce that many readers are more interested in our data than in our analysis of our data, suggesting that data-only papers can be well appreciated and that public data release can speed up the propagation of scientific results by many months. We also find that providing, and keeping, the data available for online access imposes substantial additional costs to connectomics research.

}, issn = {1662-5196}, doi = {10.3389/fninf.2022.896292}, author = {Plaza, Stephen M and Clements, Jody and Dolafi, Tom and Umayam, Lowell and Neubarth, Nicole N and Scheffer, Louis K and Berg, Stuart} } @article {67965, title = {Neural Algorithms and Circuits for Motor Planning.}, journal = {Annual Reviews Neuroscience}, year = {2022}, month = {2022 Feb 22}, abstract = {

The brain plans and executes volitional movements. The underlying patterns of neural population activity have been explored in the context of movements of the eyes, limbs, tongue, and head in nonhuman primates and rodents. How do networks of neurons produce the slow neural dynamics that prepare specific movements and the fast dynamics that ultimately initiate these movements? Recent work exploits rapid and calibrated perturbations of neural activity to test specific dynamical systems models that are capable of producing the observed neural activity. These joint experimental and computational studies show that cortical dynamics during motor planning reflect fixed points of neural activity (attractors). Subcortical control signals reshape and move attractors over multiple timescales, causing commitment to specific actions and rapid transitions to movement execution. Experiments in rodents are beginning to reveal how these algorithms are implemented at the level of brain-wide neural circuits. Expected final online publication date for the , Volume 45 is July 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-092021-121730}, author = {Inagaki, Hidehiko K and Chen, Susu and Daie, Kayvon and Finklestein, Arseny and Fontolan, Lorenzo and Romani, Sandro and Svoboda, Karel} } @article {68224, title = {Neural Algorithms and Circuits for Motor Planning.}, journal = {Annual Review Neuroscience}, volume = {45}, year = {2022}, month = {2022 Jul 08}, pages = {249-271}, abstract = {

The brain plans and executes volitional movements. The underlying patterns of neural population activity have been explored in the context of movements of the eyes, limbs, tongue, and head in nonhuman primates and rodents. How do networks of neurons produce the slow neural dynamics that prepare specific movements and the fast dynamics that ultimately initiate these movements? Recent work exploits rapid and calibrated perturbations of neural activity to test specific dynamical systems models that are capable of producing the observed neural activity. These joint experimental and computational studies show that cortical dynamics during motor planning reflect fixed points of neural activity (attractors). Subcortical control signals reshape and move attractors over multiple timescales, causing commitment to specific actions and rapid transitions to movement execution. Experiments in rodents are beginning to reveal how these algorithms are implemented at the level of brain-wide neural circuits.

}, keywords = {Algorithms, Animals, Brain, Motor Cortex, Movement, Neurons}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-092021-121730}, author = {Inagaki, Hidehiko K and Chen, Susu and Daie, Kayvon and Finkelstein, Arseny and Fontolan, Lorenzo and Romani, Sandro and Svoboda, Karel} } @article {67895, title = {A neural circuit linking learning and sleep in Drosophila long-term memory.}, journal = {Nature Communications}, volume = {13}, year = {2022}, month = {2022 Feb 01}, pages = {609}, abstract = {

Animals retain some but not all experiences in long-term memory (LTM). Sleep supports LTM retention across animal species. It is well established that learning experiences enhance post-learning sleep. However, the underlying mechanisms of how learning mediates sleep for memory retention are not clear. Drosophila males display increased amounts of sleep after courtship learning. Courtship learning depends on Mushroom Body (MB) neurons, and post-learning sleep is mediated by the sleep-promoting ventral Fan-Shaped Body neurons (vFBs). We show that post-learning sleep is regulated by two opposing output neurons\ (MBONs) from the MB, which encode a measure of learning. Excitatory MBONs-γ2α{\textquoteright}1 becomes increasingly active upon increasing time of learning, whereas inhibitory MBONs-β{\textquoteright}2mp is activated only by a short learning experience. These MB outputs are integrated by SFS neurons, which excite vFBs to promote sleep after prolonged but not short training. This circuit may ensure that only longer or more intense learning experiences induce sleep and are thereby consolidated into LTM.

}, issn = {2041-1723}, doi = {10.1038/s41467-022-28256-1}, author = {Lei, Zhengchang and Henderson, Kristin and Keleman, Krystyna} } @article {68148, title = {Neural circuit pathology driven by Shank3 mutation disrupts social behaviors.}, journal = {Cell Reports}, volume = {39}, year = {2022}, month = {2022 Jun 07}, pages = {110906}, abstract = {

Dysfunctional sociability is a core symptom in autism spectrum disorder (ASD) that may arise from neural-network dysconnectivity between multiple brain regions. However, pathogenic neural-network mechanisms underlying social dysfunction are largely unknown. Here, we demonstrate that circuit-selective mutation (ctMUT) of ASD-risk Shank3 gene within a unidirectional projection from the prefrontal cortex to the basolateral amygdala alters spine morphology and excitatory-inhibitory balance of the circuit. Shank3 ctMUT mice show reduced sociability as well as elevated neural activity and its amplitude variability, which is consistent with the neuroimaging results from human ASD patients. Moreover, the circuit hyper-activity disrupts the temporal correlation of socially tuned neurons to the events of social interactions. Finally, optogenetic circuit activation in wild-type mice partially recapitulates the reduced sociability of Shank3 ctMUT mice, while circuit inhibition in Shank3 ctMUT mice partially rescues social behavior. Collectively, these results highlight a circuit-level pathogenic mechanism of Shank3 mutation that drives social dysfunction.

}, keywords = {Animals, Autism Spectrum Disorder, Disease Models, Animal, Humans, Mice, Microfilament Proteins, Mutation, Nerve Tissue Proteins, Optogenetics, Prefrontal Cortex, Social Behavior}, issn = {2211-1247}, doi = {10.1016/j.celrep.2022.110906}, author = {Kim, Sunwhi and Kim, Yong-Eun and Song, Inuk and Ujihara, Yusuke and Kim, Namsoo and Jiang, Yong-Hui and Yin, Henry H and Lee, Tae-Ho and Kim, Il Hwan} } @article {68569, title = {Neural coding of distinct motor patterns during Drosophila courtship song}, journal = {bioRxiv}, year = {2022}, month = {2022 Dec 15}, abstract = {

Animals flexibly switch between different actions by changing neural activity patterns for motor control. Courting\ Drosophila melanogaster\ males produce two different acoustic signals, pulse and sine song, each of which can be promoted by artificial activation of distinct neurons. However, how the activity of these neurons implements flexible song production is unknown. Here, we developed an assay to record neuronal calcium signals in the ventral nerve cord, which contains the song motor circuit, in singing flies. We found that sine-promoting neurons, but not pulse-promoting neurons, show strong activation during sine song. In contrast, both pulse- and sine-promoting neurons are active during pulse song. Furthermore, population calcium imaging in the song circuit suggests that sine song involves activation of a subset of neurons that are also active during pulse song. Thus, differential activation of overlapping, rather than distinct, neural populations underlies flexible motor actions during acoustic communication in\ D. melanogaster.

}, doi = {10.1101/2022.12.14.520499}, url = {https://doi.org/10.1101/2022.12.14.520499}, author = {Hiroshi M. Shiozaki and Kaiyu Wang and Joshua L. Lillvis and Min Xu and Barry J. Dickson and David L. Stern} } @article {68273, title = {Neural network organization for courtship-song feature detection in Drosophila.}, journal = {Current Biology}, volume = {32}, year = {2022}, month = {2022 Aug 08}, pages = {3317-3333.e7}, abstract = {

Animals communicate using sounds in a wide range of contexts, and auditory systems must encode behaviorally relevant acoustic features to drive appropriate reactions. How feature detection emerges along auditory pathways has been difficult to solve due to challenges in mapping the underlying circuits and characterizing responses to behaviorally relevant features. Here, we study auditory activity in the Drosophila melanogaster brain and investigate feature selectivity for the two main modes of fly courtship song, sinusoids and pulse trains. We identify 24 new cell types of the intermediate layers of the auditory pathway, and using a new connectomic resource, FlyWire, we map all synaptic connections between these cell types, in addition to connections to known early and higher-order auditory neurons-this represents the first circuit-level map of the auditory pathway. We additionally determine the sign (excitatory or inhibitory) of most synapses in this auditory connectome. We find that auditory neurons display a continuum of preferences for courtship song modes and that neurons with different song-mode preferences and response timescales are highly interconnected in a network that lacks hierarchical structure. Nonetheless, we find that the response properties of individual cell types within the connectome are predictable from their inputs. Our study thus provides new insights into the organization of auditory coding within the Drosophila brain.

}, keywords = {Animals, Auditory Perception, Courtship, Drosophila, Drosophila melanogaster, Neural Networks, Computer, Sexual Behavior, Animal, Vocalization, Animal}, issn = {1879-0445}, doi = {10.1016/j.cub.2022.06.019}, author = {Baker, Christa A and McKellar, Claire and Pang, Rich and Nern, Aljoscha and Dorkenwald, Sven and Pacheco, Diego A and Eckstein, Nils and Funke, Jan and Dickson, Barry J and Murthy, Mala} } @article {68379, title = {The Neurodata Without Borders ecosystem for neurophysiological data science.}, journal = {eLife}, volume = {11}, year = {2022}, month = {2022 Oct 04}, abstract = {

The neurophysiology of cells and tissues are monitored electrophysiologically and optically in diverse experiments and species, ranging from flies to humans. Understanding the brain requires integration of data across this diversity, and thus these data must be findable, accessible, interoperable, and reusable (FAIR). This requires a standard language for data and metadata that can coevolve with neuroscience. We describe design and implementation principles for a language for neurophysiology data. Our open-source software (Neurodata Without Borders, NWB) defines and modularizes the interdependent, yet separable, components of a data language. We demonstrate NWB{\textquoteright}s impact through unified description of neurophysiology data across diverse modalities and species. NWB exists in an ecosystem, which includes data management, analysis, visualization, and archive tools. Thus, the NWB data language enables reproduction, interchange, and reuse of diverse neurophysiology data. More broadly, the design principles of NWB are generally applicable to enhance discovery across biology through data FAIRness.

}, keywords = {Data Science, Ecosystem, Humans, Metadata, Neurophysiology, Software}, issn = {2050-084X}, doi = {10.7554/eLife.78362}, author = {Rubel, Oliver and Tritt, Andrew and Ly, Ryan and Dichter, Benjamin K and Ghosh, Satrajit and Niu, Lawrence and Baker, Pamela and Soltesz, Ivan and Ng, Lydia and Svoboda, Karel and Frank, Loren and Bouchard, Kristofer E} } @article {67949, title = {Neuromuscular embodiment of feedback control elements in Drosophila flight}, journal = {bioRxiv}, year = {2022}, month = {2022 Mar 07}, abstract = {

While insects like\ Drosophila\ are flying, aerodynamic instabilities require that they make millisecond-timescale adjustments to their wing motion to stay aloft and on course. These stabilization reflexes can be modeled as a proportional-integral (PI) controller; however, it is unclear how such control might be instantiated in insects at the level of muscles and neurons. Here, we show that the b1 and b2 motor units{\textemdash}prominent components of the fly{\textquoteright}s steering muscles system{\textemdash}modulate specific elements of the PI controller: the angular displacement (integral, I) and angular velocity (proportional, P), respectively. Moreover, these effects are observed only during the stabilization of pitch. Our results provide evidence for an organizational principle in which each muscle contributes to a specific functional role in flight control, a finding that highlights the power of using top-down behavioral modeling to guide bottom-up cellular manipulation studies.

}, doi = {10.1101/2022.02.22.481344}, url = {https://doi.org/10.1101/2022.02.22.481344}, author = {Samuel C. Whitehead and Sofia Leone and Theodore Lindsay and Matthew Meiselman and Noah Cowan and Michael Dickinson and Nilay Yapici and David Stern and Troy Shirangi and Itai Cohen} } @article {67914, title = {Neuromuscular embodiment of feedback control elements in Drosophila flight.}, journal = {bioRxiv}, year = {2022}, month = {2022 Feb 24}, abstract = {

While insects like\ Drosophila\ are flying, aerodynamic instabilities require that they make millisecond-timescale adjustments to their wing motion to stay aloft and on course. These stabilization reflexes can be modeled as a proportional-integral (PI) controller; however, it is unclear how such control might be instantiated in insects at the level of muscles and neurons. Here, we show that the b1 and b2 motor units{\textemdash}prominent components of the fly{\textquoteright}s steering muscles system{\textemdash}modulate specific elements of the PI controller: the angular displacement (integral, I) and angular velocity (proportional, P), respectively. Moreover, these effects are observed only during the stabilization of pitch. Our results provide evidence for an organizational principle in which each muscle contributes to a specific functional role in flight control, a finding that highlights the power of using top-down behavioral modeling to guide bottom-up cellular manipulation studies.

}, doi = {10.1101/2022.02.22.481344}, author = {Samuel C Whitehead and Sofia Leone and Theodore Lindsay and Matthew R Meiselman and Noah Cowan and Michael H Dickinson and Nilay Yapici and David Stern and Troy Shirangi and Itai Cohen} } @article {68557, title = {Neuromuscular embodiment of feedback control elements in flight.}, journal = {Science Advances}, volume = {8}, year = {2022}, month = {2022 Dec 14}, pages = {eabo7461}, abstract = {

While insects such as are flying, aerodynamic instabilities require that they make millisecond time scale adjustments to their wing motion to stay aloft and on course. These stabilization reflexes can be modeled as a proportional-integral (PI) controller; however, it is unclear how such control might be instantiated in insects at the level of muscles and neurons. Here, we show that the b1 and b2 motor units-prominent components of the fly{\textquoteright}s steering muscle system-modulate specific elements of the PI controller: the angular displacement (integral) and angular velocity (proportional), respectively. Moreover, these effects are observed only during the stabilization of pitch. Our results provide evidence for an organizational principle in which each muscle contributes to a specific functional role in flight control, a finding that highlights the power of using top-down behavioral modeling to guide bottom-up cellular manipulation studies.

}, issn = {2375-2548}, doi = {10.1126/sciadv.abo7461}, author = {Whitehead, Samuel C and Leone, Sofia and Lindsay, Theodore and Meiselman, Matthew R and Cowan, Noah J and Dickinson, Michael H and Yapici, Nilay and Stern, David L and Shirangi, Troy and Cohen, Itai} } @article {68501, title = {Neuronal cell types, projections, and spatial organization of the central amygdala}, journal = {iScience}, volume = {25}, year = {2022}, month = {2022 Dec 22}, pages = {105497}, abstract = {

The central amygdala (CEA) has been richly studied for interpreting function and behavior according to specific cell types and circuits. Such work has typically defined molecular cell types by classical inhibitory marker genes; consequently, whether marker-gene-defined cell types exhaustively cover the CEA and co-vary with connectivity remains unresolved. Here, we combined single-cell RNA sequencing, multiplexed fluorescent\ in situ\ hybridization, immunohistochemistry, and long-range projection mapping to derive a {\textquotedblleft}bottom-up{\textquotedblright} understanding of CEA cell types. In doing so, we identify two major cell types, encompassing one-third of all CEA neurons, that have gone unresolved in previous studies. In spatially mapping these novel types, we identify a non-canonical CEA subdomain associated with\ Nr2f2\ expression and uncover an\ Isl1-expressing medial cell type that accounts for many long-range CEA projections. Our results reveal new CEA organizational principles across cell types and spatial scales and provide a framework for future work examining cell-type-specific behavior and function.

}, issn = {25890042}, doi = {10.1016/j.isci.2022.105497}, url = {https://linkinghub.elsevier.com/retrieve/pii/S2589004222017692}, author = {O{\textquoteright}Leary, Timothy P. and Kendrick, Rennie M. and Bristow, Brianna N. and Sullivan, Kaitlin E. and Wang, Lihua and Clements, Jody and Lemire, Andrew L. and Cembrowski, Mark S.} } @article {68225, title = {Neuronal circuits integrating visual motion information in Drosophila melanogaster.}, journal = {Current Biology}, volume = {32}, year = {2022}, month = {2022 Aug 22}, pages = {3529-3544}, abstract = {

The detection of visual motion enables sophisticated animal navigation, and studies on flies have provided profound insights into the cellular and circuit bases of this neural computation. The fly{\textquoteright}s directionally selective T4 and T5 neurons encode ON and OFF motion, respectively. Their axons terminate in one of the four retinotopic layers in the lobula plate, where each layer encodes one of the four directions of motion. Although the input circuitry of the directionally selective neurons has been studied in detail, the synaptic connectivity of circuits integrating T4/T5 motion signals is largely unknown. Here, we report a 3D electron microscopy reconstruction, wherein we comprehensively identified T4/T5{\textquoteright}s synaptic partners in the lobula plate, revealing a diverse set of new cell types and attributing new connectivity patterns to the known cell types. Our reconstruction explains how the ON- and OFF-motion pathways converge. T4 and T5 cells that project to the same layer connect to common synaptic partners and comprise a core motif together with bilayer interneurons, detailing the circuit basis for computing motion opponency. We discovered pathways that likely encode new directions of motion by integrating vertical and horizontal motion signals from upstream T4/T5 neurons. Finally, we identify substantial projections into the lobula, extending the known motion pathways and suggesting that directionally selective signals shape feature detection there. The circuits we describe enrich the anatomical basis for experimental and computations analyses of motion vision and bring us closer to understanding complete sensory-motor pathways.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2022.06.061}, author = {Shinomiya, Kazunori and Nern, Aljoscha and Meinertzhagen, Ian A and Plaza, Stephen M and Reiser, Michael B} } @article {67801, title = {A neuropeptidergic circuit gates selective escape behavior of Drosophila larvae.}, journal = {Current Biology}, volume = {32}, year = {2022}, month = {2022 Jan 10}, pages = {149-63}, abstract = {

Animals display selective escape behaviors when faced with environmental threats. Selection of the appropriate response by the underlying neuronal network is key to maximizing chances of survival, yet the underlying network mechanisms are so far not fully understood. Using synapse-level reconstruction of the Drosophila larval network paired with physiological and behavioral readouts, we uncovered a circuit that gates selective escape behavior for noxious light through acute and input-specific neuropeptide action. Sensory neurons required for avoidance of noxious light and escape in response to harsh touch, each converge on discrete domains of neuromodulatory hub neurons. We show that acute release of hub neuron-derived insulin-like peptide 7 (Ilp7) and cognate relaxin family receptor (Lgr4) signaling in downstream neurons are required for noxious light avoidance, but not harsh touch responses. Our work highlights a role for compartmentalized circuit organization and neuropeptide release from regulatory hubs, acting as central circuit elements gating escape responses.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2021.10.069}, author = {Imambocus, Bibi Nusreen and Zhou, Fangmin and Formozov, Andrey and Wittich, Annika and Tenedini, Federico M and Hu, Chun and Sauter, Kathrin and Macarenhas Varela, Ednilson and Her{\'e}dia, Fabiana and Casimiro, Andreia P and Macedo, Andr{\'e} and Schlegel, Philipp and Yang, Chung-Hui and Miguel-Aliaga, Irene and Wiegert, J Simon and Pankratz, Michael J and Gontijo, Alisson M and Cardona, Albert and Soba, Peter} } @article {68253, title = {Not so spontaneous: Multi-dimensional representations of behaviors and context in sensory areas.}, journal = {Neuron}, volume = {110}, year = {2022}, month = {2022 Oct 05}, pages = {3064}, abstract = {

Sensory areas are spontaneously active in the absence of sensory stimuli. This spontaneous activity has long been studied; however, its functional role remains largely unknown. Recent advances in technology, allowing large-scale neural recordings in the awake and behaving animal, have transformed our understanding of spontaneous activity. Studies using these recordings have discovered high-dimensional spontaneous activity patterns, correlation between spontaneous activity and behavior, and dissimilarity between spontaneous and sensory-driven activity patterns. These findings are supported by evidence from developing animals, where a transition toward these characteristics is observed as the circuit matures, as well as by evidence from mature animals across species. These newly revealed characteristics call for the formulation of a new role for spontaneous activity in neural sensory computation.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2022.06.019}, author = {Avitan, Lilach and Stringer, Carsen} } @article {68012, title = {Nuclear lamin isoforms differentially contribute to LINC complex-dependent nucleocytoskeletal coupling and whole-cell mechanics.}, journal = {Proceedings of the National Academy of Sciences of the U.S.A.}, volume = {119}, year = {2022}, month = {2022 Apr 19}, pages = {e2121816119}, abstract = {

SignificanceInteractions between the cell nucleus and cytoskeleton regulate cell mechanics and are facilitated by the interplay between the nuclear lamina and linker of nucleoskeleton and cytoskeleton (LINC) complexes. To date, the specific contribution of the four lamin isoforms to nucleocytoskeletal connectivity and whole-cell mechanics remains unknown. We discover that A- and B-type lamins distinctively interact with LINC complexes that bind F-actin and vimentin filaments to differentially modulate cortical stiffness, cytoplasmic stiffness, and contractility of mouse embryonic fibroblasts (MEFs). We propose and experimentally verify an integrated lamin-LINC complex-cytoskeleton model that explains cellular mechanical phenotypes in lamin-deficient MEFs. Our findings uncover potential mechanisms for cellular defects in human laminopathies and many cancers associated with mutations or modifications in lamin isoforms.

}, keywords = {Animals, Cell Nucleus, Cytoskeleton, Fibroblasts, Lamin Type A, Lamin Type B, Mice, Nuclear Lamina, Nuclear Matrix, Protein Isoforms}, issn = {1091-6490}, doi = {10.1073/pnas.2121816119}, author = {Vahabikashi, Amir and Sivagurunathan, Suganya and Nicdao, Fiona Ann Sadsad and Han, Yu Long and Park, Chan Young and Kittisopikul, Mark and Wong, Xianrong and Tran, Joseph R and Gundersen, Gregg G and Reddy, Karen L and Luxton, G W Gant and Guo, Ming and Fredberg, Jeffrey J and Zheng, Yixian and Adam, Stephen A and Goldman, Robert D} } @article {68512, title = {Oligodendrocyte precursor cells ingest axons in the mouse neocortex.}, journal = {Proceedings of the National Academies of Science of the U.S.A.}, volume = {119}, year = {2022}, month = {2022 Nov 29}, pages = {e2202580119}, abstract = {

Neurons in the developing brain undergo extensive structural refinement as nascent circuits adopt their mature form. This physical transformation of neurons is facilitated by the engulfment and degradation of axonal branches and synapses by surrounding glial cells, including microglia and astrocytes. However, the small size of phagocytic organelles and the complex, highly ramified morphology of glia have made it difficult to define the contribution of these and other glial cell types to this crucial process. Here, we used large-scale, serial section transmission\ electron microscopy (TEM) with computational volume segmentation to reconstruct the complete 3D morphologies of distinct glial types in the mouse visual cortex, providing unprecedented resolution of their morphology and composition. Unexpectedly, we discovered that the fine processes of oligodendrocyte precursor cells (OPCs), a population of abundant, highly dynamic glial progenitors, frequently surrounded small branches of axons. Numerous phagosomes and phagolysosomes (PLs) containing fragments of axons and vesicular structures were present inside their processes, suggesting that OPCs engage in axon pruning. Single-nucleus RNA sequencing from the developing mouse cortex revealed that OPCs express key phagocytic genes at this stage, as well as neuronal transcripts, consistent with active axon engulfment. Although microglia are thought to be responsible for the majority of synaptic pruning and structural refinement, PLs were ten times more abundant in OPCs than in microglia at this stage, and these structures were markedly less abundant in newly generated oligodendrocytes, suggesting that OPCs contribute substantially to the refinement of neuronal circuits during cortical development.

}, keywords = {Animals, Axons, Mice, Neocortex, Neurons, Oligodendrocyte Precursor Cells, Oligodendroglia}, issn = {1091-6490}, doi = {10.1073/pnas.2202580119}, author = {Buchanan, JoAnn and Elabbady, Leila and Collman, Forrest and Jorstad, Nikolas L and Bakken, Trygve E and Ott, Carolyn and Glatzer, Jenna and Bleckert, Adam A and Bodor, Agnes L and Brittain, Derrick and Bumbarger, Daniel J and Mahalingam, Gayathri and Seshamani, Sharmishtaa and Schneider-Mizell, Casey and Takeno, Marc M and Torres, Russel and Yin, Wenjing and Hodge, Rebecca D and Castro, Manuel and Dorkenwald, Sven and Ih, Dodam and Jordan, Chris S and Kemnitz, Nico and Lee, Kisuk and Lu, Ran and Macrina, Thomas and Mu, Shang and Popovych, Sergiy and Silversmith, William M and Tartavull, Ignacio and Turner, Nicholas L and Wilson, Alyssa M and Wong, William and Wu, Jingpeng and Zlateski, Aleksandar and Zung, Jonathan and Lippincott-Schwartz, Jennifer and Lein, Ed S and Seung, H Sebastian and Bergles, Dwight E and Reid, R Clay and da Costa, Nuno Ma{\c c}arico} } @article {68410, title = {Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation.}, journal = {Nature Methods}, year = {2022}, month = {2022 Oct 17}, abstract = {

Advances in microscopy hold great promise for allowing quantitative and precise measurement of morphological and molecular phenomena at the single-cell level in bacteria; however, the potential of this approach is ultimately limited by the availability of methods to faithfully segment cells independent of their morphological or optical characteristics. Here, we present Omnipose, a deep neural network image-segmentation algorithm. Unique network outputs such as the gradient of the distance field allow Omnipose to accurately segment cells on which current algorithms, including its predecessor, Cellpose, produce errors. We show that Omnipose achieves unprecedented segmentation performance on mixed bacterial cultures, antibiotic-treated cells and cells of elongated or branched morphology. Furthermore, the benefits of Omnipose extend to non-bacterial subjects, varied imaging modalities and three-dimensional objects. Finally, we demonstrate the utility of Omnipose in the characterization of extreme morphological phenotypes that arise during interbacterial antagonism. Our results distinguish Omnipose as a powerful tool for characterizing diverse and arbitrarily shaped cell types from imaging data.

}, issn = {1548-7105}, doi = {10.1038/s41592-022-01639-4}, author = {Cutler, Kevin J and Stringer, Carsen and Lo, Teresa W and Rappez, Luca and Stroustrup, Nicholas and Brook Peterson, S and Wiggins, Paul A and Mougous, Joseph D} } @article {68254, title = {Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation}, journal = {bioRxiv}, year = {2022}, month = {2022 Jul 27}, abstract = {

Advances in microscopy hold great promise for allowing quantitative and precise readouts of morphological and molecular phenomena at the single cell level in bacteria. However, the potential of this approach is ultimately limited by the availability of methods to perform unbiased cell segmentation, defined as the ability to faithfully identify cells independent of their morphology or optical characteristics. In this study, we present a new algorithm, Omnipose, which accurately segments samples that present significant challenges to current algorithms, including mixed bacterial cultures, antibiotic-treated cells, and cells of extended or branched morphology. We show that Omnipose achieves generality and performance beyond leading algorithms and its predecessor, Cellpose, by virtue of unique neural network outputs such as the gradient of the distance field. Finally, we demonstrate the utility of Omnipose in the characterization of extreme morphological phenotypes that arise during interbacterial antagonism and on the segmentation of non-bacterial objects. Our results distinguish Omnipose as a uniquely powerful tool for answering diverse questions in bacterial cell biology.

}, doi = {10.1101/2021.11.03.467199}, url = {https://doi.org/10.1101/2021.11.03.467199}, author = {Kevin J. Cutler and Carsen Stringer and Paul A. Wiggins and Joseph D. Mougous} } @article {68113, title = {One engram two readouts: stimulus dynamics switch a learned behavior in Drosophila}, journal = {bioRxiv}, year = {2022}, month = {2022 May 26}, abstract = {

Memory guides the choices an animal makes across widely varying conditions in dynamic environments. Consequently, the most adaptive choice depends on the options available. How can a single memory support optimal behavior across different sets of choice options? We address this using olfactory learning in Drosophila. Even when we restrict an odor-punishment association to a single set of synapses using optogenetics, we find that flies still show choice behavior that depends on the options it encounters. Here we show that how the odor choices are presented to the animal influences memory recall itself. Presenting two similar odors in sequence enabled flies to not only discriminate them behaviorally but also at the level of neural activity. However, when the same odors were encountered as solitary stimuli, no such differences were detectable. These results show that memory recall is not simply a comparison to a static learned template, but can be adaptively modulated by stimulus dynamics.

}, doi = {10.1101/2022.05.24.492551}, url = {https://doi.org/10.1101/2022.05.24.492551}, author = {Mehrab N Modi and Adithya Rajagopalan and Herv{\'e} Rouault and Yoshinori Aso and Glenn C Turner} } @article {67930, title = {Online learning for orientation estimation during translation in an insect ring attractor network.}, journal = {Scientific Reports}, volume = {12}, year = {2022}, month = {2022 Feb 25}, pages = {3210}, abstract = {

Insect neural systems are a promising source of inspiration for new navigation algorithms, especially on low size, weight, and power platforms. There have been unprecedented recent neuroscience breakthroughs with Drosophila in behavioral and neural imaging experiments as well as the mapping of detailed connectivity of neural structures. General mechanisms for learning orientation in the central complex (CX) of Drosophila have been investigated previously; however, it is unclear how these underlying mechanisms extend to cases where there is translation through an environment (beyond only rotation), which is critical for navigation in robotic systems. Here, we develop a CX neural connectivity-constrained model that performs sensor fusion, as well as unsupervised learning of visual features for path integration; we demonstrate the viability of this circuit for use in robotic systems in simulated and physical environments. Furthermore, we propose a theoretical understanding of how distributed online unsupervised network weight modification can be leveraged for learning in a trajectory through an environment by minimizing orientation estimation error. Overall, our results may enable a new class of CX-derived low power robotic navigation algorithms and lead to testable predictions to inform future neuroscience experiments.

}, issn = {2045-2322}, doi = {10.1038/s41598-022-05798-4}, author = {Robinson, Brian S and Norman-Tenazas, Raphael and Cervantes, Martha and Symonette, Danilo and Johnson, Erik C and Joyce, Justin and Rivlin, Patricia K and Hwang, Grace and Zhang, Kechen and Gray-Roncal, William} } @article {67873, title = {Open-source, Python-based, hardware and software for controlling behavioural neuroscience experiments.}, journal = {eLife}, volume = {11}, year = {2022}, month = {2022 Jan 19}, abstract = {

Laboratory behavioural tasks are an essential research tool. As questions asked of behaviour and brain activity become more sophisticated, the ability to specify and run richly structured tasks becomes more important. An increasing focus on reproducibility also necessitates accurate communication of task logic to other researchers. To these ends, we developed pyControl, a system of open-source hardware and software for controlling behavioural experiments comprising a simple yet flexible Python-based syntax for specifying tasks as extended state machines, hardware modules for building behavioural setups, and a graphical user interface designed for efficiently running high-throughput experiments on many setups in parallel, all with extensive online documentation. These tools make it quicker, easier, and cheaper to implement rich behavioural tasks at scale. As important, pyControl facilitates communication and reproducibility of behavioural experiments through a highly readable task definition syntax and self-documenting features. Here, we outline the system{\textquoteright}s design and rationale, present validation experiments characterising system performance, and demonstrate example applications in freely moving and head-fixed mouse behaviour.

}, issn = {2050-084X}, doi = {10.7554/eLife.67846}, author = {Akam, Thomas and Lustig, Andy and Rowland, James M and Kapanaiah, Sampath Kt and Esteve-Agraz, Joan and Panniello, Mariangela and M{\'a}rquez, Cristina and Kohl, Michael M and K{\"a}tzel, Dennis and Costa, Rui M and Walton, Mark E} } @article {68300, title = {Organization of translating secretome mRNAS on endoplasmic reticulum}, journal = {Biophysical Journal}, volume = {121}, year = {2022}, month = {2022 Feb 01}, pages = {33a}, abstract = {

The endoplasmic reticulum (ER) has a complex morphology comprised of stacked sheets, tubules, and three-way junctions, which together function as a platform for protein synthesis of membrane and secretory proteins. Specific ER subdomains are thought to be spatially organized to enable protein synthesis activity, but precisely where these domains are localized is unclear, especially relative to the plethora of organelle interactions taking place on the ER. Here, we use single-molecule tracking of ribosomes and mRNA in combination with simultaneous imaging of ER to assess the sites of membrane protein synthesis on the ER. We found that ribosomes were widely distributed throughout different ER morphologies, but the synthesis of membrane proteins (including Type I, II, and multi-spanning) and an ER luminal protein (Calreticulin) occurred primarily at three-way junctions. Lunapark played a key role in stabilizing transmembrane protein mRNA at three-way junctions. We additionally found that translating mRNAs coding for transmembrane proteins are in the vicinity of lysosomes and translate through a cap-independent but eIF2-dependent mechanism. These results support the idea that discrete ER subdomains co-exist with lysosomes to support specific types of protein synthesis activities, with ER-lysosome interactions playing an important role in the translation of secretome mRNAs.

}, issn = {00063495}, doi = {10.1016/j.bpj.2021.11.2550}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0006349521035256}, author = {Choi, Heejun and Liao, Ya-Cheng and Yoon, Young J. and Grimm, Jonathan and Lavis, Luke D. and Singer, Robert H. and Lippincott-Schwartz, Jennifer} } @article {68042, title = {Partial resistance to citalopram in a Wistar-Kyoto rat model of depression: An evaluation using resting-state functional MRI and graph analysis.}, journal = {Journal of Psychiatric Research}, volume = {151}, year = {2022}, month = {2022 Jul 01}, pages = {242-251}, abstract = {

Wistar-Kyoto (WKY) rats as an endogenous depression model partially lack a response to classic selective serotonin reuptake inhibitors (SSRIs). Thus, this strain has the potential to be established as a model of treatment-resistant depression (TRD). However, the SSRI resistance in WKY rats is still not fully understood. In this study, WKY and control rats were subjected to a series of tests, namely, a forced swim test (FST), a sucrose preference test (SPT), and an open field test (OFT), and were scanned in a 7.0-T MRI scanner before and after three-week citalopram or saline administration. Behavioral results demonstrated that WKY rats had increased immobility in the FST and decreased sucrose preference in the SPT and central time spent in the OFT. However, citalopram did not improve immobility in the FST. The amplitude of low-frequency fluctuation (ALFF) analysis showed regional changes in the striatum and hippocampus of WKY rats. However, citalopram partially reversed the ALFF value in the dorsal part of the two regions. Functional connectivity (FC) analysis showed that FC strengths were decreased in WKY rats compared with controls. Nevertheless, citalopram partially increased FC strengths in WKY rats. Based on FC, global graph analysis demonstrated decreased network efficiency in WKY\ +\ saline group compared with control\ +\ saline group, but citalopram showed weak network efficiency improvement. In conclusion, resting-state fMRI results implied widely affected brain function at both regional and global levels in WKY rats. Citalopram had only partial effects on these functional changes, indicating a potential treatment resistance mechanism.

}, issn = {1879-1379}, doi = {10.1016/j.jpsychires.2022.04.010}, author = {Li, Qi and Zhao, Wentao and Liu, Sha and Zhao, Yu and Pan, Weixing and Wang, Xiao and Liu, Zhifen and Xu, Yong} } @article {68102, title = {Perceptual decisions exhibit hallmarks of dynamic Bayesian inference}, journal = {bioRxiv}, year = {2022}, month = {2022 May 24}, abstract = {

To interpret the sensory environment, the brain combines ambiguous sensory measurements with context-specific prior experience. But environmental contexts can change abruptly and unpredictably, resulting in uncertainty about the current context. Here we address two questions: how should context-specific prior knowledge optimally guide the interpretation of sensory stimuli in changing environments, and do human decision-making strategies resemble this optimum? We probe these questions with a task in which subjects report the orientation of ambiguous visual stimuli that were drawn from three dynamically switching distributions, representing different environmental contexts. We derive predictions for an ideal Bayesian observer that leverages the statistical structure of the task to maximize decision accuracy and show that its decisions are biased by task context. The magnitude of this decision bias is not a fixed property of the sensory measurement but depends on the observer{\textquoteright}s belief about the current context. The model therefore predicts that decision bias will grow with the reliability of the context cue, the stability of the environment, and with the number of trials since the last context switch. Analysis of human choice data validates all three predictions, providing evidence that the brain continuously updates probabilistic representations of the environment to best interpret an uncertain, ever-changing world.

}, doi = {10.1101/2022.05.23.493109}, url = {https://doi.org/10.1101/2022.05.23.493109}, author = {Julie A. Charlton and Wiktor F. M{\l}ynarski and Yoon H. Bai and Ann M. Hermundstad and Robbe L. T. Goris} } @article {67994, title = {Petascale pipeline for precise alignment of images from serial section electron microscopy.}, journal = {bioRxiv}, year = {2022}, month = {2022 Mar 27}, abstract = {

The reconstruction of neural circuits from serial section electron microscopy (ssEM) images is being accelerated by automatic image segmentation methods. Segmentation accuracy is often limited by the preceding step of aligning 2D section images to create a 3D image stack. Precise and robust alignment in the presence of image artifacts is challenging, especially as datasets are attaining the petascale. We present a computational pipeline for aligning ssEM images with several key elements. Self-supervised convolutional nets are trained via metric learning to encode and align image pairs, and they are used to initialize iterative fine-tuning of alignment. A procedure called vector voting increases robustness to image artifacts or missing image data. For speedup the series is divided into blocks that are distributed to computational workers for alignment. The blocks are aligned to each other by composing transformations with decay, which achieves a global alignment without resorting to a time-consuming global optimization. We apply our pipeline to a whole fly brain dataset, and show improved accuracy relative to prior state of the art. We also demonstrate that our pipeline scales to a cubic millimeter of mouse visual cortex. Our pipeline is publicly available through two open source Python packages.

}, doi = {10.1101/2022.03.25.485816}, url = {https://doi.org/10.1101/2022.03.25.485816}, author = {Sergiy Popovych and Thomas Macrina and Nico Kemnitz and Manuel Castro and Barak Nehoran and Zhen Jia and J. Alexander Bae and Eric Mitchell and Shang Mu and Eric T. Trautman and Stephan Saalfeld and Kai Li and Sebastian Seung} } @article {68116, title = {Plasticity-induced actin polymerization in the dendritic shaft regulates intracellular AMPA receptor trafficking.}, journal = {bioRxiv}, year = {2022}, month = {2022 May 29}, abstract = {

AMPA-type receptors (AMPARs) are rapidly inserted into synapses undergoing long-term potentiation (LTP) to increase synaptic transmission, but how AMPAR-containing vesicles are selectively trafficked to these synapses during LTP is not known. Here we developed a strategy to label AMPAR GluA1 subunits expressed from the endogenous loci of rat hippocampal neurons such that the motion of GluA1-containing vesicles in time-lapse sequences can be characterized using single-particle tracking and mathematical modeling. We find that GluA1-containing vesicles are confined and concentrated near sites of stimulation-induced plasticity. We show that confinement is mediated by actin polymerization, which hinders the active transport of GluA1-containing vesicles along the length of the dendritic shaft by modulating the rheological properties of the cytoplasm. Actin polymerization also facilitates myosin-mediated transport of GluA1-containing vesicles to exocytic sites. We conclude that neurons utilize F-actin to increase vesicular GluA1 reservoirs and promote exocytosis proximal to the sites of neuronal activity.

}, doi = {10.1101/2022.05.29.493906}, url = {https://doi.org/10.1101/2022.05.29.493906}, author = {V. C. Wong and P.R. Houlihan and H. Liu and D. Walpita and M.C. DeSantis and Z. Liu and E. K. O{\textquoteright}Shea} } @article {67892, title = {A population of descending neurons that regulates the flight motor of Drosophila.}, journal = {Current Biology}, volume = {32}, year = {2022}, month = {2022 Mar 14}, pages = {1189-1196}, abstract = {

Similar to many insect species, Drosophila melanogaster is capable of maintaining a stable flight trajectory for periods lasting up to several hours. Because aerodynamic torque is roughly proportional to the fifth power of wing length, even small asymmetries in wing size require the maintenance of subtle bilateral differences in flapping motion to maintain a stable path. Flies can even fly straight after losing half of a wing, a feat they accomplish via very large, sustained kinematic changes to both the damaged and intact wings. Thus, the neural network responsible for stable flight must be capable of sustaining fine-scaled control over wing motion across a large dynamic range. In this study, we describe an unusual type of descending neuron (DNg02) that projects directly from visual output regions of the brain to the dorsal flight neuropil of the ventral nerve cord. Unlike many descending neurons, which exist as single bilateral pairs with unique morphology, there is a population of at least 15 DNg02 cell pairs with nearly identical shape. By optogenetically activating different numbers of DNg02 cells, we demonstrate that these neurons regulate wingbeat amplitude over a wide dynamic range via a population code. Using two-photon functional imaging, we show that DNg02 cells are responsive to visual motion during flight in a manner that would make them well suited to continuously regulate bilateral changes in wing kinematics. Collectively, we have identified a critical set of descending neurons that provides the sensitivity and dynamic range required for flight control.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2022.01.008}, author = {Namiki, Shigehiro and Ros, Ivo G and Morrow, Carmen and Rowell, William J and Card, Gwyneth M and Korff, Wyatt and Dickinson, Michael H} } @article {68983, title = {Post-gastrulation synthetic embryos generated ex utero from mouse naive ESCs}, journal = {Cell}, volume = {185}, year = {2022}, month = {09/2022}, pages = {3290-3306.e25}, abstract = {

Summary In\ vitro cultured stem cells with distinct developmental capacities can contribute to embryonic or extraembryonic tissues after microinjection into pre-implantation mammalian embryos. However, whether cultured stem cells can independently give rise to entire gastrulating embryo-like structures with embryonic and extraembryonic compartments remains unknown. Here, we adapt a recently established platform for prolonged ex utero growth of natural embryos to generate mouse post-gastrulation synthetic whole embryo models (sEmbryos), with both embryonic and extraembryonic compartments, starting solely from naive ESCs. This was achieved by co-aggregating non-transduced ESCs, with naive ESCs transiently expressing Cdx2 or Gata4 to promote their priming toward trophectoderm and primitive endoderm lineages, respectively. sEmbryos adequately accomplish gastrulation, advance through key developmental milestones, and develop organ progenitors within complex extraembryonic compartments similar to E8.5 stage mouse embryos. Our findings highlight the plastic potential of naive pluripotent cells to self-organize and functionally reconstitute and model the entire mammalian embryo beyond gastrulation.

}, keywords = {embryogenesis, embryoids, ESCs, ex utero, extra-embryonic Tissues, iPSCs, naive pluripotency, PGCs, synthetic embryos}, issn = {0092-8674}, doi = {https://doi.org/10.1016/j.cell.2022.07.028}, url = {https://www.sciencedirect.com/science/article/pii/S0092867422009813}, author = {Shadi Tarazi and Alejandro Aguilera-Castrejon and Carine Joubran and Nadir Ghanem and Shahd Ashouokhi and Francesco Roncato and Emilie Wildschutz and Montaser Haddad and Bernardo Oldak and Elidet Gomez-Cesar and Nir Livnat and Sergey Viukov and Dmitry Lokshtanov and Segev Naveh-Tassa and Max Rose and Suhair Hanna and Calanit Raanan and Ori Brenner and Merav Kedmi and Hadas Keren-Shaul and Tsvee Lapidot and Itay Maza and Noa Novershtern and Jacob H. Hanna} } @article {68409, title = {Practical considerations for quantitative light sheet fluorescence microscopy.}, journal = {Nature Methods}, volume = {19}, year = {2022}, month = {2022 Dec 01}, pages = {1538-49}, abstract = {

Fluorescence microscopy has evolved from a purely observational tool to a platform for quantitative, hypothesis-driven research. As such, the demand for faster and less phototoxic imaging modalities has spurred a rapid growth in light sheet fluorescence microscopy (LSFM). By restricting the excitation to a thin plane, LSFM reduces the overall light dose to a specimen while simultaneously improving image contrast. However, the defining characteristics of light sheet microscopes subsequently warrant unique considerations in their use for quantitative experiments. In this Perspective, we outline many of the pitfalls in LSFM that can compromise analysis and confound interpretation. Moreover, we offer guidance in addressing these caveats when possible. In doing so, we hope to provide a useful resource for life scientists seeking to adopt LSFM to quantitatively address complex biological hypotheses.

}, issn = {1548-7105}, doi = {10.1038/s41592-022-01632-x}, author = {Hobson, Chad M and Guo, Min and Vishwasrao, Harshad D and Wu, Yicong and Shroff, Hari and Chew, Teng-Leong} } @article {68370, title = {A proliferative to invasive switch is mediated by srGAP1 downregulation through the activation of TGF-β2 signaling.}, journal = {Cell Reports}, volume = {40}, year = {2022}, month = {2022 Sep 20}, pages = {111358}, abstract = {

Many breast cancer (BC) patients suffer from complications of metastatic disease. To form metastases, cancer cells must become migratory and coordinate both invasive and proliferative programs at distant organs. Here, we identify srGAP1 as a regulator of a proliferative-to-invasive switch in BC cells. High-resolution light-sheet microscopy demonstrates that BC cells can form actin-rich protrusions during extravasation. srGAP1 cells display a motile and invasive phenotype that facilitates their extravasation from blood vessels, as shown in zebrafish and mouse models, while attenuating tumor growth. Interestingly, a population of srGAP1 cells remain as solitary disseminated tumor cells in the lungs of mice bearing BC tumors. Overall, srGAP1 cells have increased Smad2 activation and TGF-β2 secretion, resulting in increased invasion and p27 levels to sustain quiescence. These findings identify srGAP1 as a mediator of a proliferative to invasive phenotypic switch in BC cells in\ vivo through a TGF-β2-mediated signaling axis.

}, keywords = {Actins, Animals, Cell Line, Tumor, Down-Regulation, Mice, Transforming Growth Factor beta2, Zebrafish}, issn = {2211-1247}, doi = {10.1016/j.celrep.2022.111358}, author = {Mondal, Chandrani and Gacha-Garay, Majo J and Larkin, Kathryn A and Adikes, Rebecca C and Di Martino, Julie S and Chien, Chen-Chi and Fraser, Madison and Eni-Aganga, Ireti and Agullo-Pascual, Esperanza and Cialowicz, Katarzyna and Ozbek, Umut and Naba, Alexandra and Gaitas, Angelo and Fu, Tian-Ming and Upadhyayula, Srigokul and Betzig, Eric and Matus, David Q and Martin, Benjamin L and Bravo-Cordero, Jose Javier} } @article {68043, title = {The PV2 cluster of parvalbumin neurons in the murine periaqueductal gray: connections and gene expression.}, journal = {Brain Structure and Function}, volume = {227}, year = {2022}, month = {2022 Jul 01}, pages = {2049-72}, abstract = {

The PV2 (Celio 1990), a cluster of parvalbumin-positive neurons located in the ventromedial region of the distal periaqueductal gray (PAG) has not been previously described as its own entity, leading us to study its extent, connections, and gene expression. It is an oval, bilateral, elongated cluster composed of approximately 475 parvalbumin-expressing neurons in a single mouse hemisphere. In its anterior portion it impinges upon the paratrochlear nucleus (Par4) and in its distal portion it is harbored in the posterodorsal raphe nucleus (PDR). It is known to receive inputs from the orbitofrontal cortex and from the parvafox nucleus in the ventrolateral hypothalamus. Using anterograde tracing methods in parvalbumin-Cre mice, the main projections of the PV2 cluster innervate the supraoculomotor periaqueductal gray (Su3) of the PAG, the parvafox nucleus of the lateral hypothalamus, the gemini nuclei of the posterior hypothalamus, the septal regions, and the diagonal band in the forebrain, as well as various nuclei within the reticular formation in the midbrain and brainstem. Within the brainstem, projections were discrete, but involved areas implicated in autonomic control. The PV2 cluster expressed various peptides and receptors, including the receptor for Adcyap1, a peptide secreted by one of its main afferences, namely, the parvafox nucleus. The expression of GAD1 and GAD2 in the region of the PV2, the presence of Vgat-1 in a subpopulation of PV2-neurons as well as the coexistence of GAD67 immunoreactivity with parvalbumin in terminal endings indicates the inhibitory nature of a subpopulation of PV2-neurons. The PV2 cluster may be part of a feedback controlling the activity of the hypothalamic parvafox and the Su3 nuclei in the periaqueductal gray.

}, issn = {1863-2661}, doi = {10.1007/s00429-022-02491-0}, author = {Leemann, Siri and Babalian, Alexandre and Girard, Franck and Davis, Fred and Celio, Marco R} } @article {67989, title = {Quantifying Molecular Dynamics within Complex Cellular Morphologies using LLSM-FRAP.}, journal = {Small Methods}, year = {2022}, month = {2022 Jun 01}, pages = {e2200149}, abstract = {

Quantifying molecular dynamics within the context of complex cellular morphologies is essential toward understanding the inner workings and function of cells. Fluorescence recovery after photobleaching (FRAP) is one of the most broadly applied techniques to measure the reaction diffusion dynamics of molecules in living cells. FRAP measurements typically restrict themselves to single-plane image acquisition within a subcellular-sized region of interest due to the limited temporal resolution and undesirable photobleaching induced by 3D fluorescence confocal or widefield microscopy. Here, an experimental and computational pipeline combining lattice light sheet microscopy, FRAP, and numerical simulations, offering rapid and minimally invasive quantification of molecular dynamics with respect to 3D cell morphology is presented. Having the opportunity to accurately measure and interpret the dynamics of molecules in 3D with respect to cell morphology has the potential to reveal unprecedented insights into the function of living cells.

}, issn = {2366-9608}, doi = {10.1002/smtd.202200149}, author = {Colin-York, Huw and Heddleston, John and Wait, Eric and Karedla, Narain and DeSantis, Michael and Khuon, Satya and Chew, Teng-Leong and Sbalzarini, Ivo F and Fritzsche, Marco} } @article {67849, title = {Rapid reconstruction of neural circuits using tissue expansion and lattice light sheet microscopy}, journal = {eLife}, year = {2022}, month = {2022 Oct 26}, abstract = {

Electron microscopy (EM) allows for the reconstruction of dense neuronal connectomes but suffers from low throughput, limiting its application to small numbers of reference specimens. We developed a protocol and analysis pipeline using tissue expansion and lattice light-sheet microscopy (ExLLSM) to rapidly reconstruct selected circuits across many samples with single synapse resolution and molecular contrast. We validate this approach in\ Drosophila, demonstrating that it yields synaptic counts similar to those obtained by EM, can be used to compare counts across sex and experience, and to correlate structural connectivity with functional connectivity. This approach fills a critical methodological gap in studying variability in the structure and function of neural circuits across individuals within and between species.

}, doi = {10.7554/eLife.81248}, url = {https://doi.org/10.7554/eLife.81248}, author = {Joshua L. Lillvis and Hideo Otsuna and Xiaoyu Ding and Igor Pisarev and Takashi Kawase and Jennifer Colonell and Konrad Rokicki and Cristian Goina and Ruixuan Gao and Amy Hu and Kaiyu Wang and John Bogovic and Daniel E. Milkie and Edward S. Boyden and Stephan Saalfeld and Paul W. Tillberg and Barry J. Dickson} } @article {67847, title = {Rapid synaptic plasticity contributes to a learned conjunctive code of position and choice-related information in the hippocampus.}, journal = {Neuron}, volume = {110}, year = {2022}, month = {2022 Jan 05}, pages = {96-108.e4}, abstract = {

To successfully perform goal-directed navigation, animals must know where they are and what they are doing-e.g., looking for water, bringing food back to the nest, or escaping from a predator. Hippocampal neurons code for these critical variables conjunctively, but little is known about how this "where/what" code is formed or flexibly routed to other brain regions. To address these questions, we performed intracellular whole-cell recordings in mouse CA1 during a cued, two-choice virtual navigation task. We demonstrate that plateau potentials in CA1 pyramidal neurons rapidly strengthen synaptic inputs carrying conjunctive information about position and choice. Plasticity-induced response fields were modulated by cues only in animals previously trained to collect rewards based on available cues. Thus, we reveal that gradual learning is required for the formation of a conjunctive population code, upstream of CA1, while plateau-potential-induced synaptic plasticity in CA1 enables flexible routing of the code to downstream brain regions.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2021.10.003}, author = {Zhao, Xinyu and Hsu, Ching-Lung and Spruston, Nelson} } @article {68986, title = {Recent insights into mammalian natural and synthetic ex utero embryogenesis}, journal = {Current Opinion in Genetics \& Development}, volume = {77}, year = {2022}, month = {12/2022}, pages = {101988}, abstract = {

Research on early postimplantation mammalian development has been limited by the small size and intrauterine confinement of the developing embryos. Owing to the inability to observe and manipulate living embryos at these stages in utero, the establishment of robust ex utero embryo-culture systems that capture prolonged periods of mouse development has been an important research goal. In the last few\ years, these methods have been significantly improved by the optimization and enhancement of in vitro culture systems sustaining embryo development during peri-implantation stages for several species, and more recently, proper growth of natural mouse embryos from pregastrulation to late organogenesis stages and of embryonic stem cell (ES)-derived synthetic embryo models until early organogenesis stages. Here, we discuss the most recent ex utero embryo-culture systems established to date for rodents, nonhuman primates, and humans. We emphasize their technical aspects and developmental timeframe and provide insights into the new opportunities that these methods will contribute to the study of natural and synthetic mammalian embryogenesis and the stem-cell field.

}, issn = {0959-437X}, doi = {https://doi.org/10.1016/j.gde.2022.101988}, url = {https://www.sciencedirect.com/science/article/pii/S0959437X22000971}, author = {Bernardo Oldak and Alejandro Aguilera-Castrejon and Jacob H Hanna} } @article {68081, title = {Recovery mechanisms in the dragonfly righting reflex.}, journal = {Science}, volume = {376}, year = {2022}, month = {2022 May 13}, pages = {754-758}, abstract = {

Insects have evolved sophisticated reflexes to right themselves in mid-air. Their recovery mechanisms involve complex interactions among the physical senses, muscles, body, and wings, and they must obey the laws of flight. We sought to understand the key mechanisms involved in dragonfly righting reflexes and to develop physics-based models for understanding the control strategies of flight maneuvers. Using kinematic analyses, physical modeling, and three-dimensional flight simulations, we found that a dragonfly uses left-right wing pitch asymmetry to roll its body 180 degrees to recover from falling upside down in ~200 milliseconds. Experiments of dragonflies with blocked vision further revealed that this rolling maneuver is initiated by their ocelli and compound eyes. These results suggest a pathway from the dragonfly{\textquoteright}s visual system to the muscles regulating wing pitch that underly the recovery. The methods developed here offer quantitative tools for inferring insects{\textquoteright} internal actions from their acrobatics, and are applicable to a broad class of natural and robotic flying systems.

}, keywords = {Animals, Biomechanical Phenomena, Flight, Animal, Insecta, Odonata, Reflex, Righting, Wings, Animal}, issn = {1095-9203}, doi = {10.1126/science.abg0946}, author = {Wang, Z Jane and Melfi, James and Leonardo, Anthony} } @article {67950, title = {Regulation of Drosophila courtship behavior by the Tlx/tailless-like nuclear receptor, dissatisfaction.}, journal = {Current Biology}, volume = {32}, year = {2022}, month = {2022 Apr 25}, pages = {1703-1714}, abstract = {

Sexually dimorphic courtship behaviors in Drosophila melanogaster develop from the activity of the sexual differentiation genes, doublesex (dsx) and fruitless (fru), functioning with other regulatory factors that have received little attention. The dissatisfaction (dsf) gene encodes an orphan nuclear receptor homologous to vertebrate Tlx and Drosophila tailless that is critical for the development of several aspects of female- and male-specific sexual behaviors. Here, we report the pattern of dsf expression in the central nervous system and show that the activity of sexually dimorphic abdominal interneurons that co-express dsf and dsx is necessary and sufficient for vaginal plate opening in virgin females, ovipositor extrusion in mated females, and abdominal curling in males during courtship. We find that dsf activity results in different neuroanatomical outcomes in females and males, promoting and suppressing, respectively, female development and function of these neurons depending upon the sexual state of dsx expression. We posit that dsf and dsx interact to specify sex differences in the neural circuitry for dimorphic abdominal behaviors.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2022.02.031}, author = {Duckhorn, Julia C and Cande, Jessica and Metkus, Mary C and Song, Hyeop and Altamirano, Sofia and Stern, David L and Shirangi, Troy R} } @article {67961, title = {Regulation of liver subcellular architecture controls metabolic homeostasis.}, journal = {Nature}, volume = {603}, year = {2022}, month = {2022 Mar 09}, pages = {736-742}, abstract = {

Cells display complex intracellular organization by compartmentalization of metabolic processes into organelles, yet the resolution of these structures in the native tissue context and their functional consequences are not well understood. Here we resolved the three-dimensional structural organization of organelles in large (more than 2.8\ {\texttimes}\ 10\ {\textmu}m) volumes of intact liver tissue (15 partial or full hepatocytes per condition) at high resolution (8\ nm isotropic pixel size) using enhanced focused ion beam scanning electron microscopy imaging followed by deep-learning-based automated image segmentation and 3D reconstruction. We also performed a comparative analysis of subcellular structures in liver tissue of lean and obese mice and found substantial alterations, particularly in hepatic endoplasmic reticulum (ER), which undergoes massive structural reorganization characterized by marked disorganization of stacks of ER sheets and predominance of ER tubules. Finally, we demonstrated the functional importance of these structural changes by monitoring the effects of experimental recovery of the subcellular organization on cellular and systemic metabolism. We conclude that the hepatic subcellular organization of\ the ER architecture are highly dynamic, integrated with the metabolic state and critical for adaptive homeostasis and tissue health.

}, issn = {1476-4687}, doi = {10.1038/s41586-022-04488-5}, author = {Parlakg{\"u}l, G{\"u}ne{\c s} and Arruda, Ana Paula and Pang, Song and Cagampan, Erika and Min, Nina and G{\"u}ney, Ekin and Lee, Grace Yankun and Inouye, Karen and Hess, Harald F and Xu, C Shan and Hotam{\i}{\c s}l{\i}gil, G{\"o}khan S} } @article {68079, title = {Rescue of behavioral and electrophysiological phenotypes in a Pitt-Hopkins syndrome mouse model by genetic restoration of expression.}, journal = {eLife}, volume = {11}, year = {2022}, month = {2022 May 10}, abstract = {

Pitt-Hopkins syndrome (PTHS) is a neurodevelopmental disorder caused by monoallelic mutation or deletion in the () gene. Individuals with PTHS typically present in the first year of life with developmental delay and exhibit intellectual disability, lack of speech, and motor incoordination. There are no effective treatments available for PTHS, but the root cause of the disorder, haploinsufficiency, suggests that it could be treated by normalizing gene expression. Here, we performed proof-of-concept viral gene therapy experiments using a conditional mouse model of PTHS and found that postnatally reinstating expression in neurons improved anxiety-like behavior, activity levels, innate behaviors, and memory. Postnatal reinstatement also partially corrected EEG abnormalities, which we characterized here for the first time, and the expression of key TCF4-regulated genes. Our results support a genetic normalization approach as a treatment strategy for PTHS, and possibly other TCF4-linked disorders.

}, keywords = {Animals, Disease Models, Animal, Facies, Hyperventilation, Intellectual Disability, Mice, Phenotype, Transcription Factor 4}, issn = {2050-084X}, doi = {10.7554/eLife.72290}, author = {Kim, Hyojin and Gao, Eric B and Draper, Adam and Berens, Noah C and Vihma, Hanna and Zhang, Xinyuan and Higashi-Howard, Alexandra and Ritola, Kimberly D and Simon, Jeremy M and Kennedy, Andrew J and Philpot, Benjamin D} } @article {65821, title = {Robotic Multi-Probe-Single-Actuator Inchworm Neural Microdrive}, journal = {eLife}, year = {2022}, month = {2022 Nov 10}, abstract = {

Electrophysiology is one of the major experimental techniques used in neuroscience. The favorable spatial and temporal resolution as well as the increasingly larger site counts of brain recording electrodes contribute to the popularity and importance of electrophysiology in neuroscience. Such electrodes are typically mechanically placed in the brain to perform acute or chronic freely moving animal measurements. The micro positioners currently used for such tasks employ a single translator per independent probe being placed into the targeted brain region, leading to significant size and weight restrictions. To overcome this limitation, we have developed a miniature robotic multi-probe neural microdrive that utilizes novel phase-change-material-filled resistive heater micro-grippers. The microscopic dimensions, gentle gripping action, independent electronic actuation control, and high packing density of the grippers allow for micrometer-precision independent positioning of multiple arbitrarily shaped parallel neural electrodes with only a single piezo actuator in an inchworm motor configuration. This multi-probe-single-actuator design allows for significant size and weight reduction, as well as remote control and potential automation of the microdrive. We demonstrate accurate placement of multiple independent recording electrodes into the CA1 region of the rat hippocampus\ in vivo\ in acute and chronic settings. Thus, our robotic neural microdrive technology is applicable towards basic neuroscience and clinical studies, as well as other multi-probe or multi-sensor micro-positioning applications.

}, doi = {10.7554/eLife.71876}, author = {Smith, R.D. and Kolb, Ilya and Tanaka, Shinsuke and Lee, A.K. and Harris, T.D. and Barbic, M.} } @article {68559, title = {Robust cell identity specifications through transitions in the collective state of growing developmental systems}, journal = {Current Opinion in Systems Biology}, volume = {31}, year = {2022}, month = {2022 Nov 08}, pages = {100437}, abstract = {

Mammalian development is characterized with transitions from homogeneous populations of precursor to heterogeneous population of specified cells. We review here the main dynamical mechanisms through which such transitions are conceptualized, and discuss that the differentiation timing, robust cell-type proportions and recovery upon perturbation are emergent property of proliferating and communicating cell populations. We argue that studying developmental systems using transitions in collective system states is necessary to describe observed experimental features, and propose additionally the basis of a novel analytical method to deduce the relationship between single-cell dynamics and the collective, symmetry-broken states in cellular populations.

}, issn = {24523100}, doi = {10.1016/j.coisb.2022.100437}, url = {https://linkinghub.elsevier.com/retrieve/pii/S2452310022000233}, author = {Stanoev, Angel and Koseska, Aneta} } @article {67774, title = {RS-FISH: Precise, interactive, fast, and scalable FISH spot detection}, journal = {Nature Methods}, volume = {19}, year = {2022}, month = {2022 Nov 17}, pages = {1563-7}, abstract = {

Fluorescent in-situ hybridization (FISH)-based methods are powerful tools to study molecular processes with subcellular resolution, relying on accurate identification and localization of diffraction-limited spots in microscopy images. We developed the Radial Symmetry-FISH (RS-FISH) software that accurately, robustly, and quickly detects single-molecule spots in two and three dimensions, making it applicable to several key assays, including single-molecule FISH (smFISH), spatial transcriptomics, and spatial genomics. RS-FISH allows interactive parameter tuning and scales to large sets of images as well as tera-byte sized image volumes such as entire brain scans using straight-forward distributed processing on workstations, clusters, and in the cloud.

}, doi = {10.1038/s41592-022-01669-y}, author = {Ella Bahry and Laura Breimann and Marwan Zouinkhi and Leo Epstein and Klim Kolyvanov and Xi Long and Kyle I S Harrington and Timoth{\'e}e Lionnet and Stephan Preibisch} } @article {68251, title = {A scalable and modular automated pipeline for stitching of large electron microscopy datasets.}, journal = {eLife}, volume = {11}, year = {2022}, month = {2022 Jul 26}, abstract = {

Serial-section electronmicroscopy (ssEM) is themethod of choice for studyingmacroscopic biological samples at extremely high resolution in three dimensions. In the nervous system, nanometer-scale images are necessary to reconstruct dense neural wiring diagrams in the brain, so called connectomes. In order to use this data, consisting of up to 10 individual EM images, it must be assembled into a volume, requiring seamless 2D stitching from each physical section followed by 3D alignment of the stitched sections. The high throughput of ssEM necessitates 2D stitching to be done at the pace of imaging, which currently produces tens of terabytes per day. To achieve this, we present a modular volume assembly software pipeline ASAP (Assembly Stitching and Alignment Pipeline) that is scalable to datasets containing petabytes of data and parallelized to work in a distributed computational environment. The pipeline is built on top of the Render (27) services used in the volume assembly of the brain of adult Drosophilamelanogaster (30). It achieves high throughput by operating on themeta-data and transformations of each image stored in a database, thus eliminating the need to render intermediate output. ASAP ismodular, allowing for easy incorporation of new algorithms without significant changes in the workflow. The entire software pipeline includes a complete set of tools for stitching, automated quality control, 3D section alignment, and final rendering of the assembled volume to disk. ASAP has been deployed for continuous stitching of several large-scale datasets of the mouse visual cortex and human brain samples including one cubic millimeter of mouse visual cortex (28; 8) at speeds that exceed imaging. The pipeline also has multi-channel processing capabilities and can be applied to fluorescence and multi-modal datasets like array tomography.

}, issn = {2050-084X}, doi = {10.7554/eLife.76534}, author = {Mahalingam, Gayathri and Torres, Russel and Kapner, Daniel and Trautman, Eric T and Fliss, Tim and Seshamani, Shamishtaa and Perlman, Eric and Young, Rob and Kinn, Samuel and Buchanan, JoAnn and Takeno, Marc M and Yin, Wenjing and Bumbarger, Daniel J and Gwinn, Ryder P and Nyhus, Julie and Lein, Ed and Smith, Steven J and Reid, R Clay and Khairy, Khaled A and Saalfeld, Stephan and Collman, Forrest and Macarico da Costa, Nuno} } @article {68278, title = {Selective Serotonin Reuptake Inhibitors Within Cells: Temporal Resolution in Cytoplasm, Endoplasmic Reticulum, and Membrane}, journal = {bioRxiv}, year = {2022}, month = {2022 Aug 12}, abstract = {

Selective serotonin reuptake inhibitors (SSRIs) are the most prescribed treatment for individuals experiencing major depressive disorder (MDD). The therapeutic mechanisms that take place before, during, or after SSRIs bind the serotonin transporter (SERT) are poorly understood, partially because no studies exist of the cellular and subcellular pharmacokinetic properties of SSRIs in living cells. We studied escitalopram and fluoxetine using new intensity- based drug-sensing fluorescent reporters ({\textquotedblleft}iDrugSnFRs{\textquotedblright}) targeted to the plasma membrane (PM), cytoplasm, or endoplasmic reticulum (ER) of cultured neurons and mammalian cell lines. We also employed chemical detection of drug within cells and phospholipid membranes. The drugs attain equilibrium in neuronal cytoplasm and ER, at approximately the same concentration as the externally applied solution, with time constants of a few s (escitalopram) or 200-300 s (fluoxetine). Simultaneously, the drugs accumulate within lipid membranes by >= 18-fold (escitalopram) or 180-fold (fluoxetine), and possibly by much larger factors. Both drugs leave cytoplasm, lumen, and membranes just as quickly during washout. We synthesized membrane-impermeant quaternary amine derivatives of the two SSRIs. The quaternary derivatives are substantially excluded from membrane, cytoplasm, and ER for \> 2.4 h. They inhibit SERT transport-associated currents 6- or 11-fold less potently than the SSRIs (escitalopram or fluoxetine derivative, respectively), providing useful probes for distinguishing compartmentalized SSRI effects. Although our measurements are orders of magnitude faster than the {\textquotedblleft}therapeutic lag{\textquotedblright} of SSRIs, these data suggest that SSRI-SERT interactions within organelles or membranes may play roles during either the therapeutic effects or the {\textquotedblleft}antidepressant discontinuation syndrome{\textquotedblright}.

}, doi = {10.1101/2022.08.09.502705}, url = {https://doi.org/10.1101/2022.08.09.502705}, author = {Aaron L. Nichols and Zack Blumenfeld and Laura Luebbert and Hailey J. Knox and Anand K. Muthusamy and Jonathan S. Marvin and Charlene H. Kim and Stephen N. Grant and David P. Walton and Bruce N. Cohen and Rebekkah Hammar and Loren L. Looger and Per Artursson and Dennis A. Dougherty and Henry A. Lester} } @article {68312, title = {A sensitive and specific genetically encoded potassium ion biosensor for in vivo applications across the tree of life.}, journal = {PLoS Biology}, volume = {20}, year = {2022}, month = {2022 Sep 06}, pages = {e3001772}, abstract = {

Potassium ion (K+) plays a critical role as an essential electrolyte in all biological systems. Genetically encoded fluorescent K+ biosensors are promising tools to further improve our understanding of K+-dependent processes under normal and pathological conditions. Here, we report the crystal structure of a previously reported genetically encoded fluorescent K+ biosensor, GINKO1, in the K+-bound state. Using structure-guided optimization and directed evolution, we have engineered an improved K+ biosensor, designated GINKO2, with higher sensitivity and specificity. We have demonstrated the utility of GINKO2 for in vivo detection and imaging of K+ dynamics in multiple model organisms, including bacteria, plants, and mice.

}, issn = {1545-7885}, doi = {10.1371/journal.pbio.3001772}, author = {Wu, Sheng-Yi and Wen, Yurong and Serre, Nelson B C and Laursen, Cathrine Charlotte Heiede and Dietz, Andrea Grost{\o}l and Taylor, Brian R and Drobizhev, Mikhail and Molina, Rosana S and Abhi Aggarwal and Rancic, Vladimir and Becker, Michael and Ballanyi, Klaus and Podgorski, Kaspar and Hirase, Hajime and Nedergaard, Maiken and Fendrych, Maty{\'a}{\v s} and Lemieux, M Joanne and Eberl, Daniel F and Kay, Alan R and Campbell, Robert E and Shen, Yi} } @article {67810, title = {A serotonergic axon-cilium synapse drives nuclear signaling to maintain chromatin accessibility}, journal = {Cell}, volume = {185}, year = {2022}, month = {2022 Sep 01}, pages = {3390-3407}, abstract = {

Chemical synapses between axons and dendrites mediate much of the brain{\textquoteright}s intercellular communication. Here we describe a new kind of synapse {\textendash} the axo-ciliary synapse - between axons and primary cilia. By employing enhanced focused ion beam {\textendash} scanning electron microscopy on samples with optimally preserved ultrastructure, we discovered synapses between the serotonergic axons arising from the brainstem, and the primary cilia of hippocampal CA1 pyramidal neurons. Functionally, these cilia are enriched in a ciliary-restricted serotonin receptor, 5-hydroxytryptamine receptor 6 (HTR6), whose mutation is associated with learning and memory defects. Using a newly developed cilia-targeted serotonin sensor, we show that optogenetic stimulation of serotonergic axons results in serotonin release onto cilia. Ciliary HTR6 stimulation activates a non-canonical Gαq/11-RhoA pathway. Ablation of this pathway results in nuclear actin and chromatin accessibility changes in CA1 pyramidal neurons. Axo-ciliary synapses serve as a distinct mechanism for neuromodulators to program neuron transcription through privileged access to the nuclear compartment.

}, doi = {10.1016/j.cell.2022.07.026}, author = {Shu-Hsien Sheu and Srigokul Upadhyayula and Vincent Dupuy and Song Pang and Andrew L. Lemire and Deepika Walpita and H. Amalia Pasolli and Fei Deng and Jinxia Wan and Lihua Wang and Justin Houser and Silvia Sanchez-Martinez and Sebastian E. Brauchi and Sambashiva Banala and Melanie Freeman and C. Shan Xu and Tom Kirchhausen and Harald F. Hess and Luke Lavis and Yu-Long Li and S{\'e}verine Chaumont-Dubel and David E. Clapham} } @article {68412, title = {Single molecule microscopy to profile the effect of zinc status on transcription factor dynamics.}, journal = {Scientific Reports}, volume = {12}, year = {2022}, month = {2022 Oct 22}, pages = {17789}, abstract = {

The regulation of transcription is a complex process that involves binding of transcription factors (TFs) to specific sequences, recruitment of cofactors and chromatin remodelers, assembly of the pre-initiation complex and recruitment of RNA polymerase II. Increasing evidence suggests that TFs are highly dynamic and interact only transiently with DNA. Single molecule microscopy techniques are powerful approaches for tracking individual TF molecules as they diffuse in the nucleus and interact with DNA. Here we employ multifocus microscopy and highly inclined laminated optical sheet microscopy to track TF dynamics in response to perturbations in labile zinc inside cells. We sought to define whether zinc-dependent TFs sense changes in the labile zinc pool by determining whether their dynamics and DNA binding can be modulated by zinc. We used fluorescently tagged versions of the glucocorticoid receptor (GR), with two C4 zinc finger domains, and CCCTC-binding factor (CTCF), with eleven C2H2 zinc finger domains. We found that GR was largely insensitive to perturbations of zinc, whereas CTCF was significantly affected by zinc depletion and its dwell time was affected by zinc elevation. These results indicate that at least some transcription factors are sensitive to zinc dynamics, revealing a potential new layer of transcriptional regulation.

}, keywords = {CCCTC-Binding Factor, Chromatin, DNA, Receptors, Glucocorticoid, RNA Polymerase II, Single Molecule Imaging, Transcription Factors, Zinc}, issn = {2045-2322}, doi = {10.1038/s41598-022-22634-x}, author = {Damon, Leah J and Aaron, Jesse and Palmer, Amy E} } @article {68105, title = {Single molecule microscopy to profile the effect of zinc status of transcription factor dynamics}, journal = {bioRxiv}, year = {2022}, month = {2022 May 11}, abstract = {

Transcription factors (TFs) are DNA binding proteins that control the expression of genes. The regulation of transcription is a complex process that involves binding of TFs to specific sequences, recruitment of cofactors and chromatin remodelers, assembly of the pre-initiation complex and ultimately the recruitment of RNA polymerase II. Increasing evidence suggests that TFs are highly dynamic and interact only transiently with DNA. Single molecule microscopy techniques are powerful approaches for visualizing and tracking individual TF molecules as they diffuse in the nucleus and interact with DNA. In this work, we employ multifocus microscopy and highly inclined and laminated optical sheet microscopy to track TF dynamics in response to perturbations in labile zinc inside cells. We sought to define whether zinc-dependent TFs sense changes in the labile zinc pool by determining whether their dynamics and DNA binding can be modulated by zinc. While it is widely appreciated that TFs need zinc to bind DNA, whether zinc occupancy and hence TF function are sensitive to\ changes\ in cellular zinc remain open questions. We utilized fluorescently tagged versions of the glucocorticoid receptor (GR), with two C4 zinc finger domains, and CCCTC-binding factor (CTCF), with eleven C2H2 zinc finger domains. We found that the biophysical dynamics of both TFs are susceptible to changes in zinc, but in subtly different ways. These results indicate that at least some transcription factors are sensitive to zinc dynamics, revealing a potential new layer of transcriptional regulation.

}, doi = {10.1101/2022.05.10.491421}, url = {https://doi.org/10.1101/2022.05.10.491421}, author = {Leah J. Damon and Jesse Aaron and Amy E. Palmer} } @article {68297, title = {A single-cell transcriptomic atlas of complete insect nervous systems across multiple life stages.}, journal = {Neural Development}, volume = {17}, year = {2022}, month = {2022 Aug 24}, pages = {8}, abstract = {

Molecular profiles of neurons influence neural development and function but bridging the gap between genes, circuits, and behavior has been very difficult. Here we used single cell RNAseq to generate a complete gene expression atlas of the Drosophila larval central nervous system composed of 131,077 single cells across three developmental stages (1\ h, 24\ h and 48\ h after hatching). We identify 67 distinct cell clusters based on the patterns of gene expression. These include 31 functional mature larval neuron clusters, 1 ring gland cluster, 8 glial clusters, 6 neural precursor clusters, and 13 developing immature adult neuron clusters. Some clusters are present across all stages of larval development, while others are stage specific (such as developing adult neurons). We identify genes that are differentially expressed in each cluster, as well as genes that are differentially expressed at distinct stages of larval life. These differentially expressed genes provide promising candidates for regulating the function of specific neuronal and glial types in the larval nervous system, or the specification and differentiation of adult neurons. The cell transcriptome Atlas of the Drosophila larval nervous system is a valuable resource for developmental biology and systems neuroscience and provides a basis for elucidating how genes regulate neural development and function.

}, keywords = {Animals, Drosophila, Gene Expression Regulation, Developmental, Larva, Neuroglia, Neurons, Transcriptome}, issn = {1749-8104}, doi = {10.1186/s13064-022-00164-6}, author = {Corrales, Marc and Cocanougher, Benjamin T and Kohn, Andrea B and Wittenbach, Jason D and Long, Xi S and Lemire, Andrew and Cardona, Albert and Singer, Robert H and Moroz, Leonid L and Zlatic, Marta} } @article {68530, title = {Small molecule inhibitors of mammalian glycosylation.}, journal = {Matrix Biology Plus}, volume = {16}, year = {2022}, month = {2022 Mar 16}, pages = {100108}, abstract = {

Glycans are one of the fundamental biopolymers encountered in living systems. Compared to polynucleotide and polypeptide biosynthesis, polysaccharide biosynthesis is a uniquely combinatorial process to which interdependent enzymes with seemingly broad specificities contribute. The resulting intracellular cell surface, and secreted glycans play key roles in health and disease, from embryogenesis to cancer progression. The study and modulation of glycans in cell and organismal biology is aided by small molecule inhibitors of the enzymes involved in glycan biosynthesis. In this review, we survey the arsenal of currently available inhibitors, focusing on agents which have been independently validated in diverse systems. We highlight the utility of these inhibitors and drawbacks to their use, emphasizing the need for innovation for basic research as well as for therapeutic applications.

}, issn = {2590-0285}, doi = {10.1016/j.mbplus.2022.100108}, author = {Almahayni, Karim and Spiekermann, Malte and Fiore, Antonio and Yu, Guoqiang and Pedram, Kayvon and M{\"o}ckl, Leonhard} } @article {68514, title = {SMP30-mediated synthesis of vitamin C activates the liver PPARα/FGF21 axis to regulate thermogenesis in mice.}, journal = {Experimental and Molecular Medicine}, volume = {54}, year = {2022}, month = {2022 Nov 25}, pages = {2036-2046}, abstract = {

The vitamin-C-synthesizing enzyme senescent marker protein 30 (SMP30) is a cold resistance gene in Drosophila, and vitamin C concentration increases in brown adipose tissue post-cold exposure. However, the roles of SMP30 in thermogenesis are unknown. Here, we tested the molecular mechanism of thermogenesis using wild-type (WT) and vitamin C-deficient SMP30-knockout (KO) mice. SMP30-KO mice gained more weight than WT mice without a change in food intake in response to short-term high-fat diet feeding. Indirect calorimetry and cold-challenge experiments indicated that energy expenditure is lower in SMP30-KO mice, which is associated with decreased thermogenesis in adipose tissues. Therefore, SMP30-KO mice do not lose weight during cold exposure, whereas WT mice lose weight markedly. Mechanistically, the levels of serum FGF21 were notably lower in SMP30-KO mice, and vitamin C supplementation in SMP30-KO mice recovered FGF21 expression and thermogenesis, with a marked reduction in body weight during cold exposure. Further experiments revealed that vitamin C activates PPARα to upregulate FGF21. Our findings demonstrate that SMP30-mediated synthesis of vitamin C activates the PPARα/FGF21 axis, contributing to the maintenance of thermogenesis in mice.

}, issn = {2092-6413}, doi = {10.1038/s12276-022-00888-9}, author = {Lee, Bonggi and An, Hye Jin and Kim, Dae Hyun and Lee, Min-Kyeong and Jeong, Hyeon Hak and Chung, Ki Wung and Go, Younghoon and Seo, Arnold Y and Kim, Il Yong and Seong, Je Kyung and Yu, Byung Pal and Lee, Jaewon and Im, Eunok and Lee, In-Kyu and Lee, Myung-Shik and Yamada, Ken-Ichi and Chung, Hae Young} } @article {68468, title = {Spatial organization of the 3D genome encodes gene co-expression programs in single cells}, journal = {bioRxiv}, year = {2022}, month = {2022 Oct 27}, abstract = {

Deconstructing the mechanism by which the 3D genome encodes genetic information to generate diverse cell types during animal development is a major challenge in biology. The contrast between the elimination of chromatin loops and domains upon Cohesin loss and the lack of downstream gene expression changes at the cell population level instigates intense debates regarding the structure-function relationship between genome organization and gene regulation. Here, by analyzing single cells after acute Cohesin removal with sequencing and spatial genome imaging techniques, we discover that, instead of dictating population-wide gene expression levels, 3D genome topology mediated by Cohesin safeguards long-range gene co-expression correlations in single cells. Notably, Cohesin loss induces gene co-activation and chromatin co-opening between active domains in\ cis\ up to tens of megabase apart, far beyond the typical length scale of enhancer-promoter communication. In addition, Cohesin separates Mediator protein hubs, prevents active genes in\ cis\ from localizing into shared hubs and blocks intersegment transfer of diverse transcriptional regulators. Together, these results support that spatial organization of the 3D genome orchestrates dynamic long-range gene and chromatin co-regulation in single living cells.

}, doi = {10.1101/2022.10.26.513917}, url = {https://doi.org/10.1101/2022.10.26.513917}, author = {Peng Dong and Shu Zhang and Liangqi Xie and Lihua Wang and Andrew L. Lemire and Arthur D. Lander and Howard Y. Chang and Zhe J. Liu} } @article {68369, title = {Structural Diversity within the Endoplasmic Reticulum-From the Microscale to the Nanoscale.}, journal = {Cold Spring Harbor Perspectives in Biology}, year = {2022}, month = {2022 Sep 19}, abstract = {

The endoplasmic reticulum (ER) is a continuous, highly dynamic membrane compartment that is crucial for numerous basic cellular functions. The ER stretches from the nuclear envelope to the outer periphery of all living eukaryotic cells. This ubiquitous organelle shows remarkable structural complexity, adopting a range of shapes, curvatures, and length scales. Canonically, the ER is thought to be composed of two simple membrane elements: sheets and tubules. However, recent advances in superresolution light microscopy and three-dimensional electron microscopy have revealed an astounding diversity of nanoscale ER structures, greatly expanding our view of ER organization. In this review, we describe these diverse ER structures, focusing on what is known of their regulation and associated functions in mammalian cells.

}, issn = {1943-0264}, doi = {10.1101/cshperspect.a041259}, author = {Obara, Christopher J and Moore, Andrew S and Lippincott-Schwartz, Jennifer} } @article {68408, title = {Structure of the OMEGA nickase IsrB in complex with ωRNA and target DNA.}, journal = {Nature}, volume = {610}, year = {2022}, month = {2022 Oct 12}, pages = {575-581}, abstract = {

RNA-guided systems, such as CRISPR-Cas, combine programmable substrate recognition with enzymatic function, a combination that has been used advantageously to develop powerful molecular technologies. Structural studies of these systems have illuminated how the RNA and protein jointly recognize and cleave their substrates, guiding rational engineering for further technology development. Recent work identified a new class of RNA-guided systems, termed OMEGA, which include IscB, the likely ancestor of Cas9, and the nickase IsrB, a homologue of IscB lacking the HNH nuclease domain. IsrB consists of only around 350 amino acids, but its small size is counterbalanced by a relatively large RNA guide (roughly 300-nt ωRNA). Here, we report the cryogenic-electron microscopy structure of Desulfovirgula thermocuniculi IsrB (DtIsrB) in complex with its cognate ωRNA and a target DNA. We find the overall structure of the IsrB protein shares a common scaffold with Cas9. In contrast to Cas9, however, which uses a recognition (REC) lobe to facilitate target selection, IsrB relies on its ωRNA, part of which forms an intricate ternary structure positioned analogously to REC. Structural analyses of IsrB and its ωRNA as well as comparisons to other RNA-guided systems highlight the functional interplay between protein and RNA, advancing our understanding of the biology and evolution of these diverse systems.

}, keywords = {CRISPR-Associated Proteins, CRISPR-Cas Systems, Cryoelectron Microscopy, Deoxyribonuclease I, DNA, RNA, Guide}, issn = {1476-4687}, doi = {10.1038/s41586-022-05324-6}, author = {Hirano, Seiichi and Kappel, Kalli and Altae-Tran, Han and Faure, Guilhem and Wilkinson, Max E and Kannan, Soumya and Demircioglu, F Esra and Yan, Rui and Shiozaki, Momoko and Yu, Zhiheng and Makarova, Kira S and Koonin, Eugene V and Macrae, Rhiannon K and Zhang, Feng} } @article {67908, title = {Structured random receptive fields enable informative sensory encodings}, journal = {bioRxiv}, year = {2022}, month = {2022 Feb 13}, abstract = {

Brains must represent the outside world so that animals survive and thrive. In early sensory systems, neural populations have diverse receptive fields structured to detect important features in inputs, yet significant variability has been ignored in classical models of sensory neurons. We model neuronal receptive fields as random, variable samples from parametrized distributions in two sensory modalities, using data from insect mechanosensors and neurons of mammalian primary visual cortex. We show that these random feature neurons perform a randomized wavelet transform on inputs which removes high frequency noise and boosts the signal. Our result makes a significant theoretical connection between the foundational concepts of receptive fields in neuroscience and random features in artificial neural networks. Further, these random feature neurons enable learning from fewer training samples and with smaller networks in artificial tasks. This structured random model of receptive fields provides a unifying, mathematically tractable framework to understand sensory encodings across both spatial and temporal domains.

}, doi = {10.1101/2021.09.09.459651}, author = {Biraj Pandey and Marius Pachitariu and Bingni W. Brunton and Kameron Decker Harris} } @article {68386, title = {Structured random receptive fields enable informative sensory encodings.}, journal = {PLoS Computational Biology}, volume = {18}, year = {2022}, month = {2022 Oct 10}, pages = {e1010484}, abstract = {

Brains must represent the outside world so that animals survive and thrive. In early sensory systems, neural populations have diverse receptive fields structured to detect important features in inputs, yet significant variability has been ignored in classical models of sensory neurons. We model neuronal receptive fields as random, variable samples from parameterized distributions and demonstrate this model in two sensory modalities using data from insect mechanosensors and mammalian primary visual cortex. Our approach leads to a significant theoretical connection between the foundational concepts of receptive fields and random features, a leading theory for understanding artificial neural networks. The modeled neurons perform a randomized wavelet transform on inputs, which removes high frequency noise and boosts the signal. Further, these random feature neurons enable learning from fewer training samples and with smaller networks in artificial tasks. This structured random model of receptive fields provides a unifying, mathematically tractable framework to understand sensory encodings across both spatial and temporal domains.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1010484}, author = {Pandey, Biraj and Pachitariu, Marius and Brunton, Bingni W and Harris, Kameron Decker} } @article {68222, title = {Structured sampling of olfactory input by the fly mushroom body.}, journal = {Current Biology}, volume = {32}, year = {2022}, month = {2022 Aug 08}, pages = {3334-3349.e6}, abstract = {

Associative memory formation and recall in the fruit fly Drosophila melanogaster is subserved by the mushroom body (MB). Upon arrival in the MB, sensory information undergoes a profound transformation from broadly tuned and stereotyped odorant responses in the olfactory projection neuron (PN) layer to narrowly tuned and nonstereotyped responses in the Kenyon cells (KCs). Theory and experiment suggest that this transformation is implemented by random connectivity between KCs and PNs. However, this hypothesis has been challenging to test, given the difficulty of mapping synaptic connections between large numbers of brain-spanning neurons. Here, we used a recent whole-brain electron microscopy volume of the adult fruit fly to map PN-to-KC connectivity at synaptic resolution. The PN-KC connectome revealed unexpected structure, with preponderantly food-responsive PN types converging at above-chance levels on downstream KCs. Axons of the overconvergent PN types tended to arborize near one another in the MB main calyx, making local KC dendrites more likely to receive input from those types. Overconvergent PN types preferentially co-arborize and connect with dendrites of αβ and α{\textquoteright}β{\textquoteright} KC subtypes. Computational simulation of the observed network showed degraded discrimination performance compared with a random network, except when all signal flowed through the overconvergent, primarily food-responsive PN types. Additional theory and experiment will be needed to fully characterize the impact of the observed non-random network structure on associative memory formation and recall.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2022.06.031}, author = {Zheng, Zhihao and Li, Feng and Fisher, Corey and Ali, Iqbal J and Sharifi, Nadiya and Calle-Schuler, Steven and Hsu, Joseph and Masoodpanah, Najla and Kmecova, Lucia and Kazimiers, Tom and Perlman, Eric and Nichols, Matthew and Li, Peter H and Jain, Viren and Bock, Davi D} } @article {68987, title = {SUMOylation of linker histone H1 drives chromatin condensation and restriction of embryonic cell fate identity}, journal = {Molecular Cell}, volume = {82}, year = {2022}, month = {01/2022}, pages = {106-122.e9}, abstract = {

Summary The fidelity of the early embryonic program is underlined by tight regulation of the chromatin. Yet, how the chromatin is organized to prohibit the reversal of the developmental program remains unclear. Specifically, the totipotency-to-pluripotency transition marks one of the most dramatic events to the chromatin, and yet, the nature of histone alterations underlying this process is incompletely characterized. Here, we show that linker histone H1 is post-translationally modulated by SUMO2/3, which facilitates its fixation onto ultra-condensed heterochromatin in embryonic stem cells (ESCs). Upon SUMOylation depletion, the chromatin becomes de-compacted and H1 is evicted, leading to totipotency reactivation. Furthermore, we show that H1 and SUMO2/3 jointly mediate the repression of totipotent elements. Lastly, we demonstrate that preventing SUMOylation on H1 abrogates its ability to repress the totipotency program in ESCs. Collectively, our findings unravel a critical role for SUMOylation of H1 in facilitating chromatin repression and desolation of the totipotent identity.

}, issn = {1097-2765}, doi = {https://doi.org/10.1016/j.molcel.2021.11.011}, url = {https://www.sciencedirect.com/science/article/pii/S1097276521009904}, author = {Daoud Sheban and Tom Shani and Roey Maor and Alejandro Aguilera-Castrejon and Nofar Mor and Bernardo Oldak and Merav D. Shmueli and Avital Eisenberg-Lerner and Jonathan Bayerl and Jakob Hebert and Sergey Viukov and Guoyun Chen and Assaf Kacen and Vladislav Krupalnik and Valeriya Chugaeva and Shadi Tarazi and Alejandra Rodr{\'\i}guez-delaRosa and Mirie Zerbib and Adi Ulman and Solaiman Masarwi and Meital Kupervaser and Yishai Levin and Efrat Shema and Yael David and Noa Novershtern and Jacob H. Hanna and Yifat Merbl} } @article {68167, title = {Super-Resolution Imaging of Fas/CD95 Reorganization Induced by Membrane-Bound Fas Ligand Reveals Nanoscale Clustering Upstream of FADD Recruitment.}, journal = {Cells}, volume = {11}, year = {2022}, month = {2022 Jun 12}, abstract = {

Signaling through the TNF-family receptor Fas/CD95 can trigger apoptosis or non-apoptotic cellular responses and is essential for protection from autoimmunity. Receptor clustering has been observed following interaction with Fas ligand (FasL), but the stoichiometry of Fas, particularly when triggered by membrane-bound FasL, the only form of FasL competent at inducing programmed cell death, is not known. Here we used super-resolution microscopy to study the behavior of single molecules of Fas/CD95 on the plasma membrane after interaction of Fas with FasL on planar lipid bilayers. We observed rapid formation of Fas protein superclusters containing more than 20 receptors after interactions with membrane-bound FasL. Fluorescence correlation imaging demonstrated recruitment of FADD dependent on an intact Fas death domain, with lipid raft association playing a secondary role. Flow-cytometric FRET analysis confirmed these results, and also showed that some Fas clustering can occur in the absence of FADD and caspase-8. Point mutations in the Fas death domain associated with autoimmune lymphoproliferative syndrome (ALPS) completely disrupted Fas reorganization and FADD recruitment, confirming structure-based predictions of the critical role that these residues play in Fas-Fas and Fas-FADD interactions. Finally, we showed that induction of apoptosis correlated with the ability to form superclusters and recruit FADD.

}, keywords = {Apoptosis, Cluster Analysis, Fas Ligand Protein, fas Receptor, Fas-Associated Death Domain Protein, Receptors, Tumor Necrosis Factor}, issn = {2073-4409}, doi = {10.3390/cells11121908}, author = {Frazzette, Nicholas and Cruz, Anthony C and Wu, Xufeng and Hammer, John A and Lippincott-Schwartz, Jennifer and Siegel, Richard M and Sengupta, Prabuddha} } @article {68328, title = {Superresolution microscopy reveals actomyosin dynamics in medioapical arrays.}, journal = {Molecular Biology of the Cell}, volume = {33}, year = {2022}, month = {2022 Sep 15}, pages = {ar94}, abstract = {

Arrays of actin filaments (F-actin) near the apical surface of epithelial cells (medioapical arrays) contribute to apical constriction and morphogenesis throughout phylogeny. Here, superresolution approaches (grazing incidence structured illumination, GI-SIM, and lattice light sheet, LLSM) microscopy resolve individual, fluorescently labeled F-actin and bipolar myosin filaments that drive amnioserosa cell shape changes during dorsal closure in . In expanded cells, F-actin and myosin form loose, apically domed meshworks at the plasma membrane. The arrays condense as cells contract, drawing the domes into the plane of the junctional belts. As condensation continues, individual filaments are no longer uniformly apparent. As cells expand, arrays of actomyosin are again resolved-some F-actin turnover likely occurs, but a large fraction of existing filaments rearrange. In morphologically isotropic cells, actin filaments are randomly oriented and during contraction are drawn together but remain essentially randomly oriented. In anisotropic cells, largely parallel actin filaments are drawn closer to one another. Our images offer unparalleled resolution of F-actin in embryonic tissue, show that medioapical arrays are tightly apposed to the plasma membrane and are continuous with meshworks of lamellar F-actin. Medioapical arrays thereby constitute modified cell cortex. In concert with other tagged array components, superresolution imaging of live specimens will offer new understanding of cortical architecture and function.

}, keywords = {Actin Cytoskeleton, Actins, Actomyosin, Animals, Drosophila, Microscopy, Myosins}, issn = {1939-4586}, doi = {10.1091/mbc.E21-11-0537}, author = {Moore, Regan P and Fogerson, Stephanie M and Tulu, U Serdar and Yu, Jason W and Cox, Amanda H and Sican, Melissa A and Li, Dong and Legant, Wesley R and Weigel, Aubrey V and Crawford, Janice M and Betzig, Eric and Kiehart, Daniel P} } @article {68078, title = {Super-resolution microscopy reveals actomyosin dynamics in medioapical arrays.}, journal = {Molecular Biology of the Cell}, year = {2022}, month = {2022 May 11}, pages = {mbcE21110537}, abstract = {

Arrays of actin filaments (F-actin) near the apical surface of epithelial cells (medioapical arrays) contribute to apical constriction and morphogenesis throughout phylogeny. Here, super-resolution approaches (grazing incidence structured illumination, GI-SIM and lattice light sheet, LLSM) microscopy resolve individual, fluorescently labeled F-actin and bipolar myosin filaments that drive amnioserosa cell shape changes during dorsal closure in . In expanded cells, F-actin and myosin form loose, apically domed meshworks at the plasma membrane. The arrays condense as cells contract, drawing the domes into the plane of the junctional belts. As condensation continues, individual filaments are no longer uniformly apparent. As cells expand, arrays of actomyosin are again resolved - some F-actin turnover likely occurs, but a large fraction of existing filaments rearrange. In morphologically isotropic cells, actin filaments are randomly oriented and during contraction, are drawn together but remain essentially randomly oriented. In anisotropic cells, largely parallel actin filaments are drawn closer to one another. Our images offer unparalleled resolution of F-actin in embryonic tissue show that medioapical arrays are tightly apposed to the plasma membrane, are continuous with meshworks of lamellar F-actin and thereby constitute modified cell cortex. In concert with other tagged array components, super-resolution imaging of live specimens will offer new understanding of cortical architecture and function. [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text].

}, issn = {1939-4586}, doi = {10.1091/mbc.E21-11-0537}, author = {Moore, Regan P and Fogerson, Stephanie M and Tulu, U Serdar and Yu, Jason W and Cox, Amanda H and Sican, Melissa A and Li, Dong and Legant, Wesley R and Weigel, Aubrey V and Crawford, Janice M and Betzig, Eric and Kiehart, Daniel P} } @article {68101, title = {Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy.}, journal = {Scientific Reports}, volume = {12}, year = {2022}, month = {2022 May 20}, pages = {8582}, abstract = {

The three-dimensional (3D) genome structure plays a fundamental role in gene regulation and cellular functions. Recent studies in 3D genomics inferred the very basic functional chromatin folding structures known as chromatin loops, the long-range chromatin interactions that are mediated by protein factors and dynamically extruded by cohesin. We combined the use of FISH staining of a very short (33\ kb) chromatin fragment, interferometric photoactivated localization microscopy (iPALM), and traveling salesman problem-based heuristic loop reconstruction algorithm from an image of the one of the strongest CTCF-mediated chromatin loops in human lymphoblastoid cells. In total, we have generated thirteen good quality images of the target chromatin region with 2-22\ nm oligo probe localization precision. We visualized the shape of the single chromatin loops with unprecedented genomic resolution which allowed us to study the structural heterogeneity of chromatin looping. We were able to compare the physical distance maps from all reconstructed image-driven computational models with contact frequencies observed by ChIA-PET and Hi-C genomic-driven methods to examine the concordance between single cell imaging and population based genomic data.

}, keywords = {Chromatin, Chromatin Immunoprecipitation Sequencing, Chromosomes, Genome, Humans, Microscopy}, issn = {2045-2322}, doi = {10.1038/s41598-022-12568-9}, author = {Parteka-Tojek, Zofia and Zhu, Jacqueline Jufen and Lee, Byoungkoo and Jodkowska, Karolina and Wang, Ping and Aaron, Jesse and Chew, Teng-Leong and Banecki, Krzysztof and Plewczy{\'n}ski, Dariusz and Ruan, Yijun} } @article {68022, title = {Systematic characterization of wing mechanosensors that monitor airflow and wing deformations.}, journal = {iScience}, volume = {25}, year = {2022}, month = {2022 Apr 15}, pages = {104150}, abstract = {

Animal wings deform during flight in ways that can enhance lift, facilitate flight control, and mitigate damage. Monitoring the structural and aerodynamic state of the wing is challenging because deformations are passive, and the flow fields are unsteady; it requires distributed mechanosensors that respond to local airflow and strain on the wing. Without a complete map of the sensor arrays, it is impossible to model control strategies underpinned by them. Here, we present the first systematic characterization of mechanosensors on the dragonfly{\textquoteright}s wings: morphology, distribution, and wiring. By combining a cross-species survey of sensor distribution with quantitative neuroanatomy and a high-fidelity finite element analysis, we show that the mechanosensors are well placed to perceive features of the wing dynamics relevant to flight. This work describes the wing sensory apparatus in its entirety and advances our understanding of the sensorimotor loop that facilitates exquisite flight control in animals with highly deformable wings.

}, issn = {2589-0042}, doi = {10.1016/j.isci.2022.104150}, author = {Fabian, Joseph and Siwanowicz, Igor and Uhrhan, Myriam and Maeda, Masateru and Bomphrey, Richard J and Lin, Huai-Ti} } @article {68145, title = {Targeting LIPA independent of its lipase activity is a therapeutic strategy in solid tumors via induction of endoplasmic reticulum stress.}, journal = {Nature Cancer}, volume = {3}, year = {2022}, month = {2022 Jun 02}, pages = {866-884}, abstract = {

Triple-negative breast cancer (TNBC) has a poor clinical outcome, due to a lack of actionable therapeutic targets. Herein we define lysosomal acid lipase A (LIPA) as a viable molecular target in TNBC and identify a stereospecific small molecule (ERX-41) that binds LIPA. ERX-41 induces endoplasmic reticulum (ER) stress resulting in cell death, and this effect is on target as evidenced by specific LIPA mutations providing resistance. Importantly, we demonstrate that ERX-41 activity is independent of LIPA lipase function but dependent on its ER localization. Mechanistically, ERX-41 binding of LIPA decreases expression of multiple ER-resident proteins involved in protein folding. This targeted vulnerability has a large therapeutic window, with no adverse effects either on normal mammary epithelial cells or in mice. Our study implicates a targeted strategy for solid tumors, including breast, brain, pancreatic and ovarian, whereby small, orally bioavailable molecules targeting LIPA block protein folding, induce ER stress and result in tumor cell death.

}, issn = {2662-1347}, doi = {10.1038/s43018-022-00389-8}, author = {Liu, Xihui and Viswanadhapalli, Suryavathi and Kumar, Shourya and Lee, Tae-Kyung and Moore, Andrew and Ma, Shihong and Chen, Liping and Hsieh, Michael and Li, Mengxing and Sareddy, Gangadhara R and Parra, Karla and Blatt, Eliot B and Reese, Tanner C and Zhao, Yuting and Chang, Annabel and Yan, Hui and Xu, Zhenming and Pratap, Uday P and Liu, Zexuan and Roggero, Carlos M and Tan, Zhenqiu and Weintraub, Susan T and Peng, Yan and Tekmal, Rajeshwar R and Arteaga, Carlos L and Lippincott-Schwartz, Jennifer and Vadlamudi, Ratna K and Ahn, Jung-Mo and Raj, Ganesh V} } @article {67948, title = {Taste quality interactions and transformations in a sensorimotor circuit}, journal = {eLife}, year = {2022}, month = {2022 Jul 06}, abstract = {

Taste detection and hunger state dynamically regulate the decision to initiate feeding. To study how context-appropriate feeding decisions are generated, we combined synaptic resolution circuit reconstruction with targeted genetic access to specific neurons to elucidate a gustatory sensorimotor circuit for feeding initiation in\ Drosophila melanogaster. This circuit connects gustatory sensory neurons to proboscis motor neurons through three intermediate layers. Most of the neurons in this pathway are necessary and sufficient for proboscis extension, a feeding initiation behavior, and respond selectively to sugar taste detection. Hunger signals act at select second-order neurons to increase feeding initiation in food-deprived animals. In contrast, a bitter taste pathway inhibits premotor neurons, illuminating a central mechanism that weighs sugar and bitter tastes to promote or inhibit feeding. Together, these studies reveal the neural circuit basis for the integration of external taste detection and internal nutritive state to flexibly execute a critical feeding decision.

}, doi = {10.1101/2022.03.06.483180}, url = {https://doi.org/10.1101/2022.03.06.483180}, author = {Philip K. Shiu and Gabriella R. Sterne and Stefanie Engert and Barry J. Dickson and Kristin Scott} } @article {68518, title = {TEMPO enables sequential genetic labeling and manipulation of vertebrate cell lineages.}, journal = {Neuron}, year = {2022}, month = {2022 Nov 18}, abstract = {

During development, regulatory factors appear in a precise order to determine cell fates over time. Consequently, to investigate complex tissue development, it is necessary to visualize and manipulate cell lineages with temporal control. Current strategies for tracing vertebrate cell lineages lack genetic access to sequentially produced cells. Here, we present TEMPO (Temporal Encoding and Manipulation in a Predefined Order), an imaging-readable genetic tool allowing differential labeling and manipulation of consecutive cell generations in vertebrates. TEMPO is based on CRISPR and powered by a cascade of gRNAs that drive orderly activation and inactivation of reporters and/or effectors. Using TEMPO to visualize zebrafish and mouse neurogenesis, we recapitulated birth-order-dependent neuronal fates. Temporally manipulating cell-cycle regulators in mouse cortex progenitors altered the proportion and distribution of neurons and glia, revealing the effects of temporal gene perturbation on serial cell fates. Thus, TEMPO enables sequential manipulation of molecular factors, crucial to study cell-type specification.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2022.10.035}, author = {Espinosa-Medina, Isabel and Feliciano, Daniel and Belmonte-Mateos, Carla and Linda Miyares, Rosa and Garcia-Marques, Jorge and Foster, Benjamin and Lindo, Sarah and Pujades, Cristina and Koyama, Minoru and Lee, Tzumin} } @article {67928, title = {Three Mutations Convert the Selectivity of a Protein Sensor From Nicotinic Agonists to S-Methadone For Use in Cells, Organelles, and Biofluids.}, journal = {Journal of the American Chemical Society}, volume = {144}, year = {2022}, month = {2022 May 18}, abstract = {

We report a reagentless, intensity-based S-methadone fluorescent sensor, iS-methadoneSnFR, consisting of a circularly permuted GFP inserted within the sequence of a mutated bacterial periplasmic binding protein (PBP). We used directed evolution to convert a previously reported nicotine-binding PBP to a selective S-methadone-binding sensor, via three mutations in the PBP{\textquoteright}s second shell and hinge regions. iS-methadoneSnFR displays sensitivity across the pharmacologically relevant range and selectivity against endogenous analytes and other opioids. Robust iS-methadoneSnFR responses in human sweat and saliva and mouse serum enable diagnostic uses. Genetic encoding and imaging in mammalian demonstrated the acid trapping of S-methadone in the Golgi apparatus where opioid receptors can signal. This work shows a straightforward strategy in adapting existing PBPs to serve real-time applications ranging from subcellular to personal pharmacokinetics.

}, doi = {10.1101/2022.02.24.481226}, author = {Anand K. Muthusamy and Charlene H. Kim and Scott C. Virgil and Hailey J. Knox and Jonathan S. Marvin and Aaron L. Nichols and Bruce N. Cohen and Dennis A. Dougherty and Loren L. Looger and Henry A. Lester} } @article {67859, title = {Toroidal topology of population activity in grid cells.}, journal = {Nature}, volume = {602}, year = {2022}, month = {2022 Jan 12}, pages = {123-128}, abstract = {

The medial entorhinal cortex is part of a neural system for mapping the position of an individual within a physical environment. Grid cells, a key component of this system, fire in a characteristic hexagonal pattern of locations, and are organized in modules that collectively form a population code for the animal{\textquoteright}s allocentric position. The invariance of the correlation structure of this population code across environments and behavioural states, independent of specific sensory inputs, has pointed to intrinsic, recurrently connected continuous attractor networks (CANs) as a possible substrate of the grid pattern. However, whether grid cell networks show continuous attractor dynamics, and how they interface with inputs from the environment, has remained unclear owing to the small samples of cells obtained so far. Here, using simultaneous recordings from many hundreds of grid cells and subsequent topological data analysis, we show that the joint activity of grid cells from an individual module resides on a toroidal manifold, as expected in a two-dimensional CAN. Positions on the torus correspond to positions of the moving animal in the environment. Individual cells are preferentially active at singular positions on the torus. Their positions are maintained between environments and from wakefulness to sleep, as predicted by CAN models for grid cells but not by alternative feedforward models. This demonstration of network dynamics on a toroidal manifold provides a population-level visualization of CAN dynamics in grid cells.

}, issn = {1476-4687}, doi = {10.1038/s41586-021-04268-7}, author = {Gardner, Richard J and Hermansen, Erik and Pachitariu, Marius and Burak, Yoram and Baas, Nils A and Dunn, Benjamin A and Moser, May-Britt and Moser, Edvard I} } @article {68295, title = {Tracing and Manipulating Drosophila Cell Lineages Based on CRISPR: CaSSA and CLADES.}, journal = {Methods in Molecular Biology}, volume = {2540}, year = {2022}, month = {2022 Sep 02}, pages = {201-217}, abstract = {

Cell lineage defines the mitotic connection between cells that make up an organism. Mapping these connections in relation to cell identity offers an extraordinary insight into the mechanisms underlying normal and pathological development. The analysis of molecular determinants involved in the acquisition of cell identity requires gaining experimental access to precise parts of cell lineages. Recently, we have developed CaSSA and CLADES, a new technology based on CRISPR that allows targeting and labeling specific lineage branches. Here we discuss how to better exploit this technology for lineage studies in Drosophila, with an emphasis on neuronal specification.

}, keywords = {Animals, Cell Lineage, Clustered Regularly Interspaced Short Palindromic Repeats, Drosophila, Neurons}, issn = {1940-6029}, doi = {10.1007/978-1-0716-2541-5_9}, author = {Garcia-Marques, Jorge and Lee, Tzumin} } @conference {68367, title = {Tracking by Weakly-Supervised Learning and Graph Optimization for Whole-Embryo C. elegans lineages}, booktitle = {International Conference on Medical Image Computing and Computer-Assisted Intervention}, year = {2022}, month = {2022 Sep 16}, publisher = {Springer Nature Switzerland}, organization = {Springer Nature Switzerland}, address = {Cham}, abstract = {

Tracking all nuclei of an embryo in noisy and dense fluorescence microscopy data is a challenging task. We build upon a recent method for nuclei tracking that combines weakly-supervised learning from a small set of nuclei center point annotations with an integer linear program (ILP) for optimal cell lineage extraction. Our work specifically addresses the following challenging properties of\ C. elegans\ embryo recordings: (1) Many cell divisions as compared to benchmark recordings of other organisms, and (2) the presence of polar bodies that are easily mistaken as cell nuclei. To cope with (1), we devise and incorporate a learnt cell division detector. To cope with (2), we employ a learnt polar body detector. We further propose automated ILP weights tuning via a structured SVM, alleviating the need for tedious manual set-up of a respective grid search.

}, isbn = {978-3-031-16439-2}, doi = {10.1007/978-3-031-16440-8}, url = {https://link.springer.com/10.1007/978-3-031-16440-8}, editor = {Wang, Linwei and Dou, Qi and Fletcher, P. Thomas and Speidel, Stefanie and Li, Shuo} } @article {68419, title = {Transcription factor Acj6 controls dendrite targeting via a combinatorial cell-surface code.}, journal = {Neuron}, volume = {110}, year = {2022}, month = {07/2022}, pages = {2299-2314.e8}, abstract = {

Transcription factors specify the fate and connectivity of developing neurons. We investigate how a lineage-specific transcription factor, Acj6, controls the precise dendrite targeting of Drosophila olfactory projection neurons (PNs) by regulating the expression of cell-surface proteins. Quantitative cell-surface proteomic profiling of wild-type and acj6 mutant PNs in intact developing brains, and a proteome-informed genetic screen identified PN surface proteins that execute Acj6-regulated wiring decisions. These include canonical cell adhesion molecules and proteins previously not associated with wiring, such as Piezo, whose mechanosensitive ion channel activity is dispensable for its function in PN dendrite targeting. Comprehensive genetic analyses revealed that Acj6 employs unique sets of cell-surface proteins in different PN types for dendrite targeting. Combined expression of Acj6 wiring executors rescued acj6 mutant phenotypes with higher efficacy and breadth than expression of individual executors. Thus, Acj6 controls wiring specificity of different neuron types by specifying distinct combinatorial expression of cell-surface executors.

}, keywords = {Animals, Dendrites, Drosophila, Drosophila Proteins, Ion Channels, Membrane Proteins, Nerve Tissue Proteins, Olfactory Pathways, Olfactory Receptor Neurons, POU Domain Factors, Proteomics, Transcription Factors}, issn = {1097-4199}, doi = {10.1016/j.neuron.2022.04.026}, author = {Xie, Qijing and Li, Jiefu and Li, Hongjie and Udeshi, Namrata D and Svinkina, Tanya and Orlin, Daniel and Kohani, Sayeh and Guajardo, Ricardo and Mani, D R and Xu, Chuanyun and Li, Tongchao and Han, Shuo and Wei, Wei and Shuster, S Andrew and Luginbuhl, David J and Quake, Stephen R and Murthy, Swetha E and Ting, Alice Y and Carr, Steven A and Luo, Liqun} } @article {67906, title = {Transgenic tools for targeted chromosome rearrangements allow construction of balancer chromosomes in non-melanogaster Drosophila species.}, journal = {G3 (Bethesda)}, year = {2022}, month = {2022 Feb 10}, abstract = {

Perhaps the most valuable single set of resources for genetic studies of Drosophila melanogaster is the collection of multiply-inverted chromosomes commonly known as balancer chromosomes. Balancers prevent the recovery of recombination exchange products within genomic regions included in inversions and allow perpetual maintenance of deleterious alleles in living stocks and the execution of complex genetic crosses. Balancer chromosomes have been generated traditionally by exposing animals to ionizing radiation and screening for altered chromosome structure or for unusual marker segregation patterns. These approaches are tedious and unpredictable, and have failed to produce the desired products in some species. Here I describe transgenic tools that allow targeted chromosome rearrangements in Drosophila species. The key new resources are engineered reporter genes containing introns with yeast recombination sites and enhancers that drive fluorescent reporter genes in multiple body regions. These tools were used to generate a doubly-inverted chromosome 3R in D. simulans that serves as an effective balancer chromosome.

}, issn = {2160-1836}, doi = {10.1093/g3journal/jkac030}, author = {Stern, David L} } @article {67988, title = {Transverse endoplasmic reticulum expansion in hereditary spastic paraplegia corticospinal axons.}, journal = {Human Molecular Genetics}, year = {2022}, month = {2022 Mar 26}, abstract = {

Hereditary spastic paraplegias (HSPs) comprise a large group of inherited neurologic disorders affecting the longest corticospinal axons (SPG1-86 plus others), with shared manifestations of lower extremity spasticity and gait impairment. Common autosomal dominant HSPs are caused by mutations in genes encoding the microtubule-severing ATPase spastin (SPAST; SPG4), the membrane-bound GTPase atlastin-1 (ATL1; SPG3A), and the reticulon-like, microtubule-binding protein REEP1 (REEP1; SPG31). These proteins bind one another and function in shaping the tubular endoplasmic reticulum (ER) network. Typically, mouse models of HSPs have mild, later-onset phenotypes, possibly reflecting far shorter lengths of their corticospinal axons relative to humans. Here, we have generated a robust, double mutant mouse model of HSP in which atlastin-1 is genetically modified with a K80A knock-in (KI) missense change that abolishes its GTPase activity, while its binding partner Reep1 is knocked out. Atl1KI/KI/Reep1-/- mice exhibit early-onset and rapidly progressive declines in several motor function tests. Also, ER in mutant corticospinal axons dramatically expands transversely and periodically in a mutation dosage-dependent manner to create a ladder-like appearance, based on reconstructions of focused ion beam-scanning electron microscopy datasets using machine learning-based auto-segmentation. In lockstep with changes in ER morphology, axonal mitochondria are fragmented and proportions of hypophosphorylated neurofilament H and M subunits are dramatically increased in Atl1KI/KI/Reep1-/- spinal cord. Co-occurrence of these findings links ER morphology changes to alterations in mitochondrial morphology and cytoskeletal organization. Atl1KI/KI/Reep1-/- mice represent an early-onset rodent HSP model with robust behavioral and cellular readouts for testing novel therapies.

}, issn = {1460-2083}, doi = {10.1093/hmg/ddac072}, author = {Zhu, Peng-Peng and Hung, Hui-Fang and Batchenkova, Natalia and Nixon-Abell, Jonathon and Henderson, James and Zheng, Pengli and Renvois{\'e}, Benoit and Pang, Song and Xu, C Shan and Saalfeld, Stephan and Funke, Jan and Xie, Yuxiang and Svara, Fabian and Hess, Harald F and Blackstone, Craig} } @article {68298, title = {Transverse endoplasmic reticulum expansion in hereditary spastic paraplegia corticospinal axons.}, journal = {Human Molecular Genetics}, volume = {31}, year = {2022}, month = {2022 Aug 23}, pages = {2779-2795}, abstract = {

Hereditary spastic paraplegias (HSPs) comprise a large group of inherited neurologic disorders affecting the longest corticospinal axons (SPG1-86 plus others), with shared manifestations of lower extremity spasticity and gait impairment. Common autosomal dominant HSPs are caused by mutations in genes encoding the microtubule-severing ATPase spastin (SPAST; SPG4), the membrane-bound GTPase atlastin-1 (ATL1; SPG3A) and the reticulon-like, microtubule-binding protein REEP1 (REEP1; SPG31). These proteins bind one another and function in shaping the tubular endoplasmic reticulum (ER) network. Typically, mouse models of HSPs have mild, later onset phenotypes, possibly reflecting far shorter lengths of their corticospinal axons relative to humans. Here, we have generated a robust, double mutant mouse model of HSP in which atlastin-1 is genetically modified with a K80A knock-in (KI) missense change that abolishes its GTPase activity, whereas its binding partner Reep1 is knocked out. Atl1KI/KI/Reep1-/- mice exhibit early onset and rapidly progressive declines in several motor function tests. Also, ER in mutant corticospinal axons dramatically expands transversely and periodically in a mutation dosage-dependent manner to create a ladder-like appearance, on the basis of reconstructions of focused ion beam-scanning electron microscopy datasets using machine learning-based auto-segmentation. In lockstep with changes in ER morphology, axonal mitochondria are fragmented and proportions of hypophosphorylated neurofilament H and M subunits are dramatically increased in Atl1KI/KI/Reep1-/- spinal cord. Co-occurrence of these findings links ER morphology changes to alterations in mitochondrial morphology and cytoskeletal organization. Atl1KI/KI/Reep1-/- mice represent an early onset rodent HSP model with robust behavioral and cellular readouts for testing novel therapies.

}, keywords = {Animals, Axons, Disease Models, Animal, Endoplasmic Reticulum, GTP Phosphohydrolases, Humans, Membrane Proteins, Membrane Transport Proteins, Mice, Mice, Knockout, Mutation, Spastic Paraplegia, Hereditary, Spastin}, issn = {1460-2083}, doi = {10.1093/hmg/ddac072}, author = {Zhu, Peng-Peng and Hung, Hui-Fang and Batchenkova, Natalia and Nixon-Abell, Jonathon and Henderson, James and Zheng, Pengli and Renvois{\'e}, Benoit and Pang, Song and Xu, C Shan and Saalfeld, Stephan and Funke, Jan and Xie, Yuxiang and Svara, Fabian and Hess, Harald F and Blackstone, Craig} } @article {68250, title = {Using Simulated Training Data of Voxel-Level Generative Models to Improve 3D Neuron Reconstruction.}, journal = {IEEE Transactions on Medical Imaging}, volume = {PP}, year = {2022}, month = {2022 Jul 14}, abstract = {

Reconstructing neuron morphologies from fluorescence microscope images plays a critical role in neuroscience studies. It relies on image segmentation to produce initial masks either for further processing or final results to represent neuronal morphologies. This has been a challenging step due to the variation and complexity of noisy intensity patterns in neuron images acquired from microscopes. Whereas progresses in deep learning have brought the goal of accurate segmentation much closer to reality, creating training data for producing powerful neural networks is often laborious. To overcome the difficulty of obtaining a vast number of annotated data, we propose a novel strategy of using two-stage generative models to simulate training data with voxel-level labels. Trained upon unlabeled data by optimizing a novel objective function of preserving predefined labels, the models are able to synthesize realistic 3D images with underlying voxel labels. We showed that these synthetic images could train segmentation networks to obtain even better performance than manually labeled data. To demonstrate an immediate impact of our work, we further showed that segmentation results produced by networks trained upon synthetic data could be used to improve existing neuron reconstruction methods.

}, issn = {1558-254X}, doi = {10.1109/TMI.2022.3191011}, author = {Liu, Chao and Wang, Deli and Zhang, Han and Wu, Wei and Sun, Wenzhi and Zhao, Ting and Zheng, Nenggan} } @article {68276, title = {A vast space of compact strategies for highly efficient decisions}, journal = {Sci. Adv.}, volume = {10}, year = {2022}, month = {2024 Jun 21}, abstract = {

Inference-based decision-making, which underlies a broad range of behavioral tasks, is typically studied using a small number of handcrafted models. We instead enumerate a complete ensemble of strategies that could be used to effectively, but not necessarily optimally, solve a dynamic foraging task. Each strategy is expressed as a behavioral "program" that uses a limited number of internal states to specify actions conditioned on past observations. We show that the ensemble of strategies is enormous-comprising a quarter million programs with up to five internal states-but can nevertheless be understood in terms of algorithmic "mutations" that alter the structure of individual programs. We devise embedding algorithms that reveal how mutations away from a Bayesian-like strategy can diversify behavior while preserving performance, and we construct a compositional description to link low-dimensional changes in algorithmic structure with high-dimensional changes in behavior. Together, this work provides an alternative approach for understanding individual variability in behavior across animals and tasks.

}, doi = {10.1101/2022.08.10.503471}, url = {https://doi.org/10.1101/2022.08.10.503471}, author = {Tzuhsuan Ma and Ann M Hermundstad} } @article {68812, title = {A viral toolbox for conditional and transneuronal gene expression in zebrafish}, journal = {eLife}, volume = {11}, year = {2022}, month = {07/2022}, pages = {e77153}, abstract = {

The zebrafish is an important model in systems neuroscience but viral tools to dissect the structure and function of neuronal circuitry are not established. We developed methods for efficient gene transfer and retrograde tracing in adult and larval zebrafish by herpes simplex viruses (HSV1). HSV1 was combined with the Gal4/UAS system to target cell types with high spatial, temporal, and molecular specificity. We also established methods for efficient transneuronal tracing by modified rabies viruses in zebrafish. We demonstrate that HSV1 and rabies viruses can be used to visualize and manipulate genetically or anatomically identified neurons within and across different brain areas of adult and larval zebrafish. An expandable library of viruses is provided to express fluorescent proteins, calcium indicators, optogenetic probes, toxins and other molecular tools. This toolbox creates new opportunities to interrogate neuronal circuits in zebrafish through combinations of genetic and viral approaches.

}, keywords = {Gene Transfer, Imaging, neuronal circuit, viral vector}, issn = {2050-084X}, doi = {10.7554/eLife.77153}, url = {https://doi.org/10.7554/eLife.77153}, author = {Satou, Chie and Neve, Rachael L and Oyibo, Hassana K and Zmarz, Pawel and Huang, Kuo-Hua and Arn Bouldoires, Estelle and Mori, Takuma and Higashijima, Shin-Ichi and Keller, Georg B and Friedrich, Rainer W}, editor = {Bagnall, Martha W and Stainier, Didier YR and Jin, Lei} } @article {66029, title = {Visualizing cellular and tissue ultrastructure using Ten-fold Robust Expansion Microscopy (TREx)}, journal = {eLife}, year = {2022}, month = {2022 Feb 18}, abstract = {

Expansion microscopy (ExM) is a powerful technique to overcome the diffraction limit of light microscopy that can be applied in both tissues and cells. In ExM, samples are embedded in a swellable polymer gel to physically expand the sample and isotropically increase resolution in x, y and z. The maximum resolution increase is limited by the expansion factor of the polymer gel, which is four-fold for the original ExM protocol. Variations on the original ExM method have been reported that allow for greater expansion factors, for example using iterative expansion, but at the cost of ease of adoption or versatility. Here, we systematically explore the ExM recipe space and present a novel method termed Ten-fold Robust Expansion Microscopy (TREx) that, like the original ExM method, requires no specialized equipment or procedures to carry out. We demonstrate that TREx gels expand ten-fold, can be handled easily, and can be applied to both thick tissue sections and cells enabling high-resolution subcellular imaging in a single expansion step. We show that applying TREx on antibody-stained samples can be combined with off-the-shelf small molecule stains for both total protein and membranes to provide ultrastructural context to subcellular protein localization.

}, doi = {https://doi.org/10.1101/2021.02.03.428837}, author = {Hugo G.J. Damstra and Boaz Mohar and Mark Eddison and Anna Akhmanova and Lukas C. Kapitein and Paul W. Tillberg} } @article {67894, title = {Visualizing Synaptic Dopamine Efflux with a 2D Nanofilm.}, journal = {eLife}, year = {2022}, month = {2022 Jul 04}, abstract = {

Chemical neurotransmission constitutes one of the fundamental modalities of communication between neurons. Monitoring release of these chemicals has traditionally been difficult to carry out at spatial and temporal scales relevant to neuron function. To understand chemical neurotransmission more fully, we need to improve the spatial and temporal resolutions of measurements for neurotransmitter release. To address this, we engineered a chemi-sensitive, two-dimensional nanofilm that facilitates subcellular visualization of the release and diffusion of the neurochemical dopamine with synaptic resolution, quantal sensitivity, and simultaneously from hundreds of release sites. Using this technology, we were able to monitor the spatiotemporal dynamics of dopamine release in dendritic processes, a poorly understood phenomenon. We found that dopamine release is broadcast from a subset of dendritic processes as hotspots that have a mean spatial spread of ≈3.2 {\textmu}m (full width at half maximum) and are observed with a mean spatial frequency of 1 hotspot per ≈7.5 {\textmu}m of dendritic length. Major dendrites of dopamine neurons and fine dendritic processes, as well as dendritic arbors and dendrites with no apparent varicose morphology participated in dopamine release. Remarkably, these release hotspots colocalized with Bassoon, suggesting that Bassoon may contribute to organizing active zones in dendrites, similar to its role in axon terminals.

}, doi = {10.7554/eLife.78773}, url = {https://doi.org/10.7554/eLife.78773}, author = {Chandima Bulumulla and Andrew T. Krasley and Deepika Walpita and Abraham G. Beyene} } @article {67991, title = {Voltage imaging identifies spinal circuits that modulate locomotor adaptation in zebrafish.}, journal = {Neuron}, volume = {110}, year = {2022}, month = {2022 Apr 06}, pages = {1211-1222.e4}, abstract = {

Motor systems must continuously adapt their output to maintain a desired trajectory. While the spinal circuits underlying rhythmic locomotion are well described, little is known about how the network modulates its output strength. A major challenge has been the difficulty of recording from spinal neurons during behavior. Here, we use voltage imaging to map the membrane potential of large populations of glutamatergic neurons throughout the spinal cord of the larval zebrafish during fictive swimming in a virtual environment. We characterized a previously undescribed subpopulation of tonic-spiking ventral V3 neurons whose spike rate correlated with swimming strength and bout length. Optogenetic activation of V3 neurons led to stronger swimming and longer bouts but did not affect tail beat frequency. Genetic ablation of V3 neurons led to reduced locomotor adaptation. The power of voltage imaging allowed us to identify V3 neurons as a critical driver of locomotor adaptation in zebrafish.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2022.01.001}, author = {B{\"o}hm, Urs L and Kimura, Yukiko and Kawashima, Takashi and Ahrens, Misha B and Higashijima, Shin-Ichi and Engert, Florian and Cohen, Adam E} } @article {67890, title = {Voltage imaging identifies spinal circuits that modulate locomotor adaptation in zebrafish.}, journal = {Neuron}, year = {2022}, month = {2022 Jan 24}, abstract = {

Motor systems must continuously adapt their output to maintain a desired trajectory. While the spinal circuits underlying rhythmic locomotion are well described, little is known about how the network modulates its output strength. A major challenge has been the difficulty of recording from spinal neurons during behavior. Here, we use voltage imaging to map the membrane potential of large populations of glutamatergic neurons throughout the spinal cord of the larval zebrafish during fictive swimming in a virtual environment. We characterized a previously undescribed subpopulation of tonic-spiking ventral V3 neurons whose spike rate correlated with swimming strength and bout length. Optogenetic activation of V3 neurons led to stronger swimming and longer bouts but did not affect tail beat frequency. Genetic ablation of V3 neurons led to reduced locomotor adaptation. The power of voltage imaging allowed us to identify V3 neurons as a critical driver of locomotor adaptation in zebrafish.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2022.01.001}, author = {B{\"o}hm, Urs L and Kimura, Yukiko and Kawashima, Takashi and Ahrens, Misha B and Higashijima, Shin-Ichi and Engert, Florian and Cohen, Adam E} } @article {68887, title = {Volume electron microscopy.}, journal = {Nature Reviews: Methods Primers}, volume = {2}, year = {2022}, month = {2022 Jul 07}, pages = {51}, abstract = {

Life exists in three dimensions, but until the turn of the century most electron microscopy methods provided only 2D image data. Recently, electron microscopy techniques capable of delving deep into the structure of cells and tissues have emerged, collectively called volume electron microscopy (vEM). Developments in vEM have been dubbed a quiet revolution as the field evolved from established transmission and scanning electron microscopy techniques, so early publications largely focused on the bioscience applications rather than the underlying technological breakthroughs. However, with an explosion in the uptake of vEM across the biosciences and fast-paced advances in volume, resolution, throughput and ease of use, it is timely to introduce the field to new audiences. In this Primer, we introduce the different vEM imaging modalities, the specialized sample processing and image analysis pipelines that accompany each modality and the types of information revealed in the data. We showcase key applications in the biosciences where vEM has helped make breakthrough discoveries and consider limitations and future directions. We aim to show new users how vEM can support discovery science in their own research fields and inspire broader uptake of the technology, finally allowing its full adoption into mainstream biological imaging.

}, issn = {2662-8449}, doi = {10.1038/s43586-022-00131-9}, author = {Peddie, Christopher J and Genoud, Christel and Kreshuk, Anna and Meechan, Kimberly and Micheva, Kristina D and Narayan, Kedar and Pape, Constantin and Parton, Robert G and Schieber, Nicole L and Schwab, Yannick and Titze, Benjamin and Verkade, Paul and Aubrey, Aubrey and Collinson, Lucy M} } @article {67987, title = {When light meets biology - how the specimen affects quantitative microscopy.}, journal = {Journal of Cell Science}, volume = {135}, year = {2022}, month = {2022 Mar 15}, abstract = {

Fluorescence microscopy images should not be treated as perfect representations of biology. Many factors within the biospecimen itself can drastically affect quantitative microscopy data. Whereas some sample-specific considerations, such as photobleaching and autofluorescence, are more commonly discussed, a holistic discussion of sample-related issues (which includes less-routine topics such as quenching, scattering and biological anisotropy) is required to appropriately guide life scientists through the subtleties inherent to bioimaging. Here, we consider how the interplay between light and a sample can cause common experimental pitfalls and unanticipated errors when drawing biological conclusions. Although some of these discrepancies can be minimized or controlled for, others require more pragmatic considerations when interpreting image data. Ultimately, the power lies in the hands of the experimenter. The goal of this Review is therefore to survey how biological samples can skew quantification and interpretation of microscopy data. Furthermore, we offer a perspective on how to manage many of these potential pitfalls.

}, issn = {1477-9137}, doi = {10.1242/jcs.259656}, author = {Reiche, Michael A and Aaron, Jesse S and Boehm, Ulrike and DeSantis, Michael C and Hobson, Chad M and Khuon, Satya and Lee, Rachel M and Chew, Teng-Leong} } @article {65905, title = {3D FIB-SEM reconstruction of microtubule-organelle interaction in whole primary mouse β cells.}, journal = {Journal of Cell Biology}, volume = {220}, year = {2021}, month = {2021 Feb 01}, abstract = {

Microtubules play a major role in intracellular trafficking of vesicles in endocrine cells. Detailed knowledge of microtubule organization and their relation to other cell constituents is crucial for understanding cell function. However, their role in insulin transport and secretion is under debate. Here, we use FIB-SEM to image islet β cells in their entirety with unprecedented resolution. We reconstruct mitochondria, Golgi apparati, centrioles, insulin secretory granules, and microtubules of seven β cells, and generate a comprehensive spatial map of microtubule-organelle interactions. We find that microtubules form nonradial networks that are predominantly not connected to either centrioles or endomembranes. Microtubule number and length, but not microtubule polymer density, vary with glucose stimulation. Furthermore, insulin secretory granules are enriched near the plasma membrane, where they associate with microtubules. In summary, we provide the first 3D reconstructions of complete microtubule networks in primary mammalian cells together with evidence regarding their importance for insulin secretory granule positioning and thus their supportive role in insulin secretion.

}, issn = {1540-8140}, doi = {10.1083/jcb.202010039}, author = {M{\"u}ller, Andreas and Schmidt, Deborah and Xu, C Shan and Pang, Song and D{\textquoteright}Costa, Joyson Verner and Kretschmar, Susanne and M{\"u}nster, Carla and Kurth, Thomas and Jug, Florian and Weigert, Martin and Hess, Harald F and Solimena, Michele} } @article {65319, title = {Accurate localization of linear probe electrodes across multiple brains.}, journal = {eNeuro}, volume = {8}, year = {2021}, month = {2021 Nov 12}, pages = {ENEURO.0241-21.2021}, author = {Liu, Liu D. and Chen, Susu and Economo, Michael N. and Li, Nuo and Svoboda, Karel} } @article {66018, title = {An Acquired and Endogenous Glycocalyx Forms a Bidirectional {\textquotedblleft}Don{\textquoteright}t Eat{\textquotedblright} and {\textquotedblleft}Don{\textquoteright}t Eat Me{\textquotedblright} Barrier to Phagocytosis}, journal = {Current Biology}, volume = {31}, year = {2021}, month = {Jan-01-2021}, pages = {77 - 89.e5}, abstract = {

Macrophages continuously survey their environment in search of pathogens or apoptotic corpses or debris. Targets intended for clearance expose ligands that initiate their phagocytosis ("eat me" signals), while others avoid phagocytosis by displaying inhibitory ligands ("don{\textquoteright}t eat me" signals). We report that such ligands can be obscured by the glycosaminoglycans and glycoproteins that coat pathogenic as well as malignant phagocytic targets. In addition, a reciprocal barrier of self-synthesized or acquired glycocalyx components on the macrophage surface shrouds phagocytic receptors, curtailing their ability to engage particles. The coating layers of macrophages and their targets hinder phagocytosis by both steric and electrostatic means. Their removal by enzymatic means is shown to markedly enhance phagocytic efficiency. In particular, we show that the removal of mucins, which are overexpressed in cancer cells, facilitates their clearance. These results shed light on the physical barriers that modulate phagocytosis, which have been heretofore underappreciated.

}, issn = {09609822}, doi = {10.1016/j.cub.2020.09.082}, url = {https://www.sciencedirect.com/science/article/pii/S0960982220314950?via\%3Dihub}, author = {Imbert, Paul R.C. and Saric, Amra and Pedram, Kayvon and Bertozzi, Carolyn R. and Grinstein, Sergio and Freeman, Spencer A.} } @article {67177, title = {Actin cables and comet tails organize mitochondrial networks in mitosis.}, journal = {Nature}, volume = {591}, year = {2021}, month = {2021 Mar 03}, pages = {659-664}, abstract = {

Symmetric cell division requires the even partitioning of genetic information and cytoplasmic contents between daughter cells. Whereas the mechanisms coordinating the segregation of the genome are well known, the processes that ensure organelle segregation between daughter cells remain less well understood. Here we identify multiple actin assemblies with distinct but complementary roles in mitochondrial organization and inheritance in mitosis. First, we find a dense meshwork of subcortical actin cables assembled throughout the mitotic cytoplasm. This network scaffolds the endoplasmic reticulum and organizes three-dimensional mitochondrial positioning to ensure the equal segregation of mitochondrial mass at cytokinesis. Second, we identify a dynamic wave of actin filaments reversibly assembling on the surface of mitochondria during mitosis. Mitochondria sampled by this wave are enveloped within actin clouds that can spontaneously break symmetry to form elongated comet tails. Mitochondrial comet tails promote randomly directed bursts of movement that shuffle mitochondrial position within the mother cell to randomize inheritance of healthy and damaged mitochondria between daughter cells. Thus, parallel mechanisms mediated by the actin cytoskeleton ensure both equal and random inheritance of mitochondria in symmetrically dividing cells.

}, issn = {1476-4687}, doi = {10.1038/s41586-021-03309-5}, author = {Moore, Andrew S and Coscia, Stephen M and Simpson, Cory L and Ortega, Fabian E and Wait, Eric C and Heddleston, John M and Nirschl, Jeffrey J and Obara, Christopher J and Guedes-Dias, Pedro and Boecker, C Alexander and Chew, Teng-Leong and Theriot, Julie A and Lippincott-Schwartz, Jennifer and Holzbaur, Erika L F} } @article {67304, title = {Activity-dependent Golgi satellite formation in dendrites reshapes the neuronal surface glycoproteome}, journal = {bioRxiv}, year = {2021}, month = {05/2021}, abstract = {

Activity-driven changes in the neuronal surface glycoproteome are known to occur with synapse formation, plasticity and related diseases, but their mechanistic basis and significance are unclear. Here, we observed that N-glycans on surface glycoproteins of dendrites shift from immature to mature forms containing sialic acid in response to increased neuronal excitation. In exploring the basis of these N-glycosylation alterations, we discovered they result from the growth and proliferation of Golgi satellites scattered throughout the dendrite. Golgi satellites that formed with neuronal excitation were in close association with ER exit sites and early endosomes and contained glycosylation machinery without the Golgi structural protein, GM130. They functioned as distal glycosylation stations in dendrites, terminally modifying sugars either on newly synthesized glycoproteins passing through the secretory pathway, or on surface glycoproteins taken up from the endocytic pathway. These activities led to major changes in the dendritic surface of excited neurons, impacting binding and uptake of lectins, as well as causing functional changes in neurotransmitter receptors such as nicotinic acetylcholine receptors. Neural activity thus boosts the activity of the dendrite{\textquoteright}s satellite micro-secretory system by redistributing Golgi enzymes involved in glycan modifications into peripheral Golgi satellites. This remodeling of the neuronal surface has potential significance for synaptic plasticity, addiction and disease.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2021.04.06.438745}, url = {https://doi.org/10.1101/2021.04.06.438745}, author = {Govind, Anitha P. and Jeyifous, Okunola and Russell, Theron A. and Yi, Zola and Weigel, Aubrey V. and Ramaprasad, Abhijit and Newell, Luke and Ramos, William and Valbuena, Fernando M. and Casler, Jason C. and Yan, Jing-Zhi and Glick, Benjamin S. and Swanson, Geoffrey T. and Lippincott-Schwartz, Jennifer and Green, William N.} } @article {67733, title = {Activity-dependent Golgi satellite formation in dendrites reshapes the neuronal surface glycoproteome.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Sep 21}, abstract = {

Activity-driven changes in the neuronal surface glycoproteome are known to occur with synapse formation, plasticity and related diseases, but their mechanistic basis and significance are unclear. Here, we observed that -glycans on surface glycoproteins of dendrites shift from immature to mature forms containing sialic acid in response to increased neuronal activation. In exploring the basis of these -glycosylation alterations, we discovered they result from the growth and proliferation of Golgi satellites scattered throughout the dendrite. Golgi satellites that formed during neuronal excitation were in close association with ER exit sites and early endosomes and contained glycosylation machinery without the Golgi structural protein, GM130. They functioned as distal glycosylation stations in dendrites, terminally modifying sugars either on newly synthesized glycoproteins passing through the secretory pathway, or on surface glycoproteins taken up from the endocytic pathway. These activities led to major changes in the dendritic surface of excited neurons, impacting binding and uptake of lectins, as well as causing functional changes in neurotransmitter receptors such as nicotinic acetylcholine receptors. Neural activity thus boosts the activity of the dendrite{\textquoteright}s satellite micro-secretory system by redistributing Golgi enzymes involved in glycan modifications into peripheral Golgi satellites. This remodeling of the neuronal surface has potential significance for synaptic plasticity, addiction and disease.

}, issn = {2050-084X}, doi = {10.7554/eLife.68910}, author = {Govind, Anitha P and Jeyifous, Okunola and Russell, Theron A and Yi, Zola and Weigel, Aubrey V and Ramaprasad, Abhijit and Newell, Luke and Ramos, William and Valbuena, Fernando M and Casler, Jason C and Yan, Jing-Zhi and Glick, Benjamin S and Swanson, Geoffrey T and Lippincott-Schwartz, Jennifer and Green, William N} } @article {67180, title = {Acupuncture modulates immunity in sepsis: Toward a science-based protocol.}, journal = {Autonomic Neuroscience}, volume = {232}, year = {2021}, month = {2021 Feb 27}, pages = {102793}, abstract = {

Sepsis is a serious medical condition in which immune dysfunction plays a key role. Previous treatments focused on chemotherapy to control immune function; however, a recognized effective compound or treatment has yet to be developed. Recent advances indicate that a neuromodulation approach with nerve stimulation allows developing a therapeutic strategy to control inflammation and improve organ functions in sepsis. As a quick, non-invasive technique of peripheral nerve stimulation, acupuncture has emerged as a promising therapy to provide significant advantages for immunomodulation in acute inflammation. Acupuncture obtains its regulatory effect by activating the somatic-autonomic-immune reflexes, including the somatic-sympathetic-splenic reflex, the somatic-sympathetic-adrenal reflex, the somatic-vagal-splenic reflex and the somatic-vagal-adrenal reflex, which produces a systemic effect. The peripheral nerve stimulation also induces local reflexes such as the somatic-sympathetic-lung-reflex, which then produces local effects. These mechanisms offer scientific guidance to design acupuncture protocols for immunomodulation and inflammation control, leading to an evidence-based comprehensive therapy recommendation.

}, issn = {1872-7484}, doi = {10.1016/j.autneu.2021.102793}, author = {Pan, Wei-Xing and Fan, Arthur Yin and Chen, Shaozong and Alemi, Sarah Faggert} } @article {67763, title = {An adaptive optics module for deep tissue multiphoton imaging in vivo.}, journal = {Nature Methods}, volume = {18}, year = {2021}, month = {2021 Oct 01}, pages = {1259-1264}, abstract = {

Understanding complex biological systems requires visualizing structures and processes deep within living organisms. We developed a compact adaptive optics module and incorporated it into two- and three-photon fluorescence microscopes, to measure and correct tissue-induced aberrations. We resolved synaptic structures in deep cortical and subcortical areas of the mouse brain, and demonstrated high-resolution imaging of neuronal structures and somatosensory-evoked calcium responses in the mouse spinal cord at great depths in vivo.

}, issn = {1548-7105}, doi = {10.1038/s41592-021-01279-0}, author = {Rodriguez, Cristina and Chen, Anderson and Rivera, Jos{\'e} A and Mohr, Manuel A and Liang, Yajie and Natan, Ryan G and Sun, Wenzhi and Milkie, Daniel E and Bifano, Thomas G and Chen, Xiaoke and Ji, Na} } @article {65895, title = {An adaptive optics module for deep tissue multiphoton imaging in vivo}, journal = {Nature Methods}, year = {2021}, month = {2021 Oct 04}, pages = {1259-64}, abstract = {

Understanding complex biological systems requires visualizing structures and processes deep within living organisms. We developed a compact adaptive optics module and incorporated it into two- and three-photon fluorescence microscopes, to measure and correct tissue-induced aberrations. We resolved synaptic structures in deep cortical and subcortical areas of the mouse brain, and demonstrated high-resolution imaging of neuronal structures and somatosensory-evoked calcium responses in the mouse spinal cord at unprecedented depths\ in vivo.

}, doi = {10.1038/s41592-021-01279-0}, author = {Cristina Rodr{\'\i}guez and Anderson Chen and Jos{\'e} A. Rivera and Manuel A. Mohr and Yajie liang and Wenzhi Sun and Daniel E. Milkie and Thomas G. Bifano and Xiaoke Chen and Na Ji} } @article {67298, title = {Adhesion-mediated mechanosignaling forces mitohormesis.}, journal = {Cell Metabolism}, volume = {33}, year = {2021}, month = {2021 July 6}, pages = {1322}, abstract = {

Mitochondria control eukaryotic cell fate by producing the energy needed to support life and the signals required to execute programed cell death. The biochemical milieu is known to affect mitochondrial function and contribute to the dysfunctional mitochondrial phenotypes implicated in cancer and the morbidities of aging. However, the physical characteristics of the extracellular matrix are also altered in cancerous and aging tissues. Here, we demonstrate that cells sense the physical properties of the extracellular matrix and activate a mitochondrial stress response that adaptively tunes mitochondrial function via solute carrier family 9 member A1-dependent ion exchange and heat shock factor 1-dependent transcription. Overall, our data indicate that adhesion-mediated mechanosignaling may play an unappreciated role in the altered mitochondrial functions observed in aging and cancer.

}, issn = {1932-7420}, doi = {10.1016/j.cmet.2021.04.017}, author = {Tharp, Kevin M and Higuchi-Sanabria, Ryo and Timblin, Greg A and Ford, Breanna and Garzon-Coral, Carlos and Schneider, Catherine and Muncie, Jonathon M and Stashko, Connor and Daniele, Joseph R and Moore, Andrew S and Frankino, Phillip A and Homentcovschi, Stefan and Manoli, Sagar S and Shao, Hao and Richards, Alicia L and Chen, Kuei-Ho and Hoeve, Johanna Ten and Ku, Gregory M and Hellerstein, Marc and Nomura, Daniel K and Saijo, Karou and Gestwicki, Jason and Dunn, Alexander R and Krogan, Nevan J and Swaney, Danielle L and Dillin, Andrew and Weaver, Valerie M} } @article {67302, title = {Advances in Confocal Microscopy and Selected Applications.}, journal = {Methods in Molecular Biology}, volume = {2304}, year = {2021}, month = {2021 May 28}, pages = {1-35}, abstract = {

Over the last 30 years, confocal microscopy has emerged as a primary tool for biological investigation across many disciplines. The simplicity of use and widespread accessibility of confocal microscopy ensure that it will have a prominent place in biological imaging for many years to come, even with the recent advances in light sheet and field synthesis microscopy. Since these more advanced technologies still require significant expertise to effectively implement and carry through to analysis, confocal microscopy-based approaches still remain the easiest way for biologists with minimal imaging experience to address fundamental questions about how their systems are arranged through space and time. In this review, we discuss a number of advanced applications of confocal microscopy for probing the spatiotemporal dynamics of biological systems.

}, issn = {1940-6029}, doi = {10.1007/978-1-0716-1402-0_1}, author = {Reilly, W Matt and Obara, Christopher J} } @article {67299, title = {Algorithms underlying flexible phototaxis in larval zebrafish.}, journal = {Journal of Experimental Biology}, volume = {224}, year = {2021}, month = {2021 May 15}, abstract = {

To thrive, organisms must maintain physiological and environmental variables in suitable ranges. Given that these variables undergo constant fluctuations over varying time scales, how do biological control systems maintain control over these values? We explored this question in the context of phototactic behavior in larval zebrafish. We demonstrate that larval zebrafish use phototaxis to maintain environmental luminance at a set point, that the value of this set point fluctuates on a time scale of seconds when environmental luminance changes, and that it is determined by calculating the mean input across both sides of the visual field. These results expand on previous studies of flexible phototaxis in larval zebrafish; they suggest that larval zebrafish exert homeostatic control over the luminance of their surroundings, and that feedback from the surroundings drives allostatic changes to the luminance set point. As such, we describe a novel behavioral algorithm with which larval zebrafish exert control over a sensory variable.

}, issn = {1477-9145}, doi = {10.1242/jeb.238386}, author = {Chen, Alex B and Deb, Diptodip and Bahl, Armin and Engert, Florian} } @article {67314, title = {Alpha-1 adrenergic receptor antagonists to prevent hyperinflammation and death from lower respiratory tract infection.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Jun 11}, abstract = {

In severe viral pneumonia, including Coronavirus disease 2019 (COVID-19), the viral replication phase is often followed by hyperinflammation, which can lead to acute respiratory distress syndrome, multi-organ failure, and death. We previously demonstrated that alpha-1 adrenergic receptor (⍺-AR) antagonists can prevent hyperinflammation and death in mice. Here, we conducted retrospective analyses in two cohorts of patients with acute respiratory distress (ARD, n = 18,547) and three cohorts with pneumonia (n = 400,907). Federated across two ARD cohorts, we find that patients exposed to ⍺-AR antagonists, as compared to unexposed patients, had a 34\% relative risk reduction for mechanical ventilation and death (OR = 0.70, p = 0.021). We replicated these methods on three pneumonia cohorts, all with similar effects on both outcomes. All results were robust to sensitivity analyses. These results highlight the urgent need for prospective trials testing whether prophylactic use of ⍺-AR antagonists ameliorates lower respiratory tract infection-associated hyperinflammation and death, as observed in COVID-19.

}, issn = {2050-084X}, doi = {10.7554/eLife.61700}, author = {Koenecke, Allison and Powell, Michael and Xiong, Ruoxuan and Shen, Zhu and Fischer, Nicole and Huq, Sakibul and Khalafallah, Adham M and Trevisan, Marco and Sparen, P{\"a}r and Carrero, Juan J and Nishimura, Akihiko and Caffo, Brian and Stuart, Elizabeth A and Bai, Renyuan and Staedtke, Verena and Thomas, David L and Papadopoulos, Nickolas and Kinzler, Ken W and Vogelstein, Bert and Zhou, Shibin and Bettegowda, Chetan and Konig, Maximilian F and Mensh, Brett D and Vogelstein, Joshua T and Athey, Susan} } @article {67235, title = {The anterior cingulate cortex directs exploration of alternative strategies.}, journal = {Neuron}, volume = {109}, year = {2021}, month = {2021 Jun 2}, pages = {1876-87}, abstract = {

The ability to adjust one{\textquoteright}s behavioral strategy in complex environments is at the core of cognition. Doing so efficiently requires monitoring the reliability of the ongoing strategy and, when appropriate, switching away from it to evaluate alternatives. Studies in humans and non-human primates have uncovered signals in the anterior cingulate cortex (ACC) that reflect the pressure to switch away from the ongoing strategy, whereas other ACC signals relate to the pursuit of alternatives. However, whether these signals underlie computations that actually underpin strategy switching or merely reflect tracking of related variables remains unclear. Here we provide causal evidence that the rodent ACC actively arbitrates between persisting with the ongoing behavioral strategy and temporarily switching away to re-evaluate alternatives. Furthermore, by individually perturbing distinct output pathways, we establish that the two associated computations-determining whether to switch strategy and committing to the pursuit of a specific alternative-are segregated in the ACC microcircuitry.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2021.03.028}, author = {Tervo, D Gowanlock R and Kuleshova, Elena and Manakov, Maxim and Proskurin, Mikhail and Karlsson, Mattias and Lustig, Andy and Behnam, Reza and Karpova, Alla Y} } @article {68475, title = {Arnold tongues in oscillator systems with nonuniform spatial driving.}, journal = {Phys Rev E}, volume = {103}, year = {2021}, month = {04/2021}, pages = {042211}, abstract = {

Nonlinear oscillator systems are ubiquitous in biology and physics, and their control is a practical problem in many experimental systems. Here we study this problem in the context of the two models of spatially coupled oscillators: the complex Ginzburg-Landau equation (CGLE) and a generalization of the CGLE in which oscillators are coupled through an external medium (emCGLE). We focus on external control drives that vary in both space and time. We find that the spatial distribution of the drive signal controls the frequency ranges over which oscillators synchronize to the drive and that boundary conditions strongly influence synchronization to external drives for the CGLE. Our calculations also show that the emCGLE has a low density regime in which a broad range of frequencies can be synchronized for low drive amplitudes. We study the bifurcation structure of these models and find that they are very similar to results for the driven Kuramoto model, a system with no spatial structure. We conclude by discussing qualitative implications of our results for controlling coupled oscillator systems such as the social amoebae Dictyostelium and populations of Belousov Zhabotinsky (BZ) catalytic particles using spatially structured external drives.

}, issn = {2470-0053}, doi = {10.1103/PhysRevE.103.042211}, author = {Golden, Alexander and Sgro, Allyson E and Mehta, Pankaj} } @article {66903, title = {The art of lineage tracing: From worm to human.}, journal = {Progress in Neurobiology}, volume = {199}, year = {2021}, month = {2021 Apr}, pages = {101966}, abstract = {

Reconstructing the genealogy of every cell that makes up an organism remains a long-standing challenge in developmental biology. Besides its relevance for understanding the mechanisms underlying normal and pathological development, resolving the lineage origin of cell types will be crucial to create these types on-demand. Multiple strategies have been deployed towards the problem of lineage tracing, ranging from direct observation to sophisticated genetic approaches. Here we discuss the achievements and limitations of past and current technology. Finally, we speculate about the future of lineage tracing and how to reach the next milestones in the field.

}, issn = {1873-5118}, doi = {10.1016/j.pneurobio.2020.101966}, author = {Garcia-Marques, Jorge and Isabel Espinosa Medina and Lee, Tzumin} } @article {67231, title = {Attractor dynamics gate cortical information flow during decision-making.}, journal = {Nature Neuroscience}, volume = {24}, year = {2021}, month = {2021 Jun 1}, pages = {843-50}, abstract = {

Decisions are held in memory until enacted, which makes them potentially vulnerable to distracting sensory input. Gating of information flow from sensory to motor areas could protect memory from interference during decision-making, but the underlying network mechanisms are not understood. Here, we trained mice to detect optogenetic stimulation of the somatosensory cortex, with a delay separating sensation and action. During the delay, distracting stimuli lost influence on behavior over time, even though distractor-evoked neural activity percolated through the cortex without attenuation. Instead, choice-encoding activity in the motor cortex became progressively less sensitive to the impact of distractors. Reverse engineering of neural networks trained to reproduce motor cortex activity revealed that the reduction in sensitivity to distractors was caused by a growing separation in the neural activity space between attractors that encode alternative decisions. Our results show that communication between brain regions can be gated via attractor dynamics, which control the degree of commitment to an action.

}, issn = {1546-1726}, doi = {10.1038/s41593-021-00840-6}, author = {Finkelstein, Arseny and Fontolan, Lorenzo and Economo, Michael N and Li, Nuo and Romani, Sandro and Svoboda, Karel} } @article {65832, title = {Automatic Detection of Synaptic Partners in a Whole-Brain Drosophila EM Dataset}, journal = {Nature Methods}, volume = {18}, year = {2021}, month = {2021 Jul 1}, pages = {771-4}, abstract = {

The study of neural circuits requires the reconstruction of neurons and the identification of synaptic connections between them. To scale the reconstruction to the size of whole-brain datasets, semi-automatic methods are needed to solve those tasks. Here, we present an automatic method for synaptic partner identification in insect brains, which uses convolutional neural networks to identify post-synaptic sites and their pre-synaptic partners. The networks can be trained from human generated point annotations alone and requires only simple post-processing to obtain final predictions. We used our method to extract 244 million putative synaptic partners in the fifty-teravoxel full adult fly brain (FAFB) electron microscopy (EM) dataset and evaluated its accuracy on 146,643 synapses from 702 neurons with a total cable length of 312 mm in four different brain regions. The predicted synaptic connections can be used together with a neuron segmentation to infer a connectivity graph with high accuracy: 96\% of edges between connected neurons are correctly classified as weakly connected (less than five synapses) and strongly connected (at least five synapses). Our synaptic partner predictions for the FAFB dataset are publicly available, together with a query library allowing automatic retrieval of up- and downstream neurons.

}, doi = {10.1038/s41592-021-01183-7}, author = {Buhmann, Julia and Sheridan, Arlo and Gerhard, Stephan and Krause, Renate and Nguyen, Tri and Heinrich, Larissa and Schlegel, Philipp and Lee, Wei-Chung Allen and Wilson, Rachel and Saalfeld, Stephan and Jefferis, Gregory and Bock, Davi and Turaga, Srinivas and Cook, Matthew and Funke, Jan} } @article {67822, title = {Bidirectional synaptic plasticity rapidly modifies hippocampal representations.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Dec 09}, abstract = {

Learning requires neural adaptations thought to be mediated by activity-dependent synaptic plasticity. A relatively non-standard form of synaptic plasticity driven by dendritic calcium spikes, or plateau potentials, has been reported to underlie place field formation in rodent hippocampal CA1 neurons. Here we found that this behavioral timescale synaptic plasticity (BTSP) can also reshape existing place fields via bidirectional synaptic weight changes that depend on the temporal proximity of plateau potentials to pre-existing place fields. When evoked near an existing place field, plateau potentials induced less synaptic potentiation and more depression, suggesting BTSP might depend inversely on postsynaptic activation. However, manipulations of place cell membrane potential and computational modeling indicated that this anti-correlation actually results from a dependence on current synaptic weight such that weak inputs potentiate and strong inputs depress. A network model implementing this bidirectional synaptic learning rule suggested that BTSP enables population activity, rather than pairwise neuronal correlations, to drive neural adaptations to experience.

}, issn = {2050-084X}, doi = {10.7554/eLife.73046}, author = {Milstein, Aaron D and Li, Yiding and Bittner, Katie C and Grienberger, Christine and Soltesz, Ivan and Magee, Jeffrey C and Romani, Sandro} } @article {67312, title = {Biomolecular Condensates and Their Links to Cancer Progression.}, journal = {Trends in Biochemical Sciences}, volume = {46}, year = {2021}, month = {2021 Jul 01}, pages = {535-549}, abstract = {

Liquid-liquid phase separation (LLPS) has emerged in recent years as an important physicochemical process for organizing diverse processes within cells via the formation of membraneless organelles termed biomolecular condensates. Emerging evidence now suggests that the formation and regulation of biomolecular condensates are also intricately linked to cancer formation and progression. We review the most recent literature linking the existence and/or dissolution of biomolecular condensates to different hallmarks of cancer formation and progression. We then discuss the opportunities that this condensate perspective provides for cancer research and the development of novel therapeutic approaches, including the perturbation of condensates by small-molecule inhibitors.

}, issn = {0968-0004}, doi = {10.1016/j.tibs.2021.01.002}, author = {Cai, Danfeng and Liu, Zhe and Lippincott-Schwartz, Jennifer} } @article {66893, title = {Biomolecular Condensates and Their Links to Cancer Progression.}, journal = {Trends in Biochemical Sciences}, year = {2021}, month = {2021 Feb 10}, abstract = {

Liquid-liquid phase separation (LLPS) has emerged in recent years as an important physicochemical process for organizing diverse processes within cells via the formation of membraneless organelles termed biomolecular condensates. Emerging evidence now suggests that the formation and regulation of biomolecular condensates are also intricately linked to cancer formation and progression. We review the most recent literature linking the existence and/or dissolution of biomolecular condensates to different hallmarks of cancer formation and progression. We then discuss the opportunities that this condensate perspective provides for cancer research and the development of novel therapeutic approaches, including the perturbation of condensates by small-molecule inhibitors.

}, issn = {0968-0004}, doi = {10.1016/j.tibs.2021.01.002}, author = {Cai, Danfeng and Liu, Zhe and Lippincott-Schwartz, Jennifer} } @article {67752, title = {Biosensors based on peptide exposure show single molecule conformations in live cells.}, journal = {Cell}, volume = {184}, year = {2021}, month = {2021 Oct 28}, pages = {5670-5685}, abstract = {

We describe an approach to study the conformation of individual proteins during single particle tracking (SPT) in living cells. "Binder/tag" is based on incorporation of a 7-mer peptide (the tag) into a protein where its solvent exposure is controlled by protein conformation. Only upon exposure can the peptide specifically interact with a reporter protein (the binder). Thus, simple fluorescence localization reflects protein conformation. Through direct excitation of bright dyes, the trajectory and conformation of individual proteins can be followed. Simple protein engineering provides highly specific biosensors suitable for SPT and FRET. We describe tagSrc, tagFyn, tagSyk, tagFAK, and an orthogonal binder/tag pair. SPT showed slowly diffusing islands of activated Src within Src clusters and dynamics of activation in adhesions. Quantitative analysis and stochastic modeling revealed in\ vivo Src kinetics. The simplicity of binder/tag can provide access to diverse proteins.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2021.09.026}, author = {Liu, Bei and Stone, Orrin J and Pablo, Michael and Herron, J Cody and Nogueira, Ana T and Dagliyan, Onur and Grimm, Jonathan B and Lavis, Luke D and Elston, Timothy C and Hahn, Klaus M} } @article {66902, title = {Brain microvasculature has a common topology with local differences in geometry that match metabolic load.}, journal = {Neuron}, volume = {109}, year = {2021}, month = {2021 April 01}, pages = {1168}, abstract = {

The microvasculature underlies the supply networks that support neuronal activity within heterogeneous brain regions. What are common versus heterogeneous aspects of the connectivity, density, and orientation of capillary networks? To address this, we imaged, reconstructed, and analyzed the microvasculature connectome in whole adult mice brains with sub-micrometer resolution. Graph analysis revealed common network topology across the brain that leads to a shared structural robustness against the rarefaction of vessels. Geometrical analysis, based on anatomically accurate reconstructions, uncovered a scaling law that links length density, i.e., the length of vessel per volume, with tissue-to-vessel distances. We then derive a formula that connects regional differences in metabolism to differences in length density and, further, predicts a common value of maximum tissue oxygen tension across the brain. Last, the orientation of capillaries is weakly anisotropic with the exception of a few strongly anisotropic regions; this variation can impact the interpretation of fMRI data.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2021.02.006}, author = {Ji, Xiang and Ferreira, Tiago and Friedman, Beth and Liu, Rui and Liechty, Hannah and Bas, Erhan and Chandrashekar, Jayaram and Kleinfeld, David} } @article {68137, title = {Budding epithelial morphogenesis driven by cell-matrix versus cell-cell adhesion}, journal = {Cell}, volume = {184}, year = {2021}, pages = {3702-3716.e30}, abstract = {

Summary Many embryonic organs undergo epithelial morphogenesis to form tree-like hierarchical structures. However, it remains unclear what drives the budding and branching of stratified epithelia, such as in the embryonic salivary gland and pancreas. Here, we performed live-organ imaging of mouse embryonic salivary glands at single-cell resolution to reveal that budding morphogenesis is driven by expansion and folding of a distinct epithelial surface cell sheet characterized by strong cell-matrix adhesions and weak cell-cell adhesions. Profiling of single-cell transcriptomes of this epithelium revealed spatial patterns of transcription underlying these cell adhesion differences. We then synthetically reconstituted budding morphogenesis by experimentally suppressing E-cadherin expression and inducing basement membrane formation in 3D spheroid cultures of engineered cells, which required β1-integrin-mediated cell-matrix adhesion for successful budding. Thus, stratified epithelial budding, the key first step of branching morphogenesis, is driven by an overall combination of strong cell-matrix adhesion and weak cell-cell adhesion by peripheral epithelial cells.

}, keywords = {branching morphogenesis, budding morphogenesis, cell-cell adhesion, cell-matrix adhesion, differential adhesion, E-cadherin, epithelial morphogenesis, integrin, salivary gland, tissue engineering}, issn = {0092-8674}, doi = {https://doi.org/10.1016/j.cell.2021.05.015}, url = {https://www.sciencedirect.com/science/article/pii/S0092867421006322}, author = {Shaohe Wang and Kazue Matsumoto and Samantha R. Lish and Alexander X. Cartagena-Rivera and Kenneth M. Yamada} } @article {67270, title = {Bursting potentiates the neuro-AI connection.}, journal = {Nature Neuroscience}, volume = {24}, year = {2021}, month = {2021 Jul 01}, pages = {905-6}, issn = {1546-1726}, doi = {10.1038/s41593-021-00844-2}, author = {Sun, Weinan and Zhao, Xinyu and Spruston, Nelson} } @article {67674, title = {The cAMP effector PKA mediates Moody GPCR signaling in blood-brain barrier formation and maturation.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Aug 12}, abstract = {

The blood-brain barrier (BBB) of is comprised of a thin epithelial layer of subperineural glia (SPG), which ensheath the nerve cord and insulate it against the potassium-rich hemolymph by forming intercellular septate junctions (SJs). Previously, we identified a novel Gi/Go protein-coupled receptor (GPCR), Moody, as a key factor in BBB formation at the embryonic stage. However, the molecular and cellular mechanisms of Moody signaling in BBB formation and maturation remain unclear. Here, we identify cAMP-dependent protein kinase A (PKA) as a crucial antagonistic Moody effector that is required for the formation, as well as for the continued SPG growth and BBB maintenance in the larva and adult stage. We show that PKA is enriched at the basal side of the SPG cell and that this polarized activity of the Moody/PKA pathway finely tunes the enormous cell growth and BBB integrity. Moody/PKA signaling precisely regulates the actomyosin contractility, vesicle trafficking, and the proper SJ organization in a highly coordinated spatiotemporal manner. These effects are mediated in part by PKA{\textquoteright}s molecular targets MLCK and Rho1. Moreover, 3D reconstruction of SJ ultrastructure demonstrates that the continuity of individual SJ segments, and not their total length, is crucial for generating a proper paracellular seal. Based on these findings, we propose that polarized Moody/PKA signaling plays a central role in controlling the cell growth and maintaining BBB integrity during the continuous morphogenesis of the SPG secondary epithelium, which is critical to maintain tissue size and brain homeostasis during organogenesis.

}, issn = {2050-084X}, doi = {10.7554/eLife.68275}, author = {Li, Xiaoling and Fetter, Richard and Schwabe, Tina and Jung, Christophe and Liu, Liren and Steller, Hermann and Gaul, Ulrike} } @article {67711, title = {Campylobacter jejuni Triggers Signaling through Host Cell Focal Adhesions To Inhibit Cell Motility.}, journal = {mBio}, volume = {12}, year = {2021}, month = {2021 Aug 24}, pages = {e0149421}, abstract = {

Campylobacter jejuni is a major foodborne pathogen that exploits the focal adhesions of intestinal cells to promote invasion and cause severe gastritis. Focal adhesions are multiprotein complexes involved in bidirectional signaling between the actin cytoskeleton and the extracellular matrix. We investigated the dynamics of focal adhesion structure and function in C. jejuni-infected cells using a comprehensive set of approaches, including confocal microscopy of live and fixed cells, immunoblotting, and superresolution interferometric photoactivated localization microscopy (iPALM). We found that C. jejuni infection of epithelial cells results in increased focal adhesion size and altered topology. These changes resulted in a persistent modulatory effect on the host cell focal adhesion, evidenced by an increase in cell adhesion strength, a decrease in individual cell motility, and a reduction in collective cell migration. We discovered that C. jejuni infection causes an increase in phosphorylation of paxillin and an alteration of paxillin turnover at the focal adhesion, which together represent a potential mechanistic basis for altered cell motility. Finally, we observed that infection of epithelial cells with the C. jejuni wild-type strain in the presence of a protein synthesis inhibitor, a C. jejuni CadF and FlpA fibronectin-binding protein mutant, or a C. jejuni flagellar export mutant blunts paxillin phosphorylation and partially reestablishes individual host cell motility and collective cell migration. These findings provide a potential mechanism for the restricted intestinal repair observed in C. jejuni-infected animals and raise the possibility that bacteria targeting extracellular matrix components can alter cell behavior after binding and internalization by manipulating focal adhesions. Campylobacter jejuni is a major foodborne pathogen that causes severe gastritis. We investigated the dynamics of focal adhesion structure and function in C. jejuni-infected epithelial cells. Focal adhesions act as signaling complexes that connect the extracellular matrix to the intracellular cytoskeleton. The key findings of this study show that C. jejuni changes the structure (size and position), composition, and function of cellular focal adhesions using a combination of virulence factors. Mechanistically, we found that the changes in focal adhesion dynamics are dependent upon the activation of host cell signaling pathways, which affect the assembly and disassembly of cellular proteins from the focal adhesion. To summarize, we have identified a new cellular phenotype in C. jejuni-infected cells that may be responsible for the restricted intestinal repair observed in C. jejuni-infected animals.

}, issn = {2150-7511}, doi = {10.1128/mBio.01494-21}, author = {Klappenbach, Courtney M and Negretti, Nicholas M and Aaron, Jesse and Chew, Teng-Leong and Konkel, Michael E} } @article {67696, title = {Campylobacter jejuni Triggers Signaling through Host Cell Focal Adhesions To Inhibit Cell Motility.}, journal = {mBio}, year = {2021}, month = {2021 Aug 24}, pages = {e0149421}, abstract = {

Campylobacter jejuni is a major foodborne pathogen that exploits the focal adhesions of intestinal cells to promote invasion and cause severe gastritis. Focal adhesions are multiprotein complexes involved in bidirectional signaling between the actin cytoskeleton and the extracellular matrix. We investigated the dynamics of focal adhesion structure and function in C. jejuni-infected cells using a comprehensive set of approaches, including confocal microscopy of live and fixed cells, immunoblotting, and superresolution interferometric photoactivated localization microscopy (iPALM). We found that C. jejuni infection of epithelial cells results in increased focal adhesion size and altered topology. These changes resulted in a persistent modulatory effect on the host cell focal adhesion, evidenced by an increase in cell adhesion strength, a decrease in individual cell motility, and a reduction in collective cell migration. We discovered that C. jejuni infection causes an increase in phosphorylation of paxillin and an alteration of paxillin turnover at the focal adhesion, which together represent a potential mechanistic basis for altered cell motility. Finally, we observed that infection of epithelial cells with the C. jejuni wild-type strain in the presence of a protein synthesis inhibitor, a C. jejuni CadF and FlpA fibronectin-binding protein mutant, or a C. jejuni flagellar export mutant blunts paxillin phosphorylation and partially reestablishes individual host cell motility and collective cell migration. These findings provide a potential mechanism for the restricted intestinal repair observed in C. jejuni-infected animals and raise the possibility that bacteria targeting extracellular matrix components can alter cell behavior after binding and internalization by manipulating focal adhesions. Campylobacter jejuni is a major foodborne pathogen that causes severe gastritis. We investigated the dynamics of focal adhesion structure and function in C. jejuni-infected epithelial cells. Focal adhesions act as signaling complexes that connect the extracellular matrix to the intracellular cytoskeleton. The key findings of this study show that C. jejuni changes the structure (size and position), composition, and function of cellular focal adhesions using a combination of virulence factors. Mechanistically, we found that the changes in focal adhesion dynamics are dependent upon the activation of host cell signaling pathways, which affect the assembly and disassembly of cellular proteins from the focal adhesion. To summarize, we have identified a new cellular phenotype in C. jejuni-infected cells that may be responsible for the restricted intestinal repair observed in C. jejuni-infected animals.

}, issn = {2150-7511}, doi = {10.1128/mBio.01494-21}, author = {Klappenbach, Courtney M and Negretti, Nicholas M and Aaron, Jesse and Chew, Teng-Leong and Konkel, Michael E} } @article {65897, title = {Cellpose: a generalist algorithm for cellular segmentation.}, journal = {Nature Methods}, volume = {18}, year = {2021}, month = {2021 Jan 07}, pages = {100-106}, abstract = {

Many biological applications require the segmentation of cell bodies, membranes and nuclei from microscopy images. Deep learning has enabled great progress on this problem, but current methods are specialized for images that have large training datasets. Here we introduce a generalist, deep learning-based segmentation method called Cellpose, which can precisely segment cells from a wide range of image types and does not require model retraining or parameter adjustments. Cellpose was trained on a new dataset of highly varied images of cells, containing over 70,000 segmented objects. We also demonstrate a three-dimensional (3D) extension of Cellpose that reuses the two-dimensional (2D) model and does not require 3D-labeled data. To support community contributions to the training data, we developed software for manual labeling and for curation of the automated results. Periodically retraining the model on the community-contributed data will ensure that Cellpose improves constantly.

}, issn = {1548-7105}, doi = {10.1038/s41592-020-01018-x}, author = {Stringer, Carsen and Wang, Tim and Michaelos, Michalis and Pachitariu, Marius} } @article {67737, title = {Cellular bases of olfactory circuit assembly revealed by systematic time-lapse imaging.}, journal = {Cell}, volume = {184}, year = {2021}, month = {2021 Sep 30}, pages = {5107}, abstract = {

Neural circuit assembly features simultaneous targeting of numerous neuronal processes from constituent neuron types, yet the dynamics is poorly understood. Here, we use the Drosophila olfactory circuit to investigate dynamic cellular processes by which olfactory receptor neurons (ORNs) target axons precisely to specific glomeruli in the ipsi- and contralateral antennal lobes. Time-lapse imaging of individual axons from 30 ORN types revealed a rich diversity in extension speed, innervation timing, and ipsilateral branch locations and identified that ipsilateral targeting occurs via stabilization of transient interstitial branches. Fast imaging using adaptive optics-corrected lattice light-sheet microscopy showed that upon approaching target, many ORN types exhibiting "exploring branches" consisted of parallel microtubule-based terminal branches emanating from an F-actin-rich hub. Antennal nerve ablations uncovered essential roles for bilateral axons in contralateral target selection and for ORN axons to facilitate dendritic refinement of postsynaptic partner neurons. Altogether, these observations provide cellular bases for wiring specificity establishment.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2021.08.030}, author = {Li, Tongchao and Fu, Tian-Ming and Wong, Kenneth Kin Lam and Li, Hongjie and Xie, Qijing and Luginbuhl, David J and Wagner, Mark J and Betzig, Eric and Luo, Liqun} } @article {67338, title = {A cerebellar-thalamocortical pathway drives behavioral context-dependent movement initiation.}, journal = {Neuron}, volume = {109}, year = {2021}, month = {2021 Jun 15}, pages = {2326-2338}, abstract = {

Executing learned motor behaviors often requires the transformation of sensory cues into patterns of motor commands that generate appropriately timed actions. The cerebellum and thalamus are two key areas involved in shaping cortical output and movement, but the contribution of a cerebellar-thalamocortical pathway to voluntary movement initiation remains poorly understood. Here, we investigated how an auditory "go cue" transforms thalamocortical activity patterns and how these changes relate to movement initiation. Population responses in dentate/interpositus-recipient regions of motor thalamus reflect a time-locked increase in activity immediately prior to movement initiation that is temporally uncoupled from the go cue, indicative of a fixed-latency feedforward motor timing signal. Blocking cerebellar or motor thalamic output suppresses movement initiation, while stimulation triggers movements in a behavioral context-dependent manner. Our findings show how cerebellar output, via the thalamus, shapes cortical activity patterns necessary for learned context-dependent movement initiation.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2021.05.016}, author = {Dacre, Joshua and Colligan, Matt and Clarke, Thomas and Ammer, Julian J and Schiemann, Julia and Chamosa-Pino, Victor and Claudi, Federico and Harston, J Alex and Eleftheriou, Constantinos and Pakan, Janelle M P and Huang, Cheng-Chiu and Hantman, Adam W and Rochefort, Nathalie L and Duguid, Ian} } @article {65971, title = {Characterization of a common progenitor pool of the epicardium and myocardium.}, journal = {Science}, year = {2021}, month = {2021 Jan 07}, abstract = {

The mammalian heart is derived from multiple cell lineages; however, our understanding of when and how the diverse cardiac cell types arise is limited. We mapped the origin of the embryonic mouse heart at single-cell resolution using a combination of transcriptomic, imaging, and genetic lineage labeling approaches. This provided a transcriptional and anatomic definition of cardiac progenitor types. Furthermore, it revealed a cardiac progenitor pool that is anatomically and transcriptionally distinct from currently known cardiac progenitors. Besides contributing to cardiomyocytes, these cells also represent the earliest progenitor of the epicardium, a source of trophic factors and cells during cardiac development and injury. This study provides detailed insights into the formation of early cardiac cell types, with particular relevance to the development of cell-based cardiac regenerative therapies.

}, issn = {1095-9203}, doi = {10.1126/science.abb2986}, author = {Tyser, Richard C V and Ibarra-Soria, Ximena and McDole, Katie and A Jayaram, Satish and Godwin, Jonathan and van den Brand, Teun A H and Miranda, Antonio M A and Scialdone, Antonio and Keller, Philipp J and Marioni, John C and Srinivas, Shankar} } @article {67189, title = {Circuit reorganization in the Drosophila mushroom body calyx accompanies memory consolidation.}, journal = {Cell Reports}, volume = {34}, year = {2021}, month = {2021 Mar 16}, pages = {108871}, abstract = {

The formation and consolidation of memories are complex phenomena involving synaptic plasticity, microcircuit reorganization, and the formation of multiple representations within distinct circuits. To gain insight into the structural aspects of memory consolidation, we focus on the calyx of the Drosophila mushroom body. In this essential center, essential for olfactory learning, second- and third-order neurons connect through large synaptic microglomeruli, which we dissect at the electron microscopy level. Focusing on microglomeruli that respond to a specific odor, we reveal that appetitive long-term memory results in increased numbers of precisely those functional microglomeruli responding to the conditioned odor. Hindering memory consolidation by non-coincident presentation of odor and reward, by blocking protein synthesis, or by including memory mutants suppress these structural changes, revealing their tight correlation with the process of memory consolidation. Thus, olfactory long-term memory is associated with input-specific structural modifications in a high-order center of the fly brain.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2021.108871}, author = {Baltruschat, Lothar and Prisco, Luigi and Ranft, Philipp and Lauritzen, J Scott and Fiala, Andr{\'e} and Bock, Davi D and Tavosanis, Gaia} } @article {67793, title = {Circuits for integrating learned and innate valences in the insect brain.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Nov 10}, abstract = {

Animal behavior is shaped both by evolution and by individual experience. Parallel brain pathways encode innate and learned valences of cues, but the way in which they are integrated during action-selection is not well understood. We used electron microscopy to comprehensively map with synaptic resolution all neurons downstream of all Mushroom Body output neurons (encoding learned valences) and characterized their patterns of interaction with Lateral Horn neurons (encoding innate valences) in larva. The connectome revealed multiple types that receive convergent Mushroom Body and Lateral Horn inputs. A subset of these receives excitatory input from positive-valence MB and LH pathways and inhibitory input from negative-valence MB pathways. We confirmed functional connectivity from LH and MB pathways and behavioral roles of two of these neurons. These neurons encode integrated odor value and bidirectionally regulate turning. Based on this we speculate that learning could potentially skew the balance of excitation and inhibition onto these neurons and thereby modulate turning. Together, our study provides insights into the circuits that integrate learned and innate valences to modify behavior.

}, issn = {2050-084X}, doi = {10.7554/eLife.62567}, author = {Eschbach, Claire and Fushiki, Akira and Winding, Michael and Afonso, Bruno and Andrade, Ingrid V and Cocanougher, Benjamin T and Eichler, Katharina and Gepner, Ruben and Si, Guangwei and Valdes-Aleman, Javier and Fetter, Richard D and Gershow, Marc and Jefferis, Gregory Sxe and Samuel, Aravinthan Dt and Truman, James W and Cardona, Albert and Zlatic, Marta} } @article {67714, title = {Classification and genetic targeting of cell types in the primary taste and premotor center of the adult brain.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Sep 02}, abstract = {

Neural circuits carry out complex computations that allow animals to evaluate food, select mates, move toward attractive stimuli, and move away from threats. In insects, the subesophageal zone (SEZ) is a brain region that receives gustatory, pheromonal, and mechanosensory inputs and contributes to the control of diverse behaviors, including feeding, grooming, and locomotion. Despite its importance in sensorimotor transformations, the study of SEZ circuits has been hindered by limited knowledge of the underlying diversity of SEZ neurons. Here, we generate a collection of split-GAL4 lines that provides precise genetic targeting of 138 different SEZ cell types in adult , comprising approximately one third of all SEZ neurons. We characterize the single cell anatomy of these neurons and find that they cluster by morphology into six supergroups that organize the SEZ into discrete anatomical domains. We find that the majority of local SEZ interneurons are not classically polarized, suggesting rich local processing, whereas SEZ projection neurons tend to be classically polarized, conveying information to a limited number of higher brain regions. This study provides insight into the anatomical organization of the SEZ and generates resources that will facilitate further study of SEZ neurons and their contributions to sensory processing and behavior.

}, issn = {2050-084X}, doi = {10.7554/eLife.71679}, author = {Sterne, Gabriella R and Otsuna, Hideo and Dickson, Barry J and Scott, Kristin} } @article {67762, title = {Coding sequence-independent homology search identifies highly divergent homopteran putative effector gene family}, journal = {bioRxiv}, year = {2021}, month = {2021 Sep 25}, abstract = {

Many genomes contain rapidly evolving and highly divergent genes whose homology to genes of known function often cannot be determined from sequence similarity alone. However, coding sequence-independent features of genes, such as intron-exon boundaries, often evolve more slowly than coding sequences and can provide complementary evidence for homology. We found that a linear logistic regression classifier using only structural features of rapidly evolving\ bicycle\ aphid effector genes identified many putative\ bicycle\ homologs in aphids, phylloxerids, and scale insects, whereas sequence similarity search methods yielded few homologs in most aphids and no homologs in phylloxerids and scale insects. Subsequent examination of sequence features and intron locations supported homology assignments. Differential expression studies of newly-identified\ bicycle\ homologs, together with prior proteomic studies, support the hypothesis that BICYCLE proteins act as plant effector proteins in many aphid species and perhaps also in phylloxerids and scale insects.

}, doi = {https://doi.org/10.1101/2021.09.24.461719}, author = {Stern, David and Han, Claire} } @article {65810, title = {Comparative Connectomics Reveals How Partner Identity, Location, and Activity Specify Synaptic Connectivity in Drosophila.}, journal = {Neuron}, volume = {109}, year = {2021}, month = {2021 Jan 06}, pages = {105-22}, abstract = {

The mechanisms by which synaptic partners recognize each other and establish appropriate numbers of connections during embryonic development to form functional neural circuits are poorly understood. We combined electron microscopy reconstruction, functional imaging of neural activity, and behavioral experiments to elucidate the roles of (1) partner identity, (2) location, and (3) activity in circuit assembly in the embryonic nerve cord of Drosophila. We found that postsynaptic partners are able to find and connect to their presynaptic partners even when these have been shifted to ectopic locations or silenced. However, orderly positioning of axon terminals by positional cues and synaptic activity is required for appropriate numbers of connections between specific partners, for appropriate balance between excitatory and inhibitory connections, and for appropriate functional connectivity and behavior. Our study reveals with unprecedented resolution the fine connectivity effects of multiple factors that work together to control the assembly of neural circuits.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2020.10.004}, author = {Valdes-Aleman, Javier and Fetter, Richard D and Sales, Emily C and Heckman, Emily L and Venkatasubramanian, Lalanti and Doe, Chris Q and Landgraf, Matthias and Cardona, Albert and Zlatic, Marta} } @article {67842, title = {CONFIRMS: A Toolkit for Scalable, Black Box Connectome Assessment and Investigation.}, journal = {Annual International Conference of the IEEE Engineering in Medicine and Biology Society}, volume = {2021}, year = {2021}, month = {2021 Nov 01}, pages = {2444-2450}, abstract = {

The nanoscale connectomics community has recently generated automated and semi-automated "wiring diagrams" of brain subregions from terabytes and petabytes of dense 3D neuroimagery. This process involves many challenging and imperfect technical steps, including dense 3D image segmentation, anisotropic nonrigid image alignment and coregistration, and pixel classification of each neuron and their individual synaptic connections. As data volumes continue to grow in size, and connectome generation becomes increasingly commonplace, it is important that the scientific community is able to rapidly assess the quality and accuracy of a connectome product to promote dataset analysis and reuse. In this work, we share our scalable toolkit for assessing the quality of a connectome reconstruction via targeted inquiry and large-scale graph analysis, and to provide insights into how such connectome proofreading processes may be improved and optimized in the future. We illustrate the applications and ecosystem on a recent reference dataset.Clinical relevance- Large-scale electron microscopy (EM) data offers a novel opportunity to characterize etiologies and neurological diseases and conditions at an unprecedented scale. EM is useful for low-level analyses such as biopsies; this increased scale offers new possibilities for research into areas such as neural networks if certain bottlenecks and problems are overcome.

}, keywords = {Connectome, Ecosystem, Imaging, Three-Dimensional, Microscopy, Electron, Neurons}, issn = {2694-0604}, doi = {10.1109/EMBC46164.2021.9630109}, author = {Bishop, Caitlyn and Matelsky, Jordan and Wilt, Miller and Downs, Joseph and Rivlin, Patricia and Plaza, Stephen and Wester, Brock and Gray-Roncal, William} } @article {67772, title = {A connectome is not enough - what is still needed to understand the brain of Drosophila?}, journal = {The Journal of Experimental Biology}, volume = {224}, year = {2021}, month = {2021 Nov 01}, abstract = {

Understanding the structure and operation of any nervous system has been a subject of research for well over a century. A near-term opportunity in this quest is to understand the brain of a model species, the fruit fly Drosophila melanogaster. This is an enticing target given its relatively small size (roughly 200,000 neurons), coupled with the behavioral richness that this brain supports, and the wide variety of techniques now available to study both brain and behavior. It is clear that within a few years we will possess a connectome for D. melanogaster: an electron-microscopy-level description of all neurons and their chemical synaptic connections. Given what we will soon have, what we already know and the research that is currently underway, what more do we need to know to enable us to understand the fly{\textquoteright}s brain? Here, we itemize the data we will need to obtain, collate and organize in order to build an integrated model of the brain of D. melanogaster.

}, issn = {1477-9145}, doi = {10.1242/jeb.242740}, author = {Scheffer, Louis K and Meinertzhagen, Ian A} } @article {67771, title = {A connectome of the central complex reveals network motifs suitable for flexible navigation and context-dependent action selection.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Oct 26}, abstract = {

Flexible behaviors over long timescales are thought to engage recurrent neural networks in deep brain regions, which are experimentally challenging to study. In insects, recurrent circuit dynamics in a brain region called the central complex (CX) enable directed locomotion, sleep, and context- and experience-dependent spatial navigation. We describe the first complete electron-microscopy-based connectome of the CX, including all its neurons and circuits at synaptic resolution. We identified new CX neuron types, novel sensory and motor pathways, and network motifs that likely enable the CX to extract the fly{\textquoteright}s head-direction, maintain it with attractor dynamics, and combine it with other sensorimotor information to perform vector-based navigational computations. We also identified numerous pathways that may facilitate the selection of CX-driven behavioral patterns by context and internal state. The CX connectome provides a comprehensive blueprint necessary for a detailed understanding of network dynamics underlying sleep, flexible navigation, and state-dependent action selection.

}, issn = {2050-084X}, doi = {10.7554/eLife.66039}, author = {Hulse, Brad K and Haberkern, Hannah and Franconville, Romain and Turner-Evans, Daniel B and Takemura, Shin-ya and Wolff, Tanya and Noorman, Marcella and Dreher, Marisa and Dan, Chuntao and Parekh, Ruchi and Hermundstad, Ann M and Rubin, Gerald M and Jayaraman, Vivek} } @article {67781, title = {Cre-Dependent Anterograde Transsynaptic Labeling and Functional Imaging in Zebrafish Using VSV With Reduced Cytotoxicity.}, journal = {Frontiers in Neuroanatomy}, volume = {15}, year = {2021}, month = {2021 Oct 06}, pages = {758350}, abstract = {

The small size and translucency of larval zebrafish () have made it a unique experimental system to investigate whole-brain neural circuit structure and function. Still, the connectivity patterns between most neuronal types remain mostly unknown. This gap in knowledge underscores the critical need for effective neural circuit mapping tools, especially ones that can integrate structural and functional analyses. To address this, we previously developed a vesicular stomatitis virus (VSV) based approach called Tracer with Restricted Anterograde Spread (TRAS). TRAS utilizes lentivirus to complement replication-incompetent VSV (VSVΔG) to allow restricted (monosynaptic) anterograde labeling from projection neurons to their target cells in the brain. Here, we report the second generation of TRAS (TRAS-M51R), which utilizes a mutant variant of VSVΔG [VSV(M51R)ΔG] with reduced cytotoxicity. Within the primary visual pathway, we found that TRAS-M51R significantly improved long-term viability of transsynaptic labeling (compared to TRAS) while maintaining anterograde spread activity. By using Cre-expressing VSV(M51R)ΔG, TRAS-M51R could selectively label excitatory ( positive) and inhibitory ( positive) retinorecipient neurons. We further show that these labeled excitatory and inhibitory retinorecipient neurons retained neuronal excitability upon visual stimulation at 5-8 days post fertilization (2-5 days post-infection). Together, these findings show that TRAS-M51R is suitable for neural circuit studies that integrate structural connectivity, cell-type identity, and neurophysiology.

}, issn = {1662-5129}, doi = {10.3389/fnana.2021.758350}, author = {Kler, Stanislav and Ma, Manxiu and Narayan, Sujatha and Ahrens, Misha B and Pan, Y Albert} } @article {67272, title = {CryoEM structure of the antibacterial target PBP1b at 3.3 {\r A} resolution.}, journal = {Nature Communications}, volume = {12}, year = {2021}, month = {2021 May 13}, pages = {2775}, abstract = {

The pathway for the biosynthesis of the bacterial cell wall is one of the most prolific antibiotic targets, exemplified by the widespread use of β-lactam antibiotics. Despite this, our structural understanding of class A penicillin binding proteins, which perform the last two steps in this pathway, is incomplete due to the inherent difficulty in their crystallization and the complexity of their substrates. Here, we determine the near atomic resolution structure of the 83 kDa class A PBP from Escherichia coli, PBP1b, using cryogenic electron microscopy and a styrene maleic acid anhydride membrane mimetic. PBP1b, in its apo form, is seen to exhibit a distinct conformation in comparison to Moenomycin-bound crystal structures. The work herein paves\ the way for the use of cryoEM in structure-guided antibiotic development for this notoriously difficult to crystalize class of proteins and their complex substrates.

}, issn = {2041-1723}, doi = {10.1038/s41467-021-23063-6}, author = {Caveney, Nathanael A and Workman, Sean D and Yan, Rui and Atkinson, Claire E and Yu, Zhiheng and Strynadka, Natalie C J} } @article {67179, title = {Cryo-EM structures of excitatory amino acid transporter 3 visualize coupled substrate, sodium, and proton binding and transport.}, journal = {Sciences Advances}, volume = {7}, year = {2021}, month = {2021 Mar 03}, abstract = {

Human excitatory amino acid transporter 3 (hEAAT3) mediates glutamate uptake in neurons, intestine, and kidney. Here, we report cryo-EM structures of hEAAT3 in several functional states where the transporter is empty, bound to coupled sodium ions only, or fully loaded with three sodium ions, a proton, and the substrate aspartate. The structures suggest that hEAAT3 operates by an elevator mechanism involving three functionally independent subunits. When the substrate-binding site is near the cytoplasm, it has a remarkably low affinity for the substrate, perhaps facilitating its release and allowing the rapid transport turnover. The mechanism of the coupled uptake of the sodium ions and the substrate is conserved across evolutionarily distant families and is augmented by coupling to protons in EAATs. The structures further suggest a mechanism by which a conserved glutamate residue mediates proton symport.

}, issn = {2375-2548}, doi = {10.1126/sciadv.abf5814}, author = {Qiu, Biao and Matthies, Doreen and Fortea, Eva and Yu, Zhiheng and Boudker, Olga} } @article {67803, title = {De novo endocytic clathrin coats develop curvature at early stages of their formation.}, journal = {Development Cell}, volume = {56}, year = {2021}, month = {2021 Nov 22}, pages = {3146-3159.e5}, abstract = {

Sculpting a flat patch of membrane into an endocytic vesicle requires curvature generation on the cell surface, which is the primary function of the endocytosis machinery. Using super-resolved live cell fluorescence imaging, we demonstrate that curvature generation by individual clathrin-coated pits can be detected in real time within cultured cells and tissues of developing organisms. Our analyses demonstrate that the footprint of clathrin coats increases monotonically during the formation of pits at different levels of plasma membrane tension. These findings are only compatible with models that predict curvature generation at the early stages of endocytic clathrin pit formation. We also found that CALM adaptors associated with clathrin plaques form clusters, whereas AP2 distribution is more homogenous. Considering the curvature sensing and driving roles of CALM, we propose that CALM clusters may increase the strain on clathrin lattices locally, eventually giving rise to rupture and subsequent pit completion at the edges of plaques.

}, issn = {1878-1551}, doi = {10.1016/j.devcel.2021.10.019}, author = {Willy, Nathan M and Ferguson, Joshua P and Akatay, Ata and Huber, Scott and Djakbarova, Umidahan and Silahli, Salih and Cakez, Cemal and Hasan, Farah and Chang, Henry C and Travesset, Alex and Li, Siyu and Zandi, Roya and Li, Dong and Betzig, Eric and Cocucci, Emanuele and Kural, Comert} } @article {67226, title = {Deep learning enables fast and dense single-molecule localization with high accuracy}, journal = {Nature Methods}, volume = {18}, year = {2021}, month = {2021 Sep 03}, abstract = {

Single-molecule localization microscopy (SMLM) has had remarkable success in imaging cellular structures with nanometer resolution, but the need for activating only single isolated emitters limits imaging speed and labeling density. Here, we overcome this major limitation using deep learning. We developed DECODE, a computational tool that can localize single emitters at high density in 3D with highest accuracy for a large range of imaging modalities and conditions. In a public software benchmark competition, it outperformed all other fitters on 12 out of 12 data-sets when comparing both detection accuracy and localization error, often by a substantial margin. DECODE allowed us to take live-cell SMLM data with reduced light exposure in just 3 seconds and to image microtubules at ultra-high labeling density. Packaged for simple installation and use, DECODE will enable many labs to reduce imaging times and increase localization density in SMLM.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2020.10.26.355164}, url = {https://www.biorxiv.org/content/early/2020/10/26/2020.10.26.355164}, author = {Speiser, Artur and M{\"u}ller, Lucas-Raphael and Matti, Ulf and Obara, Christopher J. and Legant, Wesley R. and Kreshuk, Anna and Macke, Jakob H. and Ries, Jonas and Turaga, Srinivas C.} } @article {67262, title = {A developmental framework linking neurogenesis and circuit formation in the Drosophila CNS.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 May 11}, abstract = {

The mechanisms specifying neuronal diversity are well-characterized, yet it remains unclear how or if these mechanisms regulate neural circuit assembly. To address this, we mapped the developmental origin of 160 interneurons from seven bilateral neural progenitors (neuroblasts), and identify them in a synapse-scale TEM reconstruction of the larval CNS. We find that lineages concurrently build the sensory and motor neuropils by generating sensory and motor hemilineages in a Notch-dependent manner. Neurons in a hemilineage share common synaptic targeting within the neuropil, which is further refined based on neuronal temporal identity. Connectome analysis shows that hemilineage-temporal cohorts share common connectivity. Finally, we show that proximity alone cannot explain the observed connectivity structure, suggesting hemilineage/temporal identity confers an added layer of specificity. Thus, we demonstrate that the mechanisms specifying neuronal diversity also govern circuit formation and function, and that these principles are broadly applicable throughout the nervous system.

}, issn = {2050-084X}, doi = {10.7554/eLife.67510}, author = {Mark, Brandon and Lai, Sen-Lin and Zarin, Aref Arzan and Manning, Laurina and Pollington, Heather Q and Litwin-Kumar, Ashok and Cardona, Albert and Truman, James W and Doe, Chris Q} } @article {65970, title = {Direct detection of SARS-CoV-2 RNA using high-contrast pH-sensitive dyes.}, journal = {Journal of Biomolecular Techniques}, volume = {32}, year = {2021}, month = {2021 Sep 01}, pages = {121-133}, abstract = {

The worldwide COVID-19 pandemic has had devastating effects on health, healthcare infrastructure, social structure, and economics. One of the limiting factors in containing the spread of this virus has been the lack of widespread availability of fast, inexpensive, and reliable methods for testing of individuals. Frequent screening for infected and often asymptomatic people is a cornerstone of pandemic management plans. Here, we introduce two pH sensitive {\textquoteleft}LAMPshade{\textquoteright} dyes as novel readouts in an isothermal RT- LAMP amplification assay for SARS-CoV-2 RNA. The resulting JaneliaLAMP (jLAMP) assay is robust, simple, inexpensive, has low technical requirements and we describe its use and performance in direct testing of contrived and clinical samples without RNA extraction.

}, doi = {https://doi.org/10.1101/2020.12.26.20248878}, author = {Timothy A. Brown and Katherine S. Schaefer and Arthur Tsang and Hyun Ah Yi and Jonathan B. Grimm and Andrew L. Lemire and Fadi M. Jradi and Charles Kim and Kevin McGowan and Kimberly Ritola and Derek T. Armstrong and Heba H. Mostafa and Wyatt Korff and Ronald D. Vale and Luke D. Lavis} } @article {67657, title = {Disrupting cortico-cerebellar communication impairs dexterity.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Jul 29}, abstract = {

To control reaching, the nervous system must generate large changes in muscle activation to drive the limb toward the target, and must also make smaller adjustments for precise and accurate behavior. Motor cortex controls the arm through projections to diverse targets across the central nervous system, but it has been challenging to identify the roles of cortical projections to specific targets. Here, we selectively disrupt cortico-cerebellar communication in the mouse by optogenetically stimulating the pontine nuclei in a cued reaching task. This perturbation did not typically block movement initiation, but degraded the precision, accuracy, duration, or success rate of the movement. Correspondingly, cerebellar and cortical activity during movement were largely preserved, but differences in hand velocity between control and stimulation conditions predicted from neural activity were correlated with observed velocity differences. These results suggest that while the total output of motor cortex drives reaching, the cortico-cerebellar loop makes small adjustments that contribute to the successful execution of this dexterous movement.

}, issn = {2050-084X}, doi = {10.7554/eLife.65906}, author = {Guo, Jian-Zhong and Sauerbrei, Britton A and Cohen, Jeremy D and Mischiati, Matteo and Graves, Austin R and Pisanello, Ferruccio and Branson, Kristin M and Hantman, Adam W} } @article {67723, title = {Dissociable contributions of phasic dopamine activity to reward and prediction.}, journal = {Cell Reports}, volume = {36}, year = {2021}, month = {2021 Sep 07}, pages = {109684}, abstract = {

Sensory cues that precede reward acquire predictive (expected value) and incentive (drive reward-seeking action) properties. Mesolimbic dopamine neurons{\textquoteright} responses to sensory cues correlate with both expected value and reward-seeking action. This has led to the proposal that phasic dopamine responses may be sufficient to inform value-based decisions, elicit actions, and/or induce motivational states; however, causal tests are incomplete. Here, we show that direct dopamine neuron stimulation, both calibrated to physiological and greater intensities, at the time of reward can be sufficient to induce and maintain reward seeking (reinforcing) although replacement of a cue with stimulation is insufficient to induce reward seeking or act as an informative cue. Stimulation of descending cortical inputs, one synapse upstream, are sufficient for reinforcement and cues to future reward. Thus, physiological activation of mesolimbic dopamine neurons can be sufficient for reinforcing properties of reward without being sufficient for the predictive and incentive properties of cues.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2021.109684}, author = {Pan, Wei-Xing and Coddington, Luke T and Dudman, Joshua T} } @article {67734, title = {Distinct genetic architectures underlie divergent thorax, leg, and wing pigmentation between Drosophila elegans and D. gunungcola.}, journal = {Heredity}, volume = {127}, year = {2021}, month = {2021 Nov 01}, pages = {467-74}, abstract = {

Pigmentation divergence between Drosophila species has emerged as a model trait for studying the genetic basis of phenotypic evolution, with genetic changes contributing to pigmentation differences often mapping to genes in the pigment synthesis pathway and their regulators. These studies of Drosophila pigmentation have tended to focus on pigmentation changes in one body part for a particular pair of species, but changes in pigmentation are often observed in multiple body parts between the same pair of species. The similarities and differences of genetic changes responsible for divergent pigmentation in different body parts of the same species thus remain largely unknown. Here we compare the genetic basis of pigmentation divergence between Drosophila elegans and D. gunungcola in the wing, legs, and thorax. Prior work has shown that regions of the genome containing the pigmentation genes yellow and ebony influence the size of divergent male-specific wing spots between these two species. We find that these same two regions of the genome underlie differences in leg and thorax pigmentation; however, divergent alleles in these regions show differences in allelic dominance and epistasis among the three body parts. These complex patterns of inheritance can be explained by a model of evolution involving tissue-specific changes in the expression of Yellow and Ebony between D. elegans and D. gunungcola.

}, issn = {1365-2540}, doi = {10.1038/s41437-021-00467-0}, author = {Massey, Jonathan H and Li, Jun and Stern, David L and Wittkopp, Patricia J} } @article {67273, title = {A Distinct Population of L6 Neurons in Mouse V1 Mediate Cross-Callosal Communication.}, journal = {Cerebral Cortex}, year = {2021}, month = {2021 May 14}, abstract = {

Through the corpus callosum, interhemispheric communication is mediated by callosal projection (CP) neurons. Using retrograde labeling, we identified a population of layer 6 (L6) excitatory neurons as the main conveyer of transcallosal information in the monocular zone of the mouse primary visual cortex (V1). Distinct from L6 corticothalamic (CT) population, V1 L6 CP neurons contribute to an extensive reciprocal network across multiple sensory cortices over two hemispheres. Receiving both local and long-range cortical inputs, they encode orientation, direction, and receptive field information, while are also highly spontaneous active. The spontaneous activity of L6 CP neurons exhibits complex relationships with brain states and stimulus presentation, distinct from the spontaneous activity patterns of the CT population. The anatomical and functional properties of these L6 CP neurons enable them to broadcast visual and nonvisual information across two hemispheres, and thus may play a role in regulating and coordinating brain-wide activity events.

}, issn = {1460-2199}, doi = {10.1093/cercor/bhab084}, author = {Liang, Yajie and Fan, Jiang Lan and Sun, Wenzhi and Lu, Rongwen and Chen, Ming and Ji, Na} } @article {67735, title = {A dominant-negative SOX18 mutant disrupts multiple regulatory layers essential to transcription factor activity.}, journal = {Nucleic Acids Research}, year = {2021}, month = {2021 Sep 27}, abstract = {

Few genetically dominant mutations involved in human disease have been fully explained at the molecular level. In cases where the mutant gene encodes a transcription factor, the dominant-negative mode of action of the mutant protein is particularly poorly understood. Here, we studied the genome-wide mechanism underlying a dominant-negative form of the SOX18 transcription factor (SOX18RaOp) responsible for both the classical mouse mutant Ragged Opossum and the human genetic disorder Hypotrichosis-lymphedema-telangiectasia-renal defect syndrome. Combining three single-molecule imaging assays in living cells together with genomics and proteomics analysis, we found that SOX18RaOp disrupts the system through an accumulation of molecular interferences which impair several functional properties of the wild-type SOX18 protein, including its target gene selection process. The dominant-negative effect is further amplified by poisoning the interactome of its wild-type counterpart, which perturbs regulatory nodes such as SOX7 and MEF2C. Our findings explain in unprecedented detail the multi-layered process that underpins the molecular aetiology of dominant-negative transcription factor function.

}, issn = {1362-4962}, doi = {10.1093/nar/gkab820}, author = {McCann, Alex J and Lou, Jieqiong and Moustaqil, Mehdi and Graus, Matthew S and Blum, Ailisa and Fontaine, Frank and Liu, Hui and Luu, Winnie and Rudolffi-Soto, Paulina and Koopman, Peter and Sierecki, Emma and Gambin, Yann and Meunier, Fr{\'e}d{\'e}ric A and Liu, Zhe and Hinde, Elizabeth and Francois, Mathias} } @article {67746, title = {A dominant-negative SOX18 mutant disrupts multiple regulatory layers essential to transcription factor activity.}, journal = {Nucleic Acids Research}, year = {2021}, month = {2021 Sep 27}, abstract = {

Few genetically dominant mutations involved in human disease have been fully explained at the molecular level. In cases where the mutant gene encodes a transcription factor, the dominant-negative mode of action of the mutant protein is particularly poorly understood. Here, we studied the genome-wide mechanism underlying a dominant-negative form of the SOX18 transcription factor (SOX18RaOp) responsible for both the classical mouse mutant Ragged Opossum and the human genetic disorder Hypotrichosis-lymphedema-telangiectasia-renal defect syndrome. Combining three single-molecule imaging assays in living cells together with genomics and proteomics analysis, we found that SOX18RaOp disrupts the system through an accumulation of molecular interferences which impair several functional properties of the wild-type SOX18 protein, including its target gene selection process. The dominant-negative effect is further amplified by poisoning the interactome of its wild-type counterpart, which perturbs regulatory nodes such as SOX7 and MEF2C. Our findings explain in unprecedented detail the multi-layered process that underpins the molecular aetiology of dominant-negative transcription factor function.

}, issn = {1362-4962}, doi = {10.1093/nar/gkab820}, author = {McCann, Alex J and Lou, Jieqiong and Moustaqil, Mehdi and Graus, Matthew S and Blum, Ailisa and Fontaine, Frank and Liu, Hui and Luu, Winnie and Rudolffi-Soto, Paulina and Koopman, Peter and Sierecki, Emma and Gambin, Yann and Meunier, Fr{\'e}d{\'e}ric A and Liu, Zhe and Hinde, Elizabeth and Francois, Mathias} } @article {67804, title = {Drosophila {\ss}-Spectrin is required in polarized ensheathing glia that form a diffusion-barrier around the neuropil.}, journal = {Nature Communications}, volume = {12}, year = {2021}, month = {2021 Nov 04}, pages = {6357}, abstract = {

In the central nervous system (CNS), functional tasks are often allocated to distinct compartments. This is also evident in the Drosophila CNS where synapses and dendrites are clustered in distinct neuropil regions. The neuropil is separated from neuronal cell bodies by ensheathing glia, which as we show using dye injection experiments, contribute to the formation of an internal diffusion barrier. We find that ensheathing glia are polarized with a basolateral plasma membrane rich in phosphatidylinositol-(3,4,5)-triphosphate (PIP) and the Na/K-ATPase Nervana2 (Nrv2) that abuts an extracellular matrix formed at neuropil-cortex interface. The apical plasma membrane is facing the neuropil and is rich in phosphatidylinositol-(4,5)-bisphosphate (PIP) that is supported by a sub-membranous {\ss}-Spectrin cytoskeleton. {\ss}-spectrin mutant larvae affect ensheathing glial cell polarity with delocalized PIP and Nrv2 and exhibit an abnormal locomotion which is similarly shown by ensheathing glia ablated larvae. Thus, polarized glia compartmentalizes the brain and is essential for proper nervous system function.

}, issn = {2041-1723}, doi = {10.1038/s41467-021-26462-x}, author = {Pogodalla, Nicole and Kranenburg, Holger and Rey, Simone and Rodrigues, Silke and Cardona, Albert and Kl{\"a}mbt, Christian} } @article {66027, title = {Drosophila uses a tripod gait across all walking speeds, and the geometry of the tripod is important for speed control.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Feb 03}, abstract = {

Changes in walking speed are characterized by changes in both the animal{\textquoteright}s gait and the mechanics of its interaction with the ground. Here we study these changes in walking . We measured the fly{\textquoteright}s center of mass (CoM) movement with high spatial resolution and the position of its footprints. Flies predominantly employ a modified tripod gait that only changes marginally with speed. The mechanics of a tripod gait can be approximated with a simple model - angular and radial spring-loaded inverted pendulum (ARSLIP) - which is characterized by two springs of an effective leg that become stiffer as the speed increases. Surprisingly, the change in the stiffness of the spring is mediated by the change in tripod shape rather than a change in stiffness of the individual leg. The effect of tripod shape on mechanics can also explain the large variation in kinematics among insects, and ARSLIP can model these variations.

}, issn = {2050-084X}, doi = {10.7554/eLife.65878}, author = {Chun, Chanwoo and Biswas, Tirthabir and Bhandawat, Vikas} } @article {67815, title = {EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization.}, journal = {Cell}, volume = {184}, year = {2021}, month = {2021 Dec 01}, pages = {6361}, abstract = {

Determining the spatial organization and morphological characteristics of molecularly defined cell types is a major bottleneck for characterizing the architecture underpinning brain function. We developed Expansion-Assisted Iterative Fluorescence In Situ Hybridization (EASI-FISH) to survey gene expression in brain tissue, as well as a turnkey computational pipeline to rapidly process large EASI-FISH image datasets. EASI-FISH was optimized for thick brain sections (300\ μm) to facilitate reconstruction of spatio-molecular domains that generalize across brains. Using the EASI-FISH pipeline, we investigated the spatial distribution of dozens of molecularly defined cell types in the lateral hypothalamic area (LHA), a brain region with poorly defined anatomical organization. Mapping cell types in the LHA revealed nine spatially and molecularly defined subregions. EASI-FISH also facilitates iterative reanalysis of scRNA-seq datasets to determine marker-genes that further dissociated spatial and morphological heterogeneity. The EASI-FISH pipeline democratizes mapping molecularly defined cell types, enabling discoveries about brain organization.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2021.11.024}, author = {Wang, Yuhan and Eddison, Mark and Fleishman, Greg and Weigert, Martin and Xu, Shengjin and Wang, Tim and Rokicki, Konrad and Goina, Cristian and Henry, Fredrick E and Lemire, Andrew L and Schmidt, Uwe and Yang, Hui and Svoboda, Karel and Myers, Eugene W and Saalfeld, Stephan and Korff, Wyatt and Sternson, Scott M and Tillberg, Paul W} } @article {67806, title = {ecDNA hubs drive cooperative intermolecular oncogene expression.}, journal = {Nature}, volume = {600}, year = {2021}, month = {2021 Dec 01}, pages = {731-6}, abstract = {

Extrachromosomal DNA (ecDNA) is prevalent in human cancers and mediates high expression of oncogenes through gene amplification and altered gene regulation. Gene induction typically involves cis-regulatory elements that contact and activate genes on the same chromosome. Here we show that ecDNA hubs-clusters of around 10-100 ecDNAs within the nucleus-enable intermolecular enhancer-gene interactions to promote oncogene overexpression. ecDNAs that encode multiple distinct oncogenes form hubs in diverse cancer cell types and primary tumours. Each ecDNA is more likely to transcribe the oncogene when spatially clustered with additional ecDNAs. ecDNA hubs are tethered by the bromodomain and extraterminal domain (BET) protein BRD4 in a MYC-amplified colorectal cancer cell line. The BET inhibitor JQ1 disperses ecDNA hubs and preferentially inhibits ecDNA-derived-oncogene transcription. The BRD4-bound PVT1 promoter is ectopically fused to MYC and duplicated in ecDNA, receiving promiscuous enhancer input to drive potent expression of MYC. Furthermore, the PVT1 promoter on an exogenous episome suffices to mediate gene activation in trans by ecDNA hubs in a JQ1-sensitive manner. Systematic silencing of ecDNA enhancers by CRISPR interference reveals intermolecular enhancer-gene activation among multiple oncogene loci that are amplified on distinct ecDNAs. Thus, protein-tethered ecDNA hubs enable intermolecular transcriptional regulation and may serve as units of oncogene function and cooperative evolution and as potential targets for cancer therapy.

}, issn = {1476-4687}, doi = {10.1038/s41586-021-04116-8}, author = {Hung, King L and Yost, Kathryn E and Xie, Liangqi and Shi, Quanming and Helmsauer, Konstantin and Luebeck, Jens and Sch{\"o}pflin, Robert and Lange, Joshua T and Chamorro Gonz{\'a}lez, Roc{\'\i}o and Weiser, Natasha E and Chen, Celine and Valieva, Maria E and Wong, Ivy Tsz-Lo and Wu, Sihan and Dehkordi, Siavash R and Duffy, Connor V and Kraft, Katerina and Tang, Jun and Belk, Julia A and Rose, John C and Corces, M Ryan and Granja, Jeffrey M and Li, Rui and Rajkumar, Utkrisht and Friedlein, Jordan and Bagchi, Anindya and Satpathy, Ansuman T and Tjian, Robert and Mundlos, Stefan and Bafna, Vineet and Henssen, Anton G and Mischel, Paul S and Liu, Zhe and Chang, Howard Y} } @article {67275, title = {Efficient and adaptive sensory codes.}, journal = {Nature Neuroscience}, volume = {24}, year = {2021}, month = {2021 Jul 01}, pages = {998-1009}, abstract = {

The ability to adapt to changes in stimulus statistics is a hallmark of sensory systems. Here, we developed a theoretical framework that can account for the dynamics of adaptation from an information processing perspective. We use this framework to optimize and analyze adaptive sensory codes, and we show that codes optimized for stationary environments can suffer from prolonged periods of poor performance when the environment changes. To mitigate the adversarial effects of these environmental changes, sensory systems must navigate tradeoffs between the ability to accurately encode incoming stimuli and the ability to rapidly detect and adapt to changes in the distribution of these stimuli. We derive families of codes that balance these objectives, and we demonstrate their close match to experimentally observed neural dynamics during mean and variance adaptation. Our results provide a unifying perspective on adaptation across a range of sensory systems, environments, and sensory tasks.

}, issn = {1097-6256}, doi = {10.1038/s41593-021-00846-0}, url = {http://www.nature.com/articles/s41593-021-00846-0}, author = {M{\l}ynarski, Wiktor F. and Hermundstad, Ann M.} } @article {67721, title = {Electrode pooling can boost the yield of extracellular recordings with switchable silicon probes.}, journal = {Nature Communications}, volume = {12}, year = {2021}, month = {2021 Sep 02}, pages = {5245}, abstract = {

State-of-the-art silicon probes for electrical recording from neurons have thousands of recording sites. However, due to volume limitations there are typically many fewer wires carrying signals off the probe, which restricts the number of channels that can be recorded simultaneously. To overcome this fundamental constraint, we propose a method called electrode pooling that uses a single wire to serve many recording sites through a set of controllable switches. Here we present the framework behind this method and an experimental strategy to support it. We then demonstrate its feasibility by implementing electrode pooling on the Neuropixels 1.0 electrode array and characterizing its effect on signal and noise. Finally we use simulations to explore the conditions under which electrode pooling saves wires without compromising the content of the recordings. We make recommendations on the design of future devices to take advantage of this strategy.

}, keywords = {Action Potentials, Animals, Brain, Electrodes, Implanted, Electrophysiology, Equipment Design, Extracellular Space, Mice, Nerve Net, Neurons, Signal Processing, Computer-Assisted, Silicon}, issn = {2041-1723}, doi = {10.1038/s41467-021-25443-4}, author = {Lee, Kyu Hyun and Ni, Yu-Li and Colonell, Jennifer and Karsh, Bill and Putzeys, Jan and Pachitariu, Marius and Harris, Timothy D and Meister, Markus} } @article {67633, title = {Enabling In Vivo Photocatalytic Activation of Rapid Bioorthogonal Chemistry by Repurposing Silicon-Rhodamine Fluorophores as Cytocompatible Far-Red Photocatalysts.}, journal = {Journal of the American Chemical Society}, volume = {143}, year = {2021}, month = {2021 Jul 21}, pages = {10793-10803}, abstract = {

Chromophores that absorb in the tissue-penetrant far-red/near-infrared window have long served as photocatalysts to generate singlet oxygen for photodynamic therapy. However, the cytotoxicity and side reactions associated with singlet oxygen sensitization have posed a problem for using long-wavelength photocatalysis to initiate other types of chemical reactions in biological environments. Herein, silicon-Rhodamine compounds (SiRs) are described as photocatalysts for inducing rapid bioorthogonal chemistry using 660 nm light through the oxidation of a dihydrotetrazine to a tetrazine in the presence of cyclooctene dienophiles. SiRs have been commonly used as fluorophores for bioimaging but have not been applied to catalyze chemical reactions. A series of SiR derivatives were evaluated, and the Janelia Fluor-SiR dyes were found to be especially effective in catalyzing photooxidation (typically 3\%). A dihydrotetrazine/tetrazine pair is described that displays high stability in both oxidation states. A protein that was site-selectively modified by cyclooctene was quantitatively conjugated upon exposure to 660 nm light and a dihydrotetrazine. By contrast, a previously described methylene blue catalyst was found to rapidly degrade the protein. SiR-red light photocatalysis was used to cross-link hyaluronic acid derivatives functionalized by dihydrotetrazine and cyclooctenes, enabling 3D culture of human prostate cancer cells. Photoinducible hydrogel formation could also be carried out in live mice through subcutaneous injection of a Cy7-labeled hydrogel precursor solution, followed by brief irradiation to produce a stable hydrogel. This cytocompatible method for using red light photocatalysis to activate bioorthogonal chemistry is anticipated to find broad applications where spatiotemporal control is needed in biological environments.

}, issn = {1520-5126}, doi = {10.1021/jacs.1c05547}, author = {Wang, Chuanqi and Zhang, He and Zhang, Tao and Zou, Xiaoyu and Wang, Hui and Rosenberger, Julia E and Vannam, Raghu and Trout, William S and Grimm, Jonathan B and Lavis, Luke D and Thorpe, Colin and Jia, Xinqiao and Li, Zibo and Fox, Joseph M} } @article {67710, title = {Endothelial junctional membrane protrusions serve as hotspots for neutrophil transmigration.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Aug 25}, abstract = {

Upon inflammation, leukocytes rapidly transmigrate across the endothelium to enter the inflamed tissue. Evidence accumulates that leukocytes use preferred exit sites, though it is not yet clear how these hotspots in the endothelium are defined and how they are recognized by the leukocyte. Using lattice light sheet microscopy, we discovered that leukocytes prefer endothelial membrane protrusions at cell junctions for transmigration. Phenotypically, these junctional membrane protrusions are present in an asymmetric manner, meaning that one endothelial cell shows the protrusion and the adjacent one does not. Consequently, leukocytes cross the junction by migrating underneath the protruding endothelial cell. These protrusions depend on Rac1 activity and by using a photo-activatable Rac1 probe, we could artificially generate local exit-sites for leukocytes. Overall, we have discovered a new mechanism that uses local induced junctional membrane protrusions to facilitate/steer the leukocyte escape/exit from inflamed vessel walls.

}, issn = {2050-084X}, doi = {10.7554/eLife.66074}, author = {Arts, Janine Jg and Mahlandt, Eike K and Gr{\"o}nloh, Max and Schimmel, Lilian and Noordstra, Ivar and Gordon, Emma and van Steen, Abraham Ci and Tol, Simon and Walzog, Barbara and van Rijssel, Jos and Nolte, Martijn A and Postma, Marten and Khuon, Satya and Heddleston, John M and Wait, Eric and Chew, Teng Leong and Winter, Mark and Montanez, Eloi and Goedhart, Joachim and van Buul, Jaap D} } @article {66006, title = {Endothelial junctional membrane protrusions serve as hotspots for neutrophil transmigration.}, journal = {bioRxiv}, year = {2021}, month = {2021 Jan 21}, abstract = {

Upon inflammation, leukocytes rapidly transmigrate across the endothelium to enter the inflamed tissue. Evidence accumulates that leukocytes use preferred exit sites, though it is not yet clear how these hotspots in the endothelium are defined and how they are recognized by the leukocyte. Using lattice light sheet microscopy, we discovered that leukocytes prefer endothelial membrane protrusions at cell junctions for transmigration. Phenotypically, these junctional membrane protrusions are present in an asymmetric manner, meaning that one endothelial cell shows the protrusion and the adjacent one does not. Consequently, leukocytes cross the junction by migrating underneath the protruding endothelial cell. These protrusions depend on Rac1 activity and by using a photo-activatable Rac1 probe, we could artificially generate local exit-sites for leukocytes. Overall, we have discovered a new mechanism that uses local induced junctional membrane protrusions to facilitate/steer the leukocyte escape/exit from inflamed vessel walls.

}, doi = {https://doi.org/10.1101/2021.01.18.427135}, author = {Janine J.G. Arts and Eike K. Mahlandt and Max L.B. Gr{\"o}nloh and Lilian Schimmel and Ivar Noordstra and Abraham C.I. van Steen and Simon Tol and Jos van Rijssel and Martijn A. Nolte and Marten Postma and Satya Khuon and John M. Heddleston and Eric Wait and Teng-Leong Chew and Mark Winter and Eloi Montanez and Joachim Goedhart and Jaap D. van Buul} } @article {67807, title = {Engineering of a fluorescent chemogenetic reporter with tunable color for advanced live-cell imaging.}, journal = {Nature Communications}, volume = {12}, year = {2021}, month = {2021 Nov 30}, pages = {6989}, abstract = {

Biocompatible fluorescent reporters with spectral properties spanning the entire visible spectrum are indispensable tools for imaging the biochemistry of living cells and organisms in real time. Here, we report the engineering of a fluorescent chemogenetic reporter with tunable optical and spectral properties. A collection of fluorogenic chromophores with various electronic properties enables to generate bimolecular fluorescent assemblies that cover the visible spectrum from blue to red using a single protein tag engineered and optimized by directed evolution and rational design. The ability to tune the fluorescence color and properties through simple molecular modulation provides a broad experimental versatility for imaging proteins in live cells, including neurons, and in multicellular organisms, and opens avenues for optimizing F{\"o}rster resonance energy transfer (FRET) biosensors in live cells. The ability to tune the spectral properties and fluorescence performance enables furthermore to match the specifications and requirements of advanced super-resolution imaging techniques.

}, issn = {2041-1723}, doi = {10.1038/s41467-021-27334-0}, author = {Benaissa, Hela and Ounoughi, Karim and Aujard, Isabelle and Fischer, Evelyne and Go{\"\i}ame, Rosette and Nguyen, Julie and Tebo, Alison G and Li, Chenge and Le Saux, Thomas and Bertolin, Giulia and Tramier, Marc and Danglot, Lydia and Pietrancosta, Nicolas and Morin, Xavier and Jullien, Ludovic and Gautier, Arnaud} } @article {67827, title = {Enhanced Photoinduced Electron Transfer Through a Tyrosine Relay in a De Novo Designed Protein Scaffold Bearing a Photoredox Unit and a Fe II S 4 Site}, journal = {ChemPhotoChem}, volume = {5}, year = {2021}, month = {03/2021}, pages = {665 - 668}, abstract = {

Electron transfer (ET) processes in biology over long distances often proceed via a series of hops, which reduces the distance dependence of the rate of ET. The protein matrix itself can be involved in mediating ET directly through the participation of redox-active amino acids. We have designed an electron transfer chain incorporated into a de novo protein scaffold, which is capable of photoinduced intramolecular electron transfer between a photoredox unit and a FeIIS4\ site through a tyrosine amino acid relay. The kinetics were characterized by nanosecond laser pulse photolysis and revealed that electron transfer from [RuIIIbpymal]3+\ proceeds most efficiently via a tyrosine located \~{}16 {\r A} from Rubpymal (bpymal=1-((1-([2,2'-bipyridin]-4-yl)-1H-1,2,3-triazol-4-yl)methyl)-1H-pyrrole-2,5-dione). Removal of the tyrosine as the electron relay station results in a 20-fold decrease in the apparent rate constant for the electron transfer.

}, issn = {2367-0932}, doi = {10.1002/cptc.v5.710.1002/cptc.202100014}, url = {https://onlinelibrary.wiley.com/toc/23670932/5/7}, author = {Tebo, Alison and Quaranta, Annamaria and Pecoraro, Vincent L. and Aukauloo, Ally} } @article {68473, title = {Erratum: Label-free imaging of fibroblast membrane interfaces and protein signatures with vibrational infrared photothermal and phase signals: publisher{\textquoteright}s note.}, journal = {Biomed Opt Express}, volume = {12}, year = {2021}, month = {09/2021}, pages = {5400}, abstract = {

[This corrects the article on p. 303 in vol. 12, PMID: 33520386.].

}, issn = {2156-7085}, doi = {10.1364/BOE.438946}, author = {Samolis, Panagis D and Langley, Daniel and O{\textquoteright}Reilly, Breanna M and Oo, Zay and Hilzenrat, Geva and Erramilli, Shyamsunder and Sgro, Allyson E and McArthur, Sally and Sander, Michelle Y} } @article {67233, title = {ER-to-Golgi protein delivery through an interwoven, tubular network extending from ER.}, journal = {Cell}, volume = {184}, year = {2021}, month = {2021 Apr 29}, pages = {2412}, abstract = {

Cellular versatility depends on accurate trafficking of diverse proteins to their organellar destinations. For the secretory pathway (followed by approximately 30\% of all proteins), the physical nature of the vessel conducting the first portage (endoplasmic reticulum [ER] to Golgi apparatus) is unclear. We provide a dynamic 3D view of early secretory compartments in mammalian cells with isotropic resolution and precise protein localization using whole-cell, focused ion beam scanning electron microscopy with cryo-structured illumination microscopy and live-cell synchronized cargo release approaches. Rather than vesicles alone, the ER spawns an elaborate, interwoven tubular network of contiguous lipid bilayers (ER exit site) for protein export. This receptacle is capable of extending microns along microtubules while still connected to the ER by a thin neck. COPII localizes to this neck region and dynamically regulates cargo entry from the ER, while COPI acts more distally, escorting the detached, accelerating tubular entity on its way to joining the Golgi apparatus through microtubule-directed movement.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2021.03.035}, author = {Weigel, Aubrey V and Chang, Chi-Lun and Shtengel, Gleb and Xu, C Shan and Hoffman, David P and Freeman, Melanie and Iyer, Nirmala and Aaron, Jesse and Khuon, Satya and Bogovic, John and Qiu, Wei and Hess, Harald F and Lippincott-Schwartz, Jennifer} } @article {66894, title = {Evaluation of multi-color genetically encoded Ca indicators in filamentous fungi.}, journal = {Fungal Genetics and Biology}, year = {2021}, month = {2021 Feb 16}, pages = {103540}, abstract = {

Genetically encoded Ca indicators (GECIs) enable long-term monitoring of cellular and subcellular dynamics of this second messenger in response to environmental and developmental cues without relying on exogenous dyes. Continued development and optimization in GECIs, combined with advances in gene manipulation, offer new opportunities for investigating the mechanism of Ca signaling in fungi, ranging from documenting Ca signatures under diverse conditions and genetic backgrounds to evaluating how changes in Ca signature impact calcium-binding proteins and subsequent cellular changes. Here, we attempted to express multi-color (green, yellow, blue, cyan, and red) circularly permuted fluorescent protein (FP)-based Ca indicators driven by multiple fungal promoters in Fusarium oxysporum, F. graminearum, and Neurospora crassa. Several variants were successfully expressed, with GCaMP5G driven by the Magnaporthe oryzae ribosomal protein 27 (P) and F. verticillioides elongation factor-1α (P) gene promoters being optimal for F. graminearum and F. oxysporum, respectively. Transformants expressing GCaMP5G were compared with those expressing YC3.60, a ratiometric Cameleon Ca indicator. Wild-type and three Ca signaling mutants of F. graminearum expressing GCaMP5G exhibited improved signal-to-noise and increased temporal and spatial resolution and are also more amenable to studies involving multiple FPs compared to strains expressing YC3.60.

}, issn = {1096-0937}, doi = {10.1016/j.fgb.2021.103540}, author = {Kim, Hye-Seon and Kim, Jung-Eun and Hwangbo, Aram and Akerboom, Jasper and Looger, Loren L and Duncan, Randall and Son, Hokyoung and Czymmek, Kirk J and Kang, Seogchan} } @article {68988, title = {Ex Utero Culture of Mouse Embryos from Pregastrulation to Advanced Organogenesis.}, journal = {J Vis Exp}, year = {2021}, month = {10/2021}, abstract = {

Postimplantation mammalian embryo culture methods have been generally inefficient and limited to brief periods after dissection out of the uterus. Platforms have been recently developed for highly robust and prolonged ex utero culture of mouse embryos from egg-cylinder stages until advanced organogenesis. These platforms enable appropriate and faithful development of pregastrulating embryos (E5.5) until the hind limb formation stage (E11). Late gastrulating embryos (E7.5) are grown in rotating bottles in these settings, while extended culture from pregastrulation stages (E5.5 or E6.5) requires a combination of static and rotating bottle cultures. In addition, sensitive regulation of O2 and CO2 concentration, gas pressure, glucose levels, and the use of a specific ex utero culture medium are critical for proper embryo development. Here, a detailed step-by-step protocol for extended ex utero mouse embryo culture is provided. The ability to grow normal mouse embryos ex utero from gastrulation to organogenesis represents a valuable tool for characterizing the effect of different experimental perturbations during embryonic development.

}, keywords = {Animals, Embryo Culture Techniques, Embryo, Mammalian, Embryonic Development, Female, Gastrulation, Mammals, Mice, Organogenesis, Pregnancy}, issn = {1940-087X}, doi = {10.3791/63160}, author = {Aguilera-Castrejon, Alejandro and Hanna, Jacob H} } @article {68989, title = {Ex utero mouse embryogenesis from pre-gastrulation to late organogenesis.}, journal = {Nature}, volume = {593}, year = {2021}, month = {05/2021}, pages = {119-124}, abstract = {

The mammalian body plan is established shortly after the embryo implants into the maternal uterus, and our understanding of post-implantation developmental processes remains limited. Although pre- and peri-implantation mouse embryos are routinely cultured in vitro, approaches for the robust culture of post-implantation embryos from egg cylinder stages until advanced organogenesis remain to be established. Here we present highly effective platforms for the ex utero culture of post-implantation mouse embryos, which enable the appropriate development of embryos from before gastrulation (embryonic day (E) 5.5) until the hindlimb formation stage (E11). Late gastrulating embryos (E7.5) are grown in three-dimensional rotating bottles, whereas extended culture from pre-gastrulation stages (E5.5 or E6.5) requires a combination of static and rotating bottle culture platforms. Histological, molecular and single-cell RNA sequencing analyses confirm that the ex utero cultured embryos recapitulate in utero development precisely. This culture system is amenable to the introduction of a variety of embryonic perturbations and micro-manipulations, the results of which can be followed ex utero for up to six days. The establishment of a system for robustly growing normal mouse embryos ex utero from pre-gastrulation to advanced organogenesis represents a valuable tool for investigating embryogenesis, as it eliminates the uterine barrier and allows researchers to mechanistically interrogate post-implantation morphogenesis and artificial embryogenesis\ in mammals.

}, keywords = {Animals, Embryo Culture Techniques, Embryo, Mammalian, Embryonic Development, Female, Gastrulation, In Vitro Techniques, Male, Mice, Organogenesis, Time Factors, Uterus}, issn = {1476-4687}, doi = {10.1038/s41586-021-03416-3}, author = {Aguilera-Castrejon, Alejandro and Oldak, Bernardo and Shani, Tom and Ghanem, Nadir and Itzkovich, Chen and Slomovich, Sharon and Tarazi, Shadi and Bayerl, Jonathan and Chugaeva, Valeriya and Ayyash, Muneef and Ashouokhi, Shahd and Sheban, Daoud and Livnat, Nir and Lasman, Lior and Viukov, Sergey and Zerbib, Mirie and Addadi, Yoseph and Rais, Yoach and Cheng, Saifeng and Stelzer, Yonatan and Keren-Shaul, Hadas and Shlomo, Raanan and Massarwa, Rada and Novershtern, Noa and Maza, Itay and Hanna, Jacob H} } @article {67243, title = {Expansion-Assisted Iterative-FISH defines lateral hypothalamus spatio-molecular organization}, journal = {bioRxiv}, year = {2021}, month = {2021 Mar 8}, abstract = {

Determining the spatial organization and morphological characteristics of molecularly defined cell types is a major bottleneck for characterizing the architecture underpinning brain function. We developed\ Expansion-Assisted Iterative\ Fluorescence\ In\ Situ\ Hybridization (EASI-FISH) to survey gene expression in brain tissue, as well as a turnkey computational pipeline to rapidly process large EASI-FISH image datasets. EASI-FISH was optimized for thick brain sections (300 {\textmu}m) to facilitate reconstruction of spatio-molecular domains that generalize across brains. Using the EASI-FISH pipeline, we investigated the spatial distribution of dozens of molecularly defined cell types in the lateral hypothalamic area (LHA), a brain region with poorly defined anatomical organization. Mapping cell types in the LHA revealed nine novel spatially and molecularly defined subregions. EASI-FISH also facilitates iterative re-analysis of scRNA-Seq datasets to determine marker-genes that further dissociated spatial and morphological heterogeneity. The EASI-FISH pipeline democratizes mapping molecularly defined cell types, enabling discoveries about brain organization.

}, doi = {10.1101/2021.03.08.434304}, url = {https://doi.org/10.1101/2021.03.08.434304}, author = {Yuhan Wang and Mark Eddison and Greg Fleishman and Martin Weigert and Shengjin Xu and Frederick E. Henry and Tim Wang and Andrew L. Lemire and Uwe Schmidt and Hui Yang and Konrad Rokicki and Cristian Goina and Karel Svoboda and Eugene W. Myers and Stephan Saalfeld and Wyatt Korff and Scott M. Sternson and Paul W. Tillberg} } @article {67659, title = {Extending the performance capabilities of isoSTED.}, journal = {Biophysical Journal}, volume = {120}, year = {2021}, month = {2021 Aug 01}, pages = {3237-3239}, issn = {1542-0086}, doi = {10.1016/j.bpj.2021.07.005}, author = {Ulrike Boehm and Galbraith, Catherine G} } @article {67199, title = {Flexible scaling and persistence of social vocal communication.}, journal = {Nature}, volume = {593}, year = {2021}, month = {2021 May 01}, pages = {108-13}, abstract = {

Innate vocal sounds such as laughing, screaming or crying convey one{\textquoteright}s feelings to others. In many species, including humans, scaling the amplitude and duration of vocalizations is essential for effective social communication. In mice, female scent triggers male mice to emit innate courtship ultrasonic vocalizations (USVs). However, whether mice flexibly scale their vocalizations and how neural circuits are structured to generate flexibility remain largely unknown. Here we identify mouse neurons from the lateral preoptic area (LPOA) that express oestrogen receptor 1 (LPOA neurons) and, when activated, elicit the complete repertoire of USV syllables emitted during natural courtship. Neural anatomy and functional data reveal a two-step, di-synaptic circuit motif in which primary long-range inhibitory LPOA neurons relieve a clamp of local periaqueductal grey (PAG) inhibition, enabling excitatory PAG USV-gating neurons to trigger vocalizations. We find that social context shapes a wide range of USV amplitudes and bout durations. This variability is absent when PAG neurons are stimulated directly; PAG-evoked vocalizations are time-locked to neural activity and stereotypically loud. By contrast, increasing the activity of LPOA neurons scales the amplitude of vocalizations, and delaying the recovery of the inhibition clamp prolongs USV bouts. Thus, the LPOA disinhibition motif contributes to flexible loudness and the duration and persistence of bouts, which are key aspects of effective vocal social communication.

}, issn = {1476-4687}, doi = {10.1038/s41586-021-03403-8}, author = {Chen, Jingyi and Markowitz, Jeffrey E and Lilascharoen, Varoth and Taylor, Sandra and Sheurpukdi, Pete and Keller, Jason A and Jensen, Jennifer R and Lim, Byung Kook and Datta, Sandeep Robert and Stowers, Lisa} } @article {67301, title = {FLIM Imaging for Metabolic Studies in Live Cells.}, journal = {Methods in Molecular Biology}, volume = {2304}, year = {2021}, month = {2021 May 28}, pages = {339-346}, abstract = {

Fluorescent biochemical sensors allow probing metabolic states in a living cell with high spatiotemporal dynamics. This chapter describes a method for the in situ detection of changes in NAD level in living cells using fluorescence lifetime imaging (FLIM).

}, issn = {1940-6029}, doi = {10.1007/978-1-0716-1402-0_18}, author = {Choi, Heejun} } @article {67715, title = {A framework for studying behavioral evolution by reconstructing ancestral repertoires.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Sep 02}, abstract = {

Although different animal species often exhibit extensive variation in many behaviors, typically scientists examine one or a small number of behaviors in any single study. Here, we propose a new framework to simultaneously study the evolution of many behaviors. We measured the behavioral repertoire of individuals from six species of fruit flies using unsupervised techniques and identified all stereotyped movements exhibited by each species. We then fit a Generalized Linear Mixed Model to estimate the intra- and inter-species behavioral covariances, and, by using the known phylogenetic relationships among species, we estimated the (unobserved) behaviors exhibited by ancestral species. We found that much of intra-specific behavioral variation has a similar covariance structure to previously described long-time scale variation in an individual{\textquoteright}s behavior, suggesting that much of the measured variation between individuals of a single species in our assay reflects differences in the status of neural networks, rather than genetic or developmental differences between individuals. We then propose a method to identify groups of behaviors that appear to have evolved in a correlated manner, illustrating how sets of behaviors, rather than individual behaviors, likely evolved. Our approach provides a new framework for identifying co-evolving behaviors and may provide new opportunities to study the mechanistic basis of behavioral evolution.

}, issn = {2050-084X}, doi = {10.7554/eLife.61806}, author = {Hern{\'a}ndez, Dami{\'a}n G and Rivera, Catalina and Cande, Jessica and Zhou, Baohua and Stern, David and Berman, Gordon J} } @article {69714, title = {FRC-QE: a robust and comparable 3D microscopy image quality metric for cleared organoids.}, journal = {Bioinformatics}, volume = {37}, year = {2021}, month = {03/2021}, pages = {3088-3090}, abstract = {

SUMMARY: Here, we propose Fourier ring correlation-based quality estimation (FRC-QE) as a new metric for automated image quality estimation in 3D fluorescence microscopy acquisitions of cleared organoids that yields comparable measurements across experimental replicates, clearing protocols and works for different microscopy modalities.

AVAILABILITY AND IMPLEMENTATION: FRC-QE is written in ImgLib2/Java and provided as an easy-to-use and macro-scriptable plugin for Fiji. Code, documentation, sample images and further information can be found under https://github.com/PreibischLab/FRC-QE.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

}, keywords = {Imaging, Three-Dimensional, Microscopy, Fluorescence, Software}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btab160}, author = {Preusser, Friedrich and Dos Santos, Nat{\'a}lia and Contzen, J{\"o}rg and Stachelscheid, Harald and Costa, {\'E}rico Tosoni and Mergenthaler, Philipp and Preibisch, Stephan} } @article {67751, title = {Functional architecture of neural circuits for leg proprioception in Drosophila.}, journal = {Current Biology}, volume = {31}, year = {2021}, month = {2021 Dec 06}, pages = {5163}, abstract = {

To effectively control their bodies, animals rely on feedback from proprioceptive mechanosensory neurons. In the Drosophila leg, different proprioceptor subtypes monitor joint position, movement direction, and vibration. Here, we investigate how these diverse sensory signals are integrated by central proprioceptive circuits. We find that signals for leg joint position and directional movement converge in second-order neurons, revealing pathways for local feedback control of leg posture. Distinct populations of second-order neurons integrate tibia vibration signals across pairs of legs, suggesting a role in detecting external substrate vibration. In each pathway, the flow of sensory information is dynamically gated and sculpted by inhibition. Overall, our results reveal parallel pathways for processing of internal and external mechanosensory signals, which we propose mediate feedback control of leg movement and vibration sensing, respectively. The existence of a functional connectivity map also provides a resource for interpreting connectomic reconstruction of neural circuits for leg proprioception.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2021.09.035}, author = {Chen, Chenghao and Agrawal, Sweta and Mark, Brandon and Mamiya, Akira and Sustar, Anne and Phelps, Jasper S and Lee, Wei-Chung Allen and Dickson, Barry J and Card, Gwyneth M and Tuthill, John C} } @article {67311, title = {The functional organization of excitatory synaptic input to place cells.}, journal = {Nature Communications}, volume = {12}, year = {2021}, month = {2021 Jun 11}, pages = {3558}, abstract = {

Hippocampal place cells contribute to mammalian spatial navigation and memory formation. Numerous models have been proposed to explain the location-specific firing of this cognitive representation, but the pattern of excitatory synaptic input leading to place firing is unknown, leaving no synaptic-scale explanation of place coding. Here we used resonant scanning two-photon microscopy to establish the pattern of synaptic glutamate input received by CA1 place cells in behaving mice. During traversals of the somatic place field, we found increased excitatory dendritic input, mainly arising from inputs with spatial tuning overlapping the somatic field, and functional clustering of this input along the dendrites over ~10 {\textmu}m. These results implicate increases in total excitatory input and co-activation of anatomically clustered synaptic input in place firing. Since they largely inherit their fields from upstream synaptic partners with similar fields, many CA1 place cells appear to be part of multi-brain-region cell assemblies forming representations of specific locations.

}, issn = {2041-1723}, doi = {10.1038/s41467-021-23829-y}, author = {Adoff, Michael D and Climer, Jason R and Davoudi, Heydar and Marvin, Jonathan S and Looger, Loren L and Dombeck, Daniel A} } @article {67805, title = {Functionally distinct roles for eEF2K in the control of ribosome availability and p-body abundance.}, journal = {Nature Communications}, volume = {12}, year = {2021}, month = {2021 Nov 23}, pages = {6789}, abstract = {

Processing bodies (p-bodies) are a prototypical phase-separated RNA-containing granule. Their abundance is highly dynamic and has been linked to translation. Yet, the molecular mechanisms responsible for coordinate control of the two processes are unclear. Here, we uncover key roles for eEF2 kinase (eEF2K) in the control of ribosome availability and p-body abundance. eEF2K acts on a sole known substrate, eEF2, to inhibit translation. We find that the eEF2K agonist nelfinavir abolishes p-bodies in sensory neurons and impairs translation. To probe the latter, we used cryo-electron microscopy. Nelfinavir stabilizes vacant 80S ribosomes. They contain SERBP1 in place of mRNA and eEF2 in the acceptor site. Phosphorylated eEF2 associates with inactive ribosomes that resist splitting in vitro. Collectively, the data suggest that eEF2K defines a population of inactive ribosomes resistant to recycling and protected from degradation. Thus, eEF2K activity is central to both p-body abundance and ribosome availability in sensory neurons.

}, issn = {2041-1723}, doi = {10.1038/s41467-021-27160-4}, author = {Smith, Patrick R and Loerch, Sarah and Kunder, Nikesh and Stanowick, Alexander D and Lou, Tzu-Fang and Campbell, Zachary T} } @article {67244, title = {A general method to improve fluorophores using deuterated auxochromes.}, journal = {JACS Au}, volume = {1}, year = {2021}, month = {2021 May 24}, pages = {690-6}, abstract = {

Fluorescence microscopy relies on dyes that absorb and then emit photons. In addition to fluorescence, fluorophores can undergo photochemical processes that decrease quantum yield or result in spectral shifts and irreversible photobleaching. Chemical strategies that suppress these undesirable pathways{\textemdash}thereby increasing the brightness and photostability of fluorophores{\textemdash}are crucial for advancing the frontier of bioimaging. Here, we describe a general method to improve small-molecule fluorophores by incorporating deuterium into the alkylamino auxochromes of rhodamines and other dyes. This strategy increases fluorescence quantum yield, inhibits photochemically induced spectral shifts, and slows irreparable photobleaching, yielding next-generation labels with improved performance in cellular imaging experiments.

}, issn = {2691-3704}, doi = {10.1021/jacsau.1c00006}, url = {https://doi.org/10.1021/jacsau.1c00006}, author = {Grimm, Jonathan B. and Xie, Liangqi and Casler, Jason C. and Patel, Ronak and Tkachuk, Ariana N. and Falco, Natalie and Choi, Heejun and Lippincott-Schwartz, Jennifer and Brown, Timothy A. and Glick, Benjamin S. and Liu, Zhe and Lavis, Luke D.} } @article {67712, title = {A genetic screen for Drosophila social isolation mutants and analysis of sex pistol.}, journal = {Scientific Reports}, volume = {11}, year = {2021}, month = {2021 Aug 30}, pages = {17395}, abstract = {

Prolonged periods of forced social isolation is detrimental to well-being, yet we know little about which genes regulate susceptibility to its effects. In the fruit fly, Drosophila melanogaster, social isolation induces stark changes in behavior including increased aggression, locomotor activity, and resistance to ethanol sedation. To identify genes regulating sensitivity to isolation, I screened a collection of sixteen hundred P-element insertion lines for mutants with abnormal levels of all three isolation-induced behaviors. The screen identified three mutants whose affected genes are likely central to regulating the effects of isolation in flies. One mutant, sex pistol (sxp), became extremely aggressive and resistant to ethanol sedation when socially isolated. sxp also had a high level of male-male courtship. The mutation in sxp reduced the expression of two minor isoforms of the actin regulator hts (adducin), as well as mildly reducing expression of CalpA, a calcium-dependent protease. As a consequence, sxp also had increased expression of the insulin-like peptide, dILP5. Analysis of the social behavior of sxp suggests that these minor hts isoforms function to limit isolation-induced aggression, while chronically high levels of dILP5 increase male-male courtship.

}, issn = {2045-2322}, doi = {10.1038/s41598-021-96871-x}, author = {Eddison, Mark} } @article {67821, title = {A genetically defined insula-brainstem circuit selectively controls motivational vigor.}, journal = {Cell}, year = {2021}, month = {2021 Dec 07}, abstract = {

The anterior insular cortex (aIC) plays a critical role in cognitive and motivational control of behavior, but the underlying neural mechanism remains elusive. Here, we show that aIC neurons expressing Fezf2 (aIC), which are the pyramidal tract neurons, signal motivational vigor and invigorate need-seeking behavior through projections to the brainstem nucleus tractus solitarii (NTS). aIC neurons and their postsynaptic NTS neurons acquire anticipatory activity through learning, which encodes the perceived value and the vigor of actions to pursue homeostatic needs. Correspondingly, aIC {\textrightarrow} NTS circuit activity controls vigor, effort, and striatal dopamine release but only if the action is learned and the outcome is needed. Notably, aIC neurons do not represent taste or valence. Moreover, aIC {\textrightarrow} NTS activity neither drives reinforcement nor influences total consumption. These results pinpoint specific functions of aIC {\textrightarrow} NTS circuit for selectively controlling motivational vigor and suggest that motivation is subserved, in part, by aIC{\textquoteright}s top-down regulation of dopamine signaling.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2021.11.019}, author = {Deng, Hanfei and Xiao, Xiong and Yang, Tao and Ritola, Kimberly and Hantman, Adam and Li, Yulong and Huang, Z Josh and Li, Bo} } @article {67816, title = {A genetically encoded fluorescent biosensor for extracellular L-lactate.}, journal = {Nature Communications}, volume = {12}, year = {2021}, month = {2021 Dec 06}, pages = {7058}, abstract = {

L-Lactate, traditionally considered a metabolic waste product, is increasingly recognized as an important intercellular energy currency in mammals. To enable investigations of the emerging roles of intercellular shuttling of L-lactate, we now report an intensiometric green fluorescent genetically encoded biosensor for extracellular L-lactate. This biosensor, designated eLACCO1.1, enables cellular resolution imaging of extracellular L-lactate in cultured mammalian cells and brain tissue.

}, issn = {2041-1723}, doi = {10.1038/s41467-021-27332-2}, author = {Nasu, Yusuke and Murphy-Royal, Ciaran and Wen, Yurong and Haidey, Jordan N and Molina, Rosana S and Abhi Aggarwal and Zhang, Shuce and Kamijo, Yuki and Paquet, Marie-Eve and Podgorski, Kaspar and Drobizhev, Mikhail and Bains, Jaideep S and Lemieux, M Joanne and Gordon, Grant R and Campbell, Robert E} } @article {67765, title = {Genetically identified amygdala-striatal circuits for valence-specific behaviors.}, journal = {Nature Neuroscience}, volume = {24}, year = {2021}, month = {2021 Oct 18}, pages = {1586-1600}, abstract = {

The basolateral amygdala (BLA) plays essential roles in behaviors motivated by stimuli with either positive or negative valence, but how it processes motivationally opposing information and participates in establishing valence-specific behaviors remains unclear. Here, by targeting Fezf2-expressing neurons in the BLA, we identify and characterize two functionally distinct classes in behaving mice, the negative-valence neurons and positive-valence neurons, which innately represent aversive and rewarding stimuli, respectively, and through learning acquire predictive responses that are essential for punishment avoidance or reward seeking. Notably, these two classes of neurons receive inputs from separate sets of sensory and limbic areas, and convey punishment and reward information through projections to the nucleus accumbens and olfactory tubercle, respectively, to drive negative and positive reinforcement. Thus, valence-specific BLA neurons are wired with distinctive input-output structures, forming a circuit framework that supports the roles of the BLA in encoding, learning and executing valence-specific motivated behaviors.

}, issn = {1546-1726}, doi = {10.1038/s41593-021-00927-0}, author = {Zhang, Xian and Guan, Wuqiang and Yang, Tao and Furlan, Alessandro and Xiao, Xiong and Yu, Kai and An, Xu and Galbavy, William and Ramakrishnan, Charu and Deisseroth, Karl and Ritola, Kimberly and Hantman, Adam and He, Miao and Josh Huang, Z and Li, Bo} } @article {67200, title = {A guide to accurate reporting in digital image processing - can anyone reproduce your quantitative analysis?}, journal = {Journal of Cell Science}, volume = {134}, year = {2021}, month = {2021 Mar 30}, abstract = {

Considerable attention has been recently paid to improving replicability and reproducibility in life science research. This has resulted in commendable efforts to standardize a variety of reagents, assays, cell lines and other resources. However, given that microscopy is a dominant tool for biologists, comparatively little discussion has been offered regarding how the proper reporting and documentation of microscopy relevant details should be handled. Image processing is a critical step of almost any microscopy-based experiment; however, improper, or incomplete reporting of its use in the literature is pervasive. The chosen details of an image processing workflow can dramatically determine the outcome of subsequent analyses, and indeed, the overall conclusions of a study. This Review aims to illustrate how proper reporting of image processing methodology improves scientific reproducibility and strengthens the biological conclusions derived from the results.

}, issn = {1477-9137}, doi = {10.1242/jcs.254151}, author = {Aaron, Jesse and Chew, Teng-Leong} } @article {67197, title = {The HaloTag as a general scaffold for far-red tunable chemigenetic indicators.}, journal = {Nature Chemical Biology}, year = {2021}, month = {2021 Apr 01}, abstract = {

Functional imaging using fluorescent indicators has revolutionized biology, but additional sensor scaffolds are needed to access properties such as bright, far-red emission. Here, we introduce a new platform for {\textquoteright}chemigenetic{\textquoteright} fluorescent indicators, utilizing the self-labeling HaloTag protein conjugated to environmentally sensitive synthetic fluorophores. We solve a crystal structure of HaloTag bound to a rhodamine dye ligand to guide engineering efforts to modulate the dye environment. We show that fusion of HaloTag with protein sensor domains that undergo conformational changes near the bound dye results in large and rapid changes in fluorescence output. This generalizable approach affords bright, far-red calcium and voltage sensors with highly tunable photophysical and chemical properties, which can reliably detect single action potentials in cultured neurons.

}, issn = {1552-4469}, doi = {10.1038/s41589-021-00775-w}, author = {Deo, Claire and Abdelfattah, Ahmed S and Bhargava, Hersh K and Berro, Adam J and Falco, Natalie and Farrants, Helen and Moeyaert, Benjamien and Chupanova, Mariam and Lavis, Luke D and Schreiter, Eric R} } @article {67211, title = {High-fidelity estimates of spikes and subthreshold waveforms from 1-photon voltage imaging in~vivo.}, journal = {Cell Reports}, volume = {35}, year = {2021}, month = {2021 Apr 06}, pages = {108954}, abstract = {

The ability to probe the membrane potential of multiple genetically defined neurons simultaneously would have a profound impact on neuroscience research. Genetically encoded voltage indicators are a promising tool for this purpose, and recent developments have achieved a high signal-to-noise ratio in\ vivo with 1-photon fluorescence imaging. However, these recordings exhibit several sources of noise and signal extraction remains a challenge. We present an improved signal extraction pipeline, spike-guided penalized matrix decomposition-nonnegative matrix factorization (SGPMD-NMF), which resolves supra- and subthreshold voltages in\ vivo. The method incorporates biophysical and optical constraints. We validate the pipeline with simultaneous patch-clamp and optical recordings from mouse layer 1 in\ vivo and with simulated and composite datasets with realistic noise. We demonstrate applications to mouse hippocampus expressing paQuasAr3-s or SomArchon1, mouse cortex expressing SomArchon1 or Voltron, and zebrafish spines expressing zArchon1.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2021.108954}, author = {Xie, Michael E and Adam, Yoav and Fan, Linlin Z and B{\"o}hm, Urs L and Kinsella, Ian and Zhou, Ding and Rozsa, Marton and Singh, Amrita and Svoboda, Karel and Paninski, Liam and Cohen, Adam E} } @article {67234, title = {High-precision coding in visual cortex.}, journal = {Cell}, volume = {184}, year = {2021}, month = {2021 May 13}, pages = {2767-78}, abstract = {

Individual neurons in visual cortex provide the brain with unreliable estimates of visual features. It is not known whether the single-neuron variability is correlated across large neural populations, thus impairing the global encoding of stimuli. We recorded simultaneously from up to 50,000 neurons in mouse primary visual cortex (V1) and in higher order visual areas and measured stimulus discrimination thresholds of 0.35{\textdegree} and 0.37{\textdegree}, respectively, in an orientation decoding task. These neural thresholds were almost 100 times smaller than the behavioral discrimination thresholds reported in mice. This discrepancy could not be explained by stimulus properties or arousal states. Furthermore, behavioral variability during a sensory discrimination task could not be explained by neural variability in V1. Instead, behavior-related neural activity arose dynamically across a network of non-sensory brain areas. These results imply that perceptual discrimination in mice is limited by downstream decoders, not by neural noise in sensory representations.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2021.03.042}, author = {Stringer, Carsen and Michaelos, Michalis and Tsyboulski, Dmitri and Lindo, Sarah E and Pachitariu, Marius} } @article {65999, title = {A high-throughput predictive method for sequence-similar fold switchers.}, journal = {Biopolymers}, volume = {112}, year = {2021}, month = {2021 Oct 01}, pages = {e23416}, abstract = {

Although most experimentally characterized proteins with similar sequences assume the same folds and perform similar functions, an increasing number of exceptions is emerging. One class of exceptions comprises sequence-similar fold switchers, whose secondary structures shift from α-helix \<-\> β-sheet through a small number of mutations, a sequence insertion, or a deletion. Predictive methods for identifying sequence-similar fold switchers are desirable because some are associated with disease and/or can perform different functions in cells. Here, we use homology-based secondary structure predictions to identify sequence-similar fold switchers from their amino acid sequences alone. To do this, we predicted the secondary structures of sequence-similar fold switchers using three different homology-based secondary structure predictors: PSIPRED, JPred4, and SPIDER3. We found that α-helix \<-\> β-strand prediction discrepancies from JPred4 discriminated between the different conformations of sequence-similar fold switchers with high statistical significance (P \< 1.8*10 ). Thus, we used these discrepancies as a classifier and found that they can often robustly discriminate between sequence-similar fold switchers and sequence-similar proteins that maintain the same folds (Matthews Correlation Coefficient of 0.82). We found that JPred4 is a more robust predictor of sequence-similar fold switchers because of (a) the curated sequence database it uses to produce multiple sequence alignments and (b) its use of sequence profiles based on Hidden Markov Models. Our results indicate that inconsistencies between JPred4 secondary structure predictions can be used to identify some sequence-similar fold switchers from their sequences alone. Thus, the negative information from inconsistent secondary structure predictions can potentially be leveraged to identify sequence-similar fold switchers from the broad base of genomic sequences.

}, issn = {1097-0282}, doi = {10.1002/bip.23416}, author = {Kim, Allen K and Looger, Loren L and Porter, Lauren L} } @article {67186, title = {Hippocampal and thalamic afferents form distinct synaptic microcircuits in the mouse frontal cortex.}, journal = {Cell Reports}, volume = {37}, year = {2021}, month = {2021 October 19}, pages = {109837}, abstract = {

Neural circuits within the frontal cortex support the flexible selection of goal-directed behaviors by integrating input from brain regions associated with sensory, emotional, episodic, and semantic memory functions. From a connectomics perspective, determining how these disparate afferent inputs target their synapses to specific cell types in the frontal cortex may prove crucial in understanding circuit-level information processing. Here, we used monosynaptic retrograde rabies mapping to examine the distribution of afferent neurons targeting four distinct classes of local inhibitory interneurons and four distinct classes of excitatory projection neurons in mouse infralimbic cortex. Interneurons expressing parvalbumin, somatostatin, or vasoactive intestinal peptide received a large proportion of inputs from hippocampal regions, while interneurons expressing neuron-derived neurotrophic factor received a large proportion of inputs from thalamic regions. A more moderate hippocampal-thalamic dichotomy was found among the inputs targeting excitatory neurons that project to the basolateral amygdala, lateral entorhinal cortex, nucleus reuniens of the thalamus, and the periaqueductal gray. Together, these results show a prominent bias among hippocampal and thalamic afferent systems in their targeting to genetically or anatomically defined sets of frontal cortical neurons. Moreover, they suggest the presence of two distinct local microcircuits that control how different inputs govern frontal cortical information processing.

}, author = {Kourtney Graham and Nelson Spruston and Erik Bloss} } @article {67263, title = {Hunger or thirst state uncertainty is resolved by outcome evaluation in medial prefrontal cortex to guide decision-making.}, journal = {Nature Neuroscience}, volume = {24}, year = {2021}, month = {2021 Jul 01}, pages = {907-912}, abstract = {

Physiological need states direct decision-making toward re-establishing homeostasis. Using a two-alternative forced choice task for mice that models elements of human decisions, we found that varying hunger and thirst states caused need-inappropriate choices, such as food seeking when thirsty. These results show limits on interoceptive knowledge of hunger and thirst states to guide decision-making. Instead, need states were identified after food and water consumption by outcome evaluation, which depended on the medial prefrontal cortex.

}, issn = {1546-1726}, doi = {10.1038/s41593-021-00850-4}, author = {Eiselt, Anne-Kathrin and Chen, Susu and Chen, Jim and Arnold, Jon and Kim, Tahnbee and Pachitariu, Marius and Sternson, Scott M} } @article {66020, title = {Idiosyncratic learning performance in flies generalizes across modalities.}, journal = {bioRxiv}, year = {2021}, month = {2021 Jan 25}, abstract = {

Individuals vary in their innate behaviors, even when they have the same genome and have been reared in the same environment. The extent of individuality in plastic behaviors, like learning, is less well characterized. Also unknown is the extent to which intragenotypic differences in learning generalize: if an individual performs well in one assay, will it perform well in other assays? We investigated this using the fruit fly\ Drosophila melanogaster, an organism long-used to study the mechanistic basis of learning and memory. We found that isogenic flies, reared in identical lab conditions, and subject to classical conditioning that associated odorants with electric shock, exhibit clear individuality in their learning responses. Flies that performed well when an odor was paired with shock tended to perform well when other odors were paired with shock, or when the original odor was paired with bitter taste. Thus, individuality in learning performance appears to be prominent in isogenic animals reared identically, and individual differences in learning performance generalize across stimulus modalities. Establishing these results in flies opens up the possibility of studying the genetic and neural circuit basis of individual differences in learning in a highly suitable model organism.

}, author = {Matthew Smith and Kyle S. Honegger and Glenn Turner and Benjamin de Bivort} } @article {66002, title = {Image-based pooled whole-genome CRISPRi screening for subcellular phenotypes.}, journal = {Journal of Cell Biology}, volume = {220}, year = {2021}, month = {2021 Feb 01}, abstract = {

Genome-wide CRISPR screens have transformed our ability to systematically interrogate human gene function, but are currently limited to a subset of cellular phenotypes. We report a novel pooled screening approach for a wider range of cellular and subtle subcellular phenotypes. Machine learning and convolutional neural network models are trained on the subcellular phenotype to be queried. Genome-wide screening then utilizes cells stably expressing dCas9-KRAB (CRISPRi), photoactivatable fluorescent protein (PA-mCherry), and a lentiviral guide RNA (gRNA) pool. Cells are screened by using microscopy and classified by artificial intelligence (AI) algorithms, which precisely identify the genetically altered phenotype. Cells with the phenotype of interest are photoactivated and isolated via flow cytometry, and the gRNAs are identified by sequencing. A proof-of-concept screen accurately identified PINK1 as essential for Parkin recruitment to mitochondria. A genome-wide screen identified factors mediating TFEB relocation from the nucleus to the cytosol upon prolonged starvation. Twenty-one of the 64 hits called by the neural network model were independently validated, revealing new effectors of TFEB subcellular localization. This approach, AI-photoswitchable screening (AI-PS), offers a novel screening platform capable of classifying a broad range of mammalian subcellular morphologies, an approach largely unattainable with current methodologies at genome-wide scale.

}, issn = {1540-8140}, doi = {10.1083/jcb.202006180}, author = {Kanfer, Gil and Sarraf, Shireen A and Maman, Yaakov and Baldwin, Heather and Dominguez-Martin, Eunice and Johnson, Kory R and Ward, Michael E and Kampmann, Martin and Lippincott-Schwartz, Jennifer and Youle, Richard J} } @article {67871, title = {Image-based representation of massive spatial transcriptomics datasets.}, journal = {bioRxiv}, year = {2021}, month = {2021 Dec 07}, abstract = {

We present STIM, an imaging-based computational framework for exploring, visualizing, and processing high-throughput spatial sequencing datasets. STIM is built on the powerful ImgLib2, N5 and BigDataViewer (BDV) frameworks enabling transfer of computer vision techniques to datasets with irregular measurement-spacing and arbitrary spatial resolution, such as spatial transcriptomics data generated by multiplexed targeted hybridization or spatial sequencing technologies. We illustrate STIM{\textquoteright}s capabilities by representing, visualizing, and automatically registering publicly available spatial sequencing data from 14 serial sections of mouse brain tissue.

}, doi = {10.1101/2021.12.07.471629}, url = {https://doi.org/10.1101/2021.12.07.471629}, author = {Stephan Preibisch and Nikos Karaiskos and Nikolaus Rajewsky} } @article {67670, title = {Imaging Africa: a strategic approach to optical microscopy training in Africa.}, journal = {Nature Methods}, volume = {18}, year = {2021}, month = {2021 Aug 20}, pages = {847-855}, issn = {1548-7105}, doi = {10.1038/s41592-021-01227-y}, author = {Reiche, Michael A and Warner, Digby F and Aaron, Jesse and Khuon, Satya and Fletcher, Daniel A and Hahn, Klaus and Rogers, Kelly L and Mhlanga, Musa and Koch, Anastasia and Quaye, Wendye and Chew, Teng-Leong} } @article {67627, title = {In~vivo glucose imaging in multiple model organisms with an engineered single-wavelength sensor.}, journal = {Cell Reports}, volume = {35}, year = {2021}, month = {2021 Jun 22}, pages = {109284}, abstract = {

Glucose is arguably the most important molecule in metabolism, and its dysregulation underlies diabetes. We describe a family of single-wavelength genetically encoded glucose sensors with a high signal-to-noise ratio, fast kinetics, and affinities varying over four orders of magnitude (1\ μM to 10\ mM). The sensors allow mechanistic characterization of glucose transporters expressed in cultured cells with high spatial and temporal resolution. Imaging of neuron/glia co-cultures revealed \~{}3-fold faster glucose changes in astrocytes. In larval Drosophila central nervous system explants, intracellular neuronal glucose fluxes suggested a rostro-caudal transport pathway in the ventral nerve cord neuropil. In zebrafish, expected glucose-related physiological sequelae of insulin and epinephrine treatments were directly visualized. Additionally, spontaneous muscle twitches induced glucose uptake in muscle, and sensory and pharmacological perturbations produced large changes in the brain. These sensors will enable rapid, high-resolution imaging of glucose influx, efflux, and metabolism in behaving animals.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2021.109284}, author = {Keller, Jacob P and Marvin, Jonathan S and Lacin, Haluk and Lemon, William C and Shea, Jamien and Kim, Soomin and Lee, Richard T and Koyama, Minoru and Keller, Philipp J and Looger, Loren L} } @article {65815, title = {In vivo optogenetics with stimulus calibration.}, journal = {Methods in Molecular Biology}, volume = {2188}, year = {2021}, month = {2020 Nov 06}, pages = {273-283}, abstract = {

Optogenetic reagents allow for depolarization and hyperpolarization of cells with light. This provides unprecedented spatial and temporal resolution to the control of neuronal activity both in vitro and in vivo. In the intact animal this requires strategies to deliver light deep into the highly scattering tissue of the brain. A general approach that we describe here is to implant optical fibers just above brain regions targeted for light delivery. In part due to the fact that expression of optogenetic proteins is accomplished by techniques with inherent variability (e.g., viral expression\ levels), it also requires strategies to measure and calibrate the effect of stimulation. Here we describe general procedures that allow one to simultaneously stimulate neurons and use photometry with genetically encoded activity indicators to precisely calibrate stimulation.

}, issn = {1940-6029}, doi = {10.1007/978-1-0716-0818-0_14}, author = {Coddington, Luke T and Dudman, Joshua T} } @article {67658, title = {An inexpensive, high-precision, modular spherical treadmill setup optimized for experiments.}, journal = {Frontiers in Behavioral Neuroscience}, volume = {15}, year = {2021}, month = {2021 Jul 16}, pages = {689573}, abstract = {

To pursue a more mechanistic understanding of the neural control of behavior, many neuroethologists study animal behavior in controlled laboratory environments. One popular approach is to measure the movements of restrained animals while presenting controlled sensory stimulation. This approach is especially powerful when applied to genetic model organisms, such as , where modern genetic tools enable unprecedented access to the nervous system for activity monitoring or targeted manipulation. While there is a long history of measuring the behavior of body- and head-fixed insects walking on an air-supported ball, the methods typically require complex setups with many custom components. Here we present a compact, simplified setup for these experiments that achieves high-performance at low cost. The simplified setup integrates existing hardware and software solutions with new component designs. We replaced expensive optomechanical and custom machined components with off-the-shelf and 3D-printed parts, and built the system around a low-cost camera that achieves 180 Hz imaging and an inexpensive tablet computer to present view-angle-corrected stimuli updated through a local network. We quantify the performance of the integrated system and characterize the visually guided behavior of flies in response to a range of visual stimuli. In this paper, we thoroughly document the improved system; the accompanying repository incorporates CAD files, parts lists, source code, and detailed instructions. We detail a complete ~$300 system, including a cold-anesthesia tethering stage, that is ideal for hands-on teaching laboratories. This represents a nearly 50-fold cost reduction as compared to a typical system used in research laboratories, yet is fully featured and yields excellent performance. We report the current state of this system, which started with a 1-day teaching lab for which we built seven parallel setups and continues toward a setup in our lab for larger-scale analysis of visual-motor behavior in flies. Because of the simplicity, compactness, and low cost of this system, we believe that high-performance measurements of tethered insect behavior should now be widely accessible and suitable for integration into many systems. This access enables broad opportunities for comparative work across labs, species, and behavioral paradigms.

}, issn = {1662-5153}, doi = {10.3389/fnbeh.2021.689573}, author = {Loesche, Frank and Reiser, Michael B} } @article {67303, title = {Information flow, cell types and stereotypy in a full olfactory connectome.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 May 25}, abstract = {

The connectome provides large scale connectivity and morphology information for the majority of the central brain of . Using this data set, we provide a complete description of the olfactory system, covering all first, second and lateral horn-associated third-order neurons. We develop a generally applicable strategy to extract information flow and layered organisation from connectome graphs, mapping olfactory input to descending interneurons. This identifies a range of motifs including highly lateralised circuits in the antennal lobe and patterns of convergence downstream of the mushroom body and lateral horn. Leveraging a second data set we provide a first quantitative assessment of inter- versus intra-individual stereotypy. Comparing neurons across two brains (three hemispheres) reveals striking similarity in neuronal morphology across brains. Connectivity correlates with morphology and neurons of the same morphological type show similar connection variability within the same brain as across two brains.

}, issn = {2050-084X}, doi = {10.7554/eLife.66018}, author = {Schlegel, Philipp and Bates, Alexander Shakeel and St{\"u}rner, Tomke and Jagannathan, Sridhar R and Drummond, Nikolas and Hsu, Joseph and Serratosa Capdevila, Laia and Javier, Alexandre and Marin, Elizabeth C and Barth-Maron, Asa and Tamimi, Imaan Fm and Li, Feng and Rubin, Gerald M and Plaza, Stephen M and Costa, Marta and Jefferis, Gregory Sxe} } @article {67656, title = {Intercellular Arc Signaling Regulates Vasodilation.}, journal = {Journal of Neuroscience}, year = {2021}, month = {2021 Jul 29}, abstract = {

Injury responses require communication between different cell types in the skin. Sensory neurons contribute to inflammation and can secrete signaling molecules that affect non-neuronal cells. Despite the pervasive role of translational regulation in nociception, the contribution of activity-dependent protein synthesis to inflammation is not well understood. To address this problem, we examined the landscape of nascent translation in murine dorsal root ganglion (DRG) neurons treated with inflammatory mediators using ribosome profiling. We identified the activity-dependent gene, Arc, as a target of translation and Inflammatory cues promote local translation of Arc in the skin. Arc-deficient male mice display exaggerated paw temperatures and vasodilation in response to an inflammatory challenge. Since Arc has recently been shown to be released from neurons in extracellular vesicles (EVs), we hypothesized that intercellular Arc signaling regulates the inflammatory response in skin. We found that the excessive thermal responses and vasodilation observed in Arc defective mice are rescued by injection of Arc-containing EVs into the skin. Our findings suggest that activity-dependent production of Arc in afferent fibers regulates neurogenic inflammation potentially through intercellular signaling.Nociceptors play prominent roles in pain and inflammation. We examined rapid changes in the landscape of nascent translation in cultured dorsal root ganglia (DRGs) treated with a combination of inflammatory mediators using ribosome profiling. We identified several hundred transcripts subject to rapid preferential translation. Among them is the immediate early gene (IEG) Arc. We provide evidence that Arc is translated in afferent fibers in the skin. Arc-deficient mice display several signs of exaggerated inflammation which is normalized on injection of Arc containing extracellular vesicles (EVs). Our work suggests that noxious cues can trigger Arc production by nociceptors which in turn constrains neurogenic inflammation in the skin.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0440-21.2021}, author = {de la Pe{\~n}a, June Bryan and Barragan-Iglesias, Paulino and Lou, Tzu-Fang and Kunder, Nikesh and Loerch, Sarah and Shukla, Tarjani and Basavarajappa, Lokesh and Song, Jane and James, Dominique N and Megat, Salim and Moy, Jamie K and Wanghzou, Andi and Ray, Pradipta R and Hoyt, Kenneth and Steward, Oswald and Price, Theodore J and Shepherd, Jason and Campbell, Zachary T} } @article {66025, title = {Internal state configures olfactory behavior and early sensory processing in larvae.}, journal = {Science Advances}, volume = {7}, year = {2021}, month = {2021 Jan 01}, abstract = {

Animals exhibit different behavioral responses to the same sensory cue depending on their internal state at a given moment. How and where in the brain are sensory inputs combined with state information to select an appropriate behavior? Here, we investigate how food deprivation affects olfactory behavior in larvae. We find that certain odors repel well-fed animals but attract food-deprived animals and that feeding state flexibly alters neural processing in the first olfactory center, the antennal lobe. Hunger differentially modulates two output pathways required for opposing behavioral responses. Upon food deprivation, attraction-mediating uniglomerular projection neurons show elevated odor-evoked activity, whereas an aversion-mediating multiglomerular projection neuron receives odor-evoked inhibition. The switch between these two pathways is regulated by the lone serotonergic neuron in the antennal lobe, CSD. Our findings demonstrate how flexible behaviors can arise from state-dependent circuit dynamics in an early sensory processing center.

}, issn = {2375-2548}, doi = {10.1126/sciadv.abd6900}, author = {Vogt, Katrin and Zimmerman, David M and Schlichting, Matthias and Hernandez-Nunez, Luis and Qin, Shanshan and Malacon, Karen and Rosbash, Michael and Pehlevan, Cengiz and Cardona, Albert and Samuel, Aravinthan D T} } @article {67210, title = {Intracellular mRNA transport and localized translation.}, journal = {Nature Reviews Molecular Cell Biology}, volume = {22}, year = {2021}, month = {2021 Jul 1}, pages = {483-504}, abstract = {

Fine-tuning cellular physiology in response to intracellular and environmental cues requires precise temporal and spatial control of gene expression. High-resolution imaging technologies to detect mRNAs and their translation state have revealed that all living organisms localize mRNAs in subcellular compartments and create translation hotspots, enabling cells to tune gene expression locally. Therefore, mRNA localization is a conserved and integral part of gene expression regulation from prokaryotic to eukaryotic cells. In this Review, we discuss the mechanisms of mRNA transport and local mRNA translation across the kingdoms of life and at organellar, subcellular and multicellular resolution. We also discuss the properties of messenger ribonucleoprotein and higher order RNA granules and how they may influence mRNA transport and local protein synthesis. Finally, we summarize the technological developments that allow us to study mRNA localization and local translation through the simultaneous detection of mRNAs and proteins in single cells, mRNA and nascent protein single-molecule imaging, and bulk RNA and protein detection methods.

}, issn = {1471-0080}, doi = {10.1038/s41580-021-00356-8}, author = {Das, Sulagna and Vera, Maria and Gandin, Valentina and Singer, Robert H and Tutucci, Evelina} } @article {67672, title = {jumps with greater velocity and acceleration than previously reported.}, journal = {MicroPublication Biology}, volume = {2021}, year = {2021}, month = {2021 Aug 02}, abstract = {

Infective juveniles of the insect-parastic nematode canjump greater than 6 times their height, a striking evolved novelty in some species of this genus. Using high-speed videography, we observed the kinematics of spontaneousjumping behavior. Our analysis places a lower bound on the velocity and acceleration of these worms.

}, issn = {2578-9430}, doi = {10.17912/micropub.biology.000435}, author = {Dillman, Adler R and Korff, Wyatt and Dickinson, Michael H and Sternberg, Paul W} } @article {68476, title = {Label-free imaging of fibroblast membrane interfaces and protein signatures with vibrational infrared photothermal and phase signals.}, journal = {Biomed Opt Express}, volume = {12}, year = {2021}, month = {12/2020}, pages = {303-319}, abstract = {

Label-free vibrational imaging of biological samples has attracted significant interest due to its integration of structural and chemical information. Vibrational infrared photothermal amplitude and phase signal (VIPPS) imaging provide label-free chemical identification by targeting the characteristic resonances of biological compounds that are present in the mid-infrared fingerprint region (3 {\textmu}m - 12 {\textmu}m). High contrast imaging of subcellular features and chemical identification of protein secondary structures in unlabeled and labeled fibroblast cells embedded in a collagen-rich extracellular matrix is demonstrated by combining contrast from absorption signatures (amplitude signals) with sensitive detection of different heat properties (lock-in phase signals). We present that the detectability of nano-sized cell membranes is enhanced to well below the optical diffraction limit since the membranes are found to act as thermal barriers. VIPPS offers a novel combination of chemical imaging and thermal diffusion characterization that paves the way towards label-free imaging of cell models and tissues as well as the study of intracellular heat dynamics.

}, issn = {2156-7085}, doi = {10.1364/BOE.411888}, author = {Samolis, Panagis D and Langley, Daniel and O{\textquoteright}Reilly, Breanna M and Oo, Zay and Hilzenrat, Geva and Erramilli, Shyamsunder and Sgro, Allyson E and McArthur, Sally and Sander, Michelle Y} } @article {66021, title = {The level of oncogenic Ras determines the malignant transformation of Lkb1 mutant tissue in vivo.}, journal = {Communications Biology}, volume = {4}, year = {2021}, month = {2021 Jan 29}, pages = {142}, abstract = {

The genetic and metabolic heterogeneity of RAS-driven cancers has confounded therapeutic strategies in the clinic. To address this, rapid and genetically tractable animal models are needed that recapitulate the heterogeneity of RAS-driven cancers in vivo. Here, we generate a Drosophila melanogaster model of Ras/Lkb1 mutant carcinoma. We show that low-level expression of oncogenic Ras (Ras) promotes the survival of Lkb1 mutant tissue, but results in autonomous cell cycle arrest and non-autonomous overgrowth of wild-type tissue. In contrast, high-level expression of oncogenic Ras (Ras) transforms Lkb1 mutant tissue resulting in lethal malignant tumors. Using simultaneous multiview light-sheet microcopy, we have characterized invasion phenotypes of Ras/Lkb1 tumors in living larvae. Our molecular analysis reveals sustained activation of the AMPK pathway in malignant Ras/Lkb1 tumors, and demonstrate the genetic and pharmacologic dependence of these tumors on CaMK-activated Ampk. We further show that LKB1 mutant human lung adenocarcinoma patients with high levels of oncogenic KRAS exhibit worse overall survival and increased AMPK activation. Our results suggest that high levels of oncogenic KRAS is a driving event in the malignant transformation of LKB1 mutant tissue, and uncovers a vulnerability that may be used to target this aggressive genetic subset of RAS-driven tumors.

}, issn = {2399-3642}, doi = {10.1038/s42003-021-01663-8}, author = {Rackley, Briana and Seong, Chang-Soo and Kiely, Evan and Parker, Rebecca E and Rupji, Manali and Dwivedi, Bhakti and Heddleston, John M and Giang, William and Anthony, Neil and Chew, Teng-Leong and Gilbert-Ross, Melissa} } @article {67792, title = {Light sheet fluorescence microscopy.}, journal = {Nature Reviews Methods Primers}, volume = {1}, year = {2021}, month = {2021 Nov 03}, abstract = {

Light sheet fluorescence microscopy (LSFM) uses a thin sheet of light to excite only fluorophores within the focal volume. Light sheet microscopes (LSMs) have a true optical sectioning capability and, hence, provide axial resolution, restrict photobleaching and phototoxicity to a fraction of the sample and use cameras to record tens to thousands of images per second. LSMs are used for in-depth analyses of large, optically cleared samples and long-term three-dimensional (3D) observations of live biological specimens at high spatio-temporal resolution. The independently operated illumination and detection trains and the canonical implementations, selective/single plane illumination microscope (SPIM) and digital scanned laser microscope (DSLM), are the basis for many LSM designs. In this Primer, we discuss various applications of LSFM for imaging multicellular specimens, developing vertebrate and invertebrate embryos, brain and heart function, 3D cell culture models, single cells, tissue sections, plants, organismic interaction and entire cleared brains. Further, we describe the combination of LSFM with other imaging approaches to allow for super-resolution or increased penetration depth and the use of sophisticated spatio-temporal manipulations to allow for observations along multiple directions. Finally, we anticipate developments of the field in the near future.

}, doi = {10.1038/s43586-021-00069-4}, url = {https://www.nature.com/articles/s43586-021-00069-4}, author = {Stelzer, Ernst H. K. and Strobl, Frederic and Chang, Bo-Jui and Preusser, Friedrich and Preibisch, Stephan and McDole, Katie and Fiolka, Reto} } @article {67339, title = {Lipid droplets in the nervous system.}, journal = {Journal of Cell Biology}, volume = {220}, year = {2021}, month = {2021 Jul 05}, abstract = {

Lipid droplets are dynamic intracellular lipid storage organelles that respond to the physiological state of cells. In addition to controlling cell metabolism, they play a protective role for many cellular stressors, including oxidative stress. Despite prior descriptions of lipid droplets appearing in the brain as early as a century ago, only recently has the role of lipid droplets in cells found in the brain begun to be understood. Lipid droplet functions have now been described for cells of the nervous system in the context of development, aging, and an increasing number of neuropathologies. Here, we review the basic mechanisms of lipid droplet formation, turnover, and function and discuss how these mechanisms enable lipid droplets to function in different cell types of the nervous system under healthy and pathological conditions.

}, issn = {1540-8140}, doi = {10.1083/jcb.202102136}, author = {Ralhan, Isha and Chang, Chi-Lun and Lippincott-Schwartz, Jennifer and Ioannou, Maria S} } @article {67309, title = {Live and Let Dye.}, journal = {Biochemistry}, year = {2021}, month = {2021 Jun 07}, abstract = {

The measurement of ion concentrations and fluxes inside living cells is key to understanding cellular physiology. Fluorescent indicators that can infiltrate and provide intel on the cellular environment are critical tools for biological research. Developing these molecular informants began with the seminal work of Racker and colleagues ( (1979) 18, 2210), who demonstrated the passive loading of fluorescein in living cells to measure changes in intracellular pH. This work continues, employing a mix of old and new tradecraft to create innovative agents for monitoring ions inside living systems.

}, issn = {1520-4995}, doi = {10.1021/acs.biochem.1c00299}, author = {Lavis, Luke D} } @article {67228, title = {Local Shape Descriptors for Neuron Segmentation}, journal = {bioRxiv}, year = {2021}, month = {2021/01}, abstract = {

We present a simple, yet effective, auxiliary learning task for the problem of neuron segmentation in electron microscopy volumes. The auxiliary task consists of the prediction of Local Shape Descriptors (LSDs), which we combine with conventional voxel-wise direct neighbor affinities for neuron boundary detection. The shape descriptors are designed to capture local statistics about the neuron to be segmented, such as diameter, elongation, and direction. On a large study comparing several existing methods across various specimen, imaging techniques, and resolutions, we find that auxiliary learning of LSDs consistently increases segmentation accuracy of affinity-based methods over a range of metrics. Furthermore, the addition of LSDs promotes affinitybased segmentation methods to be on par with the current state of the art for neuron segmentation (Flood-Filling Networks, FFN), while being two orders of magnitudes more efficient{\textemdash}a critical requirement for the processing of future petabyte-sized datasets. Implementations of the new auxiliary learning task, network architectures, training, prediction, and evaluation code, as well as the datasets used in this study are publicly available as a benchmark for future method contributions.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2021.01.18.427039}, url = {https://www.biorxiv.org/content/early/2021/01/18/2021.01.18.427039}, author = {Sheridan, Arlo and Nguyen, Tri and Deb, Diptodip and Lee, Wei-Chung Allen and Saalfeld, Stephan and Turaga, Srini and Manor, Uri and Funke, Jan} } @article {67313, title = {Locating Macromolecular Assemblies in Cells by 2D Template Matching with TEM.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Jun 11}, abstract = {

For a more complete understanding of molecular mechanisms, it is important to study macromolecules and their assemblies in the broader context of the cell. This context can be visualized at nanometer resolution in three dimensions (3D) using electron cryo-tomography, which requires tilt series to be recorded and computationally aligned, currently limiting throughput. Additionally, the high-resolution signal preserved in the raw tomograms is currently limited by a number of technical difficulties, leading to an increased false-positive detection rate when using 3D template matching to find molecular complexes in tomograms. We have recently described a 2D template matching approach that addresses these issues by including high-resolution signal preserved in single-tilt images. A current limitation of this approach is the high computational cost that limits throughput. We describe here a GPU-accelerated implementation of 2D template matching in the image processing software TEM that allows for easy scaling and improves the accessibility of this approach. We apply 2D template matching to identify ribosomes in images of frozen-hydrated cells with high precision and sensitivity, demonstrating that this is a versatile tool for visual proteomics and structure determination. We benchmark the results with 3D template matching of tomograms acquired on identical sample locations and identify strengths and weaknesses of both techniques, which offer complementary information about target localization and identity.

}, issn = {2050-084X}, doi = {10.7554/eLife.68946}, author = {Lucas, Bronwyn A and Himes, Benjamin A and Xue, Liang and Grant, Tim and Mahamid, Julia and Grigorieff, Nikolaus} } @article {67738, title = {The LRRK2 G2019S mutation alters astrocyte-to-neuron communication via extracellular vesicles and induces neuron atrophy in a human iPSC-derived model of Parkinson{\textquoteright}s disease}, journal = {eLife}, year = {2021}, month = {2021 Sep 30}, abstract = {

Astrocytes are essential cells of the central nervous system, characterized by dynamic relationships with neurons that range from functional metabolic interactions and regulation of neuronal firing activities, to the release of neurotrophic and neuroprotective factors. In Parkinson{\textquoteright}s disease (PD), dopaminergic neurons are progressively lost during the course of the disease, but the effects of PD on astrocytes and astrocyte-to-neuron communication remains largely unknown. This study focuses on the effects of the PD-related mutation LRRK2 G2019S in astrocytes generated from patient-derived induced pluripotent stem cells. We report the alteration of extracellular vesicle (EV) biogenesis in astrocytes, and we identify the abnormal accumulation of key PD-related proteins within multi vesicular bodies (MVBs). We found that dopaminergic neurons internalize astrocyte-secreted EVs and that LRRK2 G2019S EVs are abnormally enriched in neurites and fail to provide full neurotrophic support to dopaminergic neurons. Thus, dysfunctional astrocyte-to-neuron communication via altered EV biological properties may participate in the progression of PD.

}, doi = {https://doi.org/10.7554/eLife.73062}, author = {Aurelie de Rus Jacquet and Jenna L. Tancredi and Andrew L. Lemire and Michael C. DeSantis and Wei-Ping Li and Erin K. O{\textquoteright}Shea} } @article {67271, title = {Lupus susceptibility region containing CDKN1B rs34330 mechanistically influences expression and function of multiple target genes, also linked to proliferation and apoptosis.}, journal = {Arthritis Rheumatology}, volume = {73}, year = {2021}, month = {2021 Dec 01}, pages = {2303-13}, abstract = {

OBJECTIVE: A recent genome-wide association study (GWAS) reported a significant genetic association between rs34330 of cyclin-dependent kinase inhibitor 1B (CDKN1B) and risk of systemic lupus erythematosus (SLE) in Han Chinese. This study aims to validate the reported association and elucidate the biochemical mechanisms underlying the variant{\textquoteright}s effect.

METHODS: We performed allelic association with SLE followed by meta-analysis across 11 independent cohorts (n=28,872). We applied in silico bioinformatics and experimental validation in SLE-relevant cell lines to determine the functional consequences of rs34330.

RESULTS: We replicated genetic association between SLE and rs34330 (P =5.29x10 , OR (95\% CI)=0.84 (0.81-0.87)). Follow-up bioinformatics and eQTL analysis suggest that rs34330 is located in active chromatin and potentially regulates several target genes. Using luciferase and ChIP-qPCR, we demonstrated substantial allele-specific promoter and enhancer activity, and allele-specific binding of three histone marks (H3K27ac, H3K4me3, H3K4me1), RNA pol II, CTCF, and a critical immune transcription factor (IRF-1). Chromosome conformation capture (3C) detected long-range chromatin interactions between rs34330 and the promoters of neighboring genes APOLD1 and DDX47, and effects on CDKN1B and the other target genes were directly validated by CRISPR-based genome editing. Finally, CRISPR-dCas9-based epigenetic activation/silencing confirmed these results. Gene-edited cell lines also showed higher levels of proliferation and apoptosis.

CONCLUSION: Collectively, these findings suggest a mechanism whereby the rs34330 risk allele (C) influences the presence of histone marks, RNA pol II, and the IRF-1 transcription factor to regulate expression of several target genes linked to proliferation and apoptosis, which potentially underlie the association of rs34330 with SLE.

}, issn = {2326-5205}, doi = {10.1002/art.41799}, author = {Singh, Bhupinder and Maiti, Guru P and Zhou, Xujie and Fazel-Najafabadi, Mehdi and Bae, Sang-Cheol and Sun, Celi and Terao, Chikashi and Okada, Yukinori and Chua, Kek Heng and Kochi, Yuta and Guthridge, Joel M and Zhang, Hong and Weirauch, Matthew and James, Judith A and Harley, John B and Varshney, Gaurav K and Looger, Loren L and Nath, Swapan K} } @article {66023, title = {Mapping Low-Dimensional Dynamics to High-Dimensional Neural Activity: A Derivation of the Ring Model from the Neural Engineering Framework.}, journal = {Neural Computation}, volume = {33}, year = {2021}, month = {2021 Mar 01}, pages = {827-52}, abstract = {

Empirical estimates of the dimensionality of neural population activity are often much lower than the population size. Similar phenomena are also observed in trained and designed neural network models. These experimental and computational results suggest that mapping low-dimensional dynamics to high-dimensional neural space is a common feature of cortical computation. Despite the ubiquity of this observation, the constraints arising from such mapping are poorly understood. Here we consider a specific example of mapping low-dimensional dynamics to high-dimensional neural activity-the neural engineering framework. We analytically solve the framework for the classic ring model-a neural network encoding a static or dynamic angular variable. Our results provide a complete characterization of the success and failure modes for this model. Based on similarities between this and other frameworks, we speculate that these results could apply to more general scenarios.

}, issn = {1530-888X}, doi = {10.1162/neco_a_01361}, author = {Barak, Omri and Romani, Sandro} } @article {67695, title = {Method for Rapid Enzymatic Cleaning for Reuse of Patch Clamp Pipettes: Increasing Throughput by Eliminating Manual Pipette Replacement between Patch Clamp Attempts.}, journal = {Bio Protocol}, volume = {11}, year = {2021}, month = {2021 Jul 20}, pages = {e4085}, abstract = {

The whole-cell patch-clamp method is a gold standard for single-cell analysis of electrical activity, cellular morphology, and gene expression. Prior to our discovery that patch-clamp pipettes could be cleaned and reused, experimental throughput and automation were limited by the need to replace pipettes manually after each experiment. This article presents an optimized protocol for pipette cleaning, which enables it to be performed quickly (\< 30 s), resulting in a high yield of whole-cell recording success rate (\> 90\%) for over 100 reuses of a single pipette. For most patch-clamp experiments (\< 30 whole-cell recordings per day), this method enables a single pipette to be used for an entire day of experiments. In addition, we describe easily implementable hardware and software as well as troubleshooting tips to help other labs implement this method in their own experiments. Pipette cleaning enables patch-clamp experiments to be performed with higher throughput, whether manually or in an automated fashion, by eliminating the tedious and skillful task of replacing pipettes. From our experience with numerous electrophysiology laboratories, pipette cleaning can be integrated into existing patch-clamp setups in approximately one day using the hardware and software described in this article. Graphic abstract: Rapid enzymatic cleaning for reuse of patch-clamp pipettes.

}, issn = {2331-8325}, doi = {10.21769/BioProtoc.4085}, author = {Landry, Corey R and Yip, Mighten C and Kolb, Ilya and Stoy, William A and Gonzalez, Mercedes M and Forest, Craig R} } @article {67305, title = {Micro-Meta App: an interactive software tool to facilitate the collection of microscopy metadata based on community-driven specifications}, journal = {bioRxiv}, year = {2021}, month = {2021 May 31}, abstract = {

For the information content of microscopy images to be appropriately interpreted, reproduced, and meet FAIR (Findable Accessible Interoperable and Reusable) principles, they should be accompanied by detailed descriptions of microscope hardware, image acquisition settings, image pixel and dimensional structure, and instrument performance. Nonetheless, the thorough documentation of imaging experiments is significantly impaired by the lack of community-sanctioned easy-to-use software tools to facilitate the extraction and collection of relevant microscopy metadata. Here we present\ Micro-Meta App, an intuitive open-source software designed to tackle these issues that was developed in the context of nascent global bioimaging community organizations, including\ BioImaging\ North\ America (BINA) and\ QUAlity Assessment and\ REProducibility in\ Light\ Microscopy (QUAREP-LiMi), whose goal is to improve reproducibility, data quality and sharing value for imaging experiments. The App provides a user-friendly interface for building comprehensive descriptions of the conditions utilized to produce individual microscopy datasets as specified by the recently proposed 4DN-BINA-OME tiered-system of Microscopy Metadata model. To achieve this goal the App provides a visual guide for a microscope-user to: 1) interactively build diagrammatic representations of hardware configurations of given microscopes that can be easily reused and shared with colleagues needing to document similar instruments. 2) Automatically extracts relevant metadata from image files and facilitates the collection of missing image acquisition settings and calibration metrics associated with a given experiment. 3) Output all collected Microscopy Metadata to interoperable files that can be used for documenting imaging experiments and shared with the community. In addition to significantly lowering the burden of quality assurance, the visual nature of Micro-Meta App makes it particularly suited for training users that have limited knowledge of the intricacies of light microscopy experiments. To ensure wide-adoption by microscope-users with different needs Micro-Meta App closely interoperates with\ MethodsJ2\ and\ OMERO.mde, two complementary tools described in parallel manuscripts.

}, author = {Alex Rigano and Shannon Ehmsen and Serkan Utku Ozturk and Joel Ryan and Alexander Balashov and Mathias Hammer and Koray Kirli and Karl Bellve and Ulrike Boehm and Claire M. Brown and James J. Chambers and Robert A. Coleman and Andrea Cosolo and Orestis Faklaris and Kevin Fogarty and Thomas Guilbert and Anna B. Hamacher and Michelle S. Itano and Daniel P. Keeley and Susanne Kunis and Judith Lacoste and Alex Laude and Willa Ma and Marco Marcello and Paula Montero-Llopis and Glyn Nelson and Roland Nitschke and Jaime A. Pimentel and Stefanie Weidtkamp-Peters and Peter J. Park and Burak Alver and David Grunwald and Caterina Strambio-De-Castillia} } @article {67811, title = {Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications.}, journal = {Nature Methods}, volume = {18}, year = {2021}, month = {2021 Dec 03}, pages = {1489-1495}, abstract = {

For quality, interpretation, reproducibility and sharing value, microscopy images should be accompanied by detailed descriptions of the conditions that were used to produce them. Micro-Meta App is an intuitive, highly interoperable, open-source software tool that was developed in the context of the 4D Nucleome (4DN) consortium and is designed to facilitate the extraction and collection of relevant microscopy metadata as specified by the recent 4DN-BINA-OME tiered-system of Microscopy Metadata specifications. In addition to substantially lowering the burden of quality assurance, the visual nature of Micro-Meta App makes it particularly suited for training purposes.

}, issn = {1548-7105}, doi = {10.1038/s41592-021-01315-z}, author = {Rigano, Alessandro and Ehmsen, Shannon and {\"O}zt{\"u}rk, Serkan Utku and Ryan, Joel and Balashov, Alexander and Hammer, Mathias and Kirli, Koray and Boehm, Ulrike and Brown, Claire M and Bellve, Karl and Chambers, James J and Cosolo, Andrea and Coleman, Robert A and Faklaris, Orestis and Fogarty, Kevin E and Guilbert, Thomas and Hamacher, Anna B and Itano, Michelle S and Keeley, Daniel P and Kunis, Susanne and Lacoste, Judith and Laude, Alex and Ma, Willa Y and Marcello, Marco and Montero-Llopis, Paula and Nelson, Glyn and Nitschke, Roland and Pimentel, Jaime A and Weidtkamp-Peters, Stefanie and Park, Peter J and Alver, Burak H and Grunwald, David and Strambio-De-Castillia, Caterina} } @article {68358, title = {Molecular, anatomical, and functional organization of lung interoceptors}, journal = {bioRxiv}, year = {2021}, month = {11/2021}, abstract = {

Interoceptors, sensory neurons that monitor internal organs and states, are essential for physiological homeostasis and generating internal perceptions. Here we describe a comprehensive transcriptomic atlas of interoceptors of the mouse lung, defining 10 molecular subtypes that differ in developmental origin, myelination, receptive fields, terminal morphologies, and cell contacts. Each subtype expresses a unique but overlapping combination of sensory receptors that detect diverse physiological and pathological stimuli, and each can signal to distinct sets of lung cells including immune cells, forming a local neuroimmune interaction network. Functional interrogation of two mechanosensory subtypes reveals exquisitely-specific homeostatic roles in breathing, one regulating inspiratory time and the other inspiratory flow. The results suggest that lung interoceptors encode diverse and dynamic sensory information rivaling that of canonical exteroceptors, and this information is used to drive myriad local cellular interactions and enable precision control of breathing, while providing only vague perceptions of organ states.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2021.11.10.468116}, url = {https://www.biorxiv.org/content/early/2021/11/13/2021.11.10.468116}, author = {Liu, Yin and Diaz de Arce, Alex J. and Krasnow, Mark A.} } @article {67648, title = {Molecular characterization of projection neuron subtypes in the mouse olfactory bulb.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Jul 22}, abstract = {

Projection neurons (PNs) in the mammalian olfactory bulb (OB) receive input from the nose and project to diverse cortical and subcortical areas. Morphological and physiological studies have highlighted functional heterogeneity, yet no molecular markers have been described that delineate PN subtypes. Here, we used viral injections into olfactory cortex and fluorescent nucleus sorting to enrich PNs for high-throughput single nucleus and bulk RNA deep sequencing. Transcriptome analysis and RNA hybridization identified distinct mitral and tufted cell populations with characteristic transcription factor network topology, cell adhesion and excitability-related gene expression. Finally, we describe a new computational approach for integrating bulk and snRNA-seq data, and provide evidence that different mitral cell populations preferentially project to different target regions. Together, we have identified potential molecular and gene regulatory mechanisms underlying PN diversity and provide new molecular entry points into studying the diverse functional roles of mitral and tufted cell subtypes.

}, issn = {2050-084X}, doi = {10.7554/eLife.65445}, author = {Zeppilli, Sara and Ackels, Tobias and Attey, Robin and Klimpert, Nell and Kimberly Ritola, Dr and Boeing, Stefan and Crombach, Anton and Schaefer, Andreas T and Fleischmann, Alexander} } @article {69336, title = {Molecular profiling of single neurons of known identity in two ganglia from the crab Cancer borealis}, journal = {Proceedings of the National Academy of Sciences}, volume = {116}, year = {2021}, month = {2021 Feb 12}, pages = {26980 - 26990}, abstract = {

Understanding circuit organization depends on identification of cell types. Recent advances in transcriptional profiling methods have enabled classification of cell types by their gene expression. While exceptionally powerful and high throughput, the ground-truth validation of these methods is difficult: If cell type is unknown, how does one assess whether a given analysis accurately captures neuronal identity? To shed light on the capabilities and limitations of solely using transcriptional profiling for cell-type classification, we performed 2 forms of transcriptional profiling{\textemdash}RNA-seq and quantitative RT-PCR, in single, unambiguously identified neurons from 2 small crustacean neuronal networks: The stomatogastric and cardiac ganglia. We then combined our knowledge of cell type with unbiased clustering analyses and supervised machine learning to determine how accurately functionally defined neuron types can be classified by expression profile alone. The results demonstrate that expression profile is able to capture neuronal identity most accurately when combined with multimodal information that allows for post hoc grouping, so analysis can proceed from a supervised perspective. Solely unsupervised clustering can lead to misidentification and an inability to distinguish between 2 or more cell types. Therefore, this study supports the general utility of cell identification by transcriptional profiling, but adds a caution: It is difficult or impossible to know under what conditions transcriptional profiling alone is capable of assigning cell identity. Only by combining multiple modalities of information such as physiology, morphology, or innervation target can neuronal identity be unambiguously determined.

}, issn = {0027-8424}, doi = {10.1073/pnas.1911413116}, url = {https://pnas.org/doi/full/10.1073/pnas.1911413116https://pnas.org/doi/pdf/10.1073/pnas.1911413116http://www.pnas.org/syndication/doi/10.1073/pnas.1911413116}, author = {Northcutt, Adam J. and Kick, Daniel R. and Otopalik, Adriane G. and Goetz, Benjamin M. and Harris, Rayna M. and Santin, Joseph M. and Hofmann, Hans A. and Marder, Eve and Schulz, David J.} } @article {68817, title = {Multimodal patterns of inhibitory activity in cerebellar cortex}, journal = {Neuron}, volume = {109}, year = {2021}, month = {05/2021}, pages = {1590-1592}, abstract = {

In this issue of Neuron, Gurnani and Silver (2021) report that activity across Golgi cells, a major type of inhibitory interneuron in the cerebellar cortex, is multidimensional and modulated by behavior. These results suggest multiple functions for inhibition in cerebellar computations.

}, issn = {0896-6273}, doi = {https://doi.org/10.1016/j.neuron.2021.04.029}, url = {https://www.sciencedirect.com/science/article/pii/S0896627321003251}, author = {Chie Satou and Rainer W. Friedrich} } @article {67813, title = {Multiplex Gene Tagging with CRISPR-Cas9 for Live-Cell Microscopy and Application to Study the Role of SARS-CoV-2 Proteins in Autophagy, Mitochondrial Dynamics, and Cell Growth.}, journal = {The CRISPR Journal}, year = {2021}, month = {2021 Nov 30}, abstract = {

The lack of efficient tools to label multiple endogenous targets in cell lines without staining or fixation has limited our ability to track physiological and pathological changes in cells over time via live-cell studies. Here, we outline the FAST-HDR vector system to be used in combination with CRISPR-Cas9 to allow visual live-cell studies of up to three endogenous proteins within the same cell line. Our approach utilizes a novel set of advanced donor plasmids for homology-directed repair and a streamlined workflow optimized for microscopy-based cell screening to create genetically modified cell lines that do not require staining or fixation to accommodate microscopy-based studies. We validated this new methodology by developing two advanced cell lines with three fluorescent-labeled endogenous proteins that support high-content imaging without using antibodies or exogenous staining. We applied this technology to study seven severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2/COVID-19) viral proteins to understand better their effects on autophagy, mitochondrial dynamics, and cell growth. Using these two cell lines, we were able to identify the protein ORF3a successfully as a potent inhibitor of autophagy, inducer of mitochondrial relocalization, and a growth inhibitor, which highlights the effectiveness of live-cell studies using this technology.

}, issn = {2573-1602}, doi = {10.1089/crispr.2021.0041}, author = {Perez-Leal, Oscar and Nixon-Abell, Jonathon and Barrero, Carlos A and Gordon, John C and Oesterling, James and Rico, Mario C} } @article {67297, title = {Near-infrared catecholamine nanosensors for high spatiotemporal dopamine imaging.}, journal = {Nature Protocols}, volume = {16}, year = {2021}, month = {2021 May 21}, pages = {3026-3048}, abstract = {

Dopamine neuromodulation of neural synapses is a process implicated in a number of critical brain functions and diseases. Development of protocols to visualize this dynamic neurochemical process is essential to understanding how dopamine modulates brain function. We have developed a non-genetically encoded, near-IR (nIR) catecholamine nanosensor (nIRCat) capable of identifying ~2-{\textmu}m dopamine release hotspots in dorsal striatal brain slices. nIRCat is readily synthesized through sonication of single walled carbon nanotubes with DNA oligos, can be readily introduced into both genetically tractable and intractable organisms and is compatible with a number of dopamine receptor agonists and antagonists. Here we describe the synthesis, characterization and implementation of nIRCat in acute mouse brain slices. We demonstrate how nIRCat can be used to image electrically or optogenetically stimulated dopamine release, and how these procedures can be leveraged to study the effects of dopamine receptor pharmacology. In addition, we provide suggestions for building or adapting wide-field microscopy to be compatible with nIRCat nIR fluorescence imaging. We discuss strategies for analyzing nIR video data to identify dopamine release hotspots and quantify their kinetics. This protocol can be adapted and implemented for imaging other neuromodulators by using probes of this class and can be used in a broad range of species without genetic manipulation. The synthesis and characterization protocols for nIRCat take ~5 h, and the preparation and fluorescence imaging of live brain slices by using nIRCats require ~6 h.

}, issn = {1750-2799}, doi = {10.1038/s41596-021-00530-4}, author = {Yang, Sarah J and Del Bonis-O{\textquoteright}Donnell, Jackson Travis and Beyene, Abraham G and Landry, Markita P} } @article {65859, title = {Neural circuit mechanisms of sexual receptivity in Drosophila females.}, journal = {Nature}, volume = {589}, year = {2021}, month = {2021 Jan 01}, pages = {577-81}, abstract = {

Choosing a mate is one of the most consequential decisions a female will make during her lifetime. A female fly signals her willingness to mate by opening her vaginal plates, allowing a courting male to copulate. Vaginal plate opening (VPO) occurs in response to the male courtship song and is dependent on the mating status\ of the female. How these exteroceptive (song) and interoceptive (mating status) inputs are integrated to regulate VPO remains unknown. Here we characterize the neural circuitry that implements mating decisions in the brain of female Drosophila melanogaster. We show that VPO is controlled by a pair of female-specific descending neurons (vpoDNs). The vpoDNs receive excitatory input from auditory neurons (vpoENs), which are tuned to specific features of the D. melanogaster song, and from pC1 neurons, which encode the mating status\ of the female. The song responses of vpoDNs, but not vpoENs, are attenuated upon mating, accounting for the reduced receptivity of mated females. This modulation is mediated by pC1 neurons. The vpoDNs thus directly integrate the external and internal signals that control the mating decisions of Drosophila females.

}, issn = {1476-4687}, doi = {10.1038/s41586-020-2972-7}, author = {Wang, Kaiyu and Wang, Fei and Forknall, Nora and Yang, Tansy and Patrick, Christopher and Parekh, Ruchi and Dickson, Barry J} } @article {65969, title = {Neuromolecular and behavioral effects of ethanol deprivation in Drosophila}, journal = {bioRxiv}, year = {2021}, month = {2021 Jan 04}, abstract = {

Alcohol use disorder (AUD) is characterized by loss of control in limiting alcohol intake. This may involve intermittent periods of abstinence followed by alcohol seeking and, consequently, relapse. However, little is understood of the molecular mechanisms underlying the impact of alcohol deprivation on behavior. Using a new\ Drosophila melanogaster\ repeated intermittent alcohol exposure model, we sought to identify how ethanol deprivation alters spontaneous behavior, determine the associated neural structures, and reveal correlated changes in brain gene expression. We found that repeated intermittent ethanol-odor exposures followed by ethanol-deprivation dynamically induces behaviors associated with a negative affect state. Although behavioral states broadly mapped to many brain regions, persistent changes in social behaviors mapped to the mushroom body and surrounding neuropil. This occurred concurrently with changes in expression of genes associated with sensory responses, neural plasticity, and immunity. Like social behaviors, immune response genes were upregulated following three-day repeated intermittent ethanol-odor exposures and persisted with one or two days of ethanol-deprivation, suggesting an enduring change in molecular function. Our study provides a framework for identifying how ethanol deprivation alters behavior with correlated underlying circuit and molecular changes.

}, doi = {https://doi.org/10.1101/2021.01.02.425101}, author = {Natalie M. D{\textquoteright}Silva and Katie S. McCullar and Ashley M. Conard and Tyler Blackwater and Reza Azanchi and Ulrike Heberlein and Erica Larschan and Karla R. Kaun} } @article {67232, title = {Neuropixels 2.0: A miniaturized high-density probe for stable, long-term brain recordings.}, journal = {Science}, volume = {372}, year = {2021}, month = {2021 Apr 16}, abstract = {

Measuring the dynamics of neural processing across time scales requires following the spiking of thousands of individual neurons over milliseconds and months. To address this need, we introduce the Neuropixels 2.0 probe together with newly designed analysis algorithms. The probe has more than 5000 sites and is miniaturized to facilitate chronic implants in small mammals and recording during unrestrained behavior. High-quality recordings over long time scales were reliably obtained in mice and rats in six laboratories. Improved site density and arrangement combined with newly created data processing methods enable automatic post hoc correction for brain movements, allowing recording from the same neurons for more than 2 months. These probes and algorithms enable stable recordings from thousands of sites during free behavior, even in small animals such as mice.

}, issn = {1095-9203}, doi = {10.1126/science.abf4588}, author = {Steinmetz, Nicholas A and Ayd{\i}n, {\c C}a{\u g}atay and Lebedeva, Anna and Okun, Michael and Pachitariu, Marius and Bauza, Marius and Beau, Maxime and Bhagat, Jai and B{\"o}hm, Claudia and Broux, Martijn and Chen, Susu and Colonell, Jennifer and Gardner, Richard J and Karsh, Bill and Kloosterman, Fabian and Kostadinov, Dimitar and Mora-Lopez, Carolina and O{\textquoteright}Callaghan, John and Park, Junchol and Putzeys, Jan and Sauerbrei, Britton and van Daal, Rik J J and Vollan, Abraham Z and Wang, Shiwei and Welkenhuysen, Marleen and Ye, Zhiwen and Dudman, Joshua T and Dutta, Barundeb and Hantman, Adam W and Harris, Kenneth D and Lee, Albert K and Moser, Edvard I and O{\textquoteright}Keefe, John and Renart, Alfonso and Svoboda, Karel and H{\"a}usser, Michael and Haesler, Sebastian and Carandini, Matteo and Harris, Timothy D} } @article {67826, title = {Nitrite reductase activity within an antiparallel de novo scaffold.}, journal = {JBIC Journal of Biological Inorganic Chemistry}, volume = {26}, year = {2021}, month = {09/2021}, pages = {855 - 862}, abstract = {

Copper nitrite reductase (CuNiR) is a copper enzyme that converts nitrite to nitric oxide and is an important part of the global nitrogen cycle in bacteria. The relatively simple CuHis3\ binding site of the CuNiR active site has made it an enticing target for small molecule modeling and de novo protein design studies. We have previously reported symmetric CuNiR models within parallel three stranded coiled coil systems, with activities that span a range of three orders of magnitude. In this report, we investigate the same CuHis3\ binding site within an antiparallel three helical bundle scaffold, which allows the design of asymmetric constructs. We determine that a simple CuHis3\ binding site can be designed within this scaffold with enhanced activity relative to the comparable construct in parallel coiled coils. Incorporating more complex designs or repositioning this binding site can decrease this activity as much as 15 times. Comparing these constructs, we reaffirm a previous result in which a blue shift in the 1s to 4p transition energy determined by Cu(I) X-ray absorption spectroscopy is correlated with an enhanced activity within imidazole-based constructs. With this step and recent successful electron transfer site designs within this scaffold, we are one step closer to a fully functional de novo designed nitrite reductase.

}, issn = {0949-8257}, doi = {10.1007/s00775-021-01889-1}, url = {https://link.springer.com/10.1007/s00775-021-01889-1}, author = {Koebke, Karl J. and Tebo, Alison G. and Manickas, Elizabeth C. and Deb, Aniruddha and Penner-Hahn, James E. and Pecoraro, Vincent L.} } @article {67773, title = {Non-preferred contrast responses in the Drosophila motion pathways reveal a receptive field structure that explains a common visual illusion.}, journal = {Current Biology}, volume = {31}, year = {2021}, month = {2021 Dec 06}, pages = {5286}, abstract = {

Diverse sensory systems, from audition to thermosensation, feature a separation of inputs into ON (increments) and OFF (decrements) signals. In the Drosophila visual system, separate ON and OFF pathways compute the direction of motion, yet anatomical and functional studies have identified some crosstalk between these channels. We used this well-studied circuit to ask whether the motion computation depends on ON-OFF pathway crosstalk. Using whole-cell electrophysiology, we recorded visual responses of T4 (ON) and T5 (OFF) cells, mapped their composite ON-OFF receptive fields, and found that they share a similar spatiotemporal structure. We fit a biophysical model to these receptive fields that accurately predicts directionally selective T4 and T5 responses to both ON and OFF moving stimuli. This model also provides a detailed mechanistic explanation for the directional preference inversion in response to the prominent reverse-phi illusion. Finally, we used the steering responses of tethered flying flies to validate the model{\textquoteright}s predicted effects of varying stimulus parameters on the behavioral turning inversion.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2021.09.072}, author = {Gruntman, Eyal and Reimers, Pablo and Romani, Sandro and Reiser, Michael B} } @article {67181, title = {A novel family of secreted insect proteins linked to plant gall development.}, journal = {Current Biology}, volume = {31}, year = {2021}, month = {2021 May 10}, pages = {1836}, abstract = {

In an elaborate form of inter-species exploitation, many insects hijack plant development to induce novel plant organs called galls that provide the insect with a source of nutrition and a temporary home. Galls result from dramatic reprogramming of plant cell biology driven by insect molecules, but the roles of specific insect molecules in gall development have not yet been determined. Here, we study the aphid Hormaphis cornu, which makes distinctive "cone" galls on leaves of witch hazel Hamamelis virginiana. We found that derived genetic variants in the aphid gene determinant of gall color (dgc) are associated with strong downregulation of dgc transcription in aphid salivary glands, upregulation in galls of seven genes involved in anthocyanin synthesis, and deposition of two red anthocyanins in galls. We hypothesize that aphids inject DGC protein into galls and that this results in differential expression of a small number of plant genes. dgc is a member of a large, diverse family of novel predicted secreted proteins characterized by a pair of widely spaced cysteine-tyrosine-cysteine (CYC) residues, which we named BICYCLE proteins. bicycle genes are most strongly expressed in the salivary glands specifically of galling aphid generations, suggesting that they may regulate many aspects of gall development. bicycle genes have experienced unusually frequent diversifying selection, consistent with their potential role controlling gall development in a molecular arms race between aphids and their host plants.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2021.01.104}, author = {Korgaonkar, Aishwarya and Han, Clair and Lemire, Andrew L and Siwanowicz, Igor and Bennouna, Djawed and Kopec, Rachel E and Andolfatto, Peter and Shigenobu, Shuji and Stern, David L} } @article {67788, title = {Open Chemistry: What if we just give everything away?}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Nov 05}, abstract = {

A group leader decided that his lab would share the fluorescent dyes they create, for free and without authorship requirements. Nearly 12,000 aliquots later, he reveals what has happened since.

}, issn = {2050-084X}, doi = {10.7554/eLife.74981}, author = {Lavis, Luke D} } @article {67753, title = {An open-access volume electron microscopy atlas of whole cells and tissues.}, journal = {Nature}, volume = {599}, year = {2021}, month = {2021 Nov 1}, pages = {147-51}, abstract = {

Understanding cellular architecture is essential for understanding biology. Electron microscopy (EM) uniquely visualizes cellular structures with nanometre resolution. However, traditional methods, such as thin-section EM or EM tomography, have limitations in that they visualize only a single slice or a relatively small volume of the cell, respectively. Focused ion beam-scanning electron microscopy (FIB-SEM) has demonstrated the ability to image small volumes of cellular samples with 4-nm isotropic voxels. Owing to advances in the\ precision and stability of FIB milling, together with enhanced signal detection and faster SEM scanning, we have increased the volume that can be imaged with 4-nm\ voxels by two orders of magnitude. Here we present a volume EM atlas at such resolution comprising ten three-dimensional datasets for whole cells and tissues, including cancer cells, immune cells, mouse pancreatic islets and Drosophila neural tissues. These open access data (via OpenOrganelle) represent the foundation of a field of high-resolution whole-cell volume EM and subsequent analyses, and we invite researchers to explore this atlas and\ pose questions.

}, issn = {1476-4687}, doi = {10.1038/s41586-021-03992-4}, author = {Xu, C Shan and Pang, Song and Shtengel, Gleb and M{\"u}ller, Andreas and Ritter, Alex T and Hoffman, Huxley K and Takemura, Shin-ya and Lu, Zhiyuan and Pasolli, H Amalia and Iyer, Nirmala and Chung, Jeeyun and Bennett, Davis and Weigel, Aubrey V and Freeman, Melanie and Van Engelenburg, Schuyler B and Walther, Tobias C and Farese, Robert V and Lippincott-Schwartz, Jennifer and Mellman, Ira and Solimena, Michele and Hess, Harald F} } @article {67274, title = {An open-source semi-automated robotics pipeline for embryo immunohistochemistry.}, journal = {Scientific Reports}, volume = {11}, year = {2021}, month = {2021 May 13}, pages = {10314}, abstract = {

A significant challenge for developmental systems biology is balancing throughput with controlled conditions that minimize experimental artifacts. Large-scale developmental screens such as unbiased mutagenesis surveys have been limited in their applicability to embryonic systems, as the technologies for quantifying precise expression patterns in whole animals has not kept pace with other sequencing-based technologies. Here, we outline an open-source semi-automated pipeline to chemically fixate, stain, and 3D-image Drosophila embryos. Central to this pipeline is a liquid handling robot, Flyspresso, which automates the steps of classical embryo fixation and staining. We provide the schematics and an overview of the technology for an engineer or someone equivalently trained to reproduce and further improve upon Flyspresso, and highlight the Drosophila embryo fixation and colorimetric or antibody staining protocols. Additionally, we provide a detailed overview and stepwise protocol for our adaptive-feedback pipeline for automated embryo imaging on confocal microscopes. We demonstrate the efficiency of this pipeline compared to classical techniques, and how it can be repurposed or scaled to other protocols and biological systems. We hope our pipeline will serve as a platform for future research, allowing a broader community of users to build, execute, and share similar experiments.

}, issn = {2045-2322}, doi = {10.1038/s41598-021-89676-5}, author = {Fuqua, Timothy and Jordan, Jeff and Halavatyi, Aliaksandr and Tischer, Christian and Richter, Kerstin and Crocker, Justin} } @article {67178, title = {Optogenetic Tools for Manipulating Protein Subcellular Localization and Intracellular Signaling at Organelle Contact Sites}, journal = {Current Protocols}, volume = {1}, year = {2021}, month = {2021 Mar 03}, abstract = {

Intracellular signaling processes are frequently based on direct interactions between proteins and organelles. A fundamental strategy to elucidate the physiological significance of such interactions is to utilize optical dimerization tools. These tools are based on the use of small proteins or domains that interact with each other upon light illumination. Optical dimerizers are particularly suitable for reproducing and interrogating a given protein-protein interaction and for investigating a protein{\textquoteright}s intracellular role in a spatially and temporally precise manner. Described in this article are genetic engineering strategies for the generation of modular light-activatable protein dimerization units and instructions for the preparation of optogenetic applications in mammalian cells. Detailed protocols are provided for the use of light-tunable switches to regulate protein recruitment to intracellular compartments, induce intracellular organellar membrane tethering, and reconstitute protein function using enhanced Magnets (eMags), a recently engineered optical dimerization system. {\textcopyright} 2021 Wiley Periodicals LLC.

}, issn = {2691-1299}, doi = {https://doi.org/10.1002/cpz1.71}, url = {https://doi.org/10.1002/cpz1.71}, author = {Benedetti, Lorena} } @inbook {67667, title = {Optogenetics}, booktitle = {Molecular Imaging: Principles and Practice, 2nd Edition}, year = {2021}, publisher = {Academic Press}, organization = {Academic Press}, edition = {2}, chapter = {16}, abstract = {

To truly understand biological systems, one must possess the ability to selectively manipulate their parts and observe the outcome. (For purposes of this review, we refer mostly to targets of neuroscience; however, the principles covered here largely extend to myriad samples from microbes to plants to the intestine, etc.).

Drugs are the most commonly employed way of introducing such perturbations, but they act on endogenous proteins that frequently exist in multiple cell types, complicating the interpretation of experiments. Whatever the applied stimulus, it is best to introduce optimized exogenous reagents into the systems under studydenabling manipulations to be targeted to speci!c cells and pathways. (It is also possible to target manipulations through other means, such as drugs that acquire cell-type speci!city through targeting via antibodies and/or cell surface receptor ligands, but as far as we are aware, existing reagents fall short in terms of necessary speci!city.) Many types of perturbations are useful in living systems and can be divided into rough categories such as the following: depolarize or hyperpolarize cells, induce or repress the activity of a speci!c pathway, induce or inhibit expression of a particular gene, activate or repress a speci!c protein, degrade a speci!c protein, etc. User-supplied triggers for such manipulations to occur include the following: addition of a small molecule ({\textquotedblleft}chemogenetics{\textquotedblright}dideally inert on endogenous proteins) [1], sound waves ({\textquotedblleft}sonogenetics{\textquotedblright}) [2], alteration of temperature ({\textquotedblleft}thermogenetics{\textquotedblright}d almost exclusively used for small invertebrates) [3], and light ({\textquotedblleft}optogenetics{\textquotedblright}). There are reports of using magnetic !elds ({\textquotedblleft}magnetogenetics{\textquotedblright}) [4], but there is no evidence that such effects are reproducible or even physically possible [5,6]. Of these, the most commonly used, for multiple reasons, is light.

Many factors make light an ideal user-controlled stimulus for the manipulation of samples. Light is quickly delivered, and most light-sensitive proteins and other molecules respond quickly to light stimuli, making many optogenetic systems relatively rapid in comparison to, for instance, drug-modulated systems. Light is also quite easy to deliver in localized patterns, allowing for targeted stimulation. Multiple wavelengths can be delivered separately to distinct (or overlapping) regions, potentially allowing combinatorial control of diverse components. Finally, light can be delivered to shallow brain regions (and peripheral sites) relatively noninvasively, and to deeper brain regions with some effort.

However, there are also a number of shortcomings of using light for control. Robust and uniform penetration of light into the sample is the most signi!cant concern. For systems requiring modulation of many cells, particularly at depth, the use of systems controlled by small molecule drugs would generally be recommended instead of optogenetic approaches. When light is delivered through the use of !bers, lenses, or other optical devices, such interventions can produce signi!- cant cellular death, scar formation, and biofouling. The foreign-body response of tissue to objects triggers substantial molecular alterations, the implications of which are incompletely de!ned, but can involve reactive astrogliosis, oxidative stress, and perturbed vascularization. Head-mounted lightdelivery devices can be heavy and/or restrictive, and thus perturb behavior, particularly for small animals (e.g., mouse behavior is much more disrupted than rat behavior). More generally, all light causes tissue heating, which can have dramatic effects on cell health, physiology, and animal behavior. This is most concerning for tiny animals such as "ies. Light itself also damages tissue, most obviously through photochemistry (e.g., oxidation and radicalization) and photobleaching of critical endogenousmolecules. Furthermore, of course, light is ubiquitous, meaning that the sample is never completely unstimulated, despite precautions. Light passes through the eyes into the brain with surprising ease, and even through the skull with modest ef!cacy [7]dwhich can disrupt animal behavior (as can the converse: stimulating light in the brain perceived as a visual stimulus through the back of the eyes.) Light-responsive proteins exist in all samples, particularly in the eyes but to some extent in all tissuesdnotably, deep-brain photoreceptors [8].

The use of optogenetic tools has accelerated research on many fronts in disparate !elds. Additional, perhaps most, limitations on the utility of optogenetics must, however, be placed squarely on the shortcomings of the current suite of tools (and potential inherent limits in their performance.) The vast majority of optogenetic effectors are gated by blue light, which has signi!cant penetration issues and can be phototoxic under high intensity; redder wavelengths would in general be preferred. Furthermore, multiplexing requires tools making use of other parts of the visible spectrum (and redder wavelengths). A related issue is that most chromophores for optogenetic reagents have very broad action spectra (w250 nm bandwidth for retinal; w200 nm bandwidth for "avin), complicating both multiplexing and their use alongside many optical imaging reagentsdnarrower action spectra would be preferred for effectors in most situations. More generally, the current classes of optogenetic effectors are\ few, mostly limited to (1) channels and pumps (most with poor ion selectivity), (2) dimerizers, and (3) a handful of enzymes. The number of optogenetic tools that perform a very speci!c function in cells is small. Although progress has undeniably been made, much additional research and engineering will be required to dramatically expand the optogenetic toolkit.

Rather than providing a survey of research !ndings, this review covers general considerations of optogenetics experiments, and then focuses largely on molecular tools: the existing suite, their features and limitations, and goals for the creation and validation of additional reagents.

}, author = {Looger, Loren L and Maria G. Paez Segala} } @article {67794, title = {The organization and development of cortical interneuron presynaptic circuits are area specific.}, journal = {Cell Reports}, volume = {37}, year = {2021}, month = {2021 Nov 09}, pages = {109993}, abstract = {

Parvalbumin and somatostatin inhibitory interneurons gate information flow in discrete cortical areas that compute sensory and cognitive functions. Despite the considerable differences between areas, individual interneuron subtypes are genetically invariant and are thought to form canonical circuits regardless of which area they are embedded in. Here, we investigate whether this is achieved through selective and systematic variations in their afferent connectivity during development. To this end, we examined the development of their inputs within distinct cortical areas. We find that interneuron afferents show little evidence of being globally stereotyped. Rather, each subtype displays characteristic regional connectivity and distinct developmental dynamics by which this connectivity is achieved. Moreover, afferents dynamically regulated during development are disrupted by early sensory deprivation and in a model of fragile X syndrome. These data provide a comprehensive map of interneuron afferents across cortical areas and reveal the logic by which these circuits are established during development.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2021.109993}, author = {Pouchelon, Gabrielle and Dwivedi, Deepanjali and Bollmann, Yannick and Agba, Chimuanya K and Xu, Qing and Mirow, Andrea M C and Kim, Sehyun and Qiu, Yanjie and Sevier, Elaine and Ritola, Kimberly D and Cossart, Rosa and Fishell, Gord} } @article {67766, title = {A pair of dopamine neurons mediate chronic stress signals to induce learning deficit in Drosophila melanogaster.}, journal = {Proceedings of the National Academy of Sciences of the U. S. A.}, volume = {118}, year = {2021}, month = {2021 Oct 19}, abstract = {

Chronic stress could induce severe cognitive impairments. Despite extensive investigations in mammalian models, the underlying mechanisms remain obscure. Here, we show that chronic stress could induce dramatic learning and memory deficits in The chronic stress-induced learning deficit (CSLD) is long lasting and associated with other depression-like behaviors. We demonstrated that excessive dopaminergic activity provokes susceptibility to CSLD. Remarkably, a pair of PPL1-γ1pedc dopaminergic neurons that project to the mushroom body (MB) γ1pedc compartment play a key role in regulating susceptibility to CSLD so that stress-induced PPL1-γ1pedc hyperactivity facilitates the development of CSLD. Consistently, the mushroom body output neurons (MBON) of the γ1pedc compartment, MBON-γ1pedc\>α/β neurons, are important for modulating susceptibility to CSLD. Imaging studies showed that dopaminergic activity is necessary to provoke the development of chronic stress-induced maladaptations in the MB network. Together, our data support that PPL1-γ1pedc mediates chronic stress signals to drive allostatic maladaptations in the MB network that lead to CSLD.

}, issn = {1091-6490}, doi = {10.1073/pnas.2023674118}, author = {Jia, Jia and He, Lei and Yang, Junfei and Shuai, Yichun and Yang, Jingjing and Wu, Yalan and Liu, Xin and Chen, Tianli and Wang, Guaxiu and Wang, Xingyu and Song, Xiaoxu and Ding, Zhaowen and Zhu, Yan and Ling-Qi Zhang and Chen, Peng and Qin, Hongtao} } @article {67241, title = {A perspective on Microscopy Metadata: data provenance and quality control}, journal = {arXiv}, year = {2021}, month = {2021 Apr 26}, abstract = {

The application of microscopy in biomedical research has come a long way since Antonie van Leeuwenhoek discovered unicellular organisms. Countless innovations have positioned light microscopy as a cornerstone of modern biology and a method of choice for connecting omics datasets to their biological and clinical correlates. Still, regardless of how convincing published imaging data looks, it does not always convey meaningful information about the conditions in which it was acquired, processed, and analyzed. Adequate record-keeping, reporting, and quality control are therefore essential to ensure experimental rigor and data fidelity, allow experiments to be reproducibly repeated, and promote the proper evaluation, interpretation, comparison, and re-use. To this end, microscopy images should be accompanied by complete descriptions detailing experimental procedures, biological samples, microscope hardware specifications, image acquisition parameters, and image analysis procedures, as well as metrics accounting for instrument performance and calibration. However, universal, community-accepted Microscopy Metadata standards and reporting specifications that would result in Findable Accessible Interoperable and Reproducible (FAIR) microscopy data have not yet been established. To understand this shortcoming and to propose a way forward, here we provide an overview of the nature of microscopy metadata and its importance for fostering data quality, reproducibility, scientific rigor, and sharing value in light microscopy. The proposal for tiered Microscopy Metadata Specifications that extend the OME Data Model put forth by the 4D Nucleome Initiative and by Bioimaging North America [1-3] as well as a suite of three complementary and interoperable tools are being developed to facilitate the process of image data documentation and are presented in related manuscripts [4-6].

}, url = {https://arxiv.org/abs/1910.11370}, author = {Maximiliaan Huisman and Mathias Hammer and Alex Rigano and Ulrike Boehm and James J. Chambers and Nathalie Gaudreault and Alison J. North and Jaime A. Pimentel and Damir Sudar and Peter Bajcsy and Claire M. Brown and Alexander D. Corbett and Orestis Faklaris and Judith Lacoste and Alex Laude and Glyn Nelson and Roland Nitschke and David Grunwald and Caterina Strambio-De-Castillia} } @article {67702, title = {Pervasive fold switching in a ubiquitous protein superfamily.}, journal = {bioRxiv}, year = {2021}, month = {2021 Jun 11}, abstract = {

Fold-switching proteins challenge the one-sequence-one-structure paradigm by adopting multiple stable folds. Nevertheless, it is uncertain whether fold switchers are naturally pervasive or rare exceptions to the well-established rule. To address this question, we developed a predictive method and applied it to the NusG superfamily of \>15,000 transcription factors. We predicted that a substantial population (25\%) of the proteins in this family switch folds. Circular dichroism and nuclear magnetic resonance spectroscopies of 10 sequence-diverse variants confirmed our predictions. Thus, we leveraged family-wide predictions to determine both conserved contacts and taxonomic distributions of fold-switching proteins. Our results indicate that fold switching is pervasive in the NusG superfamily and that the single-fold paradigm significantly biases structure-prediction strategies.

}, doi = {10.1101/2021.06.10.447921}, author = {Lauren L. Porter and Allen K. Kim and Loren L. Looger and Anaya Majumdar and Mary Starich} } @article {68751, title = {Polo-like kinase 1 independently controls microtubule-nucleating capacity and size of the centrosome}, journal = {Journal of Cell Biology}, volume = {220}, year = {2021}, month = {01/2021}, abstract = {

Centrosomes are composed of a centriolar core surrounded by a pericentriolar material (PCM) matrix that docks microtubule-nucleating γ-tubulin complexes. During mitotic entry, the PCM matrix increases in size and nucleating capacity in a process called centrosome maturation. Polo-like kinase 1 (PLK1) is recruited to centrosomes and phosphorylates PCM matrix proteins to drive their self-assembly, which leads to PCM expansion. Here, we show that in addition to controlling PCM expansion, PLK1 independently controls the generation of binding sites for γ-tubulin complexes on the PCM matrix. Selectively preventing the generation of PLK1-dependent γ-tubulin docking sites led to spindle defects and impaired chromosome segregation without affecting PCM expansion, highlighting the importance of phospho-regulated centrosomal γ-tubulin docking sites in spindle assembly. Inhibiting both γ-tubulin docking and PCM expansion by mutating substrate target sites recapitulated the effects of loss of centrosomal PLK1 on the ability of centrosomes to catalyze spindle assembly.

}, issn = {0021-9525}, doi = {10.1083/jcb.202009083}, url = {https://doi.org/10.1083/jcb.202009083}, author = {Ohta, Midori and Zhao, Zhiling and Wu, Di and Wang, Shaohe and Harrison, Jennifer L. and G{\'o}mez-Cavazos, J. Sebasti{\'a}n and Desai, Arshad and Oegema, Karen F.} } @article {67825, title = {The power of peer networking for improving STEM faculty job applications: a successful pilot program}, journal = {bioRxiv}, year = {2021}, month = {10/2021}, abstract = {

In order to successfully obtain a faculty position, postdoctoral fellows or {\textquoteleft}postdocs{\textquoteright}, must submit an application which requires considerable time and effort to produce. These job applications are often reviewed by mentors and colleagues, but rarely are postdocs offered the opportunity to solicit feedback multiple times from reviewers with the same breadth of expertise often found on an academic search committee. To address this gap, this manuscript describes an international peer reviewing program for small groups of postdocs with a broad range of expertise to reciprocally and iteratively provide feedback to each other on their application materials. Over 145 postdocs have participated, often multiple times, over three years. A survey of participants in this program revealed that nearly all participants would recommend participation in such a program to other faculty applicants. Furthermore, this program was more likely to attract participants who struggled to find mentoring and support elsewhere, either because they changed fields or because of their identity as a woman or member of an underrepresented population in STEM. Participation in programs like this one could provide early career academics like postdocs with a diverse and supportive community of peer mentors during the difficult search for a faculty position. Such psychosocial support and encouragement has been shown to prevent attrition of individuals from these populations and programs like this one target the largest {\textquoteleft}leak{\textquoteright} in the pipeline, that of postdoc to faculty. Implementation of similar peer reviewing programs by universities or professional scientific societies could provide a valuable mechanism of support and increased chances of success for early-career academics in their search for independence.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2021.10.16.464662}, url = {https://www.biorxiv.org/content/early/2021/10/18/2021.10.16.464662}, author = {Guardia, Carlos M. and Kane, Erin and Tebo, Alison G. and Sanders, Anna A.W.M. and Kaya, Devrim and Grogan, Kathleen E.} } @article {66000, title = {Precision Mapping of COVID-19 Vulnerable Locales by Epidemiological and Socioeconomic Risk Factors, Developed Using South Korean Data.}, journal = {International Journal of Environmental Research and Public Health}, volume = {18}, year = {2021}, month = {2021 Jan 12}, abstract = {

COVID-19 has severely impacted socioeconomically disadvantaged populations. To support pandemic control strategies, geographically weighted negative binomial regression (GWNBR) mapped COVID-19 risk related to epidemiological and socioeconomic risk factors using South Korean incidence data (January 20, 2020 to July 1, 2020). We constructed COVID-19-specific socioeconomic and epidemiological themes using established social theoretical frameworks and created composite indexes through principal component analysis. The risk of COVID-19 increased with higher area morbidity, risky health behaviours, crowding, and population mobility, and with lower social distancing, healthcare access, and education. Falling COVID-19 risks and spatial shifts over three consecutive time periods reflected effective public health interventions. This study provides a globally replicable methodological framework and precision mapping for COVID-19 and future pandemics.

}, issn = {1660-4601}, doi = {10.3390/ijerph18020604}, author = {Weinstein, Bayarmagnai and da Silva, Alan R and Kouzoukas, Dimitrios E and Bose, Tanima and Kim, Gwang-Jin and Correa, Paola A and Pondugula, Santhi and Lee, YoonJung and Kim, Jihoo and Carpenter, David O} } @article {68990, title = {Principles of signaling pathway modulation for enhancing human naive pluripotency induction.}, journal = {Cell Stem Cell}, volume = {28}, year = {2021}, month = {09/2021}, pages = {1549-1565.e12}, abstract = {

Isolating human MEK/ERK signaling-independent pluripotent stem cells (PSCs) with naive pluripotency characteristics while maintaining differentiation competence and (epi)genetic integrity remains challenging. Here, we engineer reporter systems that allow the screening for defined conditions that induce molecular and functional features of human naive pluripotency. Synergistic inhibition of WNT/β-CATENIN, protein kinase C (PKC), and SRC signaling consolidates the induction of teratoma-competent naive human PSCs, with the capacity to differentiate into trophoblast stem cells (TSCs) and extraembryonic naive endodermal (nEND) cells in\ vitro. Divergent signaling and transcriptional requirements for boosting naive pluripotency were found between mouse and human. P53 depletion in naive hPSCs increased their contribution to mouse-human cross-species chimeric embryos upon priming and differentiation. Finally, MEK/ERK inhibition can be substituted with the inhibition of NOTCH/RBPj, which induces alternative naive-like hPSCs with a diminished risk for deleterious global DNA hypomethylation. Our findings set a framework for defining the signaling foundations of human naive pluripotency.

}, keywords = {Animals, Cell Differentiation, Embryo, Mammalian, Humans, Mice, Pluripotent Stem Cells, Signal Transduction, Trophoblasts}, issn = {1875-9777}, doi = {10.1016/j.stem.2021.04.001}, author = {Bayerl, Jonathan and Ayyash, Muneef and Shani, Tom and Manor, Yair Shlomo and Gafni, Ohad and Massarwa, Rada and Kalma, Yael and Aguilera-Castrejon, Alejandro and Zerbib, Mirie and Amir, Hadar and Sheban, Daoud and Geula, Shay and Mor, Nofar and Weinberger, Leehee and Naveh Tassa, Segev and Krupalnik, Vladislav and Oldak, Bernardo and Livnat, Nir and Tarazi, Shadi and Tawil, Shadi and Wildschutz, Emilie and Ashouokhi, Shahd and Lasman, Lior and Rotter, Varda and Hanna, Suhair and Ben-Yosef, Dalit and Novershtern, Noa and Viukov, Sergey and Hanna, Jacob H} } @booklet {67972, title = {Programmable 3D snapshot microscopy with Fourier convolutional networks}, year = {2021}, abstract = {

3D snapshot microscopy enables fast volumetric imaging by capturing a 3D volume in a single 2D camera image and performing computational reconstruction. Fast volumetric imaging has a variety of biological applications such as whole brain imaging of rapid neural activity in larval zebrafish. The optimal microscope design for this optical 3D-to-2D encoding is both sample- and task-dependent, with no general solution known. Deep learning based decoders can be combined with a differentiable simulation of an optical encoder for end-to-end optimization of both the deep learning decoder and optical encoder. This technique has been used to engineer local optical encoders for other problems such as depth estimation, 3D particle localization, and lensless photography. However, 3D snapshot microscopy is known to require a highly non-local optical encoder which existing UNet-based decoders are not able to engineer. We show that a neural network architecture based on global kernel Fourier convolutional neural networks can efficiently decode information from multiple depths in a volume, globally encoded across a 3D snapshot image. We show in simulation that our proposed networks succeed in engineering and reconstructing optical encoders for 3D snapshot microscopy where the existing state-of-the-art UNet architecture fails. We also show that our networks outperform the state-of-the-art learned reconstruction algorithms for a computational photography dataset collected on a prototype lensless camera which also uses a highly non-local optical encoding.

}, keywords = {Computer Vision and Pattern Recognition (cs.CV), electronic engineering, FOS: Computer and information sciences, FOS: Electrical engineering, Image and Video Processing (eess.IV), information engineering, Machine Learning (cs.LG)}, doi = {10.48550/ARXIV.2104.10611}, url = {https://arxiv.org/abs/2104.10611}, author = {Deb, Diptodip and Jiao, Zhenfei and Chen, Alex B. and Broxton, Michael and Ahrens, Misha B. and Podgorski, Kaspar and Turaga, Srinivas C.} } @article {67300, title = {Protein-Retention Expansion Microscopy (ExM): Scalable and Convenient Super-Resolution Microscopy.}, journal = {Methods in Molecular Biology}, volume = {2304}, year = {2021}, month = {2021 May 28}, pages = {147-156}, abstract = {

Expansion microscopy (ExM) is a method to expand biological specimens ~fourfold in each dimension by embedding in a hyper-swellable gel material. The expansion is uniform across observable length scales, enabling imaging of structures previously too small to resolve. ExM is compatible with any microscope and does not require expensive materials or specialized software, offering effectively sub-diffraction-limited imaging capabilities to labs that are not equipped to use traditional super-resolution imaging methods. Expanded specimens are ~99\% water, resulting in strongly reduced optical scattering and enabling imaging of sub-diffraction-limited structures throughout specimens up to several hundred microns in (pre-expansion) thickness.

}, issn = {1940-6029}, doi = {10.1007/978-1-0716-1402-0_7}, author = {Tillberg, Paul} } @article {66901, title = {Protocol for preparation of heterogeneous biological samples for 3D electron microscopy: a case study for insects.}, journal = {Scientific Reports}, volume = {11}, year = {2021}, month = {2021 Feb 25}, pages = {4717}, abstract = {

Modern morphological and structural studies are coming to a new level by incorporating the latest methods of three-dimensional electron microscopy (3D-EM). One of the key problems for the wide usage of these methods is posed by difficulties with sample preparation, since the methods work poorly with heterogeneous (consisting of tissues different in structure and in chemical composition) samples and require expensive equipment and usually much time. We have developed a simple protocol allows preparing heterogeneous biological samples suitable for 3D-EM in a laboratory that has a standard supply of equipment and reagents for electron microscopy. This protocol, combined with focused ion-beam scanning electron microscopy, makes it possible to study 3D ultrastructure of complex biological samples, e.g., whole insect heads, over their entire volume at the cellular and subcellular levels. The protocol provides new opportunities for many areas of study, including connectomics.

}, issn = {2045-2322}, doi = {10.1038/s41598-021-83936-0}, author = {Polilov, Alexey A and Makarova, Anastasia A and Pang, Song and Shan Xu, C and Hess, Harald} } @article {66900, title = {pyControl: Open source, Python based, hardware and software for controlling behavioural neuroscience experiments}, journal = {bioRxiv}, year = {2021}, month = {2021 Feb 23}, abstract = {

Laboratory behavioural tasks are an essential research tool. As questions asked of behaviour and brain activity become more sophisticated, the ability to specify and run richly structured tasks becomes more important. An increasing focus on reproducibility also necessitates accurate communication of task logic to other researchers. To these ends we developed pyControl, a system of open source hardware and software for controlling behavioural experiments comprising; a simple yet flexible Python-based syntax for specifying tasks as extended state machines, hardware modules for building behavioural setups, and a graphical user interface designed for efficiently running high throughput experiments on many setups in parallel, all with extensive online documentation. These tools make it quicker, easier and cheaper to implement rich behavioural tasks at scale. As important, pyControl facilitates communication and reproducibility of behavioural experiments through a highly readable task definition syntax and self-documenting features.

}, doi = {https://doi.org/10.1101/2021.02.22.432227}, author = {Thomas Akam and Andy Lustig and James Rowland and Sampath K.T. Kapanaiah and Joan Esteve-Agraz and Mariangela Panniello and Cristina Marquez and Michael Kohl and Dennis K{\"a}tzel and Rui M. Costa and Mark Walton} } @article {67905, title = {PyNeval: A Python Toolbox for Evaluating Neuron Reconstruction Performance.}, journal = {Frontiers in Neuroinformatics}, volume = {15}, year = {2021}, month = {2022 Jan 28}, pages = {767936}, abstract = {

Quality assessment of tree-like structures obtained from a neuron reconstruction algorithm is necessary for evaluating the performance of the algorithm. The lack of user-friendly software for calculating common metrics motivated us to develop a Python toolbox called PyNeval, which is the first open-source toolbox designed to evaluate reconstruction results conveniently as far as we know. The toolbox supports popular metrics in two major categories, geometrical metrics and topological metrics, with an easy way to configure custom parameters for each metric. We tested the toolbox on both synthetic data and real data to show its reliability and robustness. As a demonstration of the toolbox in real applications, we used the toolbox to improve the performance of a tracing algorithm successfully by integrating it into an optimization procedure.

}, issn = {1662-5196}, doi = {10.3389/fninf.2021.767936}, author = {Zhang, Han and Liu, Chao and Yu, Yifei and Dai, Jianhua and Zhao, Ting and Zheng, Nenggan} } @article {67295, title = {QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy.}, journal = {Nature Methods}, year = {2021}, month = {2021 May 21}, issn = {1548-7105}, doi = {10.1038/s41592-021-01162-y}, author = {Ulrike Boehm and Nelson, Glyn and Brown, Claire M and Bagley, Steve and Bajcsy, Peter and Bischof, Johanna and Dauphin, Aurelien and Dobbie, Ian M and Eriksson, John E and Faklaris, Orestis and Fernandez-Rodriguez, Julia and Ferrand, Alexia and Gelman, Laurent and Gheisari, Ali and Hartmann, Hella and Kukat, Christian and Laude, Alex and Mitkovski, Miso and Munck, Sebastian and North, Alison J and Rasse, Tobias M and Resch-Genger, Ute and Schuetz, Lucas C and Seitz, Arne and Strambio-De-Castillia, Caterina and Swedlow, Jason R and Nitschke, Roland} } @article {66009, title = {QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy}, journal = {Journal of Microscopy}, volume = {284}, year = {2021}, month = {2021 Oct 01}, pages = {56-73}, abstract = {

In April 2020, the QUality Assessment and REProducibility for Instruments and Images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models, and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper 1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; 2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers, and observers of such; 3) outlines the current actions of the QUAREP-LiMi initiative, and 4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.

}, url = {https://arxiv.org/abs/2101.09153}, author = {Glyn Nelson and Ulrike Boehm and Steve Bagley and Peter Bajcsy and Johanna Bischof and Claire M Brown and Aurelien Dauphin and Ian M Dobbie and John E Eriksson and Orestis Faklaris and Julia Fernandez-Rodriguez and Alexia Ferrand and Ali Gheisari and Hella Hartmann and Christian Kukat and Alex Laude and Miso Mitkovski and Sebastian Munck and Alison J North and Tobias M Rasse and Ute Resch-Genger and Lucas C Schuetz and Arne Seitz and Caterina Strambio-De-Castillia and Jason R Swedlow and Ioannis Alexopoulos and Karin Aumayr and Sergiy Avilov and Gert-Jan Bakker and Rodrigo R Bammann and Andrea Bassi and Hannes Beckert and Sebastian Beer and Yury Belyaev and Jakob Bierwagen and Konstantin A Birngruber and Manel Bosch and Juergen Breitlow and Lisa A Cameron and Joe Chalfoun and James J Chambers and Chieh-Li Chen and Eduardo Conde-Sousa and Alexander D Corbett and Fabrice P Cordelieres and Elaine Del Nery and Ralf Dietzel and Frank Eismann and Elnaz Fazeli and Andreas Felscher and Hans Fried and Nathalie Gaudreault and Wah Ing Goh and Thomas Guilbert and Roland Hadleigh and Peter Hemmerich and Gerhard A Holst and Michelle S Itano and Claudia B Jaffe and Helena K Jambor and Stuart C Jarvis and Antje Keppler and David Kirchenbuechler and Marcel Kirchner and Norio Kobayashi and Gabriel Krens and Susanne Kunis and Judith Lacoste and Marco Marcell and Gabriel G Martins and Daniel J Metcalf and Claire A Mitchell and Joshua Moore and Tobias Mueller and Michael S Nelson and Stephen Ogg and Shuichi Onami and Alexandra L Palmer and Perrine Paul-Gilloteaux and Jaime A Pimentel and Laure Plantard and Santosh Podder and Elton Rexhepaj and Arnaud Royon and Markku A Saari and Damien Schapman and Vincent Schoonderwoert and Britta Schroth-Diez and Stanley Schwartz and Michael Shaw and Martin Spitaler and Martin T Stoeckl and Damir Sudar and Jeremie Teillon and Stefan Terjung and Roland Thuenauer and Christian D Wilms and Graham D Wright and Roland Nitschke and Laurent Gelman} } @article {67767, title = {Rapid synaptic plasticity contributes to a learned conjunctive code of position and choice-related information in the hippocampus}, journal = {Neuron}, year = {2021}, month = {2021 Oct 14}, abstract = {

To successfully perform goal-directed navigation, animals must know where they are and what they are doing{\textemdash}e.g., looking for water, bringing food back to the nest, or escaping from a predator. Hippocampal neurons code for these critical variables conjunctively, but little is known about how this where/what code is formed or flexibly routed to other brain regions. To address these questions, we performed intracellular whole-cell recordings in mouse CA1 during a cued, two-choice virtual navigation task. We demonstrate that plateau potentials in CA1 pyramidal neurons rapidly strengthen synaptic inputs carrying conjunctive information about position and choice. Plasticity-induced response fields were modulated by cues only in animals previously trained to collect rewards based on these cues. Thus, we reveal that gradual learning is required for the formation of a conjunctive population code, upstream of CA1, while plateau-potential-induced synaptic plasticity in CA1 enables flexible routing of the code to downstream brain regions.

}, doi = {https://doi.org/10.1101/2021.06.30.450574}, author = {Xinyu Zhao and Ching-Lung Hsu and Nelson Spruston} } @article {65833, title = {Reconstruction of motor control circuits in adult Drosophila using automated transmission electron microscopy}, journal = {Cell}, volume = {184}, year = {2021}, month = {2021 Feb 04}, abstract = {

Many animals use coordinated limb movements to interact with and navigate through the environment. To investigate circuit mechanisms underlying locomotor behavior, we used serial-section electron microscopy (EM) to map synaptic connectivity within a neuronal network that controls limb movements. We present a synapse-resolution EM dataset containing the ventral nerve cord (VNC) of an adult female Drosophila melanogaster. To generate this dataset, we developed GridTape, a technology that combines automated serial-section collection with automated high-throughput transmission EM. Using this dataset, we reconstructed 507 motor neurons, including all those that control the legs and wings. We show that a specific class of leg sensory neurons directly synapse onto the largest-caliber motor neuron axons on both sides of the body, representing a unique feedback pathway for fast limb control. We provide open access to the dataset and reconstructions registered to a standard atlas to permit matching of cells between EM and light microscopy data. We also provide GridTape instrumentation designs and software to make large-scale EM data acquisition more accessible and affordable to the scientific community.

}, doi = {10.1101/2020.01.10.902478}, author = {Maniates-Selvin, Jasper T. and Hildebrand, David Grant Colburn and Graham, Brett J. and Kuan, Aaron T. and Thomas, Logan A. and Nguyen, Tri and Buhmann, Julia and Azevedo, Anthony W. and Shanny, Brendan L. and Funke, Jan and Tuthill, John C. and Lee, Wei-Chung Allen} } @article {66904, title = {Recording Electrical Currents across the Plasma Membrane of Mammalian Sperm Cells.}, journal = {Journal of Visualized Experiments: JOVE}, year = {2021}, month = {2021 Feb 14}, abstract = {

Recording of the electrical activity from one of the smallest cells of a mammalian organism- a sperm cell- has been a challenging task for electrophysiologists for many decades. The method known as "spermatozoan patch clamp" was introduced in 2006. It has enabled the direct recording of ion channel activity in whole-cell and cell-attached configurations and has been instrumental in describing sperm cell physiology and the molecular identity of various calcium, potassium, sodium, chloride, and proton ion channels. However, recording from single spermatozoa requires advanced skills and training in electrophysiology. This detailed protocol summarizes the step-by-step procedure and highlights several {\textquoteright}tricks-of-the-trade{\textquoteright} in order to make it available to anyone who wishes to explore the fascinating physiology of the sperm cell. Specifically, the protocol describes recording from human and murine sperm cells but can be adapted to essentially any mammalian sperm cell of any species. The protocol covers important details of the application of this technique, such as isolation of sperm cells, selection of reagents and equipment, immobilization of the highly motile cells, formation of the tight (Gigaohm) seal between a recording electrode and the plasma membrane of the sperm cells, transition into the whole-spermatozoan mode (also known as break-in), and exemplary recordings of the sperm cell calcium ion channel, CatSper, from six mammalian species. The advantages and limitations of the sperm patch clamp method, as well as the most critical steps, are discussed.

}, issn = {1940-087X}, doi = {10.3791/62049}, author = {Liu, Boheng and Mundt, Nadine and Miller, Melissa and Clapham, David E and Kirichok, Yuriy and Lishko, Polina V} } @article {67709, title = {Regulated exocytosis: Renal Aquaporin-2 3D Vesicular Network Organization and Association with F-actin.}, journal = {American Journal of Physiology: Cell Physiology}, volume = {321}, year = {2021}, month = {2021 Dec 01}, abstract = {

Regulated vesicle exocytosis is a key response to extracellular stimuli in diverse physiological processes; including hormone regulated short-term urine concentration. In the renal collecting duct, the water channel aquaporin-2 localizes to the apical plasma membrane as well as small, sub-apical vesicles. In response to stimulation with the antidiuretic hormone, arginine vasopressin, aquaporin-2 containing vesicles fuse with the plasma membrane, which increases collecting duct water reabsorption and thus, urine concentration. The nano-scale size of these vesicles has limited analysis of their 3D organization. Using a cell system combined with 3D super resolution microscopy, we provide the first direct analysis of the 3D network of aquaporin-2 containing exocytic vesicles in a cell culture system. We show that aquaporin-2 vesicles are 43 {\textpm} 3nm in diameter, a size similar to synaptic vesicles, and that one fraction of AQP2 vesicles localized with the sub-cortical F-actin layer and the other localized in between the F-actin layer and the plasma membrane. Aquaporin-2 vesicles associated with F-actin and this association was enhanced in a serine 256 phospho-mimic of aquaporin-2, whose phosphorylation is a key event in antidiuretic hormone-mediated aquaporin-2 vesicle exocytosis.

}, issn = {1522-1563}, doi = {10.1152/ajpcell.00255.2021}, author = {Holst, Mikkel R and Gammelgaard, Louis and Aaron, Jesse and Login, Fr{\'e}d{\'e}ric H and Rajkumar, Sampavi and Hahn, Ute and Nejsum, Lene N} } @article {67296, title = {Regulation of coordinated muscular relaxation in Drosophila larvae by a pattern-regulating intersegmental circuit.}, journal = {Nature Communications}, volume = {12}, year = {2021}, month = {2021 May 19}, pages = {2943}, abstract = {

Typical patterned movements in animals are achieved through combinations of contraction and delayed relaxation of groups of muscles. However, how intersegmentally coordinated patterns of muscular relaxation are regulated by the neural circuits remains poorly understood. Here, we identify Canon, a class of higher-order premotor interneurons, that regulates muscular relaxation during backward locomotion of Drosophila larvae. Canon neurons are cholinergic interneurons present in each abdominal neuromere and show wave-like activity during fictive backward locomotion. Optogenetic activation of Canon neurons induces relaxation of body wall muscles, whereas inhibition of these neurons disrupts timely muscle relaxation. Canon neurons provide excitatory outputs to inhibitory premotor interneurons. Canon neurons also connect with each other to form an intersegmental circuit and regulate their own wave-like activities. Thus, our results demonstrate how coordinated muscle relaxation can be realized by an intersegmental circuit that regulates its own patterned activity and sequentially terminates motor activities along the anterior-posterior axis.

}, issn = {2041-1723}, doi = {10.1038/s41467-021-23273-y}, author = {Hiramoto, Atsuki and Jonaitis, Julius and Niki, Sawako and Kohsaka, Hiroshi and Fetter, Richard D and Cardona, Albert and Pulver, Stefan R and Nose, Akinao} } @article {66024, title = {RNA transport and local translation in neurodevelopmental and neurodegenerative disease.}, journal = {Nature Neuroscience}, volume = {24}, year = {2021}, month = {2021 May 01}, pages = {622-32}, abstract = {

Neurons decentralize protein synthesis from the cell body to support the active metabolism of remote dendritic and axonal compartments. The neuronal RNA transport apparatus, composed of cis-acting RNA regulatory elements, neuronal transport granule proteins, and motor adaptor complexes, drives the long-distance RNA trafficking required for local protein synthesis. Over the past decade, advances in human genetics, subcellular biochemistry, and high-resolution imaging have implicated each member of the apparatus in several neurodegenerative diseases, establishing failed RNA transport and associated processes as a unifying pathomechanism. In this review, we deconstruct the RNA transport apparatus, exploring each constituent{\textquoteright}s role in RNA localization and illuminating their unique contributions to neurodegeneration.

}, issn = {1546-1726}, doi = {10.1038/s41593-020-00785-2}, author = {Fernandopulle, Michael S and Lippincott-Schwartz, Jennifer and Ward, Michael E} } @article {67703, title = {A sequence-based method for predicting extant fold switchers that undergo α-helix <-> β-strand transitions}, journal = {Biopolymers}, volume = {112}, year = {2021}, month = {2021 Oct 01}, abstract = {

Extant fold-switching proteins remodel their secondary structures and change their functions in response to cellular stimuli, regulating biological processes and affecting human health. In spite of their biological importance, these proteins remain understudied. Few representative examples of fold switchers are available in the Protein Data Bank, and they are difficult to predict. In fact, all 96 experimentally validated examples of extant fold switchers were stumbled upon by chance. Thus, predictive methods are needed to expedite the process of discovering and characterizing more of these shapeshifting proteins. Previous approaches require a solved structure or all-atom simulations, greatly constraining their use. Here, we propose a high-throughput sequence-based method for predicting extant fold switchers that transition from α-helix in one conformation to β-strand in the other. This method leverages two previous observations: (1) α-helix \<-\> β-strand prediction discrepancies from JPred4 are a robust predictor of fold switching, and (2) the fold-switching regions (FSRs) of some extant fold switchers have different secondary structure propensities when expressed in isolation (isolated FSRs) than when expressed within the context of their parent protein (contextualized FSRs). Combining these two observations, we ran JPred4 on the sequences of isolated and contextualized FSRs from 14 known extant fold switchers and found α-helix \<-\>β-strand prediction discrepancies in every case. To test the overall robustness of this finding, we randomly selected regions of proteins not expected to switch folds (single-fold proteins) and found significantly fewer α-helix \<-\> β-strand prediction discrepancies (p \< 4.2*10-20, Kolmogorov-Smirnov test). Combining these discrepancies with the overall percentage of predicted secondary structure, we developed a classifier that often robustly identifies extant fold switchers (Matthews Correlation Coefficient of 0.70). Although this classifier had a high false negative rate (6/14), its false positive rate was very low (1/211), suggesting that it can be used to predict a subset of extant fold switchers from billions of available genomic sequences.

}, doi = {10.1101/2021.01.14.426714}, author = {Soumya Mishra and Loren L. Looger and Lauren L. Porter} } @article {69334, title = {Sexual arousal gates visual processing during Drosophila courtship}, journal = {Nature}, volume = {595}, year = {2021}, month = {2022 Oct 7}, pages = {549 - 553}, abstract = {

Long-lasting internal arousal states motivate and pattern ongoing behaviour, enabling the temporary emergence of innate behavioural programs\ that serve the needs of an animal, such as fighting, feeding, and mating. However, how internal states shape sensory processing or behaviour remains unclear. In\ Drosophila, male flies perform a lengthy and elaborate courtship ritual that is triggered by the activation of sexually dimorphic P1 neurons1,2,3,4,5, during which they faithfully follow and sing to a female6,7. Here, by recording from males as they court a virtual {\textquoteleft}female{\textquoteright}, we gain insight into how the salience of visual cues is transformed by a male{\textquoteright}s internal arousal state to give rise to persistent courtship pursuit. The gain of LC10a visual projection neurons is selectively increased during courtship, enhancing their sensitivity to moving targets. A concise network model indicates that visual signalling through the LC10a circuit, once amplified by P1-mediated arousal, almost fully specifies a male{\textquoteright}s tracking of a female. Furthermore, P1 neuron activity correlates with ongoing fluctuations in the intensity of a male{\textquoteright}s pursuit to continuously tune the gain of the LC10a pathway. Together, these results reveal how a male{\textquoteright}s internal state can dynamically modulate the propagation of visual signals through a high-fidelity visuomotor circuit to guide his moment-to-moment performance of courtship.

}, issn = {0028-0836}, doi = {10.1038/s41586-021-03714-w}, url = {https://www.nature.com/articles/s41586-021-03714-whttp://www.nature.com/articles/s41586-021-03714-w.pdfhttp://www.nature.com/articles/s41586-021-03714-w.pdfhttp://www.nature.com/articles/s41586-021-03714-w}, author = {Hindmarsh Sten, Tom and Li, Rufei and Otopalik, Adriane and Ruta, Vanessa} } @article {67632, title = {Single-cell imaging of genome organization and dynamics.}, journal = {Molecular Systems Biology}, volume = {17}, year = {2021}, month = {2021 Jul 01}, pages = {e9653}, abstract = {

Probing the architecture, mechanism, and dynamics of genome folding is fundamental to our understanding of genome function in homeostasis and disease. Most chromosome conformation capture studies dissect the genome architecture with population- and time-averaged snapshots and thus have limited capabilities to reveal 3D nuclear organization and dynamics at the single-cell level. Here, we discuss emerging imaging techniques ranging from light microscopy to electron microscopy that enable investigation of genome folding and dynamics at high spatial and temporal resolution. Results from these studies complement genomic data, unveiling principles underlying the spatial arrangement of the genome and its potential functional links to diverse biological activities in the nucleus.

}, issn = {1744-4292}, doi = {10.15252/msb.20209653}, author = {Xie, Liangqi and Liu, Zhe} } @article {68425, title = {Single-cell transcriptomes of developing and adult olfactory receptor neurons in Drosophila}, journal = {Elife}, volume = {10}, year = {2021}, month = {02/2021}, abstract = {

Recognition of environmental cues is essential for the survival of all organisms. Transcriptional changes occur to enable the generation and function of the neural circuits underlying sensory perception. To gain insight into these changes, we generated single-cell transcriptomes of olfactory- (ORNs), thermo-, and hygro-sensory neurons at an early developmental and adult stage using single-cell and single-nucleus RNA sequencing. We discovered that ORNs maintain expression of the same olfactory receptors across development. Using receptor expression and computational approaches, we matched transcriptomic clusters corresponding to anatomically and physiologically defined neuron types across multiple developmental stages. We found that cell-type-specific transcriptomes partly reflected axon trajectory choices in development and sensory modality in adults. We uncovered stage-specific genes that could regulate the wiring and sensory responses of distinct ORN types. Collectively, our data reveal transcriptomic features of sensory neuron biology and provide a resource for future studies of their development and physiology.

}, keywords = {Animals, Drosophila melanogaster, Drosophila Proteins, Female, Male, Olfactory Receptor Neurons, Sequence Analysis, RNA, Single-Cell Analysis, Smell, Transcriptome}, issn = {2050-084X}, doi = {10.7554/eLife.63856}, author = {McLaughlin, Colleen N and Brbi{\'c}, Maria and Xie, Qijing and Li, Tongchao and Horns, Felix and Kolluru, Sai Saroja and Kebschull, Justus M and Vacek, David and Xie, Anthony and Li, Jiefu and Jones, Robert C and Leskovec, Jure and Quake, Stephen R and Luo, Liqun and Li, Hongjie} } @article {67647, title = {Single-molecule imaging of chromatin remodelers reveals role of ATPase in promoting fast kinetics of target search and dissociation from chromatin.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Jul 27}, abstract = {

Conserved ATP-dependent chromatin remodelers establish and maintain genome-wide chromatin architectures of regulatory DNA during cellular lifespan, but the temporal interactions between remodelers and chromatin targets have been obscure. We performed live-cell single-molecule tracking for RSC, SWI/SNF, CHD1, ISW1, ISW2, and INO80 remodeling complexes in budding yeast and detected hyperkinetic behaviors for chromatin-bound molecules that frequently transition to the free state for all complexes. Chromatin-bound remodelers display notably higher diffusion than nucleosomal histones, and strikingly fast dissociation kinetics with 4-7 s mean residence times. These enhanced dynamics require ATP binding or hydrolysis by the catalytic ATPase, uncovering an additional function to its established role in nucleosome remodeling. Kinetic simulations show that multiple remodelers can repeatedly occupy the same promoter region on a timescale of minutes, implicating an unending {\textquoteright}tug-of-war{\textquoteright} that controls a temporally shifting window of accessibility for the transcription initiation machinery.

}, issn = {2050-084X}, doi = {10.7554/eLife.69387}, author = {Kim, Jee Min and Visanpattanasin, Pat and Jou, Vivian and Liu, Sheng and Tang, Xiaona and Zheng, Qinsi and Li, Kai Yu and Snedeker, Jonathan and Lavis, Luke D and Lionnet, Timoth{\'e}e and Wu, Carl} } @article {67872, title = {Small-molecule ligands can inhibit -1 programmed ribosomal frameshifting in a broad spectrum of coronaviruses.}, journal = {bioRxiv}, year = {2021}, month = {2021 Aug 06}, abstract = {

Recurrent outbreaks of novel zoonotic coronavirus (CoV) diseases since 2000 have high-lighted the importance of developing therapeutics with broad-spectrum activity against CoVs. Because all CoVs use -1 programmed ribosomal frameshifting (-1 PRF) to control expression of key viral proteins, the frameshift signal in viral mRNA that stimulates -1 PRF provides a promising potential target for such therapeutics. To test the viability of this strategy, we explored a group of 6 small-molecule ligands, evaluating their activity against the frameshift signals from a panel of representative bat CoVs{\textemdash}the most likely source of future zoonoses{\textemdash}as well as SARS-CoV-2 and MERS-CoV. We found that whereas some ligands had notable activity against only a few of the frameshift signals, the serine protease inhibitor nafamostat suppressed -1 PRF significantly in several of them, while having limited to no effect on -1 PRF caused by frameshift signals from other viruses used as negative controls. These results suggest it is possible to find small-molecule ligands that inhibit -1 PRF specifically in a broad spectrum of CoVs, establishing the frameshift signal as a viable target for developing pan-coronaviral therapeutics.

}, doi = {10.1101/2021.08.06.455424}, url = {https://doi.org/10.1101/2021.08.06.455424}, author = {Sneha Munshi and Krishna Neupane and Sandaru M. Ileperuma and Matthew T.J. Halma and Jamie A. Kelly and Clarissa F. Halpern and Jonathan D. Dinman and Sarah Loerch and Michael T. Woodside} } @article {67201, title = {SNT: a unifying toolbox for quantification of neuronal anatomy.}, journal = {Nature Methods}, volume = {18}, year = {2021}, month = {2021 Apr 01}, pages = {374-377}, abstract = {

SNT is an end-to-end framework for neuronal morphometry and whole-brain connectomics that supports tracing, proof-editing, visualization, quantification and modeling of neuroanatomy. With an open architecture, a large user base, community-based documentation, support for complex imagery and several model organisms, SNT is a flexible resource for the broad neuroscience community. SNT is both a desktop application and multi-language scripting library, and it is available through the Fiji distribution of ImageJ.

}, issn = {1548-7105}, doi = {10.1038/s41592-021-01105-7}, author = {Arshadi, Cameron and G{\"u}nther, Ulrik and Eddison, Mark and Harrington, Kyle I S and Ferreira, Tiago A} } @article {67229, title = {SongExplorer: A deep learning workflow for discovery and segmentation of animal acoustic communication signals}, journal = {bioRxiv}, year = {2021}, month = {03/2021}, abstract = {

Many animals produce distinct sounds or substrate-borne vibrations, but these signals have proved challenging to segment with automated algorithms. We have developed SongExplorer, a web-browser based interface wrapped around a deep-learning algorithm that supports an interactive workflow for (1) discovery of animal sounds, (2) manual annotation, (3) supervised training of a deep convolutional neural network, and (4) automated segmentation of recordings. Raw data can be explored by simultaneously examining song events, both individually and in the context of the entire recording, watching synced video, and listening to song. We provide a simple way to visualize many song events from large datasets within an interactive low-dimensional visualization, which facilitates detection and correction of incorrectly labelled song events. The machine learning model we implemented displays higher accuracy than existing heuristic algorithms and similar accuracy as two expert human annotators. We show that SongExplorer allows rapid detection of all song types from new species and of novel song types in previously well-studied species.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2021.03.26.437280}, url = {https://www.biorxiv.org/content/early/2021/03/26/2021.03.26.437280}, author = {Arthur, Benjamin J. and Ding, Yun and Sosale, Medhini and Khalif, Faduma and Kim, Elizabeth and Waddell, Peter and Turaga, Srinivas C. and Stern, David L.} } @article {67673, title = {Spatially patterned excitatory neuron subtypes and projections of the claustrum.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Aug 16}, abstract = {

The claustrum is a functionally and structurally complex brain region, whose very spatial extent remains debated. Histochemical-based approaches typically treat the claustrum as a relatively narrow anatomical region that primarily projects to the neocortex, whereas circuit-based approaches can suggest a broader claustrum region containing projections to the neocortex and other regions. Here, in the mouse, we took a bottom-up and cell-type-specific approach to complement and possibly unite these seemingly disparate conclusions. Using single-cell RNA-sequencing, we found that the claustrum comprises two excitatory neuron subtypes that are differentiable from the surrounding cortex. Multicolor retrograde tracing in conjunction with 12-channel multiplexed in situ hybridization revealed a core-shell spatial arrangement of these subtypes, as well as differential downstream targets. Thus, the claustrum comprises excitatory neuron subtypes with distinct molecular and projection properties, whose spatial patterns reflect the narrower and broader claustral extents debated in previous research. This subtype-specific heterogeneity likely shapes the functional complexity of the claustrum.

}, issn = {2050-084X}, doi = {10.7554/eLife.68967}, author = {Erwin, Sarah R and Bristow, Brianna N and Sullivan, Kaitlin E and Kendrick, Rennie M and Marriott, Brian and Wang, Lihua and Clements, Jody and Lemire, Andrew L and Jackson, Jesse and Cembrowski, Mark S} } @article {67671, title = {Spatiotemporal coordination of transcription preinitiation complex assembly in live cells.}, journal = {Molecular Cell}, volume = {81}, year = {2021}, month = {2021 Sep 02}, pages = {3560-3575}, abstract = {

Transcription initiation by RNA polymerase II (RNA Pol II) requires preinitiation complex (PIC) assembly at gene promoters. In the dynamic nucleus, where thousands of promoters are broadly distributed in chromatin, it is unclear how multiple individual components converge on any target to establish the PIC. Here we use live-cell, single-molecule tracking in S.\ cerevisiae to visualize constrained exploration of the nucleoplasm by PIC components and Mediator{\textquoteright}s key role in guiding this process. On chromatin, TFIID/TATA-binding protein (TBP), Mediator, and RNA Pol II instruct assembly of a short-lived PIC, which occurs infrequently but efficiently within a few seconds on average. Moreover, PIC exclusion by nucleosome encroachment underscores regulated promoter accessibility by chromatin remodeling. Thus, coordinated nuclear exploration and recruitment to accessible targets underlies dynamic PIC establishment in yeast. Our study provides a global spatiotemporal model for transcription initiation in live cells.

}, issn = {1097-4164}, doi = {10.1016/j.molcel.2021.07.022}, author = {Nguyen, Vu Q and Ranjan, Anand and Liu, Sheng and Tang, Xiaona and Ling, Yick Hin and Wisniewski, Jan and Mizuguchi, Gaku and Li, Kai Yu and Jou, Vivian and Zheng, Qinsi and Lavis, Luke D and Lionnet, Timoth{\'e}e and Wu, Carl} } @article {67820, title = {Structure and RNA template requirements of RNA-DEPENDENT RNA POLYMERASE 2.}, journal = {Proceedings of the National Academy of Sciences of the U.S.A.}, volume = {118}, year = {2021}, month = {2021 Dec 21}, abstract = {

RNA-dependent RNA polymerases play essential roles in RNA-mediated gene silencing in eukaryotes. In , RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) physically interacts with DNA-dependent NUCLEAR RNA POLYMERASE IV (Pol IV) and their activities are tightly coupled, with Pol IV transcriptional arrest, induced by the nontemplate DNA strand, somehow enabling RDR2 to engage Pol IV transcripts and generate double-stranded RNAs. The double-stranded RNAs are then released from the Pol IV-RDR2 complex and diced into short-interfering RNAs that guide RNA-directed DNA methylation and silencing. Here we report the structure of full-length RDR2, at an overall resolution of 3.1 {\r A}, determined by cryoelectron microscopy. The N-terminal region contains an RNA-recognition motif adjacent to a positively charged channel that leads to a catalytic center with striking structural homology to the catalytic centers of multisubunit DNA-dependent RNA polymerases. We show that RDR2 initiates 1 to 2 nt internal to the 3{\textquoteright} ends of its templates and can transcribe the RNA of an RNA/DNA hybrid, provided that 9 or more nucleotides are unpaired at the RNA{\textquoteright}s 3{\textquoteright} end. Using a nucleic acid configuration that mimics the arrangement of RNA and DNA strands upon Pol IV transcriptional arrest, we show that displacement of the RNA 3{\textquoteright} end occurs as the DNA template and nontemplate strands reanneal, enabling RDR2 transcription. These results suggest a model in which Pol IV arrest and backtracking displaces the RNA 3{\textquoteright} end as the DNA strands reanneal, allowing RDR2 to engage the RNA and synthesize the complementary strand.

}, issn = {1091-6490}, doi = {10.1073/pnas.2115899118}, author = {Fukudome, Akihito and Singh, Jasleen and Mishra, Vibhor and Reddem, Eswar and Martinez-Marquez, Francisco and Wenzel, Sabine and Yan, Rui and Shiozaki, Momoko and Yu, Zhiheng and Wang, Joseph Che-Yen and Takagi, Yuichiro and Pikaard, Craig S} } @article {67675, title = {Structured patterns of activity in pulse-coupled oscillator networks with varied connectivity.}, journal = {PLoS One}, volume = {16}, year = {2021}, month = {2021 Aug 11}, pages = {e0256034}, abstract = {

Identifying coordinated activity within complex systems is essential to linking their structure and function. We study collective activity in networks of pulse-coupled oscillators that have variable network connectivity and integrate-and-fire dynamics. Starting from random initial conditions, we see the emergence of three broad classes of behaviors that differ in their collective spiking statistics. In the first class ("temporally-irregular"), all nodes have variable inter-spike intervals, and the resulting firing patterns are irregular. In the second ("temporally-regular"), the network generates a coherent, repeating pattern of activity in which all nodes fire with the same constant inter-spike interval. In the third ("chimeric"), subgroups of coherently-firing nodes coexist with temporally-irregular nodes. Chimera states have previously been observed in networks of oscillators; here, we find that the notions of temporally-regular and chimeric states encompass a much richer set of dynamical patterns than has yet been described. We also find that degree heterogeneity and connection density have a strong effect on the resulting state: in binomial random networks, high degree variance and intermediate connection density tend to produce temporally-irregular dynamics, while low degree variance and high connection density tend to produce temporally-regular dynamics. Chimera states arise with more frequency in networks with intermediate degree variance and either high or low connection densities. Finally, we demonstrate that a normalized compression distance, computed via the Lempel-Ziv complexity of nodal spike trains, can be used to distinguish these three classes of behavior even when the phase relationship between nodes is arbitrary.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0256034}, author = {Kadhim, Kyra L and Hermundstad, Ann M and Brown, Kevin S} } @article {66028, title = {Structure-Function Dataset Reveals Environment Effects within a Fluorescent Protein Model System.}, journal = {Angew Chemie (International Edition English)}, year = {2021}, month = {2021 Feb 04}, abstract = {

Anisotropic environments can drastically alter the spectroscopy and photochemistry of molecules, leading to complex structure-function relationships. We examined this using fluorescent proteins as easy-to-modify model systems. Starting from a single scaffold, we have developed a range of 27 photochromic fluorescent proteins that cover a broad range of spectroscopic properties, including the determination of 43 crystal structures. Correlation and principal component analysis confirmed the complex relationship between structure and spectroscopy, but also allowed us to identify consistent trends and to relate these to the spatial organization. We find that changes in spectroscopic properties can come about through multiple underlying mechanisms, of which polarity, hydrogen bonding and presence of water molecules are key modulators. We anticipate that our findings and rich structure/spectroscopy dataset can open opportunities for the development and evaluation of new and existing protein engineering methods.

}, issn = {1521-3773}, doi = {10.1002/anie.202015201}, author = {De Zitter, Elke and Hugelier, Siewert and Duw{\'e}, Sam and Vandenberg, Wim and Tebo, Alison G and Van Meervelt, Luc and Dedecker, Peter} } @article {66008, title = {Survey of spiking in the mouse visual system reveals functional hierarchy.}, journal = {Nature}, volume = {592(7852):86-92}, year = {2021}, month = {2021 Jan 20}, pages = {86-92}, abstract = {

The anatomy of the mammalian visual system, from the retina to the neocortex, is organized hierarchically. However, direct observation of cellular-level functional interactions across this hierarchy is lacking due to the challenge of simultaneously recording activity across numerous regions. Here we describe a large, open dataset-part of the Allen Brain Observatory-that surveys spiking from tens of thousands of units in six cortical and two thalamic regions in the brains of mice responding to a battery of visual stimuli. Using cross-correlation analysis, we reveal that the organization of inter-area functional connectivity during visual stimulation mirrors the anatomical hierarchy from the Allen Mouse Brain Connectivity Atlas. We find that four classical hierarchical measures-response latency, receptive-field size, phase-locking to drifting gratings and response decay timescale-are all correlated with the hierarchy. Moreover, recordings obtained during a visual task reveal that the correlation between neural activity and behavioural choice also increases along the hierarchy. Our study provides a foundation for understanding coding and signal propagation across hierarchically organized cortical and thalamic visual areas.

}, issn = {1476-4687}, doi = {10.1038/s41586-020-03171-x}, author = {Siegle, Joshua H and Jia, Xiaoxuan and Durand, Severine and Gale, Sam and Bennett, Corbett and Graddis, Nile and Heller, Greggory and Ramirez, Tamina K and Choi, Hannah and Luviano, Jennifer A and Groblewski, Peter A and Ahmed, Ruweida and Arkhipov, Anton and Bernard, Amy and Billeh, Yazan N and Brown, Dillan and Buice, Michael A and Cain, Nicolas and Caldejon, Shiella and Casal, Linzy and Cho, Andrew and Chvilicek, Maggie and Cox, Timothy C and Dai, Kael and Denman, Daniel J and de Vries, Saskia E J and Dietzman, Roald and Esposito, Luke and Farrell, Colin and Feng, David and Galbraith, John and Garrett, Marina and Gelfand, Emily C and Hancock, Nicole and Harris, Julie A and Howard, Robert and Hu, Brian and Hytnen, Ross and Iyer, Ramakrishnan and Jessett, Erika and Johnson, Katelyn and Kato, India and Kiggins, Justin and Lambert, Sophie and Lecoq, Jerome and Ledochowitsch, Peter and Lee, Jung Hoon and Leon, Arielle and Li, Yang and Liang, Elizabeth and Long, Fuhui and Mace, Kyla and Melchior, Jose and Millman, Daniel and Mollenkopf, Tyler and Nayan, Chelsea and Ng, Lydia and Ngo, Kiet and Nguyen, Thuyahn and Nicovich, Philip R and North, Kat and Ocker, Gabriel Koch and Ollerenshaw, Doug and Oliver, Michael and Pachitariu, Marius and Perkins, Jed and Reding, Melissa and Reid, David and Robertson, Miranda and Ronellenfitch, Kara and Seid, Sam and Slaughterbeck, Cliff and Stoecklin, Michelle and Sullivan, David and Sutton, Ben and Swapp, Jackie and Thompson, Carol and Turner, Kristen and Wakeman, Wayne and Whitesell, Jennifer D and Williams, Derric and Williford, Ali and Young, Rob and Zeng, Hongkui and Naylor, Sarah and Phillips, John W and Reid, R Clay and Mihalas, Stefan and Olsen, Shawn R and Koch, Christof} } @article {67843, title = {Synaptic targets of photoreceptors specialized to detect color and skylight polarization in .}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Dec 16}, abstract = {

Color and polarization provide complementary information about the world and are detected by specialized photoreceptors. However, the downstream neural circuits that process these distinct modalities are incompletely understood in any animal. Using electron microscopy, we have systematically reconstructed the synaptic targets of the photoreceptors specialized to detect color and skylight polarization in Drosophila, and we have used light microscopy to confirm many of our findings. We identified known and novel downstream targets that are selective for different wavelengths or polarized light, and followed their projections to other areas in the optic lobes and the central brain. Our results revealed many synapses along the photoreceptor axons between brain regions, new pathways in the optic lobes, and spatially segregated projections to central brain regions. Strikingly, photoreceptors in the polarization-sensitive dorsal rim area target fewer cell types, and lack strong connections to the lobula, a neuropil involved in color processing. Our reconstruction identifies shared wiring and modality-specific specializations for color and polarization vision, and provides a comprehensive view of the first steps of the pathways processing color and polarized light inputs.

}, issn = {2050-084X}, doi = {10.7554/eLife.71858}, author = {Kind, Emil and Longden, Kit D and Nern, Aljoscha and Zhao, Arthur and Sancer, Gizem and Flynn, Miriam A and Laughland, Connor W and Gezahegn, Bruck and Ludwig, Henrique Df and Thomson, Alex G and Obrusnik, Tessa and Alarc{\'o}n, Paula G and Dionne, Heather and Bock, Davi D and Rubin, Gerald M and Reiser, Michael B and Wernet, Mathias F} } @article {67713, title = {Synchronous and opponent thermosensors use flexible cross-inhibition to orchestrate thermal homeostasis.}, journal = {Science Advances}, volume = {7}, year = {2021}, month = {2021 Aug 27}, abstract = {

Body temperature homeostasis is essential and reliant upon the integration of outputs from multiple classes of cooling- and warming-responsive cells. The computations that integrate these outputs are not understood. Here, we discover a set of warming cells (WCs) and show that the outputs of these WCs combine with previously described cooling cells (CCs) in a cross-inhibition computation to drive thermal homeostasis in larval WCs and CCs detect temperature changes using overlapping combinations of ionotropic receptors: Ir68a, Ir93a, and Ir25a for WCs and Ir21a, Ir93a, and Ir25a for CCs. WCs mediate avoidance to warming while cross-inhibiting avoidance to cooling, and CCs mediate avoidance to cooling while cross-inhibiting avoidance to warming. Ambient temperature-dependent regulation of the strength of WC- and CC-mediated cross-inhibition keeps larvae near their homeostatic set point. Using neurophysiology, quantitative behavioral analysis, and connectomics, we demonstrate how flexible integration between warming and cooling pathways can orchestrate homeostatic thermoregulation.

}, issn = {2375-2548}, doi = {10.1126/sciadv.abg6707}, author = {Hernandez-Nunez, Luis and Chen, Alicia and Budelli, Gonzalo and Berck, Matthew E and Richter, Vincent and Rist, Anna and Thum, Andreas S and Cardona, Albert and Klein, Mason and Garrity, Paul and Samuel, Aravinthan D T} } @article {67853, title = {Systems Neuroscience of Natural Behaviors in Rodents}, journal = {Journal of Neuroscience}, volume = {41}, year = {2021}, month = {02/2021}, pages = {911{\textendash}919}, abstract = {

Animals evolved in complex environments, producing a wide range of behaviors, including navigation, foraging, prey capture, and conspecific interactions, which vary over timescales ranging from milliseconds to days. Historically, these behaviors have been the focus of study for ecology and ethology, while systems neuroscience has largely focused on short timescale behaviors that can be repeated thousands of times and occur in highly artificial environments. Thanks to recent advances in machine learning, miniaturization, and computation, it is newly possible to study freely moving animals in more natural conditions while applying systems techniques: performing temporally specific perturbations, modeling behavioral strategies, and recording from large numbers of neurons while animals are freely moving. The authors of this review are a group of scientists with deep appreciation for the common aims of systems neuroscience, ecology, and ethology. We believe it is an extremely exciting time to be a neuroscientist, as we have an opportunity to grow as a field, to embrace interdisciplinary, open, collaborative research to provide new insights and allow researchers to link knowledge across disciplines, species, and scales. Here we discuss the origins of ethology, ecology, and systems neuroscience in the context of our own work and highlight how combining approaches across these fields has provided fresh insights into our research. We hope this review facilitates some of these interactions and alliances and helps us all do even better science, together.

}, issn = {0270-6474}, doi = {10.1523/JNEUROSCI.1877-20.2020}, url = {https://www.jneurosci.org/content/41/5/911}, author = {Dennis, Emily Jane and El Hady, Ahmed and Michaiel, Angie and Clemens, Ann and Tervo, Dougal R. Gowan and Voigts, Jakob and Datta, Sandeep Robert} } @article {66001, title = {Systems Neuroscience of Natural Behaviors in Rodents.}, journal = {Journal of Neuroscience}, volume = {41}, year = {2021}, month = {2021 Feb 03}, pages = {911-1}, abstract = {

Animals evolved in complex environments, producing a wide range of behaviors, including navigation, foraging, prey capture, and conspecific interactions, which vary over timescales ranging from milliseconds to days. Historically, these behaviors have been the focus of study for ecology and ethology, while systems neuroscience has largely focused on short timescale behaviors that can be repeated thousands of times and occur in highly artificial environments. Thanks to recent advances in machine learning, miniaturization, and computation, it is newly possible to study freely moving animals in more natural conditions while applying systems techniques: performing temporally specific perturbations, modeling behavioral strategies, and recording from large numbers of neurons while animals are freely moving. The authors of this review are a group of scientists with deep appreciation for the common aims of systems neuroscience, ecology, and ethology. We believe it is an extremely exciting time to be a neuroscientist, as we have an opportunity to grow as a field, to embrace interdisciplinary, open, collaborative research to provide new insights and allow researchers to link knowledge across disciplines, species, and scales. Here we discuss the origins of ethology, ecology, and systems neuroscience in the context of our own work and highlight how combining approaches across these fields has provided fresh insights into our research. We hope this review facilitates some of these interactions and alliances and helps us all do even better science, together.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.1877-20.2020}, author = {Dennis, Emily Jane and El Hady, Ahmed and Michaiel, Angie and Clemens, Ann and Gowan Tervo, Dougal R and Voigts, Jakob and Datta, Sandeep Robert} } @article {66007, title = {Targeted photostimulation uncovers circuit motifs supporting short-term memory.}, journal = {Nature Neuroscience}, volume = {24}, year = {2021}, month = {2021 Jan 25}, pages = {259-265}, abstract = {

Short-term memory is associated with persistent neural activity that is maintained by positive feedback between neurons. To explore the neural circuit motifs that produce memory-related persistent activity, we measured coupling between functionally characterized motor cortex neurons in mice performing a memory-guided response task. Targeted two-photon photostimulation of small (\<10) groups of neurons produced sparse calcium responses in coupled neurons over approximately 100 μm. Neurons with similar task-related selectivity were preferentially coupled. Photostimulation of different groups of neurons modulated activity in different subpopulations of coupled neurons. Responses of stimulated and coupled neurons persisted for seconds, far outlasting the duration of the photostimuli. Photostimuli produced behavioral biases that were predictable based on the selectivity of the perturbed neuronal population, even though photostimulation preceded the behavioral response by seconds. Our results suggest that memory-related neural circuits contain intercalated, recurrently connected modules, which can independently maintain selective persistent activity.

}, issn = {1546-1726}, doi = {10.1038/s41593-020-00776-3}, author = {Daie, Kayvon and Svoboda, Karel and Druckmann, Shaul} } @article {68342, title = {TEMPO: A system to sequentially label and genetically manipulate vertebrate cell lineages}, journal = {bioRxiv}, year = {2021}, month = {10/2021}, abstract = {

During development, regulatory factors appear in a precise order to determine cell fates over time. To investigate complex tissue development, one should not just label cell lineages but further visualize and manipulate cells with temporal control. Current strategies for tracing vertebrate cell lineages lack genetic access to sequentially produced cells. Here we present TEMPO (Temporal Encoding and Manipulation in a Predefined Order), an imaging-readable genetic tool allowing differential labelling and manipulation of consecutive cell generations in vertebrates. TEMPO is based on CRISPR and powered by a cascade of gRNAs that drive orderly activation/inactivation of reporters/effectors. Using TEMPO to visualize zebrafish and mouse neurogenesis, we recapitulated birth-order-dependent neuronal fates. Temporally manipulating cell-cycle regulators in mouse cortex progenitors altered the proportion and distribution of neurons and glia, revealing the effects of temporal gene perturbation on serial cell fates. Thus, TEMPO enables sequential manipulation of molecular factors, crucial to study cell-type specification.One-Sentence Summary Gaining sequential genetic access to vertebrate cell lineages.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2021.10.27.466134}, url = {https://www.biorxiv.org/content/early/2021/10/28/2021.10.27.466134}, author = {Espinosa-Medina, Isabel and Feliciano, Daniel and Belmonte-Mateos, Carla and Garcia-Marques, Jorge and Foster, Benjamin and Miyares, Rosa Linda and Pujades, Cristina and Koyama, Minoru and Lee, Tzumin} } @article {68426, title = {Temporal evolution of single-cell transcriptomes of olfactory projection neurons.}, journal = {Elife}, volume = {10}, year = {2021}, month = {01/2021}, abstract = {

Neurons undergo substantial morphological and functional changes during development to form precise synaptic connections and acquire specific physiological properties. What are the underlying transcriptomic bases? Here, we obtained the single-cell transcriptomes of olfactory projection neurons (PNs) at four developmental stages. We decoded the identity of 21 transcriptomic clusters corresponding to 20 PN types and developed methods to match transcriptomic clusters representing the same PN type across development. We discovered that PN transcriptomes reflect unique biological processes unfolding at each stage-neurite growth and pruning during metamorphosis at an early pupal stage; peaked transcriptomic diversity during olfactory circuit assembly at mid-pupal stages; and neuronal signaling in adults. At early developmental stages, PN types with adjacent birth order share similar transcriptomes. Together, our work reveals principles of cellular diversity during brain development and provides a resource for future studies of neural development in PNs and other neuronal types.

}, keywords = {Animals, Drosophila melanogaster, Neurites, Olfactory Nerve, Single-Cell Analysis, Time Factors, Transcriptome}, issn = {2050-084X}, doi = {10.7554/eLife.63450}, author = {Xie, Qijing and Brbi{\'c}, Maria and Horns, Felix and Kolluru, Sai Saroja and Jones, Robert C and Li, Jiefu and Reddy, Anay R and Xie, Anthony and Kohani, Sayeh and Li, Zhuoran and McLaughlin, Colleen N and Li, Tongchao and Xu, Chuanyun and Vacek, David and Luginbuhl, David J and Leskovec, Jure and Quake, Stephen R and Luo, Liqun and Li, Hongjie} } @article {67242, title = {Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model.}, journal = {bioRxiv}, year = {2021}, month = {2021 Apr 28}, abstract = {

Digital light microscopy provides powerful tools for quantitatively probing the real-time dynamics of subcellular structures. While the power of modern microscopy techniques is undeniable, rigorous record-keeping and quality control are required to ensure that imaging data may be properly interpreted\ (quality),\ reproduced\ (reproducibility),\ and used to extract reliable information and scientific knowledge which can be shared for further analysis (value). Keeping notes on microscopy experiments and quality control procedures ought to be straightforward, as the microscope is a machine whose components are defined and the performance measurable. Nevertheless, to this date, no universally adopted community-driven specifications exist that delineate the required information about the microscope hardware and acquisition settings (i.e., microscopy {\textquotedblleft}data provenance{\textquotedblright} metadata) and the minimally accepted calibration metrics (i.e., microscopy quality control metadata) that should be automatically recorded by both commercial microscope manufacturers and customized microscope developers. In the absence of agreed guidelines, it is inherently difficult for scientists to create comprehensive records of imaging experiments and ensure the quality of resulting image data or for manufacturers to incorporate standardized reporting and performance metrics. To add to the confusion, microscopy experiments vary greatly in aim and complexity, ranging from purely descriptive work to complex, quantitative and even sub-resolution studies that require more detailed reporting and quality control measures.

}, doi = {10.1101/2021.04.25.441198v1}, url = {https://www.biorxiv.org/content/10.1101/2021.04.25.441198v1}, author = {Mathias Hammer and Maximiliaan Huisman and Alex Rigano and Ulrike Boehm and James J. Chambers and Nathalie Gaudreault and Alison J. North and Jaime A. Pimentel and Damir Sudar and Peter Bajcsy and Claire M. Brown and Alexander D. Corbett and Orestis Faklaris and Judith Lacoste and Alex Laude and Glyn Nelson and Roland Nitschke and Farzin Farzam and Carlas S. Smith and David Grunwald and Caterina Strambio-De-Castillia} } @article {67812, title = {Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model.}, journal = {Nature Methods}, volume = {18}, year = {2021}, month = {2021 Dec 03}, pages = {1427-1440}, issn = {1548-7105}, doi = {10.1038/s41592-021-01327-9}, author = {Hammer, Mathias and Huisman, Maximiliaan and Rigano, Alessandro and Boehm, Ulrike and Chambers, James J and Gaudreault, Nathalie and North, Alison J and Pimentel, Jaime A and Sudar, Damir and Bajcsy, Peter and Brown, Claire M and Corbett, Alexander D and Faklaris, Orestis and Lacoste, Judith and Laude, Alex and Nelson, Glyn and Nitschke, Roland and Farzam, Farzin and Smith, Carlas S and Grunwald, David and Strambio-De-Castillia, Caterina} } @article {65998, title = {A transcriptomic taxonomy of circadian neurons around the clock.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Jan 13}, abstract = {

Many different functions are regulated by circadian rhythms, including those orchestrated by discrete clock neurons within animal brains. To comprehensively characterize and assign cell identity to the 75 pairs of circadian neurons, we optimized a single cell RNA sequencing method and assayed clock neuron gene expression at different times of day. The data identify at least 17 clock neuron categories with striking spatial regulation of gene expression. Transcription factor regulation is prominent and likely contributes to the robust circadian oscillation of many transcripts, including those that encode cell-surface proteins previously shown to be important for cell recognition and synapse formation during development. The many other clock-regulated genes also constitute an important resource for future mechanistic and functional studies between clock neurons and/or for temporal signaling to circuits elsewhere in the fly brain.

}, issn = {2050-084X}, doi = {10.7554/eLife.63056}, author = {Ma, Dingbang and Przybylski, Dariusz and Abruzzi, Katharine C and Schlichting, Matthias and Li, Qunlong and Long, Xi and Rosbash, Michael} } @article {67845, title = {Unraveling Single-Particle Trajectories Confined in Tubular Networks}, journal = {arXiv}, year = {2021}, month = {2021 Dec 11}, abstract = {

The analysis of single particle trajectories plays an important role in elucidating dynamics within complex environments such as those found in living cells. However, the characterization of intracellular particle motion is often confounded by confinement of the particles within non-trivial subcellular geometries. Here, we focus specifically on the case of particles undergoing Brownian motion within a tubular network, as found in some cellular organelles. An unraveling algorithm is developed to uncouple particle motion from the confining network structure, allowing for an accurate extraction of the diffusion coefficient, as well as differentiating between Brownian and fractional Brownian dynamics. We validate the algorithm with simulated trajectories and then highlight its application to an example system: analyzing the motion of membrane proteins confined in the tubules of the peripheral endoplasmic reticulum in mammalian cells. We show that these proteins undergo diffusive motion with a well-characterized diffusivity. Our algorithm provides a generally applicable approach for disentangling geometric morphology and particle dynamics in networked architectures.

}, url = {https://arxiv.org/abs/2112.05884}, author = {Yunhao Sun and Zexi Yu and Christopher Obara and Keshav Mittal and Jennifer Lippincott-Schwarz and Elena F Koslover} } @article {67310, title = {Unveiling the sensory and interneuronal pathways of the neuroendocrine connectome in Drosophila.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Jun 04}, abstract = {

Neuroendocrine systems in animals maintain organismal homeostasis and regulate stress response. Although a great deal of work has been done on the neuropeptides and hormones that are released and act on target organs in the periphery, the synaptic inputs onto these neuroendocrine outputs in the brain are less well understood. Here, we use the transmission electron microscopy reconstruction of a whole central nervous system in the larva to elucidate the sensory pathways and the interneurons that provide synaptic input to the neurosecretory cells projecting to the endocrine organs. Predicted by network modeling, we also identify a new carbon dioxide-responsive network that acts on a specific set of neurosecretory cells and that includes those expressing corazonin (Crz) and diuretic hormone 44 (Dh44) neuropeptides. Our analysis reveals a neuronal network architecture for combinatorial action based on sensory and interneuronal pathways that converge onto distinct combinations of neuroendocrine outputs.

}, issn = {2050-084X}, doi = {10.7554/eLife.65745}, author = {H{\"u}ckesfeld, Sebastian and Schlegel, Philipp and Miroschnikow, Anton and Schoofs, Andreas and Zinke, Ingo and Haubrich, Andr{\'e} N and Schneider-Mizell, Casey M and Truman, James W and Fetter, Richard D and Cardona, Albert and Pankratz, Michael J} } @article {68474, title = {Ventral stress fibers induce plasma membrane deformation in human fibroblasts.}, journal = {Mol Biol Cell}, volume = {32}, year = {2021}, month = {08/2021}, pages = {1707-1723}, abstract = {

Interactions between the actin cytoskeleton and the plasma membrane are important in many eukaryotic cellular processes. During these processes, actin structures deform the cell membrane outward by applying forces parallel to the fiber{\textquoteright}s major axis (as in migration) or they deform the membrane inward by applying forces perpendicular to the fiber{\textquoteright}s major axis (as in the contractile ring during cytokinesis). Here we describe a novel actin-membrane interaction in human dermal myofibroblasts. When labeled with a cytosolic fluorophore, the myofibroblasts displayed prominent fluorescent structures on the ventral side of the cell. These structures are present in the cell membrane and colocalize with ventral actin stress fibers, suggesting that the stress fibers bend the membrane to form a "cytosolic pocket" that the fluorophores diffuse into, creating the observed structures. The existence of this pocket was confirmed by transmission electron microscopy. While dissolving the stress fibers, inhibiting fiber protein binding, or inhibiting myosin II binding of actin removed the observed pockets, modulating cellular contractility did not remove them. Taken together, our results illustrate a novel actin-membrane bending topology where the membrane is deformed outward rather than being pinched inward, resembling the topological inverse of the contractile ring found in cytokinesis.

}, keywords = {Actins, Cell Membrane, Cells, Cultured, Cytochalasin D, Cytosol, Fibroblasts, Fluorescent Dyes, Humans, Infant, Myosin Type II, Ouabain, Skin, Stress Fibers, Transforming Growth Factor beta1}, issn = {1939-4586}, doi = {10.1091/mbc.E21-03-0096}, author = {Ghilardi, Samuel J and Aronson, Mark S and Sgro, Allyson E} } @article {67833, title = {Versatile On-Demand Fluorescent Labeling of Fusion Proteins Using Fluorescence-Activating and Absorption-Shifting Tag (FAST).}, journal = {Methods Mol Biol}, volume = {2350}, year = {2021}, month = {2021}, pages = {253-265}, abstract = {

Observing the localization, the concentration, and the distribution of proteins in cells or organisms is essential to understand theirs functions. General and versatile methods allowing multiplexed imaging of proteins under a large variety of experimental conditions are thus essential for deciphering the inner workings of cells and organisms. Here, we present a general method based on the non-covalent labeling of a small protein tag, named FAST (fluorescence-activating and absorption-shifting tag), with various fluorogenic ligands that light up upon labeling, which makes the simple, robust, and versatile on-demand labeling of fusion proteins in a wide range of experimental systems possible.

}, keywords = {Animals, Cell Line, Flow Cytometry, Fluorescent Dyes, Humans, Microscopy, Fluorescence, Molecular Structure, Recombinant Fusion Proteins, Staining and Labeling, Zebrafish}, issn = {1940-6029}, doi = {10.1007/978-1-0716-1593-5_16}, author = {Gautier, Arnaud and Jullien, Ludovic and Li, Chenge and Plamont, Marie-Aude and Tebo, Alison G and Thauvin, Marion and Volovitch, Michel and Vriz, Sophie} } @article {67736, title = {Visualizing the Invisible: Advanced Optical Microscopy as a Tool to Measure Biomechanical Forces.}, journal = {Frontiers in Cell and Developmental Biology}, volume = {9}, year = {2021}, month = {2021 Sep 06}, pages = {706126}, abstract = {

The importance of mechanical force in biology is evident across diverse length scales, ranging from tissue morphogenesis during embryo development to mechanotransduction across single adhesion proteins at the cell surface. Consequently, many force measurement techniques rely on optical microscopy to measure forces being applied by cells on their environment, to visualize specimen deformations due to external forces, or even to directly apply a physical perturbation to the sample via photoablation or optogenetic tools. Recent developments in advanced microscopy offer improved approaches to enhance spatiotemporal resolution, imaging depth, and sample viability. These advances can be coupled with already existing force measurement methods to improve sensitivity, duration and speed, amongst other parameters. However, gaining access to advanced microscopy instrumentation and the expertise necessary to extract meaningful insights from these techniques is an unavoidable hurdle. In this Live Cell Imaging special issue Review, we survey common microscopy-based force measurement techniques and examine how they can be bolstered by emerging microscopy methods. We further explore challenges related to the accompanying data analysis in biomechanical studies and discuss the various resources available to tackle the global issue of technology dissemination, an important avenue for biologists to gain access to pre-commercial instruments that can be leveraged for biomechanical studies.

}, issn = {2296-634X}, doi = {10.3389/fcell.2021.706126}, author = {Hobson, Chad M and Aaron, Jesse S and Heddleston, John M and Chew, Teng-Leong} } @article {67230, title = {VolPy: Automated and scalable analysis pipelines for voltage imaging datasets.}, journal = {PLoS Computational Biology}, volume = {17}, year = {2021}, month = {2021 Apr 14}, pages = {e1008806}, abstract = {

Voltage imaging enables monitoring neural activity at sub-millisecond and sub-cellular scale, unlocking the study of subthreshold activity, synchrony, and network dynamics with unprecedented spatio-temporal resolution. However, high data rates (\>800MB/s) and low signal-to-noise ratios create bottlenecks for analyzing such datasets. Here we present VolPy, an automated and scalable pipeline to pre-process voltage imaging datasets. VolPy features motion correction, memory mapping, automated segmentation, denoising and spike extraction, all built on a highly parallelizable, modular, and extensible framework optimized for memory and speed. To aid automated segmentation, we introduce a corpus of 24 manually annotated datasets from different preparations, brain areas and voltage indicators. We benchmark VolPy against ground truth segmentation, simulations and electrophysiology recordings, and we compare its performance with existing algorithms in detecting spikes. Our results indicate that VolPy{\textquoteright}s performance in spike extraction and scalability are state-of-the-art.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1008806}, author = {Cai, Changjia and Friedrich, Johannes and Singh, Amrita and Eybposh, M Hossein and Pnevmatikakis, Eftychios A and Podgorski, Kaspar and Giovannucci, Andrea} } @article {67315, title = {Which image-based phenotypes are most promising for using AI to understand cellular functions and why?}, journal = {Cell Systems}, volume = {12}, year = {2021}, month = {2021 May 19}, pages = {384-387}, issn = {2405-4720}, doi = {10.1016/j.cels.2021.04.012}, author = {Lundberg, Emma and Funke, Jan and Uhlmann, Virginie and Gerlich, Daniel and Walter, Thomas and Carpenter, Ann and Coehlo, Luis Pedro} } @article {67750, title = {Whole-cell organelle segmentation in volume electron microscopy.}, journal = {Nature}, volume = {599}, year = {2021}, month = {2021 Nov 01}, pages = {141-46}, abstract = {

Cells contain hundreds of organelles and macromolecular assemblies. Obtaining a complete understanding of their intricate organization requires the nanometre-level, three-dimensional reconstruction of whole cells, which is only feasible with robust and scalable automatic methods. Here, to support the development of such methods, we annotated up to 35 different cellular organelle classes-ranging from endoplasmic reticulum to microtubules to ribosomes-in diverse sample volumes from multiple cell types imaged at a near-isotropic resolution of 4 nm per voxel with focused ion beam scanning electron microscopy (FIB-SEM). We trained deep learning architectures to segment these structures in 4 nm and 8 nm per voxel FIB-SEM volumes, validated their performance and showed that automatic reconstructions can be used to directly quantify previously inaccessible metrics including spatial interactions between cellular components. We also show that such reconstructions can be used to automatically register light and electron microscopy images for correlative studies. We have created an open data and open-source web repository, {\textquoteright}OpenOrganelle{\textquoteright}, to share the data, computer code and trained models, which will enable scientists everywhere to query and further improve automatic reconstruction of these datasets.

}, issn = {1476-4687}, doi = {10.1038/s41586-021-03977-3}, author = {Heinrich, Larissa and Bennett, Davis and Ackerman, David and Park, Woohyun and Bogovic, John and Eckstein, Nils and Petruncio, Alyson and Clements, Jody and Pang, Song and Xu, C Shan and Funke, Jan and Korff, Wyatt and Hess, Harald F and Lippincott-Schwartz, Jennifer and Saalfeld, Stephan and Weigel, Aubrey V} } @article {67646, title = {YAP1 nuclear efflux and transcriptional reprograming follow membrane diminution upon VSV-G-induced cell fusion.}, journal = {Nature Communications}, volume = {12}, year = {2021}, month = {2021 Jul 23}, pages = {4502}, abstract = {

Cells in many tissues, such as bone, muscle, and placenta, fuse into syncytia to acquire new functions and transcriptional programs. While it is known that fused cells are specialized, it is unclear whether cell-fusion itself contributes to programmatic-changes that generate the new cellular state. Here, we address this by employing a fusogen-mediated, cell-fusion system to create syncytia from undifferentiated cells.\ RNA-Seq analysis reveals VSV-G-induced cell fusion precedes transcriptional changes. To gain mechanistic insights, we measure the plasma membrane surface area after cell-fusion and observe it diminishes through increases in endocytosis. Consequently, glucose transporters internalize, and cytoplasmic glucose and ATP transiently decrease. This reduced energetic state activates AMPK, which inhibits YAP1, causing transcriptional-reprogramming and cell-cycle arrest. Impairing either endocytosis or AMPK activity prevents YAP1 inhibition and cell-cycle arrest after fusion. Together, these data demonstrate plasma membrane diminishment upon cell-fusion causes transient nutrient stress that may promote transcriptional-reprogramming independent from extrinsic cues.

}, issn = {2041-1723}, doi = {10.1038/s41467-021-24708-2}, author = {Feliciano, Daniel and Ott, Carolyn M and Isabel Espinosa Medina and Weigel, Aubrey V and Benedetti, Lorena and Milano, Kristin M and Tang, Zhonghua and Lee, Tzumin and Kliman, Harvey J and Guller, Seth M and Lippincott-Schwartz, Jennifer} } @article {68752, title = {ZCCHC8 is required for the degradation of pervasive transcripts originating from multiple genomic regulatory features}, journal = {bioRxiv}, year = {2021}, month = {02/2021}, abstract = {

The vast majority of mammalian genomes are transcribed as non-coding RNA in what is referred to as {\textquotedblleft}pervasive transcription.{\textquotedblright} Recent studies have uncovered various families of non-coding RNA transcribed upstream of transcription start sites. In particular, highly unstable promoter upstream transcripts known as PROMPTs have been shown to be targeted for exosomal degradation by the nuclear exosome targeting complex (NEXT) consisting of the RNA helicase MTR4, the zinc-knuckle scaffold ZCCHC8, and the RNA binding protein RBM7. Here, we report that in addition to its known RNA substrates, ZCCHC8 is required for the targeted degradation of pervasive transcripts produced at CTCF binding sites, open chromatin regions, promoters, promoter flanking regions, and transcription factor binding sites. Additionally, we report that a significant number of RIKEN cDNAs and predicted genes display the hallmarks of PROMPTs and are also substrates for ZCCHC8 and/or NEXT complex regulation suggesting these are unlikely to be functional genes. Our results suggest that ZCCHC8 and/or the NEXT complex may play a larger role in the global regulation of pervasive transcription than previously reported.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2021.01.29.428898}, url = {https://www.biorxiv.org/content/early/2021/02/06/2021.01.29.428898}, author = {Joshua W. Collins and Daniel Martin and Genomics and Computational Biology Core and Shaohe Wang and Kenneth M. Yamada} } @article {65368, title = {3D ATAC-PALM: super-resolution imaging of the accessible genome.}, journal = {Nature Methods}, volume = {17}, year = {2020}, month = {2020 Apr 01}, pages = {430-6}, abstract = {

To image the accessible genome at nanometer scale in situ, we developed three-dimensional assay for transposase-accessible chromatin-photoactivated localization microscopy (3D ATAC-PALM) that integrates an assay for transposase-accessible chromatin with visualization, PALM super-resolution imaging and lattice light-sheet microscopy. Multiplexed with oligopaint DNA{\textendash}fluorescence in situ hybridization (FISH), RNA{\textendash}FISH and protein fluorescence, 3D ATAC-PALM connected microscopy and genomic data, revealing spatially segregated accessible chromatin domains (ACDs) that enclose active chromatin and transcribed genes. Using these methods to analyze genetically perturbed cells, we demonstrated that genome architectural protein CTCF prevents excessive clustering of accessible chromatin and decompacts ACDs. These results highlight 3D ATAC-PALM as a useful tool to probe the structure and organizing mechanism of the genome.

}, issn = {1548-7091}, doi = {10.1038/s41592-020-0775-2}, url = {http://www.nature.com/articles/s41592-020-0775-2}, author = {Xie, Liangqi and Dong, Peng and Chen, Xingqi and Hsieh, Tsung-Han S. and Banala, Sambashiva and De Marzio, Margherita and English, Brian P. and Qi, Yifeng and Jung, Seol Kyoung and Kieffer-Kwon, Kyong-Rim and Legant, Wesley R. and Hansen, Anders S. and Schulmann, Anton and Casellas, Rafael and Zhang, Bin and Betzig, Eric and Lavis, Luke D. and Chang, Howard Y. and Tjian, Robert and Liu, Zhe} } @article {68841, title = {Accelerated EM Connectome Reconstruction using 3D Visualization and Segmentation Graphs}, journal = {bioRxiv}, year = {2020}, month = {2020 Jan 17}, abstract = {

Recent advances in automatic image segmentation and synapse prediction in electron microscopy (EM) datasets of the brain enable more efficient reconstruction of neural connectivity. In these datasets, a single neuron can span thousands of images containing complex tree-like arbors with thousands of synapses. While image segmentation algorithms excel within narrow fields of views, the algorithms sometimes struggle to correctly segment large neurons, which require large context given their size and complexity. Conversely, humans are comparatively good at reasoning with large objects. In this paper, we introduce several semi-automated strategies that combine 3D visualization and machine guidance to accelerate connectome reconstruction. In particular, we introduce a strategy to quickly correct a segmentation through merging and\ cleaving, or splitting a segment along supervoxel boundaries, with both operations driven by affinity scores in the underlying segmentation. We deploy these algorithms as streamlined workflows in a tool called\ Neu3\ and demonstrate superior performance compared to prior work, thus enabling efficient reconstruction of much larger datasets. The insights into proofreading from our work clarify the trade-offs to consider when tuning the parameters of image segmentation algorithms.

}, doi = {10.1101/2020.01.17.909572}, url = {https://doi.org/10.1101/2020.01.17.909572}, author = {Philip M. Hubbard and Stuart Berg and Ting Zhao and Donald J. Olbris and Lowell Umayam and Jeremy Maitin-Shepard and Michal Januszewski and William T. Katz and Erika R. Neace and Stephen M. Plaza} } @article {65276, title = {Accurate measurement of fast endocytic recycling kinetics in real time.}, journal = {Journal of Cell Science}, volume = {133}, year = {2020}, month = {2020 Jan 22}, abstract = {

The fast turnover of membrane components through endocytosis and recycling allows precise control of the composition of the plasma membrane. Endocytic recycling can be rapid with some molecules returning to the plasma membrane with a \<5 minutes. Existing methods to study these trafficking pathways utilize chemical, radioactive, or fluorescent labeling of cell surface receptors in pulse-chase experiments, which require tedious washing steps and manual collection of samples. Here, we introduce a live-cell endocytic recycling assay, based on a newly designed cell-impermeable, fluorogenic ligand for HaloTag: {\textquoteright}Janelia Fluor 635i{\textquoteright} (JFi; i=impermeant) which allows real-time detection of membrane receptor recycling at steady state. We used this method to study the effect of iron depletion on transferrin receptor (TfR) recycling using the chelator desferrioxamine. We found this perturbation significantly increases the TfR recycling rate. The high temporal resolution and simplicity of this assay provides a clear advantage over extant methods and makes it ideal for large scale cellular imaging studies. This assay can be adapted to examine other cellular kinetic parameters such as protein turnover and biosynthetic trafficking.

}, issn = {1477-9137}, doi = {10.1242/jcs.231225}, author = {Jonker, Caspar T H and Deo, Claire and Zager, Patrick J and Tkachuk, Ariana N and Weinstein, Alan M and Rodriguez-Boulan, Enrique and Lavis, Luke D and Schreiner, Ryan} } @article {65678, title = {Actin chromobody imaging reveals sub-organellar actin dynamics.}, journal = {Nature Methods}, volume = {17}, year = {2020}, month = {2020 Sep 01}, pages = {917-21}, abstract = {

The actin cytoskeleton plays multiple critical roles in cells, from cell migration to organelle dynamics. The small and transient actin structures regulating organelle dynamics are challenging to detect with fluorescence microscopy, making it difficult to determine whether actin filaments are directly associated with specific membranes. To address these limitations, we developed fluorescent-protein-tagged actin nanobodies, termed {\textquoteright}actin chromobodies{\textquoteright} (ACs), targeted to organelle membranes to enable high-resolution imaging of sub-organellar actin dynamics.

}, issn = {1548-7105}, doi = {10.1038/s41592-020-0926-5}, author = {Schiavon, Cara R and Zhang, Tong and Zhao, Bing and Moore, Andrew S and Wales, Pauline and Andrade, Leonardo R and Wu, Melissa and Sung, Tsung-Chang and Dayn, Yelena and Feng, Jasmine W and Quintero, Omar A and Shadel, Gerald S and Grosse, Robert and Manor, Uri} } @article {65313, title = {The anatomy and physiology of claustrum-cortex interactions.}, journal = {Annual Review of Neuroscience}, volume = {43}, year = {2020}, month = {2020 Jul 1}, pages = {231-47}, abstract = {

The claustrum is one of the most widely connected regions of the forebrain, yet its function has remained obscure, largely due to the experimentally challenging nature of targeting this small, thin, and elongated brain area. However, recent advances in molecular techniques have enabled the anatomy and physiology of the claustrum to be studied with the spatiotemporal and cell type-specific precision required to eventually converge on what this area does. Here we review early anatomical and electrophysiological results from cats and primates, as well as recent work in the rodent, identifying the connectivity, cell types, and physiological circuit mechanisms underlying the communication between the claustrum and the cortex. The emerging picture is one in which the rodent claustrum is closely tied to frontal/limbic regions and plays a role in processes, such as attention, that are associated with these areas. Expected final online publication date for the , Volume 43 is July 8, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-092519-101637}, author = {Jackson, Jesse and Smith, Jared B and Lee, Albert K} } @article {65615, title = {Arousal modulates retinal output.}, journal = {Neuron}, volume = {107}, year = {2020}, month = {2020 Aug 01}, pages = {487}, abstract = {

At various stages of the visual system, visual responses are modulated by arousal. Here, we find that in mice this modulation operates as early as in the first synapse from the retina and even in retinal axons. To measure retinal activity in the awake, intact brain, we imaged the synaptic boutons of retinal axons in the superior colliculus. Their activity depended not only on vision but also on running speed and pupil size, regardless of retinal illumination. Arousal typically reduced their visual responses and selectivity for direction and orientation. Recordings from retinal axons in the optic tract revealed that arousal modulates the firing of some retinal ganglion cells. Arousal had similar effects postsynaptically in colliculus neurons, independent of activity in the other main source of visual inputs to the colliculus, the primary visual cortex. These results indicate that arousal modulates activity at every stage of the mouse visual system.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2020.04.026}, author = {Schr{\"o}der, Sylvia and Steinmetz, Nicholas A and Krumin, Michael and Pachitariu, Marius and Rizzi, Matteo and Lagnado, Leon and Harris, Kenneth D and Carandini, Matteo} } @article {69335, title = {An arousal-gated visual circuit controls pursuit during Drosophila courtship}, journal = {bioRxiv}, year = {2020}, month = {2020 Aug 31}, abstract = {

Long-lasting internal states, like hunger, aggression, and sexual arousal, pattern ongoing behavior by defining how the sensory world is translated to specific actions that subserve the needs of an animal. Yet how enduring internal states shape sensory processing or behavior has remained unclear. In Drosophila, male flies will perform a lengthy and elaborate courtship ritual, triggered by activation of sexually-dimorphic P1 neurons, in which they faithfully follow and sing to a female. Here, by recording from males as they actively court a fictive {\textquoteleft}female{\textquoteright} in a virtual environment, we gain insight into how the salience of female visual cues is transformed by a male{\textquoteright}s internal arousal state to give rise to persistent courtship pursuit. We reveal that the gain of LCt0a visual projection neurons is strongly increased during courtship, enhancing their sensitivity to moving targets. A simple network model based on the LCt0a circuit accurately predicts a male{\textquoteright}s tracking of a female over hundreds of seconds, underscoring that LCt0a visual signals, once released by P1-mediated arousal, become coupled to motor pathways to deterministically control his visual pursuit. Furthermore, we find that P1 neuron activity correlates with fluctuations in the intensity of a male{\textquoteright}s pursuit, and that their acute activation is sufficient to boost the gain of the LCt0 pathways. Together, these results reveal how alterations in a male{\textquoteright}s internal arousal state can dynamically modulate the propagation of visual signals through a high-fidelity visuomotor circuit to guide his moment-to-moment performance of courtship.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2020.08.31.275883}, url = {https://www.biorxiv.org/content/early/2020/08/31/2020.08.31.275883}, author = {Tom Hindmarsh Sten and Rufei Li and Adriane Otopalik and Vanessa Ruta} } @article {65857, title = {The art of lineage tracing: from worm to human.}, journal = {Progress in Neurobiology}, year = {2020}, month = {2020 Nov 26}, pages = {101966}, abstract = {

Reconstructing the genealogy of every cell that makes up an organism remains a long-standing challenge in developmental biology. Besides its relevance for understanding the mechanisms underlying normal and pathological development, resolving the lineage origin of cell types will be crucial to create these types on-demand. Multiple strategies have been deployed towards the problem of lineage tracing, ranging from direct observation to sophisticated genetic approaches. Here we discuss the achievements and limitations of past and current technology. Finally, we speculate about the future of lineage tracing and how to reach the next milestones in the field.

}, issn = {1873-5118}, doi = {10.1016/j.pneurobio.2020.101966}, author = {Garcia-Marques, Jorge and Isabel Espinosa Medina and Lee, Tzumin} } @article {65240, title = {Aurora B functions at the apical surface after specialized cytokinesis during morphogenesis in C. elegans.}, journal = {Development}, volume = {147}, year = {2020}, month = {2020 Jan}, pages = {1-16}, abstract = {

While cytokinesis has been intensely studied, the way it is executed during development is not well understood, despite a long-standing appreciation that various aspects of cytokinesis vary across cell and tissue types. To address this, we investigated cytokinesis during the invariant embryonic divisions and found several reproducibly altered parameters at different stages. During early divisions, furrow ingression asymmetry and midbody inheritance is consistent, suggesting specific regulation of these events. During morphogenesis, we found several unexpected alterations to cytokinesis including apical midbody migration in polarizing epithelial cells of the gut, pharynx and sensory neurons. Aurora B kinase, which is essential for several aspects of cytokinesis, remains apically localized in each of these tissues after internalization of midbody ring components. Aurora B inactivation disrupts cytokinesis and causes defects in apical structures, even if inactivated post-mitotically. Therefore, cytokinesis is implemented in a specialized way during epithelial polarization and Aurora B has a new role in the formation of the apical surface.

}, issn = {1477-9129}, doi = {10.1242/dev.181099}, author = {Bai, Xiaofei and Melesse, Michael and Sorensen Turpin, Christopher G and Sloan, Dillon and Chen, Chin-Yi and Wang, Wen-Cheng and Lee, Po-Yi and Simmons, James R and Nebenfuehr, Benjamin and Mitchell, Diana and Klebanow, Lindsey R and Mattson, Nicholas and Betzig, Eric and Chen, Bi-Chang and Cheerambathur, Dhanya and Bembenek, Joshua N} } @article {65389, title = {Basal ganglia circuits for action specification.}, journal = {Annual Review Neuroscience}, volume = {43}, year = {2020}, month = {2020 Jul 8}, pages = {485-507}, abstract = {

Behavior is readily classified into patterns of movements with inferred common goals-actions. Goals may be discrete; movements are continuous. Through the careful study of isolated movements in laboratory settings, or via introspection, it has become clear that animals can exhibit exquisite graded specification to their movements. Moreover, graded control can be as fundamental to success as the selection of which action to perform under many naturalistic scenarios: a predator adjusting its speed to intercept moving prey, or a tool-user exerting the perfect amount of force to complete a delicate task. The basal ganglia are a collection of nuclei in vertebrates that extend from the forebrain (telencephalon) to the midbrain (mesencephalon), constituting a major descending extrapyramidal pathway for control over midbrain and brainstem premotor structures. Here we discuss how this pathway contributes to the continuous specification of movements that endows our voluntary actions with vigor and grace. Expected final online publication date for the , Volume 43 is July 8, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-070918-050452}, author = {Park, Junchol and Coddington, Luke T and Dudman, Joshua T} } @article {68753, title = {Basement Membrane Regulates Fibronectin Organization Using Sliding Focal Adhesions Driven by a Contractile Winch}, journal = {Developmental Cell}, volume = {52}, year = {2020}, month = {03/2020}, pages = {631-646.e4}, abstract = {

Summary We have discovered that basement membrane and its major components can induce rapid, strikingly robust fibronectin organization. In this new matrix assembly mechanism, α5β1 integrin-based focal adhesions slide actively on the underlying matrix toward the ventral cell center through the dynamic shortening of myosin IIA-associated actin stress fibers to drive rapid fibronectin fibrillogenesis distal to the adhesion. This mechanism contrasts with classical fibronectin assembly based on stable or fixed-position focal adhesions containing αVβ3 integrins plus α5β1 integrin translocation into proximal fibrillar adhesions. On basement membrane components, these sliding focal adhesions contain standard focal adhesion constituents but completely lack classical αVβ3 integrins. Instead, peripheral α3β1 or α2β1 adhesions mediate initial cell attachment but over time are switched to α5β1 integrin-based sliding focal adhesions to assemble fibronectin matrix. This basement-membrane-triggered mechanism produces rapid fibronectin fibrillogenesis, providing a mechanistic explanation for the well-known widespread accumulation of fibronectin at many organ basement membranes.

}, keywords = {basement membrane, Extracellular Matrix, fibrillogenesis, fibronectin, focal adhesion, integrin, matrix assembly}, issn = {1534-5807}, doi = {https://doi.org/10.1016/j.devcel.2020.01.007}, url = {https://www.sciencedirect.com/science/article/pii/S1534580720300083}, author = {Jiaoyang Lu and Andrew D. Doyle and Yoshinari Shinsato and Shaohe Wang and Molly A. Bodendorfer and Minhua Zheng and Kenneth M. Yamada} } @article {65311, title = {Behavioral features of motivated response to alcohol in Drosophila.}, journal = {bioRxiv}, year = {2020}, month = {2020 Feb 17}, abstract = {

Animals avoid predators and find the best food and mates by learning from the consequences of their behavior. However, reinforcers are not always uniquely appetitive or aversive but can have complex properties. Most intoxicating substances fall within this category; provoking aversive sensory and physiological reactions while simultaneously inducing overwhelming appetitive properties. Here we describe the subtle behavioral features associated with continued seeking for alcohol despite aversive consequences. We developed an automated runway apparatus to measure how Drosophila respond to consecutive exposures of a volatilized substance. Behavior within this Behavioral Expression of Ethanol Reinforcement Runway (BEER Run) demonstrated a defined shift from aversive to appetitive responses to volatilized ethanol. Behavioral metrics attained by combining computer vision and machine learning methods, reveal that a subset of 9 classified behaviors and component behavioral features associate with this shift. We propose this combination of 9 be

}, author = {Catalano, Jamie L. and Mei, Nicholas and Azanchi, Reza and Song, Sophia and Blackwater, Tyler and Heberlein, Ulrike and Kaun, Karla R.} } @article {65798, title = {Behavioral state coding by molecularly defined paraventricular hypothalamic cell type ensembles.}, journal = {Science}, volume = {370}, year = {2020}, month = {2020 Oct 16}, abstract = {

Brains encode behaviors using neurons amenable to systematic classification by gene expression. The contribution of molecular identity to neural coding is not understood because of the challenges involved with measuring neural dynamics and molecular information from the same cells. We developed CaRMA (calcium and RNA multiplexed activity) imaging based on recording in vivo single-neuron calcium dynamics followed by gene expression analysis. We simultaneously monitored activity in hundreds of neurons in mouse paraventricular hypothalamus (PVH). Combinations of cell-type marker genes had predictive power for neuronal responses across 11 behavioral states. The PVH uses combinatorial assemblies of molecularly defined neuron populations for grouped-ensemble coding of survival behaviors. The neuropeptide receptor neuropeptide Y receptor type 1 (Npy1r) amalgamated multiple cell types with similar responses. Our results show that molecularly defined neurons are important processing units for brain function.

}, issn = {1095-9203}, doi = {10.1126/science.abb2494}, author = {Xu, Shengjin and Yang, Hui and Menon, Vilas and Lemire, Andrew L and Wang, Lihua and Henry, Fredrick E and Turaga, Srinivas C and Sternson, Scott M} } @article {65797, title = {Brain-wide, scale-wide physiology underlying behavioral flexibility in zebrafish.}, journal = {Current Opinion in Neurobiology}, volume = {64}, year = {2020}, month = {2020 Oct 19}, pages = {151-160}, abstract = {

The brain is tasked with choosing actions that maximize an animal{\textquoteright}s chances of survival and reproduction. These choices must be flexible and informed by the current state of the environment, the needs of the body, and the outcomes of past actions. This information is physiologically encoded and processed across different brain regions on a wide range of spatial scales, from molecules in single synapses to networks of brain areas. Uncovering these spatially distributed neural interactions underlying behavior requires investigations that span a similar range of spatial scales. Larval zebrafish, given their small size, transparency, and ease of genetic access, are a good model organism for such investigations, allowing the use of modern microscopy, molecular biology, and computational techniques. These approaches are yielding new insights into the mechanistic basis of behavioral states, which we review here and compare to related studies in mammalian species.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2020.08.013}, author = {Mu, Yu and Narayan, Sujatha and Mensh, Brett D and Ahrens, Misha B} } @article {65650, title = {Bright and high-performance genetically encoded Ca indicator based on mNeonGreen fluorescent protein.}, journal = {ACS Sensors}, year = {2020}, month = {2020 Jul 08}, abstract = {

Genetically encodable calcium ion (Ca) indicators (GECIs) based on green fluorescent proteins (GFP) are powerful tools for imaging of cell signaling and neural activity in model organisms. Following almost 2 decades of steady improvements in the GFP-based GCaMP series of GECIs, the performance of the most recent generation (i.e., jGCaMP7) may have reached its practical limit due to the inherent properties of GFP. In an effort to sustain the steady progression toward ever-improved GECIs, we undertook the development of a new GECI based on the bright monomeric GFP, mNeonGreen (mNG). The resulting indicator, mNG-GECO1, is 60\% brighter than GCaMP6s in vitro and provides comparable performance as demonstrated by imaging Ca dynamics in cultured cells, primary neurons, and in vivo in larval zebrafish. These results suggest that mNG-GECO1 is a promising next-generation GECI that could inherit the mantle of GCaMP and allow the steady improvement of GECIs to continue for generations to come.

}, issn = {2379-3694}, doi = {10.1021/acssensors.0c00279}, author = {Zarowny, Landon and Abhi Aggarwal and Rutten, Virginia M S and Kolb, Ilya and Patel, Ronak and Huang, Hsin-Yi and Chang, Yu-Fen and Phan, Tiffany and Kanyo, Richard and Ahrens, Misha B and Allison, W Ted and Podgorski, Kaspar and Campbell, Robert E} } @article {65274, title = {Bright and tunable far-red chemigenetic indicators.}, journal = {bioRxiv}, year = {2020}, month = {2020 Jan 9}, author = {Deo, Claire and Abdelfattah, Ahmed S and Bhargava, Hersh K. and Berro, Adam J. and Falco, Natalie and Moeyaert, Benjamien and Chupanova,Mariam and Lavis, Luke D and Schreiter, Eric R} } @article {66015, title = {Bump-and-Hole Engineering Identifies Specific Substrates of Glycosyltransferases in Living Cells}, journal = {Molecular Cell}, volume = {78}, year = {2020}, month = {Jan-06-2020}, pages = {824 - 834.e15}, abstract = {

Studying posttranslational modifications classically relies on experimental strategies that oversimplify the complex biosynthetic machineries of living cells. Protein glycosylation contributes to essential biological processes, but correlating glycan structure, underlying protein, and disease-relevant biosynthetic regulation is currently elusive. Here, we engineer living cells to tag glycans with editable chemical functionalities while providing information on biosynthesis, physiological context, and glycan fine structure. We introduce a non-natural substrate biosynthetic pathway and use engineered glycosyltransferases to incorporate chemically tagged sugars into the cell surface glycome of the living cell. We apply the strategy to a particularly redundant yet disease-relevant human glycosyltransferase family, the polypeptide\ N-acetylgalactosaminyl transferases. This approach bestows a gain-of-chemical-functionality modification on cells, where the products of individual glycosyltransferases can be selectively characterized or manipulated to understand glycan contribution to major physiological processes.

}, issn = {10972765}, doi = {10.1016/j.molcel.2020.03.030}, url = {https://www.sciencedirect.com/science/article/pii/S1097276520301982?via\%3Dihub}, author = {Schumann, Benjamin and Malaker, Stacy Alyse and Wisnovsky, Simon Peter and Debets, Marjoke Froukje and Agbay, Anthony John and Fernandez, Daniel and Wagner, Lauren Jan Sarbo and Lin, Liang and Li, Zhen and Choi, Junwon and Fox, Douglas Michael and Peh, Jessie and Gray, Melissa Anne and Pedram, Kayvon and Kohler, Jennifer Jean and Mrksich, Milan and Bertozzi, Carolyn Ruth} } @article {65371, title = {CAMIO: a transgenic CRISPR pipeline to create diverse targeted genome deletions in Drosophila.}, journal = {Nucleic Acids Research}, year = {2020}, month = {2020 Mar 18}, abstract = {

The genome is the blueprint for an organism. Interrogating the genome, especially locating critical cis-regulatory elements, requires deletion analysis. This is conventionally performed using synthetic constructs, making it cumbersome and non-physiological. Thus, we created Cas9-mediated Arrayed Mutagenesis of Individual Offspring (CAMIO) to achieve comprehensive analysis of a targeted region of native DNA. CAMIO utilizes CRISPR that is spatially restricted to generate independent deletions in the intact Drosophila genome. Controlled by recombination, a single guide RNA is stochastically chosen from a set targeting a specific DNA region. Combining two sets increases variability, leading to either indels at 1-2 target sites or inter-target deletions. Cas9 restriction to male germ cells elicits autonomous double-strand-break repair, consequently creating offspring with diverse mutations. Thus, from a single population cross, we can obtain a deletion matrix covering a large expanse of DNA at both coarse and fine resolution. We demonstrate the ease and power of CAMIO by mapping 5{\textquoteright}UTR sequences crucial for chinmo{\textquoteright}s post-transcriptional regulation.

}, issn = {1362-4962}, doi = {10.1093/nar/gkaa177}, author = {Chen, Hui-Min and Marques, Jorge Garcia and Sugino, Ken and Wei, Dingjun and Miyares, Rosa Linda and Lee, Tzumin} } @article {65909, title = {Canonical goal-selective representations are absent from prefrontal cortex in a spatial working memory task requiring behavioral flexibility.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Dec 24}, abstract = {

The prefrontal cortex (PFC){\textquoteright}s functions are thought to include working memory, as its activity can reflect information that must be temporarily maintained to realize the current goal. We designed a flexible spatial working memory task that required rats to navigate - after distractions and a delay - to multiple possible goal locations from different starting points and via multiple routes. This made the current goal location the key variable to remember, instead of a particular direction or route to the goal. However, across a broad population of PFC neurons, we found no evidence of current-goal-specific memory in any previously reported form - that is differences in the rate, sequence, phase, or covariance of firing. This suggests that such patterns do not hold working memory in the PFC when information must be employed flexibly. Instead, the PFC grouped locations representing behaviorally equivalent task features together, consistent with a role in encoding long-term knowledge of task structure.

}, issn = {2050-084X}, doi = {10.7554/eLife.63035}, author = {B{\"o}hm, Claudia and Lee, Albert K} } @article {67190, title = {Canonical goal-selective representations are absent from prefrontal cortex in a spatial working memory task requiring behavioral flexibility}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Dec 24}, abstract = {

The prefrontal cortex (PFC){\textquoteright}s functions are thought to include working memory, as its activity can reflect information that must be temporarily maintained to realize the current goal. We designed a flexible spatial working memory task that required rats to navigate - after distractions and a delay - to multiple possible goal locations from different starting points and via multiple routes. This made the current goal location the key variable to remember, instead of a particular direction or route to the goal. However, across a broad population of PFC neurons, we found no evidence of current-goal-specific memory in any previously reported form - that is differences in the rate, sequence, phase, or covariance of firing. This suggests that such patterns do not hold working memory in the PFC when information must be employed flexibly. Instead, the PFC grouped locations representing behaviorally equivalent task features together, consistent with a role in encoding long-term knowledge of task structure.

}, doi = {10.7554/eLife.63035}, url = {https://elifesciences.org/articles/63035}, author = {B{\"o}hm, Claudia and Lee, Albert K} } @article {65816, title = {Cell types and neuronal circuitry underlying female aggression in Drosophila.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Nov 03}, abstract = {

Aggressive social interactions are used to compete for limited resources and are regulated by complex sensory cues and the organism{\textquoteright}s internal state. While both sexes exhibit aggression, its neuronal underpinnings are understudied in females. Here, we identify a population of sexually dimorphic aIPg neurons in the adult central brain whose optogenetic activation increased, and genetic inactivation reduced, female aggression. Analysis of GAL4 lines identified in an unbiased screen for increased female chasing behavior revealed the involvement of another sexually dimorphic neuron, pC1d, and implicated aIPg and pC1d neurons as core nodes regulating female aggression. Connectomic analysis demonstrated that aIPg neurons and pC1d are interconnected and suggest that aIPg neurons may exert part of their effect by gating the flow of visual information to descending neurons. Our work reveals important regulatory components of the neuronal circuitry that underlies female aggressive social interactions and provides tools for their manipulation.

}, issn = {2050-084X}, doi = {10.7554/eLife.58942}, author = {Schretter, Catherine E and Aso, Yoshi and Robie, Alice A and Dreher, Marisa and Dolan, Michael-John and Chen, Nan and Ito, Masayoshi and Yang, Tansy and Parekh, Ruchi and Branson, Kristin M and Rubin, Gerald M} } @article {65659, title = {Cell types promoting goosebumps form a niche to regulate hair follicle stem cells.}, journal = {Cell}, volume = {182}, year = {2020}, month = {2020 Aug 6}, pages = {578}, abstract = {

Piloerection (goosebumps) requires concerted actions of the hair follicle, the arrector pili muscle (APM), and the sympathetic nerve, providing a model to study interactions across epithelium, mesenchyme, and nerves. Here, we show that APMs and sympathetic nerves form a dual-component niche to modulate hair follicle stem cell (HFSC) activity. Sympathetic nerves form synapse-like structures with HFSCs and regulate HFSCs through norepinephrine, whereas APMs maintain sympathetic innervation to HFSCs. Without norepinephrine signaling, HFSCs enter deep quiescence by down-regulating the cell cycle and metabolism while up-regulating quiescence regulators Foxp1 and Fgf18. During development, HFSC progeny secretes Sonic Hedgehog (SHH) to direct the formation of this APM-sympathetic nerve niche, which in turn controls hair follicle regeneration in adults. Our results reveal a reciprocal interdependence between a regenerative tissue and its niche at different stages and demonstrate sympathetic nerves can modulate stem cells through synapse-like connections and neurotransmitters to couple tissue production with demands.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2020.06.031}, author = {Shwartz, Yulia and Gonzalez-Celeiro, Meryem and Chen, Chih-Lung and Pasolli, H Amalia and Sheu, Shu-Hsien and Fan, Sabrina Mai-Yi and Shamsi, Farnaz and Assaad, Steven and Lin, Edrick Tai-Yu and Zhang, Bing and Tsai, Pai-Chi and He, Megan and Tseng, Yu-Hua and Lin, Sung-Jan and Hsu, Ya-Chieh} } @article {65294, title = {Cellpose: a generalist algorithm for cellular segmentation}, journal = {bioRxiv}, year = {2020}, month = {2020 Feb 03}, abstract = {

Many biological applications require the segmentation of cell bodies, membranes and nuclei from microscopy images. Deep learning has enabled great progress on this problem, but current methods are specialized for images that have large training datasets. Here we introduce a generalist, deep learning-based segmentation algorithm called Cellpose, which can very precisely segment a wide range of image types out-of-the-box and does not require model retraining or parameter adjustments. We trained Cellpose on a new dataset of highly-varied images of cells, containing over 70,000 segmented objects. To support community contributions to the training data, we developed software for manual labelling and for curation of the automated results, with optional direct upload to our data repository. Periodically retraining the model on the community-contributed data will ensure that Cellpose improves constantly.

}, doi = {10.1101/2020.02.02.931238}, author = {Stringer, Carsen and Michaelos, Michalis and Pachitariu, Marius} } @article {68429, title = {Cell-Surface Proteomic Profiling in the Fly Brain Uncovers Wiring Regulators.}, journal = {Cell}, volume = {180}, year = {2020}, month = {01/2020}, pages = {373-386.e15}, abstract = {

Molecular interactions at the cellular interface mediate organized assembly of single cells into tissues and, thus, govern the development and physiology of multicellular organisms. Here, we developed a cell-type-specific, spatiotemporally resolved approach to profile cell-surface proteomes in intact tissues. Quantitative profiling of cell-surface proteomes of Drosophila olfactory projection neurons (PNs) in pupae and adults revealed global downregulation of wiring molecules and upregulation of synaptic molecules in the transition from developing to mature PNs. A proteome-instructed in\ vivo screen identified 20 cell-surface molecules regulating neural circuit assembly, many of which belong to evolutionarily conserved protein families not previously linked to neural development. Genetic analysis further revealed that the lipoprotein receptor LRP1 cell-autonomously controls PN dendrite targeting, contributing to the formation of a precise olfactory map. These findings highlight the power of temporally resolved in situ cell-surface proteomic profiling in discovering regulators of brain wiring.

}, keywords = {Animals, Axons, Brain, Dendrites, Drosophila melanogaster, Drosophila Proteins, Gene Expression Profiling, Gene Expression Regulation, Developmental, Membrane Proteins, Neurogenesis, Olfactory Nerve, Olfactory Pathways, Olfactory Receptor Neurons, Proteomics, Receptors, Lipoprotein, Smell}, issn = {1097-4172}, doi = {10.1016/j.cell.2019.12.029}, author = {Li, Jiefu and Han, Shuo and Li, Hongjie and Udeshi, Namrata D and Svinkina, Tanya and Mani, D R and Xu, Chuanyun and Guajardo, Ricardo and Xie, Qijing and Li, Tongchao and Luginbuhl, David J and Wu, Bing and McLaughlin, Colleen N and Xie, Anthony and Kaewsapsak, Pornchai and Quake, Stephen R and Carr, Steven A and Ting, Alice Y and Luo, Liqun} } @article {65361, title = {Cell-type specific outcome representation in primary motor cortex.}, journal = {Neuron}, volume = {107}, year = {2020}, month = {2020 Sep 9}, pages = {954-71}, abstract = {

Adaptive movements are critical to animal survival. To guide future actions, the brain monitors different outcomes, including achievement of movement and appetitive goals. The nature of outcome signals and their neuronal and network realization in motor cortex (M1), which commands the performance of skilled movements, is largely unknown. Using a dexterity task, calcium imaging, optogenetic perturbations, and behavioral manipulations, we studied outcome signals in murine M1. We find two populations of layer 2-3 neurons, {\textquotedblleft}success{\textquotedblright}- and {\textquotedblleft}failure{\textquotedblright} related neurons that develop with training and report end-result of trials. In these neurons, prolonged responses were recorded after success or failure trials, independent of reward and kinematics. In contrast, the initial state of layer-5 pyramidal tract neurons contains a memory trace of the previous trial{\textquoteright}s outcome. Inter-trial cortical activity was needed to learn new task requirements. These M1 reflective layer-specific performance outcome signals, can support reinforcement motor learning of skilled behavior.

}, doi = {10.1016/j.neuron.2020.06.006}, author = {Lavzin, Maria and Levy, Shahar and Benisty, Hadas and Dubin, Uri and Brosh, Zohar and Aeed, Fadi and Mensh, Brett D. and Schiller, Yitzhak and Meir, Ron and Barak, Omri and Talmon, Ronen and Hantman, Adam W. and Schiller, Jackie} } @article {65860, title = {Central processing of leg proprioception in Drosophila.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Dec 02}, abstract = {

Proprioception, the sense of self-movement and position, is mediated by mechanosensory neurons that detect diverse features of body kinematics. Although proprioceptive feedback is crucial for accurate motor control, little is known about how downstream circuits transform limb sensory information to guide motor output. Here, we investigate neural circuits in that process proprioceptive information from the fly leg. We identify three cell-types from distinct developmental lineages that are positioned to receive input from proprioceptor subtypes encoding tibia position, movement, and vibration. 13Bα neurons encode femur-tibia joint angle and mediate postural changes in tibia position. 9Aα neurons also drive changes in leg posture, but encode a combination of directional movement, high frequency vibration, and joint angle. Activating 10Bα neurons, which encode tibia vibration at specific joint angles, elicits pausing in walking flies. Altogether, our results reveal that central circuits integrate information across proprioceptor subtypes to construct complex sensorimotor representations that mediate diverse behaviors, including reflexive control of limb posture and detection of leg vibration.

}, issn = {2050-084X}, doi = {10.7554/eLife.60299}, author = {Agrawal, Sweta and Dickinson, Evyn S and Sustar, Anne and Gurung, Pralaksha and Shepherd, David and Truman, James W and Tuthill, John C} } @article {65363, title = {Characterization of the Genetic Architecture Underlying Eye Size Variation Within Drosophila melanogaster and Drosophila simulans.}, journal = {Genes|Genomes|Genetics}, volume = {10}, year = {2020}, month = {2020 Mar 01}, pages = {1005-18}, doi = {10.1534/g3.119.400877}, url = {http://g3journal.org/lookup/doi/10.1534/g3.119.400877https://syndication.highwire.org/content/doi/10.1534/g3.119.400877}, author = {Gaspar, Pedro and Arif, Saad and Sumner-Rooney, Lauren and Kittelmann, Maike and Bodey, Andrew J. and Stern, David L. and Nunes, Maria D. S. and McGregor, Alistair P.} } @article {65614, title = {Chloroplast Sec14-like 1 (CPSFL1) is essential for normal chloroplast development and affects carotenoid accumulation in Chlamydomonas.}, journal = {Proceedings of the National Academy of Sciences of the U S A}, volume = {117}, year = {2020}, month = {2020 Jun 2}, pages = {1-12}, abstract = {

Plastid isoprenoid-derived carotenoids serve essential roles in chloroplast development and photosynthesis. Although nearly all enzymes that participate in the biosynthesis of carotenoids in plants have been identified, the complement of auxiliary proteins that regulate synthesis, transport, sequestration, and degradation of these molecules and their isoprenoid precursors have not been fully described. To identify such proteins that are necessary for the optimal functioning of oxygenic photosynthesis, we screened a large collection of nonphotosynthetic (acetate-requiring) DNA insertional mutants of and isolated The mutant is extremely light-sensitive and susceptible to photoinhibition and photobleaching. The gene encodes a CRAL-TRIO hydrophobic ligand-binding (Sec14) domain protein. Proteins containing this domain are limited to eukaryotes, but some may have been retargeted to function in organelles of endosymbiotic origin. The mutant showed decreased accumulation of plastidial isoprenoid-derived pigments, especially carotenoids, and whole-cell focused ion-beam scanning-electron microscopy revealed a deficiency of carotenoid-rich chloroplast structures (e.g., eyespot and plastoglobules). The low carotenoid content resulted from impaired biosynthesis at a step prior to phytoene, the committed precursor to carotenoids. The CPSFL1 protein bound phytoene and β-carotene when expressed in and phosphatidic acid in vitro. We suggest that CPSFL1 is involved in the regulation of phytoene synthesis and carotenoid transport and thereby modulates carotenoid accumulation in the chloroplast.

}, issn = {1091-6490}, doi = {10.1073/pnas.1916948117}, author = {Garc{\'\i}a-Cerd{\'a}n, Jos{\'e} G and Schmid, Eva M and Takeuchi, Tomomi and McRae, Ian and McDonald, Kent L and Yordduangjun, Nichakarn and Hassan, Ahmed M and Grob, Patricia and Xu, C Shan and Hess, Harald F and Fletcher, Daniel A and Nogales, Eva and Niyogi, Krishna K} } @article {65757, title = {Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin.}, journal = {Science Advances}, volume = {6}, year = {2020}, month = {2020 Sep 23}, abstract = {

Three-dimensional (3D) chromatin organization plays a key role in regulating mammalian genome function; however, many of its physical features at the single-cell level remain underexplored. Here, we use live- and fixed-cell 3D super-resolution and scanning electron microscopy to analyze structural and functional nuclear organization in somatic cells. We identify chains of interlinked ~200- to 300-nm-wide chromatin domains (CDs) composed of aggregated nucleosomes that can overlap with individual topologically associating domains and are distinct from a surrounding RNA-populated interchromatin compartment. High-content mapping uncovers confinement of cohesin and active histone modifications to surfaces and enrichment of repressive modifications toward the core of CDs in both hetero- and euchromatic regions. This nanoscale functional topography is temporarily relaxed in postreplicative chromatin but remarkably persists after ablation of cohesin. Our findings establish CDs as physical and functional modules of mesoscale genome organization.

}, issn = {2375-2548}, doi = {10.1126/sciadv.aba8811}, author = {Miron, Ezequiel and Oldenkamp, Roel and Brown, Jill M and Pinto, David M S and Xu, C Shan and Faria, Ana R and Shaban, Haitham A and Rhodes, James D P and Innocent, Cassandravictoria and de Ornellas, Sara and Hess, Harald F and Buckle, Veronica and Schermelleh, Lothar} } @article {65683, title = {Circuit and behavioral mechanisms of sexual rejection by drosophila females.}, journal = {Current Biology}, volume = {30}, year = {2020}, month = {2020 Oct 05}, abstract = {

The mating decisions of Drosophila melanogaster females are primarily revealed through either of two discrete actions: opening of the vaginal plates to allow copulation, or extrusion of the ovipositor to reject the male. Both actions are triggered by the male courtship song, and both are dependent upon the female{\textquoteright}s mating status. Virgin females are more likely to open their vaginal plates in response to song; mated females are more likely to extrude their ovipositor. Here, we examine the neural cause and behavioral consequence of ovipositor extrusion. We show that the DNp13 descending neurons act as command-type neurons for ovipositor extrusion, and that ovipositor extrusion is an effective deterrent only when performed by females that have previously mated. The DNp13 neurons respond to male song via direct synaptic input from the pC2l auditory neurons. Mating status does not modulate the song responses of DNp13 neurons, but rather how effectively they can engage the motor circuits for ovipositor extrusion. We present evidence that mating status information is mediated by ppk sensory neurons in the uterus, which are activated upon ovulation. Vaginal plate opening and ovipositor extrusion are thus controlled by anatomically and functionally distinct circuits, highlighting the diversity of neural decision-making circuits even in the context of closely related behaviors with shared exteroceptive and interoceptive inputs.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2020.07.083}, author = {Wang, Fei and Wang, Kaiyu and Forknall, Nora and Parekh, Ruchi and Dickson, Barry J} } @article {65900, title = {Cis-regulatory variation in the shavenbaby gene underlies intraspecific phenotypic variation, mirroring interspecific divergence in the same trait.}, journal = {Evolution}, year = {2020}, month = {2020 Dec 14}, abstract = {

Despite considerable progress in recent decades in dissecting the genetic causes of natural morphological variation, there is limited understanding of how variation within species ultimately contributes to species differences. We have studied patterning of the non-sensory hairs, commonly known as "trichomes," on the dorsal cuticle of first-instar larvae of Drosophila. Most Drosophila species produce a dense lawn of dorsal trichomes, but a subset of these trichomes were lost in D. sechellia and D. ezoana due entirely to regulatory evolution of the shavenbaby (svb) gene. Here, we describe intraspecific variation in dorsal trichome patterns of first-instar larvae of D. virilis that is similar to the trichome pattern variation identified previously between species. We found that a single large effect QTL, which includes svb, explains most of the trichome number difference between two D. virilis strains and that svb expression correlates with the trichome difference between strains. This QTL does not explain the entire difference between strains, implying that additional loci contribute to variation in trichome numbers. Thus, the genetic architecture of intraspecific variation exhibits similarities and differences with interspecific variation that may reflect differences in long-term and short-term evolutionary processes.

}, issn = {1558-5646}, doi = {10.1111/evo.14142}, author = {Soverna, Ana Faigon and Rodriguez, Nahuel Cabrera and Korgaonkar, Aishwarya and Hasson, Esteban and Stern, David L and Frankel, Nicol{\'a}s} } @article {65872, title = {The claustrum.}, journal = {Current Biology}, volume = {30}, year = {2020}, month = {2020 Dec 07}, pages = {R1401-R1406}, abstract = {

The claustrum is a brain region that has been investigated for over 200 years, yet its precise function remains unknown. In the final posthumously released article of Francis Crick, written with Christof Koch, the claustrum was suggested to be critically linked to consciousness. Though the claustrum remained relatively obscure throughout the last half century, it has enjoyed a renewed interest in the last 15 years since Crick and Koch{\textquoteright}s article. During this time, the claustrum, like many other brain regions, has been studied with the myriad of modern systems neuroscience tools that have been made available by the intersection of genetic and viral technologies. This has uncovered new information about its anatomical connectivity and physiological properties and begun to reveal aspects of its function. From these studies, one clear consensus has emerged which supports Crick and Koch{\textquoteright}s primary interest in the claustrum: the claustrum has widespread extensive connectivity with the entire cerebral cortex, suggesting a prominent role in {\textquoteright}higher order processes{\textquoteright}.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2020.09.069}, author = {Smith, Jared B and Lee, Albert K and Jackson, Jesse} } @article {65585, title = {Co-evolving wing spots and mating displays are genetically separable traits in Drosophila.}, journal = {Evolution}, volume = {74}, year = {2020}, month = {2020 May 03}, pages = {1098-1111}, abstract = {

The evolution of sexual traits often involves correlated changes in morphology and behavior. For example, in Drosophila, divergent mating displays are often accompanied by divergent pigment patterns. To better understand how such traits co-evolve, we investigated the genetic basis of correlated divergence in wing pigmentation and mating display between the sibling species Drosophila elegans and D. gunungcola. Drosophila elegans males have an area of black pigment on their wings known as a wing spot and appear to display this spot to females by extending their wings laterally during courtship. By contrast, D. gunungcola lost both of these traits. Using Multiplexed Shotgun Genotyping (MSG), we identified a \~{}440 kb region on the X chromosome that behaves like a genetic switch controlling the presence or absence of male-specific wing spots. This region includes the candidate gene optomotor-blind (omb), which plays a critical role in patterning the Drosophila wing. The genetic basis of divergent wing display is more complex, with at least two loci on the X chromosome and two loci on autosomes contributing to its evolution. Introgressing the X-linked region affecting wing spot development from D. gunungcola into D. elegans reduced pigmentation in the wing spots but did not affect the wing display, indicating that these are genetically separable traits. Consistent with this observation, broader sampling of wild D. gunungcola populations confirmed the wing spot and wing display are evolving independently: some D. gunungcola males performed wing displays similar to D. elegans despite lacking wing spots. These data suggest that correlated selection pressures rather than physical linkage or pleiotropy are responsible for the coevolution of these morphological and behavioral traits. They also suggest that the change in morphology evolved prior to the change in behavior. This article is protected by copyright. All rights reserved.

}, issn = {1558-5646}, doi = {10.1111/evo.13990}, author = {Massey, Jonathan H and Rice, Gavin R and Firdaus, Anggun and Chen, Chi-Yang and Yeh, Shu-Dan and Stern, David L and Wittkopp, Patricia J} } @article {65809, title = {A community for Black chemists.}, journal = {Nature Chemistry}, volume = {12}, year = {2020}, month = {2020 Nov 01}, pages = {988-989}, issn = {1755-4349}, doi = {10.1038/s41557-020-00572-3}, author = {Beyene, Abraham G and Panescu, Priera} } @article {67225, title = {Comparative single-cell transcriptomics of complete insect nervous systems}, journal = {bioRxiv}, year = {2020}, month = {01/2020}, abstract = {

Molecular profiles of neurons influence information processing, but bridging the gap between genes, circuits, and behavior has been very difficult. Furthermore, the behavioral state of an animal continuously changes across development and as a result of sensory experience. How behavioral state influences molecular cell state is poorly understood. Here we present a complete atlas of the Drosophila larval central nervous system composed of over 200,000 single cells across four developmental stages. We develop polyseq, a python package, to perform cell-type analyses. We use single-molecule RNA-FISH to validate our scRNAseq findings. To investigate how internal state affects cell state, we optogentically altered internal state with high-throughput behavior protocols designed to mimic wasp sting and over activation of the memory system. We found nervous system-wide and neuron-specific gene expression changes. This resource is valuable for developmental biology and neuroscience, and it advances our understanding of how genes, neurons, and circuits generate behavior.

}, doi = {10.1101/785931}, url = {https://www.biorxiv.org/content/early/2020/01/16/785931}, author = {Cocanougher, Benjamin T. and Wittenbach, Jason D. and Long, Xi Salina and Kohn, Andrea B. and Norekian, Tigran P. and Yan, Jinyao and Colonell, Jennifer and Masson, Jean-Baptiste and Truman, James W. and Cardona, Albert and Turaga, Srinivas C. and Singer, Robert H. and Moroz, Leonid L. and Zlatic, Marta} } @article {65726, title = {A comparison of neuronal population dynamics measured with calcium imaging and electrophysiology.}, journal = {PLoS Computational Biology}, volume = {16}, year = {2020}, month = {2020 Sep 15}, pages = {e1008198}, abstract = {

Calcium imaging with fluorescent protein sensors is widely used to record activity in neuronal populations. The transform between neural activity and calcium-related fluorescence involves nonlinearities and low-pass filtering, but the effects of the transformation on analyses of neural populations are not well understood. We compared neuronal spikes and fluorescence in matched neural populations in behaving mice. We report multiple discrepancies between analyses performed on the two types of data, including changes in single-neuron selectivity and population decoding. These were only partially resolved by spike inference algorithms applied to fluorescence. To model the relation between spiking and fluorescence we simultaneously recorded spikes and fluorescence from individual neurons. Using these recordings we developed a model transforming spike trains to synthetic-imaging data. The model recapitulated the differences in analyses. Our analysis highlights challenges in relating electrophysiology and imaging data, and suggests forward modeling as an effective way to understand differences between these data.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1008198}, author = {Wei, Ziqiang and Lin, Bei-Jung and Chen, Tsai-Wen and Daie, Kayvon and Svoboda, Karel and Druckmann, Shaul} } @article {65645, title = {Complete connectomic reconstruction of olfactory projection neurons in the fly brain.}, journal = {Current Biology}, volume = {30}, year = {2020}, month = {2020 Aug 17}, pages = {3183-99}, abstract = {

Nervous systems contain sensory neurons, local neurons, projection neurons, and motor neurons. To understand how these building blocks form whole circuits, we must distil these broad classes into neuronal cell types and describe their network connectivity. Using an electron micrograph dataset for an entire Drosophila melanogaster brain, we reconstruct the first complete inventory of olfactory projections connecting the antennal lobe, the insect analog of the mammalian olfactory bulb, to higher-order brain regions in an adult animal brain. We then connect this inventory to extant data in the literature, providing synaptic-resolution "holotypes" both for heavily investigated and previously unknown cell types. Projection neurons are approximately twice as numerous as reported by light level studies; cell types are stereotyped, but not identical, in cell and synapse numbers between brain hemispheres. The lateral horn, the insect analog of the mammalian cortical amygdala, is the main target for this olfactory information and has been shown to guide innate behavior. Here, we find new connectivity motifs, including axo-axonic connectivity between projection neurons, feedback, and lateral inhibition of these axons by a large population of neurons, and the convergence of different inputs, including non-olfactory inputs and memory-related feedback onto third-order olfactory neurons. These features are less prominent in the mushroom body calyx, the insect analog of the mammalian piriform cortex and a center for associative memory. Our work provides a complete neuroanatomical platform for future studies of the adult Drosophila olfactory system.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2020.06.042}, author = {Bates, Alexander S and Schlegel, Philipp and Roberts, Ruair{\'\i} J V and Drummond, Nikolas and Tamimi, Imaan F M and Turnbull, Robert and Zhao, Xincheng and Marin, Elizabeth C and Popovici, Patricia D and Dhawan, Serene and Jamasb, Arian and Javier, Alexandre and Serratosa Capdevila, Laia and Li, Feng and Rubin, Gerald M and Waddell, Scott and Bock, Davi D and Costa, Marta and Jefferis, Gregory S X E} } @article {65646, title = {Comprehensive imaging of sensory-evoked activity of entire neurons within the awake developing brain using ultrafast AOD-based random-access two-photon microscopy.}, journal = {Frontiers in Neural Circuits}, volume = {14}, year = {2020}, month = {2020 Jun 16}, pages = {33}, abstract = {

Determining how neurons transform synaptic input and encode information in action potential (AP) firing output is required for understanding dendritic integration, neural transforms and encoding. Limitations in the speed of imaging 3D volumes of brain encompassing complex dendritic arbors using conventional galvanometer mirror-based laser-scanning microscopy has hampered fully capturing fluorescent sensors of activity throughout an individual neuron{\textquoteright}s entire complement of synaptic inputs and somatic APs. To address this problem, we have developed a two-photon microscope that achieves high-speed scanning by employing inertia-free acousto-optic deflectors (AODs) for laser beam positioning, enabling random-access sampling of hundreds to thousands of points-of-interest restricted to a predetermined neuronal structure, avoiding wasted scanning of surrounding extracellular tissue. This system is capable of comprehensive imaging of the activity of single neurons within the intact and awake vertebrate brain. Here, we demonstrate imaging of tectal neurons within the brains of albino tadpoles labeled using single-cell electroporation for expression of a red space-filling fluorophore to determine dendritic arbor morphology, and either the calcium sensor jGCaMP7s or the glutamate sensor iGluSnFR as indicators of neural activity. Using discrete, point-of-interest scanning we achieve sampling rates of 3 Hz for saturation sampling of entire arbors at 2 μm resolution, 6 Hz for sequentially sampling 3 volumes encompassing the dendritic arbor and soma, and 200-250 Hz for scanning individual planes through the dendritic arbor. This system allows investigations of sensory-evoked information input-output relationships of neurons within the intact and awake brain.

}, issn = {1662-5110}, doi = {10.3389/fncir.2020.00033}, author = {Sakaki, Kelly D R and Podgorski, Kaspar and Dellazizzo Toth, Tristan A and Coleman, Patrick and Haas, Kurt} } @article {65273, title = {Comprehensive transcriptome analysis of cochlear spiral ganglion neurons at multiple ages.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Jan 08}, abstract = {

Inner ear cochlear spiral ganglion neurons (SGNs) transmit auditory information to the brainstem. Recent single cell RNA-Seq studies have revealed heterogeneities within SGNs. Nonetheless, much remains unknown about the transcriptome of SGNs, especially which genes are specifically expressed in SGNs. To address these questions we needed a deeper and broader gene coverage than that in previous studies. We performed bulk RNA-Seq on mouse SGNs at five ages, and on two reference cell types (hair cells and glia). Their transcriptome comparison identified genes previously unknown to be specifically expressed in SGNs. To validate our dataset and provide useful genetic tools for this research field, we generated two knockin mouse strains: and . Our comprehensive analysis confirmed the SGN-selective expression of the candidate genes, testifying to the quality of our transcriptome data. These two mouse strains can be used to temporally label SGNs or to sort them.

}, issn = {2050-084X}, doi = {10.7554/eLife.50491}, author = {Li, Chao and Li, Xiang and Bi, Zhenghong and Sugino, Ken and Wang, Guangqin and Zhu, Tong and Liu, Zhiyong} } @article {68507, title = {A connectome and analysis of the adult Drosophila central brain.}, journal = {Elife}, volume = {9}, year = {2020}, month = {2020 Sep 07}, abstract = {

The neural circuits responsible for animal behavior remain largely unknown. We summarize new methods and present the circuitry of a large fraction of the brain of the fruit fly . Improved methods include new procedures to prepare, image, align, segment, find synapses in, and proofread such large data sets. We define cell types, refine computational compartments, and provide an exhaustive atlas of cell examples and types, many of them novel. We provide detailed circuits consisting of neurons and their chemical synapses for most of the central brain. We make the data public and simplify access, reducing the effort needed to answer circuit questions, and provide procedures linking the neurons defined by our analysis with genetic reagents. Biologically, we examine distributions of connection strengths, neural motifs on different scales, electrical consequences of compartmentalization, and evidence that maximizing packing density is an important criterion in the evolution of the fly{\textquoteright}s brain.

}, keywords = {Animals, Brain, Connectome, Drosophila melanogaster, Female, Male, Neurons, Synapses}, issn = {2050-084X}, doi = {10.7554/eLife.57443}, author = {Scheffer, Louis K and Xu, C Shan and Januszewski, Michal and Lu, Zhiyuan and Takemura, Shin-ya and Hayworth, Kenneth J and Huang, Gary B and Shinomiya, Kazunori and Maitlin-Shepard, Jeremy and Berg, Stuart and Clements, Jody and Hubbard, Philip M and Katz, William T and Umayam, Lowell and Zhao, Ting and Ackerman, David and Blakely, Tim and Bogovic, John and Dolafi, Tom and Kainmueller, Dagmar and Kawase, Takashi and Khairy, Khaled A and Leavitt, Laramie and Li, Peter H and Lindsey, Larry and Neubarth, Nicole and Olbris, Donald J and Otsuna, Hideo and Trautman, Eric T and Ito, Masayoshi and Bates, Alexander S and Goldammer, Jens and Wolff, Tanya and Svirskas, Robert and Schlegel, Philipp and Neace, Erika and Knecht, Christopher J and Alvarado, Chelsea X and Bailey, Dennis A and Ballinger, Samantha and Borycz, Jolanta A and Canino, Brandon S and Cheatham, Natasha and Cook, Michael and Dreher, Marisa and Duclos, Octave and Eubanks, Bryon and Fairbanks, Kelli and Finley, Samantha and Forknall, Nora and Francis, Audrey and Hopkins, Gary Patrick and Joyce, Emily M and Kim, SungJin and Kirk, Nicole A and Kovalyak, Julie and Lauchie, Shirley A and Lohff, Alanna and Maldonado, Charli and Manley, Emily A and McLin, Sari and Mooney, Caroline and Ndama, Miatta and Ogundeyi, Omotara and Okeoma, Nneoma and Ordish, Christopher and Padilla, Nicholas and Patrick, Christopher M and Paterson, Tyler and Phillips, Elliott E and Phillips, Emily M and Rampally, Neha and Ribeiro, Caitlin and Robertson, Madelaine K and Rymer, Jon Thomson and Ryan, Sean M and Sammons, Megan and Scott, Anne K and Scott, Ashley L and Shinomiya, Aya and Smith, Claire and Smith, Kelsey and Smith, Natalie L and Sobeski, Margaret A and Suleiman, Alia and Swift, Jackie and Takemura, Satoko and Talebi, Iris and Tarnogorska, Dorota and Tenshaw, Emily and Tokhi, Temour and Walsh, John J and Yang, Tansy and Horne, Jane Anne and Li, Feng and Parekh, Ruchi and Rivlin, Patricia K and Jayaraman, Vivek and Costa, Marta and Jefferis, Gregory Sxe and Ito, Kei and Saalfeld, Stephan and George, Reed and Meinertzhagen, Ian A and Rubin, Gerald M and Hess, Harald F and Jain, Viren and Plaza, Stephen M} } @article {65899, title = {The connectome of the adult mushroom body provides insights into function.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Dec 14}, abstract = {

Making inferences about the computations performed by neuronal circuits from synapse-level connectivity maps is an emerging opportunity in neuroscience. The mushroom body (MB) is well positioned for developing and testing such an approach due to its conserved neuronal architecture, recently completed dense connectome, and extensive prior experimental studies of its roles in learning, memory and activity regulation. Here we identify new components of the MB circuit in , including extensive visual input and MB output neurons (MBONs) with direct connections to descending neurons. We find unexpected structure in sensory inputs, in the transfer of information about different sensory modalities to MBONs, and in the modulation of that transfer by dopaminergic neurons (DANs). We provide insights into the circuitry used to integrate MB outputs, connectivity between the MB and the central complex and inputs to DANs, including feedback from MBONs. Our results provide a foundation for further theoretical and experimental work.

}, issn = {2050-084X}, doi = {10.7554/eLife.62576}, author = {Li, Feng and Lindsey, Jack W and Marin, Elizabeth C and Otto, Nils and Dreher, Marisa and Dempsey, Georgia and Stark, Ildiko and Bates, Alexander S and Pleijzier, Markus William and Schlegel, Philipp and Nern, Aljoscha and Takemura, Shin-ya and Eckstein, Nils and Yang, Tansy and Francis, Audrey and Braun, Amalia and Parekh, Ruchi and Costa, Marta and Scheffer, Louis K and Aso, Yoshi and Jefferis, Gregory Sxe and Abbott, Larry F and Litwin-Kumar, Ashok and Waddell, Scott and Rubin, Gerald M} } @article {65643, title = {Connectomics analysis reveals first-, second-, and third-order thermosensory and hygrosensory neurons in the adult Drosophila brain.}, journal = {Current Biology}, volume = {30}, year = {2020}, month = {2020 Aug 17}, pages = {3167-82}, abstract = {

Animals exhibit innate and learned preferences for temperature and humidity-conditions critical for their survival and reproduction. Leveraging a whole-brain electron microscopy volume, we studied the adult Drosophila melanogaster circuitry associated with antennal thermo- and hygrosensory neurons. We have identified two new target glomeruli in the antennal lobe, in addition to the five known ones, and the ventroposterior projection neurons (VP PNs) that relay thermo- and hygrosensory information to higher brain centers, including the mushroom body and lateral horn, seats of learned and innate behavior. We present the first connectome of a thermo- and hygrosensory neuropil, the lateral accessory calyx (lACA), by reconstructing neurons downstream of heating- and cooling-responsive VP PNs. A few mushroom body-intrinsic neurons solely receive thermosensory input from the lACA, while most receive additional olfactory and thermo- and/or hygrosensory PN inputs. Furthermore, several classes of lACA-associated neurons form a local network with outputs to other brain neuropils, suggesting that the lACA serves as a hub for thermo- and hygrosensory circuitry. For example, DN1a neurons link thermosensory PNs in the lACA to the circadian clock via the accessory medulla. Finally, we survey strongly connected downstream partners of VP PNs across the protocerebrum; these include a descending neuron targeted by dry-responsive VP PNs, meaning that just two synapses might separate hygrosensory inputs from motor circuits. These data provide a comprehensive first- and second-order layer analysis of Drosophila thermo- and hygrosensory systems and an initial survey of third-order neurons that could directly modulate behavior.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2020.06.028}, author = {Marin, Elizabeth C and B{\"u}ld, Laurin and Theiss, Maria and Sarkissian, Tatevik and Roberts, Ruair{\'\i} J V and Turnbull, Robert and Tamimi, Imaan F M and Pleijzier, Markus W and Laursen, Willem J and Drummond, Nik and Schlegel, Philipp and Bates, Alexander S and Li, Feng and Landgraf, Matthias and Costa, Marta and Bock, Davi D and Garrity, Paul A and Jefferis, Gregory S X E} } @article {65382, title = {Conservation and divergence of related neuronal lineages in the central brain.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Apr 07}, abstract = {

Wiring a complex brain requires many neurons with intricate cell specificity, generated by a limited number of neural stem cells. central brain lineages are a predetermined series of neurons, born in a specific order. To understand how lineage identity translates to neuron morphology, we mapped 18 central brain lineages. While we found large aggregate differences between lineages, we also discovered shared patterns of morphological diversification. Lineage identity plus Notch-mediated sister fate govern primary neuron trajectories, whereas temporal fate diversifies terminal elaborations. Further, morphological neuron types may arise repeatedly, interspersed with other types. Despite the complexity, related lineages produce similar neuron types in comparable temporal patterns. Different stem cells even yield two identical series of dopaminergic neuron types, but with unrelated sister neurons. Together, these phenomena suggest that straightforward rules drive incredible neuronal complexity, and that large changes in morphology can result from relatively simple fating mechanisms.

}, issn = {2050-084X}, doi = {10.7554/eLife.53518}, author = {Lee, Ying-Jou and Yang, Ching-Po and Miyares, Rosa L and Huang, Yu-Fen and He, Yisheng and Ren, Qingzhong and Chen, Hui-Min and Kawase, Takashi and Ito, Masayoshi and Otsuna, Hideo and Sugino, Ken and Aso, Yoshi and Ito, Kei and Lee, Tzumin} } @article {68991, title = {Context-dependent functional compensation between Ythdf mA reader proteins.}, journal = {Genes Dev}, volume = {34}, year = {2020}, month = {10/2020}, pages = {1373-1391}, abstract = {

The N6-methyladenosine (mA) modification is the most prevalent post-transcriptional mRNA modification, regulating mRNA decay and splicing. It plays a major role during normal development, differentiation, and disease progression. The modification is regulated by a set of writer, eraser, and reader proteins. The YTH domain family of proteins consists of three homologous mA-binding proteins, Ythdf1, Ythdf2, and Ythdf3, which were suggested to have different cellular functions. However, their sequence similarity and their tendency to bind the same targets suggest that they may have overlapping roles. We systematically knocked out (KO) the Mettl3 writer, each of the Ythdf readers, and the three readers together (triple-KO). We then estimated the effect in vivo in mouse gametogenesis, postnatal viability, and in vitro in mouse embryonic stem cells (mESCs). In gametogenesis, severity is increased as the deletion occurs earlier in the process, and Ythdf2 has a dominant role that cannot be compensated by Ythdf1 or Ythdf3, due to differences in readers{\textquoteright} expression pattern across different cell types, both in quantity and in spatial location. Knocking out the three readers together and systematically testing viable offspring genotypes revealed a redundancy in the readers{\textquoteright} role during early development that is gene dosage-dependent. Finally, in mESCs there is compensation between the three Ythdf reader proteins, since the resistance to differentiate and the significant effect on mRNA decay occur only in the triple-KO cells and not in the single KOs. Thus, we suggest a new model for the Ythdf readers function, in which there is profound dosage-dependent redundancy when all three readers are equivalently coexpressed in the same cell types.

}, keywords = {Animals, Cell Line, Dosage Compensation, Genetic, Embryonic Stem Cells, Fertility, Gametogenesis, Gene Deletion, Gene Expression Profiling, Gene Expression Regulation, Developmental, Methyltransferases, Mice, Mice, Knockout, RNA-Binding Proteins}, issn = {1549-5477}, doi = {10.1101/gad.340695.120}, author = {Lasman, Lior and Krupalnik, Vladislav and Viukov, Sergey and Mor, Nofar and Aguilera-Castrejon, Alejandro and Schneir, Dan and Bayerl, Jonathan and Mizrahi, Orel and Peles, Shani and Tawil, Shadi and Sathe, Shashank and Nachshon, Aharon and Shani, Tom and Zerbib, Mirie and Kilimnik, Itay and Aigner, Stefan and Shankar, Archana and Mueller, Jasmine R and Schwartz, Schraga and Stern-Ginossar, Noam and Yeo, Gene W and Geula, Shay and Novershtern, Noa and Hanna, Jacob H} } @article {65642, title = {Controlling motor neurons of every muscle for fly proboscis reaching.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Jun 25}, abstract = {

We describe the anatomy of all the primary motor neurons in the fly proboscis and characterize their contributions to its diverse reaching movements. Pairing this behavior with the wealth of genetic tools offers the possibility to study motor control at single-neuron resolution, and soon throughout entire circuits. As an entry to these circuits, we provide detailed anatomy of proboscis motor neurons, muscles, and joints. We create a collection of fly strains to individually manipulate every proboscis muscle through control of its motor neurons, the first such collection for an appendage. We generate a model of the action of each proboscis joint, and find that only a small number of motor neurons are needed to produce proboscis reaching. Comprehensive control of each motor element in this numerically simple system paves the way for future study of both reflexive and flexible movements of this appendage.

}, issn = {2050-084X}, doi = {10.7554/eLife.54978}, author = {McKellar, Claire E and Siwanowicz, Igor and Dickson, Barry J and Simpson, Julie H} } @article {65600, title = {The corazonin-PTTH neuronal axis controls systemic body growth by regulating basal ecdysteroid biosynthesis in Drosophila melanogaster.}, journal = {Current Biology}, volume = {30}, year = {2020}, month = {2020 Jun 8}, pages = {2156-65}, abstract = {

Steroid hormones play key roles in development, growth, and reproduction in various animal phyla [1]. The insect steroid hormone, ecdysteroid, coordinates growth and maturation, represented by molting and metamorphosis [2]. In Drosophila melanogaster, the prothoracicotropic hormone (PTTH)-producing neurons stimulate peak levels of ecdysteroid biosynthesis for maturation [3]. Additionally, recent studies on PTTH signaling indicated that basal levels of ecdysteroid negatively affect systemic growth prior to maturation [4-8]. However, it remains unclear how PTTH signaling is regulated for basal ecdysteroid biosynthesis. Here, we report that Corazonin (Crz)-producing neurons regulate basal ecdysteroid biosynthesis by affecting PTTH neurons. Crz belongs to gonadotropin-releasing hormone (GnRH) superfamily, implying an analogous role in growth and maturation [9]. Inhibition of Crz neuronal activity increased pupal size, whereas it hardly affected pupariation timing. This phenotype resulted from enhanced growth rate and a delay in ecdysteroid elevation during the mid-third instar larval (L3) stage. Interestingly, Crz receptor (CrzR) expression in PTTH neurons was higher during the mid- than the late-L3 stage. Silencing of CrzR in PTTH neurons increased pupal size, phenocopying the inhibition of Crz neuronal activity. When Crz neurons were optogenetically activated, a strong calcium response was observed in PTTH neurons during the mid-L3, but not the late-L3, stage. Furthermore, we found that octopamine neurons contact Crz neurons in the subesophageal zone (SEZ), transmitting signals for systemic growth. Together, our results suggest that the Crz-PTTH neuronal axis modulates ecdysteroid biosynthesis in response to octopamine, uncovering a regulatory neuroendocrine system in the developmental transition from growth to maturation.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2020.03.050}, author = {Imura, Eisuke and Shimada-Niwa, Yuko and Nishimura, Takashi and H{\"u}ckesfeld, Sebastian and Schlegel, Philipp and Ohhara, Yuya and Kondo, Shu and Tanimoto, Hiromu and Cardona, Albert and Pankratz, Michael J and Niwa, Ryusuke} } @article {68479, title = {Core Competencies for Undergraduates in Bioengineering and Biomedical Engineering: Findings, Consequences, and Recommendations.}, journal = {Ann Biomed Eng}, volume = {48}, year = {2020}, month = {04/2020}, pages = {905-912}, abstract = {

This paper provides a synopsis of discussions related to biomedical engineering core curricula that occurred at the Fourth BME Education Summit held at Case Western Reserve University in Cleveland, Ohio in May 2019. This summit was organized by the Council of Chairs of Bioengineering and Biomedical Engineering, and participants included over 300 faculty members from 100+ accredited undergraduate programs. This discussion focused on six key questions: QI: Is there a core curriculum, and if so, what are its components? QII: How does our purported core curriculum prepare students for careers, particularly in industry? QIII: How does design distinguish BME/BIOE graduates from other engineers? QIV: What is the state of engineering analysis and systems-level modeling in BME/BIOE curricula? QV: What is the role of data science in BME/BIOE undergraduate education? QVI: What core experimental skills are required for BME/BIOE undergrads?\ s. Indeed, BME/BIOI core curricula exists and has matured to emphasize interdisciplinary topics such as physiology, instrumentation, mechanics, computer programming, and mathematical modeling. Departments demonstrate their own identities by highlighting discipline-specific sub-specialties. In addition to technical competence, Industry partners most highly value our students{\textquoteright} capacity for problem solving and communication. As such, BME/BIOE curricula includes open-ended projects that address unmet patient and clinician needs as primary methods to prepare graduates for careers in industry. Culminating senior design experiences distinguish BME/BIOE graduates through their development of client-centered engineering solutions to healthcare problems. Finally, the overall BME/BIOE curriculum is not stagnant-it is clear that data science will become an ever-important element of our students{\textquoteright} training and that new methods to enhance student engagement will be of pedagogical importance as we embark on the next decade.

}, keywords = {Biomedical Engineering, Curriculum, Data Science, Humans, Students, Universities}, issn = {1573-9686}, doi = {10.1007/s10439-020-02468-2}, author = {White, John A and Gaver, Donald P and Butera, Robert J and Choi, Bernard and Dunlop, Mary J and Grande-Allen, K Jane and Grosberg, Anna and Hitchcock, Robert W and Huang-Saad, Aileen Y and Kotche, Miiri and Kyle, Aaron M and Lerner, Amy L and Linehan, John H and Linsenmeier, Robert A and Miller, Michael I and Papin, Jason A and Setton, Lori and Sgro, Allyson and Smith, Michael L and Zaman, Muhammad and Lee, Abraham P} } @article {65372, title = {Correcting for physical distortions in visual stimuli improves reproducibility in zebrafish neuroscience.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Mar 24}, abstract = {

Breakthrough technologies for monitoring and manipulating single-neuron activity provide unprecedented opportunities for whole-brain neuroscience in larval zebrafish1{\textendash}9. Understanding the neural mechanisms of visually guided behavior also requires precise stimulus control, but little prior research has accounted for physical distortions that result from refraction and reflection at an air-water interface that usually separates the projected stimulus from the fish10{\textendash}12. Here we provide a computational tool that transforms between projected and received stimuli in order to detect and control these distortions. The tool considers the most commonly encountered interface geometry, and we show that this and other common configurations produce stereotyped distortions. By correcting these distortions, we reduced discrepancies in the literature concerning stimuli that evoke escape behavior13,14, and we expect this tool will help reconcile other confusing aspects of the literature. This tool also aids experimental design, and we illustrate the dangers that uncorrected stimuli pose to receptive field mapping experiments.

}, doi = {10.7554/eLife.53684}, url = {https://elifesciences.org/articles/53684https://cdn.elifesciences.org/articles/53684/elife-53684-v1.pdfhttps://cdn.elifesciences.org/articles/53684/elife-53684-v1.xml}, author = {Dunn, Timothy W and Fitzgerald, James E} } @article {65281, title = {Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells.}, journal = {Science}, volume = {367}, year = {2020}, month = {2020 Jan 17}, abstract = {

Within cells, the spatial compartmentalization of thousands of distinct proteins serves a multitude of diverse biochemical needs. Correlative super-resolution (SR) fluorescence and electron microscopy (EM) can elucidate protein spatial relationships to global ultrastructure, but has suffered from tradeoffs of structure preservation, fluorescence retention, resolution, and field of view. We developed a platform for three-dimensional cryogenic SR and focused ion beam-milled block-face EM across entire vitreously frozen cells. The approach preserves ultrastructure while enabling independent SR and EM workflow optimization. We discovered unexpected protein-ultrastructure relationships in mammalian cells including intranuclear vesicles containing endoplasmic reticulum-associated proteins, web-like adhesions between cultured neurons, and chromatin domains subclassified on the basis of transcriptional activity. Our findings illustrate the value of a comprehensive multimodal view of ultrastructural variability across whole cells.

}, issn = {1095-9203}, doi = {10.1126/science.aaz5357}, author = {Hoffman, David P and Shtengel, Gleb and Xu, C Shan and Campbell, Kirby R and Freeman, Melanie and Wang, Lei and Milkie, Daniel E and Pasolli, H Amalia and Iyer, Nirmala and Bogovic, John A and Stabley, Daniel R and Shirinifard, Abbas and Pang, Song and Peale, David and Schaefer, Kathy and Pomp, Wim and Chang, Chi-Lun and Lippincott-Schwartz, Jennifer and Kirchhausen, Tom and Solecki, David J and Betzig, Eric and Hess, Harald F} } @article {65259, title = {Cortical pattern generation during dexterous movement is input-driven.}, journal = {Nature}, volume = {577}, year = {2020}, month = {2020 Jan 16}, pages = {386-91}, abstract = {

The motor cortex controls skilled arm movement by sending temporal patterns of activity to lower motor centres. Local cortical dynamics are thought to shape these patterns throughout movement execution. External inputs have been implicated in setting the initial state of the motor cortex, but they may also have a pattern-generating role. Here we dissect the contribution of local dynamics and inputs to cortical pattern generation during a prehension task in mice. Perturbing cortex to an aberrant state prevented movement initiation, but after the perturbation was released, cortex either bypassed the normal initial state and immediately generated the pattern that controls reaching or failed to generate this pattern. The difference in these two outcomes was probably a result of external inputs. We directly investigated the role of inputs by inactivating the thalamus; this perturbed cortical activity and disrupted limb kinematics at any stage of the movement. Activation of thalamocortical axon terminals at different frequencies disrupted cortical activity and arm movement in a graded manner. Simultaneous recordings revealed that both thalamic activity and the current state of cortex predicted changes in cortical activity. Thus, the pattern generator for dexterous arm movement is distributed across multiple, strongly interacting brain regions.

}, issn = {1476-4687}, doi = {10.1038/s41586-019-1869-9}, author = {Sauerbrei, Britton A and Guo, Jian-Zhong and Cohen, Jeremy D and Mischiati, Matteo and Guo, Wendy and Kabra, Mayank and Verma, Nakul and Mensh, Brett and Branson, Kristin and Hantman, Adam W} } @article {65697, title = {Cortical RORβ is required for layer 4 transcriptional identity and barrel integrity.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Aug 27}, abstract = {

Retinoic Acid-Related Orphan Receptor Beta (RORβ) is a transcription factor (TF) and marker of layer 4 (L4) neurons, which are distinctive both in transcriptional identity and the ability to form aggregates such as barrels in rodent somatosensory cortex. However, the relationship between transcriptional identity and L4 cytoarchitecture is largely unknown. We find RORβ is required in the cortex for L4 aggregation into barrels and thalamocortical afferent (TCA) segregation. Interestingly, barrel organization also degrades with age in wildtype mice. Loss of RORβ delays excitatory input and disrupts gene expression and chromatin accessibility, with down-regulation of L4 and up-regulation of L5 genes, suggesting a disruption in cellular specification. Expression and binding site accessibility change for many other TFs, including closure of neurodevelopmental TF binding sites and increased expression and binding capacity of activity-regulated TFs. Lastly, a putative target of RORβ, , is down-regulated without RORβ, and knock-out alone disrupts TCA organization in adult barrels.

}, issn = {2050-084X}, doi = {10.7554/eLife.52370}, author = {Clark, Erin A and Rutlin, Michael and Capano, Lucia and Aviles, Samuel and Saadon, Jordan R and Taneja, Praveen and Zhang, Qiyu and Bullis, James B and Lauer, Timothy and Myers, Emma and Schulmann, Anton and Forrest, Douglas and Nelson, Sacha B} } @article {65869, title = {Cryo-EM structure of the inhibited (10S) form of myosin II.}, journal = {Nature}, volume = {588}, year = {2020}, month = {2020 Dec 02}, pages = {521-25}, abstract = {

Myosin II is the motor protein that enables muscle cells to contract and nonmuscle cells to move and change shape. The molecule has two identical heads attached to an elongated tail, and can exist in two conformations: 10S and 6S, named for their sedimentation coefficients. The 6S conformation has an extended tail and assembles into polymeric filaments, which pull on actin filaments to generate force and motion. In 10S myosin, the tail is folded into three segments and the heads bend back and interact with each other and the tail, creating a compact conformation in which ATPase activity, actin activation and filament assembly are all highly inhibited. This switched-off structure appears to function as a key energy-conserving storage molecule in muscle and nonmuscle cells, which can be activated to form functional filaments as needed-but the mechanism of its inhibition is not understood. Here we have solved the structure of smooth muscle 10S myosin by cryo-electron microscopy with sufficient resolution to enable improved understanding of the function of the head and tail regions of the molecule and of the key intramolecular contacts that cause inhibition. Our results suggest an atomic model for\ the off state of myosin II, for its activation and unfolding by phosphorylation, and for understanding the clustering of disease-causing mutations near sites of intramolecular interaction.

}, issn = {1476-4687}, doi = {10.1038/s41586-020-3007-0}, author = {Yang, Shixin and Tiwari, Prince and Lee, Kyoung Hwan and Sato, Osamu and Ikebe, Mitsuo and Padr{\'o}n, Ra{\'u}l and Craig, Roger} } @article {65698, title = {A cytometry-based assay to determine optimal Janelia Fluor dye labelling of Halo and SNAP tags.}, journal = {Journal of Biomolecular Techniques}, volume = {31}, year = {2020}, month = {2020 Aug}, pages = {S26}, abstract = {

When used in combination, self-labelling protein tags such as Halo, SNAP, and CLIP allow for the simultaneous visualization of proteins across a wide fluorescence spectrum. However, the combination of cell type, ligand binding and fluorescent dye chemistry introduces several variables that need to be determined to achieve orthogonal labelling. The Janelia Cell Culture Shared Resource in collaboration with a Research Scientist, and the Lavis Lab have developed a high throughput cytometry-based assay to determine optimal conditions for various combinations of cell type, ligand and JF dyes.

}, issn = {1943-4731}, author = {Schaefer, Kathy and Xie, Frank Liangqi and Weis-Garcia, Frances and White, Nicole} } @article {65799, title = {Dense and pleiotropic regulatory information in a developmental enhancer.}, journal = {Nature}, volume = {587}, year = {2020}, month = {2020 Nov 01}, pages = {235-39}, abstract = {

Changes in gene regulation underlie much of phenotypic evolution. However, our understanding of the potential for regulatory evolution is biased, because most evidence comes from either natural variation or limited experimental perturbations. Using an automated robotics pipeline, we surveyed an unbiased mutation library for a developmental enhancer in Drosophila melanogaster. We found that almost all mutations altered gene expression and that parameters of gene expression-levels, location, and state-were convolved. The widespread pleiotropic effects of most mutations may constrain the evolvability of developmental enhancers. Consistent with these observations, comparisons of diverse Drosophila larvae revealed apparent biases in the phenotypes influenced by the enhancer. Developmental enhancers may encode a higher density of regulatory information than has been appreciated previously, imposing constraints on regulatory evolution.

}, issn = {1476-4687}, doi = {10.1038/s41586-020-2816-5}, author = {Fuqua, Timothy and Jordan, Jeff and van Breugel, Maria Elize and Halavatyi, Aliaksandr and Tischer, Christian and Polidoro, Peter and Abe, Namiko and Tsai, Albert and Mann, Richard S and Stern, David L and Crocker, Justin} } @article {65725, title = {Dense neuronal reconstruction through X-ray holographic nano-tomography.}, journal = {Nature Neuroscience}, volume = {23}, year = {2020}, month = {2020 Dec -1}, pages = {1637-43}, abstract = {

Imaging neuronal networks provides a foundation for understanding the nervous system, but resolving dense nanometer-scale structures over large volumes remains challenging for light microscopy (LM) and electron microscopy (EM). Here we show that X-ray holographic nano-tomography (XNH) can image millimeter-scale volumes with sub-100-nm resolution, enabling reconstruction of dense wiring in Drosophila melanogaster and mouse nervous tissue. We performed correlative XNH and EM to reconstruct hundreds of cortical pyramidal cells and show that more superficial cells receive stronger synaptic inhibition on their apical dendrites. By combining multiple XNH scans, we imaged an adult Drosophila leg with sufficient resolution to comprehensively catalog mechanosensory neurons and trace individual motor axons from muscles to the central nervous system. To accelerate neuronal reconstructions, we trained a convolutional neural network to automatically segment neurons from XNH volumes. Thus, XNH bridges a key gap between LM and EM, providing a new avenue for neural circuit discovery.

}, issn = {1546-1726}, doi = {10.1038/s41593-020-0704-9}, author = {Kuan, Aaron T and Phelps, Jasper S and Thomas, Logan A and Nguyen, Tri M and Han, Julie and Chen, Chiao-Lin and Azevedo, Anthony W and Tuthill, John C and Funke, Jan and Cloetens, Peter and Pacureanu, Alexandra and Lee, Wei-Chung Allen} } @article {68341, title = {Dense reconstruction of elongated cell lineages: overcoming suboptimum lineage encoding and sparse cell sampling}, journal = {bioRxiv}, year = {2020}, month = {07/2020}, abstract = {

Acquiring both lineage and cell-type information during brain development could elucidate transcriptional programs underling neuronal diversification. This is now feasible with single-cell RNA-seq combined with CRISPR-based lineage tracing, which generates genetic barcodes with cumulative CRISPR edits. This technique has not yet been optimized to deliver high-resolution lineage reconstruction of protracted lineages. Drosophila neuronal lineages are an ideal model to consider, as multiple lineages have been morphologically mapped at single-cell resolution. Here we find the parameter ranges required to encode a representative neuronal lineage emanating from 100 stem cell divisions. We derive the optimum editing rate to be inversely proportional to lineage depth, enabling encoding to persist across lineage progression. Further, we experimentally determine the editing rates of a Cas9-deaminase in cycling neural stem cells, finding near ideal rates to map elongated Drosophila neuronal lineages. Moreover, we propose and evaluate strategies to separate recurring cell-types for lineage reconstruction. Finally, we present a simple method to combine multiple experiments, which permits dense reconstruction of protracted cell lineages despite suboptimum lineage encoding and sparse cell sampling.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2020.07.27.223321}, url = {https://www.biorxiv.org/content/early/2020/07/29/2020.07.27.223321}, author = {Sugino, Ken and Miyares, Rosa L. and Espinosa-Medina, Isabel and Chen, Hui-Min and Potter, Christopher J and Lee, Tzumin} } @conference {65612, title = {Detecting the Starting Frame of Actions in Video}, booktitle = {2020 IEEE Winter Conference on Applications of Computer Vision (WACV)}, year = {2020}, month = {2020 May 14}, publisher = {IEEE}, organization = {IEEE}, address = {Snowmass Village, CO, USA}, abstract = {

In this work, we address the problem of precisely localizing key frames of an action, for example, the precise time that a pitcher releases a baseball, or the precise time that a crowd begins to applaud. Key frame localization is a largely overlooked and important action-recognition problem, for example in the field of neuroscience, in which we would like to understand the neural activity that produces the start of a bout of an action. To address this problem, we introduce a novel structured loss function that properly weights the types of errors that matter in such applications: it more heavily penalizes extra and missed action start detections over small misalignments. Our structured loss is based on the best matching between predicted and labeled action starts. We train recurrent neural networks (RNNs) to minimize differentiable approximations of this loss. To evaluate these methods, we introduce the Mouse Reach Dataset, a large, annotated video dataset of mice performing a sequence of actions. The dataset was collected and labeled by experts for the purpose of neuroscience research. On this dataset, we demonstrate that our method outperforms related approaches and baseline methods using an unstructured loss.

}, doi = {10.1109/WACV45572.202010.1109/WACV45572.2020.9093405}, url = {https://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=9087828}, author = {Kwak, Iljung S. and Guo, Jian-Zhong and Hantman, Adam and Branson, Kristin and Kriegman, David} } @article {65644, title = {Dielectric confinement and excitonic effects in two-dimensional nanoplatelets.}, journal = {ACS Nano}, year = {2020}, month = {2020 Jul 01}, abstract = {

Quasi-two-dimensional (2D) semiconductor nanoplatelets manifest strong quantum confinement with exceptional optical characteristics of narrow photoluminescence peaks with energies tunable by thickness with monolayer precision. We employed scanning tunneling spectroscopy (STS) in conjunction with optical measurements to probe the thickness-dependent band gap and density of excited states in a series of CdSe nanoplatelets. The tunneling spectra, measured in the double-barrier tunnel junction configuration, reveal the effect of quantum confinement on the band gap taking place mainly through a blue-shift of the conduction band edge, along with a signature of 2D electronic structure intermixed with finite lateral-size and/or defects effects. The STS fundamental band gaps are larger than the optical gaps as expected from the contributions of exciton binding in the absorption, as confirmed by theoretical calculations. The calculations also point to strong valence band mixing between the light- and split-off hole levels. Strikingly, the energy difference between the heavy-hole and light-hole levels in the tunneling spectra are significantly larger than the corresponding values extracted from the absorption spectra. Possible explanations for this, including an interplay of nanoplatelet charging, dielectric confinement, and difference in exciton binding energy for light and heavy holes, are analyzed and discussed.

}, issn = {1936-086X}, doi = {10.1021/acsnano.0c01950}, author = {Ji, Botao and Rabani, Eran and Efros, Alexander L and Vaxenburg, Roman and Ashkenazi, Or and Azulay, Doron and Banin, Uri and Millo, Oded} } @article {65902, title = {Directed Evolution of a Selective and Sensitive Serotonin Sensor via Machine Learning.}, journal = {Cell}, volume = {183}, year = {2020}, month = {2020 Dec 23}, pages = {1986-2002.e26}, abstract = {

Serotonin plays a central role in cognition and is the target of most pharmaceuticals for psychiatric disorders. Existing drugs have limited efficacy; creation of improved versions will require better understanding of serotonergic circuitry, which has been hampered by our inability to monitor serotonin release and transport with high spatial and temporal resolution. We developed and applied a binding-pocket redesign strategy, guided by machine learning, to create a high-performance, soluble, fluorescent serotonin sensor (iSeroSnFR), enabling optical detection of millisecond-scale serotonin transients. We demonstrate that iSeroSnFR can be used to detect serotonin release in freely behaving mice during fear conditioning, social interaction, and sleep/wake transitions. We also developed a robust assay of serotonin transporter function and modulation by drugs. We expect that both machine-learning-guided binding-pocket redesign and iSeroSnFR will have broad utility for the development of other sensors and in\ vitro and in\ vivo serotonin detection, respectively.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2020.11.040}, author = {Unger, Elizabeth K and Keller, Jacob P and Altermatt, Michael and Liang, Ruqiang and Matsui, Aya and Dong, Chunyang and Hon, Olivia J and Yao, Zi and Sun, Junqing and Banala, Samba and Flanigan, Meghan E and Jaffe, David A and Hartanto, Samantha and Carlen, Jane and Mizuno, Grace O and Borden, Phillip M and Shivange, Amol V and Cameron, Lindsay P and Sinning, Steffen and Underhill, Suzanne M and Olson, David E and Amara, Susan G and Temple Lang, Duncan and Rudnick, Gary and Marvin, Jonathan S and Lavis, Luke D and Lester, Henry A and Alvarez, Veronica A and Fisher, Andrew J and Prescher, Jennifer A and Kash, Thomas L and Yarov-Yarovoy, Vladimir and Gradinaru, Viviana and Looger, Loren L and Tian, Lin} } @article {65871, title = {Distributed control of motor circuits for backward walking in Drosophila.}, journal = {Nature Communications}, volume = {11}, year = {2020}, month = {2020 Dec 02}, pages = {6166}, abstract = {

How do descending inputs from the brain control leg motor circuits to change how an animal walks? Conceptually, descending neurons are thought to function either as command-type neurons, in which a single type of descending neuron exerts a high-level control to elicit a coordinated change in motor output, or through a population coding mechanism, whereby a group of neurons, each with local effects, act in combination to elicit a global motor response. The Drosophila Moonwalker Descending Neurons (MDNs), which alter leg motor circuit dynamics so that the fly walks backwards, exemplify the command-type mechanism. Here, we identify several dozen MDN target neurons within the leg motor circuits, and show that two of them mediate distinct and highly-specific changes in leg muscle activity during backward walking: LBL40 neurons provide the hindleg power stroke during stance phase; LUL130 neurons lift the legs at the end of stance to initiate swing. Through these two effector neurons, MDN directly controls both the stance and swing phases of the backward stepping cycle. These findings suggest that command-type descending neurons can also operate through the distributed control of local motor circuits.

}, issn = {2041-1723}, doi = {10.1038/s41467-020-19936-x}, author = {Feng, Kai and Sen, Rajyashree and minegishi, ryo and D{\"u}bbert, Michael and Bockem{\"u}hl, Till and B{\"u}schges, Ansgar and Dickson, Barry J} } @article {65904, title = {DNA damage alters nuclear mechanics through chromatin reorganization.}, journal = {Nucleic Acids Research}, year = {2020}, month = {2020 Dec 16}, abstract = {

DNA double-strand breaks drive genomic instability. However, it remains unknown how these processes may affect the biomechanical properties of the nucleus and what role nuclear mechanics play in DNA damage and repair efficiency. Here, we have used Atomic Force Microscopy to investigate nuclear mechanical changes, arising from externally induced DNA damage. We found that nuclear stiffness is significantly reduced after cisplatin treatment, as a consequence of DNA damage signalling. This softening was linked to global chromatin decondensation, which improves molecular diffusion within the organelle. We propose that this can increase recruitment for repair factors. Interestingly, we also found that reduction of nuclear tension, through cytoskeletal relaxation, has a protective role to the cell and reduces accumulation of DNA damage. Overall, these changes protect against further genomic instability and promote DNA repair. We propose that these processes may underpin the development of drug resistance.

}, issn = {1362-4962}, doi = {10.1093/nar/gkaa1202}, author = {Dos Santos, {\'A}lia and Cook, Alexander W and Gough, Rosemarie E and Schilling, Martin and Olszok, Nora A and Brown, Ian and Wang, Lin and Aaron, Jesse and Martin-Fernandez, Marisa L and Rehfeldt, Florian and Toseland, Christopher P} } @article {65655, title = {The Drosophila mushroom body: From architecture to algorithm in a learning circuit.}, journal = {Annual Review of Neuroscience}, volume = {43}, year = {2020}, month = {2020 Jul 08}, pages = {465-484}, abstract = {

The brain contains a relatively simple circuit for forming Pavlovian associations, yet it achieves many operations common across memory systems. Recent advances have established a clear framework for learning and revealed the following key operations: ) pattern separation, whereby dense combinatorial representations of odors are preprocessed to generate highly specific, nonoverlapping odor patterns used for learning; ) convergence, in which sensory information is funneled to a small set of output neurons that guide behavioral actions; ) plasticity, where changing the mapping of sensory input to behavioral output requires a strong reinforcement signal, which is also modulated by internal state and environmental context; and ) modularization, in which a memory consists of multiple parallel traces, which are distinct in stability and flexibility and exist in anatomically well-defined modules within the network. Cross-module interactions allow for higher-order effects where past experience influences future learning. Many of these operations have parallels with processes of memory formation and action selection in more complex brains.

}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-080317-0621333}, author = {Modi, Mehrab N and Shuai, Yichun and Turner, Glenn C} } @article {68477, title = {Eco-evolutionary significance of "loners".}, journal = {PLoS Biol}, volume = {18}, year = {2020}, month = {03/2020}, pages = {e3000642}, abstract = {

Loners-individuals out of sync with a coordinated majority-occur frequently in nature. Are loners incidental byproducts of large-scale coordination attempts, or are they part of a mosaic of life-history strategies? Here, we provide empirical evidence of naturally occurring heritable variation in loner behavior in the model social amoeba Dictyostelium discoideum. We propose that Dictyostelium loners-cells that do not join the multicellular life stage-arise from a dynamic population-partitioning process, the result of each cell making a stochastic, signal-based decision. We find evidence that this imperfectly synchronized multicellular development is affected by both abiotic (environmental porosity) and biotic (signaling) factors. Finally, we predict theoretically that when a pair of strains differing in their partitioning behavior coaggregate, cross-signaling impacts slime-mold diversity across spatiotemporal scales. Our findings suggest that loners could be critical to understanding collective and social behaviors, multicellular development, and ecological dynamics in D. discoideum. More broadly, across taxa, imperfect coordination of collective behaviors might be adaptive by enabling diversification of life-history strategies.

}, keywords = {Biological Evolution, Dictyostelium, Models, Biological, Quorum Sensing, Spatio-Temporal Analysis, Stochastic Processes}, issn = {1545-7885}, doi = {10.1371/journal.pbio.3000642}, author = {Rossine, Fernando W and Martinez-Garcia, Ricardo and Sgro, Allyson E and Gregor, Thomas and Tarnita, Corina E} } @article {65583, title = {Effect of circuit structure on odor representation in the insect olfactory system.}, journal = {eNeuro}, volume = {7}, year = {2020}, month = {2020 May}, pages = {1-12}, abstract = {

In Neuroscience, the structure of a circuit has often been used to intuit function - an inversion of Louis Kahn{\textquoteright}s famous dictum, {\textquoteleft}Form follows function{\textquoteright} (Kristan and Katz 2006). However, different brain networks may utilize different network architectures to solve the same problem. The olfactory circuits of two insects, the Locust, and the fruit fly, , serve the same function - to identify and discriminate odors. The neural circuitry that achieves this shows marked structural differences. Projection neurons (PN) in the antennal lobe (AL) innervate Kenyon cells (KC) of the mushroom body (MB). In locust, each KC receives inputs from \~{}50\% PNs, a scheme that maximizes the difference between inputs to any two of \~{}50,000 KCs. In contrast, in drosophila, this number is only 5\% and appears sub-optimal. Using a computational model of the olfactory system, we show the activity of KCs is sufficiently high-dimensional that it can separate similar odors regardless of the divergence of PN-KC connections. However, when temporal patterning encodes odor attributes, dense connectivity outperforms sparse connections.Increased separability comes at the cost of reliability. The disadvantage of sparse connectivity can be mitigated by incorporating other aspects of circuit architecture seen in drosophila. Our simulations predict that drosophila and locust circuits lie at different ends of a continuum where the drosophila gives up on the ability to resolve similar odors to generalize across varying environments, while the locust separates odor representations but risks misclassifying noisy variants of the same odor. How does the structure of a network affect its function? We address this question in the context of two olfactory systems that serve the same function, to distinguish the attributes of different odorants, but do so using markedly distinct architectures. In the locust, the probability of connections between projection neurons and Kenyon cells - a layer downstream - is nearly 50\%. In contrast, this number is merely 5\% in drosophila. We developed computational models of these networks to understand the relative advantages of each connectivity. Our analysis reveals that the two systems exist along a continuum of possibilities that balance two conflicting goals - separating the representations of similar odors while grouping together noisy variants of the same odor.

}, issn = {2373-2822}, doi = {10.1523/ENEURO.0130-19.2020}, author = {Rajagopalan, Adithya and Assisi, Collins} } @article {65675, title = {Efficient coding of natural scene statistics predicts discrimination thresholds for grayscale textures.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Aug 3}, abstract = {

Previously, in (Hermundstad et al., 2014), we showed that when sampling is limiting, the efficient coding principle leads to a {\textquoteright}variance is salience{\textquoteright} hypothesis, and that this hypothesis accounts for visual sensitivity to binary image statistics. Here, using extensive new psychophysical data and image analysis, we show that this hypothesis accounts for visual sensitivity to a large set of grayscale image statistics at a striking level of detail, and also identify the limits of the prediction. We define a 66-dimensional space of local grayscale light-intensity correlations, and measure the relevance of each direction to natural scenes. The {\textquoteright}variance is salience{\textquoteright} hypothesis predicts that two-point correlations are most salient, and predicts their relative salience. We tested these predictions in a texture-segregation task using un-natural, synthetic textures. As predicted, correlations beyond second order are not salient, and predicted thresholds for over 300 second-order correlations match psychophysical thresholds closely (median fractional error \< 0:13).

}, doi = {10.7554/eLife.54347}, url = {https://elifesciences.org/articles/54347}, author = {Tesileanu, Tiberiu and Conte, Mary M and Briguglio, John J and Hermundstad, Ann M and Victor, Jonathan D and Balasubramanian, Vijay} } @article {65626, title = {Employing NaChBac for cryo-EM analysis of toxin action on voltage-gated Na+ channels in nanodisc}, journal = {Proceedings of the National Academy of Sciences of the U.S.A.}, volume = {117}, year = {2020}, month = {2020 Jun 23}, pages = {14187-93}, abstract = {

NaChBac, the first bacterial voltage-gated Na+\ (Nav) channel to be characterized, has been the prokaryotic prototype for studying the structure{\textendash}function relationship of Nav\ channels. Discovered nearly two decades ago, the structure of NaChBac has not been determined. Here we present the single particle electron cryomicroscopy (cryo-EM) analysis of NaChBac in both detergent micelles and nanodiscs. Under both conditions, the conformation of NaChBac is nearly identical to that of the potentially inactivated NavAb. Determining the structure of NaChBac in nanodiscs enabled us to examine gating modifier toxins (GMTs) of Nav\ channels in lipid bilayers. To study GMTs in mammalian Nav\ channels, we generated a chimera in which the extracellular fragment of the S3 and S4 segments in the second voltage-sensing domain from Nav1.7 replaced the corresponding sequence in NaChBac. Cryo-EM structures of the nanodisc-embedded chimera alone and in complex with HuwenToxin IV (HWTX-IV) were determined to 3.5 and 3.2 {\r A} resolutions, respectively. Compared to the structure of HWTX-IV{\textendash}bound human Nav1.7, which was obtained at an overall resolution of 3.2 {\r A}, the local resolution of the toxin has been improved from \~{}6 to \~{}4 {\r A}. This resolution enabled visualization of toxin docking. NaChBac can thus serve as a convenient surrogate for structural studies of the interactions between GMTs and Nav\ channels in a membrane environment.

}, issn = {0027-8424}, doi = {10.1073/pnas.1922903117}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1922903117https://syndication.highwire.org/content/doi/10.1073/pnas.1922903117}, author = {Gao, Shuai and Valinsky, William C. and On, Nguyen Cam and Houlihan, Patrick R. and Qu, Qian and Liu, Lei and Pan, Xiaojing and Clapham, David E. and Yan, Nieng} } @article {65622, title = {Enhanced Golic+: Highly effective CRISPR gene targeting and transgene HACKing in .}, journal = {Development}, year = {2020}, month = {2020 May 28}, abstract = {

Gene targeting is an incredibly valuable technique. Sometimes however, it can also be extremely challenging for various intrinsic reasons (e.g. low target accessibility or nature/extent of gene modification). To bypass these barriers, we designed a transgene-based system in Drosophila that increases the number of independent gene targeting events while at the same time enriching for correctly targeted progeny. Unfortunately, with particularly challenging gene targeting experiments, our original design yielded numerous false positives. Here we deliver a much-improved technique named Enhanced Golic+ (E-Golic+). E-Golic+ incorporates genetic modifications to tighten lethality-based selection while simultaneously boosting efficiency. With E-Golic+, we easily achieve previously unattainable gene targeting. Additionally, we built an E-Golic+ based, high-efficiency genetic pipeline for transgene swapping. We demonstrate its utility by transforming GAL4 enhancer-trap lines into tissue-specific Cas9-expressing lines. Given the superior efficiency, specificity and scalability, E-Golic+ promises to expedite development of additional sophisticated genetic/genomic tools in .

}, issn = {1477-9129}, doi = {10.1242/dev.181974}, author = {Chen, Hui-Min and Yao, Xiaohao and Ren, Qingzhong and Chang, Chuan-Chie and Liu, Ling-Yu and Miyares, Rosa Linda and Lee, Tzumin} } @article {66017, title = {An enzymatic toolkit for selective proteolysis, detection, and visualization of mucin-domain glycoproteins}, journal = {Proceedings of the National Academy of Sciences}, volume = {117}, year = {2020}, month = {Jan-09-2020}, pages = {21299 - 21307}, abstract = {

Densely O-glycosylated mucin domains are found in a broad range of cell surface and secreted proteins, where they play key physiological roles. In addition, alterations in mucin expression and glycosylation are common in a variety of human diseases, such as cancer, cystic fibrosis, and inflammatory bowel diseases. These correlations have been challenging to uncover and establish because tools that specifically probe mucin domains are lacking. Here, we present a panel of bacterial proteases that cleave mucin domains via distinct peptide- and glycan-based motifs, generating a diverse enzymatic toolkit for mucin-selective proteolysis. By mutating catalytic residues of two such enzymes, we engineered mucin-selective binding agents with retained glycoform preferences. StcEE447D\ is a pan-mucin stain derived from enterohemorrhagic\ Escherichia coli\ that is tolerant to a wide range of glycoforms. BT4244E575A\ derived from\ Bacteroides thetaiotaomicron\ is selective for truncated, asialylated core 1 structures commonly associated with malignant and premalignant tissues. We demonstrated that these catalytically inactive point mutants enable robust detection and visualization of mucin-domain glycoproteins by flow cytometry, Western blot, and immunohistochemistry. Application of our enzymatic toolkit to ascites fluid and tissue slices from patients with ovarian cancer facilitated characterization of patients based on differences in mucin cleavage and expression patterns.

}, issn = {0027-8424}, doi = {10.1073/pnas.2012196117}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.2012196117https://syndication.highwire.org/content/doi/10.1073/pnas.2012196117http://www.pnas.org/syndication/doi/10.1073/pnas.2012196117}, author = {Shon, D. Judy and Malaker, Stacy A. and Pedram, Kayvon and Yang, Emily and Krishnan, Venkatesh and Dorigo, Oliver and Bertozzi, Carolyn R.} } @article {65367, title = {ER membranes exhibit phase behavior at sites of organelle contact.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, year = {2020}, month = {2020 March 31}, pages = {7225-7235}, abstract = {

The endoplasmic reticulum (ER) is the site of synthesis of secretory and membrane proteins and contacts every organelle of the cell, exchanging lipids and metabolites in a highly regulated manner. How the ER spatially segregates its numerous and diverse functions, including positioning nanoscopic contact sites with other organelles, is unclear. We demonstrate that hypotonic swelling of cells converts the ER and other membrane-bound organelles into micrometer-scale large intracellular vesicles (LICVs) that retain luminal protein content and maintain contact sites with each other through localized organelle tethers. Upon cooling, ER-derived LICVs phase-partition into microscopic domains having different lipid-ordering characteristics, which is reversible upon warming. Ordered ER lipid domains mark contact sites with ER and mitochondria, lipid droplets, endosomes, or plasma membrane, whereas disordered ER lipid domains mark contact sites with lysosomes or peroxisomes. Tethering proteins concentrate at ER{\textendash}organelle contact sites, allowing time-dependent behavior of lipids and proteins to be studied at these sites. These findings demonstrate that LICVs provide a useful model system for studying the phase behavior and interactive properties of organelles in intact cells.

}, issn = {0027-8424}, doi = {10.1073/pnas.1910854117}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1910854117}, author = {King, Christopher and Sengupta, Prabuddha and Seo, Arnold Y. and Lippincott-Schwartz, Jennifer} } @article {65727, title = {Erasable labeling of neuronal activity using a reversible calcium marker.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Sep 15}, abstract = {

Understanding how the brain encodes and processes information requires the recording of neural activity that underlies different behaviors. Recent efforts in fluorescent protein engineering have succeeded in developing powerful tools for visualizing neural activity, in general by coupling neural activity to different properties of a fluorescent protein scaffold. Here, we take advantage of a previously unexploited class of reversibly switchable fluorescent proteins to engineer a new type of calcium sensor. We introduce rsCaMPARI, a genetically encoded calcium marker engineered from a reversibly switchable fluorescent protein that enables spatiotemporally precise marking, erasing, and remarking of active neuron populations under brief, user-defined time windows of light exposure. rsCaMPARI photoswitching kinetics are modulated by calcium concentration when illuminating with blue light, and the fluorescence can be reset with violet light. We demonstrate the utility of rsCaMPARI for marking and remarking active neuron populations in freely swimming zebrafish.

}, issn = {2050-084X}, doi = {10.7554/eLife.57249}, author = {Sha, Fern and Abdelfattah, Ahmed S and Patel, Ronak and Schreiter, Eric R} } @article {65295, title = {Estimating the power of sequence covariation for detecting conserved RNA structure.}, journal = {Bioinformatics}, volume = {36}, year = {2020}, month = {2020 May 01}, pages = {3072-76}, abstract = {

Pairwise sequence covariations are a signal of conserved RNA secondary structure. We describe a method for distinguishing when lack of covariation signal can be taken as evidence against a conserved RNA structure, as opposed to when a sequence alignment merely has insufficient variation to detect covariations. We find that alignments for several long noncoding RNAs previously shown to lack covariation support do have adequate covariation detection power, providing additional evidence against their proposed conserved structures.

}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btaa080}, url = {https://doi.org/10.1093/bioinformatics/btaa080}, author = {Rivas, Elena and Clements, Jody and Eddy, Sean R}, editor = {Ponty, Yann} } @article {65858, title = {The evolution of a cell biologist.}, journal = {Molecular Biology of the Cell}, volume = {31}, year = {2020}, month = {2020 Dec 01}, pages = {2763-2767}, abstract = {

I am honored and humbled to receive the E. B. Wilson Medal and happy to share some reflections on my journey as a cell biologist. It took me a while to realize that my interest in biology would center on how cells are spatially and dynamically organized. From an initial fascination with cellular structures I came to appreciate that cells exhibit dynamism across all scales-from their molecules, to molecular complexes, to organelles. Uncovering the principles of this dynamism, including new ways to observe and quantify it, has been the guiding star of my work.

}, issn = {1939-4586}, doi = {10.1091/mbc.E20-09-0603}, author = {Lippincott-Schwartz, Jennifer} } @article {65737, title = {Exploring internal state-coding across the rodent brain.}, journal = {Current Opinion in Neurobiology}, volume = {65}, year = {2020}, month = {2020 Sep 17}, pages = {20-26}, abstract = {

The influence of peripheral physiology on goal-directed behavior involves specialized interoceptive sensory neurons that signal internal state to the brain. Here, we review recent progress to examine the impact of these specialized cell types on neurons and circuits throughout the central nervous system. These new approaches are important for understanding how the needs of the body interact and guide goal-directed behaviors.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2020.08.009}, author = {Sternson, Scott M} } @article {65720, title = {Extensive and spatially variable within-cell-type heterogeneity across the basolateral amygdala.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Sep 01}, abstract = {

The basolateral amygdala complex (BLA), extensively connected with both local amygdalar nuclei as well as long-range circuits, is involved in a diverse array of functional roles. Understanding the mechanisms of such functional diversity will be greatly informed by understanding the cell-type-specific landscape of the BLA. Here, beginning with single-cell RNA sequencing, we identified both discrete and graded continuous gene-expression differences within the mouse BLA. Via in situ hybridization, we next mapped this discrete transcriptomic heterogeneity onto a sharp spatial border between the basal and lateral amygdala nuclei, and identified continuous spatial gene-expression gradients within each of these regions. These discrete and continuous spatial transformations of transcriptomic cell-type identity were recapitulated by local morphology as well as long-range connectivity. Thus, BLA excitatory neurons are a highly heterogenous collection of neurons that spatially covary in molecular, cellular, and circuit properties. This heterogeneity likely drives pronounced spatial variation in BLA computation and function.

}, issn = {2050-084X}, doi = {10.7554/eLife.59003}, author = {O{\textquoteright}Leary, Timothy P and Sullivan, Kaitlin E and Wang, Lihua and Clements, Jody and Lemire, Andrew L and Cembrowski, Mark S} } @article {67704, title = {Extracellular glutamate and GABA transients at the transition from interictal spiking to seizures}, journal = {bioRxiv}, year = {2020}, month = {2020 Nov 15}, abstract = {

Focal epilepsy is associated with intermittent brief population discharges (interictal spikes), which resemble sentinel spikes that often occur at the onset of seizures. Why interictal spikes self-terminate whilst seizures persist and propagate is incompletely understood. Here we use fluorescent glutamate and GABA sensors in an awake rodent model of neocortical seizures to resolve the spatiotemporal evolution of both neurotransmitters in the extracellular space. Interictal spikes are accompanied by brief glutamate transients which are maximal at the initiation site and rapidly propagate centrifugally. GABA transients last longer than glutamate transients and are maximal ~1.5 mm from the focus where they propagate centripetally. At the transition to seizures, GABA transients are attenuated, whilst glutamate transients increase in spatial extent. The data imply that an annulus of feed-forward GABA release intermittently collapses, allowing seizures to escape from local inhibitory restraint.

}, doi = {10.1101/2020.11.13.381707}, author = {Yoshiteru Shimoda and Vincent Magloire and Jonathan S Marvin and Marco Leite and Loren L Looger and Dimitri M Kullmann} } @article {65763, title = {A far-red fluorescent chemogenetic reporter for in vivo molecular imaging}, journal = {Angewandte Chemie International Edition}, year = {2020}, month = {06/2020}, abstract = {

Far-red emitting fluorescent labels are highly desirable for spectral multiplexing and deep tissue imaging. Here, we describe the generation of frFAST (far-red Fluorescence Activating and absorption Shifting Tag), a 14-kDa monomeric protein that forms a bright far-red fluorescent assembly with (4-hydroxy-3-methoxy-phenyl)allylidene rhodanine (HPAR-3OM). As HPAR-3OM is essentially non- fluorescent in solution and in cells, frFAST can be imaged with high contrast in presence of free HPAR-3OM, which allowed the rapid and efficient imaging of frFAST fusions in live cells, zebrafish embryo/larvae and chicken embryo. Beyond enabling genetic encoding of far-red fluorescence, frFAST allowed the design of a far- red chemogenetic reporter of protein-protein interactions, demonstrating its great potential for the design of innovative far-red emitting biosensors.

}, issn = {1433-7851}, doi = {10.1002/anie.202006576}, author = {Li, Chenge and Tebo, Alison G and Thauvin, Marion and Plamont, Marie-Aude and Volovitch, Michel and Morin, Xavier and Vriz, Sophie and Gautier, Arnaud} } @article {65300, title = {A fast genetically encoded fluorescent sensor for faithful in vivo acetylcholine detection in mice, fish, worms and flies.}, journal = {bioRxiv}, year = {2020}, month = {2020 Feb 8}, abstract = {

Here we design and optimize a genetically encoded fluorescent indicator, iAChSnFR, for the ubiquitous neurotransmitter acetylcholine, based on a bacterial periplasmic binding protein. iAChSnFR shows large fluorescence changes, rapid rise and decay kinetics, and insensitivity to most cholinergic drugs. iAChSnFR revealed large transients in a variety of slice and\ in vivo\ preparations in mouse, fish, fly and worm. iAChSnFR will be useful for the study of acetylcholine in all animals.

}, doi = {https://doi.org/10.1101/2020.02.07.939504}, author = {Borden, Philip and Zhang, Peng and Shivange, Amol V and Marvin, Jonathan S and Cichon, Joseph and Dan, Chuntao and Podgorski, Kaspar and Figueiredo, Antonio and Novak, Ondrej and Tanimoto, Masashi and Shigetomi, Eiji and Lobas, Mark A and Kim, Hyuntae and Zhu, Paula and Zhang, Yajun and Zheng, W. Sharon and Fan, ChengCheng and Wang, Guangfu and Xiang, Bowen and Gan, Li and Zhang, Guang-Xian and Guo, Kaiming and Lin, Li and Cai, Yuan and Yee, Andrew G. and Aggarwal, Aman and Ford, Christopher P. and Rees, Douglas C. and Dietrich, Dirk and Khakh, Baljit S. and Dittman, Jeremy S. and Gan, Wen-Biao and Koyama, Minoru and Jayaraman, Vivek and Cheer, Joseph F. and Lester, Henry A. and Zhu, J. Julius and Looger, Loren L.} } @article {65625, title = {First occurrence of the pest Drosophila suzukii (Diptera: Drosophilidae) in the Comoros Archipelago (Western Indian Ocean)}, journal = {African Entomology}, volume = {28}, year = {2020}, month = {2020 Jun 04}, pages = {78}, abstract = {

Drosophila suzukii\ (Matsumura, 1931) is an Asian pest of grapes and other soft fruits that has invaded North America and Europe during the last decade. Here we report its recent occurrence on two islands of the Comoros archipelago in the Mozambique Channel, namely Mayotte and Ngazidja (Grande Comore), in April 2017 and November 2018, respectively. We also document its absence from other African islands in the Mozambique Channel and the Western Indian Ocean including Mayotte until 2013.\ Drosophila ashburneriTsacas, 1984\ is the only member of the\ suzukii\ species subgroup known from the Comoros, but it is morphologically distinct and likely distantly related to\ D.\ suzukii.\ Drosophila suzukii\ has likely been recently introduced to the Comoros archipelago, perhaps from La R{\'e}union island where it first appeared in November 2013. On all of these tropical islands,\ D.\ suzukii\ was found in high-altitude habitats in agreement with its adaptation to cold environments. These results suggest the high susceptibility of highlands in eastern and southern Africa to be infested by this pest in the near future.

}, doi = {10.4001/003.028.0078}, url = {https://bioone.org/journals/african-entomology/volume-28/issue-1/003.028.0078/First-occurrence-of-the-pest-Drosophila-suzukii-Diptera--Drosophilidae/10.4001/003.028.0078.full}, author = {Hassani, I.M. and Behrman, E.L. and Prigent, S.R. and Gidaszewski, N. and Ravaomanarivo, L.H. Raveloson and Suwalski, A. and Debat, V. and David, J.R. and Yassin, A.} } @article {65602, title = {FMNL2 regulates dynamics of fascin in filopodia.}, journal = {Journal of Cell Biology}, volume = {219}, year = {2020}, month = {2020 May 04}, abstract = {

Filopodia are peripheral F-actin-rich structures that enable cell sensing of the microenvironment. Fascin is an F-actin-bundling protein that plays a key role in stabilizing filopodia to support efficient adhesion and migration. Fascin is also highly up-regulated in human cancers, where it increases invasive cell behavior and correlates with poor patient prognosis. Previous studies have shown that fascin phosphorylation can regulate F-actin bundling, and that this modification can contribute to subcellular fascin localization and function. However, the factors that regulate fascin dynamics within filopodia remain poorly understood. In the current study, we used advanced live-cell imaging techniques and a fascin biosensor to demonstrate that fascin phosphorylation, localization, and binding to F-actin are highly dynamic and dependent on local cytoskeletal architecture in cells in both 2D and 3D environments. Fascin dynamics within filopodia are under the control of formins, and in particular FMNL2, that binds directly to dephosphorylated fascin. Our data provide new insight into control of fascin dynamics at the nanoscale and into the mechanisms governing rapid cytoskeletal adaptation to environmental changes. This filopodia-driven exploration stage may represent an essential regulatory step in the transition from static to migrating cancer cells.

}, issn = {1540-8140}, doi = {10.1083/jcb.201906111}, author = {Pfisterer, Karin and Levitt, James and Lawson, Campbell D and Marsh, Richard J and Heddleston, John M and Wait, Eric and Ameer-Beg, Simon Morris and Cox, Susan and Parsons, Maddy} } @article {64543, title = {Freeze-frame imaging of synaptic activity using SynTagMA.}, journal = {Nature Communications}, volume = {11}, year = {2020}, month = {2020 May 18}, pages = {2464}, abstract = {

Information within the brain travels from neuron to neuron across synapses. At any given moment, only a few synapses within billions will be active and are thought to transmit key information about the environment, a behavior being executed or memory being recalled. Here we present SynTagMA, which marks active synapses within a ~2 s time window. Upon violet illumination, the genetically expressed tag converts from green to red fluorescence if bound to calcium. Targeted to presynaptic terminals, preSynTagMA allows discrimination between active and silent axons. Targeted to excitatory postsynapses, postSynTagMA creates a snapshot of synapses active just before photoconversion. To analyze large datasets, we developed an analysis program that automatically identifies and tracks the fluorescence of thousands of individual synapses in tissue. Together, these tools provide a high throughput method for repeatedly mapping active synapses in vitro and in vivo.

}, doi = {10.1038/s41467-020-16315-4}, author = {Perez-Alvarez, Alberto and Fearey, Brenna C and Schulze, Christian and O{\textquoteright}Toole, Ryan J and Moeyaert, Benjamien and Mohr, Manuel Alexander and Arganda-Carreras, Ignacio and Yang, Wei and Wiegert, J Simon and Schreiter, Eric R and Gee, Christine E and Hoppa, Michael B and Oertner, Thomas G} } @article {65601, title = {Frontline science: dynamic cellular and subcellular features of migrating leukocytes revealed by in vivo lattice lightsheet microscopy.}, journal = {Journal of Leukocyte Biology}, year = {2020}, month = {2020 Apr 23}, abstract = {

Neutrophil and macrophage (Mϕ) migration underpin the inflammatory response. However, the fast velocity, multidirectional instantaneous movement, and plastic, ever-changing shape of phagocytes confound high-resolution intravital imaging. Lattice lightsheet microscopy (LLSM) captures highly dynamic cell morphology at exceptional spatiotemporal resolution. We demonstrate the first extensive application of LLSM to leukocytes in vivo, utilizing optically transparent zebrafish, leukocyte-specific reporter lines that highlighted subcellular structure, and a wounding assay for leukocyte migration. LLSM revealed details of migrating leukocyte morphology, and permitted intricate, volumetric interrogation of highly dynamic activities within their native physiological setting. Very thin, recurrent uropod extensions must now be considered a characteristic feature of migrating neutrophils. LLSM resolved trailing uropod extensions, demonstrating their surprising length, and permitting quantitative assessment of cytoskeletal contributions to their evanescent form. Imaging leukocytes in blood vessel microenvironments at LLSM{\textquoteright}s spatiotemporal resolution displayed blood-flow-induced neutrophil dynamics and demonstrated unexpected leukocyte-endothelial interactions such as leukocyte-induced endothelial deformation against the intravascular pressure. LLSM of phagocytosis and cell death provided subcellular insights and uncovered novel behaviors. Collectively, we provide high-resolution LLSM examples of leukocyte structures (filopodia lamellipodia, uropod extensions, vesicles), and activities (interstitial and intravascular migration, leukocyte rolling, phagocytosis, cell death, and cytoplasmic ballooning). Application of LLSM to intravital leukocyte imaging sets the stage for transformative studies into the cellular and subcellular complexities of phagocyte biology.

}, issn = {1938-3673}, doi = {10.1002/JLB.3HI0120-589R}, author = {Manley, Harriet R and Potter, David L and Heddleston, John M and Chew, Teng-Leong and Keightley, M Cristina and Lieschke, Graham J} } @article {68813, title = {Functional Diversity of Glycinergic Commissural Inhibitory Neurons in Larval Zebrafish}, journal = {Cell Reports}, volume = {30}, year = {2020}, month = {03/2020}, pages = {3036-3050.e4}, abstract = {

Summary Commissural inhibitory neurons in the spinal cord of aquatic vertebrates coordinate left-right body alternation during swimming. Their developmental origin, however, has been elusive. We investigate this by comparing the anatomy and function of two commissural inhibitory neuron types, dI6dmrt3a and V0d, derived from the pd6 and p0 progenitor domains, respectively. We find that both of these commissural neuron types have monosynaptic, inhibitory connections to neuronal populations active during fictive swimming, supporting their role in providing inhibition to the contralateral side. V0d neurons tend to fire during faster and stronger movements, while dI6dmrt3a neurons tend to fire more consistently during normal fictive swimming. Ablation of dI6dmrt3a neurons leads to an impairment of left-right alternating activity through abnormal co-activation of ventral root neurons on both sides of the spinal cord. Our results suggest that dI6dmrt3a and V0d commissural inhibitory neurons synergistically provide inhibition to the opposite side across different swimming behaviors.

}, keywords = {commissural inhibitory neurons, dI6~ neurons, glycinergic interneuons, mid cycle inhibition, spinal cord circuit, V0d neurons, Zebrafish}, issn = {2211-1247}, doi = {https://doi.org/10.1016/j.celrep.2020.02.015}, url = {https://www.sciencedirect.com/science/article/pii/S2211124720301698}, author = {Chie Satou and Takumi Sugioka and Yuto Uemura and Takashi Shimazaki and Pawel Zmarz and Yukiko Kimura and Shin-ichi Higashijima} } @article {65283, title = {Fundamental law of memory recall.}, journal = {Physical Review Letters}, volume = {124}, year = {2020}, month = {2020 Jan 10}, pages = {018101}, abstract = {

Human memory appears to be fragile and unpredictable. Free recall of random lists of words is a standard paradigm used to probe episodic memory. We proposed an associative search process that can be reduced to a deterministic walk on random graphs defined by the structure of memory representations. The corresponding graph model can be solved analytically, resulting in a novel parameter-free prediction for the average number of memory items recalled (R) out of M items in memory: R=sqrt[3πM/2]. This prediction was verified with a specially designed experimental protocol combining large-scale crowd-sourced free recall and recognition experiments with randomly assembled lists of words or common facts. Our results show that human memory can be described by universal laws derived from first principles.

}, issn = {1079-7114}, doi = {10.1103/PhysRevLett.124.018101}, author = {Naim, Michelangelo and Katkov, Mikhail and Romani, Sandro and Tsodyks, Misha} } @article {65582, title = {Gene expression analysis in the mouse brainstem identifies Cart and Nesfatin as neuropeptides co-expressed in the Calbindin-positive neurons of the Nucleus papilio.}, journal = {Sleep}, year = {2020}, month = {2020 Apr 28}, abstract = {

The brainstem contains several neuronal populations, heterogeneous in term of neurotransmitter/neuropeptide content, which are important for controlling various aspects of the REM phase of sleep. Among these populations are the Calbindin (Calb)-immunoreactive NPCalb neurons, located in the Nucleus papilio, within the dorsal paragigantocellular nucleus (DPGi), and recently shown to control eye movement during the REM phase of sleep. We performed in depth data-mining of the in-situ hybridization data collected at the Allen Brain Atlas, in order to identify potentially interesting genes expressed in this brainstem nucleus. Our attention focused on genes encoding neuropeptides, including Cart (Cocaine and Amphetamine Regulated Transcripts) and Nesfatin1. While Nesfatin1 appeared ubiquitously expressed in this Calb-positive neuronal population, Cart was co-expressed in only a subset of these glutamatergic NPCalb neurons. Furthermore, a REM sleep deprivation and rebound assay performed with mice revealed that the Cart-positive neuronal population within the DPGi was activated during REM sleep (as measured by c-fos immunoreactivity), suggesting a role of this neuropeptide in regulating some aspects of REM sleep. The assembled information could afford functional clues to investigators, conducive to further experimental pursuits.

}, issn = {1550-9109}, doi = {10.1093/sleep/zsaa085}, author = {Girard, F and von Siebenthal, M and Davis, F P and Celio, M R} } @article {65378, title = {A general approach to engineer positive-going eFRET voltage indicators}, journal = {Nature Communications}, volume = {11}, year = {2020}, month = {2020 Jul 10}, abstract = {

We engineered electrochromic fluorescence resonance energy transfer (eFRET) genetically encoded voltage indicators (GEVIs) with {\textquotedblleft}positive-going{\textquotedblright} fluorescence response to membrane depolarization through rational manipulation of the native proton transport pathway in microbial rhodopsins. We transformed the state-of-the-art eFRET GEVI Voltron into Positron, with kinetics and sensitivity equivalent to Voltron but flipped fluorescence signal polarity. We further applied this general approach to GEVIs containing different voltage sensitive rhodopsin domains and various fluorescent dye and fluorescent protein reporters.

}, author = {Abdelfattah, Ahmed S and Valenti, Rosario and Zheng, Jihong and Wong, Allan and Podgorski, Kaspar and Koyama, Minoru and Kim, Douglas S. and Schreiter, Eric R and Project Team GENIE} } @article {65667, title = {A general method to optimize and functionalize red-shifted rhodamine dyes.}, journal = {Nature Methods}, year = {2020}, month = {2020 Jul 27}, abstract = {

Expanding the palette of fluorescent dyes is vital to push the frontier of biological imaging. Although rhodamine dyes remain the premier type of small-molecule fluorophore owing to their bioavailability and brightness, variants excited with far-red or near-infrared light suffer from poor performance due to their propensity to adopt a lipophilic, nonfluorescent form. We report a framework for rationalizing rhodamine behavior in biological environments and a general chemical modification for rhodamines that optimizes long-wavelength variants and enables facile functionalization with different chemical groups. This strategy yields red-shifted {\textquoteright}Janelia Fluor{\textquoteright} (JF) dyes useful for biological imaging experiments in cells and in vivo.

}, issn = {1548-7105}, doi = {10.1038/s41592-020-0909-6}, author = {Grimm, Jonathan B and Tkachuk, Ariana N and Xie, Liangqi and Choi, Heejun and Mohar, Boaz and Falco, Natalie and Schaefer, Kathy and Patel, Ronak and Zheng, Qinsi and Liu, Zhe and Lippincott-Schwartz, Jennifer and Brown, Timothy A and Lavis, Luke D} } @article {65282, title = {A genetic, genomic, and computational resource for exploring neural circuit function.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Jan 15}, abstract = {

The anatomy of many neural circuits is being characterized with increasing resolution, but their molecular properties remain mostly unknown. Here, we characterize gene expression patterns in distinct neural cell types of the visual system using genetic lines to access individual cell types, the TAPIN-seq method to measure their transcriptomes, and a probabilistic method to interpret these measurements. We used these tools to build a resource of high-resolution transcriptomes for 100 driver lines covering 67 cell types, available at http://www.opticlobe.com. Combining these transcriptomes with recently reported connectomes helps characterize how information is transmitted and processed across a range of scales, from individual synapses to circuit pathways. We describe examples that include identifying neurotransmitters, including cases of apparent co-release, generating functional hypotheses based on receptor expression, as well as identifying strong commonalities between different cell types.

}, issn = {2050-084X}, doi = {10.7554/eLife.50901}, author = {Davis, Fred P and Nern, Aljoscha and Picard, Serge and Reiser, Michael B and Rubin, Gerald M and Eddy, Sean R and Henry, Gilbert L} } @article {65739, title = {A genetically defined compartmentalized striatal direct pathway for negative reinforcement.}, journal = {Cell}, volume = {181}, year = {2020}, month = {2020 Oct 1}, pages = {211}, abstract = {

The striosome compartment within the dorsal striatum has been implicated in reinforcement learning and regulation of motivation, but how striosomal neurons contribute to these functions remains elusive. Here, we show that a genetically identified striosomal population, which expresses the Teashirt family zinc finger 1 (Tshz1) and belongs to the direct pathway, drives negative reinforcement and is essential for aversive learning in mice. Contrasting a "conventional" striosomal direct pathway, the Tshz1 neurons cause aversion, movement suppression, and negative reinforcement once activated, and they receive a distinct set of synaptic inputs. These neurons are predominantly excited by punishment rather than reward and represent the anticipation of punishment or the motivation for avoidance. Furthermore, inhibiting these neurons impairs punishment-based learning without affecting reward learning or movement. These results establish a major role of striosomal neurons in behaviors reinforced by punishment and moreover uncover functions of the direct pathway unaccounted for in classic models.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2020.08.032}, author = {Xiao, Xiong and Deng, Hanfei and Furlan, Alessandro and Yang, Tao and Zhang, Xian and Hwang, Ga-Ram and Tucciarone, Jason and Wu, Priscilla and He, Miao and Palaniswamy, Ramesh and Ramakrishnan, Charu and Ritola, Kimberly and Hantman, Adam and Deisseroth, Karl and Osten, Pavel and Huang, Z Josh and Li, Bo} } @article {65636, title = {Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.}, journal = {Science Advances}, volume = {6}, year = {2020}, month = {2020 Jun 17}, pages = {eaaz6699}, abstract = {

Transcriptional bursting is the stochastic activation and inactivation of promoters, contributing to cell-to-cell heterogeneity in gene expression. However, the mechanism underlying the regulation of transcriptional bursting kinetics (burst size and frequency) in mammalian cells remains elusive. In this study, we performed single-cell RNA sequencing to analyze the intrinsic noise and mRNA levels for elucidating the transcriptional bursting kinetics in mouse embryonic stem cells. Informatics analyses and functional assays revealed that transcriptional bursting kinetics was regulated by a combination of promoter- and gene body-binding proteins, including the polycomb repressive complex 2 and transcription elongation factors. Furthermore, large-scale CRISPR-Cas9-based screening identified that the Akt/MAPK signaling pathway regulated bursting kinetics by modulating transcription elongation efficiency. These results uncovered the key molecular mechanisms underlying transcriptional bursting and cell-to-cell gene expression noise in mammalian cells.

}, issn = {2375-2548}, doi = {10.1126/sciadv.aaz6699}, author = {Ochiai, Hiroshi and Hayashi, Tetsutaro and Umeda, Mana and Yoshimura, Mika and Harada, Akihito and Shimizu, Yukiko and Nakano, Kenta and Saitoh, Noriko and Liu, Zhe and Yamamoto, Takashi and Okamura, Tadashi and Ohkawa, Yasuyuki and Kimura, Hiroshi and Nikaido, Itoshi} } @article {65657, title = {Growth cone-localized microtubule organizing center establishes microtubule orientation in dendrites.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Jul 13}, abstract = {

A polarized arrangement of neuronal microtubule arrays is the foundation of membrane trafficking and subcellular compartmentalization. Conserved among both invertebrates and vertebrates, axons contain exclusively {\textquoteright}plus-end-out{\textquoteright} microtubules while dendrites contain a high percentage of {\textquoteright}minus-end-out{\textquoteright} microtubules, the origins of which have been a mystery. Here we show that in the dendritic growth cone contains a non-centrosomal microtubule organizing center, which generates minus-end-out microtubules along outgrowing dendrites and plus-end-out microtubules in the growth cone. RAB-11-positive endosomes accumulate in this region and co-migrate with the microtubule nucleation complex γ-TuRC. The MTOC tracks the extending growth cone by kinesin-1/UNC-116-mediated endosome movements on distal plus-end-out microtubules and dynein clusters this advancing MTOC. Critically, perturbation of the function or localization of the MTOC causes reversed microtubule polarity in dendrites. These findings unveil the endosome-localized dendritic MTOC as a critical organelle for establishing axon-dendrite polarity.

}, issn = {2050-084X}, doi = {10.7554/eLife.56547}, author = {Liang, Xing and Kokes, Marcela and Fetter, Richard D and Sallee, Maria Danielle and Moore, Adrian W and Feldman, Jessica L and Shen, Kang} } @article {65972, title = {High throughput instrument to screen fluorescent proteins under two-photon excitation.}, journal = {Biomedical Optics Express}, volume = {11}, year = {2020}, month = {2020 Dec 01}, pages = {7192-7203}, abstract = {

Two-photon microscopy together with fluorescent proteins and fluorescent protein-based biosensors are commonly used tools in neuroscience. To enhance their experimental scope, it is important to optimize fluorescent proteins for two-photon excitation. Directed evolution of fluorescent proteins under one-photon excitation is common, but many one-photon properties do not correlate with two-photon properties. A simple system for expressing fluorescent protein mutants is colonies on an agar plate. The small focal volume of two-photon excitation makes creating a high throughput screen in this system a challenge for a conventional point-scanning approach. We present an instrument and accompanying software that solves this challenge by selectively scanning each colony based on a colony map captured under one-photon excitation. This instrument, called the GIZMO, can measure the two-photon excited fluorescence of 10,000 colonies in 7 hours. We show that the GIZMO can be used to evolve a fluorescent protein under two-photon excitation.

}, issn = {2156-7085}, doi = {10.1364/BOE.409353}, author = {Molina, Rosana S and King, Jonathan and Franklin, Jacob and Clack, Nathan and McRaven, Christopher and Goncharov, Vasily and Flickinger, Daniel and Svoboda, Karel and Drobizhev, Mikhail and Hughes, Thomas E} } @article {65377, title = {High-throughput cellular-resolution synaptic connectivity mapping in vivo with concurrent two-photon optogenetics and volumetric Ca2+ imaging}, journal = {bioRxiv}, year = {2020}, month = {2020 Feb 25}, abstract = {

The ability to measure synaptic connectivity and properties is essential for understanding neuronal circuits. However, existing methods that allow such measurements at cellular resolution are laborious and technically demanding. Here, we describe a system that allows such measurements in a high-throughput way by combining two-photon optogenetics and volumetric Ca2+\ imaging with whole-cell recording. We reveal a circuit motif for generating fast undulatory locomotion in zebrafish.

}, doi = {https://doi.org/10.1101/2020.02.21.959650}, author = {McRaven, Christopher and Tanese, Dimitrii and Zhang, Lixia and Yang, Chao-Tsung and Ahrens, Misha B and Emiliani, Valentina and Koyama, Minoru} } @article {65696, title = {Hindbrain double-negative feedback mediates palatability-guided food and water consumption.}, journal = {Cell}, volume = {182}, year = {2020}, month = {2020 Sep 17}, pages = {1589-1605}, abstract = {

Hunger and thirst have distinct goals but control similar ingestive behaviors, and little is known about neural processes that are shared between these behavioral states. We identify glutamatergic neurons in the peri-locus coeruleus (periLC neurons) as a polysynaptic convergence node from separate energy-sensitive and hydration-sensitive cell populations. We develop methods for stable hindbrain calcium imaging in free-moving mice, which show that periLC neurons are tuned to ingestive behaviors and respond similarly to food or water consumption. PeriLC neurons are scalably inhibited by palatability and homeostatic need during consumption. Inhibition of periLC neurons is rewarding and increases consumption by enhancing palatability and prolonging ingestion duration. These properties comprise a double-negative feedback relationship that sustains food or water consumption without affecting food- or water-seeking. PeriLC neurons are a hub between hunger and thirst that specifically controls motivation for food and water ingestion, which is a factor that contributes to hedonic overeating and obesity.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2020.07.031}, author = {Gong, Rong and Xu, Shengjin and Hermundstad, Ann and Yu, Yang and Sternson, Scott M} } @article {65825, title = {Hypothesis-driven quantitative fluorescence microscopy - the importance of reverse-thinking in experimental design.}, journal = {Journal of Cell Science}, volume = {133}, year = {2020}, month = {2020 Nov 05}, abstract = {

One of the challenges in modern fluorescence microscopy is to reconcile the conventional utilization of microscopes as exploratory instruments with their emerging and rapidly expanding role as a quantitative tools. The contribution of microscopy to observational biology will remain enormous owing to the improvements in acquisition speed, imaging depth, resolution and biocompatibility of modern imaging instruments. However, the use of fluorescence microscopy to facilitate the quantitative measurements necessary to challenge hypotheses is a relatively recent concept, made possible by advanced optics, functional imaging probes and rapidly increasing computational power. We argue here that to fully leverage the rapidly evolving application of microscopes in hypothesis-driven biology, we not only need to ensure that images are acquired quantitatively but must also re-evaluate how microscopy-based experiments are designed. In this Opinion, we present a reverse logic that guides the design of quantitative fluorescence microscopy experiments. This unique approach starts from identifying the results that would quantitatively inform the hypothesis and map the process backward to microscope selection. This ensures that the quantitative aspects of testing the hypothesis remain the central focus of the entire experimental design.

}, issn = {1477-9137}, doi = {10.1242/jcs.250027}, author = {Wait, Eric C and Reiche, Michael A and Chew, Teng-Leong} } @article {65637, title = {Identification of dopaminergic neurons that can both establish associative memory and acutely terminate its behavioral expression.}, journal = {Journal of Neuroscience}, volume = {40}, year = {2020}, month = {2020 Jul 29}, pages = {5990-6006}, abstract = {

An adaptive transition from exploring the environment in search of vital resources to exploiting these resources once the search is successful is important to all animals. Here we study the neuronal circuitry that allows larval of either sex to negotiate this exploration-exploitation transition. We do so by combining Pavlovian conditioning with high-resolution behavioral tracking, optogenetic manipulation of individually identified neurons, and EM-data-based analyses of synaptic organization. We find that optogenetic activation of the dopaminergic neuron DAN-i1 can both establish memory during training, and acutely terminate learned search behavior in a subsequent recall test. Its activation leaves innate behavior unaffected, however. Specifically, DAN-i1 activation can establish associative memories of opposite valence upon paired and unpaired training with odor, and its activation during the recall test can terminate the search behavior resulting from either of these memories. Our results further suggest that in its behavioral significance DAN-i1 activation resembles but does not equal sugar reward. Dendrogram analyses of all the synaptic connections between DAN-i1 and its two main targets, the Kenyon cells and the mushroom body output neuron MBON-i1, further suggest that the DAN-i1 signals during training and during the recall test could be delivered to the Kenyon cells and to MBON-i1, respectively, within previously unrecognized, locally confined branching structures. This would provide an elegant circuit motif to terminate search upon its successful completion.In the struggle for survival animals have to explore their environment in search of food. Once food is found, however, it is adaptive to prioritize exploiting it over continuing a search that would now be as pointless as searching for the glasses you are wearing. This exploration-exploitation trade-off is important for animals and humans, as well as for technical search devices. We investigate which of the only 10,000 neurons of a fruit fly larva can tip the balance in this trade-off, and identify a single dopamine neuron called DAN-i1 that can do so. Given the similarities in dopamine neuron function across the animal kingdom, this may reflect a general principle of how search is terminated once it is successful.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0290-20.2020}, author = {Schleyer, Michael and Weiglein, Ali{\'c}e and Thoener, Juliane and Strauch, Martin and Hartenstein, Volker and Kantar Weigelt, Melisa and Schuller, Sarah and Saumweber, Timo and Eichler, Katharina and Rohwedder, Astrid and Merhof, Dorit and Zlatic, Marta and Thum, Andreas S and Gerber, Bertram} } @article {65301, title = {Identifying neural substrates of competitive interactions and sequence transitions during mechanosensory responses in Drosophila.}, journal = {PLoS Genetics}, volume = {16}, year = {2020}, month = {2020 Feb 14}, pages = {e1008589}, abstract = {

Nervous systems have the ability to select appropriate actions and action sequences in response to sensory cues. The circuit mechanisms by which nervous systems achieve choice, stability and transitions between behaviors are still incompletely understood. To identify neurons and brain areas involved in controlling these processes, we combined a large-scale neuronal inactivation screen with automated action detection in response to a mechanosensory cue in Drosophila larva. We analyzed behaviors from 2.9x105 larvae and identified 66 candidate lines for mechanosensory responses out of which 25 for competitive interactions between actions. We further characterize in detail the neurons in these lines and analyzed their connectivity using electron microscopy. We found the neurons in the mechanosensory network are located in different regions of the nervous system consistent with a distributed model of sensorimotor decision-making. These findings provide the basis for understanding how selection and transition between behaviors are controlled by the nervous system.

}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1008589}, author = {Masson, Jean-Baptiste and Laurent, Francois and Cardona, Albert and Barre, Chloe and Skatchkovsky, Nicolas and Zlatic, Marta and Jovanic, Tihana} } @article {65130, title = {Idiosyncratic neural coding and neuromodulation of olfactory individuality in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, year = {2020}, month = {2020 Sep 22}, pages = {23292-23297}, abstract = {

Innate behavioral biases and preferences can vary significantly among individuals of the same genotype. Though individuality is a fundamental property of behavior, it is not currently understood how individual differences in brain structure and physiology produce idiosyncratic behaviors. Here we present evidence for idiosyncrasy in olfactory behavior and neural responses in We show that individual female from a highly inbred laboratory strain exhibit idiosyncratic odor preferences that persist for days. We used in vivo calcium imaging of neural responses to compare projection neuron (second-order neurons that convey odor information from the sensory periphery to the central brain) responses to the same odors across animals. We found that, while odor responses appear grossly stereotyped, upon closer inspection, many individual differences are apparent across antennal lobe (AL) glomeruli (compact microcircuits corresponding to different odor channels). Moreover, we show that neuromodulation, environmental stress in the form of altered nutrition, and activity of certain AL local interneurons affect the magnitude of interfly behavioral variability. Taken together, this work demonstrates that individual exhibit idiosyncratic olfactory preferences and idiosyncratic neural responses to odors, and that behavioral idiosyncrasies are subject to neuromodulation and regulation by neurons in the AL.

}, issn = {1091-6490}, doi = {10.1073/pnas.1901623116}, author = {Honegger, Kyle S and Smith, Matthew A-Y and Churgin, Matthew A and Turner, Glenn C and de Bivort, Benjamin L} } @inbook {65285, title = {Imaging Cellular Proteins and Structures}, booktitle = {The Liver : Biology and Pathobiology}, year = {2020}, pages = {965 - 978}, publisher = {Wiley}, organization = {Wiley}, edition = {1}, abstract = {

This chapter describes many of the technologies, which have the potential to provide new insights into fundamental aspects of liver biology. Imaging live liver tissue in an animal with multiphoton microscopy coupled with photoactivatable fluorescent proteins and/or additional fluorescent proteins could be used to follow the lineage and fates of individual transplanted stem cells or developing transgenic cells in liver. Proteins or other molecules are labeled with a dye that can be excited with light source. Cells and proteins are generally too small to detect with the naked eye, relatively transparent when imaged by light microscopy, and are highly dynamic. With the increased signal to noise, isotropic and volumetric imaging and high speeds lattice light sheet allows for 3D super-resolution microscopy, as well. Photomultiplier tubes, while capable of detecting and counting single photons, are less useful for high-speed imaging because they normally only detect a single pixel at a time.

}, isbn = {9781119436829}, doi = {10.1002/978111943681210.1002/9781119436812.ch72}, url = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/9781119436812.ch72}, author = {Weigel, Aubrey V. and Snapp, Erik Lee}, editor = {Arias, Irwin M. and Alter, Harvey J. and Boyer, James L. and Cohen, David E. and Shafritz, David A. and Thorgeirsson, Snorri S. and Wolkoff, Allan W.} } @article {65854, title = {Improved genetically encoded near-infrared fluorescent calcium ion indicators for in vivo imaging.}, journal = {PLoS Biology}, volume = {18}, year = {2020}, month = {2020 Nov 24}, pages = {e3000965}, abstract = {

Near-infrared (NIR) genetically encoded calcium ion (Ca2+) indicators (GECIs) can provide advantages over visible wavelength fluorescent GECIs in terms of reduced phototoxicity, minimal spectral cross talk with visible light excitable optogenetic tools and fluorescent probes, and decreased scattering and absorption in mammalian tissues. Our previously reported NIR GECI, NIR-GECO1, has these advantages but also has several disadvantages including lower brightness and limited fluorescence response compared to state-of-the-art visible wavelength GECIs, when used for imaging of neuronal activity. Here, we report 2 improved NIR GECI variants, designated NIR-GECO2 and NIR-GECO2G, derived from NIR-GECO1. We characterized the performance of the new NIR GECIs in cultured cells, acute mouse brain slices, and Caenorhabditis elegans and Xenopus laevis in vivo. Our results demonstrate that NIR-GECO2 and NIR-GECO2G provide substantial improvements over NIR-GECO1 for imaging of neuronal Ca2+ dynamics.

}, issn = {1545-7885}, doi = {10.1371/journal.pbio.3000965}, author = {Qian, Yong and Cosio, Danielle M Orozco and Piatkevich, Kiryl D and Aufmkolk, Sarah and Su, Wan-Chi and Celiker, Orhan T and Schohl, Anne and Murdock, Mitchell H and Abhi Aggarwal and Chang, Yu-Fen and Wiseman, Paul W and Ruthazer, Edward S and Boyden, Edward S and Campbell, Robert E} } @article {65275, title = {Improved HaloTag Ligand Enables BRET Imaging With NanoLuc}, journal = {Frontiers in Chemistry}, volume = {7}, year = {2020}, month = {2020 Jan 14}, doi = {10.3389/fchem.2019.0093810.3389/fchem.2019.00938.s001}, url = {https://www.frontiersin.org/article/10.3389/fchem.2019.00938/fullhttps://www.frontiersin.org/article/10.3389/fchem.2019.00938/fullhttps://www.frontiersin.org/articles/10.3389/fchem.2019.00938/supplementary-material/10.3389/fchem.2019.00938.s001}, author = {Thirukkumaran, Ovia Margaret and Wang, Congrong and Asouzu, Nnamdi Joseph and Fron, Eduard and Rocha, Susana and Hofkens, Johan and Lavis, Luke D. and Mizuno, Hideaki} } @article {65896, title = {In situ differentiation of iridophore crystallotypes underlies zebrafish stripe patterning.}, journal = {Nature Communications}, volume = {11}, year = {2020}, month = {2020 Dec 15}, pages = {6391}, abstract = {

Skin color patterns are ubiquitous in nature, impact social behavior, predator avoidance, and protection from ultraviolet irradiation. A leading model system for vertebrate skin patterning is the zebrafish; its alternating blue stripes and yellow interstripes depend on light-reflecting cells called iridophores. It was suggested that the zebrafish{\textquoteright}s color pattern arises from a single type of iridophore migrating differentially to stripes and interstripes. However, here we find that iridophores do not migrate between stripes and interstripes but instead differentiate and proliferate in-place, based on their micro-environment. RNA-sequencing analysis further reveals that stripe and interstripe iridophores have different transcriptomic states, while cryogenic-scanning-electron-microscopy and micro-X-ray diffraction identify different crystal-arrays architectures, indicating that stripe and interstripe iridophores are different cell types. Based on these results, we present an alternative model of skin patterning in zebrafish in which distinct iridophore crystallotypes containing specialized, physiologically responsive, organelles arise in stripe and interstripe by in-situ differentiation.

}, keywords = {Animals, Cell Differentiation, Cell Proliferation, Chromatophores, Microphthalmia-Associated Transcription Factor, Mutagenesis, Skin, Skin Pigmentation, Transcriptome, X-Ray Diffraction, Zebrafish, Zebrafish Proteins}, issn = {2041-1723}, doi = {10.1038/s41467-020-20088-1}, author = {Gur, Dvir and Bain, Emily J and Johnson, Kory R and Aman, Andy J and Pasoili, H Amalia and Flynn, Jessica D and Allen, Michael C and Deheyn, Dimitri D and Lee, Jennifer C and Lippincott-Schwartz, Jennifer and Parichy, David M} } @article {65235, title = {In situ structure determination at nanometer resolution using TYGRESS.}, journal = {Nature Methods}, volume = {17}, year = {2020}, month = {2020 Feb 01}, pages = {201-08}, abstract = {

The resolution of subtomogram averages calculated from cryo-electron tomograms (cryo-ET) of crowded cellular environments is often limited owing to signal loss in, and misalignment of, the subtomograms. By contrast, single-particle cryo-electron microscopy (SP-cryo-EM) routinely reaches near-atomic resolution of isolated complexes. We report a method called {\textquoteright}tomography-guided 3D reconstruction of subcellular structures{\textquoteright} (TYGRESS) that is a hybrid of cryo-ET and SP-cryo-EM, and is able to achieve close-to-nanometer resolution of complexes inside crowded cellular environments. TYGRESS combines the advantages of SP-cryo-EM (images with good signal-to-noise ratio and contrast, as well as minimal radiation damage) and subtomogram averaging (three-dimensional alignment of macromolecules in a complex sample). Using TYGRESS, we determined the structure of the intact ciliary axoneme with up to resolution of 12 {\r A}. These results reveal many structural details that were not visible by cryo-ET alone. TYGRESS is generally applicable to cellular complexes that are amenable to subtomogram averaging.

}, issn = {1548-7105}, doi = {10.1038/s41592-019-0651-0}, author = {Song, Kangkang and Shang, Zhiguo and Fu, Xiaofeng and Lou, Xiaochu and Grigorieff, Nikolaus and Nicastro, Daniela} } @conference {65835, title = {Inpainting Networks Learn to Separate Cells in Microscopy Images}, booktitle = {British Machine Vision Conference}, year = {2020}, month = {2020 Sep}, abstract = {

Deep neural networks trained to inpaint partially occluded images show a deep understanding of image composition and have even been shown to remove objects from images convincingly. In this work, we investigate how this implicit knowledge of image composition can be be used to separate cells in densely populated microscopy images. We propose a measure for the independence of two image regions given a fully self-supervised inpainting network and separate objects by maximizing this independence. We evaluate our method on two cell segmentation datasets and show that cells can be separated completely unsupervised. Furthermore, combined with simple foreground detection, our method yields instance segmentation of similar quality to fully supervised methods.

}, url = {https://www.bmvc2020-conference.com/assets/papers/0528.pdf}, author = {Wolf, Steffen and Hamprecht, Fred A and Funke, Jan} } @article {65314, title = {Input connectivity reveals additional heterogeneity of dopaminergic reinforcement in Drosophila}, journal = {Current Biology}, volume = {30}, year = {2020}, month = {2020 Aug 17}, pages = {3200-11}, abstract = {

Different types of\ Drosophila\ dopaminergic neurons (DANs) reinforce memories of unique valence and provide state-dependent motivational control [1]. Prior studies suggest that the compartment architecture of the mushroom body (MB) is the relevant resolution for distinct DAN functions [2,\ 3]. Here we used a recent electron microscope volume of the fly brain [4] to reconstruct the fine anatomy of individual DANs within three MB compartments. We find the 20 DANs of the γ5 compartment, at least some of which provide reward teaching signals, can be clustered into 5 anatomical subtypes that innervate different regions within γ5. Reconstructing 821 upstream neurons reveals input selectivity, supporting the functional relevance of DAN sub-classification. Only one PAM-γ5 DAN subtype (γ5fb) receives direct recurrent input from γ5β{\textquoteright}2a mushroom body output neurons (MBONs) and behavioral experiments distinguish a role for these DANs in memory revaluation from those reinforcing sugar memory. Other DAN subtypes receive major, and potentially reinforcing, inputs from putative gustatory interneurons or lateral horn neurons, which can also relay indirect feedback from the MB. We similarly reconstructed the single aversively reinforcing PPL1-γ1pedc DAN. The γ1pedc DAN inputs are mostly different to those of γ5 DANs and are clustered onto distinct branches of its dendritic tree, presumably separating its established roles in aversive reinforcement and appetitive motivation [5,\ 6]. Additional tracing identified neurons that provide broad input to γ5, β{\textquoteright}2a and γ1pedc DANs suggesting that distributed DAN populations can be coordinately regulated. These connectomic and behavioral analyses therefore reveal additional complexity of dopaminergic reinforcement circuits between and within MB compartments.

}, author = {Otto, Nils and Pleijzier, Markus W. and Morgan, Isabel C. and Edmondson-Stait, Amelia J and Heinz, Konrad J. and Stark, Ildiko and Dempsey, Georgia and Ito, Masayoshi and Kapoor, Ishaan and Hsu, Joseph and Schlegel, Philipp M. and Bates, Alexander S. and Costa, Marta and Ito, Kei and Bock, Davi D. and Rubin, Gerald M. and Jefferis, Gregory S.X.E. and Waddell, Scott} } @article {65762, title = {Integrated structure-function dataset reveals key mechanisms underlying photochromic fluorescent proteins}, journal = {bioRxiv}, year = {2020}, month = {09/2020}, pages = {2020.09.25.313528}, abstract = {

Photochromic fluorescent proteins have become versatile tools in the life sciences, though our understanding of their structure-function relation is limited. Starting from a single scaffold, we have developed a range of 27 photochromic fluorescent proteins that cover a broad range of spectroscopic properties, yet differ only in one or two mutations. We also determined 43 different crystal structures of these mutants. Correlation and principal component analysis of the spectroscopic and structural properties confirmed the complex relationship between structure and spectroscopy, suggesting that the observed variability does not arise from a limited number of mechanisms, but also allowed us to identify consistent trends and to relate these to the spatial organization around the chromophore. We find that particular changes in spectroscopic properties can come about through multiple different underlying mechanisms, of which the polarity of the chromophore environment and hydrogen bonding of the chromophore are key modulators. Furthermore, some spectroscopic parameters, such as the photochromism, appear to be largely determined by a single or a few structural properties, while other parameters, such as the absorption maximum, do not allow a clear identification of a single cause. We also highlight the role of water molecules close to the chromophore in influencing photochromism. We anticipate that our dataset can open opportunities for the development and evaluation of new and existing protein engineering methods.

}, doi = {10.1101/2020.09.25.313528}, author = {Zitter, Elke De and Hugelier, Siewert and Duw{\'e}, Sam and Vandenberg, Wim and Tebo, Alison G. and Meervelt, Luc Van and Dedecker, Peter} } @article {68478, title = {Intracellular signaling dynamics and their role in coordinating tissue repair.}, journal = {Wiley Interdiscip Rev Syst Biol Med}, volume = {12}, year = {2020}, month = {05/2020}, pages = {e1479}, abstract = {

Tissue repair is a complex process that requires effective communication and coordination between cells across multiple tissues and organ systems. Two of the initial intracellular signals that encode injury signals and initiate tissue repair responses are calcium and extracellular signal-regulated kinase (ERK). However, calcium and ERK signaling control a variety of cellular behaviors important for injury repair including cellular motility, contractility, and proliferation, as well as the activity of several different transcription factors, making it challenging to relate specific injury signals to their respective repair programs. This knowledge gap ultimately hinders the development of new wound healing therapies that could take advantage of native cellular signaling programs to more effectively repair tissue damage. The objective of this review is to highlight the roles of calcium and ERK signaling dynamics as mechanisms that link specific injury signals to specific cellular repair programs during epithelial and stromal injury repair. We detail how the signaling networks controlling calcium and ERK can now also be dissected using classical signal processing techniques with the advent of new biosensors and optogenetic signal controllers. Finally, we advocate the importance of recognizing calcium and ERK dynamics as key links between injury detection and injury repair programs that both organize and execute a coordinated tissue repair response between cells across different tissues and organs. This article is categorized under: Models of Systems Properties and Processes \> Mechanistic Models Biological Mechanisms \> Cell Signaling Laboratory Methods and Technologies \> Imaging Models of Systems Properties and Processes \> Organ, Tissue, and Physiological Models.

}, keywords = {Animals, Calcium, Cell Movement, Epithelial Cells, Extracellular Signal-Regulated MAP Kinases, Humans, Models, Biological, NF-kappa B, Signal Transduction, Wound Healing}, issn = {1939-005X}, doi = {10.1002/wsbm.1479}, author = {Ghilardi, Samuel J and O{\textquoteright}Reilly, Breanna M and Sgro, Allyson E} } @article {65618, title = {jYCaMP: an optimized calcium indicator for two-photon imaging at fiber laser wavelengths.}, journal = {Nature Methods}, volume = {17}, year = {2020}, month = {2020 May 25}, pages = {694-97}, abstract = {

Femtosecond lasers at fixed wavelengths above 1,000 nm are powerful, stable and inexpensive, making them promising sources for two-photon microscopy. Biosensors optimized for these wavelengths are needed for both next-generation microscopes and affordable turn-key systems. Here we report jYCaMP1, a yellow variant of the calcium indicator jGCaMP7 that outperforms its parent in mice and flies at excitation wavelengths above 1,000 nm and enables improved two-color calcium imaging with red fluorescent protein-based indicators.

}, issn = {1548-7105}, doi = {10.1038/s41592-020-0835-7}, author = {Mohr, Manuel Alexander and Bushey, Daniel and Abhi Aggarwal and Marvin, Jonathan S and Kim, Jeong Jun and Marquez, Emiliano Jimenez and Liang, Yajie and Patel, Ronak and Macklin, John J and Lee, Chi-Yu and Tsang, Arthur and Tsegaye, Getahun and Ahrens, Allison M and Chen, Jerry L and Kim, Douglas S and Wong, Allan M and Looger, Loren L and Schreiter, Eric R and Podgorski, Kaspar} } @article {65322, title = {Kilohertz two-photon fluorescence microscopy imaging of neural activity in vivo.}, journal = {Nature Methods}, volume = {17}, year = {2020}, month = {2020 Mar 02}, pages = {287-290}, abstract = {

Understanding information processing in the brain requires monitoring neuronal activity at high spatiotemporal resolution. Using an ultrafast two-photon fluorescence microscope empowered by all-optical laser scanning, we imaged neuronal activity in vivo at up to 3,000 frames per second and submicrometer spatial resolution. This imaging method enabled monitoring of both supra- and subthreshold electrical activity down to 345 μm below the brain surface in head-fixed awake mice.

}, issn = {1548-7105}, doi = {10.1038/s41592-020-0762-7}, author = {Wu, Jianglai and Liang, Yajie and Chen, Shuo and Hsu, Ching-Lung and Chavarha, Mariya and Evans, Stephen W and Shi, Dongqing and Lin, Michael Z and Tsia, Kevin K and Ji, Na} } @article {65362, title = {A large genomic insertion containing a duplicated follistatin gene is linked to the pea aphid male wing dimorphism.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Mar 06}, abstract = {

Wing dimorphisms have long served as models for examining the ecological and evolutionary tradeoffs associated with alternative phenotypes. Here, we investigated the genetic cause of the pea aphid () male wing dimorphism, wherein males exhibit one of two morphologies that differ in correlated traits that include the presence or absence of wings. We mapped this trait difference to a single genomic region and, using third generation, long-read sequencing, we identified a 120 kb insertion in the wingless allele. This insertion includes a duplicated gene, which is a strong candidate gene in the minimal mapped interval to cause the dimorphism. We found that both alleles were present prior to pea aphid biotype lineage diversification, we estimated that the insertion occurred millions of years ago, and we propose that both alleles have been maintained in the species, likely due to balancing selection.

}, issn = {2050-084X}, doi = {10.7554/eLife.50608}, author = {Li, Binshuang and Bickel, Ryan D and Parker, Benjamin J and Saleh Ziabari, Omid and Liu, Fangzhou and Vellichirammal, Neetha Nanoth and Simon, Jean-Christophe and Stern, David L and Brisson, Jennifer A} } @article {68842, title = {Latent Feature Representation via Unsupervised Learning for Pattern Discovery in Massive Electron Microscopy Image Volumes}, journal = {arXiv}, year = {2020}, month = {2020 Dec 22}, abstract = {

We propose a method to facilitate exploration and analysis of new large data sets. In particular, we give an unsupervised deep learning approach to learning a latent representation that captures semantic similarity in the data set. The core idea is to use data augmentations that preserve semantic meaning to generate synthetic examples of elements whose feature representations should be close to one another.
We demonstrate the utility of our method applied to nano-scale electron microscopy data, where even relatively small portions of animal brains can require terabytes of image data. Although supervised methods can be used to predict and identify known patterns of interest, the scale of the data makes it difficult to mine and analyze patterns that are not known a priori. We show the ability of our learned representation to enable query by example, so that if a scientist notices an interesting pattern in the data, they can be presented with other locations with matching patterns. We also demonstrate that clustering of data in the learned space correlates with biologically-meaningful distinctions. Finally, we introduce a visualization tool and software ecosystem to facilitate user-friendly interactive analysis and uncover interesting biological patterns. In short, our work opens possible new avenues in understanding of and discovery in large data sets, arising in domains such as EM analysis.

}, doi = {10.48550/arXiv.2012.12175}, url = {http://doi.org/10.48550/arXiv.2012.12175}, author = {Gary B Huang and Huei-Fang Yang and Shin-ya Takemura and Pat Rivlin and Stephen M Plaza} } @article {65366, title = {Layer 6b Is driven by intracortical long-range projection neurons.}, journal = {Cell Reports}, volume = {30}, year = {2020}, month = {2020 Mar 10}, pages = {3492 - 3505.e5}, abstract = {

Layer 6b (L6b), the deepest neocortical layer, projects to cortical targets and higher-order thalamus and is the only layer responsive to the wake-promoting neuropeptide orexin/hypocretin. These characteristics suggest that L6b can strongly modulate brain state, but projections to L6b and their influence remain unknown. Here, we examine the inputs to L6b\ ex\ vivo\ in the mouse primary somatosensory cortex with rabies-based retrograde tracing and channelrhodopsin-assisted circuit mapping in brain slices. We find that L6b receives its strongest excitatory input from intracortical long-range projection neurons, including those in the contralateral hemisphere. In contrast, local intracortical input and thalamocortical input were significantly weaker. Moreover, our data suggest that L6b receives far less thalamocortical input than other cortical layers. L6b was most strongly inhibited by PV and SST interneurons. This study shows that L6b integrates long-range intracortical information and is not part of the traditional thalamocortical loop.

}, issn = {22111247}, doi = {10.1016/j.celrep.2020.02.044}, url = {https://linkinghub.elsevier.com/retrieve/pii/S2211124720302059}, author = {Zolnik, Timothy A. and Ledderose, Julia and Toumazou, Maria and Trimbuch, Thorsten and Oram, Tess and Rosenmund, Christian and Eickholt, Britta J. and Sachdev, Robert N.S. and Larkum, Matthew E.} } @conference {67227, title = {Learning Guided Electron Microscopy with Active Acquisition}, booktitle = {Medical Image Computing and Computer Assisted Intervention {\textendash} MICCAI 2020}, year = {2020}, month = {10/2020}, publisher = {Springer International Publishing}, organization = {Springer International Publishing}, address = {Cham}, abstract = {

Single-beam scanning electron microscopes (SEM) are widely used to acquire massive datasets for biomedical study, material analysis, and fabrication inspection. Datasets are typically acquired with uniform acquisition: applying the electron beam with the same power and duration to all image pixels, even if there is great variety in the pixels{\textquoteright} importance for eventual use. Many SEMs are now able to move the beam to any pixel in the field of view without delay, enabling them, in principle, to invest their time budget more effectively with non-uniform imaging.

}, isbn = {978-3-030-59722-1}, url = {https://link.springer.com/chapter/10.1007/978-3-030-59722-1_8}, author = {Mi, Lu and Wang, Hao and Meirovitch, Yaron and Schalek, Richard and Turaga, Srinivas C. and Lichtman, Jeff W. and Samuel, Aravinthan D. T. and Shavit, Nir}, editor = {Martel, Anne L. and Abolmaesumi, Purang and Stoyanov, Danail and Mateus, Diana and Zuluaga, Maria A. and Zhou, S. Kevin and Racoceanu, Daniel and Joskowicz, Leo} } @article {65824, title = {Linking axon morphology to gene expression: a strategy for neuronal cell-type classification.}, journal = {Current Opinion in Neurobiology}, volume = {65}, year = {2020}, month = {2020 Dec 01}, pages = {70-76}, abstract = {

To study how the brain drives cognition and behavior we need to understand its cellular composition. Advances in single-cell transcriptomics have revolutionized our ability to characterize neuronal diversity. To arrive at meaningful descriptions of cell types, however, gene expression must be linked to structural and functional properties. Axonal projection patterns are an appropriate measure, as they are diverse, change only gradually over time, and they influence and constrain circuit function. Here, we consider how efforts to map transcriptional and morphological diversity in the mouse brain could be linked to generate a modern taxonomy of the mouse brain.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2020.10.006}, author = {Winnubst, Johan and Spruston, Nelson and Harris, Julie A} } @article {65908, title = {Linking axon morphology to gene expression: a strategy for neuronal cell-type classification.}, journal = {Current Opinion in Neurobiology}, volume = {65}, year = {2020}, month = {2020 Dec 01}, pages = {70-76}, abstract = {

To study how the brain drives cognition and behavior we need to understand its cellular composition. Advances in single-cell transcriptomics have revolutionized our ability to characterize neuronal diversity. To arrive at meaningful descriptions of cell types, however, gene expression must be linked to structural and functional properties. Axonal projection patterns are an appropriate measure, as they are diverse, change only gradually over time, and they influence and constrain circuit function. Here, we consider how efforts to map transcriptional and morphological diversity in the mouse brain could be linked to generate a modern taxonomy of the mouse brain.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2020.10.006}, author = {Winnubst, Johan and Spruston, Nelson and Harris, Julie A} } @article {65624, title = {Live-cell imaging in the era of too many microscopes.}, journal = {Current Opinion in Cell Biology}, volume = {66}, year = {2020}, month = {2020 May 26}, pages = {34-42}, abstract = {

At the time of this writing, searching Google Scholar for {\textquoteright}light-sheet microscopy{\textquoteright} returns almost 8500 results; over three-quarters of which were published in the last 5 years alone. Searching for other advanced imaging methods in the last 5 years yields similar results: {\textquoteright}super-resolution microscopy{\textquoteright} (\>16 000), {\textquoteright}single-molecule imaging{\textquoteright} (almost 10 000), SPIM (Single Plane Illumination Microscopy, 5000), and {\textquoteright}lattice light-sheet{\textquoteright} (1300). The explosion of new imaging methods has also produced a dizzying menagerie of acronyms, with over 100 different species of {\textquoteright}light-sheet{\textquoteright} alone, from SPIM to UM (Ultra microscopy) to SiMView (Simultaneous MultiView) to iSPIM (inclined SPIM, not to be confused with iSPIM, inverted SPIM). How then is the average biologist, without an advanced degree in physics, optics, or computer science supposed to make heads or tails of which method is best suited for their needs? Let us also not forget the plight of the optical physicist, who at best might need help with obtaining healthy samples and keeping them that way, or at worst may not realize the impact their newest technique could have for biologists. This review will not attempt to solve all\ these problems, but instead highlight some of the most recent, successful mergers between biology and advanced imaging technologies, as well as hopefully provide some guidance for anyone interested in journeying into the world of live-cell imaging.

}, issn = {1879-0410}, doi = {10.1016/j.ceb.2020.04.008}, author = {Lemon, William C and McDole, Katie} } @article {65581, title = {Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Apr 27}, abstract = {

The H2A.Z histone variant, a genome-wide hallmark of permissive chromatin, is enriched near transcription start sites in all eukaryotes. H2A.Z is deposited by the SWR1 chromatin remodeler and evicted by unclear mechanisms. We tracked H2A.Z in living yeast at single-molecule resolution, and found that H2A.Z eviction is dependent on RNA Polymerase II (Pol II) and the Kin28/Cdk7 kinase, which phosphorylates Serine 5 of heptapeptide repeats on the carboxy-terminal domain of the largest Pol II subunit Rpb1. These findings link H2A.Z eviction to transcription initiation, promoter escape and early elongation activities of Pol II. Because passage of Pol II through +1 nucleosomes genome-wide would obligate H2A.Z turnover, we propose that global transcription at yeast promoters is responsible for eviction of H2A.Z. Such usage of yeast Pol II suggests a general mechanism coupling eukaryotic transcription to erasure of the H2A.Z epigenetic signal.

}, issn = {2050-084X}, doi = {10.7554/eLife.55667}, author = {Ranjan, Anand and Nguyen, Vu Q and Liu, Sheng and Wisniewski, Jan and Kim, Jee Min and Tang, Xiaona and Mizuguchi, Gaku and Elalaoui, Ejlal and Nickels, Timothy J and Jou, Vivian and English, Brian P and Zheng, Qinsi and Luk, Ed and Lavis, Luke D and Lionnet, Timoth{\'e}e and Wu, Carl} } @article {66016, title = {Lysosome-targeting chimaeras for degradation of extracellular proteins}, journal = {Nature}, volume = {584}, year = {2020}, month = {Jan-08-2021}, pages = {291 - 297}, abstract = {

The majority of therapies that target individual proteins rely on specific activity-modulating interactions with the target protein{\textemdash}for example, enzyme inhibition or ligand blocking. However, several major classes of therapeutically relevant proteins have unknown or inaccessible activity profiles and so cannot be targeted by such strategies. Protein-degradation platforms such as proteolysis-targeting chimaeras (PROTACs)1,2\ and others (for example, dTAGs3, Trim-Away4, chaperone-mediated autophagy targeting5\ and SNIPERs6) have been developed for proteins that are typically difficult to target; however, these methods involve the manipulation of intracellular protein degradation machinery and are therefore fundamentally limited to proteins that contain cytosolic domains to which ligands can bind and recruit the requisite cellular components. Extracellular and membrane-associated proteins{\textemdash}the products of 40\% of all protein-encoding genes7{\textemdash}are key agents in cancer, ageing-related diseases and autoimmune disorders8, and so a general strategy to selectively degrade these proteins has the potential to improve human health. Here we establish the targeted degradation of extracellular and membrane-associated proteins using conjugates that bind both a cell-surface lysosome-shuttling receptor and the extracellular domain of a target protein. These initial lysosome-targeting chimaeras, which we term LYTACs, consist of a small molecule or antibody fused to chemically synthesized glycopeptide ligands that are agonists of the cation-independent mannose-6-phosphate receptor (CI-M6PR). We use LYTACs to develop a CRISPR interference screen that reveals the biochemical pathway for CI-M6PR-mediated cargo internalization in cell lines, and uncover the exocyst complex as a previously unidentified{\textemdash}but essential{\textemdash}component of this pathway. We demonstrate the scope of this platform through the degradation of therapeutically relevant proteins, including apolipoprotein\ E4, epidermal growth factor receptor, CD71 and programmed death-ligand 1. Our results establish a modular strategy for directing secreted and membrane proteins for lysosomal degradation, with broad implications for biochemical research and for therapeutics.

}, issn = {0028-0836}, doi = {10.1038/s41586-020-2545-9}, url = {http://www.nature.com/articles/s41586-020-2545-9http://www.nature.com/articles/s41586-020-2545-9.pdfhttp://www.nature.com/articles/s41586-020-2545-9.pdfhttp://www.nature.com/articles/s41586-020-2545-9}, author = {Banik, Steven M. and Pedram, Kayvon and Wisnovsky, Simon and Ahn, Green and Riley, Nicholas M. and Bertozzi, Carolyn R.} } @article {65631, title = {Mechanisms of procollagen and HSP47 sorting during ER-to-Golgi trafficking}, journal = {Matrix Biology}, volume = {93}, year = {2020}, month = {2020 Nov 01}, pages = {79-94}, abstract = {

Efficient quality control and export of procollagen from the cell is crucial for extracellular matrix homeostasis, yet it is still incompletely understood. One of the debated questions is the role of a collagen-specific ER chaperone HSP47 in these processes. Most ER chaperones preferentially bind to unfolded polypeptide chains, enabling selective export of natively folded proteins from the ER after chaperone release. In contrast, HSP47 preferentially binds to the natively folded procollagen and is believed to be released only in the ER-Golgi intermediate compartment (ERGIC) or cis-Golgi. HSP47 colocalization with procollagen in punctate structures observed by immunofluorescence imaging of fixed cells has thus been interpreted as evidence for HSP47 export from the ER together with procollagen in transport vesicles destined for ERGIC or Golgi. To understand the mechanism of this co-trafficking and its physiological significance, we imaged the dynamics of fluorescently tagged type I procollagen and HSP47 punctate structures in live MC3T3 murine osteoblasts with up to 120 nm spatial and 500 ms time resolution. Contrary to the prevailing model, we discovered that most bona fide carriers delivering procollagen from ER exit sites (ERESs) to Golgi contained no HSP47, unless the RDEL signal for ER retention in HSP47 was deleted or mutated. These transport intermediates exhibited characteristic rapid, directional motion along microtubules, while puncta with colocalized HSP47 and procollagen similar to the ones described before had only limited, stochastic motion. Live cell imaging and fluorescence recovery after photobleaching revealed that the latter puncta (including the ones induced by ARF1 inhibition) were dilated regions of ER lumen, ERESs, or autophagic structures surrounded by lysosomal membranes. Procollagen was colocalized with HSP47 and ERGIC53 at ERESs. It was colocalized with ERGIC53 but not HSP47 in Golgi-bound transport intermediates. Our results suggest that procollagen and HSP47 sorting occurs at ERES before procollagen is exported from the ER in Golgi-bound transport intermediates, providing new insights into mechanisms of procollagen trafficking.

}, issn = {0945053X}, doi = {10.1016/j.matbio.2020.06.002}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0945053X20300676}, author = {Omari, Shakib and Makareeva, Elena and Gorrell, Laura and Jarnik, Michal and Lippincott-Schwartz, Jennifer and Leikin, Sergey} } @article {68359, title = {Meissner corpuscles and their spatially intermingled afferents underlie gentle touch perception}, journal = {Science}, volume = {368}, year = {2020}, month = {06/2020}, pages = {eabb2751}, abstract = {

The Meissner corpuscle, a mechanosensory end organ, was discovered more than 165 years ago and has since been found in the glabrous skin of all mammals, including that on human fingertips. Although prominently featured in textbooks, the function of the Meissner corpuscle is unknown. Neubarth et al. generated adult mice without Meissner corpuscles and used them to show that these corpuscles alone mediate behavioral responses to, and perception of, gentle forces (see the Perspective by Marshall and Patapoutian). Each Meissner corpuscle is innervated by two molecularly distinct, yet physiologically similar, mechanosensory neurons. These two neuronal subtypes are developmentally interdependent and their endings are intertwined within the corpuscle. Both Meissner mechanosensory neuron subtypes are homotypically tiled, ensuring uniform and complete coverage of the skin, yet their receptive fields are overlapping and offset with respect to each other. Science, this issue p. eabb2751; see also p. 1311 Light touch perception and fine sensorimotor control arise from spatially overlapping mechanoreceptors of the Meissner corpuscle. Meissner corpuscles are mechanosensory end organs that densely occupy mammalian glabrous skin. We generated mice that selectively lacked Meissner corpuscles and found them to be deficient in both perceiving the gentlest detectable forces acting on glabrous skin and fine sensorimotor control. We found that Meissner corpuscles are innervated by two mechanoreceptor subtypes that exhibit distinct responses to tactile stimuli. The anatomical receptive fields of these two mechanoreceptor subtypes homotypically tile glabrous skin in a manner that is offset with respect to one another. Electron microscopic analysis of the two Meissner afferents within the corpuscle supports a model in which the extent of lamellar cell wrappings of mechanoreceptor endings determines their force sensitivity thresholds and kinetic properties.

}, doi = {10.1126/science.abb2751}, url = {https://www.science.org/doi/abs/10.1126/science.abb2751}, author = {Nicole L. Neubarth and Alan J. Emanuel and Yin Liu and Mark W. Springel and Annie Handler and Qiyu Zhang and Brendan P. Lehnert and Chong Guo and Lauren L. Orefice and Amira Abdelaziz and Michelle M. DeLisle and Michael Iskols and Julia Rhyins and Soo J. Kim and Stuart J. Cattel and Wade Regehr and Christopher D. Harvey and Jan Drugowitsch and David D. Ginty} } @article {65617, title = {Membrane potential dynamics underlying context-dependent sensory responses in the hippocampus.}, journal = {Nature Neuroscience}, volume = {23}, year = {2020}, month = {2020 Jul 1}, pages = {881-91}, abstract = {

As animals navigate, they must identify features within context. In the mammalian brain, the hippocampus has the ability to separately encode different environmental contexts, even when they share some prominent features. To do so, neurons respond to sensory features in a context-dependent manner; however, it is not known how this encoding emerges. To examine this, we performed electrical recordings in the hippocampus as mice navigated in two distinct virtual environments. In CA1, both synaptic input to single neurons and population activity strongly tracked visual cues in one environment, whereas responses were almost completely absent when the same cue was presented in a second environment. A very similar, highly context-dependent pattern of cue-driven spiking was also observed in CA3. These results indicate that CA1 inherits a complex spatial code from upstream regions, including CA3, that have already computed a context-dependent representation of environmental features.

}, issn = {1546-1726}, doi = {10.1038/s41593-020-0646-2}, author = {Zhao, Xinyu and Wang, Yingxue and Spruston, Nelson and Magee, Jeffrey C} } @article {65826, title = {Metabolic determinants of cellular fitness dependent on mitochondrial reactive oxygen species.}, journal = {Science Advances}, volume = {6}, year = {2020}, month = {2020 Nov 04}, abstract = {

Mitochondria-derived reactive oxygen species (mROS) are required for the survival, proliferation, and metastasis of cancer cells. The mechanism by which mitochondrial metabolism regulates mROS levels to support cancer cells is not fully understood. To address this, we conducted a metabolism-focused CRISPR-Cas9 genetic screen and uncovered that loss of genes encoding subunits of mitochondrial complex I was deleterious in the presence of the mitochondria-targeted antioxidant mito-vitamin E (MVE). Genetic or pharmacologic inhibition of mitochondrial complex I in combination with the mitochondria-targeted antioxidants, MVE or MitoTEMPO, induced a robust integrated stress response (ISR) and markedly diminished cell survival and proliferation in vitro. This was not observed following inhibition of mitochondrial complex III. Administration of MitoTEMPO in combination with the mitochondrial complex I inhibitor phenformin decreased the leukemic burden in a mouse model of T cell acute lymphoblastic leukemia. Thus, mitochondrial complex I is a dominant metabolic determinant of mROS-dependent cellular fitness.

}, issn = {2375-2548}, doi = {10.1126/sciadv.abb7272}, author = {Kong, Hyewon and Reczek, Colleen R and McElroy, Gregory S and Steinert, Elizabeth M and Wang, Tim and Sabatini, David M and Chandel, Navdeep S} } @article {65695, title = {Metabolic rate through the life-course: From the organism to the organelle.}, journal = {Experimental Gerontology}, volume = {140}, year = {2020}, month = {2020 Aug 13}, pages = {111059}, issn = {1873-6815}, doi = {10.1016/j.exger.2020.111059}, author = {Seo, Arnold Y and Speakman, John R and Selman, Colin} } @article {65658, title = {Microdomains form on the luminal face of neuronal extracellular vesicle membranes.}, journal = {Scientific Reports}, volume = {10}, year = {2020}, month = {2020 Jul 20}, pages = {11953}, abstract = {

Extracellular vesicles (EVs) are important mediators of cell-to-cell communication and have been implicated in several pathologies including those of the central nervous system. They are released by all cell types, including neurons, and are highly heterogenous in size and composition. Yet much remains unknown regarding the biophysical characteristics of different EVs. Here, using cryo-electron microscopy (cryoEM), we analyzed the size distribution and morphology of EVs released from primary cortical neurons. We discovered massive macromolecular clusters on the luminal face of EV membranes. These clusters are predominantly found on medium-sized vesicles, suggesting that they may be specific to microvesicles as opposed to exosomes. We propose that these clusters serve as microdomains for EV signaling and play an important role in EV physiology.

}, issn = {2045-2322}, doi = {10.1038/s41598-020-68436-x}, author = {Matthies, Doreen and Lee, Nathanael Y J and Gatera, Ian and Pasolli, H Amalia and Zhao, Xiaowei and Liu, Hui and Walpita, Deepika and Liu, Zhe and Yu, Zhiheng and Ioannou, Maria S} } @conference {65837, title = {Microtubule Tracking in Electron Microscopy Volumes}, booktitle = {International Conference on Medical Image Computing and Computer-Assisted Intervention}, year = {2020}, month = {2020 Sep 17}, abstract = {

We present a method for microtubule tracking in electron microscopy volumes. Our method first identifies a sparse set of voxels that likely belong to microtubules. Similar to prior work, we then enumerate potential edges between these voxels, which we represent in a candidate graph. Tracks of microtubules are found by selecting nodes and edges in the candidate graph by solving a constrained optimization problem incorporating biological priors on microtubule structure. For this, we present a novel integer linear programming formulation, which results in speed-ups of three orders of magnitude and an increase of 53\% in accuracy compared to prior art (evaluated on three 1 . 2 {\texttimes} 4 {\texttimes} 4{\textmu}m volumes of Drosophila neural tissue). We also propose a scheme to solve the optimization problem in a block-wise fashion, which allows distributed tracking and is necessary to process very large electron microscopy volumes. Finally, we release a benchmark dataset for microtubule tracking, here used for training, testing and validation, consisting of eight 30 x 1000 x 1000 voxel blocks (1 . 2 {\texttimes} 4 {\texttimes} 4{\textmu}m) of densely annotated microtubules in the CREMI data set (https://github.com/nilsec/micron).

}, author = {Nils Eckstein and Julia Buhmann and Matthew Cook and Jan Funke} } @article {65738, title = {The mind of a mouse.}, journal = {Cell}, volume = {182}, year = {2020}, month = {2020 Sep 17}, pages = {1372-1376}, abstract = {

Large scientific projects in genomics and astronomy are influential not because they answer any single question but because they enable investigation of continuously arising new questions from the same data-rich sources. Advances in automated mapping of the brain{\textquoteright}s synaptic connections (connectomics) suggest that the complicated circuits underlying brain function are ripe for analysis. We discuss benefits of mapping a mouse brain at the level of synapses.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2020.08.010}, author = {Abbott, Larry F and Bock, Davi D and Callaway, Edward M and Denk, Winfried and Dulac, Catherine and Fairhall, Adrienne L and Fiete, Ila and Harris, Kristen M and Helmstaedter, Moritz and Jain, Viren and Kasthuri, Narayanan and LeCun, Yann and Lichtman, Jeff W and Littlewood, Peter B and Luo, Liqun and Maunsell, John H R and Reid, R Clay and Rosen, Bruce R and Rubin, Gerald M and Sejnowski, Terrence J and Seung, H Sebastian and Svoboda, Karel and Tank, David W and Tsao, Doris and Van Essen, David C} } @article {65613, title = {mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 May 19}, abstract = {

Although the elongating ribosome is an efficient helicase, certain mRNA stem-loop structures are known to impede ribosome movement along mRNA and stimulate programmed ribosome frameshifting via mechanisms that are not well understood. Using biochemical and single-molecule F{\"o}rster resonance energy transfer (smFRET) experiments, we studied how frameshift-inducing stem-loops from mRNA and the transcript of Human Immunodeficiency Virus (HIV) perturb translation elongation. We find that upon encountering the ribosome, the stem-loops strongly inhibit A-site tRNA binding and ribosome intersubunit rotation that accompanies translation elongation. Electron cryo-microscopy (cryo-EM) reveals that the HIV stem-loop docks into the A site of the ribosome. Our results suggest that mRNA stem-loops can transiently escape the ribosome helicase by binding to the A site. Thus, the stem-loops can modulate gene expression by sterically hindering tRNA binding and inhibiting translation elongation.

}, issn = {2050-084X}, doi = {10.7554/eLife.55799}, author = {Bao, Chen and Loerch, Sarah and Ling, Clarence and Korostelev, Andrei A and Grigorieff, Nikolaus and Ermolenko, Dmitri N} } @article {65791, title = {The mTORC1/S6K/PDCD4/eIF4A axis determines outcome of mitotic arrest.}, journal = {Cell Reports}, volume = {33}, year = {2020}, month = {2020 Oct 06}, pages = {108230}, abstract = {

mTOR is a serine/threonine kinase and a master regulator of cell growth and proliferation. Raptor, a scaffolding protein that recruits substrates to mTOR complex 1 (mTORC1), is known to be phosphorylated during mitosis, but the significance of this phosphorylation remains largely unknown. Here we show that raptor expression and mTORC1 activity are dramatically reduced in cells arrested in mitosis. Expression of a non-phosphorylatable raptor mutant reactivates mTORC1 and significantly reduces cytotoxicity of the mitotic poison Taxol. This effect is mediated via degradation of PDCD4, a tumor suppressor protein that inhibits eIF4A activity and is negatively regulated by the mTORC1/S6K pathway. Moreover, pharmacological inhibition of eIF4A is able to enhance the effects of Taxol and restore sensitivity in Taxol-resistant cancer cells. These findings indicate that the mTORC1/S6K/PDCD4/eIF4A axis has a pivotal role in the death versus slippage decision during mitotic arrest and may be exploited clinically to treat tumors resistant to anti-mitotic agents.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2020.108230}, author = {Moustafa-Kamal, Mohamed and Kucharski, Thomas J and El-Assaad, Wissal and Abbas, Yazan M and Gandin, Valentina and Nagar, Bhushan and Pelletier, Jerry and Topisirovic, Ivan and Teodoro, Jose G} } @article {65653, title = {Multifield and inverse-contrast switching of magnetocaloric high contrast ratio MRI labels.}, journal = {Magnetic Resonance in Medicine}, volume = {85}, year = {2020}, month = {2020 Jul 07}, pages = {506-17}, abstract = {

PURPOSE: Demonstrating multifield and inverse contrast switching of magnetocaloric high contrast ratio MRI labels that either have increasing or decreasing moment versus temperature slopes depending on the material at physiological temperatures and different MRI magnetic field strengths.

METHODS: Two iron-rhodium samples of different purity (99\% and 99.9\%) and a lanthanum-iron-silicon sample were obtained from commercial vendors. Temperature and magnetic field-dependent magnetic moment measurements of the samples were performed on a vibrating sample magnetometer. Temperature-dependent MRI of different iron-rhodium and lanthanum-iron-silicon samples were performed on 3 different MRI scanners at 1 Tesla (T), 4.7T, and 7T.

RESULTS: Sharp, first-order magnetic phase transition of each iron-rhodium sample at a physiologically relevant temperature (~37{\textdegree}C) but at different MRI magnetic fields (1T, 4.7T, and 7T, depending on the sample) showed clear image contrast changes in temperature-dependent MRI. Iron-rhodium and lanthanum-iron-silicon samples with sharp, first-order magnetic phase transitions at the same MRI field of 1T and physiological temperature of 37{\textdegree}C, but with positive and negative slope of magnetization versus temperature, respectively, showed clear inverse contrast image changes. Temperature-dependent MRI on individual microparticle samples of lanthanum-iron-silicon also showed sharp image contrast changes.

CONCLUSION: Magnetocaloric materials of different purity and composition were demonstrated to act as diverse high contrast ratio switchable MRI contrast agents. Thus, we show that a range of magnetocaloric materials can be optimized for unique image contrast response under MRI-appropriate conditions at physiological temperatures and be controllably switched in situ.

}, issn = {1522-2594}, doi = {10.1002/mrm.28400}, author = {Barbic, Mladen and Dodd, Stephen J and ElBidweihy, Hatem and Dilley, Neil R and Marcheschi, Barbara and Huston, Alan L and Morris, H Douglas and Koretsky, Alan P} } @article {65316, title = {Multiple network properties overcome random connectivity to enable stereotypic sensory responses.}, journal = {Nature Communications}, volume = {11}, year = {2020}, month = {2020 Feb 24}, pages = {1023}, abstract = {

Connections between neuronal populations may be genetically hardwired or random. In the insect olfactory system, projection neurons of the antennal lobe connect randomly to Kenyon cells of the mushroom body. Consequently, while the odor responses of the projection neurons are stereotyped across individuals, the responses of the Kenyon cells are variable. Surprisingly, downstream of Kenyon cells, mushroom body output neurons show stereotypy in their responses. We found that the stereotypy is enabled by the convergence of inputs from many Kenyon cells onto an output neuron, and does not require learning. The stereotypy emerges in the total response of the Kenyon cell population using multiple odor-specific features of the projection neuron responses, benefits from the nonlinearity in the transfer function, depends on the convergence:randomness ratio, and is constrained by sparseness. Together, our results reveal the fundamental mechanisms and constraints with which convergence enables stereotypy in sensory responses despite random connectivity.

}, issn = {2041-1723}, doi = {10.1038/s41467-020-14836-6}, author = {Mittal, Aarush Mohit and Gupta, Diksha and Singh, Amrita and Lin, Andrew C and Gupta, Nitin} } @conference {65385, title = {Multiplexed 3-photon microscopy for functional connectomics of mammalian brains.}, booktitle = {Multiphoton Microscopy in the Biomedical Sciences XXMultiphoton Microscopy in the Biomedical Sciences XX}, year = {2020}, month = {2020 Feb 14}, publisher = {SPIE}, organization = {SPIE}, address = {San Francisco, United States}, abstract = {

3-photon excitation enables in vivo fluorescence microscopy deep in densely labeled and highly scattering samples, while maintaining high resolution and contrast. We designed and characterized a dual-plane 3-photon microscope with temporal multiplexing and remote focusing, and performed simultaneous in vivo calcium imaging of two planes deep in the cortex of a transgenic mouse expressing GCaMP6s in nearly all excitatory neurons.

}, doi = {10.1117/12.2543232 }, url = {https://www.spiedigitallibrary.org/conference-proceedings-of-spie/11244/2543232/Multiplexed-3-photon-microscopy-for-functional-connectomics-of-mammalian-brains/10.1117/12.2543232.full}, author = {Takasaki, Kevin and Tsyboulski, Dmitri A. and Waters, Jack} } @article {65852, title = {Multi-regional circuits underlying visually guided decision-making in Drosophila.}, journal = {Current Opinion in Neurobiology}, volume = {65}, year = {2020}, month = {2020 Nov 17}, pages = {77-87}, abstract = {

Visually guided decision-making requires integration of information from distributed brain areas, necessitating a brain-wide approach to examine its neural mechanisms. New tools in Drosophila melanogaster enable circuits spanning the brain to be charted with single cell-type resolution. Here, we highlight recent advances uncovering the computations and circuits that transform and integrate visual information across the brain to make behavioral choices. Visual information flows from the optic lobes to three primary central brain regions: a sensorimotor mapping area and two {\textquoteright}higher{\textquoteright} centers for memory or spatial orientation. Rapid decision-making during predator evasion emerges from the spike timing dynamics in parallel sensorimotor cascades. Goal-directed decisions may occur through memory, navigation and valence processing in the central complex and mushroom bodies.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2020.10.010}, author = {Cheong, Han and Siwanowicz, Igor and Card, Gwyneth M} } @article {65907, title = {Multi-regional circuits underlying visually guided decision-making in Drosophila.}, journal = {Current Opinion in Neurobiology}, volume = {65}, year = {2020}, month = {2020 Dec 01}, pages = {77-87}, abstract = {

Visually guided decision-making requires integration of information from distributed brain areas, necessitating a brain-wide approach to examine its neural mechanisms. New tools in Drosophila melanogaster enable circuits spanning the brain to be charted with single cell-type resolution. Here, we highlight recent advances uncovering the computations and circuits that transform and integrate visual information across the brain to make behavioral choices. Visual information flows from the optic lobes to three primary central brain regions: a sensorimotor mapping area and two {\textquoteright}higher{\textquoteright} centers for memory or spatial orientation. Rapid decision-making during predator evasion emerges from the spike timing dynamics in parallel sensorimotor cascades. Goal-directed decisions may occur through memory, navigation and valence processing in the central complex and mushroom bodies.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2020.10.010}, author = {Cheong, Han Sj and Siwanowicz, Igor and Card, Gwyneth M} } @article {65386, title = {The Mushroom Body: From Architecture to Algorithm in a Learning Circuit.}, journal = {Annual Review of Neuroscience}, year = {2020}, month = {2020 Apr 13}, abstract = {

The brain contains a relatively simple circuit for forming Pavlovian associations, yet it achieves many operations common across memory systems. Recent advances have established a clear framework for learning and revealed the following key operations: ) pattern separation, whereby dense combinatorial representations of odors are preprocessed to generate highly specific, nonoverlapping odor patterns used for learning; ) convergence, in which sensory information is funneled to a small set of output neurons that guide behavioral actions; ) plasticity, where changing the mapping of sensory input to behavioral output requires a strong reinforcement signal, which is also modulated by internal state and environmental context; and ) modularization, in which a memory consists of multiple parallel traces, which are distinct in stability and flexibility and exist in anatomically well-defined modules within the network. Cross-module interactions allow for higher-order effects where past experience influences future learning. Many of these operations have parallels with processes of memory formation and action selection in more complex brains. Expected final online publication date for the , Volume 43 is July 8, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-080317-0621333}, author = {Modi, Mehrab N and Shuai, Yichun and Turner, Glenn C} } @article {65262, title = {Nanoscale subcellular architecture revealed by multicolor three-dimensional salvaged fluorescence imaging.}, journal = {Nature Methods}, volume = {17}, year = {2020}, month = {2020 Jan 06}, pages = {225-231}, abstract = {

Combining the molecular specificity of fluorescent probes with three-dimensional imaging at nanoscale resolution is critical for investigating the spatial organization and interactions of cellular organelles and protein complexes. We present a 4Pi single-molecule switching super-resolution microscope that enables ratiometric multicolor imaging of mammalian cells at 5-10-nm localization precision in three dimensions using {\textquoteright}salvaged fluorescence{\textquoteright}. Imaging two or three fluorophores simultaneously, we show fluorescence images that resolve the highly convoluted Golgi apparatus and the close contacts between the endoplasmic reticulum and the plasma membrane, structures that have traditionally been the imaging realm of electron microscopy. The salvaged fluorescence approach is equally applicable in most single-objective microscopes.

}, issn = {1548-7105}, doi = {10.1038/s41592-019-0676-4}, author = {Zhang, Yongdeng and Schroeder, Lena K and Lessard, Mark D and Kidd, Phylicia and Chung, Jeeyun and Song, Yuanbin and Benedetti, Lorena and Li, Yiming and Ries, Jonas and Grimm, Jonathan B and Lavis, Luke D and De Camilli, Pietro and Rothman, James E and Baddeley, David and Bewersdorf, Joerg} } @article {65604, title = {Nanoscopic visualization of restricted nonvolume cholinergic and monoaminergic transmission with genetically encoded sensors.}, journal = {Nano Letters}, volume = {20}, year = {2020}, month = {2020 Jun}, pages = {4073-83}, abstract = {

How neuromodulatory transmitters diffuse into the extracellular space remains an unsolved fundamental biological question, despite wide acceptance of the volume transmission model. Here, we report development of a method combining genetically encoded fluorescent sensors with high-resolution imaging and analysis algorithms which permits the first direct visualization of neuromodulatory transmitter diffusion at various neuronal and non-neuronal cells. Our analysis reveals that acetylcholine and monoamines diffuse at individual release sites with a spread length constant of \~{}0.75 μm. These transmitters employ varied numbers of release sites, and when spatially close-packed release sites coactivate they can spillover into larger subcellular areas. Our data indicate spatially restricted (i.e., nonvolume) neuromodulatory transmission to be a prominent intercellular communication mode, reshaping current thinking of control and precision of neuromodulation crucial for understanding behaviors and diseases.

}, issn = {1530-6992}, doi = {10.1021/acs.nanolett.9b04877}, author = {Zhu, Paula K and Zheng, W Sharon and Zhang, Peng and Jing, Miao and Borden, Philip M and Ali, Farhan and Guo, Kaiming and Feng, Jiesi and Marvin, Jonathan S and Wang, Yali and Wan, Jinxia and Gan, Li and Kwan, Alex C and Lin, Li and Looger, Loren L and Li, Yulong and Zhang, Yajun} } @article {65317, title = {Neural circuitry linking mating and egg laying in Drosophila females.}, journal = {Nature}, volume = {579}, year = {2020}, month = {2020 Mar 02}, pages = {101-105}, abstract = {

Mating and egg laying are tightly cooordinated events in the reproductive life of\ all oviparous females. Oviposition is typically rare in virgin females but is initiated after copulation. Here we identify the neural circuitry that links egg laying to mating status in Drosophila melanogaster. Activation of female-specific oviposition descending neurons (oviDNs) is necessary and sufficient for egg laying, and is equally potent in virgin and mated females. After mating, sex peptide-a protein from the male seminal fluid-triggers many behavioural and physiological changes in the female, including the onset of egg laying. Sex peptide is detected by sensory neurons in the uterus, and silences these neurons and their postsynaptic ascending neurons in the abdominal ganglion. We show that these\ abdominal ganglion neurons directly activate the female-specific pC1 neurons. GABAergic (γ-aminobutyric-acid-releasing) oviposition inhibitory neurons (oviINs) mediate feed-forward inhibition from pC1 neurons to both oviDNs and their major excitatory input, the oviposition excitatory neurons (oviENs). By attenuating the abdominal ganglion inputs to pC1 neurons and oviINs, sex peptide disinhibits oviDNs to enable egg laying after mating. This circuitry thus coordinates the two key events in female reproduction: mating and egg laying.

}, issn = {1476-4687}, doi = {10.1038/s41586-020-2055-9}, author = {Wang, Fei and Wang, Kaiyu and Forknall, Nora and Patrick, Christopher and Yang, Tansy and Parekh, Ruchi and Bock, Davi and Dickson, Barry J} } @article {65598, title = {A neural representation of naturalistic motion-guided behavior in the zebrafish brain.}, journal = {Current Biology}, volume = {30}, year = {2020}, month = {2020 Jun 22}, pages = {2321-33}, abstract = {

All animals must transform ambiguous sensory data into successful behavior. This requires sensory representations that accurately reflect the statistics of natural stimuli and behavior. Multiple studies show that visual motion processing is tuned for accuracy under naturalistic conditions, but the sensorimotor circuits extracting these cues and implementing motion-guided behavior remain unclear. Here we show that the larval zebrafish retina extracts a diversity of naturalistic motion cues, and the retinorecipient pretectum organizes these cues around the elements of behavior. We find that higher-order motion stimuli, gliders, induce optomotor behavior matching expectations from natural scene analyses. We then image activity of retinal ganglion cell terminals and pretectal neurons. The retina exhibits direction-selective responses across glider stimuli, and anatomically clustered pretectal neurons respond with magnitudes matching behavior. Peripheral computations thus reflect natural input statistics, whereas central brain activity precisely codes information needed for behavior. This general principle could organize sensorimotor transformations across animal species.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2020.04.043}, author = {Yildizoglu, Tugce and Riegler, Clemens and Fitzgerald, James E and Portugues, Ruben} } @article {65722, title = {The neuroanatomical ultrastructure and function of a biological ring attractor.}, journal = {Neuron}, volume = {108}, year = {2020}, month = {2020 Oct 14}, pages = {145-63}, abstract = {

Neural representations of head direction (HD) have been discovered in many species. Theoretical work has proposed that the dynamics associated with these representations are generated, maintained, and updated by recurrent network structures called ring attractors. We evaluated this theorized structure-function relationship by performing electron-microscopy-based circuit reconstruction and RNA profiling of identified cell types in the HD system of Drosophila melanogaster. We identified motifs that have been hypothesized to maintain the HD representation in darkness, update it when the animal turns, and tether it to visual cues. Functional studies provided support for the proposed roles of individual excitatory or inhibitory circuit elements in shaping activity. We also discovered recurrent connections between neuronal arbors with mixed pre- and postsynaptic specializations. Our results confirm that the Drosophila HD network contains the core components of a ring attractor while also revealing unpredicted structural features that might enhance the network{\textquoteright}s computational power.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2020.08.006}, author = {Turner-Evans, Daniel B and Jensen, Kristopher T and Ali, Saba and Paterson, Tyler and Sheridan, Arlo and Ray, Robert P and Wolff, Tanya and Lauritzen, J Scott and Rubin, Gerald M and Bock, Davi D and Jayaraman, Vivek} } @article {65374, title = {Neuronal upregulation of Prospero protein is driven by alternative mRNA polyadenylation and Syncrip-mediated mRNA stabilisation.}, journal = {Biology Open}, volume = {9}, year = {2020}, month = {2020 May}, abstract = {

During and vertebrate brain development, the conserved transcription factor Prospero/Prox1 is an important regulator of the transition between proliferation and differentiation. Prospero level is low in neural stem cells and their immediate progeny, but is upregulated in larval neurons and it is unknown how this process is controlled. Here, we use single molecule fluorescent hybridisation to show that larval neurons selectively transcribe a long mRNA isoform containing a 15 kb 3{\textquoteright} untranslated region, which is bound in the brain by the conserved RNA-binding protein Syncrip/hnRNPQ. Syncrip binding increases the mRNA stability of the long isoform, which allows an upregulation of Prospero protein production. Adult flies selectively lacking the long isoform show abnormal behaviour that could result from impaired locomotor or neurological activity. Our findings highlight a regulatory strategy involving alternative polyadenylation followed by differential post-transcriptional regulation.

}, issn = {2046-6390}, doi = {10.1242/bio.049684}, author = {Samuels, Tamsin J and Arava, Yoav and J{\"a}rvelin, Aino I and Robertson, Francesca and Lee, Jeffrey Y and Yang, Lu and Yang, Ching-Po and Lee, Tzumin and Ish-Horowicz, David and Davis, Ilan} } @article {65263, title = {The neuropeptide Drosulfakinin regulates social isolation-induced aggression in Drosophila.}, journal = {Journal of Experimental Biology}, volume = {223}, year = {2020}, month = {2020 Jan 03}, abstract = {

Social isolation strongly modulates behavior across the animal kingdom. We utilized the fruit fly to study social isolation-driven changes in animal behavior and gene expression in the brain. RNA-seq identified several head-expressed genes strongly responding to social isolation or enrichment. Of particular interest, social isolation downregulated expression of the gene encoding the neuropeptide (), the homologue of vertebrate cholecystokinin (CCK), which is critical for many mammalian social behaviors. knockdown significantly increased social isolation-induced aggression. Genetic activation or silencing of neurons each similarly increased isolation-driven aggression. Our results suggest a U-shaped dependence of social isolation-induced aggressive behavior on signaling, similar to the actions of many neuromodulators in other contexts.

}, issn = {1477-9145}, doi = {10.1242/jeb.207407}, author = {Agrawal, Pavan and Kao, Damian and Chung, Phuong and Looger, Loren L} } @article {65318, title = {Nicotine exposure and neuronal activity regulate Golgi membrane dispersal and distribution}, journal = {bioRxiv}, year = {2020}, month = {2020 Feb 26}, abstract = {

How nicotine exposure produces long-lasting changes that remodel neural circuits with addiction is unknown. Here, we report that long-term nicotine exposure alters the trafficking of α4β2-type nicotinic acetylcholine receptors (α4β2Rs) by dispersing and redistributing the Golgi apparatus. In cultured neurons, dispersed Golgi membranes were distributed throughout somata, dendrites and axons. Small, mobile vesicles in dendrites and axons lacked standard Golgi markers and were identified by other Golgi enzymes that modify glycans. Nicotine exposure increased levels of dispersed Golgi membranes, which required α4β2R expression. Similar nicotine-induced changes occurred\ in vivo\ at dopaminergic neurons at mouse nucleus accumbens terminals, consistent with these events contributing to nicotine{\textquoteright}s addictive effects. Characterization\ in vitro\ demonstrated that dispersal was reversible, that dispersed Golgi membranes were functional, and that membranes were heterogenous in size, with smaller vesicles emerging from larger {\textquotedblleft}ministacks{\textquotedblright}, similar to Golgi dispersal induced by nocadazole. Protocols that increased cultured neuronal synaptic excitability also increased Golgi dispersal, without the requirement of α4β2R expression. Our findings reveal novel activity- and nicotine-dependent changes in neuronal intracellular morphology. These changes regulate levels and location of dispersed Golgi membranes at dendrites and axons, which function in local trafficking at subdomains.

}, author = {Govind, Anitha P. and Jeyifous, Okunola and Russell, Theron A. and Vaasjo, Lee O. and Yi, Zola and Weigel, Aubrey V. and Newell, Luke and Koranda, Jessica L. and Singh, Karanveer and Valbuena, Fernando and Glick, Benjamin S. and Mukherjee, Jogeshwar and Lippincott-Schwartz, Jennifer and Zhuang, Xiaoxi and Green, William N.} } @article {65724, title = {Novel fluorescent ligands enable single-molecule localization microscopy of the dopamine transporter.}, journal = {ACS Chemical Neuroscience}, year = {2020}, month = {2020 Sep 14}, abstract = {

The dopamine transporter (DAT) is critical for spatiotemporal control of dopaminergic neurotransmission and the target for therapeutic agents, including ADHD medications, and abused substances, such as cocaine. Here, we develop new fluorescently labeled ligands that bind DAT with high affinity and enable single-molecule detection of the transporter. The cocaine analogue MFZ2-12 (1) was conjugated to novel rhodamine-based Janelia Fluorophores (JF549 and JF646). High affinity binding of the resulting ligands to DAT was demonstrated by potent inhibition of [3H]dopamine uptake in DAT transfected CAD cells and by competition radioligand binding experiments on rat striatal membranes. Visualization of binding was substantiated by confocal or TIRF microscopy revealing selective binding of the analogues to DAT transfected CAD cells. Single particle tracking experiments were performed with JF549-conjugated DG3-80 (3) and JF646-conjugated DG4-91 (4) on DAT transfected CAD cells enabling quantification and categorization of the dynamic behavior of DAT into four distinct motion classes (immobile, confined, Brownian, and directed). Finally, we show that the ligands can be used in direct stochastic optical reconstruction microscopy (dSTORM) experiments permitting further analyses of DAT distribution on the nanoscale. In summary, these novel fluorescent ligands are promising new tools for studying DAT localization and regulation with single-molecule resolution.

}, issn = {1948-7193}, doi = {10.1021/acschemneuro.0c00397}, author = {Guthrie, Daryl and Klein Herenbrink, Carmen and Lycas, Matthew and Ku, Therese and Bonifazi, Alessandro and DeVree, Brian and Mathiasen, Signe and Javitch, Jonathan and Grimm, Jonathan B and Lavis, Luke D and Gether, Ulrik and Newman, Amy Hauck} } @article {65758, title = {Nuclear crowding and nonlinear diffusion during interkinetic nuclear migration in the zebrafish retina.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Oct 06}, abstract = {

An important question in early neural development is the origin of stochastic nuclear movement between apical and basal surfaces of neuroepithelia during interkinetic nuclear migration. Tracking of nuclear subpopulations has shown evidence of diffusion - mean squared displacements growing linearly in time - and suggested crowding from cell division at the apical surface drives basalward motion. Yet, this hypothesis has not yet been tested, and the forces involved not quantified. We employ long-term, rapid light-sheet and two-photon imaging of early zebrafish retinogenesis to track entire populations of nuclei within the tissue. The time-varying concentration profiles show clear evidence of crowding as nuclei reach close-packing and are quantitatively described by a nonlinear diffusion model. Considerations of nuclear motion constrained inside the enveloping cell membrane show that concentration-dependent stochastic forces inside cells, compatible in magnitude to those found in cytoskeletal transport, can explain the observed magnitude of the diffusion constant.

}, issn = {2050-084X}, doi = {10.7554/eLife.58635}, author = {Azizi, Afnan and Herrmann, Anne and Wan, Yinan and Buse, Salvador Jrp and Keller, Philipp J and Goldstein, Raymond E and Harris, William A} } @article {68427, title = {Nurturing Undergraduate Researchers in Biomedical Sciences.}, journal = {Cell}, volume = {182}, year = {2020}, month = {07/2020}, pages = {1-4}, abstract = {

Undergraduate researchers are the next-generation scientists. Here, we call for more attention from our community to the proper training of undergraduates in biomedical research laboratories. By dissecting common pitfalls, we suggest how to better mentor undergraduates and prepare them for flourishing careers.

}, keywords = {Biomedical Research, Communication, Mentoring, Mentors, Research Personnel}, issn = {1097-4172}, doi = {10.1016/j.cell.2020.05.008}, author = {Li, Jiefu and Luo, Liqun} } @article {67668, title = {Optimization of Fluorescent Proteins and Techniques for In-resin Correlative Light and Electron Microscopy}, journal = {Microscopy and Microanalysis}, volume = {26}, year = {2020}, month = {07/2020}, pages = {1036{\textendash}1039}, abstract = {

Correlative light and electron microscopy (CLEM) combines the power of electron microscopy, with its excellent resolution and contrast, with that of fluorescence imaging, which allows the staining of specific molecules, organelles, and cell populations. Fluorescence imaging is also readily compatible with live cells and behaving animals, facilitating real-time visualization of cellular processes, potentially followed by electron microscopic reconstruction. Super-resolution single-molecule localization microscopy is a relatively new modality that harnesses the ability of some fluorophores to photoconvert, through which localization precision better than Abbe{\textquoteright}s diffraction limit is achieved through iterative high-resolution localization of single-molecule emitters. Here we describe our lab{\textquoteright}s recent progress in the development of reagents and techniques for super-resolution single-molecule localization CLEM and their applications to biological problems.

}, doi = {10.1017/S143192762001675X}, author = {Paez-Segala, Maria and Wang, Yalin and Iyer, Nirmala and Li, Wei-Ping and Rivlin, Patricia and Looger, Loren} } @article {65827, title = {Optimized Vivid-derived Magnets photodimerizers for subcellular optogenetics in mammalian cells.}, journal = {Elife}, volume = {9}, year = {2020}, month = {2020 Nov 11}, abstract = {

Light-inducible dimerization protein modules enable precise temporal and spatial control of biological processes in non-invasive fashion. Among them, Magnets are small modules engineered from the photoreceptor Vivid by orthogonalizing the homodimerization interface into complementary heterodimers. Both Magnets components, which are well-tolerated as protein fusion partners, are photoreceptors requiring simultaneous photoactivation to interact, enabling high spatiotemporal confinement of dimerization with a single-excitation wavelength. However, Magnets require concatemerization for efficient responses and cell preincubation at 28C to be functional. Here we overcome these limitations by engineering an optimized Magnets pair requiring neither concatemerization nor low temperature preincubation. We validated these {\textquoteright}enhanced{\textquoteright} Magnets (eMags) by using them to rapidly and reversibly recruit proteins to subcellular organelles, to induce organelle contacts, and to reconstitute OSBP-VAP ER-Golgi tethering implicated in phosphatidylinositol-4-phosphate transport and metabolism. eMags represent a very effective tool to optogenetically manipulate physiological processes over whole cells or in small subcellular volumes.

}, issn = {2050-084X}, doi = {10.7554/eLife.63230}, author = {Benedetti, Lorena and Marvin, Jonathan S and Falahati, Hanieh and Guill{\'e}n-Samander, Andres and Looger, Loren L and De Camilli, Pietro} } @article {65761, title = {Orthogonal fluorescent chemogenetic reporters for multicolor imaging}, journal = {Nature Chemical Biology}, year = {2020}, month = {04/2020}, pages = {1{\textendash}9}, abstract = {

Spectrally separated fluorophores allow the observation of multiple targets simultaneously inside living cells, leading to a deeper understanding of the molecular interplay that regulates cell function and fate. Chemogenetic systems combining a tag and a synthetic fluorophore provide certain advantages over fluorescent proteins since there is no requirement for chromophore maturation. Here, we present the engineering of a set of spectrally orthogonal fluorogen-activating tags based on the fluorescence-activating and absorption shifting tag (FAST) that are compatible with two-color, live-cell imaging. The resulting tags, greenFAST and redFAST, demonstrate orthogonality not only in their fluorogen recognition capabilities, but also in their one- and two-photon absorption profiles. This pair of orthogonal tags allowed the creation of a two-color cell cycle sensor capable of detecting very short, early cell cycles in zebrafish development and the development of split complementation systems capable of detecting multiple protein{\textendash}protein interactions by live-cell fluorescence microscopy. The fluorescent chemogenetic reporters greenFAST and redFAST were engineered by protein engineering. They display orthogonal fluorogen recognition and spectral properties allowing efficient multicolor imaging of proteins in live cells and organisms.

}, issn = {1552-4450}, doi = {10.1038/s41589-020-0611-0}, author = {Tebo, Alison G. and Moeyaert, Benjamien and Thauvin, Marion and Carlon-Andres, Irene and B{\"o}ken, Dorothea and Volovitch, Michel and Padilla-Parra, Sergi and Dedecker, Peter and Vriz, Sophie and Gautier, Arnaud} } @article {65312, title = {Parvalbumin+ and Npas1+ Pallidal neurons have distinct circuit topology and function.}, journal = {Journal of Neuroscience}, year = {2020}, month = {2020 Aug 30}, author = {Pamukcu, Arin and Cui, Qiaoling and Xenias, Harry S. and Berceau, Brianna L. and Augustine, Elizabeth C. and Fan, Isabel and Hantman, Adam W and Lerner, Talia N. and Boca, Simina M. and Chan, C. Savio} } @article {65694, title = {A post-invasion role for type III effector TarP in modulating the dynamics and organization of host cell focal adhesions.}, journal = {Journal of Biological Chemistry}, volume = {295}, year = {2020}, month = {2020 Oct 23}, pages = {14763-14779}, abstract = {

The human pathogen targets epithelial cells lining the genital mucosa. We observed that infection of various cell types, including fibroblasts and epithelial cells resulted in the formation of unusually stable and mature focal adhesions that resisted disassembly induced by the myosin II inhibitor, blebbistatin. Super-resolution microscopy revealed in infected cells the vertical displacement of paxillin and FAK from the signaling layer of focal adhesions; while vinculin remained in its normal position within the force transduction layer. The candidate type III effector TarP which localized to focal adhesions during infection and when expressed ectopically, was sufficient to mimic both the reorganization and blebbistatin-resistant phenotypes. These effects of TarP, including its localization to focal adhesions, required a post-invasion interaction with the host protein vinculin through a specific domain at the C-terminus of TarP. This interaction is repurposed from an actin-recruiting and -remodeling complex to one that mediates nano-architectural and dynamic changes of focal adhesions. The consequence of -stabilized focal adhesions was restricted cell motility and enhanced attachment to the extracellular matrix. Thus, via a novel mechanism, inserts TarP within focal adhesions to alter their organization and stability.

}, issn = {1083-351X}, doi = {10.1074/jbc.RA120.015219}, author = {Pedrosa, Antonio T and Murphy, Korinn N and Nogueira, Ana T and Brinkworth, Amanda J and Thwaites, Tristan R and Aaron, Jesse and Chew, Teng-Leong and Carabeo, Rey A} } @article {65634, title = {Precision Calcium Imaging of Dense Neural Populations via a Cell-Body-Targeted Calcium Indicator.}, journal = {Neuron}, volume = {107}, year = {2020}, month = {2020 Aug 01}, pages = {470}, abstract = {

Methods for one-photon fluorescent imaging of calcium dynamics can capture the activity of hundreds of neurons across large fields of view at a low equipment complexity and cost. In contrast to two-photon methods, however, one-photon methods suffer from higher levels of crosstalk from neuropil, resulting in a decreased signal-to-noise ratio and artifactual correlations of neural activity. We address this problem by engineering cell-body-targeted variants of the fluorescent calcium indicators GCaMP6f and GCaMP7f. We screened fusions of GCaMP to natural, as well as artificial, peptides and identified fusions that localized GCaMP to within 50\ μm of the cell body of neurons in mice and larval zebrafish. One-photon imaging of soma-targeted GCaMP in dense neural circuits reported fewer artifactual spikes from neuropil, an increased signal-to-noise ratio, and decreased artifactual correlation across neurons. Thus, soma-targeting of fluorescent calcium indicators facilitates usage of simple, powerful, one-photon methods for imaging neural calcium dynamics.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2020.05.029}, author = {Shemesh, Or A and Linghu, Changyang and Piatkevich, Kiryl D and Goodwin, Daniel and Celiker, Orhan Tunc and Gritton, Howard J and Romano, Michael F and Gao, Ruixuan and Yu, Chih-Chieh Jay and Tseng, Hua-An and Bensussen, Seth and Narayan, Sujatha and Yang, Chao-Tsung and Freifeld, Limor and Siciliano, Cody A and Gupta, Ishan and Wang, Joyce and Pak, Nikita and Yoon, Young-Gyu and Ullmann, Jeremy F P and Guner-Ataman, Burcu and Noamany, Habiba and Sheinkopf, Zoe R and Park, Won Min and Asano, Shoh and Keating, Amy E and Trimmer, James S and Reimer, Jacob and Tolias, Andreas S and Bear, Mark F and Tye, Kay M and Han, Xue and Ahrens, Misha B and Boyden, Edward S} } @article {65721, title = {Preventing cytokine storm syndrome in COVID-19 using α-1 adrenergic receptor antagonists.}, journal = {The Journal of Clinical Investigatio}, volume = {130}, year = {2020}, month = {2020 Jul 01}, pages = {3345-47}, keywords = {Adrenergic alpha-1 Receptor Antagonists, Clinical Trials as Topic, Coronavirus Infections, Cytokine Release Syndrome, Humans, Pandemics, Pneumonia, Viral}, issn = {1558-8238}, doi = {10.1172/JCI139642}, author = {Konig, Maximilian F and Powell, Mike and Staedtke, Verena and Bai, Ren-Yuan and Thomas, David L and Fischer, Nicole and Huq, Sakibul and Khalafallah, Adham M and Koenecke, Allison and Xiong, Ruoxuan and Mensh, Brett and Papadopoulos, Nickolas and Kinzler, Kenneth W and Vogelstein, Bert and Vogelstein, Joshua T and Athey, Susan and Zhou, Shibin and Bettegowda, Chetan} } @article {65884, title = {Probabilistic Models of Larval Zebrafish Behavior Reveal Structure on Many Scales}, journal = {Current Biology}, volume = {30}, year = {2020}, month = {01/2020}, pages = {70 - 82.e4}, abstract = {

Nervous systems have evolved to combine environmental information with internal state to select and generate adaptive behavioral sequences. To better understand these computations and their implementation in neural circuits, natural behavior must be carefully measured and quantified. Here, we collect high spatial resolution video of single zebrafish larvae swimming in a naturalistic environment and develop models of their action selection across exploration and hunting. Zebrafish larvae swim in punctuated bouts separated by longer periods of rest called interbout intervals. We take advantage of this structure by categorizing bouts into discrete types and representing their behavior as labeled sequences of bout types emitted over time. We then construct probabilistic models{\textemdash}specifically, marked renewal processes{\textemdash}to evaluate how bout types and interbout intervals are selected by the fish as a function of its internal hunger state, behavioral\ history, and the locations and properties of nearby prey. Finally, we evaluate the models by their predictive likelihood and their ability to generate realistic trajectories of virtual fish swimming through simulated environments. Our simulations capture multiple timescales of structure in larval zebrafish behavior and expose many ways in which hunger state influences their action selection to promote food seeking during hunger and safety during satiety.

}, keywords = {behavioral models, behavioral simulations, exploration, hunger, hunting, natural behavior, Zebrafish}, issn = {0960-9822}, doi = {https://doi.org/10.1016/j.cub.2019.11.026}, url = {http://www.sciencedirect.com/science/article/pii/S0960982219314654}, author = {Robert Evan Johnson and Scott Linderman and Thomas Panier and Caroline Lei Wee and Erin Song and Kristian Joseph Herrera and Andrew Miller and Florian Engert} } @article {65669, title = {A programmable sequence of reporters for lineage analysis.}, journal = {Nature Neuroscience}, volume = {23}, year = {2020}, month = {2020 Dec 01}, pages = {1618-28}, abstract = {

We present CLADES (cell lineage access driven by an edition sequence), a technology for cell lineage studies based on CRISPR-Cas9 techniques. CLADES relies on a system of genetic switches to activate and inactivate reporter genes in a predetermined order. Targeting CLADES to progenitor cells allows the progeny to inherit a sequential cascade of reporters, thereby coupling birth order to reporter expression. This system, which can also be temporally induced by heat shock, enables the temporal resolution of lineage development and can therefore be used to deconstruct an extended cell lineage by tracking the reporters expressed in the progeny. When targeted to the germ line, the same cascade progresses across animal generations, predominantly marking each generation with the corresponding combination of reporters. CLADES therefore offers an innovative strategy for making programmable cascades of genes that can be used for genetic manipulation or to record serial biological events.

}, issn = {1546-1726}, doi = {10.1038/s41593-020-0676-9}, author = {Garcia-Marques, Jorge and Isabel Espinosa Medina and Ku, Kai-Yuan and Yang, Ching-Po and Koyama, Minoru and Yu, Hung-Hsiang and Lee, Tzumin} } @article {65321, title = {Rapid mesoscale volumetric imaging of neural activity with synaptic resolution.}, journal = {Nature Methods}, volume = {17}, year = {2020}, month = {2020 Mar 02}, pages = {291-4}, abstract = {

Imaging neurons and neural circuits over large volumes at high speed and subcellular resolution is a difficult task. Incorporating a Bessel focus module into a two-photon fluorescence mesoscope, we achieved rapid volumetric imaging of neural activity over the mesoscale with synaptic resolution. We applied the technology to calcium imaging of entire dendritic spans of neurons as well as neural ensembles within multiple cortical regions over two hemispheres of the awake mouse brain.

}, issn = {1548-7105}, doi = {10.1038/s41592-020-0760-9}, author = {Lu, Rongwen and Liang, Yajie and Meng, Guanghan and Zhou, Pengcheng and Svoboda, Karel and Paninski, Liam and Ji, Na} } @article {65668, title = {Rational design of bioavailable photosensitizers for manipulation and imaging of biological systems.}, journal = {Cell Chemical Biology}, volume = {27}, year = {2020}, month = {2020 Aug 20}, pages = {1063-72}, abstract = {

Light-mediated chemical reactions are powerful methods for manipulating and interrogating biological systems. Photosensitizers, compounds that generate reactive oxygen species upon excitation with light, can be utilized for numerous biological experiments, but the repertoire of bioavailable photosensitizers is limited. Here, we describe the synthesis, characterization, and utility of two photosensitizers based upon the widely used rhodamine scaffold and demonstrate their efficacy for chromophore-assisted light inactivation, cell ablation in culture and in\ vivo, and photopolymerization of diaminobenzidine for electron microscopy. These chemical tools will facilitate a broad range of applications spanning from targeted destruction of proteins to high-resolution imaging.

}, issn = {2451-9448}, doi = {10.1016/j.chembiol.2020.07.001}, author = {Binns, Thomas C and Ayala, Anthony X and Grimm, Jonathan B and Tkachuk, Ariana N and Castillon, Guillaume A and Phan, Sebastien and Zhang, Lixia and Brown, Timothy A and Liu, Zhe and Adams, Stephen R and Ellisman, Mark H and Koyama, Minoru and Lavis, Luke D} } @article {65373, title = {Recurrent architecture for adaptive regulation of learning in the insect brain.}, journal = {Nature Neuroscience}, volume = {23}, year = {2020}, month = {2020 Mar 23}, pages = {544-55}, abstract = {

Dopaminergic neurons (DANs) drive learning across the animal kingdom, but the upstream circuits that regulate their activity and thereby learning remain poorly understood. We provide a synaptic-resolution connectome of the circuitry upstream of all DANs in a learning center, the mushroom body of Drosophila larva. We discover afferent sensory pathways and a large population of neurons that provide feedback from mushroom body output neurons and link distinct memory systems (aversive and appetitive). We combine this with functional studies of DANs and their presynaptic partners and with comprehensive circuit modeling. We find that DANs compare convergent feedback from aversive and appetitive systems, which enables the computation of integrated predictions that may improve future learning. Computational modeling reveals that the discovered feedback motifs increase model flexibility and performance on learning tasks. Our study provides the most detailed view to date of biological circuit motifs that support associative learning.

}, issn = {1546-1726}, doi = {10.1038/s41593-020-0607-9}, author = {Eschbach, Claire and Fushiki, Akira and Winding, Michael and Schneider-Mizell, Casey M and Shao, Mei and Arruda, Rebecca and Eichler, Katharina and Valdes-Aleman, Javier and Ohyama, Tomoko and Thum, Andreas S and Gerber, Bertram and Fetter, Richard D and Truman, James W and Litwin-Kumar, Ashok and Cardona, Albert and Zlatic, Marta and Cardona, Albert and Zlatic, Marta} } @article {65364, title = {Recurrent interactions in local cortical circuits.}, journal = {Nature}, volume = {579}, year = {2020}, month = {2020 Mar 04}, pages = {256-59}, abstract = {

Most cortical synapses are local and excitatory. Local recurrent circuits could implement amplification, allowing pattern completion and other computations. Cortical circuits contain subnetworks that consist of neurons with similar receptive fields and increased connectivity relative to the network average. Cortical neurons that encode different types of information are spatially intermingled and distributed over large brain volumes, and this complexity has hindered attempts to probe the function of these subnetworks by perturbing them individually. Here we use computational modelling, optical recordings and manipulations to probe the function of recurrent coupling in layer 2/3 of the mouse vibrissal somatosensory cortex during active tactile discrimination. A neural circuit model of layer 2/3 revealed that recurrent excitation enhances sensory signals by amplification, but only for subnetworks with increased connectivity. Model networks with high amplification were sensitive to damage: loss of a few members of the subnetwork degraded stimulus encoding. We tested this prediction by mapping neuronal selectivity and photoablating neurons with specific selectivity. Ablation of a small proportion of layer 2/3 neurons (10-20, less than 5\% of the total) representing touch markedly reduced responses in the spared touch representation, but not in other representations. Ablations most strongly affected neurons with stimulus responses that were similar to those of the ablated population, which is also consistent with network models. Recurrence among cortical neurons with similar selectivity therefore drives input-specific amplification during behaviour.

}, issn = {1476-4687}, doi = {10.1038/s41586-020-2062-x}, author = {Peron, Simon and Pancholi, Ravi and Voelcker, Bettina and Wittenbach, Jason D and {\'O}lafsd{\'o}ttir, H Freyja and Freeman, Jeremy and Svoboda, Karel} } @article {65654, title = {Revisiting Membrane Microdomains and Phase Separation: A Viral Perspective}, journal = {Viruses}, volume = {12}, year = {2020}, month = {2020 Jul 10}, pages = {745}, abstract = {

Retroviruses selectively incorporate a specific subset of host cell proteins and lipids into their outer membrane when they bud out from the host plasma membrane. This specialized viral membrane composition is critical for both viral survivability and infectivity. Here, we review recent findings from live cell imaging of single virus assembly demonstrating that proteins and lipids sort into the HIV retroviral membrane by a mechanism of lipid-based phase partitioning. The findings showed that multimerizing HIV Gag at the assembly site creates a liquid-ordered lipid phase enriched in cholesterol and sphingolipids. Proteins with affinity for this specialized lipid environment partition into it, resulting in the selective incorporation of proteins into the nascent viral membrane. Building on this and other work in the field, we propose a model describing how HIV Gag induces phase separation of the viral assembly site through a mechanism involving transbilayer coupling of lipid acyl chains and membrane curvature changes. Similar phase-partitioning pathways in response to multimerizing structural proteins likely help sort proteins into the membranes of other budding structures within cells.

}, doi = {10.3390/v12070745}, url = {https://www.mdpi.com/1999-4915/12/7/745}, author = {Sengupta, Prabuddha and Lippincott-Schwartz, Jennifer} } @article {65670, title = {Seeing the forest for the trees in obesity.}, journal = {Nature Metabolism}, year = {2020}, month = {2020 Jul 27}, issn = {2522-5812}, doi = {10.1038/s42255-020-0259-9}, author = {Sternson, Scott M} } @article {65760, title = {Sensing cellular biochemistry with fluorescent chemical{\textendash}genetic hybrids}, journal = {Current Opinion in Chemical Biology}, volume = {57}, year = {2020}, month = {08/2020}, pages = {58{\textendash}64}, abstract = {

Fluorescent biosensors are powerful tools\ for the detection of biochemical events inside cells with high spatiotemporal resolution. Biosensors based on fluorescent proteins often suffer from issues with photostability and brightness. On the other hand, hybrid, chemical{\textendash}genetic systems present unique opportunities to combine the strengths of synthetic, organic chemistry with biological macromolecules to generate exquisitely tailored semisynthetic sensors.

}, issn = {1367-5931}, doi = {10.1016/j.cbpa.2020.04.005}, author = {Gautier, Arnaud and Tebo, Alison G.} } @article {68428, title = {Single-Cell Transcriptomes Reveal Diverse Regulatory Strategies for Olfactory Receptor Expression and Axon Targeting.}, journal = {Curr Biol}, volume = {30}, year = {2020}, month = {04/2020}, pages = {1189-1198.e5}, abstract = {

The regulatory mechanisms by which neurons coordinate their physiology and connectivity are not well understood. The Drosophila olfactory receptor neurons (ORNs) provide an excellent system to investigate this question. Each ORN type expresses a unique olfactory receptor, or a combination thereof, and sends their axons to a stereotyped glomerulus. Using single-cell RNA sequencing, we identified 33 transcriptomic clusters for ORNs and mapped 20 to their glomerular types, demonstrating that transcriptomic clusters correspond well with anatomically and physiologically defined ORN types. Each ORN type expresses hundreds of transcription factors. Transcriptome-instructed genetic analyses revealed that (1) one broadly expressed transcription factor (Acj6) only regulates olfactory receptor expression in one ORN type and only wiring specificity in another type, (2) one type-restricted transcription factor (Forkhead) only regulates receptor expression, and (3) another type-restricted transcription factor (Unplugged) regulates both events. Thus, ORNs utilize diverse strategies and complex regulatory networks to coordinate their physiology and connectivity.

}, keywords = {Animals, Axons, Drosophila melanogaster, Drosophila Proteins, Forkhead Transcription Factors, Homeodomain Proteins, Nerve Tissue Proteins, Olfactory Receptor Neurons, POU Domain Factors, Receptors, Odorant, Single-Cell Analysis, Smell, Transcriptome}, issn = {1879-0445}, doi = {10.1016/j.cub.2020.01.049}, author = {Li, Hongjie and Li, Tongchao and Horns, Felix and Li, Jiefu and Xie, Qijing and Xu, Chuanyun and Wu, Bing and Kebschull, Justus M and McLaughlin, Colleen N and Kolluru, Sai Saroja and Jones, Robert C and Vacek, David and Xie, Anthony and Luginbuhl, David J and Quake, Stephen R and Luo, Liqun} } @article {65383, title = {Size-dependent secretory protein reflux into the cytosol in association with acute endoplasmic reticulum stress.}, journal = {Traffic}, year = {2020}, month = {2020 Apr 04}, abstract = {

Once secretory proteins have been targeted to the endoplasmic reticulum (ER) lumen, the proteins typically remain partitioned from the cytosol. If the secretory proteins misfold, they can be unfolded and retrotranslocated into the cytosol for destruction by the proteasome by ER-associated protein Degradation (ERAD). Here, we report that correctly folded and targeted luminal ER fluorescent protein reporters accumulate in the cytosol during acute misfolded secretory protein stress in yeast. Photoactivation fluorescence microscopy experiments reveal that luminal reporters already localized to the ER relocalize to the cytosol, even in the absence of essential ERAD machinery. We named this process "ER reflux." Reflux appears to be regulated in a size-dependent manner for reporters. Interestingly, prior heat shock stress also prevents ER stress-induced reflux. Together, our findings establish a new ER stress-regulated pathway for relocalization of small luminal secretory proteins into the cytosol, distinct from the ERAD and pre-emptive quality control pathways. Importantly, our results highlight the value of fully characterizing the cell biology of reporters and describe a simple modification to maintain luminal ER reporters in the ER during acute ER stress. This article is protected by copyright. All rights reserved.

}, issn = {1600-0854}, doi = {10.1111/tra.12729}, author = {Lajoie, Patrick and Snapp, Erik L} } @article {65870, title = {Social hierarchy is established and maintained with distinct acts of aggression in male Drosophila melanogaster.}, journal = {Journal of Experimental Biology}, year = {2020}, month = {2020 Dec 02}, abstract = {

Social interactions pivot on an animal{\textquoteright}s experiences, internal states, and feedback from others. This complexity drives the need for precise descriptions of behavior to dissect the fine detail of its genetic and neural circuit bases. In laboratory assays, male reliably exhibit aggression, and its extent is generally measured by scoring lunges, a feature of aggression in which one male quickly thrusts onto his opponent. Here, we introduce an explicit approach to identify both the onset and reversals in hierarchical status between opponents and observe that distinct aggressive acts reproducibly precede, concur, or follow the establishment of dominance. We find that lunges are insufficient for establishing dominance. Rather, lunges appear to reflect the dominant state of a male and help in maintaining his social status. Lastly, we characterize the recurring and escalating structure of aggression that emerges through subsequent reversals in dominance. Collectively, this work provides a framework for studying the complexity of agonistic interactions in male flies enabling its neurogenetic basis to be understood with precision.

}, issn = {1477-9145}, doi = {10.1242/jeb.232439}, author = {Simon, Jasper C and Heberlein, Ulrike} } @article {65584, title = {A Sparse, Spatially Biased Subtype of Mature Granule Cell Dominates Recruitment in Hippocampal-Associated Behaviors.}, journal = {Cell Reports}, volume = {31}, year = {2020}, month = {2020 Apr 28}, pages = {107551}, abstract = {

Animals can store information about experiences by activating specific neuronal populations, and subsequent reactivation of these neural ensembles can lead to recall of salient experiences. In the hippocampus, granule cells of the dentate gyrus participate in such memory engrams; however, whether there is an underlying logic to granule cell participation has not been examined. Here, we find that a range of novel experiences preferentially activates granule cells of the suprapyramidal blade relative to the infrapyramidal blade. Motivated by this, we identify a suprapyramidal-blade-enriched population of granule cells with distinct spatial, morphological, physiological, and developmental properties. Via transcriptomics, we map these traits onto a sparse and discrete granule cell subtype that is recruited at a 10-fold greater frequency than expected by subtype prevalence, constituting the majority of all recruited granule cells. Thus, in behaviors known to involve hippocampal-dependent memory formation, a rare and spatially localized subtype dominates overall granule cell recruitment.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2020.107551}, author = {Erwin, Sarah R and Sun, Weinan and Copeland, Monique and Lindo, Sarah and Spruston, Nelson and Cembrowski, Mark S} } @article {65847, title = {Spatial readout of visual looming in the central brain of Drosophila.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Nov 18}, abstract = {

Visual systems can exploit spatial correlations in the visual scene by using retinotopy. However, retinotopy is often lost, such as when visual pathways are integrated with other sensory modalities. How is spatial information processed outside of strictly visual brain areas? Here, we focused on visual looming responsive LC6 cells in , a population whose dendrites collectively cover the visual field, but whose axons form a single glomerulus-a structure without obvious retinotopic organization-in the central brain. We identified multiple cell types downstream of LC6 in the glomerulus and found that they more strongly respond to looming in different portions of the visual field, unexpectedly preserving spatial information. Through EM reconstruction of all LC6 synaptic inputs to the glomerulus, we found that LC6 and downstream cell types form circuits within the glomerulus that enable spatial readout of visual features and contralateral suppression-mechanisms that transform visual information for behavioral control.

}, issn = {2050-084X}, doi = {10.7554/eLife.57685}, author = {Morimoto, Mai M and Nern, Aljoscha and Zhao, Arthur and Rogers, Edward M and Wong, Allan and Isaacson, Mathew D and Bock, Davi and Rubin, Gerald M and Reiser, Michael B} } @article {65792, title = {The Statistical Structure of the Hippocampal Code for Space as a Function of Time, Context, and Value.}, journal = {Cell}, volume = {183}, year = {2020}, month = {2020 Oct 29}, pages = {620-35}, abstract = {

Hippocampal activity represents many behaviorally important variables, including context, an animal{\textquoteright}s location within a given environmental context, time, and reward. Using longitudinal calcium imaging in mice, multiple large virtual environments, and differing reward contingencies, we derived a unified probabilistic model of CA1 representations centered on a single feature-the field propensity. Each cell{\textquoteright}s propensity governs how many place fields it has per unit space, predicts its reward-related activity, and is preserved across distinct environments and over months. Propensity is broadly distributed-with many low, and some very high, propensity cells-and thus strongly shapes hippocampal representations. This results in a range of spatial codes, from sparse to dense. Propensity varied \~{}10-fold between adjacent cells in salt-and-pepper fashion, indicating substantial functional differences within a presumed cell type. Intracellular recordings linked propensity to cell excitability. The stability of each cell{\textquoteright}s propensity across conditions suggests this fundamental property has anatomical, transcriptional, and/or developmental origins.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2020.09.024}, author = {Lee, Jae Sung and Briguglio, John J and Cohen, Jeremy D and Romani, Sandro and Lee, Albert K} } @article {65853, title = {The structural basis of Rubisco phase separation in the pyrenoid.}, journal = {Nature Plants}, year = {2020}, month = {2020 Nov 23}, abstract = {

Approximately one-third of global CO fixation occurs in a phase-separated algal organelle called the pyrenoid. The existing data suggest that the pyrenoid forms by the phase separation of the CO-fixing enzyme Rubisco with a linker protein; however, the molecular interactions underlying this phase separation remain unknown. Here we present the structural basis of the interactions between Rubisco and its intrinsically disordered linker protein Essential Pyrenoid Component 1 (EPYC1) in the model alga Chlamydomonas reinhardtii. We find that EPYC1 consists of five evenly spaced Rubisco-binding regions that share sequence similarity. Single-particle cryo-electron microscopy of these regions in complex with Rubisco indicates that each Rubisco holoenzyme has eight binding sites for EPYC1, one on each Rubisco small subunit. Interface mutations disrupt binding, phase separation and pyrenoid formation. Cryo-electron tomography supports a model in which EPYC1 and Rubisco form a codependent multivalent network of specific low-affinity bonds, giving the matrix liquid-like properties. Our results advance the structural and functional understanding of the phase separation underlying the pyrenoid, an organelle that plays a fundamental role in the global carbon cycle.

}, issn = {2055-0278}, doi = {10.1038/s41477-020-00811-y}, author = {He, Shan and Chou, Hui-Ting and Matthies, Doreen and Wunder, Tobias and Meyer, Moritz T and Atkinson, Nicky and Martinez-Sanchez, Antonio and Jeffrey, Philip D and Port, Sarah A and Patena, Weronika and He, Guanhua and Chen, Vivian K and Hughson, Frederick M and McCormick, Alistair J and Mueller-Cajar, Oliver and Engel, Benjamin D and Yu, Zhiheng and Jonikas, Martin C} } @article {65901, title = {The structural basis of Rubisco phase separation in the pyrenoid.}, journal = {Nature Plants}, volume = {6}, year = {2020}, month = {2020 Dec 01}, pages = {1480-1490}, abstract = {

Approximately one-third of global CO fixation occurs in a phase-separated algal organelle called the pyrenoid. The existing data suggest that the pyrenoid forms by the phase separation of the CO-fixing enzyme Rubisco with a linker protein; however, the molecular interactions underlying this phase separation remain unknown. Here we present the structural basis of the interactions between Rubisco and its intrinsically disordered linker protein Essential Pyrenoid Component 1 (EPYC1) in the model alga Chlamydomonas reinhardtii. We find that EPYC1 consists of five evenly spaced Rubisco-binding regions that share sequence similarity. Single-particle cryo-electron microscopy of these regions in complex with Rubisco indicates that each Rubisco holoenzyme has eight binding sites for EPYC1, one on each Rubisco small subunit. Interface mutations disrupt binding, phase separation and pyrenoid formation. Cryo-electron tomography supports a model in which EPYC1 and Rubisco form a codependent multivalent network of specific low-affinity bonds, giving the matrix liquid-like properties. Our results advance the structural and functional understanding of the phase separation underlying the pyrenoid, an organelle that plays a fundamental role in the global carbon cycle.

}, issn = {2055-0278}, doi = {10.1038/s41477-020-00811-y}, author = {He, Shan and Chou, Hui-Ting and Matthies, Doreen and Wunder, Tobias and Meyer, Moritz T and Atkinson, Nicky and Martinez-Sanchez, Antonio and Jeffrey, Philip D and Port, Sarah A and Patena, Weronika and He, Guanhua and Chen, Vivian K and Hughson, Frederick M and McCormick, Alistair J and Mueller-Cajar, Oliver and Engel, Benjamin D and Yu, Zhiheng and Jonikas, Martin C} } @article {65759, title = {Structural insight into the ATP-driven exporter of virulent peptide toxins.}, journal = {Science Advances}, volume = {6}, year = {2020}, month = {2020 Sep 30}, abstract = {

is a major human pathogen that has acquired alarming broad-spectrum antibiotic resistance. One group of secreted toxins with key roles during infection is the phenol-soluble modulins (PSMs). PSMs are amphipathic, membrane-destructive cytolytic peptides that are exported to the host-cell environment by a designated adenosine 5{\textquoteright}-triphosphate (ATP)-binding cassette (ABC) transporter, the PSM transporter (PmtABCD). Here, we demonstrate that the minimal Pmt unit necessary for PSM export is PmtCD and provide its first atomic characterization by single-particle cryo-EM and x-ray crystallography. We have captured the transporter in the ATP-bound state at near atomic resolution, revealing a type II ABC exporter fold, with an additional cytosolic domain. Comparison to a lower-resolution nucleotide-free map displaying an "open" conformation and putative hydrophobic inner chamber of a size able to accommodate the binding of two PSM peptides provides mechanistic insight and sets the foundation for therapeutic design.

}, issn = {2375-2548}, doi = {10.1126/sciadv.abb8219}, author = {Zeytuni, N and Dickey, S W and Hu, J and Chou, H T and Worrall, L J and Alexander, J A N and Carlson, M L and Nosella, M and Duong, F and Yu, Z and Otto, M and Strynadka, N C J} } @article {65286, title = {Structure and assembly of calcium homeostasis modulator proteins.}, journal = {Nature Structural and Molecular Biology}, volume = {27}, year = {2020}, month = {2020 Jan 27}, pages = {150-9}, abstract = {

The biological membranes of many cell types contain large-pore channels through which a wide variety of ions and metabolites permeate. Examples include connexin, innexin and pannexin, which form gap junctions and/or bona fide cell surface channels. The most recently identified large-pore channels are the calcium homeostasis modulators (CALHMs), through which ions and ATP permeate in a voltage-dependent manner to control neuronal excitability, taste signaling and pathologies of depression and Alzheimer{\textquoteright}s disease. Despite such critical biological roles, the structures and patterns of their oligomeric assembly remain unclear. Here, we reveal the structures of two CALHMs, chicken CALHM1 and human CALHM2, by single-particle cryo-electron microscopy (cryo-EM), which show novel assembly of the four transmembrane helices into channels of octamers and undecamers, respectively. Furthermore, molecular dynamics simulations suggest that lipids can favorably assemble into a bilayer within the larger CALHM2 pore, but not within CALHM1, demonstrating the potential correlation between pore size, lipid accommodation and channel activity.

}, issn = {1545-9985}, doi = {10.1038/s41594-019-0369-9}, author = {Syrjanen, Johanna L and Michalski, Kevin and Chou, Tsung-Han and Grant, Timothy and Rao, Shanlin and Simorowski, Noriko and Tucker, Stephen J and Grigorieff, Nikolaus and Furukawa, Hiro} } @article {65635, title = {Structure of human GABA receptor in an inactive state.}, journal = {Nature}, volume = {584}, year = {2020}, month = {2020 Aug 01}, pages = {304-9}, abstract = {

The human GABA receptor-a member of the class C family of G-protein-coupled receptors (GPCRs)-mediates inhibitory neurotransmission and has been implicated in epilepsy, pain and addiction. A unique GPCR that is known to require heterodimerization for function, the GABA receptor has two subunits, GABA and GABA, that are structurally homologous but perform distinct and complementary functions. GABA recognizes orthosteric ligands, while GABA couples with G proteins. Each subunit is characterized by an extracellular Venus flytrap (VFT) module, a descending peptide linker, a seven-helix transmembrane domain and a cytoplasmic tail. Although the VFT heterodimer structure has been resolved, the structure of the full-length receptor and its transmembrane signalling mechanism remain unknown. Here we present a near full-length structure of the GABA receptor at atomic resolution, captured in an inactive state by cryo-electron microscopy. Our structure reveals several ligands that preassociate with the receptor, including two large endogenous phospholipids that are embedded within the transmembrane domains to maintain receptor integrity and modulate receptor function. We also identify a previously unknown heterodimer interface between transmembrane helices 3 and 5 of both subunits, which serves as a signature of the inactive conformation. A unique {\textquoteright}intersubunit latch{\textquoteright} within this transmembrane interface maintains the inactive state, and its disruption leads to constitutive receptor activity.

}, issn = {1476-4687}, doi = {10.1038/s41586-020-2452-0}, author = {Park, Jinseo and Fu, Ziao and Frangaj, Aurel and Liu, Jonathan and Mosyak, Lidia and Shen, Tong and Slavkovich, Vesna N and Ray, Kimberly M and Taura, Jaume and Cao, Baohua and Geng, Yong and Zuo, Hao and Kou, Yongjun and Grassucci, Robert and Chen, Shaoxia and Liu, Zheng and Lin, Xin and Williams, Justin P and Rice, William J and Eng, Edward T and Huang, Rick K and Soni, Rajesh K and Kloss, Brian and Yu, Zhiheng and Javitch, Jonathan A and Hendrickson, Wayne A and Slesinger, Paul A and Quick, Matthias and Graziano, Joseph and Yu, Hongtao and Fiehn, Oliver and Clarke, Oliver B and Frank, Joachim and Fan, Qing R} } @article {65898, title = {Structure of the radial spoke head and insights into its role in mechanoregulation of ciliary beating.}, journal = {Nature Structural Molecular Biology}, volume = {28}, year = {2020}, month = {2020 Dec 14}, pages = {20-28}, abstract = {

Motile cilia power cell locomotion and drive extracellular fluid flow by propagating bending waves from their base to tip. The coordinated bending of cilia requires mechanoregulation by the radial spoke (RS) protein complexes and the microtubule central pair (CP). Despite their importance for ciliary motility across eukaryotes, the molecular function of the RSs is unknown. Here, we reconstituted the Chlamydomonas reinhardtii RS head that abuts the CP and determined its structure using single-particle cryo-EM to 3.1-{\r A} resolution, revealing a flat, negatively charged surface supported by a rigid core of tightly intertwined proteins. Mutations in this core, corresponding to those involved in human ciliopathies, compromised the stability of the recombinant complex, providing a molecular basis for disease. Partially reversing the negative charge on the RS surface impaired motility in C. reinhardtii. We propose that the RS-head architecture is well-suited for mechanoregulation of ciliary beating through physical collisions with the CP.

}, issn = {1545-9985}, doi = {10.1038/s41594-020-00519-9}, author = {Grossman-Haham, Iris and Coudray, Nicolas and Yu, Zanlin and Wang, Feng and Zhang, Nan and Bhabha, Gira and Vale, Ronald D} } @article {65277, title = {Structure of the vesicular stomatitis virus L protein in complex with Its phosphoprotein cofactor.}, journal = {Cell Reports}, volume = {30}, year = {2020}, month = {2020 Jan 07}, pages = {53-60.e5}, abstract = {

The large (L) proteins of non-segmented, negative-strand RNA viruses are multifunctional enzymes that produce capped, methylated, and polyadenylated mRNA and replicate the viral genome. A phosphoprotein (P), required for efficient RNA-dependent RNA polymerization from the viral ribonucleoprotein (RNP) template, regulates the function and conformation of the L protein. We report the structure of vesicular stomatitis virus L in complex with its P cofactor determined by electron cryomicroscopy at 3.0\ {\r A} resolution, enabling us to visualize bound segments of P. The contacts of three P segments with multiple L domains show how P induces a closed, compact, initiation-competent conformation. Binding of P to L positions its N-terminal domain adjacent to a putative RNA exit channel for efficient encapsidation of newly synthesized genomes with the nucleoprotein and orients its C-terminal domain to interact with an RNP template. The model shows that a conserved tryptophan in the priming loop can support the initiating 5{\textquoteright} nucleotide.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2019.12.024}, author = {Jenni, Simon and Bloyet, Louis-Marie and Diaz-Avalos, Ruben and Liang, Bo and Whelan, Sean P J and Grigorieff, Nikolaus and Harrison, Stephen C} } @article {65616, title = {Super-Resolution Fluorescence Imaging Reveals That Serine Incorporator Protein 5 Inhibits Human Immunodeficiency Virus Fusion by Disrupting Envelope Glycoprotein Clusters.}, journal = {ACS Nano}, year = {2020}, month = {2020 May 22}, abstract = {

Serine incorporator protein 5 (SERINC5) is the host anti-retroviral factor that reduces HIV-1 infectivity by incorporating into virions and inhibiting the envelope glycoprotein (Env) mediated virus fusion with target cells. We and others have shown that SERINC5 incorporation into virions alters the Env structure and sensitizes the virus to broadly neutralizing antibodies targeting cryptic Env epitopes. We have also found that SERINC5 accelerates the loss of Env function over time compared to control viruses. However, the exact mechanism by which SERINC5 inhibits HIV-1 fusion is not understood. Here, we utilized 2D and 3D super-resolution microscopy to examine the effect of SERINC5 on the distribution of Env glycoproteins on single HIV-1 particles. We find that, in agreement with a previous report, Env glycoproteins form clusters on the surface of mature virions. Importantly, incorporation of SERINC5, but not SERINC2, which lacks antiviral activity, disrupted Env clusters without affecting the overall Env content. We also show that SERINC5 and SERINC2 also form clusters on single virions. Unexpectedly, Env and SERINCs molecules exhibited poor co-distribution on virions, as evidenced by much greater Env-SERINC pairwise distances compare to Env-Env distances. This observation is inconsistent with the previously reported interaction between Env and SERINC5 and suggests an indirect effect of SERINC5 on Env cluster formation. Collectively, our results reveal a multifaceted mechanism of SERINC5-mediated restriction of HIV-1 fusion that, aside from the effects on individual Env trimers, involves disruption of Env clusters, which likely serve as sites of viral fusion with target cells.

}, issn = {1936-086X}, doi = {10.1021/acsnano.0c02699}, author = {Chen, Yen-Cheng and Sood, Chetan and Marin, Mariana and Aaron, Jesse and Gratton, Enrico and Salaita, Khalid and Melikyan, Gregory B} } @article {65855, title = {Super-resolution ophthalmoscopy: Virtually structured detection for resolution improvement in retinal imaging.}, journal = {Experimental Biology and Medicine (Maywood)}, year = {2020}, month = {2020 Nov 27}, pages = {1535370220970533}, abstract = {

Quantitative retinal imaging is essential for advanced study and clinical management of eye diseases. However, spatial resolution of retinal imaging has been limited due to available numerical aperture and optical aberration of the ocular optics. Structured illumination microscopy has been established to break the diffraction-limit resolution in conventional light microscopy. However, practical implementation of structured illumination microscopy for ophthalmoscopy of the retina is challenging due to inevitable eye movements that can produce phase artifacts. Recently, we have demonstrated the feasibility of using virtually structured detection as one alternative to structured illumination microscopy for super-resolution imaging. By providing the flexibility of digital compensation of eye movements, the virtually structured detection provides a feasible, phase-artifact-free strategy to achieve super-resolution ophthalmoscopy. In this article, we summarize the technical rationale of virtually structured detection, and its implementations for super-resolution imaging of freshly isolated retinas, intact animals, and awake human subjects.

}, issn = {1535-3699}, doi = {10.1177/1535370220970533}, author = {Yao, Xincheng and Lu, Rongwen and Wang, Benquan and Lu, Yiming and Kim, Tae-Hoon} } @article {65723, title = {A systematic nomenclature for the Drosophila ventral nerve cord.}, journal = {Neuron}, volume = {107}, year = {2020}, month = {2020 Sep 14}, pages = {1071-79}, abstract = {

Drosophila melanogaster is an established model for neuroscience research with relevance in biology and medicine. Until recently, research on the Drosophila brain was hindered by the lack of a complete and uniform nomenclature. Recognizing this, Ito et\ al. (2014) produced an authoritative nomenclature for the adult insect brain, using Drosophila as the reference. Here, we extend this nomenclature to the adult thoracic and abdominal neuromeres, the ventral nerve cord (VNC), to provide an anatomical description of this major component of the Drosophila nervous system. The VNC is the locus for the reception and integration of sensory information and involved in generating most of the locomotor actions that underlie fly behaviors. The aim is to create a nomenclature, definitions, and spatial boundaries for the Drosophila VNC that are consistent with other insects. The work establishes an anatomical framework that provides a powerful tool for analyzing the functional organization of the VNC.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2020.08.005}, author = {Court, Robert and Namiki, Shigehiro and Armstrong, J Douglas and Borner, Jana and Card, Gwyneth and Costa, Marta and Dickinson, Michael and Duch, Carsten and Korff, Wyatt and Mann, Richard and Merritt, David and Murphey, Rod K and Seeds, Andrew M and Shirangi, Troy and Simpson, Julie H and Truman, James W and Tuthill, John C and Williams, Darren W and Shepherd, David} } @booklet {67224, title = {Teaching deep neural networks to localize single molecules for super-resolution microscopy}, year = {2020}, abstract = {

Single-molecule localization fluorescence microscopy constructs super-resolution images by sequential imaging and computational localization of sparsely activated fluorophores. Accurate and efficient fluorophore localization algorithms are key to the success of this computational microscopy method. We present a novel localization algorithm based on deep learning which significantly improves upon the state of the art. Our contributions are a novel network architecture for simultaneous detection and localization, and new loss function which phrases detection and localization as a Bayesian inference problem, and thus allows the network to provide uncertainty-estimates. In contrast to standard methods which independently process imaging frames, our network architecture uses temporal context from multiple sequentially imaged frames to detect and localize molecules. We demonstrate the power of our method across a variety of datasets, imaging modalities, signal to noise ratios, and fluorophore densities. While existing localization algorithms can achieve optimal localization accuracy at low fluorophore densities, they are confounded by high densities. Our method is the first deep-learning based approach which achieves state-of-the-art on the SMLM2016 challenge. It achieves the best scores on 12 out of 12 data-sets when comparing both detection accuracy and precision, and excels at high densities. Finally, we investigate how unsupervised learning can be used to make the network robust against mismatch between simulated and real data. The lessons learned here are more generally relevant for the training of deep networks to solve challenging Bayesian inverse problems on spatially extended domains in biology and physics.

}, url = {https://arxiv.org/abs/1907.00770}, author = {Artur Speiser and Lucas-Raphael M{\"u}ller and Ulf Matti and Christopher J. Obara and Wesley R. Legant and Jonas Ries and Jakob H. Macke and Srinivas C. Turaga} } @article {65390, title = {Temperature-dependent sex determination is mediated by pSTAT3 repression of Kdm6b..}, journal = {Science}, volume = {368}, year = {2020}, month = {2020 Apr 17}, pages = {303-306}, abstract = {

In many reptiles, including the red-eared slider turtle (), sex is determined by ambient temperature during embryogenesis. We previously showed that the epigenetic regulator is elevated at the male-producing temperature and essential to activate the male pathway. In this work, we established a causal link between temperature and transcriptional regulation of We show that signal transducer and activator of transcription 3 (STAT3) is phosphorylated at the warmer, female-producing temperature, binds the locus, and represses transcription, blocking the male pathway. Influx of Ca, a mediator of STAT3 phosphorylation, is elevated at the female temperature and acts as a temperature-sensitive regulator of STAT3 activation.

}, issn = {1095-9203}, doi = {10.1126/science.aaz4165}, author = {Weber, Ceri and Zhou, Yingjie and Lee, Jong Gwan and Looger, Loren L and Qian, Guoying and Ge, Chutian and Capel, Blanche} } @article {65856, title = {Theoretical principles for illuminating sensorimotor processing with brain-wide neuronal recordings.}, journal = {Current Opinion in Neurobiology}, volume = {65}, year = {2020}, month = {2020 Nov 25}, pages = {138-145}, abstract = {

Modern recording techniques now permit brain-wide sensorimotor circuits to be observed at single neuron resolution in small animals. Extracting theoretical understanding from these recordings requires principles that organize findings and guide future experiments. Here we review theoretical principles that shed light onto brain-wide sensorimotor processing. We begin with an analogy that conceptualizes principles as streetlamps that illuminate the empirical terrain, and we illustrate the analogy by showing how two familiar principles apply in new ways to brain-wide phenomena. We then focus the bulk of the review on describing three more principles that have wide utility for mapping brain-wide neural activity, making testable predictions from highly parameterized mechanistic models, and investigating the computational determinants of neuronal response patterns across the brain.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2020.10.021}, author = {Biswas, Tirthabir and Bishop, William E and Fitzgerald, James E} } @article {65272, title = {Tiled reconstruction improves structured illumination microscopy.}, journal = {bioRxiv}, year = {2020}, month = {2020 Jan 11}, abstract = {

Structured illumination microscopy (SIM) is widely used for fast, long-term, live-cell super-resolution imaging. However, SIM images can contain substantial artifacts if the sample does not conform to the underlying assumptions of the reconstruction algorithm. Here we describe a simple, easy to implement, process that can be combined with any reconstruction algorithm to alleviate many common SIM reconstruction artifacts and briefly discuss possible extensions.

}, doi = {10.1101/2020.01.06.895318}, author = {Hoffman, David P. and Betzig, Eric} } @article {65253, title = {Tissue clearing and its applications in neuroscience}, journal = {Nature Reviews Neuroscience}, year = {2020}, month = {2020 Feb 1}, abstract = {

State-of-the-art tissue-clearing methods provide subcellular-level optical access to intact tissues from individual organs and even to some entire mammals. When combined with light-sheet microscopy and automated approaches to image analysis, existing tissue-clearing methods can speed up and may reduce the cost of conventional histology by several orders of magnitude. In addition, tissue-clearing chemistry allows whole-organ antibody labelling, which can be applied even to thick human tissues. By combining the most powerful labelling, clearing, imaging and data-analysis tools, scientists are extracting structural and functional cellular and subcellular information on complex mammalian bodies and large human specimens at an accelerated pace. The rapid generation of terabyte-scale imaging data furthermore creates a high demand for efficient computational approaches that tackle challenges in large-scale data analysis and management. In this Review, we discuss how tissue-clearing methods could provide an unbiased, system-level view of mammalian bodies and human specimens and discuss future opportunities for the use of these methods in human neuroscience.

}, issn = {1471-003X}, doi = {10.1038/s41583-019-0250-1}, url = {http://www.nature.com/articles/s41583-019-0250-1}, author = {Ueda, Hiroki R. and Ert{\"u}rk, Ali and Chung, Kwanghun and Gradinaru, Viviana and Ch{\'e}dotal, Alain and Tomancak, Pavel and Keller, Philipp J.} } @article {65264, title = {Tissue clearing and its applications in~neuroscience.}, journal = {Nature Reviews Neuroscience}, volume = {21}, year = {2020}, month = {2020 Jan 02}, pages = {61-79}, abstract = {

State-of-the-art tissue-clearing methods provide subcellular-level optical access to intact tissues from individual organs and even to some entire mammals. When combined with light-sheet microscopy and automated approaches to image analysis, existing tissue-clearing methods can speed up and may reduce the cost of conventional histology by several orders of magnitude. In addition, tissue-clearing chemistry allows whole-organ antibody labelling, which can be applied even to thick human tissues. By combining the most powerful labelling, clearing, imaging and data-analysis tools, scientists are extracting structural and functional cellular and subcellular information on complex mammalian bodies and large human specimens at an accelerated pace. The rapid generation of terabyte-scale imaging data furthermore creates a high demand for efficient computational approaches that tackle challenges in large-scale data analysis and management. In this Review, we discuss how tissue-clearing methods could provide an unbiased, system-level view of mammalian bodies and human specimens and discuss future opportunities for the use of these methods in human neuroscience.

}, issn = {1471-0048}, doi = {10.1038/s41583-019-0250-1}, author = {Ueda, Hiroki R and Ert{\"u}rk, Ali and Chung, Kwanghun and Gradinaru, Viviana and Ch{\'e}dotal, Alain and Tomancak, Pavel and Keller, Philipp J} } @article {65284, title = {Toward nanoscale localization of memory engrams in Drosophila.}, journal = {Journal of Neurogenetics}, volume = {34}, year = {2020}, month = {2020 Mar 01}, pages = {151-55}, abstract = {

The Mushroom Body (MB) is the primary location of stored associative memories in the Drosophila brain. We discuss recent advances in understanding the MB{\textquoteright}s neuronal circuits made using advanced light microscopic methods and cell-type-specific genetic tools. We also review how the compartmentalized nature of the MB{\textquoteright}s organization allows this brain area to form and store memories with widely different dynamics.

}, issn = {1563-5260}, doi = {10.1080/01677063.2020.1715973}, author = {Aso, Yoshinori and Rubin, Gerald M} } @article {65660, title = {Towards accurate and unbiased imaging-based differentiation of Parkinson{\textquoteright}s disease, progressive supranuclear palsy and corticobasal syndrome.}, journal = {Brain Communications}, volume = {2}, year = {2020}, month = {2020 Jul 1}, pages = {fcaa051}, abstract = {

The early and accurate differential diagnosis of parkinsonian disorders is still a significant challenge for clinicians. In recent years, a number of studies have used magnetic resonance imaging data combined with machine learning and statistical classifiers to successfully differentiate between different forms of Parkinsonism. However, several questions and methodological issues remain, to minimize bias and artefact-driven classification. In this study, we compared different approaches for feature selection, as well as different magnetic resonance imaging modalities, with well-matched patient groups and tightly controlling for data quality issues related to patient motion. Our sample was drawn from a cohort of 69 healthy controls, and patients with idiopathic Parkinson{\textquoteright}s disease (= 35), progressive supranuclear palsy Richardson{\textquoteright}s syndrome (= 52) and corticobasal syndrome (= 36). Participants underwent standardized T1-weighted and diffusion-weighted magnetic resonance imaging. Strict data quality control and group matching reduced the control and patient numbers to 43, 32, 33 and 26, respectively. We compared two different methods for feature selection and dimensionality reduction: whole-brain principal components analysis, and an anatomical region-of-interest based approach. In both cases, support vector machines were used to construct a statistical model for pairwise classification of healthy controls and patients. The accuracy of each model was estimated using a leave-two-out cross-validation approach, as well as an independent validation using a different set of subjects. Our cross-validation results suggest that using principal components analysis for feature extraction provides higher classification accuracies when compared to a region-of-interest based approach. However, the differences between the two feature extraction methods were significantly reduced when an independent sample was used for validation, suggesting that the principal components analysis approach may be more vulnerable to overfitting with cross-validation. Both T1-weighted and diffusion magnetic resonance imaging data could be used to successfully differentiate between subject groups, with neither modality outperforming the other across all pairwise comparisons in the cross-validation analysis. However, features obtained from diffusion magnetic resonance imaging data resulted in significantly higher classification accuracies when an independent validation cohort was used. Overall, our results support the use of statistical classification approaches for differential diagnosis of parkinsonian disorders. However, classification accuracy can be affected by group size, age, sex and movement artefacts. With appropriate controls and out-of-sample cross validation, diagnostic biomarker evaluation including magnetic resonance imaging based classifiers may be an important adjunct to clinical evaluation.

}, issn = {2632-1297}, doi = {10.1093/braincomms/fcaa051}, author = {Correia, Marta M and Rittman, Timothy and Barnes, Christopher L and Coyle-Gilchrist, Ian T and Ghosh, Boyd and Hughes, Laura E and Rowe, James B} } @article {65320, title = {Transcriptional co-repressor Sin3a regulates hippocampal synaptic plasticity via Homer1/mGluR5.}, journal = {JCI Insight}, year = {2020}, month = {2020 Feb 18}, abstract = {

Long-term memory depends on the control of activity-dependent neuronal gene expression, which is regulated by epigenetic modifications. The epigenetic modification of histones is orchestrated by the opposing activities of two classes of regulatory complexes: permissive co-activators and silencing co-repressors. Much work has focused on co-activator complexes, but little is known about the co-repressor complexes that suppress the expression of plasticity-related genes. Here, we define a critical role for the co-repressor SIN3A in memory and synaptic plasticity, showing that postnatal neuronal deletion of Sin3a enhances hippocampal long-term potentiation and long-term contextual fear memory. SIN3A regulates the expression of genes encoding proteins in the post-synaptic density. Loss of SIN3A increases expression of the synaptic scaffold Homer1, alters the mGluR1α- and mGluR5-dependence of long-term potentiation, and increases activation of extracellular signal regulated kinase (ERK) in the hippocampus after learning. Our studies define a critical role for co-repressors in modulating neural plasticity and memory consolidation and reveal that Homer1/mGluR signaling pathways may be central molecular mechanisms for memory enhancement.

}, issn = {2379-3708}, doi = {10.1172/jci.insight.92385}, author = {Bridi, Morgan S and Schoch, Hannah and Florian, C{\'e}drick and Poplawski, Shane G and Banerjee, Anamika and Hawk, Joshua D and Banks, Giulia S and Lejards, Camille and Hahn, Chang-Gyu and Giese, Karl Peter and Havekes, Robbert and Spruston, Nelson and Abel, Ted} } @article {65256, title = {Trans-endocytosis of intact IL-15Rα-IL-15 complex from presenting cells into NK cells favors signaling for proliferation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, year = {2020}, month = {2020 Jan 07}, pages = {522-531}, abstract = {

Interleukin 15 (IL-15) is an essential cytokine for the survival and proliferation of natural killer (NK) cells. IL-15 activates signaling by the β and common γ (γ) chain heterodimer of the IL-2 receptor through -presentation by cells expressing IL-15 bound to the α chain of the IL-15 receptor (IL-15Rα). We show here that membrane-associated IL-15Rα-IL-15 complexes are transferred from presenting cells to NK cells through -endocytosis and contribute to the phosphorylation of ribosomal protein S6 and NK cell proliferation. NK cell interaction with soluble or surface-bound IL-15Rα-IL-15 complex resulted in Stat5 phosphorylation and NK cell survival at a concentration or density of the complex much lower than required to stimulate S6 phosphorylation. Despite this efficient response, Stat5 phosphorylation was reduced after inhibition of metalloprotease-induced IL-15Rα-IL-15 shedding from -presenting cells, whereas S6 phosphorylation was unaffected. Conversely, inhibition of -endocytosis by silencing of the small GTPase TC21 or expression of a dominant-negative TC21 reduced S6 phosphorylation but not Stat5 phosphorylation. Thus, -endocytosis of membrane-associated IL-15Rα-IL-15 provides a mode of regulating NK cells that is not afforded to IL-2 and is distinct from activation by soluble IL-15. These results may explain the strict IL-15 dependence of NK cells and illustrate how the cellular compartment in which receptor-ligand interaction occurs can influence functional outcome.

}, issn = {1091-6490}, doi = {10.1073/pnas.1911678117}, author = {Anton, Olga M and Peterson, Mary E and Hollander, Michael J and Dorward, David W and Arora, Gunjan and Traba, Javier and Rajagopalan, Sumati and Snapp, Erik L and Garcia, K Christopher and Waldmann, Thomas A and Long, Eric O} } @article {65632, title = {Two-parameter mobility assessments discriminate diverse regulatory factor behaviors in chromatin.}, journal = {Molecular Cell}, volume = {79}, year = {2020}, month = {2020 Aug 1}, pages = {677}, abstract = {

Enzymatic probes of chromatin structure reveal accessible versus inaccessible chromatin states, while super-resolution microscopy reveals a continuum of chromatin compaction states. Characterizing histone H2B movements by single-molecule tracking (SMT), we resolved chromatin domains ranging from low to high mobility and displaying different subnuclear localizations patterns. Heterochromatin constituents correlated with the lowest mobility chromatin, whereas transcription factors varied widely with regard to their respective mobility with low- or high-mobility chromatin. Pioneer transcription factors, which bind nucleosomes, can access the low-mobility chromatin domains, whereas weak or non-nucleosome binding factors are excluded from the domains and enriched in higher mobility domains. Nonspecific DNA and nucleosome binding accounted for most of the low mobility of strong nucleosome interactor FOXA1. Our analysis shows how the parameters of the mobility of chromatin-bound factors, but not their diffusion behaviors or SMT-residence times within chromatin, distinguish functional characteristics of different chromatin-interacting proteins.

}, issn = {1097-4164}, doi = {10.1016/j.molcel.2020.05.036}, author = {Lerner, Jonathan and Gomez-Garcia, Pablo Aurelio and McCarthy, Ryan L and Liu, Zhe and Lakadamyali, Melike and Zaret, Kenneth S} } @article {65903, title = {Two-parameter single-molecule analysis for measurement of chromatin mobility.}, journal = {STAR Protocols}, volume = {1}, year = {2020}, month = {2020 Dec 13}, pages = {100223}, abstract = {

This protocol provides a two-parameter analysis of single-molecule tracking (SMT) trajectories of Halo-tagged histones in living adherent cell lines and unveils a chromatin mobility landscape composed of five chromatin types, ranging from low to high mobility. When the analysis is applied to Halo-tagged, chromatin-binding proteins, it associates chromatin interaction properties with known functions in a way that previously used SMT parameters did not. For complete information on the use and execution of this protocol, please refer to Lerner et\ al. (2020).

}, issn = {2666-1667}, doi = {10.1016/j.xpro.2020.100223}, author = {Lerner, Jonathan and Gomez-Garcia, Pablo Aurelio and McCarthy, Ryan L and Liu, Zhe and Lakadamyali, Melike and Zaret, Kenneth S} } @article {65603, title = {Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization.}, journal = {Nature Communications}, volume = {11}, year = {2020}, month = {2020 May 01}, pages = {2120}, abstract = {

The human genome is extensively folded into 3-dimensional organization. However, the detailed 3D chromatin folding structures have not been fully visualized due to the lack of robust and ultra-resolution imaging capability. Here, we report the development of an electron microscopy method that combines serial block-face scanning electron microscopy with in situ hybridization (3D-EMISH) to visualize 3D chromatin folding at targeted genomic regions with ultra-resolution (5 {\texttimes} 5 {\texttimes} 30 nm in xyz dimensions) that is superior to the current super-resolution by fluorescence light microscopy. We apply 3D-EMISH to human lymphoblastoid cells at a 1.7 Mb segment of the genome and visualize a large number of distinctive 3D chromatin folding structures in ultra-resolution. We further quantitatively characterize the reconstituted chromatin folding structures by identifying sub-domains, and uncover a high level heterogeneity of chromatin folding ultrastructures in individual nuclei, suggestive of extensive dynamic fluidity in 3D chromatin states.

}, issn = {2041-1723}, doi = {10.1038/s41467-020-15987-2}, author = {Trzaskoma, Pawe{\l} and Ruszczycki, B{\l}a{\.z}ej and Lee, Byoungkoo and Pels, Katarzyna K and Krawczyk, Katarzyna and Bokota, Grzegorz and Szczepankiewicz, Andrzej A and Aaron, Jesse and Walczak, Agnieszka and {\'S}liwi{\'n}ska, Ma{\l}gorzata A and Magalska, Adriana and Kadlof, Michal and Wolny, Artur and Parteka, Zofia and Arabasz, Sebastian and Kiss-Arabasz, Magdalena and Plewczy{\'n}ski, Dariusz and Ruan, Yijun and Wilczy{\'n}ski, Grzegorz M} } @article {65597, title = {Unanticipated stressful and rewarding experiences engage the same prefrontal cortex and ventral tegmental area neuronal populations.}, journal = {eNeuro}, year = {2020}, month = {2020 May 08}, abstract = {

Brain networks that mediate motivated behavior in the context of aversive and rewarding experiences involve the prefrontal cortex (PFC) and ventral tegmental area (VTA). Neurons in both regions are activated by stress and reward, and by learned cues that predict aversive or appetitive outcomes. Recent studies have proposed that separate neuronal populations and circuits in these regions encode learned aversive versus appetitive contexts. But how about the actual experience? Do the same or different PFC and VTA neurons encode unanticipated aversive and appetitive experiences? To address this, we recorded unit activity and local field potentials (LFP) in the dorsomedial PFC (dmPFC) and VTA of male rats as they were exposed, in the same recording session, to reward (sucrose) or stress (tail pinch) spaced one hour apart. As expected, experience-specific neuronal responses were observed. About 15-25\% of single units in each region responded by excitation or inhibition to either stress or reward, and only stress increased LFP theta oscillation power in both regions and coherence between regions. But the largest number of responses (29\% dmPFC and 30\% VTA units) involved dual-valence neurons that responded to both stress and reward exposure. Moreover, the temporal profile of neuronal population activity in dmPFC and VTA as assessed by principal component analysis were similar during both types of experiences. These results reveal that aversive and rewarding experiences engage overlapping neuronal populations in the dmPFC and the VTA. These populations may provide a locus of vulnerability for stress related disorders, which are often associated with anhedonia. Animals must recognize unexpected harmful and rewarding events in order to survive. How the brain represents these competing experiences is not fully understood. Two interconnected brain regions implicated in encoding both rewarding and stressful events are the dmPFC and the VTA. In either region, separate neurons and associated circuitry are assumed to respond to events with positive or negative valence. We find, however, that a significant subpopulation of neurons in dmPFC and VTA encode both rewarding and aversive experiences. These dual-valence neurons may provide a computational advantage for flexible planning of behavior when organisms face unexpected rewarding and harmful experiences.

}, issn = {2373-2822}, doi = {10.1523/ENEURO.0029-20.2020}, author = {Del Arco, Alberto and Park, Junchol and Moghaddam, Bita} } @article {65910, title = {An unbiased template of the Drosophila brain and ventral nerve cord.}, journal = {PLoS One}, volume = {15}, year = {2020}, month = {2020 Dec 31}, pages = {e0236495}, abstract = {

The fruit fly Drosophila melanogaster is an important model organism for neuroscience with a wide array of genetic tools that enable the mapping of individual neurons and neural subtypes. Brain templates are essential for comparative biological studies because they enable analyzing many individuals in a common reference space. Several central brain templates exist for Drosophila, but every one is either biased, uses sub-optimal tissue preparation, is imaged at low resolution, or does not account for artifacts. No publicly available Drosophila ventral nerve cord template currently exists. In this work, we created high-resolution templates of the Drosophila brain and ventral nerve cord using the best-available technologies for imaging, artifact correction, stitching, and template construction using groupwise registration. We evaluated our central brain template against the four most competitive, publicly available brain templates and demonstrate that ours enables more accurate registration with fewer local deformations in shorter time.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0236495}, author = {Bogovic, John A and Otsuna, Hideo and Heinrich, Larissa and Ito, Masayoshi and Jeter, Jennifer and Meissner, Geoffrey and Nern, Aljoscha and Colonell, Jennifer and Malkesman, Oz and Ito, Kei and Saalfeld, Stephan} } @article {65375, title = {Unc-4 acts to promote neuronal identity and development of the take-off circuit in the Drosophila CNS.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Mar 27}, doi = {10.7554/eLife.55007}, url = {https://elifesciences.org/articles/55007}, author = {Lacin, Haluk and Williamson, W Ryan and Card, Gwyneth M and Skeath, James B and Truman, James W} } @article {65297, title = {A versatile vector system for the fast generation of knock-in cell lines with CRISPR.}, journal = {bioRxiv}, year = {2020}, month = {2020 Feb 06}, abstract = {

Until recent advancements in genome editing via CRISPR/Cas9 technology, understanding protein function typically involved artificially overexpressing proteins of interest. Despite that CRISPR/Cas9 has ushered in a new era of possibilities for modifying endogenous genes with labeling tags (knock-in) to more accurately study proteins under physiological conditions, the technique is largely underutilized due to its tedious, multi-step process. Here we outline a homologous recombination system (FAST-HDR) to be used in combination with CRISPR/Cas9 that significantly simplifies and accelerates this process while introducing multiplexing to allow live-cell studies of 3 endogenous proteins within the same cell line. Furthermore, the recombination vectors are assembled in a single reaction that is enhanced for eliminating false positives and reduces the overall creation time for the knockin cell line from\ ~8 weeks to \<15 days. Finally, the system utilizes a modular construction to allow for seamlessly swapping labeling tags to ensure flexibility according to the area under study. We validated this new methodology by developing advanced cell lines with 3 fluorescent-labeled endogenous proteins that support high-content phenotypic drug screening without using antibodies or exogenous staining. Therefore, Fast-HDR cell lines provide a robust alternative for studying multiple proteins of interest in live cells without artificially overexpressing labeled proteins.

}, doi = {10.1101/2020.02.06.927384}, author = {Perez-Leal, Oscar and Nixon-Abell, Jonathon and Barrero, Carlos A. and Gordon, John and Rico, Mario C.} } @article {65278, title = {When does midbrain dopamine activity exert its effects on behavior?}, journal = {Nature Neuroscience}, volume = {23}, year = {2020}, month = {2020 Jan 13}, pages = {154-6}, issn = {1546-1726}, doi = {10.1038/s41593-019-0577-y}, author = {Coddington, Luke T} } @article {65633, title = {Whole-brain profiling of cells and circuits in mammals by tissue clearing and light-sheet microscopy.}, journal = {Neuron}, volume = {106}, year = {2020}, month = {2020 May 06}, pages = {369-387}, abstract = {

Tissue clearing and light-sheet microscopy have a 100-year-plus history, yet these fields have been combined only recently to facilitate novel experiments and measurements in neuroscience. Since tissue-clearing methods were first combined with modernized light-sheet microscopy a decade ago, the performance of both technologies has rapidly improved, broadening their applications. Here, we review the state of the art of tissue-clearing methods and light-sheet microscopy and discuss applications of these techniques in profiling cells and circuits in mice. We examine outstanding challenges and future opportunities for expanding these techniques to achieve brain-wide profiling of cells and circuits in primates and humans. Such integration will help provide a systems-level understanding of the physiology and pathology of our central nervous system.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2020.03.004}, author = {Ueda, Hiroki R and Dodt, Hans-Ulrich and Osten, Pavel and Economo, Michael N and Chandrashekar, Jayaram and Keller, Philipp J} } @article {65599, title = {Whole-brain profiling of cells and circuits in mammals by tissue clearing and light-sheet microscopy.}, journal = {Neuron}, volume = {106}, year = {2020}, month = {2020 May 06}, pages = {369-387}, abstract = {

Tissue clearing and light-sheet microscopy have a 100-year-plus history, yet these fields have been combined only recently to facilitate novel experiments and measurements in neuroscience. Since tissue-clearing methods were first combined with modernized light-sheet microscopy a decade ago, the performance of both technologies has rapidly improved, broadening their applications. Here, we review the state of the art of tissue-clearing methods and light-sheet microscopy and discuss applications of these techniques in profiling cells and circuits in mice. We examine outstanding challenges and future opportunities for expanding these techniques to achieve brain-wide profiling of cells and circuits in primates and humans. Such integration will help provide a systems-level understanding of the physiology and pathology of our central nervous system.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2020.03.004}, author = {Ueda, Hiroki R and Dodt, Hans-Ulrich and Osten, Pavel and Economo, Michael N and Chandrashekar, Jayaram and Keller, Philipp J} } @article {65656, title = {The wiring logic of an identified serotonergic neuron that spans sensory networks.}, journal = {Journal of Neuroscience}, volume = {40}, year = {2020}, month = {2020 Aug 12}, pages = {6309-27}, abstract = {

Serotonergic neurons project widely throughout the brain to modulate diverse physiological and behavioral processes. However, a single cell resolution understanding of the connectivity of serotonergic neurons is currently lacking. Using a whole-brain EM dataset of a female , we comprehensively determine the wiring logic of a broadly projecting serotonergic neuron (the "CSDn") that spans several olfactory regions. Within the antennal lobe, the CSDn differentially innervates each glomerulus, yet surprisingly, this variability reflects a diverse set of presynaptic partners, rather than glomerulus-specific differences in synaptic output, which is predominately to local interneurons. Moreover, the CSDn has distinct connectivity relationships with specific local interneuron subtypes, suggesting that the CSDn influences distinct aspects of local network processing. Across olfactory regions, the CSDn has different patterns of connectivity, even having different connectivity with individual projection neurons that also span these regions. Whereas the CSDn targets inhibitory local neurons in the antennal lobe, the CSDn has more distributed connectivity in the LH, preferentially synapsing with principal neuron types based on transmitter content. Lastly, we identify individual novel synaptic partners associated with other sensory domains that provide strong, top-down input to the CSDn. Taken together, our study reveals the complex connectivity of serotonergic neurons which combine the integration of local and extrinsic synaptic input in a nuanced, region-specific manner.All sensory systems receive serotonergic modulatory input. However, a comprehensive understanding of the synaptic connectivity of individual serotonergic neurons is lacking. In this study, we use a whole-brain EM microscopy dataset to comprehensively determine the wiring logic of a broadly projecting serotonergic neuron in the olfactory system of Collectively, our study demonstrates at a single cell level, the complex connectivity of serotonergic neurons within their target networks, identifies specific cell classes heavily targeted for serotonergic modulation in the olfactory system, and reveals novel extrinsic neurons that provide strong input to this serotonergic system outside of the context of olfaction. Elucidating the connectivity logic of individual modulatory neurons provides a ground plan for the seemingly heterogeneous effects of modulatory systems.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0552-20.2020}, author = {Coates, Kaylynn E and Calle-Schuler, Steven A and Helmick, Levi M and Knotts, Victoria L and Martik, Brennah N and Salman, Farzaan and Warner, Lauren T and Valla, Sophia V and Bock, Davi D and Dacks, Andrew M} } @article {65296, title = {Wiring patterns from auditory sensory neurons to the escape and song-relay pathways in fruit flies.}, journal = {Journal of Comparative Neurology}, volume = {528}, year = {2020}, month = {2020 Aug 01}, pages = {2068}, abstract = {

Many animals rely on acoustic cues to decide what action to take next. Unraveling the wiring patterns of the auditory neural pathways is prerequisite for understanding such information processing. Here we reconstructed the first step of the auditory neural pathway in the fruit fly brain, from primary to secondary auditory neurons, at the resolution of transmission electron microscopy. By tracing axons of two major subgroups of auditory sensory neurons in fruit flies, low-frequency tuned Johnston{\textquoteright}s organ (JO)-B neurons and high-frequency tuned JO-A neurons, we observed extensive connections from JO-B neurons to the main second-order neurons in both the song-relay and escape pathways. In contrast, JO-A neurons connected strongly to a neuron in the escape pathway. Our findings suggest that heterogeneous JO neuronal populations could be recruited to modify escape behavior whereas only specific JO neurons contribute to courtship behavior. We also found that all JO neurons have postsynaptic sites at their axons. Presynaptic modulation at the output sites of JO neurons could affect information processing of the auditory neural pathway in flies. This article is protected by copyright. All rights reserved.

}, issn = {1096-9861}, doi = {10.1002/cne.24877}, author = {Kim, Hyunsoo and Horigome, Mihoko and Ishikawa, Yuki and Li, Feng and Lauritzen, J Scott and Card, Gwyneth and Bock, Davi D and Kamikouchi, Azusa} } @article {64784, title = {An actin-based protrusion originating from a podosome-enriched region initiates macrophage fusion.}, journal = {Molecular Biology of the Cell}, volume = {30}, year = {2019}, month = {2019 Aug 1}, pages = {2254-67}, abstract = {

Macrophage fusion resulting in the formation of multinucleated giant cells occurs in a variety of chronic inflammatory diseases, yet the mechanism responsible for initiating macrophage fusion is unknown. Here, we used live cell imaging to show that actin-based protrusions at the leading edge initiate macrophage fusion. Phase contrast video microscopy demonstrated that in the majority of events, short protrusions (3 {\textpm} 1 μm) between two closely apposed cells initiated fusion, but occasionally we observed long protrusions (16 {\textpm} 7 μm). Using macrophages isolated from LifeAct mice and imaging with lattice light sheet microscopy, we further found that fusion-competent actin-based protrusions formed at sites enriched in podosomes. Inducing fusion in mixed populations of GFP- and mRFP-LifeAct macrophages showed rapid spatial overlap between GFP and RFP signal at the site of fusion. Cytochalasin B strongly reduced fusion and when rare fusion events occurred, protrusions were not observed. Fusion of macrophages deficient in Wiskott-Aldrich syndrome protein and Cdc42, key molecules involved in the formation of actin-based protrusions and podosomes, was also impaired both in vitro and in vivo. Finally, inhibiting the activity of the Arp2/3 complex decreased fusion and podosome formation. Together these data indicate that an actin-based protrusion formed at the leading edge macrophage fusion.

}, doi = {10.1101/538314}, author = {Faust, James J and Balabiyev, Arnat and Heddleston, John M and Podolnikova, Nataly P and Baluch, Debra Page and Chew, Teng-Leong and Ugarova, Tatiana P} } @article {64890, title = {Amino acid signatures of HLA Class-I and II molecules are strongly associated with SLE susceptibility and autoantibody production in Eastern Asians.}, journal = {PLoS Genetics}, volume = {15}, year = {2019}, month = {2019 Apr 25}, pages = {e1008092}, abstract = {

Human leukocyte antigen (HLA) is a key genetic factor conferring risk of systemic lupus erythematosus (SLE), but precise independent localization of HLA effects is extremely challenging. As a result, the contribution of specific HLA alleles and amino-acid residues to the overall risk of SLE and to risk of specific autoantibodies are far from completely understood. Here, we dissected (a) overall SLE association signals across HLA, (b) HLA-peptide interaction, and (c) residue-autoantibody association. Classical alleles, SNPs, and amino-acid residues of eight HLA genes were imputed across 4,915 SLE cases and 13,513 controls from Eastern Asia. We performed association followed by conditional analysis across HLA, assessing both overall SLE risk and risk of autoantibody production. DR15 alleles HLA-DRB1*15:01 (P = 1.4x10-27, odds ratio (OR) = 1.57) and HLA-DQB1*06:02 (P = 7.4x10-23, OR = 1.55) formed the most significant haplotype (OR = 2.33). Conditioned protein-residue signals were stronger than allele signals and mapped predominantly to HLA-DRB1 residue 13 (P = 2.2x10-75) and its proxy position 11 (P = 1.1x10-67), followed by HLA-DRB1-37 (P = 4.5x10-24). After conditioning on HLA-DRB1, novel associations at HLA-A-70 (P = 1.4x10-8), HLA-DPB1-35 (P = 9.0x10-16), HLA-DQB1-37 (P = 2.7x10-14), and HLA-B-9 (P = 6.5x10-15) emerged. Together, these seven residues increased the proportion of explained heritability due to HLA to 2.6\%. Risk residues for both overall disease and hallmark autoantibodies (i.e., nRNP: DRB1-11, P = 2.0x10-14; DRB1-13, P = 2.9x10-13; DRB1-30, P = 3.9x10-14) localized to the peptide-binding groove of HLA-DRB1. Enrichment for specific amino-acid characteristics in the peptide-binding groove correlated with overall SLE risk and with autoantibody presence. Risk residues were in primarily negatively charged side-chains, in contrast with rheumatoid arthritis. We identified novel SLE signals in HLA Class I loci (HLA-A, HLA-B), and localized primary Class II signals to five residues in HLA-DRB1, HLA-DPB1, and HLA-DQB1. These findings provide insights about the mechanisms by which the risk residues interact with each other to produce autoantibodies and are involved in SLE pathophysiology.

}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1008092}, author = {Molineros, Julio E and Looger, Loren L and Kim, Kwangwoo and Okada, Yukinori and Terao, Chikashi and Sun, Celi and Zhou, Xu-Jie and Raj, Prithvi and Kochi, Yuta and Suzuki, Akari and Akizuki, Shuji and Nakabo, Shuichiro and Bang, So-Young and Lee, Hye-Soon and Kang, Young Mo and Suh, Chang-Hee and Chung, Won Tae and Park, Yong-Beom and Choe, Jung-Yoon and Shim, Seung-Cheol and Lee, Shin-Seok and Zuo, Xiaoxia and Yamamoto, Kazuhiko and Li, Quan-Zhen and Shen, Nan and Porter, Lauren L and Harley, John B and Chua, Kek Heng and Zhang, Hong and Wakeland, Edward K and Tsao, Betty P and Bae, Sang-Cheol and Nath, Swapan K} } @article {65059, title = {Analysis of phosphatidylinositol transfer at ER-PM junctions in receptor-stimulated live cells.}, journal = {Methods in Molecular Biology}, volume = {1949}, year = {2019}, month = {2019 Feb 23}, pages = {1-11}, abstract = {

Phosphatidylinositol (PI) is an inositol-containing phospholipid synthesized in the endoplasmic reticulum (ER). PI is a precursor lipid for PI 4,5-bisphosphate (PI(4,5)P) in the plasma membrane (PM) important for Ca signaling in response to extracellular stimuli. Thus, ER-to-PM PI transfer becomes essential for cells to maintain PI(4,5)P homeostasis during receptor stimulation. In this chapter, we discuss two live-cell imaging protocols to analyze ER-to-PM PI transfer at ER-PM junctions, where the two membrane compartments make close appositions accommodating PI transfer. First, we describe how to monitor PI(4,5)P replenishment following receptor stimulation, as a readout of PI transfer, using a PI(4,5)P biosensor and total internal reflection fluorescence\ microscopy. The second protocol directly visualizes PI transfer proteins that accumulate at ER-PM junctions and mediate PI(4,5)P replenishment with PI in the ER in stimulated cells. These methods provide spatial and temporal analysis of ER-to-PM PI transfer during receptor stimulation and can be adapted to other research questions related to this topic.

}, keywords = {Biological Transport, Biosensing Techniques, Cell Membrane, Endoplasmic Reticulum, Hela Cells, Humans, Image Processing, Computer-Assisted, Microscopy, Phosphatidylinositol 4,5-Diphosphate, Phosphatidylinositols}, issn = {1940-6029}, doi = {10.1007/978-1-4939-9136-5_1}, author = {Chang, Chi-Lun and Liou, Jen} } @article {68818, title = {Associative conditioning remaps odor representations and modifies inhibition in a higher olfactory brain area.}, journal = {Nat Neurosci}, volume = {22}, year = {2019}, month = {11/2019}, pages = {1844-1856}, abstract = {

Intelligent behavior involves associations between high-dimensional sensory representations and behaviorally relevant qualities such as valence. Learning of associations involves plasticity of excitatory connectivity, but it remains poorly understood how information flow is reorganized in networks and how inhibition contributes to this process. We trained adult zebrafish in an appetitive odor discrimination task and analyzed odor representations in a specific compartment of the posterior zone of the dorsal telencephalon (Dp), the homolog of mammalian olfactory cortex. Associative conditioning enhanced responses with a preference for the positively conditioned odor. Moreover, conditioning systematically remapped odor representations along an axis in coding space that represented attractiveness (valence). Interindividual variations in this mapping predicted variations in behavioral odor preference. Photoinhibition of interneurons resulted in specific modifications of odor representations that mirrored effects of conditioning and reduced experience-dependent, interindividual variations in odor-valence mapping. These results reveal an individualized odor-to-valence map that is shaped by inhibition and reorganized during learning.

}, keywords = {Animals, Animals, Genetically Modified, Association Learning, Brain Mapping, Discrimination Learning, Female, Individuality, Male, Neural Inhibition, Odorants, Olfactory Cortex, Olfactory Perception, Zebrafish}, issn = {1546-1726}, doi = {10.1038/s41593-019-0495-z}, author = {Frank, Thomas and M{\"o}nig, Nila R and Satou, Chie and Higashijima, Shin-Ichi and Friedrich, Rainer W} } @article {65180, title = {Asymmetric ON-OFF processing of visual motion cancels variability induced by the structure of natural scenes.}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Oct 15}, abstract = {

Animals detect motion using a variety of visual cues that reflect regularities in the natural world. Experiments in animals across phyla have shown that motion percepts incorporate both pairwise and triplet spatiotemporal correlations that could theoretically benefit motion computation. However, it remains unclear how visual systems assemble these cues to build accurate motion estimates. Here we used systematic behavioral measurements of fruit fly motion perception to show how flies combine local pairwise and triplet correlations to reduce variability in motion estimates across natural scenes. By generating synthetic images with statistics controlled by maximum entropy distributions, we show that the triplet correlations are useful only when images have light-dark asymmetries that mimic natural ones. This suggests that asymmetric ON-OFF processing is tuned to the particular statistics of natural scenes. Since all animals encounter the world{\textquoteright}s light-dark asymmetries, many visual systems are likely to use asymmetric ON-OFF processing to improve motion estimation.

}, issn = {2050-084X}, doi = {10.7554/eLife.47579}, author = {Chen, Juyue and Mandel, Holly B and Fitzgerald, James E and Clark, Damon A} } @article {64847, title = {Attachment of the blastoderm to the vitelline envelope affects gastrulation of insects.}, journal = {Nature}, year = {2019}, month = {2019 Mar 27}, abstract = {

During gastrulation, physical forces reshape the simple embryonic tissue to form the complex body plans of multicellular organisms. These forces often cause large-scale asymmetric movements of the embryonic tissue. In many embryos, the gastrulating tissue is surrounded by a rigid protective shell. Although it is well-recognized that gastrulation movements depend on forces that are generated by tissue-intrinsic contractility,\ it is not known whether interactions between the tissue and the protective shell provide additional forces that affect gastrulation. Here we show that a particular part of the blastoderm tissue of the red flour beetle (Tribolium castaneum) tightly adheres in a temporally coordinated manner to the vitelline envelope that surrounds the embryo. This attachment generates an additional force that counteracts tissue-intrinsic contractile forces to create asymmetric tissue movements. This localized attachment depends on an αPS2 integrin (inflated), and the knockdown of this integrin leads to a gastrulation phenotype that is consistent with complete loss of attachment. Furthermore, analysis of another integrin (the αPS3 integrin, scab) in the fruit fly (Drosophila melanogaster) suggests that gastrulation in this organism also relies on adhesion between the blastoderm and the vitelline envelope. Our findings reveal a conserved mechanism through which the spatiotemporal pattern of tissue adhesion to the vitelline envelope provides controllable, counteracting forces that shape gastrulation movements in insects.

}, doi = {10.1038/s41586-019-1044-3}, author = {Muenster, Stefan and Jain, Akanksha and Mietke, Alexander and Pavlopoulos, Anastasios and Grill, Stephan W and Tomancak, Pavel} } @article {64942, title = {Augmin accumulation on long-lived microtubules drives amplification and kinetochore-directed growth.}, journal = {Journal of Cell Biology}, volume = {218}, year = {2019}, month = {2019 Jul 01}, pages = {2150-68}, abstract = {

Dividing cells reorganize their microtubule cytoskeleton into a bipolar spindle, which moves one set of sister chromatids to each nascent daughter cell. Early spindle assembly models postulated that spindle pole-derived microtubules search the cytoplasmic space until they randomly encounter a kinetochore to form a stable attachment. More recent work uncovered several additional, centrosome-independent microtubule generation pathways, but the contributions of each pathway to spindle assembly have remained unclear. Here, we combined live microscopy and mathematical modeling to show that most microtubules nucleate at noncentrosomal regions in dividing human cells. Using a live-cell probe that selectively labels aged microtubule lattices, we demonstrate that the distribution of growing microtubule plus ends can be almost entirely explained by Augmin-dependent amplification of long-lived microtubule lattices. By ultrafast 3D lattice light-sheet microscopy, we observed that this mechanism results in a strong directional bias of microtubule growth toward individual kinetochores. Our systematic quantification of spindle dynamics reveals highly coordinated microtubule growth during kinetochore fiber assembly.

}, issn = {1540-8140}, doi = {10.1083/jcb.201805044}, author = {David, Ana F and Roudot, Philippe and Legant, Wesley R and Betzig, Eric and Danuser, Gaudenz and Gerlich, Daniel W} } @article {65001, title = {Automated reconstruction of a serial-section EM drosophila brain with flood-filling networks and local realignment.}, journal = {bioRxiv}, year = {2019}, month = {2019 Apr 11}, abstract = {

Reconstruction of neural circuitry at single-synapse resolution is an attractive target for improving understanding of the nervous system in health and disease. Serial section transmission electron microscopy (ssTEM) is among the most prolific imaging methods employed in pursuit of such reconstructions. We demonstrate how Flood-Filling Networks (FFNs) can be used to computationally segment a forty-teravoxel whole-brain\ Drosophila\ ssTEM volume. To compensate for data irregularities and imperfect global alignment, FFNs were combined with procedures that locally re-align serial sections and dynamically adjust image content. The proposed approach produced a largely merger-free segmentation of the entire ssTEM\ Drosophila\ brain, which we make freely available. As compared to manual tracing using an efficient skeletonization strategy, the segmentation enabled circuit reconstruction and analysis workflows that were an order of magnitude faster.

}, doi = {10.1101/605634}, author = {Peter H. Li and Larry F. Lindsey and Micha{\l} Januszewski and Zhihao Zheng and Alexander Shakeel Bates and Istv{\'a}n Taisz and Mike Tyka and Matthew Nichols and Feng Li and Eric Perlman and Jeremy Maitin-Shepard and Tim Blakely and Laramie Leavitt and Gregory S.X.E. Jefferis and Davi Bock and Viren Jain} } @article {65090, title = {An automatic behavior recognition system classifies animal behaviors using movements and their temporal context.}, journal = {Journal of Neuroscience Methods}, volume = {326}, year = {2019}, month = {2019 Aug 12}, pages = {108352}, abstract = {

Animals can perform complex and purposeful behaviors by executing simpler movements in flexible sequences. It is particularly challenging to analyze behavior sequences when they are highly variable, as is the case in language production, certain types of birdsong and, as in our experiments, flies grooming. High sequence variability necessitates rigorous quantification of large amounts of data to identify organizational principles and temporal structure of such behavior. To cope with large amounts of data, and minimize human effort and subjective bias, researchers often use automatic behavior recognition software. Our standard grooming assay involves coating flies in dust and videotaping them as they groom to remove it. The flies move freely and so perform the same movements in various orientations. As the dust is removed, their appearance changes. These conditions make it difficult to rely on precise body alignment and anatomical landmarks such as eyes or legs and thus present challenges to existing behavior classification software. Human observers use speed, location, and shape of the movements as the diagnostic features of particular grooming actions. We applied this intuition to design a new automatic behavior recognition system (ABRS) based on spatiotemporal features in the video data, heavily weighted for temporal dynamics and invariant to the animal{\textquoteright}s position and orientation in the scene. We use these spatiotemporal features in two steps of supervised classification that reflect two time-scales at which the behavior is structured. As a proof of principle, we show results from quantification and analysis of a large data set of stimulus-induced fly grooming behaviors that would have been difficult to assess in a smaller dataset of human-annotated ethograms. While we developed and validated this approach to analyze fly grooming behavior, we propose that the strategy of combining alignment-invariant features and multi-timescale analysis may be generally useful for movement-based classification of behavior from video data.

}, issn = {01650270}, doi = {10.1016/j.jneumeth.2019.108352}, author = {Ravbar, Primoz and Branson, Kristin and Simpson, Jie H.} } @article {65198, title = {A bidirectional network for appetite control in larval zebrafish.}, journal = {Elife}, volume = {8}, year = {2019}, month = {2019 Oct 18}, abstract = {

Medial and lateral hypothalamic loci are known to suppress and enhance appetite, respectively, but the dynamics and functional significance of their interaction have yet to be explored. Here we report that, in larval zebrafish, primarily serotonergic neurons of the ventromedial caudal hypothalamus (cH) become increasingly active during food deprivation, whereas activity in the lateral hypothalamus (LH) is reduced. Exposure to food sensory and consummatory cues reverses the activity patterns of these two nuclei, consistent with their representation of opposing internal hunger states. Baseline activity is restored as food-deprived animals return to satiety via voracious feeding. The antagonistic relationship and functional importance of cH and LH activity patterns were confirmed by targeted stimulation and ablation of cH neurons. Collectively, the data allow us to propose a model in which these hypothalamic nuclei regulate different phases of hunger and satiety and coordinate energy balance via antagonistic control of distinct behavioral outputs.

}, issn = {2050-084X}, doi = {10.7554/eLife.43775}, author = {Wee, Caroline Lei and Song, Erin Yue and Johnson, Robert Evan and Ailani, Deepak and Randlett, Owen and Kim, Ji-Yoon and Nikitchenko, Maxim and Bahl, Armin and Yang, Chao-Tsung and Ahrens, Misha B and Kawakami, Koichi and Engert, Florian and Kunes, Sam} } @article {65079, title = {BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples.}, journal = {Nature Methods}, volume = {16}, year = {2019}, month = {2019 Sep}, pages = {870-74}, abstract = {

Light-sheet imaging of cleared and expanded samples creates terabyte-sized datasets that consist of many unaligned three-dimensional image tiles, which must be reconstructed before analysis. We developed the BigStitcher software to address this challenge. BigStitcher enables interactive visualization, fast and precise alignment, spatially resolved quality estimation, real-time fusion and deconvolution of dual-illumination, multitile, multiview datasets. The software also compensates for optical effects, thereby improving accuracy and enabling subsequent biological analysis.

}, issn = {1548-7091}, doi = {10.1038/s41592-019-0501-0}, url = {http://www.nature.com/articles/s41592-019-0501-0http://www.nature.com/articles/s41592-019-0501-0.pdfhttp://www.nature.com/articles/s41592-019-0501-0.pdfhttp://www.nature.com/articles/s41592-019-0501-0}, author = {H{\"o}rl, David and Rojas Rusak, Fabio and Preusser, Friedrich and Tillberg, Paul and Randel, Nadine and Chhetri, Raghav K. and Cardona, Albert and Keller, Philipp J. and Harz, Hartmann and Leonhardt, Heinrich and Treier, Mathias and Preibisch, Stephan} } @article {65242, title = {Biosensors show the pharmacokinetics of S-Ketamine in the endoplasmic reticulum.}, journal = {Frontiers in Cellular Neuroscience}, volume = {13}, year = {2019}, month = {2019 Nov 12}, pages = {499}, abstract = {

The target for the "rapid" (\<24 h) antidepressant effects of S-ketamine is unknown, vitiating programs to rationally develop more effective rapid antidepressants. To describe a drug{\textquoteright}s target, one must first understand the compartments entered by the drug, at all levels-the organ, the cell, and the organelle. We have, therefore, developed molecular tools to measure the subcellular, organellar pharmacokinetics of S-ketamine. The tools are genetically encoded intensity-based S-ketamine-sensing fluorescent reporters, iSKetSnFR1 and iSKetSnFR2. In solution, these biosensors respond to S-ketamine with a sensitivity, S-slope = delta(F/F)/(delta[S-ketamine]) of 0.23 and 1.9/μM, respectively. The iSKetSnFR2 construct allows measurements at \<0.3 μM S-ketamine. The iSKetSnFR1 and iSKetSnFR2 biosensors display \>100-fold selectivity over other ligands tested, including R-ketamine. We targeted each of the sensors to either the plasma membrane (PM) or the endoplasmic reticulum (ER). Measurements on these biosensors expressed in Neuro2a cells and in human dopaminergic neurons differentiated from induced pluripotent stem cells (iPSCs) show that S-ketamine enters the ER within a few seconds after appearing in the external solution near the PM, then leaves as rapidly after S-ketamine is removed from the extracellular solution. In cells, S-slopes for the ER and PM-targeted sensors differ by \<2-fold, indicating that the ER [S-ketamine] is less than 2-fold different from the extracellular [S-ketamine]. Organelles represent potential compartments for the engagement of S-ketamine with its antidepressant target, and potential S-ketamine targets include organellar ion channels, receptors, and transporters.

}, issn = {1662-5102}, doi = {10.3389/fncel.2019.00499}, author = {Bera, Kallol and Kamajaya, Aron and Shivange, Amol V and Muthusamy, Anand K and Nichols, Aaron L and Borden, Philip M and Grant, Stephen and Jeon, Janice and Lin, Elaine and Bishara, Ishak and Chin, Theodore M and Cohen, Bruce N and Kim, Charlene H and Unger, Elizabeth K and Tian, Lin and Marvin, Jonathan S and Looger, Loren L and Lester, Henry A} } @article {65081, title = {Bright and photostable chemigenetic indicators for extended in vivo voltage imaging.}, journal = {Science}, volume = {365}, year = {2019}, month = {2019 Aug 13}, pages = {699-704}, abstract = {

Imaging changes in membrane potential using genetically encoded fluorescent voltage indicators (GEVIs) has great potential for monitoring neuronal activity with high spatial and temporal resolution. Brightness and photostability of fluorescent proteins and rhodopsins have limited the utility of existing GEVIs. We engineered a novel GEVI, "Voltron", that utilizes bright and photostable synthetic dyes instead of protein-based fluorophores, extending the combined duration of imaging and number of neurons imaged simultaneously by more than tenfold relative to existing GEVIs. We used Voltron for in vivo voltage imaging in mice, zebrafish, and fruit flies. In mouse cortex, Voltron allowed single-trial recording of spikes and subthreshold voltage signals from dozens of neurons simultaneously, over 15 min of continuous imaging. In larval zebrafish, Voltron enabled the precise correlation of spike timing with behavior.

}, issn = {1095-9203}, doi = {10.1126/science.aav6416}, author = {Abdelfattah, Ahmed S and Kawashima, Takashi and Singh, Amrita and Novak, Ondrej and Liu, Hui and Shuai, Yichun and Huang, Yi-Chieh and Campagnola, Luke and Seeman, Stephanie C and Yu, Jianing and Zheng, Jihong and Grimm, Jonathan B and Patel, Ronak and Friedrich, Johannes and Mensh, Brett D and Paninski, Liam and Macklin, John J and Murphy, Gabe J and Podgorski, Kaspar and Lin, Bei-Jung and Chen, Tsai-Wen and Turner, Glenn C and Liu, Zhe and Koyama, Minoru and Svoboda, Karel and Ahrens, Misha B and Lavis, Luke D and Schreiter, Eric R} } @article {64937, title = {Busted! A dope ring with activity clocked at dawn and dusk.}, journal = {Neuron}, volume = {102}, year = {2019}, month = {2019 May 22}, pages = {713-5}, abstract = {Clock neurons generate circadian rhythms in behavioral activity, but the relevant pathways remain poorly understood. In this issue of Neuron, Liang et al. (2019) show that distinct clock neurons independently drive movement-promoting {\textquotedblleft}ring neurons{\textquotedblright} in Drosophila through dopaminergic relays to support morning and evening locomotor activity.}, doi = {10.1016/j.neuron.2019.05.004}, author = {Hulse, Brad and Jayaraman, Vivek} } @article {67280, title = {CaImAn an open source tool for scalable calcium imaging data analysis}, journal = {eLife}, volume = {8}, year = {2019}, month = {01/2019}, abstract = {

Advances in fluorescence microscopy enable monitoring larger brain areas in-vivo with finer time resolution. The resulting data rates require reproducible analysis pipelines that are reliable, fully automated, and scalable to datasets generated over the course of months. We present CaImAn, an open-source library for calcium imaging data analysis. CaImAn\ provides automatic and scalable methods to address problems common to pre-processing, including motion correction, neural activity identification, and registration across different sessions of data collection. It does this while requiring minimal user intervention, with good scalability on computers ranging from laptops to high-performance computing clusters. CaImAn\ is suitable for two-photon and one-photon imaging, and also enables real-time analysis on streaming data. To benchmark the performance of CaImAn\ we collected and combined a corpus of manual annotations from multiple labelers on nine mouse two-photon datasets. We demonstrate that CaImAn\ achieves near-human performance in detecting locations of active neurons

}, doi = {10.7554/eLife.38173}, url = {https://elifesciences.org/articles/38173}, author = {Giovannucci, Andrea and Friedrich, Johannes and Gunn, Pat and Kalfon, J{\'e}r{\'e}mie and Brown, Brandon L and Koay, Sue Ann and Taxidis, Jiannis and Najafi, Farzaneh and Gauthier, Jeffrey L and Zhou, Pengcheng and Khakh, Baljit S and Tank, David W and Chklovskii, Dmitri B and Pnevmatikakis, Eftychios A} } @article {65137, title = {Can one concurrently record electrical spikes from every neuron in a mammalian brain?}, journal = {Neuron}, volume = {103}, year = {2019}, month = {2019 Sep 25}, pages = {1005}, abstract = {

The classic approach to measure the spiking response of neurons involves the use of metal electrodes to record extracellular potentials. Starting over 60 years ago with a single recording site, this technology now extends to ever larger numbers and densities of sites. We argue, based on the mechanical and electrical properties of existing materials, estimates of signal-to-noise ratios, assumptions regarding extracellular space in the brain, and estimates of heat generation by the electronic interface, that it should be possible to fabricate rigid electrodes to concurrently record from essentially every neuron in the cortical mantle. This will involve fabrication with existing yet nontraditional materials and procedures. We further emphasize the need to advance materials for improved flexible electrodes as an essential advance to record from neurons in brainstem and spinal cord in moving animals.

}, issn = {08966273}, doi = {10.1016/j.neuron.2019.08.011}, author = {Kleinfeld, David and Luan, Lan and Mitra, Partha P. and Robinson, Jacob T. and Sarpeshkar, Rahul and Shepard, Kenneth and Xie, Chong and Harris, Timothy D.} } @proceedings {65054, title = {Cellular level analysis of the locomotor neural circuits in Drosophila melanogaster.}, year = {2019}, month = {2019 Jul 6}, pages = {334-7}, author = {minegishi, ryo and Feng, Kai and Dickson, Barry} } @article {64850, title = {Cellular localization of tolyporphins, unusual tetrapyrroles, in a microbial photosynthetic community determined using hyperspectral confocal fluorescence microscopy.}, journal = {Photosynthesis Research}, volume = {141}, year = {2019}, month = {2019 Sep 1}, pages = {259-71}, abstract = {

The cyanobacterial culture HT-58-2, composed of a filamentous cyanobacterium and accompanying community bacteria, produces chlorophyll a as well as the tetrapyrrole macrocycles known as tolyporphins. Almost all known tolyporphins (A-M except K) contain a dioxobacteriochlorin chromophore and exhibit an absorption spectrum somewhat similar to that of chlorophyll a. Here, hyperspectral confocal fluorescence microscopy was employed to noninvasively probe the locale of tolyporphins within live cells under various growth conditions (media, illumination, culture age). Cultures grown in nitrate-depleted media (BG-11 vs. nitrate-rich, BG-11) are known to increase the production of tolyporphins by orders of magnitude (rivaling that of chlorophyll a) over a period of 30-45 days. Multivariate curve resolution (MCR) was applied to an image set containing images from each condition to obtain pure component spectra of the endogenous pigments. The relative abundances of these components were then calculated for individual pixels in each image in the entire set, and 3D-volume renderings were obtained. At 30 days in media with or without nitrate, the chlorophyll a and phycobilisomes (combined phycocyanin and phycobilin components) co-localize in the filament outer cytoplasmic region. Tolyporphins localize in a distinct peripheral pattern in cells grown in BG-11 versus a diffuse pattern (mimicking the chlorophyll a localization) upon growth in BG-11. In BG-11, distinct puncta of tolyporphins were commonly found at the septa between cells and at the end of filaments. This work quantifies the relative abundance and envelope localization of tolyporphins in single cells, and illustrates the ability to identify novel tetrapyrroles in the presence of chlorophyll a in a photosynthetic microorganism within a non-axenic culture.

}, issn = {1573-5079}, doi = {10.1007/s11120-019-00625-w}, author = {Barnhart-Dailey, Meghan and Zhang, Yunlong and Zhang, Ran and Anthony, Stephen M and Aaron, Jesse S and Miller, Eric S and Lindsey, Jonathan S and Timlin, Jerilyn A} } @article {65042, title = {Changes throughout a genetic network mask the contribution of Hox gene evolution.}, journal = {Current Biology}, volume = {29}, year = {2019}, month = {2019 Jul 08}, pages = {2157-66}, abstract = {

Hox genes pattern the anterior-posterior axis of animals and are posited to drive animal body plan evolution, yet their precise role in evolution has been difficult to determine. Here, we identified evolutionary modifications in the Hox gene\ Abd-Bthat dramatically altered its expression along the body plan of\ Drosophila santomea.\ Abd-B\ is required for pigmentation in\ Drosophila yakuba, the sister species of\ D.\ santomea, and changes to Abd-B expression would be predicted to make large contributions to the loss of body pigmentation in\ D.\ santomea. However, manipulating\ Abd-B\ expression in current-day\ D.\ santomea\ does not affect pigmentation. We attribute this epistatic interaction to four other genes within the\ D.\ santomea\ pigmentation network, three of which have evolved expression patterns that do not respond to Abd-B. Our results demonstrate how body plans may evolve through small evolutionary steps distributed throughout Hox-regulated networks. Polygenicity and epistasis may hinder efforts to identify genes and mechanisms underlying macroevolutionary traits.

}, issn = {09609822}, doi = {10.1016/j.cub.2019.05.074}, author = {Liu, Yang and Ramos-Womack, Margarita and Han, Clair and Reilly, Patrick and Brackett, Kelly LaRue and Rogers, William and Williams, Thomas M. and Andolfatto, Peter and Stern, David L. and Rebeiz, Mark} } @article {49582, title = {Characterization of neurite dystrophy after trauma by high speed structured illumination microscopy and lattice light sheet microscopy.}, journal = {Journal of Neuroscience Methods}, volume = {312}, year = {2019}, month = {2019 Jan 15}, pages = {154-61}, abstract = {

BACKGROUND: Unbiased screening studies have repeatedly identified actin-related proteins as one of the families of proteins most influenced by neurotrauma. Nevertheless, the status quo model of cytoskeletal reorganization after neurotrauma excludes actin and incorporates only changes in microtubules and intermediate filaments. Actin is excluded in part because it is difficult to image with conventional techniques. However, recent innovations in fluorescent microscopy provide an opportunity to image the actin cytoskeleton at super-resolution resolution in living cells. This study applied these innovations to an in vitro model of neurotrauma.

NEW METHOD: New methods are introduced for traumatizing neurons before imaging them with high speed structured illumination microscopy or lattice light sheet microscopy. Also, methods for analyzing structured illumination microscopy images to quantify post-traumatic neurite dystrophy are presented.

RESULTS: Human induced pluripotent stem cell-derived neurons exhibited actin organization typical of immature neurons. Neurite dystrophy increased after trauma but was not influenced by jasplakinolide treatment. The F-actin content of dystrophies varied greatly from one dystrophy to another.

COMPARISON WITH EXISTING METHODS: In contrast to fixation dependent methods, these methods capture the evolution of the actin cytoskeleton over time in a living cell. In contrast to prior methods based on counting dystrophies, this quantification scheme parameterizes the severity of a given dystrophy as it evolves from a local swelling to an almost-perfect spheroid that threatens to transect the neurite.

CONCLUSIONS: These methods can be used to investigate genetic factors and therapeutic interventions that modulate the course of neurite dystrophy after trauma.

}, issn = {1872-678X}, doi = {10.1016/j.jneumeth.2018.12.005}, author = {Phillips, Jack K and Sherman, Sydney A and Cotton, Kristen Y and Heddleston, John M and Taylor, Aaron B and Finan, John D} } @article {64880, title = {Chemistry of photosensitive fluorophores for single-molecule localization microscopy.}, journal = {ACS Chemical Biology}, volume = {14}, year = {2019}, month = {2019 Jun 21}, pages = {1077-90}, abstract = {

The development of single-molecule localization microscopy (SMLM) has sparked a revolution in biological imaging, allowing {\textquoteright}super-resolution{\textquoteright} fluorescence microscopy below the diffraction limit of light. The last decade has seen an explosion in not only optical hardware for SMLM but also the development or repurposing of fluorescent proteins and small-molecule fluorescent probes for this technique. In this review, written by chemists for chemists, we detail the history of single-molecule localization microscopy and collate the collection of probes with demonstrated utility in SMLM. We hope it will serve as a primer for probe choice in localization microscopy as well as an inspiration for the development of new fluorophores that enable imaging of biological samples with exquisite detail.

}, issn = {1554-8937}, doi = {10.1021/acschembio.9b00197}, author = {Jradi, Fadi M and Lavis, Luke D} } @article {65058, title = {CHP1 regulates compartmentalized glycerolipid synthesis by activating GPAT4.}, journal = {Molecular Cell}, volume = {74}, year = {2019}, month = {2019 Apr 4}, pages = {45-58.e7}, abstract = {

Cells require a constant supply of fatty acids to survive and proliferate. Fatty acids incorporate into membrane and storage glycerolipids through a series of endoplasmic reticulum (ER) enzymes, but how these enzymes are regulated is not well understood. Here, using a combination of CRISPR-based genetic screens and unbiased lipidomics, we identified calcineurin B homologous protein 1 (CHP1) as a major regulator of ER glycerolipid synthesis. Loss of\ CHP1 severely reduces fatty acid incorporation and storage in mammalian cells and invertebrates. Mechanistically, CHP1 binds and activates GPAT4, which catalyzes the initial rate-limiting step in glycerolipid synthesis. GPAT4 activity requires CHP1 to be N-myristoylated, forming a key molecular interface between the two proteins. Interestingly, upon CHP1 loss, the peroxisomal enzyme, GNPAT, partially compensates for the loss of ER lipid synthesis, enabling cell proliferation. Thus, our work identifies a conserved regulator of glycerolipid metabolism and reveals plasticity in lipid synthesis of proliferating cells.

}, keywords = {3T3 Cells, Acyltransferases, Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Calcium-Binding Proteins, Cell Proliferation, Drosophila melanogaster, Drosophila Proteins, Endoplasmic Reticulum, Enzyme Activation, Gene Expression Regulation, Enzymologic, Glycerides, Glycerol-3-Phosphate O-Acyltransferase, HEK293 Cells, Hela Cells, Hep G2 Cells, Humans, Jurkat Cells, Lipogenesis, Mice, Palmitic Acid, Protein Binding}, issn = {1097-4164}, doi = {10.1016/j.molcel.2019.01.037}, author = {Zhu, Xiphias Ge and Nicholson Puthenveedu, Shirony and Shen, Yihui and La, Konnor and Ozlu, Can and Wang, Tim and Klompstra, Diana and Gultekin, Yetis and Chi, Jingyi and Fidelin, Justine and Peng, Tao and Molina, Henrik and Hang, Howard C and Min, Wei and Birsoy, K{\i}van{\c c}} } @article {64814, title = {Chronology-based architecture of descending circuits that underlie the development of locomotor repertoire after birth.}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Feb 25}, abstract = {

The emergence of new and increasingly sophisticated behaviors after birth is accompanied by dramatic increase of newly established synaptic connections in the nervous system. Little is known, however, of how nascent connections are organized to support such new behaviors alongside existing ones. To understand this, in the larval zebrafish we examined the development of spinal pathways from hindbrain V2a neurons and the role of these pathways in the development of locomotion. We found that new projections are continually layered laterally to existing neuropil, and give rise to distinct pathways that function in parallel to existing pathways. Across these chronologically layered pathways, the connectivity patterns and biophysical properties vary systematically to support a behavioral repertoire with a wide range of kinematics and dynamics. Such layering of new parallel circuits equipped with systematically changing properties may be central to the postnatal diversification and increasing sophistication of an animal{\textquoteright}s behavioral repertoire.

}, issn = {2050-084X}, doi = {10.7554/eLife.42135}, author = {Pujala, Avinash and Koyama, Minoru} } @article {65379, title = {CLADES: a programmable sequence of reporters for lineage analysis}, journal = {bioRxiv}, year = {2019}, month = {2019 May 30}, abstract = {

We present CLADES (Cell Lineage Access Driven by an Edition Sequence), a technology for cell lineage studies based on CRISPR/Cas9. CLADES relies on a system of genetic switches to activate and inactivate reporter genes in a pre-determined order. Targeting CLADES to progenitor cells allows the progeny to inherit a sequential cascade of reporters, coupling birth order with reporter expression. This gives us temporal resolution of lineage development that can be used to deconstruct an extended cell lineage by tracking the reporters expressed in the progeny. When targeted to the germ line, the same cascade progresses across animal generations, marking each generation with the corresponding combination of reporters. CLADES thus offers an innovative strategy for making programmable cascades of genes that can be used for genetic manipulation or to record serial biological events.

}, doi = {https://doi.org/10.1101/655308}, author = {Garcia-Marques, Jorge and Yang, Ching-Po and Isabel Espinosa Medina and Koyama, Minoru and Lee, Tzumin} } @article {65082, title = {Comparing 3D ultrastructure of presynaptic and postsynaptic mitochondria.}, journal = {Biology Open}, volume = {8}, year = {2019}, month = {2019 Aug 01}, abstract = {

Serial-section electron microscopy such as FIB-SEM (focused ion beam scanning electron microscopy) has become an important tool for neuroscientists to trace the trajectories and global architecture of neural circuits in the brain, as well as to visualize the 3D ultrastructure of cellular organelles in neurons. In this study, we examined 3D features of mitochondria in electron microscope images generated from serial sections of four regions of mouse brains: nucleus accumbens (NA), hippocampal CA1, somatosensory cortex and dorsal cochlear nucleus (DCN). We compared mitochondria in the presynaptic terminals to those in the postsynaptic/dendritic compartments, and we focused on the shape and size of mitochondria. A common feature of mitochondria among the four brain regions is that presynaptic mitochondria generally are small and short, and most of them do not extend beyond presynaptic terminals. In contrast, the majority of postsynaptic/dendritic mitochondria are large and many of them spread through significant portions of the dendrites. Comparing among the brain areas, the cerebral cortex and DCN have even larger postsynaptic/dendritic mitochondria than the NA and CA1. Our analysis reveals that mitochondria in neurons are differentially sized and arranged according to their subcellular locations, suggesting a spatial organizing principle of mitochondria at the synapse.

}, issn = {2046-6390}, doi = {10.1242/bio.044834}, author = {Delgado, Thomas and Petralia, Ronald S and Freeman, David W and Sedlacek, Miloslav and Wang, Ya-Xian and Brenowitz, Stephan D and Sheu, Shu-Hsien and Gu, Jeffrey W and Kapogiannis, Dimitrios and Mattson, Mark P and Yao, Pamela J} } @article {51252, title = {Comparisons between the ON- and OFF-edge motion pathways in the brain.}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Jan 09}, abstract = {

Understanding the circuit mechanisms behind motion detection is a long-standing question in visual neuroscience. In , recent synapse-level connectomes in the optic lobe, particularly in ON-pathway (T4) receptive-field circuits, in concert with physiological studies, suggest an increasingly intricate motion model compared with the ubiquitous Hassenstein-Reichardt model, while our knowledge of OFF-pathway (T5) has been incomplete. Here we present a conclusive and comprehensive connectome that for the first time integrates detailed connectivity information for inputs to both T4 and T5 pathways in a single EM dataset covering the entire optic lobe. With novel reconstruction methods using automated synapse prediction suited to such a large connectome, we successfully corroborate previous findings in the T4 pathway and comprehensively identify inputs and receptive fields for T5. While the two pathways are likely evolutionarily linked and indeed exhibit many similarities, we uncover interesting differences and interactions that may underlie their distinct functional properties.

}, issn = {2050-084X}, doi = {10.7554/eLife.40025}, author = {Shinomiya, Kazunori and Huang, Gary and Lu, Zhiyuan and Parag, Toufiq and Xu, C Shan and Aniceto, Roxanne and Ansari, Namra and Cheatham, Natasha and Lauchie, Shirley and Neace, Erika and Ogundeyi, Omotara and Ordish, Christopher and Peel, David and Shinomiya, Aya and Smith, Claire and Takemura, Satoko and Talebi, Iris and Rivlin, Patricia K and Nern, Aljoscha and Scheffer, Louis K and Plaza, Stephen M and Meinertzhagen, Ian A} } @article {65246, title = {The computation of directional selectivity in the OFF motion pathway.}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Dec 11}, abstract = {

In flies, the direction of moving ON and OFF features is computed separately. T4 (ON) and T5 (OFF) are the first neurons in their respective pathways to extract a directionally selective response from their non-selective inputs. Our recent study of T4 found that the integration of offset depolarizing and hyperpolarizing inputs is critical for the generation of directional selectivity. However, T5s lack small-field inhibitory inputs, suggesting they may use a different mechanism. Here we used whole-cell recordings of T5 neurons and found a similar receptive field structure: fast depolarization and persistent, spatially offset hyperpolarization. By assaying pairwise interactions of local stimulation across the receptive field, we found no amplifying responses, only suppressive responses to the non-preferred motion direction. We then evaluated passive, biophysical models and found that a model using direct inhibition, but not the removal of excitation, can accurately predict T5 responses to a range of moving stimuli.

}, issn = {2050-084X}, doi = {10.7554/eLife.50706}, author = {Gruntman, Eyal and Romani, Sandro and Reiser, Michael B} } @inbook {65065, title = {Computational methods for stitching, alignment, and artifact correction of serial section data.}, booktitle = {Methods in Cell Biology}, volume = {152}, year = {2019}, pages = {261 - 276}, publisher = {Elsevier}, organization = {Elsevier}, abstract = {

Imaging large samples at the resolution offered by\ electron microscopy\ is typically achieved by sequentially recording overlapping tiles that are later combined to seamless\ mosaics. Mosaics of serial sections are aligned to reconstruct three-dimensional volumes. To achieve this, image distortions and artifacts as introduced during sample preparation or imaging need to be removed.

In this chapter, we will discuss typical sources of artifacts and distortion, and we will learn how to use the open source software TrakEM2 to correct them.

}, isbn = {9780128170182}, issn = {0091679X}, doi = {10.1016/bs.mcb.2019.04.007}, url = {https://doi.org/10.1016/bs.mcb.2019.04.007}, author = {Saalfeld, Stephan} } @article {65179, title = {Computational neuroethology: A call to action.}, journal = {Neuron}, volume = {104}, year = {2019}, month = {2019 Oct 09}, pages = {11-24}, abstract = {

The brain is worthy of study because it is in charge of behavior. A flurry of recent technical advances in measuring and quantifying naturalistic behaviors provide an important opportunity for advancing brain science. However, the problem of understanding unrestrained behavior in the context of neural recordings and manipulations remains unsolved, and developing approaches to addressing this challenge is critical. Here we discuss considerations in computational neuroethology-the science of quantifying naturalistic behaviors for understanding the brain-and propose strategies to evaluate progress. We point to open questions that require resolution and call upon the broader systems neuroscience community to further develop and leverage measures of naturalistic, unrestrained behavior, which will enable us to more effectively probe the richness and complexity of the brain.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2019.09.038}, author = {Datta, Sandeep Robert and Anderson, David J and Branson, Kristin and Perona, Pietro and Leifer, Andrew} } @article {65128, title = {Constraining computational models using electron microscopy wiring diagrams.}, journal = {Current Opinion in Neurobiology}, volume = {58}, year = {2019}, month = {2019 Aug 27}, pages = {94-100}, abstract = {

Numerous efforts to generate "connectomes," or synaptic wiring diagrams, of large neural circuits or entire nervous systems are currently underway. These efforts promise an abundance of data to guide theoretical models of neural computation and test their predictions. However, there is not yet a standard set of tools for incorporating the connectivity constraints that these datasets provide into the models typically studied in theoretical neuroscience. This article surveys recent approaches to building models with constrained wiring diagrams and the insights they have provided. It also describes challenges and the need for new techniques to scale these approaches to ever more complex datasets.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2019.07.007}, author = {Litwin-Kumar, Ashok and Turaga, Srinivas C} } @article {51795, title = {Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution.}, journal = {Science (New York, N.Y.)}, volume = {363}, year = {2019}, month = {2019 Jan 18}, pages = {eaau8302}, abstract = {

Optical and electron microscopy have made tremendous inroads toward understanding the complexity of the brain. However, optical microscopy offers insufficient resolution to reveal subcellular details, and electron microscopy lacks the throughput and molecular contrast to visualize specific molecular constituents over millimeter-scale or larger dimensions. We combined expansion microscopy and lattice light-sheet microscopy to image the nanoscale spatial relationships between proteins across the thickness of the mouse cortex or the entire\ Drosophila\ brain. These included synaptic proteins at dendritic spines, myelination along axons, and presynaptic densities at dopaminergic neurons in every fly brain region. The technology should enable statistically rich, large-scale studies of neural development, sexual dimorphism, degree of stereotypy, and structural correlations to behavior or neural activity, all with molecular contrast.

}, doi = {10.1126/science.aau8302}, author = {Gao, Ruixuan and Asano, Shoh M and Upadhyayula, Srigokul and Pisarev, Igor and Milkie, Daniel E and Liu, Tsung-Li and Singh, Ved and Graves, Austin R and Huynh, Grace H and Zhao, Yongxin and Bogovic, John A and Colonell, Jennifer and Ott, Carolyn M and Zugates, Christopher T and Tappan, Susan and Rodriguez, Alfredo and Mosaliganti, Kishore R and Sheu, Shu-Hsien and Pasolli, H Amalia and et al} } @article {64833, title = {Cryo-EM fibril structures from systemic AA amyloidosis reveal the species complementarity of pathological amyloids.}, journal = {Nature Communications}, volume = {10}, year = {2019}, month = {2019 Mar 07}, pages = {1104}, abstract = {

Systemic AA amyloidosis is a worldwide occurring protein misfolding disease of humans and animals. It arises from the formation of amyloid fibrils from the acute phase protein serum amyloid A. Here, we report the purification and electron cryo-microscopy analysis of amyloid fibrils from a mouse and a human patient with systemic AA amyloidosis. The obtained resolutions are 3.0 {\r A} and 2.7 {\r A} for the murine and human fibril, respectively. The two fibrils differ in fundamental properties, such as presence of right-hand or left-hand twisted cross-β sheets and overall fold of the fibril proteins. Yet, both proteins adopt highly similar β-arch conformations within the N-terminal ~21 residues. Our data demonstrate the importance of the fibril protein N-terminus for the stability of the analyzed amyloid fibril morphologies and suggest strategies of combating this disease by interfering with specific fibril polymorphs.

}, issn = {2041-1723}, doi = {10.1038/s41467-019-09033-z}, author = {Liberta, Falk and Loerch, Sarah and Rennegarbe, Matthies and Schierhorn, Angelika and Westermark, Per and Westermark, Gunilla T and Hazenberg, Bouke P C and Grigorieff, Nikolaus and F{\"a}ndrich, Marcus and Schmidt, Matthias} } @article {51793, title = {Cryo-EM of retinoschisin branched networks suggests an intercellular adhesive scaffold in the retina.}, journal = {The Journal of Cell Biology}, volume = {218}, year = {2019}, month = {2019 Jan 10}, pages = {1027-38}, abstract = {

Mutations in the retinal protein retinoschisin (RS1) cause progressive loss of vision in young males, a form of macular degeneration called X-linked retinoschisis (XLRS). We previously solved the structure of RS1, a 16-mer composed of paired back-to-back octameric rings. Here, we show by cryo-electron microscopy that RS1 16-mers can assemble into extensive branched networks. We classified the different configurations, finding four types of interaction between the RS1 molecules. The predominant configuration is a linear strand with a wavy appearance. Three less frequent types constitute the branch points of the network. In all cases, the "spikes" around the periphery of the double rings are involved in these interactions. In the linear strand, a loop (usually referred to as spike 1) occurs on both sides of the interface between neighboring molecules. Mutations in this loop suppress secretion, indicating the possibility of intracellular higher-order assembly. These observations suggest that branched networks of RS1 may play a stabilizing role in maintaining the integrity of the retina.

}, issn = {1540-8140}, doi = {10.1083/jcb.201806148}, author = {Heymann, J Bernard and Vijayasarathy, Camasamudram and Huang, Rick K and Dearborn, Altaira D and Sieving, Paul A and Steven, Alasdair C} } @article {64782, title = {Cryo-EM structure of the homohexameric T3SS ATPase-central stalk complex reveals rotary ATPase-like asymmetry.}, journal = {Nature Communications}, volume = {10}, year = {2019}, month = {2019 Feb 07}, pages = {626}, abstract = {

Many Gram-negative bacteria, including causative agents of dysentery, plague, and typhoid fever, rely on a type III secretion system - a multi-membrane spanning syringe-like apparatus - for their pathogenicity. The cytosolic ATPase complex of this injectisome is proposed to play an important role in energizing secretion events and substrate recognition. We present the 3.3 {\r A} resolution cryo-EM structure of the enteropathogenic Escherichia coli ATPase EscN in complex with its central stalk EscO. The structure shows an asymmetric pore with different functional states captured in its six catalytic sites, details directly supporting a rotary catalytic mechanism analogous to that of the heterohexameric F/V-ATPases despite its homohexameric nature. Situated at the C-terminal opening of the EscN pore is one molecule of EscO, with primary interaction mediated through an electrostatic interface. The EscN-EscO structure provides significant atomic insights into how the ATPase contributes to type III secretion, including torque generation and binding of chaperone/substrate complexes.

}, issn = {2041-1723}, doi = {10.1038/s41467-019-08477-7}, author = {Majewski, Dorothy D and Worrall, Liam J and Hong, Chuan and Atkinson, Claire E and Vuckovic, Marija and Watanabe, Nobuhiko and Yu, Zhiheng and Strynadka, Natalie C J} } @article {65211, title = {Cryo-EM structure of the human FLCN-FNIP2-Rag-Ragulator complex.}, journal = {Cell}, volume = {179}, year = {2019}, month = {2019 Nov 27}, pages = {1319-29}, issn = {00928674}, doi = {10.1016/j.cell.2019.10.036}, author = {Shen, Kuang and Rogala, Kacper B. and Chou, Hui-Ting and Huang, Rick K. and Yu, Zhiheng and Sabatini, David M.} } @article {64831, title = {Cytoskeletal actin patterns shape mast cell activation.}, journal = {Communications Biology}, volume = {2}, year = {2019}, month = {2019}, pages = {93}, abstract = {

Activation of immune cells relies on a dynamic actin cytoskeleton. Despite detailed knowledge of molecular actin assembly, the exact processes governing actin organization during activation remain elusive. Using advanced microscopy, we here show that Rat Basophilic Leukemia (RBL) cells, a model mast cell line, employ an orchestrated series of reorganization events within the cortical actin network during activation. In response to IgE antigen-stimulation of FCε receptors (FCεR) at the RBL cell surface, we observed symmetry breaking of the F-actin network and subsequent rapid disassembly of the actin cortex. This was followed by a reassembly process that may be driven by the coordinated transformation of distinct nanoscale F-actin architectures, reminiscent of self-organizing actin patterns. Actin patterns co-localized with zones of Arp2/3 nucleation, while network reassembly was accompanied by myosin-II activity. Strikingly, cortical actin disassembly coincided with zones of granule secretion, suggesting that cytoskeletal actin patterns contribute to orchestrate RBL cell activation.

}, issn = {2399-3642}, doi = {10.1038/s42003-019-0322-9}, author = {Colin-York, Huw and Li, Dong and Korobchevskaya, Kseniya and Chang, Veronica T and Betzig, Eric and Eggeling, Christian and Fritzsche, Marco} } @article {64852, title = {Cytoskeletal control of antigen-dependent T cell activation.}, journal = {Cell Reports}, volume = {26}, year = {2019}, month = {2019 Mar 19}, pages = {3369-3379.e5}, abstract = {

Cytoskeletal actin dynamics is essential for T\ cell activation. Here, we show evidence that the binding kinetics of the antigen engaging the T\ cell receptor influences the nanoscale actin organization and mechanics of the immune synapse. Using an engineered T\ cell system expressing a specific T\ cell receptor and stimulated by a range of antigens, we found that the peak force experienced by the T\ cell receptor during activation was independent of the unbinding kinetics of the stimulating antigen. Conversely, quantification of the actin retrograde flow velocity at the synapse revealed a striking dependence on the antigen unbinding kinetics. These findings suggest that the dynamics of the actin cytoskeleton actively adjusted to normalize the force experienced by the T\ cell receptor in an antigen-specific manner. Consequently, tuning actin dynamics in response to antigen kinetics may thus\ be a mechanism that allows T\ cells to adjust the lengthscale and timescale of T\ cell receptor signaling.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2019.02.074}, author = {Colin-York, Huw and Javanmardi, Yousef and Skamrahl, Mark and Kumari, Sudha and Chang, Veronica T and Khuon, Satya and Taylor, Aaron and Chew, Teng-Leong and Betzig, Eric and Moeendarbary, Emad and Cerundolo, Vincenzo and Eggeling, Christian and Fritzsche, Marco} } @article {64918, title = {De novo design of tunable, pH-driven conformational changes.}, journal = {Science}, volume = {364}, year = {2019}, month = {2019 May 17}, pages = {658-64}, abstract = {

The ability of naturally occurring proteins to change conformation in response to environmental changes is critical to biological function. Although there have been advances in the de novo design of stable proteins with a single, deep free-energy minimum, the design of conformational switches remains challenging. We present a general strategy to design pH-responsive protein conformational changes by precisely preorganizing histidine residues in buried hydrogen-bond networks. We design homotrimers and heterodimers that are stable above pH 6.5 but undergo cooperative, large-scale conformational changes when the pH is lowered and electrostatic and steric repulsion builds up as the network histidine residues become protonated. The transition pH and cooperativity can be controlled through the number of histidine-containing networks and the strength of the surrounding hydrophobic interactions. Upon disassembly, the designed proteins disrupt lipid membranes both in vitro and after being endocytosed in mammalian cells. Our results demonstrate that environmentally triggered conformational changes can now be programmed by de novo protein design.

}, doi = {10.1126/science.aav7897}, author = {Boyken, Scott E and Benhaim, Mark A and Busch, Florian and Jia, Mengxuan and Back, Matthew J and Choi, Heejun and Klima, Jason C and Chen, Zibo and Walkey, Carl and Mileant, Alexander and Sahasrabuddhe, Aniruddha and Wei, Kathy Y and Hodge, Edgar A and Byron, Sarah and Quijano-Rubio, Alfredo and Sankaran, Banumathi and King, Neil P and Lippincott-Schwartz, Jennifer and Wysocki, Vicki H and et al} } @article {64546, title = {Determining the pharmacokinetics of nicotinic drugs in the endoplasmic reticulum using biosensors.}, journal = {The Journal of General Physiology}, year = {2019}, month = {2019 Feb 04}, abstract = {

Nicotine dependence is thought to arise in part because nicotine permeates into the endoplasmic reticulum (ER), where it binds to nicotinic receptors (nAChRs) and begins an "inside-out" pathway that leads to up-regulation of nAChRs on the plasma membrane. However, the dynamics of nicotine entry into the ER are unquantified. Here, we develop a family of genetically encoded fluorescent biosensors for nicotine, termed iNicSnFRs. The iNicSnFRs are fusions between two proteins: a circularly permutated GFP and a periplasmic choline-/betaine-binding protein engineered to bind nicotine. The biosensors iNicSnFR3a and iNicSnFR3b respond to nicotine by increasing fluorescence at [nicotine] \<1 {\textmu}M, the concentration in the plasma and cerebrospinal fluid of a smoker. We target iNicSnFR3 biosensors either to the plasma membrane or to the ER and measure nicotine kinetics in HeLa, SH-SY5Y, N2a, and HEK293 cell lines, as well as mouse hippocampal neurons and human stem cell-derived dopaminergic neurons. In all cell types, we find that nicotine equilibrates in the ER within 10 s (possibly within 1 s) of extracellular application and leaves as rapidly after removal from the extracellular solution. The [nicotine] in the ER is within twofold of the extracellular value. We use these data to run combined pharmacokinetic and pharmacodynamic simulations of human smoking. In the ER, the inside-out pathway begins when nicotine becomes a stabilizing pharmacological chaperone for some nAChR subtypes, even at concentrations as low as \~{}10 nM. Such concentrations would persist during the 12 h of a typical smoker{\textquoteright}s day, continually activating the inside-out pathway by \>75\%. Reducing nicotine intake by 10-fold decreases activation to \~{}20\%. iNicSnFR3a and iNicSnFR3b also sense the smoking cessation drug varenicline, revealing that varenicline also permeates into the ER within seconds. Our iNicSnFRs enable optical subcellular pharmacokinetics for nicotine and varenicline during an early event in the inside-out pathway.

}, issn = {1540-7748}, doi = {10.1085/jgp.201812201}, author = {Shivange, Amol V and Borden, Philip M and Muthusamy, Anand K and Nichols, Aaron L and Bera, Kallol and Bao, Huan and Bishara, Ishak and Jeon, Janice and Mulcahy, Matthew J and Cohen, Bruce and O{\textquoteright}Riordan, Saidhbhe L and Kim, Charlene and Dougherty, Dennis A and Chapman, Edwin R and Marvin, Jonathan and Looger, Loren and Lester, Henry A} } @article {64783, title = {Determining the pharmacokinetics of nicotinic drugs in the endoplasmic reticulum using biosensors.}, journal = {The Journal of General Physiology}, volume = {151}, year = {2019}, month = {2019 Feb 04}, pages = {738-57}, abstract = {

Nicotine dependence is thought to arise in part because nicotine permeates into the endoplasmic reticulum (ER), where it binds to nicotinic receptors (nAChRs) and begins an "inside-out" pathway that leads to up-regulation of nAChRs on the plasma membrane. However, the dynamics of nicotine entry into the ER are unquantified. Here, we develop a family of genetically encoded fluorescent biosensors for nicotine, termed iNicSnFRs. The iNicSnFRs are fusions between two proteins: a circularly permutated GFP and a periplasmic choline-/betaine-binding protein engineered to bind nicotine. The biosensors iNicSnFR3a and iNicSnFR3b respond to nicotine by increasing fluorescence at [nicotine] \<1 {\textmu}M, the concentration in the plasma and cerebrospinal fluid of a smoker. We target iNicSnFR3 biosensors either to the plasma membrane or to the ER and measure nicotine kinetics in HeLa, SH-SY5Y, N2a, and HEK293 cell lines, as well as mouse hippocampal neurons and human stem cell-derived dopaminergic neurons. In all cell types, we find that nicotine equilibrates in the ER within 10 s (possibly within 1 s) of extracellular application and leaves as rapidly after removal from the extracellular solution. The [nicotine] in the ER is within twofold of the extracellular value. We use these data to run combined pharmacokinetic and pharmacodynamic simulations of human smoking. In the ER, the inside-out pathway begins when nicotine becomes a stabilizing pharmacological chaperone for some nAChR subtypes, even at concentrations as low as \~{}10 nM. Such concentrations would persist during the 12 h of a typical smoker{\textquoteright}s day, continually activating the inside-out pathway by \>75\%. Reducing nicotine intake by 10-fold decreases activation to \~{}20\%. iNicSnFR3a and iNicSnFR3b also sense the smoking cessation drug varenicline, revealing that varenicline also permeates into the ER within seconds. Our iNicSnFRs enable optical subcellular pharmacokinetics for nicotine and varenicline during an early event in the inside-out pathway.

}, issn = {1540-7748}, doi = {10.1085/jgp.201812201}, author = {Shivange, Amol V and Borden, Philip M and Muthusamy, Anand K and Nichols, Aaron L and Bera, Kallol and Bao, Huan and Bishara, Ishak and Jeon, Janice and Mulcahy, Matthew J and Cohen, Bruce and O{\textquoteright}Riordan, Saidhbhe L and Kim, Charlene and Dougherty, Dennis A and Chapman, Edwin R and Marvin, Jonathan and Looger, Loren and Lester, Henry A} } @article {68993, title = {Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules.}, journal = {Cell Stem Cell}, volume = {24}, year = {2019}, month = {02/2019}, pages = {328-341.e9}, abstract = {

The epigenetic dynamics of induced pluripotent stem cell (iPSC) reprogramming in correctly reprogrammed cells at high resolution and throughout the entire process remain largely undefined. Here, we characterize conversion of mouse fibroblasts into iPSCs using Gatad2a-Mbd3/NuRD-depleted and highly efficient reprogramming systems. Unbiased high-resolution profiling of dynamic changes in levels of gene expression, chromatin engagement, DNA accessibility, and DNA methylation were obtained. We identified two distinct and synergistic transcriptional modules that dominate successful reprogramming, which are associated with cell identity and biosynthetic genes. The pluripotency module is governed by dynamic alterations in epigenetic modifications to promoters and binding by Oct4, Sox2, and Klf4, but not Myc. Early DNA demethylation at certain enhancers prospectively marks cells fated to reprogram. Myc activity drives expression of the essential biosynthetic module and is associated with optimized changes in tRNA codon usage. Our functional validations highlight interweaved epigenetic- and Myc-governed essential reconfigurations that rapidly commission and propel deterministic reprogramming toward naive pluripotency.

}, keywords = {Animals, Cell Lineage, Cellular Reprogramming, Chromatin, Demethylation, Epigenesis, Genetic, Humans, Induced Pluripotent Stem Cells, Kruppel-Like Factor 4, Mice, Protein Binding, Proto-Oncogene Proteins c-myc, RNA, Transfer, Transcription Factors, Transcription, Genetic}, issn = {1875-9777}, doi = {10.1016/j.stem.2018.11.014}, author = {Zviran, Asaf and Mor, Nofar and Rais, Yoach and Gingold, Hila and Peles, Shani and Chomsky, Elad and Viukov, Sergey and Buenrostro, Jason D and Scognamiglio, Roberta and Weinberger, Leehee and Manor, Yair S and Krupalnik, Vladislav and Zerbib, Mirie and Hezroni, Hadas and Jaitin, Diego Adhemar and Larastiaso, David and Gilad, Shlomit and Benjamin, Sima and Gafni, Ohad and Mousa, Awni and Ayyash, Muneef and Sheban, Daoud and Bayerl, Jonathan and Aguilera-Castrejon, Alejandro and Massarwa, Rada and Maza, Itay and Hanna, Suhair and Stelzer, Yonatan and Ulitsky, Igor and Greenleaf, William J and Tanay, Amos and Trumpp, Andreas and Amit, Ido and Pilpel, Yitzhak and Novershtern, Noa and Hanna, Jacob H} } @article {65168, title = {Developmental organization of central neurons in the adult Drosophila ventral nervous system.}, journal = {Journal of Comparative Neurology}, volume = {527}, year = {2019}, month = {2019 Oct 15}, pages = {2573-2598}, abstract = {

We have used MARCM to reveal the adult morphology of the post embryonically produced neurons in the thoracic neuromeres of the Drosophila VNS. The work builds on previous studies of the origins of the adult VNS neurons to describe the clonal organization of the adult VNS. We present data for 58 of 66 postembryonic thoracic lineages, excluding the motor neuron producing lineages (15 and 24) which have been described elsewhere. MARCM labels entire lineages but where both A and B hemilineages survive (e.g., lineages 19, 12, 13, 6, 1, 3, 8, and 11), the two hemilineages can be discriminated and we have described each hemilineage separately. Hemilineage morphology is described in relation to the known functional domains of the VNS neuropil and based on the anatomy we are able to assign broad functional roles for each hemilineage. The data show that in a thoracic hemineuromere, 16 hemilineages are primarily involved in controlling leg movements and walking, 9 are involved in the control of wing movements, and 10 interface between both leg and wing control. The data provide a baseline of understanding of the functional organization of the adult Drosophila VNS. By understanding the morphological organization of these neurons, we can begin to define and test the rules by which neuronal circuits are assembled during development and understand the functional logic and evolution of neuronal networks.

}, issn = {1096-9861}, doi = {10.1002/cne.24690}, author = {Shepherd, David and Sahota, Virender and Court, Robert and Williams, Darren W and Truman, James W} } @article {56202, title = {Developmentally arrested precursors of pontine neurons establish an embryonic blueprint of the Drosophila central complex.}, journal = {Current Biology : CB}, volume = {29}, year = {2019}, month = {2019 Jan 15}, pages = {412-25}, abstract = {

Serial electron microscopic analysis shows that the Drosophila brain at hatching possesses a large fraction of developmentally arrested neurons with a small soma, heterochromatin-rich nucleus, and unbranched axon lacking synapses. We digitally reconstructed all 802 "small undifferentiated" (SU) neurons and assigned them to the known brain lineages. By establishing the coordinates and reconstructing trajectories of the SU neuron tracts, we provide a framework of landmarks for the ongoing analyses of the L1 brain circuitry. To address the later fate of SU neurons, we focused on the 54 SU neurons belonging to the DM1-DM4 lineages, which generate all columnar neurons of the central complex. Regarding their topologically ordered projection pattern, these neurons form an embryonic nucleus of the fan-shaped body ("FB pioneers"). Fan-shaped body pioneers survive into the adult stage, where they develop into a specific class of bi-columnar elements, the pontine neurons. Later born, unicolumnar DM1-DM4 neurons fasciculate with the fan-shaped body pioneers. Selective ablation of the fan-shaped body pioneers altered the architecture of the larval fan-shaped body primordium but did not result in gross abnormalities of the trajectories of unicolumnar neurons, indicating that axonal pathfinding of the two systems may be controlled independently. Our comprehensive spatial and developmental analysis of the SU neurons adds to our understanding of the establishment of neuronal circuitry.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2018.12.012}, author = {Andrade, Ingrid V and Riebli, Nadia and Nguyen, Bao-Chau M and Omoto, Jaison J and Cardona, Albert and Hartenstein, Volker} } @article {65127, title = {Differential nanoscale organisation of LFA-1 modulates T cell migration.}, journal = {Journal of Cell Science}, volume = {132}, year = {2019}, month = {2019 Aug 29}, pages = {1-28}, issn = {0021-9533}, doi = {10.1242/jcs.232991}, url = {http://jcs.biologists.org/lookup/doi/10.1242/jcs.23299}, author = {Shannon, Michael J. and Pineau, Judith and Griffi{\'e}, Juliette and Aaron, Jesse and Peel, Tamlyn and Williamson, David J. and Zamoyska, Rose and Cope, Andrew P. and Cornish, Georgina H. and Owen, Dylan M.} } @article {65043, title = {Direct wavefront sensing enables functional imaging of infragranular axons and spines.}, journal = {Nature Methods}, volume = {16}, year = {2019}, month = {2019 Jul}, pages = {615-618}, abstract = {

We advance two-photon microscopy for near-diffraction-limited imaging up to 850 {\textmu}m below the pia in awake mice. Our approach combines direct wavefront sensing of light from a guidestar (formed by descanned fluorescence from Cy5.5-conjugated dextran in brain microvessels) with adaptive optics to compensate for tissue-induced aberrations in the wavefront. We achieve high signal-to-noise ratios in recordings of glutamate release from thalamocortical axons and calcium transients in spines of layer 5b basal dendrites during active tactile sensing.

}, issn = {1548-7105}, doi = {10.1038/s41592-019-0434-7}, author = {Liu, Rui and Li, Zengyi and Marvin, Jonathan S and Kleinfeld, David} } @article {64781, title = {Discrete attractor dynamics underlies persistent activity in the frontal cortex.}, journal = {Nature}, volume = {566}, year = {2019}, month = {2019 Feb 06}, pages = {212-7}, abstract = {

Short-term memories link events separated in time, such as past sensation and future actions. Short-term memories are correlated with slow neural dynamics, including selective persistent activity, which can be maintained over seconds. In a delayed response task that requires short-term memory, neurons in the mouse anterior lateral motor cortex (ALM) show persistent activity that instructs future actions. To determine the principles that underlie this persistent activity, here we combined intracellular and extracellular electrophysiology with optogenetic perturbations and network modelling. We show that during the delay epoch, the activity of ALM neurons moved towards discrete end points that correspond to specific movement directions. These end points were robust to transient shifts in ALM activity caused by optogenetic perturbations. Perturbations occasionally switched the population dynamics to the other end point, followed by incorrect actions. Our results show that discrete attractor dynamics underlie short-term memory related to motor planning.

}, issn = {1476-4687}, doi = {10.1038/s41586-019-0919-7}, author = {Inagaki, Hidehiko K and Fontolan, Lorenzo and Romani, Sandro and Svoboda, Karel} } @article {65203, title = {Drosulfakinin signaling in fruitless circuitry antagonizes P1 neurons to regulate sexual arousal in Drosophila.}, journal = {Nature Communications}, volume = {10}, year = {2019}, month = {2019 Oct 18}, pages = {4770}, abstract = {

Animals perform or terminate particular behaviors by integrating external cues and internal states through neural circuits. Identifying neural substrates and their molecular modulators promoting or inhibiting animal behaviors are key steps to understand how neural circuits control behaviors. Here, we identify the Cholecystokinin-like peptide Drosulfakinin (DSK) that functions at single-neuron resolution to suppress male sexual behavior in Drosophila. We found that Dsk neurons physiologically interact with male-specific P1 neurons, part of a command center for male sexual behaviors, and function oppositely to regulate multiple arousal-related behaviors including sex, sleep and spontaneous walking. We further found that the DSK-2 peptide functions through its receptor CCKLR-17D3 to suppress sexual behaviors in flies. Such a neuropeptide circuit largely overlaps with the fruitless-expressing neural circuit that governs most aspects of male sexual behaviors. Thus DSK/CCKLR signaling in the sex circuitry functions antagonistically with P1 neurons to balance arousal levels and modulate sexual behaviors.

}, issn = {2041-1723}, doi = {10.1038/s41467-019-12758-6}, author = {Wu, Shunfan and Guo, Chao and Zhao, Huan and Sun, Mengshi and Chen, Jie and Han, Caihong and Peng, Qionglin and Qiao, Huanhuan and Peng, Ping and Liu, Yan and Luo, Shengzhan D and Pan, Yufeng} } @article {65241, title = {Dual-plane 3-photon microscopy with remote focusing.}, journal = {Biomedical Optics Express}, volume = {10}, year = {2019}, month = {2019 Nov 1}, pages = {5585-5599}, abstract = {

3-photon excitation enables fluorescence microscopy deep in densely labeled and highly scattering samples. To date, 3-photon excitation has been restricted to scanning a single focus, limiting the speed of volume acquisition. Here, for the first time to our knowledge, we implemented and characterized dual-plane 3-photon microscopy with temporal multiplexing and remote focusing, and performed simultaneous calcium imaging of two planes beyond 600 {\textmu}m deep in the cortex of a pan-excitatory GCaMP6s transgenic mouse with a per-plane framerate of 7 Hz and an effective 2 MHz laser repetition rate. This method is a straightforward and generalizable modification to single-focus 3PE systems, doubling the rate of volume (column) imaging with off-the-shelf components and minimal technical constraints.

}, issn = {2156-7085}, doi = {10.1364/BOE.10.005585}, author = {Takasaki, Kevin T and Tsyboulski, Dmitri and Waters, Jack} } @article {64542, title = {DVID: Distributed versioned image-oriented dataservice.}, journal = {Frontiers in Neural Circuits}, volume = {13}, year = {2019}, month = {2019 Feb 05}, abstract = {

Open-source software development has skyrocketed in part due to community tools like github.com, which allows publication of code as well as the ability to create branches and push accepted modifications back to the original repository. As the number and size of EM-based datasets increases, the connectomics community faces similar issues when we publish snapshot data corresponding to a publication. Ideally, there would be a mechanism where remote collaborators could modify branches of the data and then flexibly reintegrate results via moderated acceptance of changes. The DVID system provides a web-based connectomics API and the first steps toward such a distributed versioning approach to EM-based connectomics datasets. Through its use as the central data resource for Janelia{\textquoteright}s FlyEM team, we have integrated the concepts of distributed versioning into reconstruction workflows, allowing support for proofreader training and segmentation experiments through branched, versioned data. DVID also supports persistence to a variety of storage systems from high-speed local SSDs to cloud-based object stores, which allows its deployment on laptops as well as large servers. The tailoring of the backend storage to each type of connectomics data leads to efficient storage and fast queries. DVID is freely available as open-source software with an increasing number of supported storage options.

}, doi = {10.3389/fncir.2019.00005}, author = {Katz, William T and Plaza, Stephen M} } @article {64889, title = {Dynamic super-resolution structured illumination imaging in the living brain.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, year = {2019}, month = {2019 Apr 26}, pages = {9586-91}, abstract = {

Cells in the brain act as components of extended networks. Therefore, to understand neurobiological processes in a physiological context, it is essential to study them in vivo. Super-resolution microscopy has spatial resolution beyond the diffraction limit, thus promising to provide structural and functional insights that are not accessible with conventional microscopy. However, to apply it to in vivo brain imaging, we must address the challenges of 3D imaging in an optically heterogeneous tissue that is constantly in motion. We optimized image acquisition and reconstruction to combat sample motion and applied adaptive optics to correcting sample-induced optical aberrations in super-resolution structured illumination microscopy (SIM) in vivo. We imaged the brains of live zebrafish larvae and mice and observed the dynamics of dendrites and dendritic spines at nanoscale resolution.

}, issn = {1091-6490}, doi = {10.1073/pnas.1819965116}, author = {Turcotte, Raphael and Liang, Yajie and Tanimoto, Masashi and Zhang, Qinrong and Li, Ziwei and Koyama, Minoru and Betzig, Eric and Ji, Na} } @article {64797, title = {Dystroglycan is a scaffold for extracellular axon guidance decisions.}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Feb 13}, abstract = {

Axon guidance requires interactions between extracellular signaling molecules and transmembrane receptors, but how appropriate context-dependent decisions are coordinated outside the cell remains unclear. Here we show that the transmembrane glycoprotein Dystroglycan interacts with a changing set of environmental cues that regulate the trajectories of extending axons throughout the mammalian brain and spinal cord. Dystroglycan operates primarily as an extracellular scaffold during axon guidance, as it functions non-cell autonomously and does not require signaling through its intracellular domain. We identify the transmembrane receptor Celsr3/Adgrc3 as a binding partner for Dystroglycan, and show that this interaction is critical for specific axon guidance events . These findings establish Dystroglycan as a multifunctional scaffold that coordinates extracellular matrix proteins, secreted cues, and transmembrane receptors to regulate axon guidance.

}, issn = {2050-084X}, doi = {10.7554/eLife.42143}, author = {Lindenmaier, L Bailey and Parmentier, Nicolas and Guo, Caiying and Tissir, Fadel and Wright, Kevin M} } @article {65115, title = {Effective dimensionality reduction for visualizing neural dynamics by laplacian eigenmaps.}, journal = {Neural Computation}, volume = {31}, year = {2019}, month = {2019 Jul}, pages = {1356-1379}, abstract = {

With the development of neural recording technology, it has become possible to collect activities from hundreds or even thousands of neurons simultaneously. Visualization of neural population dynamics can help neuroscientists analyze large-scale neural activities efficiently. In this letter, Laplacian eigenmaps is applied to this task for the first time, and the experimental results show that the proposed method significantly outperforms the commonly used methods. This finding was confirmed by the systematic evaluation using nonhuman primate data, which contained the complex dynamics well suited for testing. According to our results, Laplacian eigenmaps is better than the other methods in various ways and can clearly visualize interesting biological phenomena related to neural dynamics.

}, issn = {1530-888X}, doi = {10.1162/neco_a_01203}, author = {Sun, G and Zhang, S and Zhang, Y and Xu, K and Zhang, Q and Zhao, T and Zheng, X} } @article {64875, title = {Enabling cell-type-specific behavioral epigenetics in Drosophila: a modified high-yield INTACT method reveals the impact of social environment on the epigenetic landscape in dopaminergic neurons.}, journal = {BMC Biology}, volume = {17}, year = {2019}, month = {2019 Apr 10}, pages = {30}, abstract = {

BACKGROUND: Epigenetic mechanisms play fundamental roles in brain function and behavior and stressors such as social isolation can alter animal behavior via epigenetic mechanisms. However, due to cellular heterogeneity, identifying cell-type-specific epigenetic changes in the brain is challenging. Here, we report the first use of a modified isolation of nuclei tagged in specific cell type (INTACT) method in behavioral epigenetics of Drosophila melanogaster, a method we call mini-INTACT.

RESULTS: Using ChIP-seq on mini-INTACT purified dopaminergic nuclei, we identified epigenetic signatures in socially isolated and socially enriched Drosophila males. Social experience altered the epigenetic landscape in clusters of genes involved in transcription and neural function. Some of these alterations could be predicted by expression changes of four transcription factors and the prevalence of their binding sites in several clusters. These transcription factors were previously identified as activity-regulated genes, and their knockdown in dopaminergic neurons reduced the effects of social experience on sleep.

CONCLUSIONS: Our work enables the use of Drosophila as a model for cell-type-specific behavioral epigenetics and establishes that social environment shifts the epigenetic landscape in dopaminergic neurons. Four activity-related transcription factors are required in dopaminergic neurons for the effects of social environment on sleep.

}, issn = {1741-7007}, doi = {10.1186/s12915-019-0646-4}, author = {Agrawal, Pavan and Chung, Phuong and Heberlein, Ulrike and Kent, Clement} } @article {65114, title = {Evolution of embryonic cis-regulatory landscapes between divergent Phallusia and Ciona ascidians.}, journal = {Developmental Biology}, volume = {448}, year = {2019}, month = {2019 Apr 15}, pages = {71-87}, abstract = {

Ascidian species of the Phallusia and Ciona genera are distantly related, their last common ancestor dating several hundred million years ago. Although their genome sequences have extensively diverged since this radiation, Phallusia and Ciona species share almost identical early morphogenesis and stereotyped cell lineages. Here, we explored the evolution of transcriptional control between P. mammillata and C. robusta. We combined genome-wide mapping of open chromatin regions in both species with a comparative analysis of the regulatory sequences of a test set of 10 pairs of orthologous early regulatory genes with conserved expression patterns. We find that ascidian chromatin accessibility landscapes obey similar rules as in other metazoa. Open-chromatin regions are short, highly conserved within each genus and cluster around regulatory genes. The dynamics of chromatin accessibility and closest-gene expression are strongly correlated during early embryogenesis. Open-chromatin regions are highly enriched in cis-regulatory elements: 73\% of 49 open chromatin regions around our test genes behaved as either distal enhancers or proximal enhancer/promoters following electroporation in Phallusia eggs. Analysis of this datasets suggests a pervasive use in ascidians of "shadow" enhancers with partially overlapping activities. Cross-species electroporations point to a deep conservation of both the trans-regulatory logic between these distantly-related ascidians and the cis-regulatory activities of individual enhancers. Finally, we found that the relative order and approximate distance to the transcription start site of open chromatin regions can be conserved between Ciona and Phallusia species despite extensive sequence divergence, a property that can be used to identify orthologous enhancers, whose regulatory activity can partially diverge.

}, issn = {1095-564X}, doi = {10.1016/j.ydbio.2019.01.003}, author = {Madgwick, Alicia and Magri, Marta Silvia and Dantec, Christelle and Gailly, Damien and Fiuza, Ulla-Maj and Guignard, Leo and Hettinger, Sabrina and Gomez-Skarmeta, Jose Luis and Lemaire, Patrick} } @article {64958, title = {Evolution of Mechanisms that Control Mating in Drosophila Males.}, journal = {Cell Reports}, volume = {27}, year = {2019}, month = {2019 May 28}, pages = {2527-2536.e4}, abstract = {

Genetically wired neural mechanisms inhibit mating between species because even naive animals rarely mate with other species. These mechanisms can evolve through changes in expression or function of key genes in sensory pathways or central circuits. Gr32a is a gustatory chemoreceptor that, in D.\ melanogaster, is essential to inhibit interspecies courtship and sense quinine. Similar to D.\ melanogaster, we find that D.\ simulans Gr32a is expressed in foreleg tarsi, sensorimotor appendages that inhibit interspecies courtship, and it is required to sense quinine. Nevertheless, Gr32a is not required to inhibit interspecies mating by D.\ simulans males. However, and similar to its function in D.\ melanogaster, Ppk25, a member of the Pickpocket family, promotes conspecific courtship in D.\ simulans. Together, we have identified distinct evolutionary mechanisms underlying chemosensory control of taste and courtship in closely related Drosophila species.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2019.04.104}, author = {Ahmed, Osama M and Avila-Herrera, Aram and Tun, Khin May and Serpa, Paula H and Peng, Justin and Parthasarathy, Srinivas and Knapp, Jon-Michael and Stern, David L and Davis, Graeme W and Pollard, Katherine S and Shah, Nirao M} } @article {65110, title = {Expansion microscopy: scalable and convenient super-resolution microscopy.}, journal = {Annual Review of Cell and Developmental Biology}, volume = {35}, year = {2019}, month = {2019 Oct 6}, pages = {683-701}, abstract = {

Expansion microscopy (ExM) is a physical form of magnification that increases the effective resolving power of any microscope. Here, we describe the fundamental principles of ExM, as well as how recently developed ExM variants build upon and apply those principles. We examine applications of ExM in cell and developmental biology for the study of nanoscale structures as well as ExM{\textquoteright}s potential for scalable mapping of nanoscale structures across large sample volumes. Finally, we explore how the unique anchoring and hydrogel embedding properties enable postexpansion molecular interrogation in a purified chemical environment. ExM promises to play an important role complementary to emerging live-cell imaging techniques, because of its relative ease of adoption and modification and its compatibility with tissue specimens up to at least 200 μm thick. Expected final online publication date for the , Volume 35 is October 7, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

}, issn = {1530-8995}, doi = {10.1146/annurev-cellbio-100818-125320}, author = {Tillberg, Paul W and Chen, Fei} } @article {68755, title = {Extracellular matrix dynamics in cell migration, invasion and tissue morphogenesis}, journal = {International Journal of Experimental Pathology}, volume = {100}, year = {2019}, month = {06/2019}, pages = {144-152}, abstract = {

Summary This review describes how direct visualization of the dynamic interactions of cells with different extracellular matrix microenvironments can provide novel insights into complex biological processes. Recent studies have moved characterization of cell migration and invasion from classical 2D culture systems into 1D and 3D model systems, revealing multiple differences in mechanisms of cell adhesion, migration and signalling{\textemdash}even though cells in 3D can still display prominent focal adhesions. Myosin II restrains cell migration speed in 2D culture but is often essential for effective 3D migration. 3D cell migration modes can switch between lamellipodial, lobopodial and/or amoeboid depending on the local matrix environment. For example, {\textquotedblleft}nuclear piston{\textquotedblright} migration can be switched off by local proteolysis, and proteolytic invadopodia can be induced by a high density of fibrillar matrix. Particularly, complex remodelling of both extracellular matrix and tissues occurs during morphogenesis. Extracellular matrix supports self-assembly of embryonic tissues, but it must also be locally actively remodelled. For example, surprisingly focal remodelling of the basement membrane occurs during branching morphogenesis{\textemdash}numerous tiny perforations generated by proteolysis and actomyosin contractility produce a microscopically porous, flexible basement membrane meshwork for tissue expansion. Cells extend highly active blebs or protrusions towards the surrounding mesenchyme through these perforations. Concurrently, the entire basement membrane undergoes translocation in a direction opposite to bud expansion. Underlying this slowly moving 2D basement membrane translocation are highly dynamic individual cell movements. We conclude this review by describing a variety of exciting research opportunities for discovering novel insights into cell-matrix interactions.

}, keywords = {3D culture, basement membrane remodelling, branching morphogenesis, cell migration, Extracellular Matrix, invasion}, doi = {https://doi.org/10.1111/iep.12329}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/iep.12329}, author = {Yamada, Kenneth M. and Collins, Joshua W. and Cruz Walma, David A. and Doyle, Andrew D. and Morales, Shaimar Gonzalez and Lu, Jiaoyang and Matsumoto, Kazue and Nazari, Shayan S. and Sekiguchi, Rei and Shinsato, Yoshinari and Wang, Shaohe} } @article {64959, title = {Fate plasticity and reprogramming in genetically distinct populations of leucophores.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, year = {2019}, month = {2019 Jun 11}, pages = {11806-11}, abstract = {

Understanding genetic and cellular bases of adult form remains a fundamental goal at the intersection of developmental and evolutionary biology. The skin pigment cells of vertebrates, derived from embryonic neural crest, are a useful system for elucidating mechanisms of fate specification, pattern formation, and how particular phenotypes impact organismal behavior and ecology. In a survey of fishes, including the zebrafish , we identified two populations of white pigment cells-leucophores-one of which arises by transdifferentiation of adult melanophores and another of which develops from a yellow-orange xanthophore or xanthophore-like progenitor. Single-cell transcriptomic, mutational, chemical, and ultrastructural analyses of zebrafish leucophores revealed cell-type-specific chemical compositions, organelle configurations, and genetic requirements. At the organismal level, we identified distinct physiological responses of leucophores during environmental background matching, and we showed that leucophore complement influences behavior. Together, our studies reveal independently arisen pigment cell types and mechanisms of fate acquisition in zebrafish and illustrate how concerted analyses across hierarchical levels can provide insights into phenotypes and their evolution.

}, issn = {1091-6490}, doi = {10.1073/pnas.1901021116}, author = {Lewis, Victor M and Saunders, Lauren M and Larson, Tracy A and Bain, Emily J and Sturiale, Samantha L and Gur, Dvir and Chowdhury, Sarwat and Flynn, Jessica D and Allen, Michael C and Deheyn, Dimitri D and Lee, Jennifer C and Simon, Julian A and Lippincott-Schwartz, Jennifer and Raible, David W and Parichy, David M} } @article {65060, title = {The fly brain atlas.}, journal = {Annual Review of Cell and Developmental Biology}, volume = {35}, year = {2019}, month = {2019 Oct 6}, pages = {637-53}, abstract = {

The brain{\textquoteright}s synaptic networks endow an animal with powerfully adaptive biological behavior. Maps of such synaptic circuits densely reconstructed in those model brains, which can be examined and manipulated by genetic means, offer the best prospect for understanding the underlying biological bases of behavior. That prospect is now technologically feasible and a scientifically enabling possibility in neurobiology, much as genomics has been in molecular biology and genetics. In , two major advances are in electron microscopic technology, using focused ion beam-scanning electron microscopy (FIB-SEM) milling to capture and align digital images, and in computer-aided reconstruction of neuron morphologies. The last decade has witnessed enormous progress in detailed knowledge of the actual synaptic circuits formed by real neurons. Advances in various brain regions that heralded identification of the motion-sensing circuits in the optic lobe are now extending to other brain regions, with the prospect of encompassing the fly{\textquoteright}s entire nervous system, both brain and ventral nerve cord. Expected final online publication date for the Volume 35 is October 7, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

}, issn = {1530-8995}, doi = {10.1146/annurev-cellbio-100818-125444}, author = {Scheffer, Louis K and Meinertzhagen, Ian A} } @article {64934, title = {Functional and anatomical specificity in a higher olfactory centre.}, journal = {Elife}, volume = {8}, year = {2019}, month = {2019 May 21}, abstract = {

Most sensory systems are organized into parallel neuronal pathways that process distinct aspects of incoming stimuli. In the insect olfactory system, second order projection neurons target both the mushroom body, required for learning, and the lateral horn (LH), proposed to mediate innate olfactory behavior. Mushroom body neurons form a sparse olfactory population code, which is not stereotyped across animals. In contrast, odor coding in the LH remains poorly understood. We combine genetic driver lines, anatomical and functional criteria to show that the LH has ~1400 neurons and \>165 cell types. Genetically labeled LHNs have stereotyped odor responses across animals and on average respond to three times more odors than single projection neurons. LHNs are better odor categorizers than projection neurons, likely due to stereotyped pooling of related inputs. Our results reveal some of the principles by which a higher processing area can extract innate behavioral significance from sensory stimuli.

}, issn = {2050-084X}, doi = {10.7554/eLife.44590}, author = {Frechter, Shahar and Bates, Alexander Shakeel and Tootoonian, Sina and Dolan, Michael-John and Manton, James D and Jamasb, Arian Rokkum and Kohl, Johannes and Bock, Davi and Jefferis, Gregory Sxe} } @article {65205, title = {Functional clustering of dendritic activity during decision-making.}, journal = {Elife}, volume = {8}, year = {2019}, month = {2019 Oct 30}, abstract = {

The active properties of dendrites can support local nonlinear operations, but previous imaging and electrophysiological measurements have produced conflicting views regarding the prevalence and selectivity of local nonlinearities in vivo. We imaged calcium signals in pyramidal cell dendrites in the motor cortex of mice performing a tactile decision task. A custom microscope allowed us to image the soma and up to 300 μm of contiguous dendrite at 15 Hz, while resolving individual spines. New analysis methods were used to estimate the frequency and spatial scales of activity in dendritic branches and spines. The majority of dendritic calcium transients were coincident with global events. However, task-associated calcium signals in dendrites and spines were compartmentalized by dendritic branching and clustered within branches over approximately 10 μm. Diverse behavior-related signals were intermingled and distributed throughout the dendritic arbor, potentially supporting a large learning capacity in individual neurons.

}, issn = {2050-084X}, doi = {10.7554/eLife.46966}, author = {Kerlin, Aaron and Boaz, Mohar and Flickinger, Daniel and MacLennan, Bryan J and Dean, Matthew B and Davis, Courtney and Spruston, Nelson and Svoboda, Karel} } @article {68431, title = {Functional divergence of Plexin B structural motifs in distinct steps of olfactory circuit assembly.}, journal = {Elife}, volume = {8}, year = {2019}, month = {06/2019}, abstract = {

Plexins exhibit multitudinous, evolutionarily conserved functions in neural development. How Plexins employ their diverse structural motifs in vivo to perform distinct roles is unclear. We previously reported that Plexin B (PlexB) controls multiple steps during the assembly of the olfactory circuit (Li et al., 2018b). Here, we systematically mutagenized structural motifs of PlexB and examined the function of these variants in these multiple steps: axon fasciculation, trajectory choice, and synaptic partner selection. We found that the extracellular Sema domain is essential for all three steps, the catalytic site of the intracellular RapGAP is engaged in none, and the intracellular GTPase-binding motifs are essential for trajectory choice and synaptic partner selection, but are dispensable for fasciculation. Moreover, extracellular PlexB cleavage serves as a regulatory mechanism of PlexB signaling. Thus, the divergent roles of PlexB motifs in distinct steps of neural development contribute to its functional versatility in neural circuit assembly.

}, keywords = {Animals, Animals, Genetically Modified, Axons, Drosophila melanogaster, Drosophila Proteins, Nerve Tissue Proteins, Neurogenesis, Olfactory Bulb, Receptors, Cell Surface, Semaphorins, Signal Transduction, Smell}, issn = {2050-084X}, doi = {10.7554/eLife.48594}, author = {Guajardo, Ricardo and Luginbuhl, David J and Han, Shuo and Luo, Liqun and Li, Jiefu} } @article {65224, title = {Gas cluster ion beam SEM for imaging of large tissue samples with 10 nm isotropic resolution.}, journal = {Nature Methods}, volume = {17}, year = {2019}, month = {2020 Jan 01}, pages = {68-71}, abstract = {

We demonstrate gas cluster ion beam scanning electron microscopy (SEM), in which wide-area ion milling is performed on a series of thick tissue sections. This three-dimensional electron microscopy technique acquires datasets with \<10 nm isotropic resolution of each section, and these can then be stitched together to span the sectioned volume. Incorporating gas cluster ion beam SEM into existing single-beam and multibeam SEM workflows should be straightforward, increasing reliability while improving z resolution by a factor of three or more.

}, issn = {1548-7105}, doi = {10.1038/s41592-019-0641-2}, author = {Hayworth, Kenneth J and Peale, David and Januszewski, Micha{\l} and Knott, Graham W and Lu, Zhiyuan and Xu, C Shan and Hess, Harald F} } @article {64823, title = {GCIB-SEM: A path to 10 nm isotropic imaging of cubic millimeter volumes.}, journal = {bioRxiv}, year = {2019}, month = {2019 Feb 28}, abstract = {Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) generates 3D datasets optimally suited for segmentation of cell ultrastructure and automated connectome tracing but is limited to small fields of view and is therefore incompatible with the new generation of ultrafast multibeam SEMs. In contrast, section-based techniques are multibeam-compatible but are limited in z-resolution making automatic segmentation of cellular ultrastructure difficult. Here we demonstrate a novel 3D electron microscopy technique, Gas Cluster Ion Beam SEM (GCIB-SEM), in which top-down, wide-area ion milling is performed on a series of thick sections, acquiring < 10 nm isotropic datasets of each which are then stitched together to span the full sectioned volume. Based on our results, incorporating GCIB-SEM into existing single beam and multibeam SEM workflows should be straightforward and should dramatically increase reliability while simultaneously improving z-resolution by a factor of 3 or more.}, doi = {10.1101/563239}, author = {Hayworth, Kenneth J and Peale, David R and Januszewski, Michal and Knott, Graham and Lu, Zhiyuan and Xu, C. Shan and Hess, Harald F} } @article {65234, title = {Generation of stable heading representations in diverse visual scenes.}, journal = {Nature}, volume = {576}, year = {2019}, month = {2019 Nov 20}, pages = {126-31}, abstract = {

Many animals rely on an internal heading representation when navigating in varied environments. How this representation is linked to the sensory cues that define different surroundings is unclear. In the fly brain, heading is represented by {\textquoteright}compass{\textquoteright} neurons that innervate a ring-shaped structure known as the ellipsoid body. Each compass neuron receives inputs from {\textquoteright}ring{\textquoteright} neurons that are selective for particular visual features; this combination provides an ideal substrate for the extraction of directional information from a visual scene. Here we combine two-photon calcium imaging and optogenetics in tethered flying flies with circuit modelling, and show how the correlated activity of compass and visual neurons drives plasticity, which flexibly transforms two-dimensional visual cues into a stable heading representation. We also describe how this plasticity enables the fly to convert a partial heading representation, established from orienting within part of a novel setting, into a complete heading representation. Our results provide mechanistic insight into the memory-related computations that are essential for flexible navigation in varied surroundings.

}, issn = {1476-4687}, doi = {10.1038/s41586-019-1767-1}, author = {Kim, Sung Soo and Hermundstad, Ann M and Romani, Sandro and Abbott, L F and Jayaraman, Vivek} } @article {65157, title = {Genetic dissection of active forgetting in labile and consolidated memories in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, year = {2019}, month = {2019 Oct 01}, pages = {21191-97}, abstract = {

Different memory components are forgotten through distinct molecular mechanisms. In , the activation of 2 Rho GTPases (Rac1 and Cdc42), respectively, underlies the forgetting of an early labile memory (anesthesia-sensitive memory, ASM) and a form of consolidated memory (anesthesia-resistant memory, ARM). Here, we dissected the molecular mechanisms that tie Rac1 and Cdc42 to the different types of memory forgetting. We found that 2 WASP family proteins, SCAR/WAVE and WASp, act downstream of Rac1 and Cdc42 separately to regulate ASM and ARM forgetting in mushroom body neurons. Arp2/3 complex, which organizes branched actin polymerization, is a canonical downstream effector of WASP family proteins. However, we found that Arp2/3 complex is required in Cdc42/WASp-mediated ARM forgetting but not in Rac1/SCAR-mediated ASM forgetting. Instead, we identified that Rac1/SCAR may function with formin Diaphanous (Dia), a nucleator that facilitates linear actin polymerization, in ASM forgetting. The present study, complementing the previously identified Rac1/cofilin pathway that regulates actin depolymerization, suggests that Rho GTPases regulate forgetting by recruiting both actin polymerization and depolymerization pathways. Moreover, Rac1 and Cdc42 may regulate different types of memory forgetting by tapping into different actin polymerization mechanisms.

}, issn = {1091-6490}, doi = {10.1073/pnas.1903763116}, author = {Gao, Yang and Shuai, Yichun and Zhang, Xuchen and Peng, Yuwei and Wang, Lianzhang and He, Jing and Zhong, Yi and Li, Qian} } @article {68360, title = {Genetic Identification of Vagal Sensory Neurons That Control Feeding}, journal = {Cell}, volume = {179}, year = {2019}, month = {11/2019}, pages = {1129-1143.e23}, abstract = {

Summary Energy homeostasis requires precise measurement of the quantity and quality of ingested food. The vagus nerve innervates the gut and can detect diverse interoceptive cues, but the identity of the key sensory neurons and corresponding signals that regulate food intake remains unknown. Here, we use an approach for target-specific, single-cell RNA sequencing to generate a map of the vagal cell types that innervate the gastrointestinal tract. We show that unique molecular markers identify vagal neurons with distinct innervation patterns, sensory endings, and function. Surprisingly, we find that food intake is most sensitive to stimulation of mechanoreceptors in the intestine, whereas nutrient-activated mucosal afferents have no effect. Peripheral manipulations combined with central recordings reveal that intestinal mechanoreceptors, but not other cell types, potently and durably inhibit hunger-promoting AgRP neurons in the hypothalamus. These findings identify a key role for intestinal mechanoreceptors in the regulation of feeding.

}, keywords = {AgRP Neurons, chemogenetics, fiber photometry, Hypothalamus, Optogenetics, RNA sequencing, Satiation, stretch, vagal afferents, vagus nerve}, issn = {0092-8674}, doi = {https://doi.org/10.1016/j.cell.2019.10.031}, url = {https://www.sciencedirect.com/science/article/pii/S009286741931181X}, author = {Ling Bai and Sheyda Mesgarzadeh and Karthik S. Ramesh and Erica L. Huey and Yin Liu and Lindsay A. Gray and Tara J. Aitken and Yiming Chen and Lisa R. Beutler and Jamie S. Ahn and Linda Madisen and Hongkui Zeng and Mark A. Krasnow and Zachary A. Knight} } @article {65056, title = {A genetically encoded fluorescent sensor for in vivo imaging of GABA.}, journal = {Nature Methods}, volume = {16}, year = {2019}, month = {2019 Jul 15}, pages = {763-770}, abstract = {

Current techniques for monitoring GABA (γ-aminobutyric acid), the primary inhibitory neurotransmitter in vertebrates, cannot follow transients in intact neural circuits. To develop a GABA sensor, we applied the design principles used to create the fluorescent glutamate receptor iGluSnFR. We used a protein derived from a previously unsequenced Pseudomonas fluorescens strain and performed structure-guided mutagenesis and library screening to obtain intensity-based GABA sensing fluorescence reporter (iGABASnFR) variants. iGABASnFR is genetically encoded, detects GABA release evoked by electric stimulation of afferent fibers in acute brain slices and produces readily detectable fluorescence increases in vivo in mice and zebrafish. We applied iGABASnFR to track mitochondrial GABA content and its modulation by an anticonvulsant, swimming-evoked, GABA-mediated transmission in zebrafish cerebellum, GABA release events during interictal spikes and seizures in awake mice, and found that GABA-mediated tone decreases during isoflurane anesthesia.

}, issn = {1548-7105}, doi = {10.1038/s41592-019-0471-2}, author = {Marvin, Jonathan S and Shimoda, Yoshiteru and Magloire, Vincent and Leite, Marco and Kawashima, Takashi and Jensen, Thomas P and Kolb, Ilya and Knott, Erika L and Novak, Ondrej and Podgorski, Kaspar and Leidenheimer, Nancy J and Rusakov, Dmitri A and Ahrens, Misha B and Kullmann, Dimitri M and Looger, Loren L} } @article {56204, title = {A genetically encoded near-infrared fluorescent calcium ion indicator.}, journal = {Nature Methods}, volume = {16}, year = {2019}, month = {2019 Jan 21}, pages = {171-4}, abstract = {

We report an intensiometric, near-infrared fluorescent, genetically encoded calcium ion (Ca) indicator (GECI) with excitation and emission maxima at 678 and 704 nm, respectively. This GECI, designated NIR-GECO1, enables imaging of Ca transients in cultured mammalian cells and brain tissue with sensitivity comparable to that of currently available visible-wavelength GECIs. We demonstrate that NIR-GECO1 opens up new vistas for multicolor Ca imaging in combination with other optogenetic indicators and actuators.

}, issn = {1548-7105}, doi = {10.1038/s41592-018-0294-6}, author = {Qian, Yong and Piatkevich, Kiryl D and Mc Larney, Benedict and Abdelfattah, Ahmed S and Mehta, Sohum and Murdock, Mitchell H and Gottschalk, Sven and Molina, Rosana S and Zhang, Wei and Chen, Yingche and Wu, Jiahui and Drobizhev, Mikhail and Hughes, Thomas E and Zhang, Jin and Schreiter, Eric R and Shoham, Shy and Razansky, Daniel and Boyden, Edward S and Campbell, Robert E} } @article {64796, title = {A genetically encoded single-wavelength sensor for imaging cytosolic and cell surface ATP.}, journal = {Nature Communications}, volume = {10}, year = {2019}, month = {2019 Feb 12}, pages = {711}, abstract = {

Adenosine 5{\textquoteright} triphosphate (ATP) is a universal intracellular energy source and an evolutionarily ancient, ubiquitous extracellular signal in diverse species. Here, we report the generation and characterization of single-wavelength genetically encoded fluorescent sensors (iATPSnFRs) for imaging extracellular and cytosolic ATP from insertion of circularly permuted superfolder GFP into the epsilon subunit of FF-ATPase from Bacillus PS3. On the cell surface and within the cytosol, iATPSnFR responds to relevant ATP concentrations (30 μM to 3 mM) with fast increases in fluorescence. iATPSnFRs can be genetically targeted to specific cell types and sub-cellular compartments, imaged with standard light microscopes, do not respond to other nucleotides and nucleosides, and when fused with a red fluorescent protein function as ratiometric indicators. After careful consideration of their modest pH sensitivity, iATPSnFRs represent promising reagents for imaging ATP in the extracellular space and within cells during a variety of settings, and for further application-specific refinements.

}, issn = {2041-1723}, doi = {10.1038/s41467-019-08441-5}, author = {Lobas, Mark A and Tao, Rongkun and Nagai, Jun and Kronschl{\"a}ger, Mira T and Borden, Philip M and Marvin, Jonathan S and Looger, Loren L and Khakh, Baljit S} } @article {65020, title = {Genetics of intellectual disability in consanguineous families.}, journal = {Mol Psychiatry}, volume = {24}, year = {2019}, month = {2018 Jan 04}, pages = {1027-1039}, abstract = {

Autosomal recessive (AR) gene defects are the leading genetic cause of intellectual disability (ID) in countries with frequent parental consanguinity, which account for about 1/7th of the world population. Yet, compared to autosomal dominant de novo mutations, which are the predominant cause of ID in Western countries, the identification of AR-ID genes has lagged behind. Here, we report on whole exome and whole genome sequencing in 404 consanguineous predominantly Iranian families with two or more affected offspring. In 219 of these, we found likely causative variants, involving 77 known and 77 novel AR-ID (candidate) genes, 21 X-linked genes, as well as 9 genes previously implicated in diseases other than ID. This study, the largest of its kind published to date, illustrates that high-throughput DNA sequencing in consanguineous families is a superior strategy for elucidating the thousands of hitherto unknown gene defects underlying AR-ID, and it sheds light on their prevalence.

}, issn = {1476-5578}, doi = {10.1038/s41380-017-0012-2}, author = {Hu, Hao and Kahrizi, Kimia and Musante, Luciana and Fattahi, Zohreh and Herwig, Ralf and Hosseini, Masoumeh and Oppitz, Cornelia and Abedini, Seyedeh Sedigheh and Suckow, Vanessa and Larti, Farzaneh and Beheshtian, Maryam and Lipkowitz, Bettina and Akhtarkhavari, Tara and Mehvari, Sepideh and Otto, Sabine and Mohseni, Marzieh and Arzhangi, Sanaz and Jamali, Payman and Mojahedi, Faezeh and Taghdiri, Maryam and Papari, Elaheh and Soltani Banavandi, Mohammad Javad and Akbari, Saeide and Tonekaboni, Seyed Hassan and Dehghani, Hossein and Ebrahimpour, Mohammad Reza and Bader, Ingrid and Davarnia, Behzad and Cohen, Monika and Khodaei, Hossein and Albrecht, Beate and Azimi, Sarah and Zirn, Birgit and Bastami, Milad and Wieczorek, Dagmar and Bahrami, Gholamreza and Keleman, Krystyna and Vahid, Leila Nouri and Tzschach, Andreas and G{\"a}rtner, Jutta and Gillessen-Kaesbach, Gabriele and Varaghchi, Jamileh Rezazadeh and Timmermann, Bernd and Pourfatemi, Fatemeh and Jankhah, Aria and Chen, Wei and Nikuei, Pooneh and Kalscheuer, Vera M and Oladnabi, Morteza and Wienker, Thomas F and Ropers, Hans-Hilger and Najmabadi, Hossein} } @article {65023, title = {Glia accumulate evidence that actions are futile and suppress unsuccessful behavior.}, journal = {Cell}, volume = {178}, year = {2019}, month = {2019 Jun 27}, pages = {27-43}, abstract = {

When a behavior repeatedly fails to achieve its goal, animals often give up and become passive, which can be strategic for preserving energy or regrouping between attempts. It is unknown how the brain identifies behavioral failures and mediates this behavioral-state switch. In larval zebrafish swimming in virtual reality, visual feedback can be withheld so that swim attempts fail to trigger expected visual flow. After tens of seconds of such motor futility, animals became passive for similar durations. Whole-brain calcium imaging revealed noradrenergic neurons that responded specifically to failed swim attempts and radial astrocytes whose calcium levels accumulated with increasing numbers of failed attempts. Using cell ablation and optogenetic or chemogenetic activation, we found that noradrenergic neurons progressively activated brainstem radial astrocytes, which then suppressed swimming. Thus, radial astrocytes perform a computation critical for behavior: they accumulate evidence that current actions are ineffective and consequently drive changes in behavioral states.

}, doi = {10.1016/j.cell.2019.05.050}, author = {Mu, Yu and Bennett, Davis V and Rubinov, Mikail and Narayan, Sujatha and Yang, Chao-Tsung and Tanimoto, Masashi and Mensh, Brett D and Looger, Loren L and Ahrens, Misha B} } @article {64904, title = {The glutamine transporter Slc38a1 regulates GABAergic neurotransmission and synaptic plasticity.}, journal = {Cerebal Cortex}, year = {2019}, month = {2019 May 03}, abstract = {

GABA signaling sustains fundamental brain functions, from nervous system development to the synchronization of population activity and synaptic plasticity. Despite these pivotal features, molecular determinants underscoring the rapid and cell-autonomous replenishment of the vesicular neurotransmitter GABA and its impact on synaptic plasticity remain elusive. Here, we show that genetic disruption of the glutamine transporter Slc38a1 in mice hampers GABA synthesis, modifies synaptic vesicle morphology in GABAergic presynapses and impairs critical period plasticity. We demonstrate that Slc38a1-mediated glutamine transport regulates vesicular GABA content, induces high-frequency membrane oscillations and shapes cortical processing and plasticity. Taken together, this work shows that Slc38a1 is not merely a transporter accumulating glutamine for metabolic purposes, but a key component regulating several neuronal functions.

}, issn = {1460-2199}, doi = {10.1093/cercor/bhz055}, author = {Qureshi, Tayyaba and S{\o}rensen, Christina and Berghuis, Paul and Jensen, Vidar and Dobszay, Marton B and Farkas, Tam{\'a}s and Dalen, Knut Tomas and Guo, Caiying and Hassel, Bj{\o}rnar and Utheim, Tor Paaske and Hvalby, {\O}ivind and Hafting, Torkel and Harkany, Tibor and Fyhn, Marianne and Chaudhry, Farrukh Abbas} } @article {64824, title = {Heterogeneity within classical cell types is the rule: lessons from hippocampal pyramidal neurons.}, journal = {Nature Reviews. Neuroscience}, volume = {20}, year = {2019}, month = {2019 Feb 18}, pages = {193-204}, abstract = {

The mechanistic operation of brain regions is often interpreted by partitioning constituent neurons into {\textquoteright}cell types{\textquoteright}. Historically, such cell types were broadly defined by their correspondence to gross features of the nervous system (such as cytoarchitecture). Modern-day neuroscientific techniques, enabling a more nuanced examination of neuronal properties, have illustrated a wealth of heterogeneity within these classical cell types. Here, we review the extent of this within-cell-type heterogeneity in one of the simplest cortical regions of the mammalian brain, the rodent hippocampus. We focus on the mounting evidence\ that the classical CA3, CA1 and subiculum pyramidal cell types all exhibit prominent\ and spatially patterned within-cell-type heterogeneity, and suggest these cell\ types\ provide a model system for exploring the organization and function of such heterogeneity. Given that the hippocampus is structurally simple and evolutionarily ancient,\ within-cell-type heterogeneity is likely to be a general and crucial feature of the\ mammalian brain.

}, issn = {1471-0048}, doi = {10.1038/s41583-019-0125-5}, author = {Cembrowski, Mark S and Spruston, Nelson} } @article {65752, title = {High precision coding in visual cortex}, journal = {BioRxiv}, year = {2019}, month = {06/2019}, pages = {679324}, abstract = {

Single neurons in visual cortex provide unreliable measurements of visual features due to their high trial-to-trial variability. It is not known if this {\textquotedblleft}noise{\textquotedblright} extends its effects over large neural populations to impair the global encoding of sensory stimuli. We recorded simultaneously from \~{}20,000 neurons in mouse visual cortex and found that the neural population had discrimination thresholds of 0.3{\textdegree} in an orientation decoding task. These thresholds are \~{}100 times smaller than those reported behaviorally in mice. The discrepancy between neural and behavioral discrimination could not be explained by the types of stimuli we used, by behavioral states or by the sequential nature of trial-by-trial perceptual learning tasks. These results imply that the limits of sensory perception in mice are not set by neural noise in sensory cortex, but by the limitations of downstream decoders.

}, doi = {https://doi.org/10.1101/679324}, author = {Stringer, Carsen and Michaelos, Michalis and Pachitariu, Marius} } @article {68757, title = {A high-content imaging approach to profile C. elegans embryonic development}, journal = {Development}, volume = {146}, year = {2019}, month = {04-2019}, abstract = {

The Caenorhabditis elegans embryo is an important model for analyzing mechanisms of cell fate specification and tissue morphogenesis. Sophisticated lineage-tracing approaches for analyzing embryogenesis have been developed but are labor intensive and do not naturally integrate morphogenetic readouts. To enable the rapid classification of developmental phenotypes, we developed a high-content method that employs two custom strains: a Germ Layer strain that expresses nuclear markers in the ectoderm, mesoderm and endoderm/pharynx; and a Morphogenesis strain that expresses markers labeling epidermal cell junctions and the neuronal cell surface. We describe a procedure that allows simultaneous live imaging of development in 80-100 embryos and provide a custom program that generates cropped, oriented image stacks of individual embryos to facilitate analysis. We demonstrate the utility of our method by perturbing 40 previously characterized developmental genes in variants of the two strains containing RNAi-sensitizing mutations. The resulting datasets yielded distinct, reproducible signature phenotypes for a broad spectrum of genes that are involved in cell fate specification and morphogenesis. In addition, our analysis provides new in vivo evidence for MBK-2 function in mesoderm fate specification and LET-381 function in elongation.

}, issn = {0950-1991}, doi = {10.1242/dev.174029}, url = {https://doi.org/10.1242/dev.174029}, author = {Wang, Shaohe and Ochoa, Stacy D. and Khaliullin, Renat N. and Gerson-Gurwitz, Adina and Hendel, Jeffrey M. and Zhao, Zhiling and Biggs, Ronald and Chisholm, Andrew D. and Desai, Arshad and Oegema, Karen and Green, Rebecca A.} } @article {49534, title = {High-dimensional geometry of population responses in visual cortex.}, journal = {Nature}, volume = {571}, year = {2019}, month = {2019 Jun 26}, pages = {361-65}, abstract = {

A neuronal population encodes information most efficiently when its activity is uncorrelated and high-dimensional, and most robustly when its activity is correlated and lower-dimensional. Here, we analyzed the correlation structure of natural image coding, in large visual cortical populations recorded from awake mice. Evoked population activity was high dimensional, with correlations obeying an unexpected power-law: the n-th principal component variance scaled as 1/n. This was not inherited from the 1/f spectrum of natural images, because it persisted after stimulus whitening. We proved mathematically that the variance spectrum must decay at least this fast if a population code is smooth, i.e. if small changes in input cannot dominate population activity. The theory also predicts larger power-law exponents for lower-dimensional stimulus ensembles, which we validated experimentally. These results suggest that coding smoothness represents a fundamental constraint governing correlations in neural population codes.

}, doi = {10.1038/s41586-019-1346-5}, author = {Stringer, Carsen and Pachitariu, Marius and Steinmetz, Nicholas A and Carandini, Matteo and Harris, Kenneth D} } @article {64986, title = {High-performance calcium sensors for imaging activity in neuronal populations and microcompartments.}, journal = {Nature Methods}, volume = {16}, year = {2019}, month = {2019 Jun 17}, pages = {649-57}, abstract = {

Calcium imaging with genetically encoded calcium indicators (GECIs) is routinely used to measure neural activity in intact nervous systems. GECIs are frequently used in one of two different modes: to track activity in large populations of neuronal cell bodies, or to follow dynamics in subcellular compartments such as axons, dendrites and individual synaptic compartments. Despite major advances, calcium imaging is still limited by the biophysical properties of existing GECIs, including affinity, signal-to-noise ratio, rise and decay kinetics and dynamic range. Using structure-guided mutagenesis and neuron-based screening, we optimized the green fluorescent protein-based GECI GCaMP6 for different modes of in vivo imaging. The resulting jGCaMP7 sensors provide improved detection of individual spikes (jGCaMP7s,f), imaging in neurites and neuropil (jGCaMP7b), and may allow tracking larger populations of neurons using two-photon (jGCaMP7s,f) or wide-field (jGCaMP7c) imaging.

}, issn = {1548-7105}, doi = {10.1038/s41592-019-0435-6}, author = {Dana, Hod and Sun, Yi and Mohar, Boaz and Hulse, Brad K and Kerlin, Aaron M and Hasseman, Jeremy P and Tsegaye, Getahun and Tsang, Arthur and Wong, Allan and Patel, Ronak and Macklin, John J and Chen, Yang and Konnerth, Arthur and Jayaraman, Vivek and Looger, Loren L and Schreiter, Eric R and Svoboda, Karel and Kim, Douglas S} } @article {64971, title = {High-resolution cryo-EM structures of outbreak strain human norovirus shells reveal size variations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, year = {2019}, month = {2019 Jun 25}, pages = {12828-32}, abstract = {

Noroviruses are a leading cause of foodborne illnesses worldwide. Although GII.4 strains have been responsible for most norovirus outbreaks, the assembled virus shell structures have been available in detail for only a single strain (GI.1). We present high-resolution (2.6- to 4.1-{\r A}) cryoelectron microscopy (cryo-EM) structures of GII.4, GII.2, GI.7, and GI.1 human norovirus outbreak strain virus-like particles (VLPs). Although norovirus VLPs have been thought to exist in a single-sized assembly, our structures reveal polymorphism between and within genogroups, with small, medium, and large particle sizes observed. Using asymmetric reconstruction, we were able to resolve a Zn2+\ metal ion adjacent to the coreceptor binding site, which affected the structural stability of the shell. Our structures serve as valuable templates for facilitating vaccine formulations.

}, doi = {10.1073/pnas.1903562116}, author = {Jung, James and Grant, Timothy and Thomas, Dennis R. and Diehnelt, Chris W. and Grigorieff, Nikolaus and Leemor, Joshua-Tor} } @article {65041, title = {High-resolution imaging reveals how the spindle midzone impacts chromosome movement.}, journal = {The Journal of Cell Biology}, volume = {218}, year = {2019}, month = {27 Jun 2019}, pages = {2529-44}, abstract = {

In the spindle midzone, microtubules from opposite half-spindles form bundles between segregating chromosomes. Microtubule bundles can either push or restrict chromosome movement during anaphase in different cellular contexts, but how these activities are achieved remains poorly understood. Here, we use high-resolution live-cell imaging to analyze individual microtubule bundles, growing filaments, and chromosome movement in dividing human cells. Within bundles, filament overlap length marked by the cross-linking protein PRC1 decreases during anaphase as chromosome segregation slows. Filament ends within microtubule bundles appear capped despite dynamic PRC1 turnover and submicrometer proximity to growing microtubules. Chromosome segregation distance and rate are increased in two human cell lines when microtubule bundle assembly is prevented via PRC1 knockdown. Upon expressing a mutant PRC1 with reduced microtubule affinity, bundles assemble but chromosome hypersegregation is still observed. We propose that microtubule overlap length reduction, typically linked to pushing forces generated within filament bundles, is needed to properly restrict spindle elongation and position chromosomes within daughter cells.

}, issn = {0021-9525}, doi = {10.1083/jcb.201904169}, url = {http://www.jcb.org/lookup/doi/10.1083/jcb.201904169https://syndication.highwire.org/content/doi/10.1083/jcb.201904169}, author = {Pamula, Melissa C. and Carlini, Lina and Forth, Scott and Verma, Priyanka and Suresh, Subbulakshmi and Legant, Wesley R. and Khodjakov, Alexey and Betzig, Eric and Kapoor, Tarun M.} } @article {65244, title = {High-throughput dense reconstruction of cell lineages.}, journal = {Open Biology}, volume = {9}, year = {2019}, month = {2019 Dec 01}, pages = {190229}, abstract = {

The first meeting exclusively dedicated to the {\textquoteright}High-throughput dense reconstruction of cell lineages{\textquoteright} took place at Janelia Research Campus (Howard Hughes Medical Institute) from 14 to 18 April 2019. Organized by Tzumin Lee, Connie Cepko, Jorge Garcia-Marques and Isabel Espinosa-Medina, this meeting echoed the recent eruption of new tools that allow the reconstruction of lineages based on the phylogenetic analysis of DNA mutations induced during development. Combined with single-cell RNA sequencing, these tools promise to solve the lineage of complex model organisms at single-cell resolution. Here, we compile the conference consensus on the technological and computational challenges emerging from the use of the new strategies, as well as potential solutions.

}, issn = {2046-2441}, doi = {10.1098/rsob.190229}, author = {Isabel Espinosa Medina and Garcia-Marques, Jorge and Cepko, Connie and Lee, Tzumin} } @article {49597, title = {High-throughput synapse-resolving two-photon fluorescence microendoscopy for deep-brain volumetric imaging .}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Jan 03}, abstract = {

Optical imaging has become a powerful tool for studying brains . The opacity of adult brains makes microendoscopy, with an optical probe such as a gradient index (GRIN) lens embedded into brain tissue to provide optical relay, the method of choice for imaging neurons and neural activity in deeply buried brain structures. Incorporating a Bessel focus scanning module into two-photon fluorescence microendoscopy, we extended the excitation focus axially and improved its lateral resolution. Scanning the Bessel focus in 2D, we imaged volumes of neurons at high-throughput while resolving fine structures such as synaptic terminals. We applied this approach to the volumetric anatomical imaging of dendritic spines and axonal boutons in the mouse hippocampus, and functional imaging of GABAergic neurons in the mouse lateral hypothalamus .

}, issn = {2050-084X}, doi = {10.7554/eLife.40805}, author = {Meng, Guanghan and Liang, Yajie and Sarsfield, Sarah and Jiang, Wan-Chen and Lu, Rongwen and Dudman, Joshua Tate and Aponte, Yeka and Ji, Na} } @article {65204, title = {High-yield, automated intracellular electrophysiology in retinal pigment epithelia.}, journal = {Journal of Neuroscience Methods}, volume = {328}, year = {2019}, month = {2019 Dec 01}, pages = {108442}, abstract = {

BACKGROUND: Recent advancements with induced pluripotent stem cell-derived (iPSC) retinal pigment epithelium (RPE) have made disease modeling and cell therapy for macular degeneration feasible. However, current techniques for intracellular electrophysiology - used to validate epithelial function - are painstaking and require manual skill; limiting experimental throughput.

NEW METHOD: A five-stage algorithm, leveraging advances in automated patch clamping, systematically derived and optimized, improves yield and reduces skill when compared to conventional, manual techniques.

RESULTS: The automated algorithm improves yield per attempt from 17\% (manually, n = 23) to 22\% (automated, n = 120) (chi-squared, p = 0.004). Specifically for RPE, depressing the local cell membrane by 6 μm and electroporating (buzzing) just prior to this depth (5 μm) maximized yield.

COMPARISON WITH EXISTING METHOD: Conventionally, intracellular epithelial electrophysiology is performed by manually lowering a pipette with a micromanipulator, blindly, towards a monolayer of cells and spontaneously stopping when the magnitude of the instantaneous measured membrane potential decreased below a predetermined threshold. The new method automatically measures the pipette tip resistance during the descent, detects the cell surface, indents the cell membrane, and briefly buzzes to electroporate the membrane while descending, overall achieving a higher yield than conventional methods.

CONCLUSIONS: This paper presents an algorithm for high-yield, automated intracellular electrophysiology in epithelia; optimized for human RPE. Automation reduces required user skill and training while, simultaneously, improving yield. This algorithm could enable large-scale exploration of drug toxicity and physiological function verification for numerous kinds of epithelia.

}, issn = {1872-678X}, doi = {10.1016/j.jneumeth.2019.108442}, author = {Lewallen, Colby F and Wan, Qin and Maminishkis, Arvydas and Stoy, William and Kolb, Ilya and Hotaling, Nathan and Bharti, Kapil and Forest, Craig R} } @article {65175, title = {Histone H3K27 acetylation precedes active transcription during zebrafish zygotic genome activation as revealed by live-cell analysis.}, journal = {Development}, volume = {146}, year = {2019}, month = {2019 Sep 30}, abstract = {

Histone post-translational modifications are key gene expression regulators, but their rapid dynamics during development remain difficult to capture. We applied a Fab-based live endogenous modification labeling technique to monitor the changes in histone modification levels during zygotic genome activation (ZGA) in living zebrafish embryos. Among various histone modifications, H3 Lys27 acetylation (H3K27ac) exhibited most drastic changes, accumulating in two nuclear foci in the 64- to 1k-cell-stage embryos. The elongating form of RNA polymerase II, which is phosphorylated at Ser2 in heptad repeats within the C-terminal domain (RNAP2 Ser2ph), and miR-430 transcripts were also concentrated in foci closely associated with H3K27ac. When treated with α-amanitin to inhibit transcription or JQ-1 to inhibit binding of acetyl-reader proteins, H3K27ac foci still appeared but RNAP2 Ser2ph and miR-430 morpholino were not concentrated in foci, suggesting that H3K27ac precedes active transcription during ZGA. We anticipate that the method presented here could be applied to a variety of developmental processes in any model and non-model organisms.

}, issn = {1477-9129}, doi = {10.1242/dev.179127}, author = {Sato, Yuko and Hilbert, Lennart and Oda, Haruka and Wan, Yinan and Heddleston, John M and Chew, Teng-Leong and Zaburdaev, Vasily and Keller, Philipp and Lionnet, Timoth{\'e}e and Vastenhouw, Nadine and Kimura, Hiroshi} } @article {64985, title = {How to design a chalk talk-the million dollar sales pitch}, journal = {Molecular Biology of the Cell}, volume = {30}, year = {2019}, month = {2019 Jun 15}, pages = {1575-1577}, abstract = {

Each faculty recruiting season, many postdocs ask, "What is a chalk talk?" The chalk talk is many things-a sales pitch, a teaching demonstration, a barrage of questions, and a description of a future research program. The chalk talk is arguably the most important component of a faculty search interview. Yet few postdocs or grad students receive training or practice in giving a chalk talk. In the following essay, I{\textquoteright}ll cover the basics of chalk talk design and preparation.

}, issn = {1939-4586}, doi = {10.1091/mbc.E19-01-0007}, author = {Snapp, Erik Lee} } @article {65177, title = {Identification of cell types from single-cell transcriptomic data.}, journal = {Methods in Molecular Biology}, volume = {1935}, year = {2019}, month = {2019 Oct 16}, pages = {45-77}, abstract = {

Unprecedented technological advances in single-cell RNA-sequencing (scRNA-seq) technology have now made it possible to profile genome-wide expression in single cells at low cost and high throughput. There is substantial ongoing effort to use scRNA-seq measurements to identify the "cell types" that form components of a complex tissue, akin to taxonomizing species in ecology. Cell type classification from scRNA-seq data involves the application of computational tools rooted in dimensionality reduction and clustering, and statistical analysis to identify molecular signatures that are unique to each type. As datasets continue to grow in size and complexity, computational challenges abound, requiring analytical methods to be scalable, flexible, and robust. Moreover, careful consideration needs to be paid to experimental biases and statistical challenges that are unique to these measurements to avoid artifacts. This chapter introduces these topics in the context of cell-type identification, and outlines an instructive step-by-step example bioinformatic pipeline for researchers entering this field.

}, keywords = {Animals, Cluster Analysis, Computational Biology, Gene Expression Profiling, Genome, High-Throughput Nucleotide Sequencing, Humans, Mice, RNA, Sequence Analysis, RNA, Single-Cell Analysis, Transcriptome}, issn = {1940-6029}, doi = {10.1007/978-1-4939-9057-3_4}, author = {Shekhar, Karthik and Menon, Vilas} } @article {49449, title = {Idiosyncratic choice bias in decision tasks naturally emerges from neuronal network dynamics.}, journal = {Nature Human Behavior}, volume = {3}, year = {2019}, month = {2019 Sep 02}, pages = {1190-1202}, abstract = {

Idiosyncratic tendency to choose one alternative over others in the absence of an identified reason, is a common observation in two-alternative forced-choice experiments. It is tempting to account for it as resulting from the (unknown) participant-specific history and thus treat it as a measurement noise. Indeed, idiosyncratic choice biases are typically considered as nuisance. Care is taken to account for them by adding an ad-hoc bias parameter or by counterbalancing the choices to average them out. Here we quantify idiosyncratic choice biases in a perceptual discrimination task and a motor task. We report substantial and significant biases in both cases. Then, we present theoretical evidence that even in idealized experiments, in which the settings are symmetric, idiosyncratic choice bias is expected to emerge from the dynamics of competing neuronal networks. We thus argue that idiosyncratic choice bias reflects the microscopic dynamics of choice and therefore is virtually inevitable in any comparison or decision task.

}, doi = {10.1101/284877}, author = {Lebovich, Lior and Darshan, Ran and Lavi, Yoni and Hansel, David and Loewenstein, Yonatan} } @article {65178, title = {ilastik: interactive machine learning for (bio)image analysis.}, journal = {Nature Methods}, volume = {16}, year = {2019}, month = {2019 Sep 30}, pages = {1226-32}, abstract = {

We present ilastik, an easy-to-use interactive tool that brings machine-learning-based (bio)image analysis to end users without substantial computational expertise. It contains pre-defined workflows for image segmentation, object classification, counting and tracking. Users adapt the workflows to the problem at hand by interactively providing sparse training annotations for a nonlinear classifier. ilastik can process data in up to five dimensions (3D, time and number of channels). Its computational back end runs operations on-demand wherever possible, allowing for interactive prediction on data larger than RAM. Once the classifiers are trained, ilastik workflows can be applied to new data from the command line without further user interaction. We describe all ilastik workflows in detail, including three case studies and a discussion on the expected performance.

}, issn = {1548-7105}, doi = {10.1038/s41592-019-0582-9}, author = {Berg, Stuart and Kutra, Dominik and Kroeger, Thorben and Straehle, Christoph N and Kausler, Bernhard X and Haubold, Carsten and Schiegg, Martin and Ales, Janez and Beier, Thorsten and Rudy, Markus and Eren, Kemal and Cervantes, Jaime I and Xu, Buote and Beuttenmueller, Fynn and Wolny, Adrian and Zhang, Chong and Koethe, Ullrich and Hamprecht, Fred A and Kreshuk, Anna} } @article {65092, title = {Imaging striatal dopamine release using a nongenetically encoded near infrared fluorescent catecholamine nanosensor.}, journal = {Science Advances}, volume = {5}, year = {2019}, month = {2019 Jul 10}, pages = {eaaw3108}, abstract = {

Neuromodulation plays a critical role in brain function in both health and disease, and new tools that capture neuromodulation with high spatial and temporal resolution are needed. Here, we introduce a synthetic catecholamine nanosensor with fluorescent emission in the near infrared range (1000{\textendash}1300 nm), near infrared catecholamine nanosensor (nIRCat). We demonstrate that nIRCats can be used to measure electrically and optogenetically evoked dopamine release in brain tissue, revealing hotspots with a median size of 2 {\textmu}m. We also demonstrated that nIRCats are compatible with dopamine pharmacology and show D2 autoreceptor modulation of evoked dopamine release, which varied as a function of initial release magnitude at different hotspots. Together, our data demonstrate that nIRCats and other nanosensors of this class can serve as versatile synthetic optical tools to monitor neuromodulatory neurotransmitter release with high spatial resolution.

}, doi = {10.1126/sciadv.aaw3108}, url = {http://advances.sciencemag.org/lookup/doi/10.1126/sciadv.aaw3108https://syndication.highwire.org/content/doi/10.1126/sciadv.aaw3108}, author = {Beyene, Abraham G. and Delevich, Kristen and Del Bonis-O{\textquoteright}Donnell, Jackson Travis and Piekarski, David J. and Lin, Wan Chen and Thomas, A. Wren and Yang, Sarah J. and Kosillo, Polina and Yang, Darwin and Prounis, George S. and Wilbrecht, Linda and Landry, Markita P.} } @article {67223, title = {Importance Weighted Adversarial Variational Autoencoders for Spike Inference from Calcium Imaging Data}, journal = {CoRR}, volume = {abs/1906.03214}, year = {2019}, month = {10/2019}, abstract = {

The Importance Weighted Auto Encoder (IWAE) objective has been shown to improve the training of generative models over the standard Variational Auto Encoder (VAE) objective. Here, we derive importance weighted extensions to Adversarial Variational Bayes (AVB) and Adversarial Autoencoder (AAE). These latent variable models use implicitly defined inference networks whose approximate posterior density qφ(z|x) cannot be directly evaluated, an essential ingredient for importance weighting. We show improved training and inference in latent variable models with our adversarially trained importance weighting method, and derive new theoretical connections between adversarial generative model training criteria and marginal likelihood based methods. We apply these methods to the important problem of inferring spiking neural activity from calcium imaging data, a challenging posterior inference problem in neuroscience, and show that posterior samples from the adversarial methods outperform factorized posteriors used in VAEs.

}, url = {http://arxiv.org/abs/1906.03214}, author = {Daniel Jiwoong Im and Sridhama Prakhya and Jinyao Yan and Srinivas C. Turaga and Kristin Branson} } @article {65024, title = {In situ structure of rotavirus VP1 RNA-dependent RNA polymerase.}, journal = {Journal of Molecular Biology}, volume = {431}, year = {2019}, month = {2019 Jun 21}, pages = {3124-38}, abstract = {

Rotaviruses, like other non-enveloped, double-strand RNA (dsRNA) viruses, package an RNA-dependent RNA polymerase (RdRp) with each duplex of their segmented genomes. Rotavirus cell entry results in loss of an outer protein layer and delivery into the cytosol of an intact, inner capsid particle (the {\textquotedblleft}double-layer particle{\textquotedblright} or DLP). The RdRp, designated VP1, is active inside the DLP; each VP1 achieves many rounds of mRNA transcription from its associated genome segment. Previous work has shown that one VP1 molecule lies close to each fivefold axis of the icosahedrally symmetric DLP, just beneath the inner surface of its protein shell, embedded in tightly packed RNA. We have determined a high-resolution structure for the rotavirus VP1 RdRp\ in situ, by local reconstruction of density around individual fivefold positions. We have analyzed intact virions ({\textquotedblleft}triple-layer particles{\textquotedblright} or TLPs), non-transcribing DLPs and transcribing DLPs. Outer layer dissociation enables the DLP to synthesize RNA,\ in vitro\ as well as\ in vivo, but appears not to induce any detectable structural change in the RdRp. Addition of NTPs, Mg2+, and S-adenosyl methionine, which allows active transcription, results in conformational rearrangements, in both VP1 and the DLP capsid shell protein, that allow a transcript to exit the polymerase and the particle. The position of VP1 (among the five symmetrically related alternatives) at one vertex does not correlate with its position at other vertices. This stochastic distribution of site occupancies limits long-range order in the 11-segment, dsRNA genome.

}, doi = {10.1016/j.jmb.2019.06.016}, author = {Jenni, Simon and Salgado, Eric N. and Herrmann, Tobias and Li, Zongli and Grant, Timothy and Grigorieff, Nikolaus and Trapani, Stefano and Estrozi, Leandro F. and Harrison, Stephen C.} } @article {64866, title = {In vivo glucose imaging in multiple model organisms with an engineered single-wavelength sensor.}, journal = {bioRxiv}, year = {2019}, month = {2019 Mar 8}, abstract = {Glucose is arguably the most important molecule in metabolism, and its mismanagement underlies diseases of vast societal import, most notably diabetes. Although glucose-related metabolism has been the subject of intense study for over a century, tools to track glucose in living organisms with high spatio-temporal resolution are lacking. We describe the engineering of a family of genetically encoded glucose sensors with high signal-to-noise ratio, fast kinetics and affinities varying over four orders of magnitude (1 {\textmu}M to 10 mM). The sensors allow rigorous mechanistic characterization of glucose transporters expressed in cultured cells with high spatial and temporal resolution. Imaging of neuron/glia co-cultures revealed \~{}3-fold higher glucose changes in astrocytes versus neurons. In larval Drosophila central nervous system explants, imaging of intracellular neuronal glucose suggested a novel rostro-caudal transport pathway in the ventral nerve cord neuropil, with paradoxically slower uptake into the peripheral cell bodies and brain lobes. In living zebrafish, expected glucose-related physiological sequelae of insulin and epinephrine treatments were directly visualized in real time. Additionally, spontaneous muscle twitches induced glucose uptake in muscle, and sensory- and pharmacological perturbations gave rise to large but enigmatic changes in the brain. These sensors will enable myriad experiments, most notably rapid, high-resolution imaging of glucose influx, efflux, and metabolism in behaving animals.}, doi = {10.1101/571422}, author = {Keller, Jacob P and Marvin, Jonathan S and Lacin, Haluk and Lemon, William C and Shea, Jamien and Kim, Soomin and Lee, Richard T and Koyama, Minoru and Keller, Philipp J and Looger, Loren L} } @article {64957, title = {Inaccurate secondary structure predictions often indicate protein fold switching.}, journal = {Protein Science}, volume = {28}, year = {2019}, month = {2019 Aug}, pages = {1487-93}, abstract = {

Although most proteins conform to the classical one-structure/one-function paradigm, an increasing number of proteins with dual structures and functions have been discovered. In response to cellular stimuli, such proteins undergo structural changes sufficiently dramatic to remodel even their secondary structures and domain organization. This "fold-switching" capability fosters protein multi-functionality, enabling cells to establish tight control over various biochemical processes. Accurate predictions of fold-switching proteins could both suggest underlying mechanisms for uncharacterized biological processes and reveal potential drug targets. Recently, we developed a prediction method for fold-switching proteins using structure-based thermodynamic calculations and discrepancies between predicted and experimentally determined protein secondary structure. Here we seek to leverage the negative information found in these secondary structure prediction discrepancies. To do this, we quantified secondary structure prediction accuracies of 192 known fold-switching regions (FSRs) within solved protein structures found in the Protein Data Bank (PDB). We find that the secondary structure prediction accuracies for these FSRs vary widely. Inaccurate secondary structure predictions are strongly associated with fold-switching proteins compared to equally long segments of non-fold-switching proteins selected at random. These inaccurate predictions are enriched in helix-to-strand and strand-to-coil discrepancies. Finally, we find that most proteins with inaccurate secondary structure predictions are underrepresented in the PDB compared with their alternatively folded cognates, suggesting that unequal representation of fold-switching conformers within the PDB could be an important cause of inaccurate secondary structure predictions. These results demonstrate that inconsistent secondary structure predictions can serve as a useful preliminary marker of fold switching. This article is protected by copyright. All rights reserved.

}, issn = {1469-896X}, doi = {10.1002/pro.3664}, author = {Mishra, Soumya and Looger, Loren L and Porter, Lauren L} } @article {69338, title = {Innexin expression in electrically coupled motor circuits}, journal = {Neuroscience Letters}, volume = {695}, year = {2019}, month = {2019 Mar 16}, pages = {19-24}, abstract = {

The many roles of innexins, the molecules that form gap junctions in invertebrates, have been explored in numerous species. Here, we present a summary of innexin expression and function in two small, central pattern generating circuits found in crustaceans: the stomatogastric ganglion and the cardiac ganglion. The two ganglia express multiple innexin genes, exhibit varying combinations of symmetrical and rectifying gap junctions, as well as gap junctions within and across different cell types. Past studies have revealed correlations in ion channel and innexin expression in coupled neurons, as well as intriguing functional relationships between ion channel conductances and electrical coupling. Together, these studies suggest a putative role for innexins in correlating activity between coupled neurons at the levels of gene expression and physiological activity during development and in the adult animal.

}, keywords = {Cardiac ganglion, Central pattern generators, Crustacean, Neuronal homeostasis, Stomatogastric ganglion}, issn = {0304-3940}, doi = {https://doi.org/10.1016/j.neulet.2017.07.016}, url = {https://www.sciencedirect.com/science/article/pii/S0304394017305785}, author = {Adriane G. Otopalik and Brian Lane and David J. Schulz and Eve Marder} } @article {65212, title = {Interactions between Dpr11 and DIP-γ control selection of amacrine neurons in color vision circuits.}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Nov 06}, abstract = {

R7 UV photoreceptors (PRs) are divided into yellow (y) and pale (p) subtypes. yR7 PRs express the Dpr11 cell surface protein and are presynaptic to Dm8 amacrine neurons (yDm8) that express Dpr11{\textquoteright}s binding partner DIP-g, while pR7 PRs synapse onto DIP-g-negative pDm8. Dpr11 and DIP-g expression patterns define {\textquoteright}yellow{\textquoteright} and {\textquoteright}pale{\textquoteright} color vision circuits. We examined Dm8 neurons in these circuits by electron microscopic reconstruction and expansion microscopy. and mutations affect the morphologies of yDm8 distal ({\textquoteright}home column{\textquoteright}) dendrites. yDm8 neurons are generated in excess during development and compete for presynaptic yR7 PRs, and interactions between Dpr11 and DIP-g are required for yDm8 survival. These interactions also allow yDm8 neurons to select yR7 PRs as their appropriate home column partners. yDm8 and pDm8 neurons do not normally compete for survival signals or R7 partners, but can be forced to do so by manipulation of R7 subtype fate.

}, issn = {2050-084X}, doi = {10.7554/eLife.48935}, author = {Menon, Kaushiki P and Kulkarni, Vivek and Takemura, Shin-ya and Anaya, Michael and Zinn, Kai} } @article {64851, title = {Interfacial actin protrusions mechanically enhance killing by cytotoxic T cells.}, journal = {Science Immunology}, volume = {4}, year = {2019}, month = {2019 Mar 22}, abstract = {

Cytotoxic T lymphocytes (CTLs) kill by forming immunological synapses with target cells and secreting toxic proteases and the pore-forming protein perforin into the intercellular space. Immunological synapses are highly dynamic structures that boost perforin activity by applying mechanical force against the target cell. Here, we used high-resolution imaging and microfabrication to investigate how CTLs exert synaptic forces and coordinate their mechanical output with perforin secretion. Using micropatterned stimulatory substrates that enable synapse growth in three dimensions, we found that perforin release occurs at the base of actin-rich protrusions that extend from central and intermediate locations within the synapse. These protrusions, which depended on the cytoskeletal regulator WASP and the Arp2/3 actin nucleation complex, were required for synaptic force exertion and efficient killing. They also mediated physical deformation of the target cell surface during CTL-target cell interactions. Our results reveal the mechanical basis of cellular cytotoxicity and highlight the functional importance of dynamic, three-dimensional architecture in immune cell-cell interfaces.

}, issn = {2470-9468}, doi = {10.1126/sciimmunol.aav5445}, author = {Tamzalit, Fella and Wang, Mitchell S and Jin, Weiyang and Tello-Lafoz, Maria and Boyko, Vitaly and Heddleston, John M and Black, Charles T and Kam, Lance C and Huse, Morgan} } @conference {56205, title = {Internal models in control, biology and neuroscience.}, booktitle = {2018 IEEE Conference on Decision and Control (CDC)}, year = {2019}, month = {2019 Jan 21}, abstract = {

This tutorial paper deals with the Internal Model Principle (IMP) from different perspectives. The goal is to start from the principle as introduced and commonly used in the control theory and then enlarge the vision to other fields where {\textquotedblleft}internal models{\textquotedblright} play a role. The biology and neuroscience fields are specifically targeted in the paper. The paper ends by presenting an {\textquotedblleft}abstract{\textquotedblright} theory of IMP applicable to a large class of systems.

}, doi = {10.1109/CDC.2018.8619624}, author = {Huang, J and Isidori, A and Marconi, L and Mischiati, Matteo and Sontag, E and Wonham, W M} } @article {65150, title = {Isomeric tuning yields bright and targetable red Ca indicators.}, journal = {Journal of the American Chemical Society}, volume = {141}, year = {2019}, month = {2019 Sep 04}, pages = {13734-13738}, abstract = {

Targeting small-molecule fluorescent indicators using genetically encoded protein tags yields new hybrid sensors for biological imaging. Optimization of such systems requires redesign of the synthetic indicator to allow cell-specific targeting without compromising the photophysical properties or cellular performance of the small-molecule probe. We developed a bright and sensitive Ca indicator by systematically exploring the relative configuration of dye and chelator, which can be targeted using the HaloTag self-labeling tag system. Our "isomeric tuning" approach is generalizable, yielding a far-red targetable indicator to visualize Ca fluxes in the primary cilium.

}, issn = {1520-5126}, doi = {10.1021/jacs.9b06092}, author = {Deo, Claire and Sheu, Shu-Hsien and Seo, Jinyoung and Clapham, David E and Lavis, Luke D} } @article {49329, title = {Kilohertz frame-rate two-photon tomography.}, journal = {Nature Methods}, volume = {16}, year = {2019}, month = {2019 Jul 29}, pages = {778-86}, abstract = {

Point-scanning two-photon microscopy enables high-resolution imaging within scattering specimens such as the mammalian brain, but sequential acquisition of voxels fundamentally limits imaging speed. We developed a two-photon imaging technique that scans lines of excitation across a focal plane at multiple angles and uses prior information to recover high-resolution images at over 1.4 billion voxels per second. Using a structural image as a prior for recording neural activity, we imaged visually-evoked and spontaneous glutamate release across hundreds of dendritic spines in mice at depths over 250 microns and frame-rates over 1 kHz. Dendritic glutamate transients in anaesthetized mice are synchronized within spatially-contiguous domains spanning tens of microns at frequencies ranging from 1-100 Hz. We demonstrate high-speed recording of acetylcholine and calcium sensors, 3D single-particle tracking, and imaging in densely-labeled cortex. Our method surpasses limits on the speed of raster-scanned imaging imposed by fluorescence lifetime.

}, doi = {10.1101/357269}, author = {Kazemipour, Abbas and Novak, Ondrej and Flickinger, Daniel and Marvin, Jonathan S and Abdelfattah, Ahmed S and King, J. and Borden, PM and Kim, JJ and Al-Abdullatif, SH and Deal, PE and Miller, EW and Schreiter, ER and Druckmann, S and Svoboda, K and Looger, LL and Podgorski, K} } @article {65033, title = {Kilohertz in vivo imaging of neural activity.}, journal = {bioRxiv}, year = {2019}, month = {2019 Feb 06}, abstract = {

Understanding information processing in the brain requires us to monitor neural activity in vivo at high spatiotemporal resolution. Using an ultrafast two-photon fluorescence microscope (2PFM) empowered by all-optical laser scanning, we imaged neural activity in vivo at 1,000 frames per second and submicron spatial resolution. This ultrafast imaging method enabled monitoring of electrical activity down to 300 μm below the brain surface in head fixed awake mice.

}, doi = {10.1101/543058}, author = {Jianglai Wu and Yajie liang and Ching-Lung Hsu and Mariya Chavarha and Stephen Evans and Dongqing Shi and Michael Lin and Kevin Tsia and Na Ji} } @article {68758, title = {The Kinetochore-Microtubule Coupling Machinery Is Repurposed in Sensory Nervous System Morphogenesis}, journal = {Developmental Cell}, volume = {48}, year = {2019}, month = {03/2019}, pages = {864-872.e7}, abstract = {

Summary Dynamic coupling of microtubule ends to kinetochores, built on the centromeres of chromosomes, directs chromosome segregation during cell division. Here, we report that the evolutionarily ancient kinetochore-microtubule\ coupling machine, the KMN (Knl1/Mis12/Ndc80-complex) network, plays a critical role in neuronal morphogenesis. We show that the KMN network concentrates in microtubule-rich dendrites of developing sensory neurons that collectively extend in a multicellular morphogenetic event that occurs during C.\ elegans embryogenesis. Post-mitotic degradation of KMN components in sensory neurons disrupts dendritic extension, leading to patterning and functional defects in the sensory nervous system. Structure-guided mutations revealed that the molecular interface that couples kinetochores to spindle microtubules also functions in neuronal development. These results identify a cell-division-independent function for the chromosome-segregation machinery and define a microtubule-coupling-dependent event in sensory nervous system morphogenesis.

}, keywords = {Chromosome Segregation, dendrite, kinetochore, KMN network, Knl1, microtubule, Mis12 complex, Mitosis, Morphogenesis, Ndc80 complex, Nervous System, sensory neuron}, issn = {1534-5807}, doi = {https://doi.org/10.1016/j.devcel.2019.02.002}, url = {https://www.sciencedirect.com/science/article/pii/S1534580719300577}, author = {Dhanya K. Cheerambathur and Bram Prevo and Tiffany-Lynn Chow and Neil Hattersley and Shaohe Wang and Zhiling Zhao and Taekyung Kim and Adina Gerson-Gurwitz and Karen Oegema and Rebecca Green and Arshad Desai} } @article {48806, title = {Large scale image segmentation with structured loss based deep learning for connectome reconstruction.}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, volume = {41}, year = {2019}, month = {2019 Jul 1}, pages = {1669-80}, abstract = {

We present a method combining affinity prediction with region agglomeration, which improves significantly upon the state of the art of neuron segmentation from electron microscopy (EM) in accuracy and scalability. Our method consists of a 3D U-net, trained to predict affinities between voxels, followed by iterative region agglomeration. We train using a structured loss based on MALIS, encouraging topologically correct segmentations obtained from affinity thresholding. Our extension consists of two parts: First, we present a quasi-linear method to compute the loss gradient, improving over the original quadratic algorithm. Second, we compute the gradient in two separate passes to avoid spurious gradient contributions in early training stages. Our predictions are accurate enough that simple learning-free percentile-based agglomeration outperforms more involved methods used earlier on inferior predictions. We present results on three diverse EM datasets, achieving relative improvements over previous results of 27\%, 15\%, and 250\%. Our findings suggest that a single method can be applied to both nearly isotropic block-face EM data and anisotropic serial sectioned EM data. The runtime of our method scales linearly with the size of the volume and achieves a throughput of ~2.6 seconds per megavoxel, qualifying our method for the processing of very large datasets.

}, doi = {10.1109/TPAMI.2018.2835450}, author = {Funke, Jan and Tschopp, Fabian D and Grisaitis, William and Sheridan, Arlo and Singh, Chandan and Saalfeld, Stephan and Turaga, Srinivas C} } @article {65171, title = {Learning from action: reconsidering movement signaling in midbrain dopamine neuron activity.}, journal = {Neuron}, volume = {104}, year = {2019}, month = {2019 Oct 09}, pages = {63-77}, abstract = {

Animals infer when and where a reward is available from experience with informative sensory stimuli and their own actions. In vertebrates, this is thought to depend upon the release of dopamine from midbrain dopaminergic neurons. Studies of the role of dopamine have focused almost exclusively on their encoding of informative sensory stimuli; however, many dopaminergic neurons are active just prior to movement initiation, even in the absence of sensory stimuli. How should current frameworks for understanding the role of dopamine incorporate these observations? To address this question, we review recent anatomical and functional evidence for action-related dopamine signaling. We conclude by proposing a framework in which dopaminergic neurons encode subjective signals of action initiation to solve an internal credit assignment problem.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2019.08.036}, author = {Coddington, Luke T and Dudman, Joshua T} } @article {65057, title = {Light-sheet microscopy and its potential for understanding developmental processes.}, journal = {Annual Review of Cell and Developmental Biology}, volume = {35}, year = {2019}, month = {2019 Oct 6}, pages = {655-81}, abstract = {

The ability to visualize and quantitatively measure dynamic biological processes in vivo and at high spatiotemporal resolution is of fundamental importance to experimental investigations in developmental biology. Light-sheet microscopy is particularly well suited to providing such data, since it offers exceptionally high imaging speed and good spatial resolution while minimizing light-induced damage to the specimen. We review core principles and recent advances in light-sheet microscopy, with a focus on concepts and implementations relevant for applications in developmental biology. We discuss how light-sheet microcopy has helped advance our understanding of developmental processes from single-molecule to whole-organism studies, assess the potential for synergies with other state-of-the-art technologies, and introduce methods for computational image and data analysis. Finally, we explore the future trajectory of light-sheet microscopy, discuss key efforts to disseminate new light-sheet technology, and identify exciting opportunities for further advances.

}, issn = {1530-8995}, doi = {10.1146/annurev-cellbio-100818-125311}, author = {Wan, Yinan and McDole, Katie and Keller, Philipp J} } @article {64863, title = {A lipid-based partitioning mechanism for selective incorporation of proteins into membranes of HIV particles.}, journal = {Nature Cell Biology}, volume = {21}, year = {2019}, month = {2019 Apr}, pages = {452-461}, abstract = {

Particles that bud off from the cell surface, including viruses and microvesicles, typically have a unique membrane protein composition distinct from that of the originating plasma membrane. This selective protein composition enables viruses to evade the immune response and infect other cells. But how membrane proteins sort into budding viruses such as human immunodeficiency virus (HIV) remains unclear. Proteins could passively distribute into HIV-assembly-site membranes producing compositions resembling pre-existing plasma-membrane domains. Here, we demonstrate that proteins instead sort actively into HIV-assembly-site membranes, generating compositions enriched in cholesterol and sphingolipids that undergo continuous remodeling. Proteins are recruited into and removed from the HIV assembly site through lipid-based partitioning, initiated by oligomerization of the HIV structural protein Gag. Changes in membrane curvature at the assembly site further amplify this sorting process. Thus, a lipid-based sorting mechanism, aided by increasing membrane curvature, generates the unique membrane composition of the HIV surface.

}, issn = {1476-4679}, doi = {10.1038/s41556-019-0300-y}, author = {Sengupta, Prabuddha and Seo, Arnold Y and Pasolli, H Amalia and Song, Yul Eum and Johnson, Marc and Lippincott-Schwartz, Jennifer} } @article {65040, title = {Local synaptic inputs support opposing, network-specific odor representations in a widely projecting modulatory neuron.}, journal = {eLife}, volume = {8}, year = {2019}, month = {2 Jul 2019}, abstract = {

Serotonin plays different roles across networks within the same sensory modality. Previously, we used whole-cell electrophysiology in\ Drosophila\ to show that serotonergic neurons innervating the first olfactory relay are inhibited by odorants (Zhang and Gaudry, 2016). Here we show that network-spanning serotonergic neurons segregate information about stimulus features, odor intensity and identity, by using opposing coding schemes in different olfactory neuropil. A pair of serotonergic neurons (the CSDns) innervate the antennal lobe and lateral horn, which are first and second order neuropils. CSDn processes in the antennal lobe are inhibited by odors in an identity independent manner. In the lateral horn, CSDn processes are excited in an odor identity dependent manner. Using functional imaging, modeling, and EM reconstruction, we demonstrate that antennal lobe derived inhibition arises from local GABAergic inputs and acts as a means of gain control on branch specific inputs that the CSDns receive within the lateral horn.

}, doi = {10.7554/eLife.46839}, url = {https://elifesciences.org/articles/46839https://cdn.elifesciences.org/articles/46839/elife-46839-v1.pdfhttps://cdn.elifesciences.org/articles/46839/elife-46839-v1.xml}, author = {Zhang, Xiaonan and Coates, Kaylynn and Dacks, Andrew M and Gunay, Cengiz and Lauritzen, J Scott and Li, Feng and Calle-Schuler, Steven A and Bock, Davi and Gaudry, Quentin} } @article {64547, title = {Looking back and looking forward at Janelia.}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Feb07}, pages = {e44826}, abstract = {

Starting a new research campus is a leap of faith. Only later, in the full measure of time, is it possible to take stock of what has worked and what could have been done better or differently. The Janelia Research Campus opened its doors 12 years ago. What has it achieved? What has it taught us? And where does Janelia go from here?

}, doi = {10.7554/eLife.44826}, author = {Rubin, Gerald M and O{\textquoteright}Shea, Erin K} } @article {65160, title = {Mamo decodes hierarchical temporal gradients into terminal neuronal fate.}, journal = {Elife}, volume = {8}, year = {2019}, month = {2019 Sep 23}, abstract = {

Temporal patterning is a seminal method of expanding neuronal diversity. Here we unravel a mechanism decoding neural stem cell temporal gene expression and transforming it into discrete neuronal fates. This mechanism is characterized by hierarchical gene expression. First, neuroblasts express opposing temporal gradients of RNA-binding proteins, Imp and Syp. These proteins promote or inhibit translation, yielding a descending neuronal gradient. Together, first and second-layer temporal factors define a temporal expression window of BTB-zinc finger nuclear protein, Mamo. The precise temporal induction of Mamo is achieved via both transcriptional and post-transcriptional regulation. Finally, Mamo is essential for the temporally defined, terminal identity of α{\textquoteright}/β{\textquoteright} mushroom body neurons and identity maintenance. We describe a straightforward paradigm of temporal fate specification where diverse neuronal fates are defined via integrating multiple layers of gene regulation. The neurodevelopmental roles of orthologous/related mammalian genes suggest a fundamental conservation of this mechanism in brain development.

}, issn = {2050-084X}, doi = {10.7554/eLife.48056}, author = {Liu, Ling-Yu and Long, Xi and Yang, Ching-Po and Miyares, Rosa L and Sugino, Ken and Singer, Robert H and Lee, Tzumin} } @article {64874, title = {Mapping the transcriptional diversity of genetically and anatomically defined cell populations in the mouse brain.}, journal = {Elife}, volume = {8}, year = {2019}, month = {2019 Apr 12}, abstract = {

Understanding the principles governing neuronal diversity is a fundamental goal for neuroscience. Here we provide an anatomical and transcriptomic database of nearly 200 genetically identified cell populations. By separately analyzing the robustness and pattern of expression differences across these cell populations, we identify two gene classes contributing distinctly to neuronal diversity. Short homeobox transcription factors distinguish neuronal populations combinatorially, and exhibit extremely low transcriptional noise, enabling highly robust expression differences. Long neuronal effector genes, such as channels and cell adhesion molecules, contribute disproportionately to neuronal diversity, based on their patterns rather than robustness of expression differences. By linking transcriptional identity to genetic strains and anatomical atlases we provide an extensive resource for further investigation of mouse neuronal cell types.

}, issn = {2050-084X}, doi = {10.7554/eLife.38619}, author = {Sugino, Ken and Clark, Erin and Schulmann, Anton and Shima, Yasuyuki and Wang, Lihua and Hunt, David L and Hooks, Bryan M and Traenkner, Dimitri and Chandrashekar, Jayaram and Picard, Serge and Lemire, Andrew L and Spruston, Nelson and Hantman, Adam W and Nelson, Sacha B} } @article {65255, title = {Mechanisms underlying the neural computation of head direction.}, journal = {Annual Review of Neuroscience}, volume = {43}, year = {2019}, month = {2020 Jul 8}, pages = {31-54}, abstract = {

Many animals use an internal sense of direction to guide their movements through the world. Neurons selective to head direction are thought to support this directional sense and have been found in a diverse range of species, from insects to primates, highlighting their evolutionary importance. Across species, most head-direction networks share four key properties: a unique representation of direction at all times, persistent activity in the absence of movement, integration of angular velocity to update the representation, and the use of directional cues to correct drift. The dynamics of theorized network structures called ring attractors elegantly account for these properties, but their relationship to brain circuits is unclear. Here, we review experiments in rodents and flies that offer insights into potential neural implementations of ring attractor networks. We suggest that a theory-guided search across model systems for biological mechanisms that enable such dynamics would uncover general principles underlying head-direction circuit function. Expected final online publication date for the , Volume 43 is July 8, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-072116-031516}, author = {Hulse, Brad K and Jayaraman, Vivek} } @article {64973, title = {Mechanistic characterization of RASGRP1 variants identifies an hnRNP K-regulated transcriptional enhancer contributing to SLE susceptibility.}, journal = {Frontiers in Immunology}, year = {2019}, month = {2019 May 20}, abstract = {

Systemic lupus erythematosus (SLE) is an autoimmune disease with a strong genetic component. We recently identified a novel SLE susceptibility locus near\ RASGRP1, which governs the ERK/MAPK kinase cascade and B-/T-cell differentiation and development. However, precise causal\ RASGRP1functional variant(s) and their mechanisms of action in SLE pathogenesis remain undefined. Our goal was to fine-map this locus, prioritize genetic variants likely to be functional, experimentally validate their biochemical mechanisms, and determine the contribution of these SNPs to SLE risk. We performed a meta-analysis across six Asian and European cohorts (9,529 cases; 22,462 controls), followed by\ in silico\ bioinformatic and epigenetic analyses to prioritize potentially functional SNPs. We experimentally validated the functional significance and mechanism of action of three SNPs in cultured T-cells. Meta-analysis identified 18 genome-wide significant (p\ \< 5 {\texttimes} 10-8) SNPs, mostly concentrated in two haplotype blocks, one intronic and the other intergenic. Epigenetic fine-mapping, allelic, eQTL, and imbalance analyses predicted three transcriptional regulatory regions with four SNPs (rs7170151, rs11631591-rs7173565, and rs9920715) prioritized for functional validation. Luciferase reporter assays indicated significant allele-specific enhancer activity for intronic rs7170151 and rs11631591-rs7173565 in T-lymphoid (Jurkat) cells, but not in HEK293 cells. Following up with EMSA, mass spectrometry, and ChIP-qPCR, we detected allele-dependent interactions between heterogeneous nuclear ribonucleoprotein K (hnRNP-K) and rs11631591. Furthermore, inhibition of hnRNP-K in Jurkat and primary T-cells downregulated\ RASGRP1\ and ERK/MAPK signaling. Comprehensive association, bioinformatics, and epigenetic analyses yielded putative functional variants of\ RASGRP1, which were experimentally validated. Notably, intronic variant (rs11631591) is located in a cell type-specific enhancer sequence, where its risk allele binds to the hnRNP-K protein and modulates\ RASGRP1\ expression in Jurkat and primary T-cells. As risk allele dosage of rs11631591 correlates with increased\ RASGRP1\ expression and ERK activity, we suggest that this SNP may underlie SLE risk at this locus.

}, doi = {10.3389/fimmu.2019.01066}, author = {Molineros, Julio E. and Singh, Bhupinder and Terao, Chikashi and Okada, Yukinori and Kaplan, Jakub and McDaniel, Barbara and Akizuki, Shuji and Sun, Celi and Webb, Carol F. and Looger, Loren L and Nath, Swapan K.} } @article {65257, title = {MeCP2 nuclear dynamics in live neurons results from low and high affinity chromatin interactions.}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Dec 23}, abstract = {

Methyl-CpG-binding-Protein 2 (MeCP2) is an abundant nuclear protein highly enriched in neurons. Here we report live-cell single-molecule imaging studies of the kinetic features of mouse MeCP2 at high spatial-temporal resolution. MeCP2 displays dynamic features that are distinct from both highly mobile transcription factors and immobile histones. Stable binding of MeCP2 in living neurons requires its methyl-binding domain and is sensitive to DNA modification levels. Diffusion of unbound MeCP2 is strongly constrained by weak, transient interactions mediated primarily by its AT-hook domains, and varies with the level of chromatin compaction and cell type. These findings extend previous studies of the role of the MeCP2 MBD in high affinity DNA binding to living neurons, and identify a new role for its AT-hooks domains as critical determinants of its kinetic behavior. They suggest that limited nuclear diffusion of MeCP2 in live neurons contributes to its local impact on chromatin structure and gene expression.

}, issn = {2050-084X}, doi = {10.7554/eLife.51449}, author = {Piccolo, Francesco M and Liu, Zhe and Dong, Peng and Hsu, Ching-Lung and Stoyanova, Elitsa I and Rao, Anjana and Tjian, Robert and Heintz, Nathaniel} } @article {64853, title = {Membrane-cytoskeletal crosstalk mediated by myosin-I regulates adhesion turnover during phagocytosis.}, journal = {Nature Communications}, volume = {10}, year = {2019}, month = {2019 03 19}, pages = {1249}, abstract = {

Phagocytosis of invading pathogens or cellular debris requires a dramatic change in cell shape driven by actin polymerization. For antibody-covered targets, phagocytosis is thought to proceed through the sequential engagement of Fc-receptors on the phagocyte with antibodies on the target surface, leading to the extension and closure of the phagocytic cup around the target. We find that two actin-dependent molecular motors, class 1 myosins myosin 1e and myosin 1f, are specifically localized to Fc-receptor adhesions and required for efficient phagocytosis of antibody-opsonized targets. Using primary macrophages lacking both myosin 1e and myosin 1f, we find that without the actin-membrane linkage mediated by these myosins, the organization of individual adhesions is compromised, leading to excessive actin polymerization, slower adhesion turnover, and deficient phagocytic internalization. This work identifies a role for class 1 myosins in coordinated adhesion turnover during phagocytosis and supports a mechanism involving membrane-cytoskeletal crosstalk for phagocytic cup closure.

}, issn = {2041-1723}, doi = {10.1038/s41467-019-09104-1}, author = {Barger, Sarah R and Reilly, Nicholas S and Shutova, Maria S and Li, Qingsen and Maiuri, Paolo and Heddleston, John M and Mooseker, Mark S and Flavell, Richard A and Svitkina, Tatyana and Oakes, Patrick W and Krendel, Mira and Gauthier, Nils C} } @article {64842, title = {Metabolic regulation of developmental cell cycles and zygotic transcription.}, journal = {Current Biology}, volume = {29}, year = {2019}, month = {2019 Mar 01}, pages = {1193-8}, abstract = {

The thirteen nuclear cleavages that give rise to the Drosophila blastoderm are some of the fastest known cell cycles. Surprisingly, the fertilized egg is provided with at most one-third of the dNTPs needed to complete the thirteen rounds of DNA replication. The rest must be synthesized by the embryo, concurrent with cleavage divisions. What is the reason for the limited supply of DNA building blocks? We propose that frugal control of dNTP synthesis contributes to the well-characterized deceleration of the cleavage cycles and is needed for robust accumulation of zygotic gene products. In support of this model, we demonstrate that when the levels of dNTPs are abnormally high, nuclear cleavages fail to sufficiently decelerate, the levels of zygotic transcription are dramatically reduced, and the embryo catastrophically fails early in gastrulation. Our work reveals a direct connection between metabolism, the cell cycle, and zygotic transcription.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2019.02.028}, author = {Djabrayan, Nareg J-V and Smits, Celia M and Krajnc, Matej and Stern, Tomer and Yamada, Shigehiro and Lemon, William C and Keller, Philipp J and Rushlow, Christine A and Shvartsman, Stanislav Y} } @article {64873, title = {MicroED data collection with SerialEM.}, journal = {Ultramicroscopy}, volume = {201}, year = {2019}, month = {2019 Mar 19}, pages = {77-80}, abstract = {

The cryoEM method Microcrystal Electron Diffraction (MicroED) involves transmission electron microscope (TEM) and electron detector working in synchrony to collect electron diffraction data by continuous rotation. We previously reported several protein, peptide, and small molecule structures by MicroED using manual control of the microscope and detector to collect data. Here we present a procedure to automate this process using a script developed for the popular open-source software package SerialEM. With this approach, SerialEM coordinates stage rotation, microscope operation, and camera functions for automated continuous-rotation MicroED data collection. Depending on crystal and substrate geometry, more than 300 datasets can be collected overnight in this way, facilitating high-throughput MicroED data collection for large-scale data analyses.

}, issn = {1879-2723}, doi = {10.1016/j.ultramic.2019.03.009}, author = {de la Cruz, M Jason and Martynowycz, Michael W and Hattne, Johan and Gonen, Tamir} } @article {59911, title = {Molecular logic of spinocerebellar tract neuron diversity and connectivity.}, journal = {Cell Reports}, volume = {27}, year = {2019}, month = {2019 May 27}, pages = {2620-35}, abstract = {

Coordinated motor behaviors depend on feedback communication between peripheral sensory systems and central circuits in the brain and spinal cord. Relay of muscle and tendon-derived sensory information to the CNS is facilitated by functionally and anatomically diverse groups of spinocerebellar tract neurons (SCTNs), but the molecular logic by which SCTN diversity and connectivity is achieved is poorly understood. We used single cell RNA sequencing and genetic manipulations to define the mechanisms governing the molecular profile and organization of SCTN subtypes. We found that SCTNs relaying proprioceptive sensory information from limb and axial muscles are generated through segmentally-restricted actions of specific Hox genes. Loss of Hox function disrupts SCTN subtype-specific transcriptional programs, leading to defects in the connections between proprioceptive sensory neurons, SCTNs, and the cerebellum. These results indicate that Hox-dependent genetic programs play essential roles in the assembly of the neural circuits required for proprioception.

}, doi = {10.1016/j.celrep.2019.04.113}, author = {Baek, Myungin and Menon, Vilas and Jessell, Thomas M and Hantman, Adam W and Dasen, Jeremy} } @article {69337, title = {Molecular Profiling to Infer Neuronal Cell Identity: Lessons from small ganglia of the Crab Cancer borealis}, journal = {bioRxiv}, year = {2019}, month = {2019 Jul 2}, abstract = {

Understanding circuit organization depends on identification of cell types. Recent advances in transcriptional profiling methods have enabled classification of cell types by their gene expression. While exceptionally powerful and high throughput, the ground-truth validation of these methods is difficult: if cell type is unknown, how does one assess whether a given analysis accurately captures neuronal identity? To shed light on the capabilities and limitations of solely using transcriptional profiling for cell type classification, we performed two forms of transcriptional profiling {\textendash} RNA-seq and quantitative RT-PCR, in single, unambiguously identified neurons from two small crustacean networks: the stomatogastric and cardiac ganglia. We then combined our knowledge of cell type with unbiased clustering analyses and supervised machine learning to determine how accurately functionally-defined neuron types can be classified by expression profile alone. Our results demonstrate that expression profile is able to capture neuronal identity most accurately when combined with multimodal information that allows for post-hoc grouping so analysis can proceed from a supervised perspective. Solely unsupervised clustering can lead to misidentification and an inability to distinguish between two or more cell types. Therefore, our study supports the general utility of cell identification by transcriptional profiling, but adds a caution: it is difficult or impossible to know under what conditions transcriptional profiling alone is capable of assigning cell identity. Only by combining multiple modalities of information such as physiology, morphology or innervation target can neuronal identity be unambiguously determined.SIGNIFICANCE STATEMENT Single cell transcriptional profiling has become a widespread tool in cell identification, particularly in the nervous system, based on the notion that genomic information determines cell identity. However, many cell type classification studies are unconstrained by other cellular attributes (e.g., morphology, physiology). Here, we systematically test how accurately transcriptional profiling can assign cell identity to well-studied anatomically- and functionally-identified neurons in two small neuronal networks. While these neurons clearly possess distinct patterns of gene expression across cell types, their expression profiles are not sufficient to unambiguously confirm their identity. We suggest that true cell identity can only be determined by combining gene expression data with other cellular attributes such as innervation pattern, morphology, or physiology.

}, doi = {10.1101/690388}, url = {https://www.biorxiv.org/content/early/2019/07/02/690388}, author = {Adam J. Northcutt and Daniel R. Kick and Adriane G. Otopalik and Benjamin M. Goetz and Rayna M. Harris and Joseph M. Santin and Hans A. Hofmann and Eve Marder and David J. Schulz} } @article {66012, title = {The mucin-selective protease StcE enables molecular and functional analysis of human cancer-associated mucins}, journal = {Proceedings of the National Academy of Sciences}, volume = {116}, year = {2019}, month = {Sep-04-2019}, pages = {7278 - 7287}, abstract = {

Mucin domains are densely\ O-glycosylated modular protein domains that are found in a wide variety of cell surface and secreted proteins. Mucin-domain glycoproteins are known to be key players in a host of human diseases, especially cancer, wherein mucin expression and glycosylation patterns are altered. Mucin biology has been difficult to study at the molecular level, in part, because methods to manipulate and structurally characterize mucin domains are lacking. Here, we demonstrate that secreted protease of C1 esterase inhibitor (StcE), a bacterial protease from\ Escherichia coli, cleaves mucin domains by recognizing a discrete peptide- and glycan-based motif. We exploited StcE{\textquoteright}s unique properties to improve sequence coverage, glycosite mapping, and glycoform analysis of recombinant human mucins by mass spectrometry. We also found that StcE digests cancer-associated mucins from cultured cells and from ascites fluid derived from patients with ovarian cancer. Finally, using StcE, we discovered that sialic acid-binding Ig-type lectin-7 (Siglec-7), a glycoimmune checkpoint receptor, selectively binds sialomucins as biological ligands, whereas the related receptor Siglec-9 does not. Mucin-selective proteolysis, as exemplified by StcE, is therefore a powerful tool for the study of mucin domain structure and function.

}, issn = {0027-8424}, doi = {10.1073/pnas.1813020116}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1813020116https://syndication.highwire.org/content/doi/10.1073/pnas.1813020116http://www.pnas.org/syndication/doi/10.1073/pnas.1813020116}, author = {Malaker, Stacy A. and Pedram, Kayvon and Ferracane, Michael J. and Bensing, Barbara A. and Krishnan, Venkatesh and Pett, Christian and Yu, Jin and Woods, Elliot C. and Kramer, Jessica R. and Westerlind, Ulrika and Dorigo, Oliver and Bertozzi, Carolyn R.} } @article {64972, title = {Multi-color single molecule imaging uncovers extensive heterogeneity in mRNA decoding.}, journal = {Cell}, volume = {178}, year = {2019}, month = {2019 Jul 11}, pages = {458-72}, abstract = {

mRNA translation is a key step in decoding genetic information. Genetic decoding is surprisingly heterogeneous, as multiple distinct polypeptides can be synthesized from a single mRNA sequence. To study translational heterogeneity, we developed the MoonTag, a new fluorescence labeling system to visualize translation of single mRNAs. When combined with the orthogonal SunTag system, the MoonTag enables dual readouts of translation, greatly expanding the possibilities to interrogate complex translational heterogeneity. By placing MoonTag and SunTag sequences in different translation reading frames, each driven by distinct translation start sites, start site selection of individual ribosomes can be visualized in real-time. We find that start site selection is largely stochastic, but that the probability of using a particular start site differs among mRNA molecules, and can be dynamically regulated over time. Together, this study provides key insights into translation start site selection heterogeneity, and provides a powerful toolbox to visualize complex translation dynamics.

}, doi = {10.1016/j.cell.2019.05.001}, author = {Boersma, Sanne and Khuperkar, Deepak and Verhagen, Bram M.P. and Sonneveld, Stijn and Grimm, Jonathan B. and Lavis, Luke D. and Tanenbaum, Marvin E.} } @article {65258, title = {A multilayer circuit architecture for the generation of distinct locomotor behaviors in .}, journal = {eLlife}, volume = {8}, year = {2019}, month = {2019 Dec 23}, abstract = {

Animals generate diverse motor behaviors, yet how the same motor neurons (MNs) generate two distinct or antagonistic behaviors remains an open question. Here we characterize larval muscle activity patterns and premotor/motor circuits to understand how they generate forward and backward locomotion. We show that all body wall MNs are activated during both behaviors, but a subset of MNs change recruitment timing for each behavior. We used TEM to reconstruct a full segment of all 60 MNs and 236 premotor neurons (PMNs), including differentially-recruited MNs. Analysis of this comprehensive connectome identified PMN-MN {\textquoteright}labeled line{\textquoteright} connectivity; PMN-MN combinatorial connectivity; asymmetric neuronal morphology; and PMN-MN circuit motifs that could all contribute to generating distinct behaviors. We generated a recurrent network model that reproduced the observed behaviors, and used functional optogenetics to validate selected model predictions. This PMN-MN connectome will provide a foundation for analyzing the full suite of larval behaviors.

}, issn = {2050-084X}, doi = {10.7554/eLife.51781}, author = {Zarin, Aref Arzan and Mark, Brandon and Cardona, Albert and Litwin-Kumar, Ashok and Doe, Chris Q} } @article {64864, title = {Multimodal in vivo brain electrophysiology with integrated glass microelectrodes.}, journal = {Nature Biomedical Engineering}, volume = {3}, year = {2019}, month = {2019 Apr 01}, pages = {741-53}, abstract = {

Electrophysiology is the most used approach for the collection of functional data in basic and translational neuroscience, but it is typically limited to either intracellular or extracellular recordings. The integration of multiple physiological modalities for the routine acquisition of multimodal data with microelectrodes could be useful for biomedical applications, yet this has been challenging owing to incompatibilities of fabrication methods. Here, we present a suite of glass pipettes with integrated microelectrodes for the simultaneous acquisition of multimodal intracellular and extracellular information in vivo, electrochemistry assessments, and optogenetic perturbations of neural activity. We used the integrated devices to acquire multimodal signals from the CA1 region of the hippocampus in mice and rats, and show that these data can serve as ground-truth validation for the performance of spike-sorting algorithms. The microdevices are applicable for basic and translational neurobiology, and for the development of next-generation brain-machine interfaces.

}, issn = {2157-846X}, doi = {10.1038/s41551-019-0373-8}, author = {Hunt, David L and Lai, Chongxi and Smith, Richard D and Lee, Albert K and Harris, Timothy D and Barbic, Mladen} } @article {64865, title = {Multiplex imaging relates quantal glutamate release to presynaptic Ca homeostasis at multiple synapses in situ.}, journal = {Nature Communications}, volume = {10}, year = {2019}, month = {2019 03 29}, pages = {1414}, abstract = {

Information processing by brain circuits depends on Ca-dependent, stochastic release of the excitatory neurotransmitter glutamate. Whilst optical glutamate sensors have enabled detection of synaptic discharges, understanding presynaptic machinery requires simultaneous readout of glutamate release and nanomolar presynaptic Ca in situ. Here, we find that the fluorescence lifetime of the red-shifted Ca indicator Cal-590 is Ca-sensitive in the nanomolar range, and employ it in combination with green glutamate sensors to relate quantal neurotransmission to presynaptic Ca kinetics. Multiplexed imaging of individual and multiple synapses in identified axonal circuits reveals that glutamate release efficacy, but not its short-term plasticity, varies with time-dependent fluctuations in presynaptic resting Ca or spike-evoked Ca entry. Within individual presynaptic boutons, we find no nanoscopic co-localisation of evoked presynaptic Ca entry with the prevalent glutamate release site, suggesting loose coupling between the two. The approach enables a better understanding of release machinery at central synapses.

}, issn = {2041-1723}, doi = {10.1038/s41467-019-09216-8}, author = {Jensen, Thomas P and Zheng, Kaiyu and Cole, Nicholas and Marvin, Jonathan S and Looger, Loren L and Rusakov, Dmitri A} } @article {65088, title = {MuscleViz: Free open-source software for muscle weakness visualization.}, journal = {Journal of Neuromuscular Diseases}, volume = {6}, year = {2019}, month = {2019 May 21}, pages = {263-266}, abstract = {

Muscle strength testing is routine in clinical practice. Here we provide an aid to the documentation and visual conceptualization of those results - MuscleViz: a free, open-source application for visualizing the results of muscle strength testing. Its use in clinical settings streamlines the communication of physical examination findings. The tool is also useful for presenting patient data in case reports or case series. A push towards free, open-source software has benefitted other areas of science; we believe a similar effort dedicated to the development of clinical tools is worth pursuing.

}, issn = {2214-3602}, doi = {10.3233/JND-190385}, author = {Wittenbach, Jason D and Cocanougher, Benjamin T and Yun, Pomi and Foley, A Reghan and B{\"o}nnemann, Carsten G} } @article {64987, title = {NDP52 tunes cortical actin interaction with astral microtubules for accurate spindle orientation.}, journal = {Cell Research}, volume = {29}, year = {2019}, month = {2019 Jun 14}, pages = {666-79}, abstract = {

Oriented cell divisions are controlled by a conserved molecular cascade involving Gαi, LGN, and NuMA. Here, we show that NDP52 regulates spindle orientation via remodeling the polar cortical actin cytoskeleton. siRNA-mediated NDP52 suppression surprisingly revealed a ring-like compact subcortical F-actin architecture surrounding the spindle in prophase/prometaphase cells, which resulted in severe defects of astral microtubule growth and an aberrant spindle orientation. Remarkably, NDP52 recruited the actin assembly factor N-WASP and regulated the dynamics of the subcortical F-actin ring in mitotic cells. Mechanistically, NDP52 was found to bind to phosphatidic acid-containing vesicles, which absorbed cytoplasmic N-WASP to regulate local filamentous actin growth at the polar cortex. Our TIRFM analyses revealed that NDP52-containing vesicles anchored N-WASP and shortened the length of actin filaments in vitro. Based on these results we propose that NDP52-containing vesicles regulate cortical actin dynamics through N-WASP to accomplish a spatiotemporal regulation between astral microtubules and the actin network for proper spindle orientation and precise chromosome segregation. In this way, intracellular vesicles cooperate with microtubules and actin filaments to regulate proper mitotic progression. Since NDP52 is absent from yeast, we reason that metazoans have evolved an elaborate spindle positioning machinery to ensure accurate chromosome segregation in mitosis.

}, issn = {1748-7838}, doi = {10.1038/s41422-019-0189-9}, author = {Yu, Huijuan and Yang, Fengrui and Dong, Peng and Liao, Shanhui and Liu, Wei R and Zhao, Gangyin and Qin, Bo and Dou, Zhen and Liu, Zhe and Liu, Wei and Zang, Jianye and Lippincott-Schwartz, Jennifer and Liu, Xing and Yao, Xuebiao} } @article {64825, title = {Neural basis for looming size and velocity encoding in the Drosophila giant fiber escape pathway.}, journal = {Current Biology : CB}, volume = {29}, year = {2019}, month = {2019 Feb 28}, pages = {1073}, abstract = {

Identified neuron classes in vertebrate cortical [1-4] and subcortical [5-8] areas and invertebrate peripheral [9-11] and central [12-14] brain neuropils encode specific visual features of a panorama. How downstream neurons integrate these features to control vital behaviors, like escape, is unclear [15]. In Drosophila, the timing of a single spike in the giant fiber (GF) descending neuron [16-18] determines whether a fly uses a short or long takeoff when escaping a looming predator [13]. We previously proposed that GF spike timing results from summation of two visual features whose detection is highly conserved across animals [19]: an object{\textquoteright}s subtended angular size and its angular velocity [5-8, 11, 20, 21]. We attributed velocity encoding to input from lobula columnar type 4 (LC4) visual projection neurons, but the size-encoding\ source remained unknown. Here, we show that lobula plate/lobula columnar, type 2 (LPLC2) visual projection neurons anatomically specialized to detect looming [22] provide the entire GF size component. We find LPLC2 neurons to be necessary for GF-mediated escape and show that LPLC2 and LC4 synapse directly onto the GF via reconstruction in a fly brain electron microscopy (EM) volume [23]. LPLC2 silencing eliminates the size component of the GF looming response in patch-clamp recordings, leaving only the velocity component. A model summing a linear function of angular velocity (provided by LC4) and a Gaussian function of angular size (provided by LPLC2) replicates GF looming response dynamics and predicts the peak response time. We thus present an identified circuit in which information from looming feature-detecting neurons is combined by a common post-synaptic target to determine behavioral output.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2019.01.079}, author = {Ache, Jan M and Polsky, Jason and Alghailani, Shada and Parekh, Ruchi and Breads, Patrick and Peek, Martin Y and Bock, Davi D and von Reyn, Catherine R and Card, Gwyneth M} } @article {65207, title = {A Neural Circuit Arbitrates between Persistence and Withdrawal in Hungry Drosophila.}, journal = {Neuron}, year = {2019}, month = {2019 Aug 09}, abstract = {

In pursuit of food, hungry animals mobilize significant energy resources and overcome exhaustion and fear. How need and motivation control the decision to continue or change behavior is not understood. Using a single fly treadmill, we show that hungry flies persistently track a food odor and increase their effort over repeated trials in the absence of reward suggesting that need dominates negative experience. We further show that odor tracking is regulated by two mushroom body output neurons (MBONs) connecting the MB to the lateral horn. These MBONs, together with dopaminergic neurons and Dop1R2 signaling, control behavioral persistence. Conversely, an octopaminergic neuron, VPM4, which directly innervates one of the MBONs, acts as a brake on odor tracking by connecting feeding and olfaction. Together, our data suggest a function for the\ MB in internal state-dependent expression of behavior that can be suppressed by external inputs conveying a competing behavioral drive.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2019.07.028}, author = {Sayin, Sercan and De Backer, Jean-Francois and Siju, K P and Wosniack, Marina E and Lewis, Laurence P and Frisch, Lisa-Marie and Gansen, Benedikt and Schlegel, Philipp and Edmondson-Stait, Amelia and Sharifi, Nadiya and Fisher, Corey B and Calle-Schuler, Steven A and Lauritzen, J Scott and Bock, Davi D and Costa, Marta and Jefferis, Gregory S X E and Gjorgjieva, Julijana and Grunwald Kadow, Ilona C} } @article {65141, title = {A neural circuit arbitrates between persistence and withdrawal in hungry drosophila.}, journal = {Neuron}, volume = {104}, year = {2019}, month = {2019 Nov 6}, pages = {544-58}, abstract = {

In pursuit of food, hungry animals mobilize significant energy resources and overcome exhaustion and fear. How need and motivation control the decision to continue or change behavior is not understood. Using a single fly treadmill, we show that hungry flies persistently track a food odor and increase their effort over repeated trials in the absence of reward suggesting that need dominates negative experience. We further show that odor tracking is regulated by two mushroom body output neurons (MBONs) connecting the MB to the lateral horn. These MBONs, together with dopaminergic neurons and Dop1R2 signaling, control behavioral persistence. Conversely, an octopaminergic neuron, VPM4, which directly innervates one of the MBONs, acts as a brake on odor tracking by connecting feeding and olfaction. Together, our data suggest a function for the\ MB in internal state-dependent expression of behavior that can be suppressed by external inputs conveying a competing behavioral drive.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2019.07.028}, author = {Sayin, Sercan and De Backer, Jean-Francois and Siju, K P and Wosniack, Marina E and Lewis, Laurence P and Frisch, Lisa-Marie and Gansen, Benedikt and Schlegel, Philipp and Edmondson-Stait, Amelia and Sharifi, Nadiya and Fisher, Corey B and Calle-Schuler, Steven A and Lauritzen, J Scott and Bock, Davi D and Costa, Marta and Jefferis, Gregory S X E and Gjorgjieva, Julijana and Grunwald Kadow, Ilona C} } @article {64917, title = {A neural circuit encoding the experience of copulation in female Drosophila.}, journal = {Neuron}, volume = {102}, year = {2019}, month = {2019 Apr 26}, pages = {1025}, abstract = {

Female behavior changes profoundly after mating. In Drosophila, the mechanisms underlying the long-term changes led by seminal products have been extensively studied. However, the effect of the sensory component of copulation on the female{\textquoteright}s internal state and behavior remains elusive. We pursued this question by dissociating the effect of coital sensory inputs from those of male ejaculate. We found that the sensory inputs of copulation cause a reduction of post-coital receptivity in females, referred to as the "copulation effect." We identified three layers of a neural circuit underlying this phenomenon. Abdominal neurons expressing the mechanosensory channel Piezo convey the signal of copulation to female-specific ascending neurons, LSANs, in the ventral nerve cord. LSANs relay this information to neurons expressing myoinhibitory peptides in the brain. We hereby provide a\ neural mechanism by which the experience of\ copulation facilitates females encoding their mating\ status, thus adjusting behavior to optimize reproduction.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2019.04.009}, author = {Shao, Lisha and Chung, Phuong and Wong, Allan and Siwanowicz, Igor and Kent, Clement F and Long, Xi and Heberlein, Ulrike} } @conference {67294, title = {Neural Correlates of Cognition in Primary Visual versus Downstream Posterior Cortices During Evidence Accumulation}, booktitle = {APS March Meeting Abstracts}, year = {2019}, month = {01/2019}, abstract = {

The ability of animals to accumulate sensory information across time is fundamental to decision-making. Using a mouse behavioral paradigm where navigational decisions are based on accumulating pulses of visual cues, I compared neural activity in primary visual (V1) to secondary visual and retrosplenial cortices. Even in V1, only a small fraction of neurons had sensory-like responses to cues. Instead, all areas were grossly similar in how neural populations contained a large variety of task-related information from sensory to cognitive, including cue timings, accumulated counts, place/time, decision and reward outcome. Across-trial influences were prevalent, possibly relevant to how animal behavior incorporates past contexts. Intriguingly, all these variables also modulated the amplitudes of sensory responses. While previous work often modeled the accumulation process as integration, the observed scaling of sensory responses by accumulated counts instead suggests a recursive process where sensory responses are gradually amplified. I show that such a multiplicative feedback-loop algorithm better explains psychophysical data than integration, particularly in how the performance transitions into following Weber-Fechner{\textquoteright}s Law only at high counts.

}, url = {https://ui.adsabs.harvard.edu/abs/2019APS..MARP67013K/abstract}, author = {Koay, Sue Ann and Tank, David and Brody, Carlos} } @article {67287, title = {Neural Correlates of Cognition in Primary Visual versus Neighboring Posterior Cortices during Visual Evidence-Accumulation-based Navigation}, journal = {bioRxiv}, year = {2019}, month = {03/2019}, abstract = {

Studies of perceptual decision-making have often assumed that the main role of sensory cortices is to provide sensory input to downstream processes that accumulate and drive behavioral decisions. We performed a systematic comparison of neural activity in primary visual (V1) to secondary visual and retrosplenial cortices, as mice performed a task where they should accumulate pulsatile visual cues through time to inform a navigational decision. Even in V1, only a small fraction of neurons had sensory-like responses to cues. Instead, in all areas neurons were sequentially active, and contained information ranging from sensory to cognitive, including cue timings, evidence, place/time, decision and reward outcome. Per-cue sensory responses were amplitude-modulated by various cognitive quantities, notably accumulated evidence. This inspired a multiplicative feedback-loop circuit hypothesis that proposes a more intricate role of sensory areas in the accumulation process, and furthermore explains a surprising observation that perceptual discrimination deviates from Weber-Fechner Law.Highlights / eTOC BlurbMice made navigational decisions based on accumulating pulsatile visual cuesThe bulk of neural activity in visual cortices was sequential and beyond-sensoryAccumulated pulse-counts modulated sensory (cue) responses, suggesting feedbackA feedback-loop neural circuit explains behavioral deviations from Weber{\textquoteright}s LawHighlights / eTOC BlurbIn a task where navigation was informed by accumulated pulsatile visual evidence, neural activity in visual cortices predominantly coded for cognitive variables across multiple timescales, including outside of a visual processing context. Even sensory responses to visual pulses were amplitude-modulated by accumulated pulse counts and other variables, inspiring a multiplicative feedback-loop circuit hypothesis that in turn explained behavioral deviations from Weber-Fechner Law.

}, doi = {10.1101/568766}, url = {https://www.biorxiv.org/content/early/2019/03/06/568766}, author = {Koay, Sue Ann and Thiberge, Stephan Y. and Brody, Carlos D. and Tank, David W.} } @article {64841, title = {Neural evolution of context-dependent fly song.}, journal = {Current Biology : CB}, volume = {29}, year = {2019}, month = {2019 Mar 08}, pages = {1089-99}, abstract = {

It is unclear where in the nervous system evolutionary changes tend to occur. To localize the source of neural evolution that has generated divergent behaviors, we developed a new approach to label and functionally manipulate homologous neurons across Drosophila species. We examined homologous descending neurons that drive courtship song in two species that sing divergent song types and localized relevant evolutionary changes in circuit function downstream of the intrinsic physiology of these descending neurons. This evolutionary change causes different species to produce divergent motor patterns in similar social contexts. Artificial stimulation of these descending neurons drives multiple song types, suggesting that multifunctional properties of song circuits may facilitate rapid evolution of song types.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2019.02.019}, author = {Ding, Yun and Lillvis, Joshua L and Cande, Jessica and Berman, Gordon J and Arthur, Benjamin J and Long, Xi and Xu, Min and Dickson, Barry J and Stern, David L} } @article {64785, title = {Neural substrates of Drosophila larval anemotaxis.}, journal = {Current Biology : CB}, volume = {29}, year = {2019}, month = {2019 Jan 29}, pages = {554-66}, abstract = {

Animals use sensory information to move toward more favorable conditions. Drosophila larvae can move up or down gradients of odors (chemotax), light (phototax), and temperature (thermotax) by modulating the probability, direction, and size of turns based on sensory input. Whether larvae can anemotax in gradients of mechanosensory cues is unknown. Further, although many of the sensory neurons that mediate taxis have been described, the central circuits are not well understood. Here, we used high-throughput, quantitative behavioral assays to demonstrate Drosophila larvae anemotax in gradients of wind speeds and to characterize the behavioral strategies involved. We found that larvae modulate the probability, direction, and size of turns to move away from higher wind speeds. This suggests that similar central decision-making mechanisms underlie taxis in somatosensory and other sensory modalities. By silencing the activity of single or very few neuron types in a behavioral screen, we found two sensory (chordotonal and multidendritic class III) and six nerve cord neuron types involved in anemotaxis. We reconstructed the identified neurons in an electron microscopy volume that spans the entire larval nervous system and found they received direct input from the mechanosensory neurons or from each other. In this way, we identified local interneurons and first- and second-order subesophageal zone (SEZ) and brain projection neurons. Finally, silencing a dopaminergic brain neuron type impairs anemotaxis. These findings suggest that anemotaxis involves both nerve cord and brain circuits. The candidate neurons and circuitry identified in our study provide a basis for future detailed mechanistic understanding of the circuit principles of anemotaxis.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2019.01.009}, author = {Jovanic, Tihana and Winding, Michael and Cardona, Albert and Truman, James W and Gershow, Marc and Zlatic, Marta} } @article {64933, title = {Neurogenetic dissection of the lateral horn reveals major outputs, diverse behavioural functions, and interactions with the mushroom body.}, journal = {Elife}, volume = {8}, year = {2019}, month = {2019 May 21}, abstract = {

Animals exhibit innate behaviours to a variety of sensory stimuli including olfactory cues. In , one higher olfactory centre, the lateral horn (LH), is implicated in innate behaviour. However, our structural and functional understanding of the LH is scant, in large part due to a lack of sparse neurogenetic tools for this region. We generate a collection of split-GAL4 driver lines providing genetic access to 82 LH cell types. We use these to create an anatomical and neurotransmitter map of the LH and link this to EM connectomics data. We find ~30\% of LH projections converge with outputs from the mushroom body, site of olfactory learning and memory. Using optogenetic activation, we identify LH cell types that drive changes in valence behavior or specific locomotor programs. In summary, we have generated a resource for manipulating and mapping LH neurons, providing new insights into the circuit basis of innate and learned olfactory behavior.

}, issn = {2050-084X}, doi = {10.7554/eLife.43079}, author = {Dolan, Michael-John and Frechter, Shahar and Bates, Alexander Shakeel and Dan, Chuntao and Huoviala, Paavo and Roberts, Ruair{\'\i} Jv and Schlegel, Philipp and Dhawan, Serene and Tabano, Remy and Dionne, Heather and Christoforou, Christina and Close, Kari and Sutcliffe, Ben and Giuliani, Bianca and Li, Feng and Costa, Marta and Ihrke, Gudrun and Meissner, Geoffrey Wilson and Bock, Davi D and Aso, Yoshinori and Rubin, Gerald M and Jefferis, Gregory Sxe} } @article {67307, title = {Neuronal activity and learning in local cortical networks are modulated by the action-perception state}, journal = {bioRxiv}, year = {2019}, month = {2019 Feb 01}, abstract = {

During sensorimotor learning, neuronal networks change to optimize the associations between action and perception. In this study, we examine how the brain harnesses neuronal patterns that correspond to the current action-perception state during learning. To this end, we recorded activity from motor cortex while monkeys either performed a familiar motor task (movement-state) or learned to control the firing rate of a target neuron using a brain-machine interface (BMI-state). Before learning, monkeys were placed in an observation-state, where no action was required. We found that neuronal patterns during the BMI-state were markedly different from the movement-state patterns. BMI-state patterns were initially similar to those in the observation-state and evolved to produce an increase in the firing rate of the target neuron. The overall activity of the non-target neurons remained similar after learning, suggesting that excitatory-inhibitory balance was maintained. Indeed, a novel neural-level reinforcement-learning network model operating in a chaotic regime of balanced excitation and inhibition predicts our results in detail. We conclude that during BMI learning, the brain can adapt patterns corresponding to the current action-perception state to gain rewards. Moreover, our results show that we can predict activity changes that occur during learning based on the pre-learning activity. This new finding may serve as a key step toward clinical brain-machine interface applications to modify impaired brain activity.

}, doi = {10.1101/537613}, url = {https://doi.org/10.1101/537613}, author = {Ben Engelhard and Ran Darshan and Nofar Ozeri-Engelhard and Zvi Israel and Uri Werner-Reiss and David Hansel and Hagai Bergman and Eilon Vaadia} } @article {69339, title = {Neuronal morphologies built for reliable physiology in a rhythmic motor circuit}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Jan 19}, pages = {e41728}, abstract = {

It is often assumed that highly-branched neuronal structures perform compartmentalized computations. However, previously we showed that the Gastric Mill (GM) neuron in the crustacean stomatogastric ganglion (STG) operates like a single electrotonic compartment, despite having thousands of branch points and total cable length \>10 mm (Otopalik et al., 2017a; 2017b). Here we show that compact electrotonic architecture is generalizable to other STG neuron types, and that these neurons present direction-insensitive, linear voltage integration, suggesting they pool synaptic inputs across their neuronal structures. We also show, using simulations of 720 cable models spanning a broad range of geometries and passive properties, that compact electrotonus, linear integration, and directional insensitivity in STG neurons arise from their neurite geometries (diameters tapering from 10-20 {\textmu}m to \uline\< 2 {\textmu}m at their terminal tips). A broad parameter search reveals multiple morphological and biophysical solutions for achieving different degrees of passive electrotonic decrement and computational strategies in the absence of active properties.

}, keywords = {cancer borealis, electrotonus, Stomatogastric ganglion, variability, voltage Integration}, issn = {2050-084X}, doi = {10.7554/eLife.41728}, url = {https://doi.org/10.7554/eLife.41728}, author = {Otopalik, Adriane G and Pipkin, Jason and Marder, Eve}, editor = {Slutsky, Inna and Calabrese, Ronald L} } @article {65107, title = {A neuronal pathway that commands deceleration in Drosophila larval light-avoidance.}, journal = {Neuroscience Bulletin}, volume = {35}, year = {2019}, month = {2019 Dec 1}, abstract = {

When facing a sudden danger or aversive condition while engaged in on-going forward motion, animals transiently slow down and make a turn to escape. The neural mechanisms underlying stimulation-induced deceleration in avoidance behavior are largely unknown. Here, we report that in Drosophila larvae, light-induced deceleration was commanded by a continuous neural pathway that included prothoracicotropic hormone neurons, eclosion hormone neurons, and tyrosine decarboxylase 2 motor neurons (the PET pathway). Inhibiting neurons in the PET pathway led to defects in light-avoidance due to insufficient deceleration and head casting. On the other hand, activation of PET pathway neurons specifically caused immediate deceleration in larval locomotion. Our findings reveal a neural substrate for the emergent deceleration response and provide a new understanding of the relationship between behavioral modules in animal avoidance responses.

}, issn = {1995-8218}, doi = {10.1007/s12264-019-00349-w}, author = {Gong, Caixia and Ouyang, Zhenhuan and Zhao, Weiqiao and Wang, Jie and Li, Kun and Zhou, Peipei and Zhao, Ting and Zheng, Nenggan and Gong, Zhefeng} } @article {64815, title = {Neuronal reactivation during post-learning sleep consolidates long-term memory in .}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Feb 25}, abstract = {

Animals consolidate some, but not all, learning experiences into long-term memory. Across the animal kingdom, sleep has been found to have a beneficial effect on the consolidation of recently formed memories into long-term storage. However, the underlying mechanisms of sleep dependent memory consolidation are poorly understood. Here, we show that consolidation of courtship long-term memory in is mediated by reactivation during sleep of dopaminergic neurons that were earlier involved in memory acquisition. We identify specific fan-shaped body neurons that induce sleep after the learning experience and activate dopaminergic neurons for memory consolidation. Thus, we provide a direct link between sleep, neuronal reactivation of dopaminergic neurons, and memory consolidation.

}, issn = {2050-084X}, doi = {10.7554/eLife.42786}, author = {Dag, Ugur and Lei, Zhengchang and Le, Jasmine Q and Wong, Allan and Bushey, Daniel and Keleman, Krystyna} } @article {68992, title = {Neuronal Transdifferentiation Potential of Human Mesenchymal Stem Cells from Neonatal and Adult Sources by a Small Molecule Cocktail.}, journal = {Stem Cells Int}, volume = {2019}, year = {2019}, month = {04/2019}, pages = {7627148}, abstract = {

Human mesenchymal stem cells (MSCs) are good candidates for brain cell replacement strategies and have already been used as adjuvant treatments in neurological disorders. MSCs can be obtained from many different sources, and the present study compares the potential of neuronal transdifferentiation in MSCs from adult and neonatal sources (Wharton{\textquoteright}s jelly (WhJ), dental pulp (DP), periodontal ligament (PDL), gingival tissue (GT), dermis (SK), placenta (PLAC), and umbilical cord blood (UCB)) with a protocol previously tested in bone marrow- (BM-) MSCs consisting of a cocktail of six small molecules: I-BET151, CHIR99021, forskolin, RepSox, Y-27632, and dbcAMP (ICFRYA). Neuronal morphology and the presence of cells positive for neuronal markers (TUJ1 and MAP2) were considered attributes of neuronal induction. The ICFRYA cocktail did not induce neuronal features in WhJ-MSCs, and these features were only partial in the MSCs from dental tissues, SK-MSCs, and PLAC-MSCs. The best response was found in UCB-MSCs, which was comparable to the response of BM-MSCs. The addition of neurotrophic factors to the ICFRYA cocktail significantly increased the number of cells with complex neuron-like morphology and increased the number of cells positive for mature neuronal markers in BM- and UCB-MSCs. The neuronal cells generated from UCB-MSCs and BM-MSCs showed increased reactivity of the neuronal genes TUJ1, MAP2, NF-H, NCAM, ND1, TAU, ENO2, GABA, and NeuN as well as down- and upregulation of MSC and neuronal genes, respectively. The present study showed marked differences between the MSCs from different sources in response to the transdifferentiation protocol used here. These results may contribute to identifying the best source of MSCs for potential cell replacement therapies.

}, issn = {1687-966X}, doi = {10.1155/2019/7627148}, author = {Cort{\'e}s-Medina, Lorena V and Pasantes-Morales, Herminia and Aguilera-Castrejon, Alejandro and Picones, Arturo and Lara-Figueroa, Cesar O and Luis, Enoch and Montesinos, Juan Jose and Cort{\'e}s-Morales, Victor A and De la Rosa Ruiz, M P and Hern{\'a}ndez-Est{\'e}vez, Erika and Bonifaz, Laura C and Alvarez-Perez, Marco Antonio and Ramos-Mandujano, Gerardo} } @article {65067, title = {Neuron-astrocyte metabolic coupling protects against activity-induced fatty acid toxicity.}, journal = {Cell}, volume = {177}, year = {2019}, month = {2019 May 30}, pages = {1522-1535.e14}, abstract = {

Metabolic coordination between neurons and astrocytes is critical for the health of the brain. However, neuron-astrocyte coupling of lipid metabolism, particularly in response to neural activity, remains largely uncharacterized. Here, we demonstrate that toxic fatty acids (FAs) produced in hyperactive neurons are transferred to astrocytic lipid droplets by ApoE-positive lipid particles. Astrocytes consume the FAs stored in lipid droplets via mitochondrial β-oxidation in response to neuronal activity and turn on a detoxification gene expression program. Our findings reveal that FA metabolism is coupled in neurons and astrocytes to protect neurons from FA toxicity during periods of enhanced activity. This coordinated mechanism for metabolizing FAs could underlie both homeostasis and a variety of disease states of the brain.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2019.04.001}, author = {Ioannou, Maria S and Jackson, Jesse and Sheu, Shu-Hsien and Chang, Chi-Lun and Weigel, Aubrey V and Liu, Hui and Pasolli, H Amalia and Xu, C Shan and Pang, Song and Matthies, Doreen and Hess, Harald F and Lippincott-Schwartz, Jennifer and Liu, Zhe} } @article {65139, title = {A neuron-glia Co-culture system for studying intercellular lipid transport.}, journal = {Curr Protoc Cell Biol}, volume = {84}, year = {2019}, month = {2019 Sep 01}, pages = {e95}, abstract = {

Neurons and glia operate in a highly coordinated fashion in the brain. Although glial cells have long been known to supply lipids to neurons via lipoprotein particles, new evidence reveals that lipid transport between neurons and glia is bidirectional. Here, we describe a co-culture system to study transfer of lipids and lipid-associated proteins from neurons to glia. The assay entails culturing neurons and glia on separate coverslips, pulsing the neurons with fluorescently labeled fatty acids, and then incubating the coverslips together. As astrocytes internalize and store neuron-derived fatty acids in lipid droplets, analyzing the number, size, and fluorescence intensity of lipid droplets containing the fluorescent fatty acids provides an easy and quantifiable measure of fatty acid transport. {\textcopyright} 2019 The Authors.

}, issn = {1934-2616}, doi = {10.1002/cpcb.95}, author = {Ioannou, Maria S and Liu, Zhe and Lippincott-Schwartz, Jennifer} } @article {65261, title = {Neuropixels data-acquisition system: A scalable platform for parallel recording of 10 000+ electrophysiological signals.}, journal = {IEEE Transactions on Biomedical Circuits and Systems}, volume = {13}, year = {2019}, month = {2019 Dec 01}, pages = {1635-1644}, abstract = {

Although CMOS fabrication has enabled a quick evolution in the design of high-density neural probes and neural-recording chips, the scaling and miniaturization of the complete data-acquisition systems has happened at a slower pace. This is mainly due to the complexity and the many requirements that change depending on the specific experimental settings. In essence, the fundamental challenge of a neural-recording system is getting the signals describing the largest possible set of neurons out of the brain and down to data storage for analysis. This requires a complete system optimization that considers the physical, electrical, thermal and signal-processing requirements, while accounting for available technology, manufacturing constraints and budget. Here we present a scalable and open-standards-based open-source data-acquisition system capable of recording from over 10,000 channels of raw neural data simultaneously. The components and their interfaces have been optimized to ensure robustness and minimum invasiveness in small-rodent electrophysiology.

}, issn = {1940-9990}, doi = {10.1109/TBCAS.2019.2943077}, author = {Putzeys, Jan and Musa, Silke and Mora Lopez, Carolina and Raducanu, Bogdan C and Carton, Alain and De Ceulaer, Jef and Karsh, Bill and Siegle, Joshua H and Van Helleputte, Nick and Harris, Timothy D and Dutta, Barundeb} } @conference {65315, title = {The Neuropixels probe: A CMOS based integrated microsystems platform for neuroscience and brain-computer interfaces.}, booktitle = {2019 IEEE International Electron Devices Meeting (IEDM)}, year = {2019}, month = {2020 Feb 13}, publisher = {IEEE}, organization = {IEEE}, address = {San Francisco, CA, USA}, abstract = {

We review recent progress in neural probes for brain recording, with a focus on the Neuropixels platform. Historically the number of neurons{\textquoteright} recorded simultaneously, follows a Moore{\textquoteright}s law like behavior, with numbers doubling every 6.7 years. Using traditional techniques of probe fabrication, continuing to scale up electrode densities is very challenging. We describe a custom CMOS process technology that enables electrode counts well beyond 1000 electrodes; with the aim to characterize large neural populations with single neuron spatial precision and millisecond timing resolution. This required integrating analog and digital circuitry with the electrode array, making it a standalone integrated electrophysiology recording system. Input referred noise and power per channel is 7.5{\textmu}V and \<50{\textmu}W respectively to ensure tissue heating \<1{\textdegree}C. This approach enables doubling the number of measured neurons every 12 months.

}, doi = {10.1109/IEDM19573.201910.1109/IEDM19573.2019.8993611}, url = {https://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=8971803https://ieeexplore.ieee.org/document/8993611/http://xplorestaging.ieee.org/ielx7/8971803/8993428/08993611.pdf?arnumber=8993611}, author = {Dutta, B. and Trautmann, E. M. and Welkenhuysen, M. and Shenoy, K. V. and Andrei, A. and Harris, T. D. and Lopez, C. M. and O{\textquoteright}Callahan, J. and Putzeys, J. and Raducanu, B. C. and Severi, S. and Stavisky, S. D.} } @article {64849, title = {Neurotransmitter identity is acquired in a lineage-restricted manner in the Drosophila CNS.}, journal = {Elife}, volume = {8}, year = {2019}, month = {2019 Mar 26}, abstract = {

The vast majority of the adult fly ventral nerve cord is composed of 34 hemilineages, which are clusters of lineally related neurons. Neurons in these hemilineages use one of the three fast-acting neurotransmitters (acetylcholine, GABA, or glutamate) for communication. We generated a comprehensive neurotransmitter usage map for the entire ventral nerve cord. We did not find any cases of neurons using more than one neurotransmitter, but found that the acetylcholine specific gene ChAT is transcribed in many glutamatergic and GABAergic neurons, but these transcripts typically do not leave the nucleus and are not translated. Importantly, our work uncovered a simple rule: All neurons within a hemilineage use the same neurotransmitter. Thus, neurotransmitter identity is acquired at the stem cell level. Our detailed transmitter- usage/lineage identity map will be a great resource for studying the developmental basis of behavior and deciphering how neuronal circuits function to regulate behavior.

}, issn = {2050-084X}, doi = {10.7554/eLife.43701}, author = {Lacin, Haluk and Chen, Hui-Min and Long, Xi and Singer, Robert H and Lee, Tzumin and Truman, James W} } @article {65227, title = {Nitric oxide acts as a cotransmitter in a subset of dopaminergic neurons to diversify memory dynamics.}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Nov 14}, abstract = {

Animals employ diverse learning rules and synaptic plasticity dynamics to record temporal and statistical information about the world. However, the molecular mechanisms underlying this diversity are poorly understood. The anatomically defined compartments of the insect mushroom body function as parallel units of associative learning, with different learning rates, memory decay dynamics and flexibility (Aso \& Rubin 2016). Here we show that nitric oxide (NO) acts as a neurotransmitter in a subset of dopaminergic neurons in . NO{\textquoteright}s effects develop more slowly than those of dopamine and depend on soluble guanylate cyclase in postsynaptic Kenyon cells. NO acts antagonistically to dopamine; it shortens memory retention and facilitates the rapid updating of memories. The interplay of NO and dopamine enables memories stored in local domains along Kenyon cell axons to be specialized for predicting the value of odors based only on recent events. Our results provide key mechanistic insights into how diverse memory dynamics are established in parallel memory systems.

}, issn = {2050-084X}, doi = {10.7554/eLife.49257}, author = {Aso, Yoshinori and Ray, Robert P and Long, Xi and Bushey, Daniel and Cichewicz, Karol and Ngo, Teri-Tb and Sharp, Brandi and Christoforou, Christina and Hu, Amy and Lemire, Andrew L and Tillberg, Paul and Hirsh, Jay and Litwin-Kumar, Ashok and Rubin, Gerald M} } @article {65035, title = {Novel Complex Interactions between Mitochondrial and Nuclear DNA in Schizophrenia and Bipolar Disorder.}, journal = {Mol Neuropsychiatry}, volume = {5}, year = {2019}, month = {2019 Mar 0}, pages = {13-27}, abstract = {

Mitochondrial dysfunction has been associated with schizophrenia (SZ) and bipolar disorder (BD). This review examines recent publications and novel associations between mitochondrial genes and SZ and BD. Associations of nuclear-encoded mitochondrial variants with SZ were found using gene- and pathway-based approaches. Two control region mitochondrial DNA (mtDNA) SNPs, T16519C and T195C, both showed an association with SZ and BD. A review of 4 studies of A15218G located in the cytochrome B oxidase gene (CYTB, SZ = 11,311, control = 35,735) shows a moderate association with SZ ( = 2.15E-03). Another mtDNA allele A12308G was nominally associated with psychosis in BD type I subjects and SZ. The first published study testing the epistatic interaction between nuclear-encoded and mitochondria-encoded genes demonstrated evidence for potential interactions between mtDNA and the nuclear genome for BD. A similar analysis for the risk of SZ revealed significant joint effects (34 nuclear-mitochondria SNP pairs with joint effect <= 5E-07) and significant enrichment of projection neurons. The mitochondria-encoded gene CYTB was found in both the epistatic interactions for SZ and BD and the single SNP association of SZ. Future efforts considering population stratification and polygenic risk scores will test the role of mitochondrial variants in psychiatric disorders.

}, issn = {2296-9209}, doi = {10.1159/000495658}, author = {Schulmann, Anton and Ryu, Euijung and Goncalves, Vanessa and Rollins, Brandi and Christiansen, Michael and Frye, Mark A and Biernacka, Joanna and Vawter, Marquis P} } @article {51253, title = {Nuclear transcriptomes of the seven neuronal cell types that constitute the mushroom bodies.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, year = {2019}, month = {2019 Jan 09}, pages = {81-94}, abstract = {

The insect mushroom body (MB) is a conserved brain structure that plays key roles in a diverse array of behaviors. The MB is the primary invertebrate model of neural circuits related to memory formation and storage, and its development, morphology, wiring, and function has been extensively studied. MBs consist of intrinsic Kenyon Cells that are divided into three major neuron classes (γ, α{\textquoteright}/β{\textquoteright} and α/β) and 7 cell subtypes (γd, γm, α{\textquoteright}/β{\textquoteright}ap, α{\textquoteright}/β{\textquoteright}m, α/βp, α/βs and α/βc) based on their birth order, morphology, and connectivity. These subtypes play distinct roles in memory processing, however the underlying transcriptional differences are unknown. Here, we used RNA sequencing (RNA-seq) to profile the nuclear transcriptomes of each MB neuronal cell subtypes. We identified 350 MB class- or subtype-specific genes, including the widely used α/β class marker and the α{\textquoteright}/β{\textquoteright} class marker Immunostaining corroborates the RNA-seq measurements at the protein level for several cases. Importantly, our data provide a full accounting of the neurotransmitter receptors, transporters, neurotransmitter biosynthetic enzymes, neuropeptides, and neuropeptide receptors expressed within each of these cell types. This high-quality, cell type-level transcriptome catalog for the MB provides a valuable resource for the fly neuroscience community.

}, issn = {2160-1836}, doi = {10.1534/g3.118.200726}, author = {Shih, Meng-Fu Maxwell and Davis, Fred Pejman and Henry, Gilbert Lee and Dubnau, Josh} } @article {59912, title = {NWB:N 2.0: An accessible data standard for neurophysiology.}, journal = {bioRxiv}, year = {2019}, month = {2019 Jan 17}, abstract = {

Neurodata Without Borders: Neurophysiology (NWB:N) is a data standard for neurophysiology, providing neuroscientists with a common standard to share, archive, use, and build common analysis tools for neurophysiology data. With NWB:N version 2.0 (NWB:N 2.0) we made significant advances towards creating a usable standard, software ecosystem, and vibrant community for standardizing neurophysiology data. In this manuscript we focus in particular on the NWB:N data standard schema and present advances towards creating an accessible data standard for neurophysiology.

}, doi = {10.1101/523035}, author = {Rubel, Oliver and Tritt, Andrew and Dichter, Benjamin and Braun, Thomas and Cain, Nicholas and Clack, Nathan G and Davidson, Thomas J and Dougherty, Max and Fillion-Rubin, Jean-Christophe and Graddis, Nile and Grauer, Michael and Kiggins, Justin T and Niu, Lawrence and Ozturk, Doruk and Schroeder, William and Soltesz, Ivan and Sommer, Friedrich T and Svoboda, Karel and Ng, Lydia and et al} } @article {51792, title = {An orderly single-trial organization of population dynamics in premotor cortex predicts behavioral variability.}, journal = {Nature Communications}, volume = {10}, year = {2019}, month = {2019 Jan 15}, pages = {216}, abstract = {

Animals are not simple input-output machines. Their responses to even very similar stimuli are variable. A key, long-standing question in neuroscience is to understand the neural correlates of such behavioral variability. To reveal these correlates, behavior and neural population activity must be related to one another on single trials. Such analysis is challenging due to the dynamical nature of brain function (e.g., in decision making), heterogeneity across neurons and limited sampling of the relevant neural population. By analyzing population recordings from mouse frontal cortex in perceptual decision-making tasks, we show that an analysis approach tailored to the coarse grain features of the dynamics is able to reveal previously unrecognized structure in the organization of population activity. This structure is similar on error and correct trials, suggesting dynamics that may be constrained by the underlying circuitry, is able to predict multiple aspects of behavioral variability and reveals long time-scale modulation of population activity.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-08141-6}, author = {Wei, Ziqiang and Inagaki, Hidehiko and Li, Nuo and Svoboda, Karel and Druckmann, Shaul} } @article {65206, title = {The organization of the second optic chiasm of the optic lobe.}, journal = {Frontiers in Neural Circuits}, volume = {13}, year = {2019}, month = {2019 Oct 11}, pages = {65}, abstract = {

Visual pathways from the compound eye of an insect relay to four neuropils, successively the lamina, medulla, lobula, and lobula plate in the underlying optic lobe. Among these neuropils, the medulla, lobula, and lobula plate are interconnected by the complex second optic chiasm, through which the anteroposterior axis undergoes an inversion between the medulla and lobula. Given their complex structure, the projection patterns through the second optic chiasm have so far lacked critical analysis. By densely reconstructing axon trajectories using a volumetric scanning electron microscopy (SEM) technique, we reveal the three-dimensional structure of the second optic chiasm of , which comprises interleaving bundles and sheets of axons insulated from each other by glial sheaths. These axon bundles invert their horizontal sequence in passing between the medulla and lobula. Axons connecting the medulla and lobula plate are also bundled together with them but do not decussate the sequence of their horizontal positions. They interleave with sheets of projection neuron axons between the lobula and lobula plate, which also lack decussations. We estimate that approximately 19,500 cells per hemisphere, about two thirds of the optic lobe neurons, contribute to the second chiasm, most being Tm cells, with an estimated additional 2,780 T4 and T5 cells each. The chiasm mostly comprises axons and cell body fibers, but also a few synaptic elements. Based on our anatomical findings, we propose that a chiasmal structure between the neuropils is potentially advantageous for processing complex visual information in parallel. The EM reconstruction shows not only the structure of the chiasm in the adult brain, the previously unreported main topic of our study, but also suggest that the projection patterns of the neurons comprising the chiasm may be determined by the proliferation centers from which the neurons develop. Such a complex wiring pattern could, we suggest, only have arisen in several evolutionary steps.

}, issn = {1662-5110}, doi = {10.3389/fncir.2019.00065}, author = {Shinomiya, Kazunori and Horne, Jane Anne and McLin, Sari and Wiederman, Meagan and Nern, Aljoscha and Plaza, Stephen M and Meinertzhagen, Ian A} } @article {64902, title = {Parametric amplification of reversible transverse susceptibility in single domain magnetic nanoparticles.}, journal = {AIP Advances}, volume = {9}, year = {2019}, month = {2019 Apr 25}, pages = {045031}, abstract = {
We propose, model, and experimentally demonstrate the enhancement of reversible transverse susceptibility in single domain magnetic nanoparticles through the principle of parametric amplification. It has previously been demonstrated that properly oriented anisotropic single domain magnetic nanoparticles have an appreciable peak in transverse susceptibility at the particle anisotropy field. Here we show theoretically and experimentally that an additional parametric AC magnetic field applied at a proper phase and at twice the frequency (2f) of the transverse field further enhances transverse susceptibility peaks through the process of parametric amplification. We model this effect numerically and describe it through the energy formalism of the single magnetic domain Stoner-Wohlfarth model. The proper phase relationships of the transverse and parametric fields to obtain either parametric amplification or attenuation of the transverse susceptibility signals are also described. We experimentally demonstrate such parametric tuning of transverse susceptibility in single domain magnetic nanoparticles of a commercial audio tape in a prototypical inductive transverse susceptibility set-up.
}, doi = {10.1063/1.5079980}, author = {El Bidweihy, Hatem and Smith, Richard D and Barbic, Mladen} } @article {51254, title = {The Pearson{\textquoteright}s correlation coefficient is not a universally superior colocalization metric. Response to {\textquoteright}Quantifying colocalization: the MOC is a hybrid coefficient - an uninformative mix of co-occurrence and correlation{\textquoteright}.}, journal = {Journal of Cell Science}, volume = {132}, year = {2019}, month = {2019 Jan 09}, issn = {1477-9137}, doi = {10.1242/jcs.227074}, author = {Aaron, Jesse S and Taylor, Aaron B and Chew, Teng-Leong} } @article {65245, title = {Phase separation of YAP reorganizes genome topology for long-term YAP target gene expression.}, journal = {Nature Cell Biology}, volume = {21}, year = {2019}, month = {2019 Dec}, pages = {1578-1589}, abstract = {

Yes-associated protein (YAP) is a transcriptional co-activator that regulates cell proliferation and survival by binding to a select set of enhancers for target gene activation. How YAP coordinates these transcriptional responses is unknown. Here, we demonstrate that YAP forms liquid-like condensates in the nucleus. Formed within seconds of hyperosmotic stress, YAP condensates compartmentalized the YAP transcription factor TEAD1 and other YAP-related co-activators, including TAZ, and subsequently induced the transcription of YAP-specific proliferation genes. Super-resolution imaging using assay for transposase-accessible chromatin with photoactivated localization microscopy revealed that the YAP nuclear condensates were areas enriched in accessible chromatin domains organized as super-enhancers. Initially devoid of RNA polymerase II, the accessible chromatin domains later acquired RNA polymerase II, transcribing RNA. The removal of the intrinsically-disordered YAP transcription activation domain prevented the formation of YAP condensates and diminished downstream YAP signalling. Thus, dynamic changes in genome organization and gene activation during YAP reprogramming is mediated by liquid-liquid phase separation.

}, issn = {1476-4679}, doi = {10.1038/s41556-019-0433-z}, author = {Cai, Danfeng and Feliciano, Daniel and Dong, Peng and Flores, Eduardo and Gruebele, Martin and Porat-Shliom, Natalie and Sukenik, Shahar and Liu, Zhe and Lippincott-Schwartz, Jennifer} } @article {66014, title = {Physical Principles of Membrane Shape Regulation by the Glycocalyx}, journal = {Cell}, volume = {177}, year = {2019}, month = {Jan-06-2019}, pages = {1757 - 1770.e21}, abstract = {

Cells bend their plasma membranes into highly curved forms to interact with the local environment, but how shape generation is regulated is not fully resolved. Here, we report a synergy between shape-generating processes in the cell interior and the external organization and composition of the cell-surface\ glycocalyx.\ Mucinbiopolymers\ and long-chain\ polysaccharides\ within the glycocalyx can generate entropic forces that favor or disfavor the projection of spherical and finger-like extensions from the cell surface. A polymer brush model of the glycocalyx successfully predicts the effects of polymer size and cell-surface density on membrane morphologies. Specific glycocalyx compositions can also induce plasma membrane instabilities to generate more exotic undulating and pearled\ membrane structures\ and drive secretion of extracellular vesicles. Together, our results suggest a fundamental role for the glycocalyx in regulating curved membrane features that serve in communication between cells and with the\ extracellular matrix.

}, issn = {00928674}, doi = {10.1016/j.cell.2019.04.017}, url = {https://www.sciencedirect.com/science/article/pii/S0092867419304039?via\%3Dihub}, author = {Shurer, Carolyn R. and Kuo, Joe Chin-Hun and Roberts, LaDeidra Mon{\'e}t and Gandhi, Jay G. and Colville, Marshall J. and Enoki, Thais A. and Pan, Hao and Su, Jin and Noble, Jade M. and Hollander, Michael J. and O{\textquoteright}Donnell, John P. and Yin, Rose and Pedram, Kayvon and M{\"o}ckl, Leonhard and Kourkoutis, Lena F. and Moerner, W.E. and Bertozzi, Carolyn R. and Feigenson, Gerald W. and Reesink, Heidi L. and Paszek, Matthew J.} } @article {64944, title = {Pleiotropic effects of ebony and tan on pigmentation and cuticular hydrocarbon composition in Drosophila melanogaster.}, journal = {Frontiers in Physiology}, volume = {10}, year = {2019}, month = {05/2019}, pages = {518}, abstract = {

Pleiotropic genes are genes that affect more than one trait. For example, many genes required for pigmentation in the fruit fly also affect traits such as circadian rhythms, vision, and mating behavior. Here, we present evidence that two pigmentation genes, and , which encode enzymes catalyzing reciprocal reactions in the melanin biosynthesis pathway, also affect cuticular hydrocarbon (CHC) composition in females. More specifically, we report that loss-of-function mutants have a CHC profile that is biased toward long (\>25C) chain CHCs, whereas loss-of-function mutants have a CHC profile that is biased toward short (\<25C) chain CHCs. Moreover, pharmacological inhibition of dopamine synthesis, a key step in the melanin synthesis pathway, reversed the changes in CHC composition seen in mutants, making the CHC profiles similar to those seen in mutants. These observations suggest that genetic variation affecting and/or activity might cause correlated changes in pigmentation and CHC composition in natural populations. We tested this possibility using the Genetic Reference Panel (DGRP) and found that CHC composition covaried with pigmentation as well as levels of and expression in newly eclosed adults in a manner consistent with the and mutant phenotypes. These data suggest that the pleiotropic effects of and might contribute to covariation of pigmentation and CHC profiles in .

}, issn = {1664-042X}, doi = {10.3389/fphys.2019.00518}, author = {Massey, Jonathan H and Akiyama, Noriyoshi and Bien, Tanja and Dreisewerd, Klaus and Wittkopp, Patricia J and Yew, Joanne Y and Takahashi, Aya} } @article {64786, title = {Possible magneto-mechanical and magneto-thermal mechanisms of ion channel activation by iron-loaded ferritin in magnetogenetics.}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Aug 02}, abstract = {

The palette of tools for stimulation and regulation of neural activity is continually expanding. One of the new methods being introduced is magnetogenetics, where mechano-sensitive and thermo-sensitive ion channels are genetically engineered to be closely coupled to the iron-storage protein ferritin. Such genetic constructs could provide a powerful new way of non-invasively activating ion channels in-vivo using external magnetic fields that easily penetrate biological tissue. Initial reports that introduced this new technology have sparked a vigorous debate on the plausibility of physical mechanisms of ion channel activation by means of external magnetic fields. I argue that the initial criticisms leveled against magnetogenetics as being physically implausible were possibly based on the overly simplistic and unnecessarily pessimistic assumptions about the magnetic spin configurations of iron in ferritin protein. Additionally, all the possible magnetic-field-based mechanisms of ion channel activation in magnetogenetics might not have been fully considered. I present and propose several new magneto-mechanical and magneto-thermal mechanisms of ion channel activation by iron-loaded ferritin protein that may elucidate and clarify some of the mysteries that presently challenge our understanding of the reported biological experiments. Finally, I present some additional puzzles that will require further theoretical and experimental investigation.

}, doi = {10.7554/eLife.45807}, author = {Barbic, Mladen} } @article {64903, title = {Practical considerations in particle and object tracking and analysis.}, journal = {Current Protocols in Cell Biology}, volume = {83}, year = {2019}, month = {2019 Jun 01}, pages = {e88}, abstract = {

The rapid advancement of live-cell imaging technologies has enabled biologists to generate high-dimensional data to follow biological movement at the microscopic level. Yet, the "perceived" ease of use of modern microscopes has led to challenges whereby sub-optimal data are commonly generated that cannot support quantitative tracking and analysis as a result of various ill-advised decisions made during image acquisition. Even optimally acquired images often require further optimization through digital processing before they can be analyzed. In writing this article, we presume our target audience to be biologists with a foundational understanding of digital image acquisition and processing, who are seeking to understand the essential steps for particle/object tracking experiments. It is with this targeted readership in mind that we review the basic principles of image-processing techniques as well as analysis strategies commonly used for tracking experiments. We conclude this technical survey with a discussion of how movement behavior can be mathematically modeled and described. {\textcopyright} 2019 by John Wiley \& Sons, Inc.

}, issn = {1934-2616}, doi = {10.1002/cpcb.88}, author = {Aaron, Jesse and Wait, Eric and DeSantis, Michael and Chew, Teng-Leong} } @article {64832, title = {Prediction of choice from competing mechanosensory and choice-memory cues during active tactile decision making.}, journal = {The Journal of Neuroscience : the official journal of the Society for Neuroscience}, volume = {39}, year = {2019}, month = {2019 May 15}, pages = {3921-33}, abstract = {

Perceptual decision making is an active process where animals move their sense organs to extract task-relevant information. To investigate how the brain translates sensory input into decisions during active sensation, we developed a mouse active touch task where the mechanosensory input can be precisely measured and that challenges animals to use multiple mechanosensory cues. Male mice were trained to localise a pole using a single whisker and to report their decision by selecting one of three choices. Using high-speed imaging and machine vision we estimated whisker-object mechanical forces at millisecond resolution. Mice solved the task by a sensory-motor strategy where both the strength and direction of whisker bending were informative cues to pole location. We found competing influences of immediate sensory input and choice memory on mouse choice. On correct trials, choice could be predicted from the direction and strength of whisker bending, but not from previous choice. In contrast, on error trials, choice could be predicted from previous choice but not from whisker bending. This study shows that animal choices during active tactile decision making can be predicted from mechanosenory and choice-memory signals; and provides a new task, well-suited for future study of the neural basis of active perceptual decisions.Due to the difficulty of measuring the sensory input to moving sense organs, active perceptual decision making remains poorly understood. The whisker system provides a way forward since it is now possible to measure the mechanical forces due to whisker-object contact during behaviour. Here we train mice in a novel behavioural task that challenges them to use rich mechanosensory cues, but can be performed using one whisker and enables task-relevant mechanical forces to be precisely estimated. This approach enables rigorous study of how sensory cues translate into action during active, perceptual decision making. Our findings provide new insight into active touch and how sensory/internal signals interact to determine behavioural choices.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2217-18.2019}, author = {Campagner, Dario and Evans, Mathew H and Chlebikova, Katarina and Colins-Rodriguez, Andrea and Loft, Michaela S E and Fox, Sarah and Pettifer, David and Humphries, Mark D and Svoboda, Karel and Petersen, Rasmus S} } @article {65236, title = {Preparation and co-culture of iPSC-derived dopaminergic neurons and astrocytes.}, journal = {Current Protocols in Cell Biology}, volume = {85}, year = {2019}, month = {2019 Dec 04}, pages = {e98}, abstract = {

Induced pluripotent stem cell (iPSC)-based models are powerful tools to study neurodegenerative diseases such as Parkinson{\textquoteright}s disease. The differentiation of patient-derived neurons and astrocytes allows investigation of the molecular mechanisms responsible for disease onset and development. In particular, these two cell types can be mono- or co-cultured to study the influence of cell-autonomous and non-cell-autonomous contributors to neurodegenerative diseases. We developed a streamlined procedure to produce high-quality/high-purity cultures of dopaminergic neurons and astrocytes that originate from the same population of midbrain floor-plate progenitors. This unit describes differentiation, quality control, culture parameters, and troubleshooting tips to ensure the highest quality and reproducibility of research results. {\textcopyright} 2019 The Authors. Basic Protocol 1: Differentiation of iPSCs into midbrain-patterned neural progenitor cells Support Protocol: Quality control of neural progenitor cells Basic Protocol 2: Differentiation of neural progenitor cells into astrocytes Basic Protocol 3: Differentiation of neural progenitor cells into dopaminergic neurons Basic Protocol 4: Co-culture of iPSC-derived neurons and astrocytes.

}, issn = {1934-2616}, doi = {10.1002/cpcb.98}, author = {de Rus Jacquet, Aurelie} } @article {64813, title = {Principles governing the dynamics of GABAergic interneurons in the barrel cortex.}, journal = {bioRxiv}, year = {2019}, month = {2019 Feb 21}, abstract = {

Information processing in the neocortex is performed by GABAergic interneurons that are integrated with excitatory neurons into precisely structured circuits. To reveal how each neuron type shapes sensory representations, we measured spikes and membrane potential of specific types of neurons in the barrel cortex while mice performed an active, whisker-dependent object localization task. Whiskers were tracked with millisecond precision. Fast-spiking (FS) neurons were activated by touch with short latency and by whisking. FS neurons track thalamic input and provide feedforward inhibition. Somatostatin (SOM)-expressing neurons were also excited by touch, but with a delay (5 ms) compared to excitatory (E) and FS neurons. SOM neurons monitor local excitation and provide feedback inhibition. Vasoactive intestinal polypeptide (VIP)-expressing neurons were not driven by touch but elevated their spike rate during whisking, disinhibiting E and FS neurons. Our data reveal rules of recruitment for specific interneuron types, providing foundations for understanding cortical computations.

}, doi = {10.1101/554949}, author = {Yu, Jianing and Hu, Hang and Agmon, Ariel and Svoboda, Karel} } @article {64780, title = {Probing nicotinic acetylcholine receptor function in mouse brain slices via laser flash photolysis of photoactivatable nicotine.}, journal = {Journal of Visualized Experiments : JoVE}, year = {2019}, month = {2019 Jan 25}, abstract = {

Acetylcholine (ACh) acts through receptors to modulate a variety of neuronal processes, but it has been challenging to link ACh receptor function with subcellular location within cells where this function is carried out. To study the subcellular location of nicotinic ACh receptors (nAChRs) in native brain tissue, an optical method was developed for precise release of nicotine at discrete locations near neuronal membranes during electrophysiological recordings. Patch-clamped neurons in brain slices are filled with dye to visualize their morphology during 2-photon laser scanning microscopy, and nicotine uncaging is executed with a light flash by focusing a 405 nm laser beam near one or more cellular membranes. Cellular current deflections are measured, and a high-resolution three-dimensional (3D) image of the recorded neuron is made to allow reconciliation of nAChR responses with cellular morphology. This method allows for detailed analysis of nAChR functional distribution in complex tissue preparations, promising to enhance the understanding of cholinergic neurotransmission.

}, issn = {1940-087X}, doi = {10.3791/58873}, author = {Arvin, Matthew C and Wokosin, David L and Banala, Sambashiva and Lavis, Luke D and Drenan, Ryan M} } @article {64935, title = {Quantitative in vivo imaging of neuronal glucose concentrations with a genetically encoded fluorescence lifetime sensor.}, journal = {Journal of Neuroscience Research}, volume = {97}, year = {2019}, month = {2019 Aug 01}, pages = {946-60}, abstract = {

Glucose is an essential source of energy for the brain. Recently, the development of genetically encoded fluorescent biosensors has allowed real time visualization of glucose dynamics from individual neurons and astrocytes. A major difficulty for this approach, even for ratiometric sensors, is the lack of a practical method to convert such measurements into actual concentrations in ex vivo brain tissue or in vivo. Fluorescence lifetime imaging provides a strategy to overcome this. In a previous study, we reported the lifetime glucose sensor iGlucoSnFR-TS (then called SweetieTS) for monitoring changes in neuronal glucose levels in response to stimulation. This genetically encoded sensor was generated by combining the Thermus thermophilus glucose-binding protein with a circularly permuted variant of the monomeric fluorescent protein T-Sapphire. Here, we provide more details on iGlucoSnFR-TS design and characterization, as well as pH and temperature sensitivities. For accurate estimation of glucose concentrations, the sensor must be calibrated at the same temperature as the experiments. We find that when the extracellular glucose concentration is in the range 2-10\ mM, the intracellular glucose concentration in hippocampal neurons from acute brain slices is ~20\% of the nominal external glucose concentration (~0.4-2\ mM). We also measured the cytosolic neuronal glucose concentration in vivo, finding a range of ~0.7-2.5\ mM in cortical neurons from awake mice.

}, issn = {1097-4547}, doi = {10.1002/jnr.24433}, author = {D{\'\i}az-Garc{\'\i}a, Carlos Manlio and Lahmann, Carolina and Mart{\'\i}nez-Fran{\c c}ois, Juan Ram{\'o}n and Li, Binsen and Koveal, Dorothy and Nathwani, Nidhi and Rahman, Mahia and Keller, Jacob P and Marvin, Jonathan S and Looger, Loren L and Yellen, Gary} } @article {66013, title = {Quantitative Super-Resolution Microscopy of the Mammalian Glycocalyx}, journal = {Developmental Cell}, volume = {50}, year = {2019}, month = {Jan-07-2019}, pages = {57 - 72.e6}, abstract = {

The mammalian glycocalyx is a heavily glycosylated extramembrane compartment found on nearly every cell. Despite its relevance in both health and disease, studies of the glycocalyx remain hampered by a paucity of methods to spatially classify its components. We combine metabolic labeling, bioorthogonal chemistry, and super-resolution localization microscopy to image two constituents of cell-surface glycans,\ N-acetylgalactosamine (GalNAc) and sialic acid, with 10{\textendash}20\ nm precision in 2D and 3D. This approach enables two measurements: glycocalyx height and the distribution of individual sugars distal from the membrane. These measurements show that the glycocalyx exhibits nanoscale organization on both cell lines and primary human tumor cells. Additionally, we observe enhanced glycocalyx height in response to epithelial-to-mesenchymal transition and to oncogenic\ KRAS\ activation. In the latter case, we trace increased height to an effector gene,\ GALNT7. These data highlight the power of advanced imaging methods to provide molecular and functional insights into glycocalyx biology.

}, issn = {15345807}, doi = {10.1016/j.devcel.2019.04.035}, url = {https://www.sciencedirect.com/science/article/pii/S1534580719303326?via\%3Dihub}, author = {M{\"o}ckl, Leonhard and Pedram, Kayvon and Roy, Anish R. and Krishnan, Venkatesh and Gustavsson, Anna-Karin and Dorigo, Oliver and Bertozzi, Carolyn R. and Moerner, W.E.} } @article {65176, title = {Rational design of fluorogenic and spontaneously blinking labels for super-resolution imaging.}, journal = {ACS Central Science}, volume = {5}, year = {2019}, month = {2019 Sep 25}, pages = {1602-1613}, abstract = {

Rhodamine dyes exist in equilibrium between a fluorescent zwitterion and a nonfluorescent lactone. Tuning this equilibrium toward the nonfluorescent lactone form can improve cell-permeability and allow creation of "fluorogenic" compounds-ligands that shift to the fluorescent zwitterion upon binding a biomolecular target. An archetype fluorogenic dye is the far-red tetramethyl-Si-rhodamine (SiR), which has been used to create exceptionally useful labels for advanced microscopy. Here, we develop a quantitative framework for the development of new fluorogenic dyes, determining that the lactone-zwitterion equilibrium constant () is sufficient to predict fluorogenicity. This rubric emerged from our analysis of known fluorophores and yielded new fluorescent and fluorogenic labels with improved performance in cellular imaging experiments. We then designed a novel fluorophore-Janelia Fluor 526 (JF)-with SiR-like properties but shorter fluorescence excitation and emission wavelengths. JF is a versatile scaffold for fluorogenic probes including ligands for self-labeling tags, stains for endogenous structures, and spontaneously blinking labels for super-resolution immunofluorescence. JF constitutes a new label for advanced microscopy experiments, and our quantitative framework will enable the rational design of other fluorogenic probes for bioimaging.

}, issn = {2374-7943}, doi = {10.1021/acscentsci.9b00676}, author = {Zheng, Qinsi and Ayala, Anthony X and Chung, Inhee and Weigel, Aubrey V and Ranjan, Anand and Falco, Natalie and Grimm, Jonathan B and Tkachuk, Ariana N and Wu, Carl and Lippincott-Schwartz, Jennifer and Singer, Robert H and Lavis, Luke D} } @article {65138, title = {Reconstruction of 1,000 projection neurons reveals new cell types and organization of long-range connectivity in the mouse brain.}, journal = {Cell}, volume = {179}, year = {2019}, month = {2019 Sep 19}, pages = {268-81}, abstract = {

Neuronal\ cell\ types\ are the nodes of neural circuits that determine the flow of information within the\ brain. Neuronal morphology, especially the shape of the axonal arbor, provides an essential descriptor of\ cell\ type and\ reveals\ how individual\ neurons\ route their output across the\ brain. Despite the importance of morphology, few\ projection\ neurons\ in the\ mouse\ brain\ have been reconstructed in their entirety. Here we present a robust and efficient platform for imaging and reconstructing complete neuronal morphologies, including axonal arbors that span substantial portions of the\ brain. We used this platform to reconstruct more than\ 1,000\ projection\ neurons\ in the motor cortex, thalamus, subiculum, and hypothalamus. Together, the reconstructed\ neurons\ constitute more than 85\ meters of axonal length and are available in a searchable online database. Axonal shapes revealed previously unknown subtypes of\ projection\ neurons\ and suggest organizational principles of\ long-range\ connectivity.

}, issn = {00928674}, doi = {10.1016/j.cell.2019.07.042}, author = {Winnubst, Johan and Bas, Erhan and Ferreira, Tiago A. and Wu, Zhuhao and Economo, Michael N. and Edson, Patrick and Arthur, Ben J. and Bruns, Christopher and Rokicki, Konrad and Schauder, David and Olbris, Donald J. and Murphy, Sean D. and Ackerman, David G. and Arshadi, Cameron and Baldwin, Perry and Blake, Regina and Elsayed, Ahmad and Hasan, Mashtura and Ramirez, Daniel and Dos Santos, Bruno and Weldon, Monet and Zafar, Amina and Dudman, Joshua T. and Gerfen, Charles R. and Hantman, Adam W. and Korff, Wyatt and Sternson, Scott M. and Spruston, Nelson and Svoboda, Karel and Chandrashekar, Jayaram} } @article {65129, title = {Recruitment of GABAergic interneurons in the barrel cortex during active tactile behavior.}, journal = {Neuron}, volume = {104}, year = {2019}, month = {2019 Oct 23}, pages = {412-27}, abstract = {

Neural computation involves diverse types of GABAergic inhibitory interneurons that are integrated with excitatory (E) neurons into precisely structured circuits. To understand how each neuron type shapes sensory representations, we measured firing patterns of defined types of neurons in the barrel cortex while mice performed an active, whisker-dependent object localization task. Touch excited fast-spiking (FS) interneurons at short latency, followed by activation of E neurons and somatostatin-expressing (SST) interneurons. Touch only weakly modulated vasoactive intestinal polypeptide-expressing (VIP) interneurons. Voluntary whisker movement activated FS neurons in the ventral posteromedial nucleus (VPM) target layers, a subset of SST neurons and a majority of VIP neurons. Together, FS neurons track thalamic input, mediating feedforward inhibition. SST neurons monitor local excitation, providing feedback inhibition. VIP neurons are activated by non-sensory inputs, disinhibiting E and FS neurons. Our data reveal rules of recruitment for interneuron types during behavior, providing foundations for understanding computation in cortical microcircuits.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2019.07.027}, author = {Yu, Jianing and Hu, Hang and Agmon, Ariel and Svoboda, Karel} } @article {65111, title = {Regionalized tissue fluidization by an actomyosin cable is required for epithelial gap closure during insect gastrulation.}, journal = {Nature Communications}, volume = {11}, year = {2019}, month = {2020 Aug 22}, pages = {5604}, abstract = {

Many animal embryos face early on in development the problem of having to pull and close an epithelial sheet around the spherical yolk-sac. During this gastrulation process, known as epiboly, the spherical geometry of the egg dictates that the epithelial sheet first expands and subsequently compacts to close around the sphere. While it is well recognized that contractile actomyosin cables can drive epiboly movements, it is unclear how pulling on the leading edge can lead to simultaneous tissue expansion and compaction. Moreover, the epithelial sheet spreading over the sphere is mechanically stressed and this stress needs to be dissipated for seamless closure. While oriented cell division is known to dissipate tissue stresses during epiboly, it is unclear how this can be achieved without cell division. Here we show that during extraembryonic tissue (serosa) epiboly in the red flour beetle Tribolium castaneum, the non-proliferative serosa becomes regionalized into two distinct territories: a dorsal region under higher tension away from the leading edge with larger, isodiametric and non-rearranging cells, and a more fluid ventral region under lower tension surrounding the leading edge with smaller, anisotropic cells undergoing cell intercalation. Our results suggest that fluidization of the leading edge is effected by a heterogeneous actomyosin cable that drives sequential eviction and intercalation of individual cells away from the serosa margin. Since this developmental solution utilized during epiboly resembles the mechanism of wound healing in other systems, we propose actomyosin cable-driven local tissue fluidization as a conserved morphogenetic module for closure of epithelial gaps.

}, doi = {https://doi.org/10.1101/744193}, author = {Jain, Akanksha and Ulman, Vladimir and Mukherjee, Argo and Prakash, Mangal and Pimpale, Lokesh and Munster, Stefan and Panfilio, Kristen A. and Jug, Florian and Grill, Stephan WA. and Tomancak, Pavel and Pavlopoulos, Anastasios} } @article {64988, title = {Regulation of forward and backward locomotion through intersegmental feedback circuits in Drosophila larvae.}, journal = {Nature Communications}, volume = {10}, year = {2019}, month = {2019 Jun 14}, pages = {2654}, abstract = {

Animal locomotion requires spatiotemporally coordinated contraction of muscles throughout the body. Here, we investigate how contractions of antagonistic groups of muscles are intersegmentally coordinated during bidirectional crawling of Drosophila larvae. We identify two pairs of higher-order premotor excitatory interneurons present in each abdominal neuromere that intersegmentally provide feedback to the adjacent neuromere during motor propagation. The two feedback neuron pairs are differentially active during either forward or backward locomotion but commonly target a group of premotor interneurons that together provide excitatory inputs to transverse muscles and inhibitory inputs to the antagonistic longitudinal muscles. Inhibition of either feedback neuron pair compromises contraction of transverse muscles in a direction-specific manner. Our results suggest that the intersegmental feedback neurons coordinate contraction of synergistic muscles by acting as delay circuits representing the phase lag between segments. The identified circuit architecture also shows how bidirectional motor networks could be economically embedded in the nervous system.

}, issn = {2041-1723}, doi = {10.1038/s41467-019-10695-y}, author = {Kohsaka, Hiroshi and Zwart, Maarten F and Fushiki, Akira and Fetter, Richard D and Truman, James W and Cardona, Albert and Nose, Akinao} } @article {59913, title = {Regulation of modulatory cell activity across olfactory structures in Drosophila melanogaster.}, journal = {bioRxiv}, year = {2019}, month = {2019 Jan 16}, abstract = {

All centralized nervous systems possess modulatory neurons that arborize broadly across multiple brain regions. Such modulatory systems are critical for proper sensory, motor, and cognitive processing. How single modulatory neurons integrate into circuits within their target destination remains largely unexplored due to difficulties in both labeling individual cells and imaging across distal parts of the CNS. Here, we take advantage of an identified modulatory neuron in Drosophila that arborizes in multiple olfactory neuropils. We demonstrate that this serotonergic neuron has opposing odor responses in its neurites of the antennal lobe and lateral horn, first and second order olfactory neuropils respectively. Specifically, processes of this neuron in the antennal lobe have responses that are inhibitory and odor-independent, while lateral horn responses are excitatory and odor-specific. The results show that widespread modulatory neurons may not function purely as integrate-and-fire cells, but rather their transmitter release is locally regulated based on neuropil. As nearly all vertebrate and invertebrate neurons are subject to synaptic inputs along their dendro-axonic axis, it is likely that our findings generalize across phylogeny and other broadly-projecting modulatory systems.

}, doi = {10.1101/522177}, author = {Zhang, Xiaonan and Coates, Kaylynn and Dacks, Andrew and Gunay, Cengiz and Lauritzen, J Scott and Li, Feng and Calle-Schuler, Steven A and Bock, Davi D and Gaudry, Quentin} } @article {65025, title = {Regulation of plasma membrane nanodomains of the water channel aquaporin-3 revealed by fixed and live photoactivated localization microscopy.}, journal = {Nano Letters}, volume = {19}, year = {2019}, month = {2019 Feb 13}, pages = {699-707}, abstract = {

Several aquaporin (AQP) water channels are short-term regulated by the messenger cyclic adenosine monophosphate (cAMP), including AQP3. Bulk measurements show that cAMP can change diffusive properties of AQP3; however, it remains unknown how elevated cAMP affects AQP3 organization at the nanoscale. Here we analyzed AQP3 nano-organization following cAMP stimulation using photoactivated localization microscopy (PALM) of fixed cells combined with pair correlation analysis. Moreover, in live cells, we combined PALM acquisitions of single fluorophores with single-particle tracking (spt-PALM). These analyses revealed that AQP3 tends to cluster and that the diffusive mobility is confined to nanodomains with radii of \~{}150 nm. This domain size increases by \~{}30\% upon elevation of cAMP, which, however, is not accompanied by a significant increase in the confined diffusion coefficient. This regulation of AQP3 organization at the nanoscale may be important for understanding the mechanisms of water AQP3-mediated water transport across plasma membranes.

}, keywords = {Animals, Aquaporin 3, Cell Membrane, Cyclic AMP, Diffusion, Dogs, Epithelial Cells, Madin Darby Canine Kidney Cells, Microscopy, Fluorescence, Photochemical Processes}, issn = {1530-6992}, doi = {10.1021/acs.nanolett.8b03721}, author = {Arnspang, Eva C and Sengupta, Prabuddha and Mortensen, Kim I and Jensen, Helene H and Hahn, Ute and Jensen, Eva B V and Lippincott-Schwartz, Jennifer and Nejsum, Lene N} } @article {65159, title = {A repeated molecular architecture across thalamic pathways.}, journal = {Nature Neuroscience}, volume = {22}, year = {2019}, month = {2019 Sep 16}, pages = {1925-35}, abstract = {

The thalamus is the central communication hub of the forebrain and provides the cerebral cortex with inputs from sensory organs, subcortical systems and the cortex itself. Multiple thalamic regions send convergent information to each cortical region, but the organizational logic of thalamic projections has remained elusive. Through comprehensive transcriptional analyses of retrogradely labeled thalamic neurons in adult mice, we identify three major profiles of thalamic pathways. These profiles exist along a continuum that is repeated across all major projection systems, such as those for vision, motor control and cognition. The largest component of gene expression variation in the mouse thalamus is topographically organized, with features conserved in humans. Transcriptional differences between these thalamic neuronal identities are tied to cellular features that are critical for function, such as axonal morphology and membrane properties. Molecular profiling therefore reveals covariation in the properties of thalamic pathways serving all major input modalities and output targets, thus establishing a molecular framework for understanding the thalamus.

}, issn = {1546-1726}, doi = {10.1038/s41593-019-0483-3}, author = {Phillips, James W and Schulmann, Anton and Hara, Erina and Winnubst, Johan and Liu, Chenghao and Valakh, Vera and Wang, Lihua and Shields, Brenda C and Korff, Wyatt and Chandrashekar, Jayaram and Lemire, Andrew L and Mensh, Brett and Dudman, Joshua T and Nelson, Sacha B and Hantman, Adam W} } @article {65080, title = {Response to "Fallacies of mice experiments".}, journal = {Neuroinformatics}, year = {2019}, month = {2019 Aug 03}, abstract = {

In a recent Editorial, De Schutter commented on our recent study on the roles of a cortico-cerebellar loop in motor planning in mice (De Schutter 2019, Neuroinformatics, 17, 181-183, Gao et al. 2018, Nature, 563, 113-116). Two issues were raised. First, De Schutter questions the involvement of the fastigial nucleus in motor planning, rather than the dentate nucleus, given previous anatomical studies in non-human primates. Second, De Schutter suggests that our study design did not delineate different components of the behavior and the fastigial nucleus might play roles in sensory discrimination rather than motor planning. These comments are based on anatomical studies in other species and homology-based arguments and ignore key anatomical data and neurophysiological experiments from our study. Here we outline our interpretation of existing data and point out gaps in knowledge where future studies are needed.

}, issn = {1559-0089}, doi = {10.1007/s12021-019-09433-y}, author = {Gao, Zhenyu and Thomas, Alyse M and Economo, Michael N and Abrego, Amada M and Svoboda, Karel and De Zeeuw, Chris I and Li, Nuo} } @article {65108, title = {Revealing the synaptic hodology of mammalian neural circuits with multiscale neurocartography.}, journal = {Frontiers in Neuroinformatics}, volume = {13}, year = {2019}, month = {2019 Jul 30}, abstract = {

The functional features of neural circuits are determined by a combination of properties that range in scale from projections systems across the whole brain to molecular interactions at the synapse. The burgeoning field of neurocartography seeks to map these relevant features of brain structure{\textemdash}spanning a volume \~{}20 orders of magnitude{\textemdash}to determine how neural circuits perform computations supporting cognitive function and complex behavior. Recent technological breakthroughs in tissue sample preparation, high-throughput electron microscopy imaging, and automated image analyses have produced the first visualizations of all synaptic connections between neurons of invertebrate model systems. However, the sheer size of the central nervous system in mammals implies that reconstruction of the first full brain maps at synaptic scale may not be feasible for decades. In this review, we outline existing and emerging technologies for neurocartography that complement electron microscopy-based strategies and are beginning to derive some basic organizing principles of circuit hodology at the mesoscale, microscale, and nanoscale. Specifically, we discuss how a host of light microscopy techniques including array tomography have been utilized to determine both long-range and subcellular organizing principles of synaptic connectivity. In addition, we discuss how new techniques, such as two-photon serial tomography of the entire mouse brain, have become attractive approaches to dissect the potential connectivity of defined cell types. Ultimately, principles derived from these techniques promise to facilitate a conceptual understanding of how connectomes, and neurocartography in general, can be effectively utilized toward reaching a mechanistic understanding of circuit function.

}, doi = {10.3389/fninf.2019.00052}, url = {https://www.frontiersin.org/article/10.3389/fninf.2019.00052/fullhttps://www.frontiersin.org/article/10.3389/fninf.2019.00052/full}, author = {Bloss, Erik B. and Hunt, David L.} } @article {64544, title = {Rhomboid distorts lipids to break the viscosity-imposed speed limit of membrane diffusion.}, journal = {Science (New York, N.Y.)}, volume = {363}, year = {2019}, month = {2019 Feb 01}, abstract = {

Enzymes that cut proteins inside membranes regulate diverse cellular events, including cell signaling, homeostasis, and host-pathogen interactions. Adaptations that enable catalysis in this exceptional environment are poorly understood. We visualized single molecules of multiple rhomboid intramembrane proteases and unrelated proteins in living cells (human and ) and planar lipid bilayers. Notably, only rhomboid proteins were able to diffuse above the Saffman-Delbr{\"u}ck viscosity limit of the membrane. Hydrophobic mismatch with the irregularly shaped rhomboid fold distorted surrounding lipids and propelled rhomboid diffusion. The rate of substrate processing in living cells scaled with rhomboid diffusivity. Thus, intramembrane proteolysis is naturally diffusion-limited, but cells mitigate this constraint by using the rhomboid fold to overcome the "speed limit" of membrane diffusion.

}, issn = {1095-9203}, doi = {10.1126/science.aao0076}, author = {Kreutzberger, Alex J B and Ji, Ming and Aaron, Jesse and Mihaljevi{\'c}, Ljubica and Urban, Sini{\v s}a} } @article {65156, title = {RNA granules hitchhike on lysosomes for long-distance transport, Using annexin A11 as a molecular tether.}, journal = {Cell}, volume = {179}, year = {2019}, month = {2019 Sep 19}, pages = {147-164.e20}, abstract = {

Long-distance RNA transport enables local protein synthesis at metabolically-active sites distant from the nucleus. This process ensures an appropriate spatial organization of proteins, vital to polarized cells such as neurons. Here, we present a mechanism for RNA transport in which RNA granules "hitchhike" on moving lysosomes. In\ vitro biophysical modeling, live-cell microscopy, and unbiased proximity labeling proteomics reveal that annexin A11 (ANXA11), an RNA granule-associated phosphoinositide-binding protein, acts as a molecular tether between RNA granules and lysosomes. ANXA11 possesses an N-terminal low complexity domain, facilitating its phase separation into membraneless RNA granules, and a C-terminal membrane binding domain, enabling interactions with lysosomes. RNA granule transport requires ANXA11, and amyotrophic lateral sclerosis (ALS)-associated mutations in ANXA11 impair RNA granule transport by disrupting their interactions with lysosomes. Thus, ANXA11 mediates neuronal RNA transport by tethering RNA granules to actively-transported lysosomes, performing a critical cellular function that is disrupted in ALS.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2019.08.050}, author = {Liao, Ya-Cheng and Fernandopulle, Michael S and Wang, Guozhen and Choi, Heejun and Hao, Ling and Drerup, Catherine M and Patel, Rajan and Qamar, Seema and Nixon-Abell, Jonathon and Shen, Yi and Meadows, William and Vendruscolo, Michele and Knowles, Tuomas P J and Nelson, Matthew and Czekalska, Magdalena A and Musteikyte, Greta and Gachechiladze, Mariam A and Stephens, Christina A and Pasolli, H Amalia and Forrest, Lucy R and St George-Hyslop, Peter and Lippincott-Schwartz, Jennifer and Ward, Michael E} } @article {68754, title = {A Semi-high-throughput Imaging Method and Data Visualization Toolkit to Analyze C. elegans Embryonic Development}, journal = {Journal of Visualized Experiments}, year = {2019}, month = {10/2019}, abstract = {

C. elegans\ is the premier system for the systematic analysis of cell fate specification and morphogenetic events during embryonic development. One challenge is that embryogenesis dynamically unfolds over a period of about 13 h; this half day-long timescale has constrained the scope of experiments by limiting the number of embryos that can be imaged. Here, we describe a semi-high-throughput protocol that allows for the simultaneous 3D time-lapse imaging of development in 80{\textendash}100 embryos at moderate time resolution, from up to 14 different conditions, in a single overnight run. The protocol is straightforward and can be implemented by any laboratory with access to a microscope with point visiting capacity. The utility of this protocol is demonstrated by using it to image two custom-built strains expressing fluorescent markers optimized to visualize key aspects of germ-layer specification and morphogenesis. To analyze the data, a custom program that crops individual embryos out of a broader field of view in all channels, z-steps, and timepoints and saves the sequences for each embryo into a separate tiff stack was built. The program, which includes a user-friendly graphical user interface (GUI), streamlines data processing by isolating, pre-processing, and uniformly orienting individual embryos in preparation for visualization or automated analysis. Also supplied is an ImageJ macro that compiles individual embryo data into a multi-panel file that displays maximum intensity fluorescence projection and brightfield images for each embryo at each time point. The protocols and tools described herein were validated by using them to characterize embryonic development following knock-down of 40 previously described developmental genes; this analysis visualized previously annotated developmental phenotypes and revealed new ones. In summary, this work details a semi-high-throughput imaging method coupled with a cropping program and ImageJ visualization tool that, when combined with strains expressing informative fluorescent markers, greatly accelerates experiments to analyze embryonic development.

}, doi = {10.3791/60362}, url = {https://www.jove.com/t/60362/a-semi-high-throughput-imaging-method-data-visualization-toolkit-tohttps://www.jove.com/t/60362/a-semi-high-throughput-imaging-method-data-visualization-toolkit-to}, author = {Khaliullin, Renat N. and Hendel, Jeffrey M. and Gerson-Gurwitz, Adina and Wang, Shaohe and Ochoa, Stacy D. and Zhao, Zhiling and Desai, Arshad and Oegema, Karen and Green, Rebecca A.} } @article {67290, title = {Sequential and efficient neural-population coding of complex task information}, journal = {bioRxiv}, year = {2019}, month = {10/2019}, abstract = {

Recent work has highlighted that many types of variables are represented in each neocortical area. How can these many neural representations be organized together without interference, and coherently maintained/updated through time? We recorded from large neural populations in posterior cortices as mice performed a complex, dynamic task involving multiple interrelated variables. The neural encoding implied that correlated task variables were represented by uncorrelated modes in an information-coding subspace. We show via theory that this can enable optimal decoding directions to be insensitive to neural noise levels. Across posterior cortex, principles of efficient coding thus applied to task-specific information, with neural-population modes as the encoding unit. Remarkably, this encoding function was multiplexed with rapidly changing, sequential neural dynamics, yet reliably followed slow changes in task-variable correlations through time. We can explain this as due to a mathematical property of high-dimensional spaces that the brain might exploit as a temporal scaffold.

}, doi = {10.1101/801654}, url = {https://www.biorxiv.org/content/early/2019/10/13/801654}, author = {Koay, Sue Ann and Thiberge, Stephan Y. and Brody, Carlos D. and Tank, David W.} } @article {65225, title = {ShuTu: Open-source software for efficient and accurate reconstruction of dendritic morphology.}, journal = {Frontiers in Neuroinformatics}, volume = {13}, year = {2019}, month = {2019 Oct 31}, pages = {68}, abstract = {

Neurons perform computations by integrating inputs from thousands of synapses-mostly in the dendritic tree-to drive action potential firing in the axon. One fruitful approach to studying this process is to record from neurons using patch-clamp electrodes, fill the recorded neurons with a substance that allows subsequent staining, reconstruct the three-dimensional architectures of the dendrites, and use the resulting functional and structural data to develop computer models of dendritic integration. Accurately producing quantitative reconstructions of dendrites is typically a tedious process taking many hours of manual inspection and measurement. Here we present ShuTu, a new software package that facilitates accurate and efficient reconstruction of dendrites imaged using bright-field microscopy. The program operates in two steps: (1) automated identification of dendritic processes, and (2) manual correction of errors in the automated reconstruction. This approach allows neurons with complex dendritic morphologies to be reconstructed rapidly and efficiently, thus facilitating the use of computer models to study dendritic structure-function relationships and the computations performed by single neurons.

}, issn = {1662-5196}, doi = {10.3389/fninf.2019.00068}, author = {Jin, Dezhe Z and Zhao, Ting and Hunt, David L and Tillage, Rachel P and Hsu, Ching-Lung and Spruston, Nelson} } @article {65764, title = {Simple imaging protocol for autofluorescence elimination and optical sectioning in fluorescence endomicroscopy}, journal = {Optica}, volume = {6}, year = {2019}, month = {07/2019}, pages = {972}, abstract = {

Fiber-optic epifluorescence imaging with one-photon excitation benefits from its ease of use, cheap light sources, and full-frame acquisition, which enables it for favorable temporal resolution of image acquisition. However, it suffers from a lack of robustness against autofluorescence and light scattering. Moreover, it cannot easily eliminate the out-of-focus background, which generally results in low-contrast images. In order to overcome these limitations, we have implemented fast out-of-phase imaging after optical modulation (Speed OPIOM) for dynamic contrast in fluorescence endomicroscopy. Using a simple and cheap optical-fiber bundle-based endomicroscope integrating modulatable light sources, we first showed that Speed OPIOM provides intrinsic optical sectioning, which restricts the observation of fluorescent labels at targeted positions within a sample. We also demonstrated that this imaging protocol efficiently eliminates the interference of autofluorescence arising from both the fiber bundle and the specimen in several biological samples. Finally, we could perform multiplexed observations of two spectrally similar fluorophores differing by their photoswitching dynamics. Such attractive features of Speed OPIOM in fluorescence endomicroscopy should find applications in bioprocessing, clinical diagnostics, plant observation, and surface imaging.

}, doi = {10.1364/optica.6.000972}, author = {Zhang, Ruikang and Chouket, Raja and Tebo, Alison G and Plamont, Marie-Aude and Kelemen, Zsolt and Gissot, Lionel and Faure, Jean-Denis and Gautier, Arnaud and Croquette, Vincent and Jullien, Ludovic and Saux, Thomas Le} } @article {65162, title = {Single-cell reconstruction of emerging population activity in an entire developing circuit.}, journal = {Cell}, volume = {179}, year = {2019}, month = {2019 Sep 23}, abstract = {

Animal survival requires a functioning nervous system to develop during embryogenesis. Newborn neurons must assemble into circuits producing activity patterns capable of instructing behaviors. Elucidating how this process is coordinated requires new methods that follow maturation and activity of all cells across a developing circuit. We present an imaging method for comprehensively tracking neuron lineages, movements, molecular identities, and activity in the entire developing zebrafish spinal cord, from neurogenesis until the emergence of patterned activity instructing the earliest spontaneous motor behavior. We found that motoneurons are active first and form local patterned ensembles with neighboring neurons. These ensembles merge, synchronize globally after reaching a threshold size, and finally recruit commissural interneurons to orchestrate the left-right alternating patterns important for locomotion in vertebrates. Individual neurons undergo functional maturation stereotypically based on their birth time and anatomical origin. Our study provides a general strategy for reconstructing how functioning circuits emerge during embryogenesis.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2019.08.039}, author = {Wan, Yinan and Wei, Ziqiang and Looger, Loren L and Koyama, Minoru and Druckmann, Shaul and Keller, Philipp J} } @article {64830, title = {Single-neuron axonal reconstruction: The search for a wiring diagram of the brain.}, journal = {The Journal of Comparative Neurology}, year = {2019}, month = {2019 Mar 12}, abstract = {

Reconstruction of the axonal projection patterns of single neurons has been an important tool for understanding both the diversity of cell types in the brain and the logic of information flow between brain regions. Innovative approaches now enable the complete reconstruction of axonal projection patterns of individual neurons with vastly increased throughput. Here we review how advances in genetic, imaging, and computational techniques have been exploited for axonal reconstruction. We also discuss how new innovations could enable the integration of genetic and physiological information with axonal morphology for producing a census of cell types in the mammalian brain at scale. This article is protected by copyright. All rights reserved.

}, issn = {1096-9861}, doi = {10.1002/cne.24674}, author = {Economo, Michael N and Winnubst, Johan and Bas, Erhan and Ferreira, Tiago A and Chandrashekar, Jayaram} } @article {65089, title = {A small number of cholinergic neurons mediate hyperaggression in female Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, year = {2019}, month = {2019 Aug 07}, pages = {17029-38}, abstract = {

In the\ Drosophila\ model of aggression, males and females fight in same-sex pairings, but a wide disparity exists in the levels of aggression displayed by the 2 sexes. A screen of\ Drosophila Flylight Gal4\ lines by driving expression of the gene coding for the temperature sensitive dTRPA1 channel, yielded a single line (GMR26E01-Gal4) displaying greatly enhanced aggression when thermoactivated. Targeted neurons were widely distributed throughout male and female nervous systems, but the enhanced aggression was seen only in females. No effects were seen on female mating behavior, general arousal, or male aggression. We quantified the enhancement by measuring fight patterns characteristic of female and male aggression and confirmed that the effect was female-specific. To reduce the numbers of neurons involved, we used an intersectional approach with our library of enhancer trap flp-recombinase lines. Several crosses reduced the populations of labeled neurons, but only 1 cross yielded a large reduction while maintaining the phenotype. Of particular interest was a small group (2 to 4 pairs) of neurons in the approximate position of the pC1 cluster important in governing male and female social behavior. Female brains have approximately 20\ doublesex (dsx)-expressing neurons within pC1 clusters. Using\ dsxFLP\ instead of\ 357FLP\ for the intersectional studies, we found that the same 2 to 4 pairs of neurons likely were identified with both. These neurons were cholinergic and showed no immunostaining for other transmitter compounds. Blocking the activation of these neurons blocked the enhancement of aggression.

}, issn = {0027-8424}, doi = {10.1073/pnas.1907042116}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1907042116https://syndication.highwire.org/content/doi/10.1073/pnas.1907042116http://www.pnas.org/syndication/doi/10.1073/pnas.1907042116}, author = {Palavicino-Maggio, Caroline B. and Chan, Yick-Bun and McKellar, Claire and Kravitz, Edward A.} } @article {65113, title = {Software for lattice light-sheet imaging of FRET biosensors, illustrated with a new Rap1 biosensor.}, journal = {The Journal of Cell Biology}, volume = {218}, year = {2019}, month = {2019 Sep 2}, pages = {3153-3160}, abstract = {

Lattice light-sheet microscopy (LLSM) is valuable for its combination of reduced photobleaching and outstanding spatiotemporal resolution in 3D. Using LLSM to image biosensors in living cells could provide unprecedented visualization of rapid, localized changes in protein conformation or posttranslational modification. However, computational manipulations required for biosensor imaging with LLSM are challenging for many software packages. The calculations require processing large amounts of data even for simple changes such as reorientation of cell renderings or testing the effects of user-selectable settings, and lattice imaging poses unique challenges in thresholding and ratio imaging. We describe here a new software package, named ImageTank, that is specifically designed for practical imaging of biosensors using LLSM. To demonstrate its capabilities, we use a new biosensor to study the rapid 3D dynamics of the small GTPase Rap1 in vesicles and cell protrusions.

}, issn = {0021-9525}, doi = {10.1083/jcb.201903019}, url = {http://www.jcb.org/lookup/doi/10.1083/jcb.201903019}, author = {O{\textquoteright}Shaughnessy, Ellen C. and Stone, Orrin J. and LaFosse, Paul K. and Azoitei, Mihai L. and Tsygankov, Denis and Heddleston, John M. and Legant, Wesley R. and Wittchen, Erika S. and Burridge, Keith and Elston, Timothy C. and Betzig, Eric and Chew, Teng-Leong and Adalsteinsson, David and Hahn, Klaus M.} } @article {64795, title = {Spastin tethers lipid droplets to peroxisomes and directs fatty acid trafficking through ESCRT-III.}, journal = {Journal of Cell Biology}, volume = {218}, year = {2019}, month = {2019 Jun 21}, pages = {2583-99}, abstract = {

Lipid droplets (LDs) are neutral lipid storage organelles that transfer lipids to various organelles including peroxisomes. Here, we show that the hereditary spastic paraplegia protein M1 Spastin, a membrane-bound AAA ATPase found on LDs, coordinates fatty acid (FA) trafficking from LDs to peroxisomes through two inter-related mechanisms. First, M1 Spastin forms a tethering complex with peroxisomal ABCD1 to promote LD-peroxisome contact formation. Second, M1 Spastin recruits the membrane-shaping ESCRT-III proteins IST1 and CHMP1B to LDs via its MIT domain to facilitate LD-to-peroxisome FA trafficking, possibly through IST1 and CHMP1B modifying LD membrane morphology. Furthermore, M1 Spastin, IST1 and CHMP1B are all required to relieve LDs of lipid peroxidation. The roles of M1 Spastin in tethering LDs to peroxisomes and in recruiting ESCRT-III components to LD-peroxisome contact sites for FA trafficking may help explain the pathogenesis of diseases associated with defective FA metabolism in LDs and peroxisomes.

}, doi = {10.1101/544023}, author = {Chang, Chi-Lun and Weigel, Aubrey V and Ioannou, Maria S and Pasolli, H Amalia and Xu, C Shan and Peale, David R and Shtengel, Gleb and Freeman, Melanie and Hess, Harald F and Blackstone, Craig and Lippincott-Schwartz, Jennifer} } @article {65226, title = {Spatiotemporal constraints on optogenetic inactivation in cortical circuits.}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Nov 18}, abstract = {

Optogenetics allows manipulations of genetically and spatially defined neuronal populations with excellent temporal control. However, neurons are coupled with other neurons over multiple length scales, and the effects of localized manipulations thus spread beyond the targeted neurons. We benchmarked several optogenetic methods to inactivate small regions of neocortex. Optogenetic excitation of GABAergic neurons produced more effective inactivation than light-gated ion pumps. Transgenic mice expressing the light-dependent chloride channel GtACR1 produced the most potent inactivation. Generally, inactivation spread substantially beyond the photostimulation light, caused by strong coupling between cortical neurons. Over some range of light intensity, optogenetic excitation of inhibitory neurons reduced activity in these neurons, together with pyramidal neurons, a signature of inhibition-stabilized neural networks ({\textquoteright}paradoxical effect{\textquoteright}). The offset of optogenetic inactivation was followed by rebound excitation in a light dose-dependent manner, limiting temporal resolution. Our data offer guidance for the design of optogenetics experiments.

}, issn = {2050-084X}, doi = {10.7554/eLife.48622}, author = {Li, Nuo and Chen, Susu and Guo, Zengcai V and Chen, Han and Huo, Yan and Inagaki, Hidehiko K and Chen, Guang and Davis, Courtney and Hansel, David and Guo, Caiying and Svoboda, Karel} } @article {67281, title = {Specialized coding of sensory, motor and cognitive variables in VTA dopamine neurons}, journal = {Nature}, volume = {570}, year = {2019}, month = {05/2019}, pages = {509 - 513}, abstract = {

There is increased appreciation that dopamine neurons in the midbrain respond not only to reward1\ and reward-predicting cues1,2, but also to other variables such as the distance to reward3, movements4,5,6,7,8,9\ and behavioural choices10,11. An important question is how the responses to these diverse variables are organized across the population of dopamine neurons. Whether individual dopamine neurons multiplex several variables, or whether there are subsets of neurons that are specialized in encoding specific behavioural variables remains unclear. This fundamental question has been difficult to resolve because recordings from large populations of individual dopamine neurons have not been performed in a behavioural task with sufficient complexity to examine these diverse variables simultaneously. Here, to address this gap, we used two-photon calcium imaging through an implanted lens to record the activity of more than 300 dopamine neurons from the ventral tegmental area of the mouse midbrain during a complex decision-making task. As mice navigated in a virtual-reality environment, dopamine neurons encoded an array of sensory, motor and cognitive variables. These responses were functionally clustered, such that subpopulations of neurons transmitted information about a subset of behavioural variables, in addition to encoding reward. These functional clusters were spatially organized, with neighbouring neurons more likely to be part of the same cluster. Together with the topography between dopamine neurons and their projections, this specialization and anatomical organization may aid downstream circuits in correctly interpreting the wide range of signals transmitted by dopamine neurons.

}, issn = {0028-0836}, doi = {10.1038/s41586-019-1261-9}, url = {http://www.nature.com/articles/s41586-019-1261-9}, author = {Engelhard, Ben and Finkelstein, Joel and Cox, Julia and Fleming, Weston and Jang, Hee Jae and Ornelas, Sharon and Koay, Sue Ann and Thiberge, Stephan Y. and Daw, Nathaniel D. and Tank, David W. and Witten, Ilana B.} } @article {65765, title = {A split fluorescent reporter with rapid and reversible complementation.}, journal = {Nature communications}, volume = {10}, year = {2019}, month = {06/2019}, pages = {2822}, abstract = {

Interactions between proteins play an essential role in metabolic and signaling pathways, cellular processes and organismal systems. We report the development of splitFAST, a fluorescence complementation system for the visualization of transient protein-protein interactions in living cells. Engineered from the fluorogenic reporter FAST (Fluorescence-Activating and absorption-Shifting Tag), which specifically and reversibly binds fluorogenic hydroxybenzylidene rhodanine (HBR) analogs, splitFAST displays rapid and reversible complementation, allowing the real-time visualization of both the formation and the dissociation of a protein assembly.

}, doi = {10.1038/s41467-019-10855-0}, author = {Tebo, Alison G and Gautier, Arnaud} } @article {64843, title = {Split-QF system for fine-tuned transgene expression in Drosophila.}, journal = {Genetics}, volume = {212}, year = {2019}, month = {2019 Mar 12}, pages = {53-63}, abstract = {

The Q-system is a binary expression system that works well across species. Here we report the development and demonstrate applications of a split-QF system that drives strong expression in , is repressible by QS and inducible by a small non-toxic molecule quinic acid. The split-QF system is fully compatible with existing split-GAL4 and split-LexA lines, thus greatly expanding the range of possible advanced intersectional experiments and anatomical, physiological and behavioural assays in and in other organisms.

}, issn = {1943-2631}, doi = {10.1534/genetics.119.302034}, author = {Riabinina, Olena and Vernon, Samuel W and Dickson, Barry J and Baines, Richard A} } @article {49187, title = {Spontaneous behaviors drive multidimensional, brain-wide population activity.}, journal = {Science}, volume = {364}, year = {2019}, month = {2019 Apr 18}, pages = {255}, abstract = {

Sensory cortices are active in the absence of external sensory stimuli. To understand the nature of this ongoing activity, we used two-photon calcium imaging to record from over 10,000 neurons in the visual cortex of mice awake in darkness while monitoring their behavior videographically. Ongoing population activity was multidimensional, exhibiting at least 100 significant dimensions, some of which were related to the spontaneous behaviors of the mice. The largest single dimension was correlated with the running speed and pupil area, while a 16-dimensional summary of orofacial behaviors could predict ~45\% of the explainable neural variance. Electrophysiological recordings with 8 simultaneous Neuropixels probes revealed a similar encoding of high-dimensional orofacial behaviors across multiple forebrain regions. Representation of motor variables continued uninterrupted during visual stimulus presentation, occupying dimensions nearly orthogonal to the stimulus responses. Our results show that a multidimensional representation of motor state is encoded across the forebrain, and is integrated with visual input by neuronal populations in primary visual cortex.

}, doi = {10.1101/306019}, author = {Stringer, Carsen and Pachitariu, Marius and Steinmetz, Nicholas A and Reddy, Charu Bai and Carandini, Matteo and Harris, Kenneth D} } @article {65050, title = {State-dependent decoupling of sensory and motor circuits underlies behavioral flexibility in Drosophila.}, journal = {Nature Neuroscience}, volume = {22}, year = {2019}, month = {2019 Jul 01}, pages = {1132-1139}, abstract = {

An approaching predator and self-motion toward an object can generate similar looming patterns on the retina, but these situations demand different rapid responses. How central circuits flexibly process visual cues to activate appropriate, fast motor pathways remains unclear. Here we identify two descending neuron (DN) types that control landing and contribute to visuomotor flexibility in Drosophila. For each, silencing impairs visually evoked landing, activation drives landing, and spike rate determines leg extension amplitude. Critically, visual responses of both DNs are severely attenuated during non-flight periods, effectively decoupling visual stimuli from the landing motor pathway when landing is inappropriate. The flight-dependence mechanism differs between DN types. Octopamine exposure mimics flight effects in one, whereas the other probably receives neuronal feedback from flight motor circuits. Thus, this sensorimotor flexibility arises from distinct mechanisms for gating action-specific descending pathways, such that sensory and motor networks are coupled or decoupled according to the behavioral state.

}, issn = {1546-1726}, doi = {10.1038/s41593-019-0413-4}, author = {Ache, Jan M and Namiki, Shigehiro and Lee, Allen and Branson, Kristin and Card, Gwyneth M} } @article {56203, title = {Structural basis for substrate binding and specificity of a sodium-alanine symporter AgcS.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, year = {2019}, month = {2019 Jan 18}, pages = {2086-90}, abstract = {

The amino acid, polyamine, and organocation (APC) superfamily is the second largest superfamily of membrane proteins forming secondary transporters that move a range of organic molecules across the cell membrane. Each transporter in the APC superfamily is specific for a unique subset of substrates, even if they possess a similar structural fold. The mechanism of substrate selectivity remains, by and large, elusive. Here, we report two crystal structures of an APC member from , the alanine or glycine:cation symporter (AgcS), with l- or d-alanine bound. Structural analysis combined with site-directed mutagenesis and functional studies inform on substrate binding, specificity, and modulation of the AgcS family and reveal key structural features that allow this transporter to accommodate glycine and alanine while excluding all other amino acids. Mutation of key residues in the substrate binding site expand the selectivity to include valine and leucine. These studies provide initial insights into substrate selectivity in AgcS symporters.

}, issn = {1091-6490}, doi = {10.1073/pnas.1806206116}, author = {Ma, Jinming and Lei, Hsiang-Ting and Reyes, Francis E and Sanchez-Martinez, Silvia and Sarhan, Maen F and Hattne, Johan and Gonen, Tamir} } @article {65260, title = {Structure of an endosomal signaling GPCR-G protein-β-arrestin megacomplex.}, journal = {Nature Structural and Molecular Biology}, volume = {26}, year = {2019}, month = {2019 Dec 26}, pages = {1123-1131}, abstract = {

Classically, G-protein-coupled receptors (GPCRs) are thought to activate G protein from the plasma membrane and are subsequently desensitized by β-arrestin (β-arr). However, some GPCRs continue to signal through G protein from internalized compartments, mediated by a GPCR-G protein-β-arr {\textquoteright}megaplex{\textquoteright}. Nevertheless, the molecular architecture of the megaplex remains unknown. Here, we present its cryo-electron microscopy structure, which shows simultaneous engagement of human G protein and bovine β-arr to the core and phosphorylated tail, respectively, of a single active human chimeric β-adrenergic receptor with the C-terminal tail of the arginine vasopressin type 2 receptor (βVR). All three components adopt their canonical active conformations, suggesting that a single megaplex GPCR is capable of simultaneously activating G protein and β-arr. Our findings provide a structural basis for GPCR-mediated sustained internalized G protein signaling.

}, issn = {1545-9985}, doi = {10.1038/s41594-019-0330-y}, author = {Nguyen, Anthony H and Thomsen, Alex R B and Cahill, Thomas J and Huang, Rick and Huang, Li-Yin and Marcink, Tara and Clarke, Oliver B and Heissel, S{\o}ren and Masoudi, Ali and Ben-Hail, Danya and Samaan, Fadi and Dandey, Venkata P and Tan, Yong Zi and Hong, Chuan and Mahoney, Jacob P and Triest, Sarah and Little, John and Chen, Xin and Sunahara, Roger and Steyaert, Jan and Molina, Henrik and Yu, Zhiheng and des Georges, Amedee and Lefkowitz, Robert J} } @article {65002, title = {Super resolution imaging of a distinct chromatin loop in human lymphoblastoid cells.}, journal = {bioRxiv}, year = {2019}, month = {2019 Apr 29}, abstract = {

The three-dimensional genome structure plays a fundamental role in gene regulation and cellular functions. Recent studies in genomics based on sequencing technologies inferred the very basic functional chromatin folding structures of the genome known as chromatin loops, the long-range chromatin interactions that are often mediated by protein factors. To visualize the looping structure of chromatin we applied super-resolution microscopy iPALM to image a specific chromatin loop in GM12878 cells. Totally, we have generated six images of the target chromatin region at the single molecule resolution. To infer the chromatin structures from the captured images, we modeled them as looping conformations using different computational algorithms and then evaluated the models by comparing with Hi-C data to examine the concordance. The results showed a good correlation between the imaging data and sequencing data, suggesting the visualization of higher-order chromatin structures for the very short genomic segments can be realized by microscopic imaging.

}, doi = {10.1101/621920}, author = {Jacqueline Jufen Zhu and Zofia Parteka and Byoungkoo Lee and Przemyslaw Szalaj and Ping Wang and Karolina Jodkowska and Jesse Aaron and Teng-Leong Chew and Dariusz Plewczynski and Yijun Ruan} } @article {65197, title = {Superresolution architecture of cornerstone focal adhesions in human pluripotent stem cells.}, journal = {Nature Communications}, volume = {10}, year = {2019}, month = {2019 Oct 18}, pages = {4756}, abstract = {

While it is clear that key transcriptional programmes are important for maintaining pluripotency, the requirement for cell adhesion to the extracellular matrix remains poorly defined. Human pluripotent stem cells\ (hPSCs) form colonies encircled by an actin ring and large stable cornerstone focal adhesions (FA). Using superresolution two-colour interferometric photo-activated localisation microscopy, we examine the three-dimensional architecture of cornerstone adhesions and report vertical lamination of FA proteins with three main structural features distinct from previously studied focal adhesions: 1) integrin β5 and talin are present at high density, at the edges of cornerstone FA, adjacent to a vertical kank-rich protein wall, 2) vinculin localises higher than previously reported, displaying a head-above-tail orientation, and 3) surprisingly, actin and α-actinin are present in two discrete z-layers. Finally, we report that depletion of kanks diminishes FA patterning, and actin organisation within the colony, indicating a role for kanks in hPSC colony architecture.

}, issn = {2041-1723}, doi = {10.1038/s41467-019-12611-w}, author = {Stubb, Aki and Guzm{\'a}n, Camilo and N{\"a}rv{\"a}, Elisa and Aaron, Jesse and Chew, Teng-Leong and Saari, Markku and Miihkinen, Mitro and Jacquemet, Guillaume and Ivaska, Johanna} } @article {65109, title = {T3S injectisome needle complex structures in four distinct states reveal the basis of membrane coupling and assembly.}, journal = {Nature Microbiology}, volume = {4}, year = {2019}, month = {2019 Aug}, pages = {2010-19}, abstract = {

The bacterial injectisome is a syringe-shaped macromolecular nanomachine utilized by many pathogenic Gram-negative bacteria, including the causative agents of plague, typhoid fever, whooping cough, sexually transmitted infections and major nosocomial infections. Bacterial proteins destined for self-assembly and host-cell targeting are translocated by the injectisome in a process known as type III secretion (T3S). The core structure is the ~4 MDa needle complex (NC), built on a foundation of three highly oligomerized ring-forming proteins that create a hollow scaffold spanning the bacterial inner membrane (IM) (24-mer ring-forming proteins PrgH and PrgK in the\ Salmonella entericaserovar Typhimurium\ Salmonella\ pathogenicity island 1 (SPI-1) type III secretion system (T3SS)) and outer membrane (OM) (15-mer InvG, a member of the broadly conserved secretin pore family). An internalized helical needle projects from the NC and bacterium, ultimately forming a continuous passage to the host, for delivery of virulence effectors. Here, we have captured snapshots of the entire prototypical SPI-1 NC in four distinct needle assembly states, including near-atomic resolution, and local reconstructions in the absence and presence of the needle. These structures reveal the precise localization and molecular interactions of the internalized SpaPQR {\textquoteleft}export apparatus{\textquoteright} complex, which is intimately encapsulated and stabilized within the IM rings in the manner of a nanodisc, and to which the PrgJ rod directly binds and functions as an initiator and anchor of needle polymerization. We also describe the molecular details of the extensive and continuous coupling interface between the OM secretin and IM rings, which is remarkably facilitated by a localized 16-mer stoichiometry in the periplasmic-most coupling domain of the otherwise 15-mer InvG oligomer.

}, doi = {10.1038/s41564-019-0545-z}, url = {http://www.nature.com/articles/s41564-019-0545-zhttp://www.nature.com/articles/s41564-019-0545-z.pdfhttp://www.nature.com/articles/s41564-019-0545-z.pdfhttp://www.nature.com/articles/s41564-019-0545-z}, author = {Hu, Jinhong and Worrall, Liam J. and Vuckovic, Marija and Hong, Chuan and Deng, Wanyin and Atkinson, Claire E. and Brett Finlay, B. and Yu, Zhiheng and Strynadka, Natalie C. J.} } @article {67222, title = {Teaching deep neural networks to localize single molecules for super-resolution microscopy}, journal = {arXiv e-prints}, year = {2019}, month = {06/2019}, pages = {arXiv:1907.00770}, abstract = {

Single-molecule localization fluorescence microscopy constructs super-resolution images by sequential imaging and computational localization of sparsely activated fluorophores. Accurate and efficient fluorophore localization algorithms are key to the success of this computational microscopy method. We present a novel localization algorithm based on deep learning which significantly improves upon the state of the art. Our contributions are a novel network architecture for simultaneous detection and localization, and new loss function which phrases detection and localization as a Bayesian inference problem, and thus allows the network to provide uncertainty-estimates. In contrast to standard methods which independently process imaging frames, our network architecture uses temporal context from multiple sequentially imaged frames to detect and localize molecules. We demonstrate the power of our method across a variety of datasets, imaging modalities, signal to noise ratios, and fluorophore densities. While existing localization algorithms can achieve optimal localization accuracy at low fluorophore densities, they are confounded by high densities. Our method is the first deep-learning based approach which achieves state-of-the-art on the SMLM2016 challenge. It achieves the best scores on 12 out of 12 data-sets when comparing both detection accuracy and precision, and excels at high densities. Finally, we investigate how unsupervised learning can be used to make the network robust against mismatch between simulated and real data. The lessons learned here are more generally relevant for the training of deep networks to solve challenging Bayesian inverse problems on spatially extended domains in biology and physics.

}, keywords = {Computer Science - Machine Learning, Electrical Engineering and Systems Science - Image and Video Processing, Statistics - Machine Learning}, url = {https://arxiv.org/abs/1907.00770}, author = {Speiser, Artur and M{\"u}ller, Lucas-Raphael and Matti, Ulf and Obara, Christopher J. and Legant, Wesley R. and Ries, Jonas and Macke, Jakob H. and Turaga, Srinivas C.} } @article {68340, title = {Theoretical modeling on CRISPR-coded cell lineages: efficient encoding and optimal reconstruction}, journal = {bioRxiv}, year = {2019}, month = {04/2019}, abstract = {

Delineating cell lineages is a prerequisite for interrogating the genesis of cell types. CRISPR/Cas9 can edit genomic sequence during development which enables to trace cell lineages. Recent studies have demonstrated the feasibility of this idea. However, the optimality of the encoding or reconstruction processes has not been adequately addressed. Here, we surveyed a multitude of reconstruction algorithms and found hierarchical clustering, with a metric based on the number of shared Cas9 edits, delivers the best reconstruction. However, the trackable depth is ultimately limited by the number of available coding units that typically decrease exponentially across cell generations. To overcome this limit, we established two strategies that better sustain the coding capacity. One involves controlling target availability via use of parallel gRNA cascades, whereas the other strategy exploits adjustable Cas9/gRNA editing rates. In summary, we provide a theoretical basis in understanding, designing, and analyzing robust CRISPR barcodes for dense reconstruction of protracted cell lineages.

}, doi = {10.1101/538488}, url = {https://www.biorxiv.org/content/early/2019/04/14/538488}, author = {Sugino, Ken and Garcia-Marques, Jorge and Espinosa-Medina, Isabel and Lee, Tzumin} } @article {64871, title = {Thirst regulates motivated behavior through modulation of brainwide neural population dynamics.}, journal = {Science}, volume = {364}, year = {2019}, month = {2019 Apr 04}, pages = {253}, abstract = {

Physiological needs produce motivational drives, such as thirst and hunger, that regulate behaviors essential to survival. Hypothalamic neurons sense these needs and must coordinate relevant brainwide neuronal activity to produce the appropriate behavior. We studied dynamics from ~24,000 neurons in 34 brain regions during thirst-motivated choice behavior, as mice consumed water and became sated. Water-predicting sensory cues elicited activity that rapidly spread throughout the brain of thirsty animals. These dynamics were gated by a brainwide mode of population activity that encoded motivational state. Focal optogenetic activation of hypothalamic thirst-sensing neurons, after satiation, returned global activity to the pre-satiation state. Thus, motivational states specify initial conditions determining how a brainwide dynamical system transforms sensory input into behavioral output.

}, issn = {1095-9203}, doi = {10.1126/science.aav3932}, author = {Allen, William E and Chen, Michael Z and Pichamoorthy, Nandini and Tien, Rebecca H and Pachitariu, Marius and Luo, Liqun and Deisseroth, Karl} } @article {56201, title = {Threshold-based ordering of sequential actions during Drosophila courtship.}, journal = {Current Biology : CB}, volume = {29}, year = {2019}, month = {2019 Jan 07}, pages = {426-34}, abstract = {

Goal-directed animal behaviors are typically composed of sequences of motor actions whose order and timing are critical for a successful outcome. Although numerous theoretical models for sequential action generation have been proposed, few have been supported by the identification of control neurons sufficient to elicit a sequence. Here, we identify a pair of descending neurons that coordinate a stereotyped sequence of engagement actions during Drosophila melanogaster male courtship behavior. These actions are initiated sequentially but persist cumulatively, a feature not explained by existing models of sequential behaviors. We find evidence consistent with a ramp-to-threshold mechanism, in which increasing neuronal activity elicits each action independently at successively higher activity thresholds.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2018.12.019}, author = {McKellar, Claire E and Lillvis, Joshua L and Bath, Daniel E and Fitzgerald, James E and Cannon, John G and Simpson, Julie H and Dickson, Barry J} } @article {64943, title = {Time-variant SRC kinase activation determines endothelial permeability response.}, journal = {Cell Chemical Biology}, volume = {26}, year = {2019}, month = {2019 Aug 15}, pages = {1081-94}, abstract = {

In the current model of endothelial barrier regulation, the tyrosine kinase SRC is purported to induce disassembly of endothelial adherens junctions (AJs) via\ phosphorylation of VE cadherin, and thereby increase\ junctional permeability. Here, using a chemical biology approach to temporally control SRC activation,\ we show that SRC exerts distinct time-variant effects on the endothelial barrier. We discovered that the immediate effect of SRC activation was to transiently enhance endothelial barrier function as the result of accumulation of VE cadherin at AJs and formation of morphologically distinct reticular AJs. Endothelial barrier enhancement via SRC required phosphorylation of VE cadherin at Y731. In contrast, prolonged SRC activation induced VE cadherin phosphorylation at Y685, resulting in increased endothelial permeability. Thus, time-variant SRC activation differentially phosphorylates VE cadherin and shapes AJs to fine-tune endothelial barrier function. Our work demonstrates important advantages of synthetic biology tools in dissecting complex signaling systems.

}, issn = {2451-9448}, doi = {10.1016/j.chembiol.2019.04.007}, author = {Klomp, Jennifer E and Shaaya, Mark and Matsche, Jacob and Rebiai, Rima and Aaron, Jesse S and Collins, Kerrie B and Huyot, Vincent and Gonzalez, Annette M and Muller, William A and Chew, Teng-Leong and Malik, Asrar B and Karginov, Andrei V} } @article {68430, title = {Transsynaptic Fish-lips signaling prevents misconnections between nonsynaptic partner olfactory neurons.}, journal = {Proc Natl Acad Sci U S A}, volume = {116}, year = {2019}, month = {08/2019}, pages = {16068-16073}, abstract = {

Our understanding of the mechanisms of neural circuit assembly is far from complete. Identification of wiring molecules with novel mechanisms of action will provide insights into how complex and heterogeneous neural circuits assemble during development. In the olfactory system, 50 classes of olfactory receptor neurons (ORNs) make precise synaptic connections with 50 classes of partner projection neurons (PNs). Here, we performed an RNA interference screen for cell surface molecules and identified the leucine-rich repeat-containing transmembrane protein known as Fish-lips (Fili) as a novel wiring molecule in the assembly of the olfactory circuit. Fili contributes to the precise axon and dendrite targeting of a small subset of ORN and PN classes, respectively. Cell-type-specific expression and genetic analyses suggest that Fili sends a transsynaptic repulsive signal to neurites of nonpartner classes that prevents their targeting to inappropriate glomeruli in the antennal lobe.

}, keywords = {Animals, Axons, Dendrites, Drosophila melanogaster, Drosophila Proteins, Leucine-Rich Repeat Proteins, Membrane Proteins, Mutation, Olfactory Receptor Neurons, Phenotype, Proteins, Signal Transduction, Synapses}, issn = {1091-6490}, doi = {10.1073/pnas.1905832116}, author = {Xie, Qijing and Wu, Bing and Li, Jiefu and Xu, Chuanyun and Li, Hongjie and Luginbuhl, David J and Wang, Xin and Ward, Alex and Luo, Liqun} } @article {65239, title = {TwoLumps ascending neurons mediate touch-evoked reversal of walking direction in Drosophila.}, journal = {Current Biology}, volume = {29}, year = {2019}, month = {2019 Nov 22}, pages = {4337-44}, abstract = {

External cues, including touch, enable walking animals to flexibly maneuver around obstacles and extricate themselves from dead-ends (for reviews, see [1-3]). In a screen for neurons that enable Drosophila melanogaster to retreat when it encounters a dead-end, we identified a pair of ascending neurons, the TwoLumps Ascending (TLA) neurons. Silencing TLA activity impairs backward locomotion, whereas optogenetic activation triggers backward walking. TLA-induced reversal is mediated in part by the Moonwalker Descending Neurons (MDNs) [4], which receive excitatory input from the TLAs. Silencing the TLAs decreases the extent to which freely walking flies back up upon encountering a physical barrier in the dark, and TLAs show calcium responses to optogenetic activation of neurons expressing the mechanosensory channel NOMPC. We infer that TLAs convey feedforward mechanosensory stimuli to transiently activate MDNs in response to anterior body touch.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2019.11.004}, author = {Sen, Rajyashree and Wang, Kaiyu and Dickson, Barry J} } @article {65254, title = {Two-photon imaging with silicon photomultipliers.}, journal = {Optics Express}, volume = {27}, year = {2019}, month = {2019 Nov 25}, pages = {35830-35841}, abstract = {

We compared performance of recently developed silicon photomultipliers (SiPMs) to GaAsP photomultiplier tubes (PMTs) for two-photon imaging of neural activity. Despite higher dark counts, SiPMs match or exceed the signal-to-noise ratio of PMTs at photon rates encountered in typical calcium imaging experiments due to their low pulse height variability. At higher photon rates encountered during high-speed voltage imaging, SiPMs substantially outperform PMTs.

}, issn = {1094-4087}, doi = {10.1364/OE.27.035830}, author = {Modi, Mehrab N and Daie, Kayvon and Turner, Glenn C and Podgorski, Kaspar} } @article {64840, title = {Ultrapotent chemogenetics for research and potential clinical applications.}, journal = {Science}, volume = {364}, year = {2019}, month = {2019 Mar 14}, pages = {eaav5282}, abstract = {

Chemogenetics enables non-invasive chemical control over cell populations in behaving animals. However, existing small molecule agonists show insufficient potency or selectivity. There is also need for chemogenetic systems compatible with both research and human therapeutic applications. We developed a new ion channel-based platform for cell activation and silencing that is controlled by low doses of the anti-smoking drug varenicline. We then synthesized novel sub-nanomolar potency agonists, called uPSEMs, with high selectivity for the chemogenetic receptors. uPSEMs and their receptors were characterized in brains of mice and a rhesus monkey by in vivo electrophysiology, calcium imaging, positron emission tomography, behavioral efficacy testing, and receptor counterscreening. This platform of receptors and selective ultrapotent agonists enables potential research and clinical applications of chemogenetics.

}, issn = {1095-9203}, doi = {10.1126/science.aav5282}, author = {Magnus, Christopher J and Lee, Peter H and Bonaventura, Jordi and Zemla, Roland and Gomez, Juan L and Ramirez, Melissa H and Hu, Xing and Galvan, Adriana and Basu, Jayeeta and Michaelides, Michael and Sternson, Scott M} } @article {65078, title = {Unlimited genetic switches for cell-type-specific manipulation.}, journal = {Neuron}, volume = {104}, year = {2019}, month = {2019 Oct 23}, pages = {227-38}, abstract = {

Gaining independent genetic access to discrete cell types is critical to interrogate their biological functions as well as to deliver precise gene therapy. Transcriptomics has allowed us to profile cell populations with extraordinary precision, revealing that cell types are typically defined by a unique combination of genetic markers. Given the lack of adequate tools to target cell types based on multiple markers, most cell types remain inaccessible to genetic manipulation. Here we present CaSSA, a platform to create unlimited genetic switches based on CRISPR/Cas9 (Ca) and the DNA repair mechanism known as single-strand annealing (SSA). CaSSA allows engineering of independent genetic switches, each responding to a specific gRNA. Expressing multiple gRNAs in specific patterns enables multiplex cell-type-specific manipulations and combinatorial genetic targeting. CaSSA is a new genetic tool that conceptually works as an unlimited number of recombinases and will facilitate genetic access to cell types in diverse organisms.

}, doi = {https://doi.org/10.1016/j.neuron.2019.07.005}, author = {Garcia-Marques, Jorge and Yang, Ching-Po and Isabel Espinosa Medina and Mok, Kent and Koyama, Minoru and Lee, Tzumin} } @article {64905, title = {Visually guided behavior and optogenetically induced learning in head-fixed flies exploring a virtual landscape.}, journal = {Current Biology : CB}, year = {2019}, month = {2019 Apr 29}, abstract = {

Studying the intertwined roles of sensation, experience, and directed action in navigation has been facilitated by the development of virtual reality (VR) environments for head-fixed animals, allowing for quantitative measurements of behavior in well-controlled conditions. VR has long featured in studies of Drosophila melanogaster, but these experiments have typically allowed the fly to change only its heading in a visual scene and not its position. Here we explore how flies move in two dimensions (2D) using a visual VR environment that more closely captures an animal{\textquoteright}s experience during free behavior. We show that flies{\textquoteright} 2D interaction with landmarks cannot be automatically derived from their orienting behavior under simpler one-dimensional (1D) conditions. Using novel paradigms, we then demonstrate that flies in 2D VR adapt their behavior in response to optogenetically delivered appetitive and aversive stimuli. Much like free-walking flies after encounters with food, head-fixed flies exploring a 2D VR respond to optogenetic activation of sugar-sensing neurons by initiating a local search, which appears not to rely on visual landmarks. Visual landmarks can, however, help flies to avoid areas in VR where they experience an aversive, optogenetically generated heat stimulus. By coupling aversive virtual heat to the flies{\textquoteright} presence near visual landmarks of specific shapes, we elicit selective learned avoidance of those landmarks. Thus, we demonstrate that head-fixed flies adaptively navigate in 2D virtual environments, but their reliance on visual landmarks is context dependent. These behavioral paradigms set the stage for interrogation of the fly brain circuitry underlying flexible navigation in complex multisensory environments.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2019.04.033}, author = {Haberkern, Hannah and Basnak, Melanie A and Ahanonu, Biafra and Schauder, David and Cohen, Jeremy D and Bolstad, Mark and Bruns, Christopher and Jayaraman, Vivek} } @article {65229, title = {The yellow gene influences Drosophila male mating success through sex comb melanization.}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Oct 15}, abstract = {

males perform a series of courtship behaviors that, when successful, result in copulation with a female. For over a century, mutations in the gene, named for its effects on pigmentation, have been known to reduce male mating success. Prior work has suggested that influences mating behavior through effects on wing extension, song, and/or courtship vigor. Here, we rule out these explanations, as well as effects on the nervous system more generally, and find instead that the effects of on male mating success are mediated by its effects on pigmentation of male-specific leg structures called sex combs. Loss of expression in these modified bristles reduces their melanization, which changes their structure and causes difficulty grasping females prior to copulation. These data illustrate why the mechanical properties of anatomy, not just neural circuitry, must be considered to fully understand the development and evolution of behavior.

}, issn = {2050-084X}, doi = {10.7554/eLife.49388}, author = {Massey, Jonathan H and Chung, Daayun and Siwanowicz, Igor and Stern, David L and Wittkopp, Patricia J} } @article {65213, title = {Zebrafish neuroscience: Using artificial neural networks to help understand brains.}, journal = {Current Biology}, volume = {29}, year = {2019}, month = {2019 Nov 04}, pages = {R1138-R1140}, abstract = {

Brains are notoriously hard to understand, and neuroscientists need all the tools they can get their hands on to have a realistic shot at it. Advances in machine learning are proving instrumental, illustrated by their recent use to shed light on navigational strategies implemented by zebrafish brains.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2019.09.039}, author = {Ahrens, Misha B} } @article {49416, title = {4D cell biology: big data image analytics and lattice light-sheet imaging reveal dynamics of clathrin-mediated endocytosis in stem cell derived intestinal organoids.}, journal = {Molecular Biology of the Cell}, year = {2018}, month = {2018 Sep 06}, pages = {mbcE18060375}, abstract = {

New methods in stem cell 3D organoid tissue culture, advanced imaging and big data image analytics now allow tissue scale 4D cell biology, but currently available analytical pipelines are inadequate for handing and analyzing the resulting gigabytes and terabytes of high-content imaging data. We expressed fluorescent protein fusions of clathrin and dynamin2 at endogenous levels in genome-edited human embryonic stem cells, which were differentiated into hESC-derived intestinal epithelial organoids. Lattice Light-Sheet Imaging with adaptive optics (AO-LLSM) allowed us to image large volumes of these organoids (70{\textmu}m x 60{\textmu}m x 40{\textmu}m xyz) at 5.7s/frame. We developed an open source data analysis package termed pyLattice to process the resulting large (\~{}60Gb) movie datasets and to track clathrin-mediated endocytosis (CME) events. CME tracks could be recorded from \~{}35 cells at a time, resulting in \~{}4000 processed tracks per movie. Based on their localization in the organoid, we classified CME tracks into apical, lateral and basal events and found that CME dynamics are similar for all three classes, despite reported differences in membrane tension. pyLattice coupled with AO-LLSM makes possible quantitative, high temporal and spatial resolution analysis of subcellular events within tissues. Movie S1 Movie S1 Thresholded 3D AO-LLSM data of an intestinal epithelial organoid showing clathrin (red) and dynamin2 (green) puncta in surface depiction. The movie zooms out from a single clathrin mediated endocytosis event that shows both clathrin and dynamin2 at the same location to eventually show the whole AO-LLSM field of view. Nuclear envelopes and the outer membranes of the tissue are depicted in transparent white. Movie S2 Movie S2 Thresholded 3D AO-LLSM data of an intestinal epithelial organoid showing clathrin (red) and dynamin2 (green) puncta in surface depiction. The movie rotates the AO-LLSM field of view. Nuclear envelopes and the outer membranes of the tissue are depicted in transparent white. Movie S3 Movie S3 Thresholded 3D AO-LLSM data of an intestinal epithelial organoid. The curved surface is of the spherical organoid is visible as the movie rotates. Clathrin puncta are visible throughout the tissue (white). Movie S4 Movie S4 The detection step in the data processing pipeline retrieves all clathrin puncta in the volume. Detected puncta are marked with a cube (blue). Movie S5 Movie S5 Zoom on one clathrin puncta in the thresholded 3D dataset. The punctum of interest is marked with a blue cube. Other puncta are also visible. Movie S6 Movie S6 Zoom on the same clathrin puncta as in M3 in non-thresholded 3D data. The surrounding fluorescence is visible as a transparent cloud.

}, issn = {1939-4586}, doi = {10.1091/mbc.E18-06-0375}, author = {Sch{\"o}neberg, Johannes and Dambournet, Daphne and Liu, Tsung-Li and Forster, Ryan and Hockemeyer, Dirk and Betzig, Eric and Drubin, David G} } @article {49151, title = {50 Hz volumetric functional imaging with continuously adjustable depth of focus.}, journal = {Biomedical Optics Express}, volume = {9}, year = {2018}, month = {2018 Apr}, pages = {1964-76}, abstract = {

Understanding how neural circuits control behavior requires monitoring a large population of neurons with high spatial resolution and volume rate. Here we report an axicon-based Bessel beam module with continuously adjustable depth of focus (CADoF), that turns frame rate into volume rate by extending the excitation focus in the axial direction while maintaining high lateral resolutions. Cost-effective and compact, this CADoF Bessel module can be easily integrated into existing two-photon fluorescence microscopes. Simply translating one of the relay lenses along its optical axis enabled continuous adjustment of the axial length of the Bessel focus. We used this module to simultaneously monitor activity of spinal projection neurons extending over 60 {\textmu}m depth in larval zebrafish at 50 Hz volume rate with adjustable axial extent of the imaged volume.

}, doi = {10.1364/BOE.9.001964}, author = {Lu, Rongwen and Tanimoto, Masashi and Koyama, Minoru and Na, Ji} } @article {49023, title = {Aberrant calcium signaling in astrocytes inhibits neuronal excitability in a human Down syndrome stem cell model.}, journal = {Cell Reports}, volume = {24}, year = {2018}, month = {2018 Jul 10}, pages = {355-65}, abstract = {

Down syndrome (DS) is a genetic disorder that causes cognitive impairment. The staggering effects associated with an extra copy of human chromosome 21 (HSA21) complicates mechanistic understanding of DS pathophysiology. We examined the neuron-astrocyte interplay in a fully recapitulated HSA21 trisomy cellular model differentiated from DS-patient-derived induced pluripotent stem cells (iPSCs). By combining calcium imaging with genetic approaches, we discovered the functional defects of DS astroglia and their effects on neuronal excitability. Compared with control isogenic astroglia, DS astroglia exhibited more-frequent spontaneous calcium fluctuations, which reduced the excitability of co-cultured neurons. Furthermore, suppressed neuronal activity could be rescued by abolishing astrocytic spontaneous calcium activity either chemically by blocking adenosine-mediated signaling or genetically by knockdown of inositol triphosphate (IP3) receptors or S100B, a calcium binding protein coded on HSA21. Our results suggest a mechanism by which DS alters the function of astrocytes, which subsequently disturbs neuronal excitability.

}, doi = {10.1101/247585}, author = {Tian, Lin and Or, Grace and Wang, Yinxue and Shi, Guilai and Wang, Yizhi and Sun, Junqing and Papadopoulos, Stelios and Broussard, Gerard and Unger, Elizabeth and Deng, Wenbin and Weick, Jason and Bhattacharyya, Anita and Chen, Chao-Yin and Yu, Guoqiang and Looger, Loren L} } @article {67283, title = {An Accumulation-of-Evidence Task Using Visual Pulses for Mice Navigating in Virtual Reality}, journal = {Frontiers in Behavioral Neuroscience}, volume = {12}, year = {2018}, month = {Jun-03-2018}, abstract = {

The gradual accumulation of sensory evidence is a crucial component of perceptual decision making, but its neural mechanisms are still poorly understood. Given the wide availability of genetic and optical tools for mice, they can be useful model organisms for the study of these phenomena; however, behavioral tools are largely lacking. Here, we describe a new evidence-accumulation task for head-fixed mice navigating in a virtual reality (VR) environment. As they navigate down the stem of a virtual T-maze, they see brief pulses of visual evidence on either side, and retrieve a reward on the arm with the highest number of pulses. The pulses occur randomly with Poisson statistics, yielding a diverse yet well-controlled stimulus set, making the data conducive to a variety of computational approaches. A large number of mice of different genotypes were able to learn and consistently perform the task, at levels similar to rats in analogous tasks. They are sensitive to side differences of a single pulse, and their memory of the cues is stable over time. Moreover, using non-parametric as well as modeling approaches, we show that the mice indeed accumulate evidence: they use multiple pulses of evidence from throughout the cue region of the maze to make their decision, albeit with a small overweighting of earlier cues, and their performance is affected by the magnitude but not the duration of evidence. Additionally, analysis of the mice{\textquoteright}s running patterns revealed that trajectories are fairly stereotyped yet modulated by the amount of sensory evidence, suggesting that the navigational component of this task may provide a continuous readout correlated to the underlying cognitive variables. Our task, which can be readily integrated with state-of-the-art techniques, is thus a valuable tool to study the circuit mechanisms and dynamics underlying perceptual decision making, particularly under more complex behavioral contexts.

}, doi = {10.3389/fnbeh.2018.00036}, url = {http://journal.frontiersin.org/article/10.3389/fnbeh.2018.00036/full}, author = {Pinto, Lucas and Koay, Sue A. and Engelhard, Ben and Yoon, Alice M. and Deverett, Ben and Thiberge, Stephan Y. and Witten, Ilana B. and Tank, David W. and Brody, Carlos D.} } @article {49128, title = {Accurate and sensitive quantification of protein-DNA binding affinity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, year = {2018}, month = {2018 Apr 02}, pages = {E3692-701}, abstract = {

Transcription factors (TFs) control gene expression by binding to genomic DNA in a sequence-specific manner. Mutations in TF binding sites are increasingly found to be associated with human disease, yet we currently lack robust methods to predict these sites. Here, we developed a versatile maximum likelihood framework named No Read Left Behind (NRLB) that infers a biophysical model of protein-DNA recognition across the full affinity range from a library of in vitro selected DNA binding sites. NRLB predicts human Max homodimer binding in near-perfect agreement with existing low-throughput measurements. It can capture the specificity of the p53 tetramer and distinguish multiple binding modes within a single sample. Additionally, we confirm that newly identified low-affinity enhancer binding sites are functional in vivo, and that their contribution to gene expression matches their predicted affinity. Our results establish a powerful paradigm for identifying protein binding sites and interpreting gene regulatory sequences in eukaryotic genomes.

}, issn = {1091-6490}, doi = {10.1073/pnas.1714376115}, author = {Rastogi, Chaitanya and Rube, H Tomas and Kribelbauer, Judith F and Crocker, Justin and Loker, Ryan E and Martini, Gabriella D and Laptenko, Oleg and Freed-Pastor, William A and Prives, Carol and Stern, David L and Mann, Richard S and Bussemaker, Harmen J} } @article {49341, title = {The actin cytoskeletal architecture of estrogen receptor positive breast cancer cells suppresses invasion.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Jul 30}, pages = {2980}, abstract = {

Estrogen promotes growth of estrogen receptor-positive (ER+) breast tumors. However, epidemiological studies examining the prognostic characteristics of breast cancer in postmenopausal women receiving hormone replacement therapy reveal a significant decrease in tumor dissemination, suggesting that estrogen has potential protective effects against cancer cell invasion. Here, we show that estrogen suppresses invasion of ER+ breast cancer cells by increasing transcription of the Ena/VASP protein, EVL, which promotes the generation of suppressive cortical actin bundles that inhibit motility dynamics, and is crucial for the ER-mediated suppression of invasion in vitro and in vivo. Interestingly, despite its benefits in suppressing tumor growth, anti-estrogenic endocrine therapy decreases EVL expression and increases local invasion in patients. Our results highlight the dichotomous effects of estrogen on tumor progression and suggest that, in contrast to its established role in promoting growth of ER+ tumors, estrogen has a significant role in suppressing invasion through actin cytoskeletal remodeling.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-05367-2}, author = {Padilla-Rodriguez, Marco and Parker, Sara S and Adams, Deanna G and Westerling, Thomas and Puleo, Julieann I and Watson, Adam W and Hill, Samantha M and Noon, Muhammad and Gaudin, Rapha{\"e}l and Aaron, Jesse and Tong, Daoqin and Roe, Denise J and Knudsen, Beatrice and Mouneimne, Ghassan} } @article {49477, title = {Active dendritic integration and mixed neocortical network representations during an adaptive sensing behavior.}, journal = {Nature Neuroscience}, volume = {21}, year = {2018}, month = {2018 Oct 22}, pages = {1583-90}, abstract = {

Animals strategically scan the environment to form an accurate perception of their surroundings. Here we investigated the neuronal representations that mediate this behavior. Ca imaging and selective optogenetic manipulation during an active sensing task reveals that layer 5 pyramidal neurons in the vibrissae cortex produce a diverse and distributed representation that is required for mice to adapt their whisking motor strategy to changing sensory cues. The optogenetic perturbation degraded single-neuron selectivity and network population encoding through a selective inhibition of active dendritic integration. Together the data indicate that active dendritic integration in pyramidal neurons produces a nonlinearly mixed network representation of joint sensorimotor parameters that is used to transform sensory information into motor commands during adaptive behavior. The prevalence of the layer 5 cortical circuit motif suggests that this is a general circuit computation.

}, issn = {1546-1726}, doi = {10.1038/s41593-018-0254-6}, author = {Ranganathan, Gayathri N and Apostolides, Pierre F and Harnett, Mark T and Xu, Ning-long and Druckmann, Shaul and Magee, Jeffrey C} } @article {49311, title = {Adaptive coding for dynamic sensory inference.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Jul 10}, abstract = {

Behavior relies on the ability of sensory systems to infer properties of the environment from incoming stimuli. The accuracy of inference depends on the fidelity with which behaviorally relevant properties of stimuli are encoded in neural responses. High-fidelity encodings can be metabolically costly, but low-fidelity encodings can cause errors in inference. Here, we discuss general principles that underlie the tradeoff between encoding cost and inference error. We then derive adaptive encoding schemes that dynamically navigate this tradeoff. These optimal encodings tend to increase the fidelity of the neural representation following a change in the stimulus distribution, and reduce fidelity for stimuli that originate from a known distribution. We predict dynamical signatures of such encoding schemes and demonstrate how known phenomena, such as burst coding and firing rate adaptation, can be understood as hallmarks of optimal coding for accurate inference.

}, issn = {2050-084X}, doi = {10.7554/eLife.32055}, author = {M{\l}ynarski, Wiktor F and Hermundstad, Ann M} } @article {49031, title = {Adaptive optical microscopy for neurobiology.}, journal = {Current Opinion in Neurobiology}, volume = {50}, year = {2018}, month = {2018 Jun}, pages = {83-91}, abstract = {

Highlights:

With the ability to correct for the aberrations introduced by biological specimens, adaptive optics{\textemdash}a method originally developed for astronomical telescopes{\textemdash}has been applied to optical microscopy to recover diffraction-limited imaging performance deep within living tissue. In particular, this technology has been used to improve image quality and provide a more accurate characterization of both structure and function of neurons in a variety of living organisms. Among its many highlights, adaptive optical microscopy has made it possible to image large volumes with diffraction-limited resolution in zebrafish larval brains, to resolve dendritic spines over 600μm deep in the mouse brain, and to more accurately characterize the orientation tuning properties of thalamic boutons in the primary visual cortex of awake mice.

}, doi = {10.1016/j.conb.2018.01.011}, author = {Rodriguez, Cristina and Ji, Na} } @article {49572, title = {Allatostatin-C/AstC-R2 is a novel pathway to modulate the circadian activity pattern in Drosophila.}, journal = {Current Biology : CB}, volume = {29}, year = {2018}, month = {2018 Dec 04}, pages = {13-22}, abstract = {

Seven neuropeptides are expressed within the Drosophila brain circadian network. Our previous mRNA profiling suggested that Allatostatin-C (AstC) is an eighth neuropeptide and specifically expressed in dorsal clock neurons (DN1s). Our results here show that AstC is, indeed, expressed in DN1s, where it oscillates. AstC is also expressed in two less well-characterized circadian neuronal clusters, the DN3s and lateral-posterior neurons (LPNs). Behavioral experiments indicate that clock-neuron-derived AstC is required to mediate evening locomotor activity under short (winter-like) and long (summer-like) photoperiods. The AstC-Receptor 2 (AstC-R2) is expressed in LNds, the clock neurons that drive evening locomotor activity, and AstC-R2 is required in these neurons to modulate the same short photoperiod evening phenotype. Ex\ vivo calcium imaging indicates that AstC directly inhibits a single LNd. The results suggest that a novel AstC/AstC-R2 signaling pathway, from dorsal circadian neurons to an LNd, regulates the evening phase in Drosophila.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2018.11.005}, author = {D{\'\i}az, Madelen M and Schlichting, Matthias and Abruzzi, Katharine C and Long, Xi and Rosbash, Michael} } @article {49533, title = {Analysis of discrete local variability and structural covariance in macromolecular assemblies using Cryo-EM and focused classification.}, journal = {Ultramicroscopy}, volume = {203}, year = {2018}, month = {2018 Nov 29}, pages = {170}, abstract = {

Single-particle electron cryo-microscopy and computational image classification can be used to analyze structural variability in macromolecules and their assemblies. In some cases, a particle may contain different regions that each display a range of distinct conformations. We have developed strategies, implemented within the Frealign and\ cisTEM image processing packages, to focus classify on specific regions of a particle and detect potential covariance. The strategies are based on masking the region of interest using either a 2-D mask applied to reference projections and particle images, or a 3-D mask applied to the 3-D volume. We show that focused classification approaches can be used to study structural covariance, a concept that is likely to gain more importance as datasets grow in size, allowing the distinction of more structural states and smaller differences between states. Finally, we apply the approaches to an experimental dataset containing the HIV-1 Transactivation Response (TAR) element RNA fused into the large bacterial ribosomal subunit to deconvolve structural mobility within localized regions of interest, and to a dataset containing assembly intermediates of the large subunit to measure structural covariance.

}, doi = {10.1016/j.ultramic.2018.11.016}, author = {Zhang, Cheng and Cantara, William and Jeon, Youngmin and Musier-Forsyth, Karin and Grigorieff, Nikolaus and Lyumkis, Dmitry} } @article {49180, title = {Analysis of global and site-specific radiation damage in cryo-EM.}, journal = {Structure (London, England : 1993)}, volume = {26}, year = {2018}, month = {2018 Apr 18}, pages = {759-66}, abstract = {

Micro-crystal electron diffraction (MicroED) combines the efficiency of electron scattering with diffraction to allow structure determination from nano-sized crystalline samples in cryoelectron microscopy (cryo-EM). It has been used to solve structures of a diverse set of biomolecules and materials, in some cases to sub-atomic resolution. However, little is known about the damaging effects of the electron beam on samples during such measurements. We assess global and site-specific damage from electron radiation on nanocrystals of proteinase K and of a prion hepta-peptide and find that the dynamics of electron-induced damage follow well-established trends observed in X-ray crystallography. Metal ions are perturbed, disulfide bonds are broken, and acidic side chains are decarboxylated while the\ diffracted intensities decay exponentially with increasing exposure. A better understanding of radiation damage in MicroED improves our assessment and processing of all types of cryo-EM data.

}, issn = {1878-4186}, doi = {10.1016/j.str.2018.03.021}, author = {Hattne, Johan and Shi, Dan and Glynn, Calina and Zee, Chih-Te and Gallagher-Jones, Marcus and Martynowycz, Michael W and Rodriguez, Jose A and Gonen, Tamir} } @inbook {49508, title = {Analysis of image similarity and relationship.}, booktitle = {Basic Confocal Microscopy}, year = {2018}, pages = {309-33}, publisher = {Springer}, organization = {Springer}, abstract = {

The ability of fluorescence microscopy to simultaneously image multiple specific molecules of interest has allowed biologists to infer macromolecular organization and colocalization in fixed and live samples. However, a number of factors could\ affect these analyses, and colocalization is a misnomer. We propose that\ image similarity coefficient\ as a better and more descriptive term. In this chapter we will discuss many of the factors involved with determining image similarity including our perception of color in images. In addition, the correct use of several commonly accepted methods such as Pearson{\textquoteright}s correlation coefficient, Manders{\textquoteright} overlap coefficient, and Spearman{\textquoteright}s ranked correlation coefficient is discussed.

}, issn = {978-3-319-97453-8}, doi = {10.1007/978-3-319-97454-5_11}, author = {Aaron, Jesse S and Chew, Teng-Leong} } @article {49493, title = {Analysis tools for large connectomes.}, journal = {Frontiers in Neural Circuits}, volume = {12}, year = {2018}, month = {2018}, pages = {85}, abstract = {

New reconstruction techniques are generating connectomes of unprecedented size. These must be analyzed to generate human comprehensible results. The analyses being used fall into three general categories. The first is interactive tools used during reconstruction, to help guide the effort, look for possible errors, identify potential cell classes, and answer other preliminary questions. The second type of analysis is support for formal documents such as papers and theses. Scientific norms here require that the data be archived and accessible, and the analysis reproducible. In contrast to some other "omic" fields such as genomics, where a few specific analyses dominate usage, connectomics is rapidly evolving and the analyses used are often specific to the connectome being analyzed. These analyses are typically performed in a variety of conventional programming language, such as Matlab, R, Python, or C++, and read the connectomic data either from a file or through database queries, neither of which are standardized. In the short term we see no alternative to the use of specific analyses, so the best that can be done is to publish the analysis code, and the interface by which it reads connectomic data. A similar situation exists for archiving connectome data. Each group independently makes their data available, but there is no standardized format and long-term accessibility is neither enforced nor funded. In the long term, as connectomics becomes more common, a natural evolution would be a central facility for storing and querying connectomic data, playing a role similar to the National Center for Biotechnology Information for genomes. The final form of analysis is the import of connectome data into downstream tools such as neural simulation or machine learning. In this process, there are two main problems that need to be addressed. First, the reconstructed circuits contain huge amounts of detail, which must be intelligently reduced to a form the downstream tools can use. Second, much of the data needed for these downstream operations must be obtained by other methods (such as genetic or optical) and must be merged with the extracted connectome.

}, issn = {1662-5110}, doi = {10.3389/fncir.2018.00085}, author = {Scheffer, Louis K} } @article {49531, title = {Analyzing image segmentation for connectomics.}, journal = {Frontiers in Neural Circuits}, volume = {12}, year = {2018}, month = {2018}, pages = {102}, abstract = {

Automatic image segmentation is critical to scale up electron microscope (EM) connectome reconstruction. To this end, segmentation competitions, such as CREMI and SNEMI, exist to help researchers evaluate segmentation algorithms with the goal of improving them. Because generating ground truth is time-consuming, these competitions often fail to capture the challenges in segmenting larger datasets required in connectomics. More generally, the common metrics for EM image segmentation do not emphasize impact on downstream analysis and are often not very useful for isolating problem areas in the segmentation. For example, they do not capture connectivity information and often over-rate the quality of a segmentation as we demonstrate later. To address these issues, we introduce a novel strategy to enable evaluation of segmentation at large scales both in a supervised setting, where ground truth is available, or an unsupervised setting. To achieve this, we first introduce new metrics more closely aligned with the use of segmentation in downstream analysis and reconstruction. In particular, these include synapse connectivity and completeness metrics that provide both meaningful and intuitive interpretations of segmentation quality as it relates to the preservation of neuron connectivity. Also, we propose measures of segmentation correctness and completeness with respect to the percentage of "orphan" fragments and the concentrations of self-loops formed by segmentation failures, which are helpful in analysis and can be computed without ground truth. The introduction of new metrics intended to be used for practical applications involving large datasets necessitates a scalable software ecosystem, which is a critical contribution of this paper. To this end, we introduce a scalable, flexible software framework that enables integration of several different metrics and provides mechanisms to evaluate and debug differences between segmentations. We also introduce visualization software to help users to consume the various metrics collected. We evaluate our framework on two relatively large public groundtruth datasets providing novel insights on example segmentations.

}, issn = {1662-5110}, doi = {10.3389/fncir.2018.00102}, author = {Plaza, Stephen M and Funke, Jan} } @article {49383, title = {Anterolateral motor cortex connects with a medial subdivision of ventromedial thalamus through cell-type-specific circuits, forming an excitatory thalamo-cortico-thalamic loop via layer 1 apical tuft dendrites of layer 5B pyramidal tract type neurons.}, journal = {The Journal of Neuroscience : the official journal of the Society for Neuroscience}, volume = {38}, year = {2018}, month = {2018 Aug 24}, pages = {8787-97}, abstract = {

The anterolateral motor cortex (ALM) and ventromedial (VM) thalamus are functionally linked to support persistent activity during motor planning. We analyzed the underlying synaptic interconnections using optogenetics and electrophysiology in mice (♀/♂). In cortex, thalamocortical (TC) axons from VM excited VM-projecting pyramidal-tract (PT) neurons in layer 5B of ALM. These axons also strongly excited layer 2/3 neurons (which strongly excite PT neurons, as previously shown) but not VM-projecting corticothalamic (CT) neurons in layer 6. The strongest connections in the VM{\textrightarrow}PT circuit were localized to apical-tuft dendrites of PT neurons, in layer 1. These tuft inputs were selectively augmented after blocking hyperpolarization-activated cyclic nucleotide-gated (HCN) channels. In thalamus, axons from ALM PT neurons excited ALM-projecting VM neurons, located medially in VM. These axons provided weak input to neurons in mediodorsal nucleus, and little or no input either to neurons in the GABAergic reticular thalamic nucleus or to neurons in VM projecting to primary motor cortex (M1). Conversely, M1 PT axons excited M1- but not ALM-projecting VM neurons. Our findings indicate, first, a set of cell-type-specific connections forming an excitatory thalamo-cortico-thalamic (T-C-T) loop for ALM<->VM communication and a circuit-level substrate for supporting reverberant activity in this system. Second, a key feature of this loop is the prominent involvement of layer 1 synapses onto apical dendrites, a subcellular compartment with distinct signaling properties, including HCN-mediated gain control. Third, the segregation of the ALM<->VM loop from M1-related circuits of VM adds cellular-level support for the concept of parallel pathway organization in the motor system.Anterolateral motor cortex (ALM), a higher-order motor area in the mouse, and ventromedial thalamus (VM) are anatomically and functionally linked, but their synaptic interconnections at the cellular level are unknown. Our results show that ALM pyramidal tract neurons monosynaptically excite ALM-projecting thalamocortical neurons in a medial subdivision of VM, and vice versa. The thalamo-cortico-thalamic loop formed by these recurrent connections constitutes a circuit-level substrate for supporting reverberant activity in this system.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.1333-18.2018}, author = {Guo, KuangHua and Yamawaki, Naoki and Svoboda, Karel and Shepherd, Gordon M G} } @article {49316, title = {Apical and basal matrix remodeling control epithelial morphogenesis.}, journal = {Developmental Cell}, volume = {46}, year = {2018}, month = {2018 Jul 02}, pages = {23-39.e5}, abstract = {

Epithelial tissues can elongate in two dimensions by polarized cell intercalation, oriented cell division, or cell shape change, owing to local or global actomyosin contractile forces acting in the plane of the tissue. In addition, epithelia can undergo morphogenetic change in three dimensions. We show that elongation of the wings and legs of Drosophila involves a columnar-to-cuboidal cell shape change that reduces cell height and expands cell width. Remodeling of the apical extracellular matrix by the Stubble protease and basal matrix by MMP1/2 proteases induces wing and leg elongation. Matrix remodeling does not occur in the haltere, a limb that fails to elongate. Limb elongation is made anisotropic by planar polarized Myosin-II, which drives convergent extension along the proximal-distal axis. Subsequently, Myosin-II relocalizes to lateral membranes to accelerate columnar-to-cuboidal transition and isotropic tissue expansion. Thus, matrix remodeling induces dynamic changes in actomyosin contractility\ to drive epithelial morphogenesis in three dimensions.

}, issn = {1878-1551}, doi = {10.1016/j.devcel.2018.06.006}, author = {Diaz-de-la-Loza, Maria-Del-Carmen and Ray, Robert P and Ganguly, Poulami S and Alt, Silvanus and Davis, John R and Hoppe, Andreas and Tapon, Nic and Salbreux, Guillaume and Thompson, Barry J} } @article {49123, title = {Architecture of the human GATOR1 and GATOR1-Rag GTPases complexes.}, journal = {Nature}, volume = {556}, year = {2018}, month = {2018 Mar 28}, pages = {64-9}, abstract = {

Nutrients, such as amino acids and glucose, signal through the Rag GTPases to activate mTORC1. The GATOR1 protein complex-comprising DEPDC5, NPRL2 and NPRL3-regulates the Rag GTPases as a GTPase-activating protein (GAP) for RAGA; loss of GATOR1 desensitizes mTORC1 signalling to nutrient starvation. GATOR1 components have no sequence homology to other proteins, so the function of GATOR1 at the molecular level is currently unknown. Here we used cryo-electron microscopy to solve structures of GATOR1 and GATOR1-Rag GTPases complexes. GATOR1 adopts an extended architecture with a cavity in the middle; NPRL2 links DEPDC5 and NPRL3, and DEPDC5 contacts the Rag GTPase heterodimer. Biochemical analyses reveal that our GATOR1-Rag GTPases structure is inhibitory, and that at least two binding modes must exist between the Rag GTPases and GATOR1. Direct interaction of DEPDC5 with RAGA inhibits GATOR1-mediated stimulation of GTP hydrolysis by RAGA, whereas weaker interactions between the NPRL2-NPRL3 heterodimer and RAGA execute GAP activity. These data reveal the structure of a component of the nutrient-sensing mTORC1 pathway and a non-canonical interaction between a GAP and its substrate GTPase.

}, issn = {1476-4687}, doi = {10.1038/nature26158}, author = {Shen, Kuang and Huang, Rick K and Brignole, Edward J and Condon, Kendall J and Valenstein, Max L and Chantranupong, Lynne and Bomaliyamu, Aimaiti and Choe, Abigail and Hong, Chuan and Yu, Zhiheng and Sabatini, David M} } @article {49475, title = {Astrocytes integrate and drive action potential firing in inhibitory subnetworks.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Oct 18}, pages = {4336}, abstract = {

Many brain functions depend on the ability of neural networks to temporally integrate transient inputs to produce sustained discharges. This can occur through cell-autonomous mechanisms in individual neurons and through reverberating activity in recurrently connected neural networks. We report a third mechanism involving temporal integration of neural activity by a network of astrocytes. Previously, we showed that some types of interneurons can generate long-lasting trains of action potentials (barrage firing) following repeated depolarizing stimuli. Here we show that calcium signaling in an astrocytic network correlates with barrage firing; that active depolarization of astrocyte networks by chemical or optogenetic stimulation enhances; and that chelating internal calcium, inhibiting release from internal stores, or inhibiting GABA transporters or metabotropic glutamate receptors inhibits barrage firing. Thus, networks of astrocytes influence the spatiotemporal dynamics of neural networks by directly integrating neural activity and driving barrages of action potentials in some populations of inhibitory interneurons.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-06338-3}, author = {Deemyad, Tara and L{\"u}thi, Joel and Spruston, Nelson} } @article {49223, title = {Atomic resolution cryo-EM structure of β-galactosidase.}, journal = {Structure (London, England : 1993)}, volume = {26}, year = {2018}, month = {2018 Apr 30}, pages = {848}, abstract = {

The advent of direct electron detectors has enabled the routine use of single-particle cryo-electron microscopy (EM) approaches to determine structures of a variety of protein complexes at near-atomic resolution. Here, we report the development of methods to account for local variations in defocus and beam-induced drift, and the implementation of a data-driven dose compensation scheme that significantly improves the extraction of high-resolution information recorded during exposure of the specimen to the electron beam. These advances enable determination of a cryo-EM density map for β-galactosidase bound to the inhibitor phenylethyl β-D-thiogalactopyranoside where the ordered regions are resolved at a level of detail seen in X-ray maps at \~{} 1.5\ {\r A} resolution. Using this density map in conjunction with constrained molecular dynamics simulations provides a measure of the local flexibility of the non-covalently bound inhibitor and offers further opportunities for structure-guided inhibitor design.

}, issn = {1878-4186}, doi = {10.1016/j.str.2018.04.004}, author = {Bartesaghi, Alberto and Aguerrebere, Cecilia and Falconieri, Veronica and Banerjee, Soojay and Earl, Lesley A and Zhu, Xing and Grigorieff, Nikolaus and Milne, Jacqueline L S and Sapiro, Guillermo and Wu, Xiongwu and Subramaniam, Sriram} } @article {49117, title = {Atomic-level evidence for packing and positional amyloid polymorphism by segment from TDP-43 RRM2.}, journal = {Nature Structural \& Molecular Biology}, year = {2018}, month = {2018 Mar 12}, abstract = {

Proteins in the fibrous amyloid state are a major hallmark of neurodegenerative disease. Understanding the multiple conformations, or polymorphs, of amyloid proteins at the molecular level is a challenge of amyloid research. Here, we detail the wide range of polymorphs formed by a segment of human TAR DNA-binding protein 43 (TDP-43) as a model for the polymorphic capabilities of pathological amyloid aggregation. Using X-ray diffraction, microelectron diffraction (MicroED) and single-particle cryo-EM, we show that theDLIIKGISVHIsegment from the second RNA-recognition motif (RRM2) forms an array of amyloid polymorphs. These associations include seven distinct interfaces displaying five different symmetry classes of steric zippers. Additionally, we find that this segment can adopt three different backbone conformations that contribute to its polymorphic capabilities. The polymorphic nature of this segment illustrates at the molecular level how amyloid proteins can form diverse fibril structures.

}, issn = {1545-9985}, doi = {10.1038/s41594-018-0045-5}, author = {Guenther, Elizabeth L and Ge, Peng and Trinh, Hamilton and Sawaya, Michael R and Cascio, Duilio and Boyer, David R and Gonen, Tamir and Zhou, Z Hong and Eisenberg, David S} } @article {49056, title = {BAK/BAX macropores facilitate mitochondrial herniation and mtDNA efflux during apoptosis.}, journal = {Science (New York, N.Y.)}, volume = {359}, year = {2018}, month = {2018 02 23}, abstract = {

Mitochondrial apoptosis is mediated by BAK and BAX, two proteins that induce mitochondrial outer membrane permeabilization, leading to cytochrome c release and activation of apoptotic caspases. In the absence of active caspases, mitochondrial DNA (mtDNA) triggers the innate immune cGAS/STING pathway, causing dying cells to secrete type I interferon. How cGAS gains access to mtDNA remains unclear. We used live-cell lattice light-sheet microscopy to examine the mitochondrial network in mouse embryonic fibroblasts. We found that after BAK/BAX activation and cytochrome c loss, the mitochondrial network broke down and large BAK/BAX pores appeared in the outer membrane. These BAK/BAX macropores allowed the inner mitochondrial membrane to herniate into the cytosol, carrying with it mitochondrial matrix components, including the mitochondrial genome. Apoptotic caspases did not prevent herniation but dismantled the dying cell to suppress mtDNA-induced innate immune signaling.

}, issn = {1095-9203}, doi = {10.1126/science.aao6047}, author = {McArthur, Kate and Whitehead, Lachlan W and Heddleston, John M and Li, Lucy and Padman, Benjamin S and Oorschot, Viola and Geoghegan, Niall D and Chappaz, Stephane and Davidson, Sophia and San Chin, Hui and Lane, Rachael M and Dramicanin, Marija and Saunders, Tahnee L and Sugiana, Canny and Lessene, Romina and Osellame, Laura D and Chew, Teng-Leong and Dewson, Grant and Lazarou, Michael and Ramm, Georg and Lessene, Guillaume and Ryan, Michael T and Rogers, Kelly L and van Delft, Mark F and Kile, Benjamin T} } @article {49535, title = {Brain-wide circuit interrogation at the cellular level guided by online analysis of neuronal function.}, journal = {Nature Methods}, volume = {15}, year = {2018}, month = {2018 Nov 30}, pages = {1117-1125}, abstract = {

Whole-brain imaging allows for comprehensive functional mapping of distributed neural pathways, but neuronal perturbation experiments are usually limited to targeting predefined regions or genetically identifiable cell types. To complement whole-brain measures of activity with brain-wide manipulations for testing causal interactions, we introduce a system that uses measuredactivity patterns to guide optical perturbations of any subset of neurons in the same fictively behaving larval zebrafish. First, a light-sheet microscope collects whole-brain data that are rapidly analyzed by a distributed computing system to generate functional brain maps. On the basis of these maps, the experimenter can then optically ablate neurons and image activity changes across the brain. We applied this method to characterize contributions of behaviorally tuned populations to the optomotor response. We extended the system to optogenetically stimulate arbitrary subsets of neurons during whole-brain imaging. These open-source methods enable delineating the contributions of neurons to brain-wide circuit dynamics and behavior in individual animals.

}, doi = {10.1038/s41592-018-0221-x}, author = {Vladimirov, Nikita and Wang, Chen and H{\"o}ckendorf, Burkhard and Pujala, Avinash and Tanimoto, Masashi and Mu, Yu and Yang, Chao-Tsung and Wittenbach, Jason and Freeman, Jeremy and Preibisch, Stephan and Koyama, Minoru and Keller, Philipp J and Ahrens, Misha B} } @article {49520, title = {Brain-wide organization of neuronal activity and convergent sensorimotor transformations in larval zebrafish.}, journal = {Neuron}, volume = {100}, year = {2018}, month = {2018 Nov 21}, pages = {876-890.e5}, abstract = {

Simultaneous recordings of large populations of neurons in behaving animals allow detailed observation of high-dimensional, complex brain activity. However, experimental approaches often focus on singular behavioral paradigms or brain areas. Here, we recorded whole-brain neuronal activity of larval zebrafish presented with a battery of visual stimuli while recording fictive motor output. We identified neurons tuned to each stimulus type and motor output and discovered groups of neurons in the anterior hindbrain that respond to different stimuli eliciting similar behavioral responses. These convergent sensorimotor representations were only weakly correlated to instantaneous motor activity, suggesting that they critically inform, but do not directly generate, behavioral choices. To catalog brain-wide activity beyond explicit sensorimotor processing, we developed an unsupervised clustering technique that organizes neurons into functional groups. These analyses enabled a broad overview of the functional organization of the brain and revealed numerous brain nuclei whose neurons exhibit concerted activity patterns.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2018.09.042}, author = {Chen, Xiuye and Mu, Yu and Hu, Yu and Kuan, Aaron T and Nikitchenko, Maxim and Randlett, Owen and Chen, Alex B and Gavornik, Jeffery P and Sompolinsky, Haim and Engert, Florian and Ahrens, Misha B} } @article {49368, title = {Building a functional connectome of the central complex.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Aug 20}, abstract = {

The central complex is a highly conserved insect brain region composed of morphologically stereotyped neurons that arborize in distinctively shaped substructures. The region is implicated in a wide range of behaviors and several modeling studies have explored its circuit computations. Most studies have relied on assumptions about connectivity between neurons based on their overlap in light microscopy images. Here, we present an extensive functional connectome of Drosophila melanogaster{\textquoteright}s central complex at cell-type resolution. Using simultaneous optogenetic stimulation, calcium imaging and pharmacology, we tested the connectivity between 70 presynaptic-to-postsynaptic cell-type pairs. We identi1ed numerous inputs to the central complex, but only a small number of output channels. Additionally, the connectivity of this highly recurrent circuit appears to be sparser than anticipated from light microscopy images. Finally, the connectivity matrix highlights the potentially critical role of a class of bottleneck interneurons. All data is provided for interactive exploration on a website.

}, issn = {2050-084X}, doi = {10.7554/eLife.37017}, author = {Franconville, Romain and Beron, Celia and Jayaraman, Vivek} } @article {67289, title = {CalmAn: An open source tool for scalable Calcium Imaging data Analysis}, journal = {bioRxiv}, year = {2018}, month = {06/2018}, abstract = {

Advances in fluorescence microscopy enable monitoring larger brain areas in-vivo with finer time resolution. The resulting data rates require reproducible analysis pipelines that are reliable, fully automated, and scalable to datasets generated over the course of months. Here we present CaImAn, an open-source library for calcium imaging data analysis. CaImAn provides automatic and scalable methods to address problems common to pre-processing, including motion correction, neural activity identification, and registration across different sessions of data collection. It does this while requiring minimal user intervention, with good performance on computers ranging from laptops to high-performance computing clusters. CaImAn is suitable for two-photon and one-photon imaging, and also enables real-time analysis on streaming data. To benchmark the performance of CaImAn we collected a corpus of ground truth annotations from multiple labelers on nine mouse two-photon datasets. We demonstrate that CaImAn achieves near-human performance in detecting locations of active neurons.

}, doi = {10.1101/339564}, url = {https://www.biorxiv.org/content/early/2018/06/05/339564}, author = {Giovannucci, Andrea and Friedrich, Johannes and Gunn, Pat and Kalfon, J{\'e}r{\'e}mie and Koay, Sue Ann and Taxidis, Jiannis and Najafi, Farzaneh and Gauthier, Jeffrey L. and Zhou, Pengcheng and Tank, David W. and Chklovskii, Dmitri and Pnevmatikakis, Eftychios A.} } @article {49061, title = {Cell type-specific variation of somatotopic precision across corticostriatal projections. }, journal = {bioRxiv}, year = {2018}, month = {2018 Feb 7}, abstract = {

The striatum shows general topographic organization and regional differences in behavioral functions. How corticostriatal topography differs across cortical areas and cell types to support these distinct functions is unclear. This study contrasted corticostriatal projections from two layer 5 cell types, intratelencephalic (IT-type) and pyramidal tract (PT-type) neurons, using viral vectors expressing fluorescent reporters in Cre-driver mice. Long-range corticostriatal projections from sensory and motor cortex are somatotopic, with a decreasing somatotopic specificity as injections move from sensory to motor and frontal areas. Somatotopic organization differs between IT-type and PT-type neurons, including injections in the same site, with IT-type neurons having higher somatotopic stereotypy than PT-type neurons. Furthermore, IT-type projections from interconnected cortical areas have stronger correlations in corticostriatal targeting than PT-type projections do. Thus, as predicted by a long-standing basal ganglia model, corticostriatal projections of interconnected cortical areas form parallel circuits in basal ganglia-thalamus-cortex loops.

}, doi = {10.1101/261446}, author = {Hooks, Bryan M and Papale, Andrew E and Paletzki, Ronald and Feroze, Muhammad and Eastwood, Brian S and Couey, Jonathan J and Winnubst, Johan and Chandrashekar, Jayaram and Gerfen, Charles R} } @article {49406, title = {Cell-specific chemical delivery using a selective Nitroreductase-Nitroaryl pair.}, journal = {ACS Chemical Biology}, volume = {13}, year = {2018}, month = {2018 Aug 29}, pages = {1888-96}, abstract = {

The utility of small molecules to probe or perturb biological systems is limited by the lack of cell-specificity. "Masking" the activity of small molecules using a general chemical modification and "unmasking" it only within target cells overcomes this limitation. To this end, we have developed a selective enzyme-substrate pair consisting of engineered variants of E. coli nitroreductase (NTR) and a 2-nitro- N-methylimidazolyl (NM) masking group. To discover and optimize this NTR-NM system, we synthesized a series of fluorogenic substrates containing different nitroaromatic masking groups, confirmed their stability in cells, and identified the best substrate for NTR. We then engineered the enzyme for improved activity in mammalian cells, ultimately yielding an enzyme variant (enhanced NTR, or eNTR) that possesses up to 100-fold increased activity over wild-type NTR. These improved NTR enzymes combined with the optimal NM masking group enable rapid, selective unmasking of dyes, indicators, and drugs to genetically defined populations of cells.

}, issn = {1554-8937}, doi = {10.1021/acschembio.8b00524}, author = {Gruber, Todd D and Krishnamurthy, Chithra and Grimm, Jonathan B and Tadross, Michael R and Wysocki, Laura M and Gartner, Zev J and Lavis, Luke D} } @article {49256, title = {Cell-type specific changes in glial morphology and glucocorticoid expression during stress and aging in the medial prefrontal cortex.}, journal = {Frontiers in Aging Neuroscience}, volume = {10}, year = {2018}, month = {2018 May 23}, abstract = {

Repeated exposure to stressors is known to produce large-scale remodeling of neurons within the prefrontal cortex (PFC). Recent work suggests stress-related forms of structural plasticity can interact with aging to drive distinct patterns of pyramidal cell morphological changes. However, little is known about how other cellular components within PFC might be affected by these challenges. Here, we examined the effects of stress exposure and aging on medial prefrontal cortical glial subpopulations. Interestingly, we found no changes in glial morphology with stress exposure but a profound morphological change with aging. Furthermore, we found an upregulation of non-nuclear glucocorticoid receptors (GR) with aging, while nuclear levels remained largely unaffected. Both changes are selective for microglia, with no stress or aging effect found in astrocytes. Lastly, we show that the changes found within microglia inversely correlated with the density of dendritic spines on layer III pyramidal cells. These findings suggest microglia play a selective role in synaptic health within the aging brain.

}, doi = {10.3389/fnagi.2018.00146}, author = {Chan, Thomas E and Grossman, Yael S and Bloss, Erik B and Janssen, William G and Lou, Wendy and McEwen, Bruce S and Dumitriu, Dani and Morrison, John H} } @article {67284, title = {Cerebellar involvement in an evidence-accumulation decision-making task}, journal = {eLife}, volume = {7}, year = {2018}, month = {08/2018}, abstract = {

To make successful evidence-based decisions, the brain must rapidly and accurately transform sensory inputs into specific goal-directed behaviors. Most experimental work on this subject has focused on forebrain mechanisms. Using a novel evidence-accumulation task for mice, we performed recording and perturbation studies of crus I of the lateral posterior cerebellum, which communicates bidirectionally with numerous forebrain regions. Cerebellar inactivation led to a reduction in the fraction of correct trials. Using two-photon fluorescence imaging of calcium, we found that Purkinje cell somatic activity contained choice/evidence-related information. Decision errors were represented by dendritic calcium spikes, which in other contexts are known to drive cerebellar plasticity. We propose that cerebellar circuitry may contribute to computations that support accurate performance in this perceptual decision-making task.

}, doi = {10.7554/eLife.36781}, url = {https://elifesciences.org/articles/36781}, author = {Deverett, Ben and Koay, Sue Ann and Oostland, Marlies and Wang, Samuel S-H} } @article {67292, title = {A cerebellar role in evidence-guided decision-making}, journal = {bioRxiv}, year = {2018}, month = {06/2018}, abstract = {

To make successful evidence-based decisions, the brain must rapidly and accurately transform sensory inputs into specific goal-directed behaviors. Most experimental work on this subject has focused on forebrain mechanisms. Here we show that during perceptual decision-making over a period of seconds, decision-, sensory-, and error-related information converge on the lateral posterior cerebellum in crus I, a structure that communicates bidirectionally with numerous forebrain regions. We trained mice on a novel evidence-accumulation task and demonstrated that cerebellar inactivation reduces behavioral accuracy without impairing motor parameters of action. Using two-photon calcium imaging, we found that Purkinje cell somatic activity encoded choice- and evidence-related variables. Decision errors were represented by dendritic calcium spikes, which are known to drive plasticity. We propose that cerebellar circuitry may contribute to the set of distributed computations in the brain that support accurate perceptual decision-making.

}, doi = {10.1101/343095}, url = {https://www.biorxiv.org/content/early/2018/06/11/343095}, author = {Deverett, Ben and Koay, Sue Ann and Oostland, Marlies and Wang, Samuel S.-H.} } @article {49021, title = {The Chlamydia type III effector TarP alters the dynamics and organization of host focal adhesions.}, journal = {bioRxiv}, year = {2018}, month = {2018 Jan 23}, abstract = {

Bacterial infection of mucosal epithelial cells triggers cell exfoliation to limit the dissemination of infection within the tissue. Therefore, mucosal pathogens must possess strategies to counteract cell extrusion in response to infection. Chlamydia trachomatis spends most of its intracellular development in the non-infectious form. Thus, premature host cell extrusion is detrimental to the pathogen. We demonstrate that C. trachomatis alters the dynamics of focal adhesions. Live-cell microscopy showed that focal adhesions in C. trachomatis-infected cells displayed increased stability. In contrast, focal adhesions in mock-infected cells readily disassembled upon inhibition of myosin II by blebbisttin. Super-resolution microscopy revealed a reorganization of paxillin and FAK in infected cells. Ectopically expressed type III effector TarP localized to focal adhesions, leading to their stabilization and reorganization in a vinculin-dependent manner. Overall, the results indicate that C. trachomatis possesses a dedicated mechanism to regulate host cell focal adhesion dynamics.

}, doi = {10.1101/250563}, author = {Pedrosa, Antonio T and Nogueira, Ana T and Thwaites, Tristan R and Aaron, Jesse and Chew, Teng-Leong and Carabeo, Rey A} } @article {65772, title = {Circularly Permuted Fluorogenic Proteins for the Design of Modular Biosensors.}, journal = {ACS Chemical Biology}, volume = {13}, year = {2018}, month = {09/2018}, pages = {2392 {\textendash} 2397}, abstract = {

Fluorescent reporters are essential components for the design of optical biosensors that are able to image intracellular analytes in living cells. Herein, we describe the development of circularly permuted variants of Fluorescence-Activating and absorption-Shifting Tag (FAST) and demonstrate their potential as reporting module in biosensors. Circularly permutated FAST (cpFAST) variants allow one to condition the binding and activation of a fluorogenic ligand (and thus fluorescence) to analyte recognition by coupling them with analyte-binding domains. We demonstrated their use for biosensor design by generating multicolor plug-and-play fluorogenic biosensors for imaging the intracellular levels of Ca2+ in living mammalian cells in real time.

}, doi = {10.1021/acschembio.8b00417}, author = {Tebo, Alison G and Pimenta, Frederico M and Zoumpoulaki, Martha and Kikuti, Carlos and Sirkia, Helena and Plamont, Marie-Aude and Houdusse, Anne and Gautier, Arnaud} } @article {49087, title = {cisTEM, User-friendly software for single-particle image processing.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Mar 07}, abstract = {

We have developed new open-source software calledTEM (computational imaging system for transmission electron microscopy) for the processing of data for high-resolution electron cryo-microscopy and single-particle averaging.TEM features a graphical user interface that is used to submit jobs, monitor their progress, and display results. It implements a full processing pipeline including movie processing, image defocus determination, automatic particle picking, 2D classification, ab-initio 3D map generation from random parameters, 3D classification, and high-resolution refinement and reconstruction. Some of these steps implement newly-developed algorithms; others were adapted from previously published algorithms. The software is optimized to enable processing of typical datasets (2000 micrographs, 200k - 300k particles) on a high-end, CPU-based workstation in half a day or less, comparable to GPU-accelerated processing. Jobs can also be scheduled on large computer clusters using flexible run profiles that can be adapted for most computing environments.TEM is available for download from cistem.org.

}, issn = {2050-084X}, doi = {10.7554/eLife.35383}, author = {Grant, Timothy and Rohou, Alexis and Grigorieff, Nikolaus} } @article {49236, title = {Color depth MIP mask search: a new tool to expedite Split-GAL4 creation.}, journal = {bioRxiv}, year = {2018}, month = {2018 May 09}, abstract = {

The GAL4-UAS system has proven its versatility in studying the function and expression patterns of neurons the Drosophila central nervous system. Although the GAL4 system has been used for 25 years, recent genetic intersectional tools have enabled genetic targeting of very small numbers of neurons aiding in the understanding of their function. This split-GAL4 system is extremely powerful for studying neuronal morphology and the neural basis of animal behavior. However, choosing lines to intersect that have overlapping patterns restricted to one to a few neurons has been cumbersome. This challenge is now growing as the collections of GAL4 driver lines has increased. Here we present a new method and software plug-in for Fiji to dramatically improve the speed of querying large databases of potential lines to intersect and aid in the split-GAL4 creation. We also provide pre-computed datasets for the Janelia GAL4 (5,738 lines) and VT GAL4 (7,429 lines) of the Drosophila central nervous system (CNS). The tool reduced our split-GAL4 creation effort dramatically.

}, doi = {10.1101/318006}, author = {Otsuna, Hideo and Ito, Masayoshi and Kawase, Takashi} } @article {49126, title = {Colour vision: A fresh view of lateral inhibition in Drosophila.}, journal = {Current Biology : CB}, volume = {28}, year = {2018}, month = {2018 Apr 02}, pages = {R308-R311}, abstract = {

A recent study reports a novel form of lateral inhibition between photoreceptors supporting colour vision in the vinegar fly, Drosophila melanogaster.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2018.02.052}, author = {Longden, Kit D} } @article {49434, title = {Communication from learned to innate olfactory processing centers is required for memory retrieval in Drosophila.}, journal = {Neuron}, volume = {100}, year = {2018}, month = {2018 Sep 19}, pages = {651-68}, abstract = {

The behavioral response to a sensory stimulus may depend on both learned and innate neuronal representations. How these circuits interact to produce appropriate behavior is unknown. In Drosophila, the lateral horn (LH) and mushroom body (MB) are thought to mediate innate and learned olfactory behavior, respectively, although LH function has not been tested directly. Here we identify two LH cell types (PD2a1 and PD2b1) that receive input from an MB output neuron required for recall of aversive olfactory memories. These neurons are required for aversive memory retrieval and modulated by training. Connectomics data demonstrate that PD2a1 and PD2b1 neurons also receive direct input from food odor-encoding neurons. Consistent with this, PD2a1 and PD2b1 are also necessary for unlearned attraction to some odors, indicating that these neurons have a dual behavioral role. This provides a circuit mechanism by which learned and innate olfactory information can interact in identified neurons to produce appropriate behavior.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2018.08.037}, author = {Dolan, Michael-John and Belliart-Gu{\'e}rin, Ghislain and Bates, Alexander Shakeel and Frechter, Shahar and Lampin-Saint-Amaux, Aur{\'e}lie and Aso, Yoshinori and Roberts, Ruair{\'\i} J V and Schlegel, Philipp and Wong, Allan and Hammad, Adnan and Bock, Davi and Rubin, Gerald M and Preat, Thomas and Placais, Pierre-Yves and Jefferis, Gregory S X E} } @article {67219, title = {Community-based benchmarking improves spike rate inference from two-photon calcium imaging data}, journal = {PLOS Computational Biology}, volume = {14}, year = {2018}, month = {Sep-05-2019}, pages = {e1006157}, abstract = {

In recent years, two-photon calcium imaging has become a standard tool to probe the function of neural circuits and to study computations in neuronal populations. However, the acquired signal is only an indirect measurement of neural activity due to the comparatively slow dynamics of fluorescent calcium indicators. Different algorithms for estimating spike rates from noisy calcium measurements have been proposed in the past, but it is an open question how far performance can be improved. Here, we report the results of the\ spikefinder\ challenge, launched to catalyze the development of new spike rate inference algorithms through crowd-sourcing. We present ten of the submitted algorithms which show improved performance compared to previously evaluated methods. Interestingly, the top-performing algorithms are based on a wide range of principles from deep neural networks to generative models, yet provide highly correlated estimates of the neural activity. The competition shows that benchmark challenges can drive algorithmic developments in neuroscience.

}, doi = {10.1371/journal.pcbi.1006157}, url = {https://journals.plos.org/ploscompbiol/article?rev=2\&id=10.1371/journal.pcbi.1006157}, author = {Berens, Philipp and Freeman, Jeremy and Deneux, Thomas and Chenkov, Nikolay and McColgan, Thomas and Speiser, Artur and Macke, Jakob H. and Turaga, Srinivas C. and Mineault, Patrick and Rupprecht, Peter and Gerhard, Stephan and Friedrich, Rainer W. and Friedrich, Johannes and Paninski, Liam and Pachitariu, Marius and Harris, Kenneth D. and Bolte, Ben and Machado, Timothy A. and Ringach, Dario and Stone, Jasmine and Rogerson, Luke E. and Sofroniew, Nicolas J. and Reimer, Jacob and Froudarakis, Emmanouil and Euler, Thomas and Rom{\'a}n Ros{\'o}n, Miroslav and Theis, Lucas and Tolias, Andreas S. and Bethge, Matthias}, editor = {Bush, Daniel} } @article {49149, title = {A community-developed Open-Source computational ecosystem for big neuro data.}, journal = {Nature Methods}, volume = {15}, year = {2018}, month = {2018 Nov}, pages = {846-7}, abstract = {

Big imaging data is becoming more prominent in brain sciences across spatiotemporal scales and phylogenies. We have developed a computational ecosystem that enables storage, visualization, and analysis of these data in the cloud, thusfar spanning 20+ publications and 100+ terabytes including nanoscale ultrastructure, microscale synaptogenetic diversity, and mesoscale whole brain connectivity, making NeuroData the largest and most diverse open repository of brain data.

}, doi = {10.1038/s41592-018-0181-1}, author = {Vogelstein, Joshua T and Perlman, Eric and Falk, Benjamin and Baden, Alex and Roncal, William Gray and Chandrashekhar, Vikram and Collman, Forrest and Seshamani, Sharmishtaa and Patsolic, Jesse and Lillaney, Kunal and Kazhdan, Michael and Hider Jr., Robert and Pryor, Derek and Matelsky, Jordan and Gion, Timothy and Manavalan, Priya and Wester, Brock and Chevillet, Mark and Trautman, Eric T and Khairy, Khaled} } @article {48620, title = {A complete electron microscopy volume of the brain of adult Drosophila melanogaster.}, journal = {Cell}, volume = {174}, year = {2018}, month = {2018 Jul 12}, pages = {730-43}, abstract = {

Drosophila melanogaster has a rich repertoire of innate and learned behaviors. Its 100,000-neuron brain is a large but tractable target for comprehensive neural circuit mapping. Only electron microscopy (EM) enables complete, unbiased mapping of synaptic connectivity; however, the fly brain is too large for conventional EM. We developed a custom high-throughput EM platform and imaged the entire brain of an adult female fly at synaptic resolution. To validate the dataset, we traced brain-spanning circuitry involving the mushroom body (MB), which has been extensively studied for its role in learning. All inputs to Kenyon cells (KCs), the intrinsic neurons of the MB, were mapped, revealing a previously unknown cell type, postsynaptic partners of KC dendrites, and unexpected clustering of olfactory projection neurons. These reconstructions show that this freely available EM volume supports mapping of brain-spanning circuits, which will significantly accelerate Drosophila neuroscience..

}, doi = {10.1016/j.cell.2018.06.019}, author = {Zheng, Zhihao and Lauritzen, J Scott and Perlman, Eric and Robinson, Camenzind G and Nichols, Matthew and Milkie, Daniel E and Torrens, Omar and Price, John and Fisher, Corey B and Sharifi, Nadiya and Calle-Schuler, Steven A and Kmecova, Lucia and Ali, Iqbal J and Karsh, Bill and Trautman, Eric T and Bogovic, John A and Hanslovsky, Philipp and Jefferis, Gregory S X E and Kazhdan, Michael and Khairy, Khaled} } @article {49092, title = {Comprehensive analysis of a cis-regulatory region reveals pleiotropy in enhancer function.}, journal = {Cell Reports}, volume = {22}, year = {2018}, month = {2018 Mar 13}, pages = {3021-3031}, abstract = {

Developmental genes can have complex cis-regulatory regions with multiple enhancers. Early work revealed remarkable modularity of enhancers, whereby distinct DNA regions drive gene expression in defined spatiotemporal domains. Nevertheless, a few reports have shown that enhancers function in multiple developmental stages, implying that enhancers can be pleiotropic. Here, we have studied the activity of the enhancers of the shavenbaby gene throughout D.\ melanogaster development. We found that all seven shavenbaby enhancers drive expression in multiple tissues and developmental stages. We explored how enhancer pleiotropy is encoded in two of these enhancers. In one enhancer,\ the same transcription factor binding sites contribute to embryonic and pupal expression, revealing site pleiotropy, whereas for a second enhancer, these roles are encoded by distinct sites. Enhancer pleiotropy may be a common feature of cis-regulatory regions of developmental genes, and site pleiotropy may constrain enhancer evolution in some cases.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2018.02.073}, author = {Preger-Ben Noon, Ella and Sabar{\'\i}s, Gonzalo and Ortiz, Daniela M and Sager, Jonathan and Liebowitz, Anna and Stern, David L and Frankel, Nicol{\'a}s} } @article {49580, title = {Computational processing of neural recordings from calcium imaging data.}, journal = {Current Opinion in Neurobiology}, volume = {55}, year = {2018}, month = {2019 Apr }, pages = {22-31}, abstract = {

Electrophysiology has long been the workhorse of neuroscience, allowing scientists to record with millisecond precision the action potentials generated by neurons in vivo. Recently, calcium imaging of fluorescent indicators has emerged as a powerful alternative. This technique has its own strengths and weaknesses and unique data processing problems and interpretation confounds. Here we review the computational methods that convert raw calcium movies to estimates of single neuron spike times with minimal human supervision. By computationally addressing the weaknesses of calcium imaging, these methods hold the promise of significantly improving data quality. We also introduce a new metric to evaluate the output of these processing pipelines, which is based on the cluster isolation distance routinely used in electrophysiology.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2018.11.005}, author = {Stringer, Carsen and Pachitariu, Marius} } @article {49290, title = {A connectome based hexagonal lattice convolutional network model of the Drosophila visual system.}, journal = {arXiv}, year = {2018}, month = {2018 Jun 12}, pages = {1806.04793 }, abstract = {

What can we learn from a connectome? We constructed a simplified model of the first two stages of the fly visual system, the lamina and medulla. The resulting hexagonal lattice convolutional network was trained using backpropagation through time to perform object tracking in natural scene videos. Networks initialized with weights from connectome reconstructions automatically discovered well-known orientation and direction selectivity properties in T4 neurons and their inputs, while networks initialized at random did not. Our work is the first demonstration, that knowledge of the connectome can enable in silico predictions of the functional properties of individual neurons in a circuit, leading to an understanding of circuit function from structure alone.

}, url = {https://arxiv.org/abs/1806.04793}, author = {Tschopp, Fabian D and Reiser, Michael B and Turaga, Srinivas C} } @article {49118, title = {Continuous variation within cell types of the nervous system.}, journal = {Trends in Neurosciences}, volume = {41}, year = {2018}, month = {2018 Mar 22}, pages = {337-48}, abstract = {

The brain is an organ of immense complexity. Next-generation RNA sequencing (RNA-seq) is becoming increasingly popular in the deconstruction of this complexity into distinct classes of {\textquoteright}cell types{\textquoteright}. Notably, in addition to revealing the organization of this distinct cell-type landscape, the technology has also begun to illustrate that continuous variation can be found within narrowly defined cell types. Here we summarize the evidence for graded transcriptomic heterogeneity being present, widespread, and functionally relevant in the nervous system. We explain how these graded differences can map onto higher-order organizational features and how they may reframe existing interpretations of higher-order heterogeneity. Ultimately, a multimodal approach incorporating continuously variable cell types will facilitate an accurate reductionist interpretation of the nervous system.

}, issn = {1878-108X}, doi = {10.1016/j.tins.2018.02.010}, author = {Cembrowski, Mark S and Menon, Vilas} } @article {49583, title = {Convergence of monosynaptic and polysynaptic sensory paths onto common motor outputs in a feeding connectome.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Dec 11}, abstract = {

We reconstructed, from a whole CNS EM volume, the synaptic map of input and output neurons that underlie food intake behavior of larvae. Input neurons originate from enteric, pharyngeal and external sensory organs and converge onto seven distinct sensory synaptic compartments within the CNS. Output neurons consist of feeding motor, serotonergic modulatory and neuroendocrine neurons. Monosynaptic connections from a set of sensory synaptic compartments cover the motor, modulatory and neuroendocrine targets in overlapping domains. Polysynaptic routes are superimposed on top of monosynaptic connections, resulting in divergent sensory paths that converge on common outputs. A completely different set of sensory compartments is connected to the mushroom body calyx. The mushroom body output neurons are connected to interneurons that directly target the feeding output neurons. Our results illustrate a circuit architecture in which monosynaptic and multisynaptic connections from sensory inputs traverse onto output neurons via a series of converging paths.

}, issn = {2050-084X}, doi = {10.7554/eLife.40247}, author = {Miroschnikow, Anton and Schlegel, Philipp and Schoofs, Andreas and Hueckesfeld, Sebastian and Li, Feng and Schneider-Mizell, Casey M and Fetter, Richard D and Truman, James W and Cardona, Albert and Pankratz, Michael J} } @article {49478, title = {Correlated evolution of two copulatory organs via a single cis-regulatory nucleotide change.}, journal = {Current Biology : CB}, volume = {28}, year = {2018}, month = {2018 Oct 05}, pages = {3450-7}, abstract = {

Diverse traits often covary between species [1-3]. The possibility that a single mutation could contribute to the evolution of several characters between species [3] is rarely investigated as relatively few cases are dissected at the nucleotide level. Drosophila santomea has evolved additional sex comb sensory teeth on its legs and has lost two sensory bristles on its genitalia. We present evidence that a single nucleotide substitution in an enhancer of the scute gene contributes to both changes. The mutation alters a binding site for the Hox protein Abdominal-B in the developing genitalia, leading to bristle loss, and for another factor in the developing leg, leading to bristle gain. Our study suggests that morphological evolution between species can occur through a single nucleotide change affecting several sexually dimorphic traits. VIDEO ABSTRACT.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2018.08.047}, author = {Nagy, Olga and Nuez, Isabelle and Savisaar, Rosina and Peluffo, Alexandre E and Yassin, Amir and Lang, Michael and Stern, David L and Matute, Daniel R and David, Jean R and Courtier-Orgogozo, Virginie} } @article {49476, title = {A cortico-cerebellar loop for motor planning.}, journal = {Nature}, volume = {563}, year = {2018}, month = {2018 Oct 17}, pages = {113-6}, abstract = {

Persistent and ramping neural activity in the frontal cortex anticipates specific movements. Preparatory activity is distributed across several brain regions, but it is unclear which brain areas are involved and how this activity is mediated by multi-regional interactions. The cerebellum is thought to be primarily involved in the short-timescale control of movement; however, roles for this structure in cognitive processes have also been proposed. In humans, cerebellar damage can cause defects in planning and working memory. Here we show that persistent representation of information in the frontal cortex during motor planning is dependent on the cerebellum. Mice performed a sensory discrimination task in which they used short-term memory to plan a future directional movement. A transient perturbation in the medial deep cerebellar nucleus (fastigial nucleus) disrupted subsequent correct responses without hampering movement execution. Preparatory activity was observed in both the frontal cortex and the cerebellar nuclei, seconds before the onset of movement. The silencing of frontal cortex activity abolished preparatory activity in the cerebellar nuclei, and fastigial activity was necessary to maintain cortical preparatory activity. Fastigial output selectively targeted the behaviourally relevant part of the frontal cortex through the thalamus, thus closing a cortico-cerebellar loop. Our results support the view that persistent neural dynamics during motor planning is maintained by neural circuits that span multiple brain regions, and that cerebellar computations extend beyond online motor control.

}, issn = {1476-4687}, doi = {10.1038/s41586-018-0633-x}, author = {Gao, Zhenyu and Davis, Courtney and Thomas, Alyse M and Economo, Michael N and Abrego, Amada M and Svoboda, Karel and De Zeeuw, Chris I and Li, Nuo} } @article {49433, title = {Cryo-EM analysis of the T3S injectisome reveals the structure of the needle and open secretin.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Sep 21}, pages = {3840}, abstract = {

The bacterial type III secretion system, or injectisome, is a syringe shaped nanomachine essential for the virulence of many disease causing Gram-negative bacteria. At the core of the injectisome structure is the needle complex, a continuous channel formed by the highly oligomerized inner and outer membrane hollow rings and a polymerized helical needle filament which spans through and projects into the infected host cell. Here we present the near-atomic resolution structure of a needle complex from the prototypical Salmonella Typhimurium SPI-1 type III secretion system, with local masking protocols allowing for model building and refinement of the major membrane spanning components of the needle complex\ base in addition to an isolated needle filament. This work provides significant insight into injectisome structure and assembly and importantly captures the molecular basis for substrate induced gating in the giant outer membrane secretin portal family.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-06298-8}, author = {Hu, J and Worrall, L J and Hong, C and Vuckovic, M and Atkinson, C E and Caveney, N and Yu, Z and Strynadka, N C J} } @article {49315, title = {Cryo-EM structure of an essential Plasmodium vivax invasion complex.}, journal = {Nature}, volume = {559}, year = {2018}, month = {2018 Jul}, pages = {135-139}, abstract = {

Plasmodium vivax is the most widely distributed malaria parasite that infects humans. P. vivax invades reticulocytes exclusively, and successful entry depends on specific interactions between the P. vivax reticulocyte-binding protein 2b (PvRBP2b) and transferrin receptor 1 (TfR1). TfR1-deficient erythroid cells are refractory to invasion by P. vivax, and anti-PvRBP2b monoclonal antibodies inhibit reticulocyte binding and block P. vivax invasion in field isolates. Here we report a high-resolution cryo-electron microscopy structure of a ternary complex of PvRBP2b bound to human TfR1 and transferrin, at 3.7 {\r A} resolution. Mutational analyses show that PvRBP2b residues involved in complex formation are conserved; this suggests that antigens could be designed that act across P. vivax strains. Functional analyses of TfR1 highlight how P. vivax hijacks TfR1, an essential housekeeping protein, by binding to sites that govern host specificity, without affecting its cellular function of transporting iron. Crystal and solution structures of PvRBP2b in complex with antibody fragments characterize the inhibitory epitopes. Our results establish a structural framework for understanding how P. vivax reticulocyte-binding protein engages its receptor and the molecular mechanism of inhibitory monoclonal antibodies, providing important information for the design of novel vaccine candidates.

}, issn = {1476-4687}, doi = {10.1038/s41586-018-0249-1}, author = {Gruszczyk, Jakub and Huang, Rick K and Chan, Li-Jin and Menant, S{\'e}bastien and Hong, Chuan and Murphy, James M and Mok, Yee-Foong and Griffin, Michael D W and Pearson, Richard D and Wong, Wilson and Cowman, Alan F and Yu, Zhiheng and Tham, Wai-Hong} } @article {49325, title = {Cryo-EM structure of the polycystin 2-l1 ion channel.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Jul 13}, abstract = {

We report the near atomic resolution (3.3 {\r A}) of the human polycystic kidney disease 2-like 1 (polycystin 2-l1) ion channel. Encoded by PKD2L1, polycystin 2-l1 is a calcium and monovalent cation-permeant ion channel in primary cilia and plasma membranes. The related primary cilium-specific polycystin-2 protein, encoded by PKD2, shares a high degree of sequence similarity, yet has distinct permeability characteristics. Here we show that these differences are reflected in the architecture of polycystin 2-l1.

}, issn = {2050-084X}, doi = {10.7554/eLife.36931}, author = {Hulse, Raymond E and Li, Zongli and Huang, Rick K and Zhang, Jin and Clapham, David E} } @article {65000, title = {Cryo-EM structure of the receptor-activated TRPC5 ion channel at 2.9 angstrom resolution.}, year = {2018}, month = {2018 Nov 11}, abstract = {

The transient receptor potential canonical subfamily member 5 (TRPC5) is a non-selective calcium-permeant cation channel. As a depolarizing channel, its function is studied in the central nervous system and kidney. TRPC5 forms heteromultimers with TRPC1, but also forms homomultimers. It can be activated by reducing agents through reduction of the extracellular disulfide bond. Here we present the 2.9 {\r A} resolution electron cryo-microscopy (cryo-EM) structure of TRPC5. The structure of TRPC5 in its apo state is partially open, which may be related to the weak activation of TRPC5 in response to extracellular pH. We also report the conserved negatively charged residues of the cation binding site located in the hydrophilic pocket between S2 and S3. Comparison of the TRPC5 structure to previously determined structures of other TRPC and TRP channels reveals differences in the extracellular pore domain and in the length of the S3 helix. Together, these results shed light on the structural features that contribute to the specific activation mechanism of the receptor-activated TRPC5.

}, doi = {10.1101/467969}, author = {Jingjing Duan and Jian Li and Gui-Lan Chen and Bo Zeng and Kechen Xie and Xiaogang Peng and Wei Zhou and Jianing Zhong and Yixing Zhang and Jie Xu and Changhu Xue and Lan Zhu and Wei Liu and Xiao-Li Tian and Jianbin Wang and David E. Clapham and Zongli Li and Jin Zhang} } @article {49264, title = {Crystal structure of arginine-bound lysosomal transporter SLC38A9 in the cytosol-open state.}, journal = {Nature Structural \& Molecular Biology}, volume = {25}, year = {2018}, month = {2018 Jun}, pages = {522-527}, abstract = {

Recent advances in understanding intracellular amino acid transport and mechanistic target of rapamycin complex 1 (mTORC1) signaling shed light on solute carrier 38, family A member 9 (SLC38A9), a lysosomal transporter responsible for the binding and translocation of several essential amino acids. Here we present the first crystal structure of SLC38A9 from Danio rerio in complex with arginine. As captured in the cytosol-open state, the bound arginine was locked in a transitional state stabilized by transmembrane helix 1 (TM1) of drSLC38A9, which was anchored at the groove between TM5 and TM7. These anchoring interactions were mediated by the highly conserved WNTMM motif in TM1, and mutations in this motif abolished arginine transport by drSLC38A9. The underlying mechanism of substrate binding is critical for sensitizing the mTORC1 signaling pathway to amino acids and for maintenance of lysosomal amino acid homeostasis. This study offers a first glimpse into a prototypical model for SLC38 transporters.

}, issn = {1545-9985}, doi = {10.1038/s41594-018-0072-2}, author = {Lei, Hsiang-Ting and Ma, Jinming and Sanchez Martinez, Silvia and Gonen, Tamir} } @article {68759, title = {CYK-4 functions independently of its centralspindlin partner ZEN-4 to cellularize oocytes in germline syncytia}, journal = {eLife}, volume = {7}, year = {2018}, month = {07/2018}, pages = {e36919}, abstract = {

Throughout metazoans, germ cells undergo incomplete cytokinesis to form syncytia connected by intercellular bridges. Gamete formation ultimately requires bridge closure, yet how bridges are reactivated to close is not known. The most conserved bridge component is centralspindlin, a complex of the Rho family GTPase-activating protein (GAP) CYK-4/MgcRacGAP and the microtubule motor ZEN-4/kinesin-6. Here, we show that oocyte production by the syncytial \textitCaenorhabditis elegans germline requires CYK-4 but not ZEN-4, which contrasts with cytokinesis, where both are essential. Longitudinal imaging after conditional inactivation revealed that CYK-4 activity is important for oocyte cellularization, but not for the cytokinesis-like events that generate syncytial compartments. CYK-4{\textquoteright}s lipid-binding C1 domain and the GTPase-binding interface of its GAP domain were both required to target CYK-4 to intercellular bridges and to cellularize oocytes. These results suggest that the conserved C1-GAP region of CYK-4 constitutes a targeting module required for closure of intercellular bridges in germline syncytia.

}, keywords = {centralspindlin, germline syncytia, intercellular bridge, Kinesin-6, MgcRacGAP, ring canal}, issn = {2050-084X}, doi = {10.7554/eLife.36919}, url = {https://doi.org/10.7554/eLife.36919}, author = {Lee, Kian-Yong and Green, Rebecca A and Gutierrez, Edgar and Gomez-Cavazos, J Sebastian and Kolotuev, Irina and Wang, Shaohe and Desai, Arshad and Groisman, Alex and Oegema, Karen}, editor = {Balasubramanian, Mohan K and Akhmanova, Anna} } @article {49125, title = {Dedicated photoreceptor pathways in Drosophila larvae mediate navigation by processing either spatial or temporal cues.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Mar 28}, pages = {1260}, abstract = {

To integrate changing environmental cues with high spatial and temporal resolution is critical for animals to orient themselves. Drosophila larvae show an effective motor program to navigate away from light sources. How the larval visual circuit processes light stimuli to control navigational decision remains unknown. The larval visual system is composed of two sensory input channels, Rhodopsin5 (Rh5) and Rhodopsin6 (Rh6) expressing photoreceptors (PRs). We here characterize how spatial and temporal information are used to control navigation. Rh6-PRs are required to perceive temporal changes of light intensity during head casts, while Rh5-PRs are required to control behaviors that allow navigation in response to spatial cues. We characterize how distinct behaviors are modulated and identify parallel acting and converging features of the visual circuit. Functional features of the larval visual circuit highlight the principle of how early in a sensory circuit distinct behaviors may be computed by partly overlapping sensory pathways.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-03520-5}, author = {Humberg, Tim-Henning and Bruegger, Pascal and Afonso, Bruno and Zlatic, Marta and Truman, James W and Gershow, Marc and Samuel, Aravinthan and Sprecher, Simon G} } @article {49127, title = {A deep (learning) dive into a cell.}, journal = {Nature Methods}, volume = {15}, year = {2018}, month = {2018 Apr 03}, pages = {253-4}, issn = {1548-7105}, doi = {10.1038/nmeth.4658}, author = {Branson, Kristin} } @article {49415, title = {Defective cortex glia plasma membrane structure underlies light-induced epilepsy in mutants.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, year = {2018}, month = {2018 Sep 05}, pages = {E8919-28}, abstract = {

Seizures induced by visual stimulation (photosensitive epilepsy; PSE) represent a common type of epilepsy in humans, but the molecular mechanisms and genetic drivers underlying PSE remain unknown, and no good genetic animal models have been identified as yet. Here, we show an animal model of PSE, in , owing to defective cortex glia. The cortex glial membranes are severely compromised in ceramide phosphoethanolamine synthase ()-null mutants and fail to encapsulate the neuronal cell bodies in the neuronal cortex. Expression of human sphingomyelin synthase 1, which synthesizes the closely related ceramide phosphocholine (sphingomyelin), rescues the cortex glial abnormalities and PSE, underscoring the evolutionarily conserved role of these lipids in glial membranes. Further, we show the compromise in plasma membrane structure that underlies the glial cell membrane collapse in mutants and leads to the PSE phenotype.

}, issn = {1091-6490}, doi = {10.1073/pnas.1808463115}, author = {Kunduri, Govind and Turner-Evans, Daniel and Konya, Yutaka and Izumi, Yoshihiro and Nagashima, Kunio and Lockett, Stephen and Holthuis, Joost and Bamba, Takeshi and Acharya, Usha and Acharya, Jairaj K} } @article {67291, title = {Detecting and Correcting False Transients in Calcium Imaging}, journal = {bioRxiv}, year = {2018}, month = {11/2018}, abstract = {

Population recordings of calcium activity are a major source of insight into neural function. Large dataset sizes often require automated methods, but automation can introduce errors that are difficult to detect. Here we show that automatic time course estimation can sometimes lead to significant misattribution errors, in which fluorescence is ascribed to the wrong cell. Misattribution arises when the shapes of overlapping cells are imperfectly defined, or when entire cells or processes are not identified, and misattribution can even be produced by methods specifically designed to handle overlap. To diagnose this problem, we develop a transient-by-transient metric and a visualization tool that allow users to quickly assess the degree of misattribution in large populations. To filter out misattribution, we also design a robust estimator that explicitly accounts for contaminating signals in a generative model. Our methods can be combined with essentially any cell finding technique, empowering users to diagnose and correct at large scale a problem that has the potential to significantly alter scientific conclusions.

}, doi = {10.1101/473470}, url = {https://www.biorxiv.org/content/early/2018/11/19/473470}, author = {Gauthier, Jeff L. and Koay, Sue Ann and Nieh, Edward H. and Tank, David W. and Pillow, Jonathan W. and Charles, Adam S.} } @article {67669, title = {Development and Applications of Fluorescent Proteins for Correlative Light and Electron Microscopy}, journal = {Microscopy and Microanalysis}, volume = {24}, year = {2018}, month = {01/2018}, pages = {2318 - 2319}, abstract = {

Recent advances in super-resolution microscopy have pushed the resolution limit of light microscopy closer to that of electron microscopy. However, as they invariably rely on fluorescence, light microscopy techniques only visualize whatever gets labeled. On the other hand, while electron microscopy reveals cellular structures at the highest resolution, it offers no specificity. The information gap between the two imaging modalities can only be bridged by correlative light and electron microscopy (CLEM). Previously we have developed a probe (mEos4) whose fluorescence and photoconversion survive 0.5-1\% OsO4 fixation, allowing super-resolution visualization of organelles and fused proteins in the context of resinembedded ultrastructure in both transmission EM (TEM) and scanning EM (SEM) [1,2].

}, issn = {1431-9276}, doi = {10.1017/S1431927618012072}, url = {https://www.cambridge.org/core/product/identifier/S1431927618012072/type/journal_article}, author = {Paez-Segala, Maria G. and Wang, Yalin and Iyer, Nirmala and Li, Wei-Ping and Rivlin, Patricia K. and Looger, Loren L.} } @article {49419, title = {The development and enhancement of FRAP as a key tool for investigating protein dynamics.}, journal = {Biophysical Journal}, volume = {115}, year = {2018}, month = {2018 Aug 17}, pages = {1146-55}, abstract = {

The saga of fluorescence recovery after photobleaching (FRAP) illustrates how disparate technical developments impact science. Starting with the classic 1976 Axelrod et\ al. work in Biophysical Journal, FRAP (originally fluorescence photobleaching recovery) opened the door to extraction of quantitative information from photobleaching experiments, laying the experimental and theoretical groundwork for quantifying both the mobility and the mobile fraction of a labeled population of proteins. Over the ensuing years, FRAP{\textquoteright}s reach dramatically expanded, with new developments in GFP technology and turn-key confocal microscopy, which enabled measurement of protein diffusion and binding/dissociation rates in virtually every compartment within the cell. The FRAP technique and data catalyzed an exchange of ideas between biophysicists studying membrane dynamics, cell biologists focused on intracellular dynamics, and systems biologists modeling the dynamics of cell activity. The outcome transformed the field of cellular biology, leading to a fundamental rethinking of long-held theories of cellular dynamism. Here, we review the pivotal FRAP studies that made these developments and conceptual changes possible, which gave rise to current models of complex cell dynamics.

}, issn = {1542-0086}, doi = {10.1016/j.bpj.2018.08.007}, author = {Lippincott-Schwartz, Jennifer and Snapp, Erik Lee and Phair, Robert D} } @article {49467, title = {Development of 2-colour and 3D SMLM data analysis methods for fibrous spatial point patterns.}, journal = {Journal of Physics D: Applied Physics}, volume = {52}, year = {2018}, month = {2018 Oct 11}, pages = {1}, abstract = {

Abstract ingle molecule localisation microscopy (SMLM), experimentally achieved over a decade ago, has become a routinely used analytical tool across the life sciences. Synergistic advances in probe chemistry, optical physics and data analysis has propelled SMLM into the quantitative realm, enabling unprecedented access to the cellular machinery at the nanoscale. In its early years, SMLM primarily served as a platform for impressive rendered images of sub diffraction scale structures, however more recently a shift towards interrogating SMLM point pattern data in a robust mathematical framework has occurred. A prevalent theme in the SMLM field is the need for quantitative analytical methods, to better understand the underlying processes on which SMLM reports and to extract statistically valid biological insights. Whilst some forms of post processing analytics, for example cluster analysis, have been widely studied, others such as fibre analysis remain in their infancy. Here, we review the current state of the art of cluster analysis and fibre analysis and present new methods for their implementation in both 3D SMLM data sets and multi-colour data.

}, doi = {10.1088/1361-6463/aae7ac}, author = {Peters, Ruby and Griffi{\'e}, Juliette and Williamson, David and Aaron, Jesse and Khuon, Satya and Owen, Dylan} } @article {65771, title = {Development of a Rubredoxin-Type Center Embedded in a de Dovo-Designed Three-Helix Bundle}, journal = {Biochemistry}, volume = {57}, year = {2018}, month = {03/2018}, pages = {2308 {\textendash} 2316}, abstract = {

Protein design is a powerful tool for interrogating the basic requirements for the function of a metal site in a way that allows for the selective incorporation of elements that are important for function. Rubredoxins are small electron transfer proteins with a reduction potential centered near 0 mV (vs normal hydrogen electrode). All previous attempts to design a rubredoxin site have focused on incorporating the canonical CXXC motifs in addition to reproducing the peptide fold or using flexible loop regions to define the morphology of the site. We have produced a rubredoxin site in an utterly different fold, a three-helix bundle. The spectra of this construct mimic the ultraviolet{\textendash}visible, M{\"o}ssbauer, electron paramagnetic resonance, and magnetic circular dichroism spectra of native rubredoxin. Furthermore, the measured reduction potential suggests that this rubredoxin analogue could function similarly. Thus, we have shown that an α-helical scaffold sustains a rubredoxin site that can cycle with the desired potential between the Fe(II) and Fe(III) states and reproduces the spectroscopic characteristics of this electron transport protein without requiring the classic rubredoxin protein fold.

}, doi = {10.1021/acs.biochem.8b00091}, url = {https://pubs-acs-org.accesdistant.sorbonne-universite.fr/doi/pdf/10.1021/acs.biochem.8b00091}, author = {Tebo, Alison G and Pinter, Tyler B J and Garc{\'\i}a-Serres, Ricardo and Speelman, Amy L and Tard, C{\'e}dric and S{\'e}n{\`e}que, Olivier and Blondin, Genevi{\`e}ve and Latour, Jean-Marc and Penner-Hahn, James and Lehnert, Nicolai and Pecoraro, Vincent L} } @article {49546, title = {Developmental pattern and structural factors of dendritic survival in cerebellar granule cells in vivo.}, journal = {Scientific Reports}, volume = {8}, year = {2018}, month = {2018 Dec 03}, pages = {17561}, abstract = {

Granule cells (GCs) in the cerebellar cortex are important for sparse encoding of afferent sensorimotor information. Modeling studies show that GCs can perform their function most effectively when they have four dendrites. Indeed, mature GCs have four short dendrites on average, each terminating in a claw-like ending that receives both excitatory and inhibitory inputs. Immature GCs, however, have significantly more dendrites-all without claws. How these redundant dendrites are refined during development is largely unclear. Here, we used in vivo time-lapse imaging and immunohistochemistry to study developmental refinement of GC dendritic arbors and its relation to synapse formation. We found that while the formation of dendritic claws stabilized the dendrites, the selection of surviving dendrites was made before claw formation, and longer immature dendrites had a significantly higher chance of survival than shorter dendrites. Using immunohistochemistry, we show that glutamatergic and GABAergic synapses are transiently formed on immature GC dendrites, and the number of GABAergic, but not glutamatergic, synapses correlates with the length of immature dendrites. Together, these results suggest a potential role of transient GABAergic synapses on dendritic selection and show that preselected dendrites are stabilized by the formation of dendritic claws-the site of mature synapses.

}, issn = {2045-2322}, doi = {10.1038/s41598-018-35829-y}, author = {Dhar, Matasha and Hantman, Adam W and Nishiyama, Hiroshi} } @article {49255, title = {Discrete flow posteriors for variational inference in discrete dynamical systems.}, journal = {arXiv}, year = {2018}, month = {2018 May 28}, pages = {1805.10958}, abstract = {

Each training step for a variational autoencoder (VAE) requires us to sample from the approximate posterior, so we usually choose simple (e.g. factorised) approximate posteriors in which sampling is an efficient computation that fully exploits GPU parallelism. However, such simple approximate posteriors are often insufficient, as they eliminate statistical dependencies in the posterior. While it is possible to use normalizing flow approximate posteriors for continuous latents, some problems have discrete latents and strong statistical dependencies. The most natural approach to model these dependencies is an autoregressive distribution, but sampling from such distributions is inherently sequential and thus slow. We develop a fast, parallel sampling procedure for autoregressive distributions based on fixed-point iterations which enables efficient and accurate variational inference in discrete state-space latent variable dynamical systems. To optimize the variational bound, we considered two ways to evaluate probabilities: inserting the relaxed samples directly into the pmf for the discrete distribution, or converting to continuous logistic latent variables and interpreting the K-step fixed-point iterations as a normalizing flow. We found that converting to continuous latent variables gave considerable additional scope for mismatch between the true and approximate posteriors, which resulted in biased inferences, we thus used the former approach. Using our fast sampling procedure, we were able to realize the benefits of correlated posteriors, including accurate uncertainty estimates for one cell, and accurate connectivity estimates for multiple cells, in an order of magnitude less time.

}, url = {https://arxiv.org/abs/1805.10958}, author = {Aitchison, Laurence and Adam, Vincent and Turaga, Srinivas C} } @article {49174, title = {Dissociable structural and functional hippocampal outputs via distinct subiculum cell classes.}, journal = {Cell}, volume = {173}, year = {2018}, month = {2018 Apr 10}, pages = {1280-92}, abstract = {

The mammalian hippocampus, comprised of serially connected subfields, participates in diverse behavioral and cognitive functions. It has been postulated that parallel circuitry embedded within hippocampal subfields may underlie such functional diversity. We sought to identify, delineate, and manipulate this putatively parallel architecture in the dorsal subiculum, the primary output subfield of the dorsal hippocampus. Population and single-cell RNA-seq revealed that the subiculum can be divided into two spatially adjacent subregions associated with prominent differences in pyramidal cell gene expression. Pyramidal cells occupying these two regions differed in their long-range inputs, local wiring, projection targets, and electrophysiological properties. Leveraging gene-expression differences across these regions, we use genetically restricted neuronal silencing to show that\ these regions differentially contribute to spatial working memory. This work provides a coherent molecular-, cellular-, circuit-, and behavioral-level demonstration that the hippocampus embeds structurally and functionally dissociable streams within its serial architecture.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2018.03.031}, author = {Cembrowski, Mark S and Phillips, Matthew G and DiLisio, Salvatore F and Shields, Brenda C and Winnubst, Johan and Chandrashekar, Jayaram and Bas, Erhan and Spruston, Nelson} } @article {49294, title = {Distinct cell types in the superficial superior colliculus project to the dorsal lateral geniculate and lateral posterior thalamic nuclei.}, journal = {Journal of Neurophysiology}, volume = {120}, year = {2018}, month = {2018 Jun 13}, pages = {1286-92}, abstract = {

The superficial layers of the superior colliculus (sSC) receive retinal input and project to thalamic regions - the dorsal lateral geniculate (dLGN) and lateral posterior (LP; or pulvinar) nuclei -that convey visual information to cortex. A critical step towards understanding the functional impact of sSC neurons on these parallel thalamo-cortical pathways is determining whether different classes of sSC neurons, which are known to respond to different features of visual stimuli, innervate overlapping or distinct thalamic targets. Here, we identified a transgenic mouse line that labels sSC neurons that project to dLGN but not LP. We utilized selective expression of fluorophores and channelrhodopsin in this and previously characterized mouse lines to demonstrate that distinct cell types give rise to sSC projections to dLGN and LP. We further show that the glutamatergic sSC cell type that projects to dLGN also provides input to the sSC cell type that projects to LP. These results clarify the cellular origin of parallel sSC-thalamo-cortical pathways and reveal an interaction between these pathways via local connections within the sSC.

}, issn = {1522-1598}, doi = {10.1152/jn.00248.2018}, author = {Gale, Samuel D and Murphy, Gabe J} } @article {49496, title = {Distinct descending motor cortex pathways and their roles in movement.}, journal = {Nature}, volume = {563}, year = {2018}, month = {2018 Nov}, pages = {79-84}, abstract = {

Activity in the motor cortex predicts movements, seconds before they are initiated. This preparatory activity has been observed across cortical layers, including in descending pyramidal tract neurons in layer 5. A key question is how preparatory activity is maintained without causing movement, and is ultimately converted to a motor command to trigger appropriate movements. Here, using single-cell transcriptional profiling and axonal reconstructions, we identify two types of pyramidal tract neuron. Both types project to several targets in the basal ganglia and brainstem. One type projects to thalamic regions that connect back to motor cortex; populations of these neurons produced early preparatory activity that persisted until the movement was initiated. The second type projects to motor centres in the medulla and mainly\ produced late preparatory activity and motor commands. These results indicate that two types of motor cortex output neurons have specialized roles in motor control.

}, issn = {1476-4687}, doi = {10.1038/s41586-018-0642-9}, author = {Economo, Michael N and Viswanathan, Sarada and Tasic, Bosiljka and Bas, Erhan and Winnubst, Johan and Menon, Vilas and Graybuck, Lucas T and Nguyen, Thuc Nghi and Smith, Kimberly A and Yao, Zizhen and Wang, Lihua and Gerfen, Charles R and Chandrashekar, Jayaram and Zeng, Hongkui and Looger, Loren L and Svoboda, Karel} } @article {49119, title = {Dynamic cues for whisker-based object localization: An analytical solution to vibration during active whisker touch.}, journal = {PLoS Computational Biology}, volume = {14}, year = {2018}, month = {2018 Mar 27}, pages = {e1006032}, abstract = {

Vibrations are important cues for tactile perception across species. Whisker-based sensation in mice is a powerful model system for investigating mechanisms of tactile perception. However, the role vibration plays in whisker-based sensation remains unsettled, in part due to difficulties in modeling the vibration of whiskers. Here, we develop an analytical approach to calculate the vibrations of whiskers striking objects. We use this approach to quantify vibration forces during active whisker touch at a range of locations along the whisker. The frequency and amplitude of vibrations evoked by contact are strongly dependent on the position of contact along the whisker. The magnitude of vibrational shear force and bending moment is comparable to quasi-static forces. The fundamental vibration frequencies are in a detectable range for mechanoreceptor properties and below the maximum spike rates of primary sensory afferents. These results suggest two dynamic cues exist that rodents can use for object localization: vibration frequency and comparison of vibrational to quasi-static force magnitude. These complement the use of quasi-static force angle as a distance cue, particularly for touches close to the follicle, where whiskers are stiff and force angles hardly change during touch. Our approach also provides a general solution to calculation of whisker vibrations in other sensing tasks.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1006032}, author = {Vaxenburg, Roman and Wyche, Isis and Svoboda, Karel and Efros, Alexander L and Hires, Samuel Andrew} } @article {49195, title = {Ejaculation induced by the activation of Crz neurons is rewarding to Drosophila males.}, journal = {Current Biology : CB}, volume = {28}, year = {2018}, month = {2018 May 07}, pages = {1445-1452.e3}, abstract = {

The reward system is a collection of circuits that reinforce behaviors necessary for survival [1, 2]. Given the importance of reproduction for survival, actions that promote successful mating induce pleasurable feeling and are positively reinforced [3, 4]. This principle is conserved in Drosophila, where successful copulation is naturally rewarding to male flies, induces long-term appetitive memories [5], increases brain levels of neuropeptide F (NPF, the fly homolog of neuropeptide Y), and prevents ethanol, known otherwise as rewarding to flies [6, 7], from being rewarding [5]. It is not clear which of the multiple sensory and motor responses performed during mating induces perception of reward. Sexual interactions with female flies that do not reach copulation are not sufficient to reduce ethanol consumption [5], suggesting that only successful mating encounters are rewarding. Here, we uncoupled the initial steps of mating from its final steps and tested the ability of ejaculation to mimic the rewarding value of full copulation. We induced ejaculation by activating neurons that express the neuropeptide corazonin (CRZ) [8] and subsequently measured different aspects of reward. We show that activating Crz-expressing neurons is rewarding to male flies, as they choose to reside in a zone that triggers optogenetic stimulation of Crz neurons and display conditioned preference for an odor paired with the activation. Reminiscent of successful mating, repeated activation of Crz neurons increases npf levels and reduces ethanol consumption. Our results demonstrate that ejaculation stimulated by Crz/Crz-receptor signaling serves as an essential part of the mating reward mechanism in Drosophila. VIDEO ABSTRACT.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2018.03.039}, author = {Zer-Krispil, Shir and Zak, Hila and Shao, Lisha and Ben-Shaanan, Shir and Tordjman, Lea and Bentzur, Assa and Shmueli, Anat and Shohat-Ophir, Galit} } @article {49175, title = {Elucidating neuronal mechanisms using intracellular recordings during behavior.}, journal = {Trends in Neurosciences}, volume = {41}, year = {2018}, month = {2018 Apr 20}, pages = {385-403}, abstract = {

Intracellular recording allows measurement and perturbation of the membrane potential of identified neurons with sub-millisecond and sub-millivolt precision. This gives intracellular recordings a unique capacity to provide rich information about individual cells (e.g., high-resolution characterization of inputs, outputs, excitability, and structure). Hence, such recordings can elucidate the mechanisms that underlie fundamental phenomena, such as brain state, sparse coding, gating, gain modulation, and learning. Technical developments have increased the range of behaviors during which intracellular recording methods can be employed, such as in freely moving animals and head-fixed animals actively performing tasks, including in virtual environments. Such advances, and the combination of intracellular recordings with genetic and imaging techniques, have enabled investigation of the mechanisms that underlie neural computations during natural and trained behaviors.

}, issn = {1878-108X}, doi = {10.1016/j.tins.2018.03.014}, author = {Lee, Albert K and Brecht, Michael} } @article {49342, title = {The ESCRT-III protein CHMP1A mediates secretion of sonic hedgehog on a distinctive subtype of extracellular vesicles.}, journal = {Cell Reports}, volume = {24}, year = {2018}, month = {2018 Jul 24}, pages = {973-986.e8}, abstract = {

Endosomal sorting complex required for transport (ESCRT) complex proteins regulate biogenesis and release of extracellular vesicles (EVs), which enable cell-to-cell communication in the nervous system essential for development and adult function. We recently showed human loss-of-function (LOF) mutations in ESCRT-III member CHMP1A cause autosomal recessive microcephaly with pontocerebellar hypoplasia, but its mechanism was unclear. Here, we show Chmp1a is required for progenitor proliferation in mouse cortex and cerebellum and progenitor maintenance in human cerebral organoids. In Chmp1a null mice, this defect is associated with impaired sonic hedgehog (Shh) secretion and intraluminal vesicle (ILV) formation in multivesicular bodies (MVBs). Furthermore, we show CHMP1A is important for release of an EV subtype that contains AXL, RAB18, and TMED10 (ART) and SHH. Our findings show CHMP1A loss impairs secretion of SHH on ART-EVs, providing molecular mechanistic insights into the role of ESCRT proteins and EVs in the brain.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2018.06.100}, author = {Coulter, Michael E and Dorobantu, Cristina M and Lodewijk, Gerrald A and Delalande, Fran{\c c}ois and Cianferani, Sarah and Ganesh, Vijay S and Smith, Richard S and Lim, Elaine T and Xu, C Shan and Pang, Song and Wong, Eric T and Lidov, Hart G W and Calicchio, Monica L and Yang, Edward and Gonzalez, Dilenny M and Schlaeger, Thorsten M and Mochida, Ganeshwaran H and Hess, Harald and Lee, Wei-Chung Allen and Lehtinen, Maria K and Kirchhausen, Tomas and Haussler, David and Jacobs, Frank M J and Gaudin, Rapha{\"e}l and Walsh, Christopher A} } @article {49150, title = {Evaluating the potential of using quantum dots for monitoring electrical signals in neurons.}, journal = {Nature Nanotechnology}, volume = {13}, year = {2018}, month = {2018 Apr}, pages = {278-288}, abstract = {

Success in the projects aimed at providing an advanced understanding of the brain is directly predicated on making critical advances in nanotechnology. This Perspective addresses the unique interface of neuroscience and nanomaterials by considering the foundational problem of sensing neuron membrane voltage and offers a potential solution that may be facilitated by a prototypical nanomaterial. Despite substantial improvements, the visualization of instantaneous voltage changes within individual neurons, whether in cell culture or in vivo, at both the single-cell and network level at high speed remains complex and problematic. The unique properties of semiconductor quantum dots (QDs) have made them powerful fluorophores for bioimaging. What is not widely appreciated, however, is that QD photoluminescence is exquisitely sensitive to proximal electric fields. This property should be suitable for sensing voltage changes that occur in the active neuronal membrane. Here, we examine the potential role of QDs in addressing the important challenge of real-time optical voltage imaging.

}, issn = {1748-3395}, doi = {10.1038/s41565-018-0107-1}, author = {Efros, Alexander L and Delehanty, James B and Huston, Alan L and Medintz, Igor L and Barbic, Mladen and Harris, Timothy D} } @article {49318, title = {Evolution of a central neural circuit underlies Drosophila mate preferences.}, journal = {Nature}, volume = {559}, year = {2018}, month = {2018 Jul 11}, pages = {564-9}, abstract = {

Courtship rituals serve to reinforce reproductive barriers between closely related species. Drosophila melanogaster and Drosophila simulans exhibit reproductive isolation, owing in part to the fact that D. melanogaster females produce 7,11-heptacosadiene, a pheromone that promotes courtship in D. melanogaster males but suppresses courtship in D. simulans males. Here we compare pheromone-processing pathways in D. melanogaster and D. simulans males to define how these sister species endow 7,11-heptacosadiene with the opposite behavioural valence to underlie species discrimination. We show that males of both species detect 7,11-heptacosadiene using homologous peripheral sensory neurons, but this signal is differentially propagated to P1 neurons, which control courtship behaviour. A change in the balance of excitation and inhibition onto courtship-promoting neurons transforms an excitatory pheromonal cue in D. melanogaster into an inhibitory cue in D. simulans. Our results reveal how species-specific pheromone responses can emerge from conservation of peripheral detection mechanisms and diversification of central circuitry, and demonstrate how flexible nodes in neural circuits can contribute to behavioural evolution.

}, issn = {1476-4687}, doi = {10.1038/s41586-018-0322-9}, author = {Seeholzer, Laura F and Seppo, Max and Stern, David L and Ruta, Vanessa} } @article {49474, title = {Expanding the optogenetics toolkit by topological inversion of rhodopsins.}, journal = {Cell}, volume = {175}, year = {2018}, month = {2018 Oct 16}, pages = {1131-40}, abstract = {

Targeted manipulation of activity in specific populations of neurons is important for investigating the neural circuit basis of behavior. Optogenetic approaches using light-sensitive microbial rhodopsins have permitted manipulations to reach a level of temporal precision that is enabling functional circuit dissection. As demand for more precise perturbations to serve specific experimental goals increases, a palette of opsins with diverse selectivity, kinetics, and spectral properties will be needed. Here, we introduce a novel approach of "topological engineering"-inversion of opsins in the plasma membrane-and demonstrate that it can produce variants with unique functional properties of interest for circuit neuroscience. In one striking example, inversion of a Channelrhodopsin variant converted it from a potent activator into a fast-acting inhibitor that operates as a cation pump. Our findings argue that membrane topology provides a useful orthogonal dimension of protein engineering that immediately permits as much as a doubling of the available toolkit.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2018.09.026}, author = {Brown, Jennifer and Behnam, Reza and Coddington, Luke and Tervo, D G R and Martin, Kathleen and Proskurin, Mikhail and Kuleshova, Elena and Park, Junchol and Phillips, James and Bergs, Amelie C F and Gottschalk, Alexander and Dudman, Joshua T and Karpova, Alla Y} } @article {49346, title = {Expansion microscopy: protocols for imaging proteins and RNA in cells and tissues.}, journal = {Current Protocols in Cell Biology}, volume = {80}, year = {2018}, month = {2018 Aug 02}, pages = {e56}, abstract = {

Expansion microscopy (ExM) is a recently developed technique that enables nanoscale-resolution imaging of preserved cells and tissues on conventional diffraction-limited microscopes via isotropic physical expansion of the specimens before imaging. In ExM, biomolecules and/or fluorescent labels in the specimen are linked to a dense, expandable polymer matrix synthesized evenly throughout the specimen, which undergoes 3-dimensional expansion by \~{}4.5 fold linearly when immersed in water. Since our first report, versions of ExM optimized for visualization of proteins, RNA, and other biomolecules have emerged. Here we describe best-practice, step-by-step ExM protocols for performing analysis of proteins (protein retention ExM, or proExM) as well as RNAs (expansion fluorescence in situ hybridization, or ExFISH), using chemicals and hardware found in a typical biology lab. Furthermore, a detailed protocol for handling and mounting expanded samples and for imaging them with confocal and light-sheet microscopes is provided. {\textcopyright} 2018 by John Wiley \& Sons, Inc.

}, issn = {1934-2616}, doi = {10.1002/cpcb.56}, author = {Asano, Shoh M and Gao, Ruixuan and Wassie, Asmamaw T and Tillberg, Paul W and Chen, Fei and Boyden, Edward S} } @article {49234, title = {Extant fold-switching proteins are widespread.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, year = {2018}, month = {2018 May 21}, pages = {5968-73}, abstract = {

A central tenet of biology is that globular proteins have a unique 3D structure under physiological conditions. Recent work has challenged this notion by demonstrating that some proteins switch folds, a process that involves remodeling of secondary structure in response to a few mutations (evolved fold switchers) or cellular stimuli (extant fold switchers). To date, extant fold switchers have been viewed as rare byproducts of evolution, but their frequency has been neither quantified nor estimated. By systematically and exhaustively searching the Protein Data Bank (PDB), we found \~{}100 extant fold-switching proteins. Furthermore, we gathered multiple lines of evidence suggesting that these proteins are widespread in nature. Based on these lines of evidence, we hypothesized that the frequency of extant fold-switching proteins may be underrepresented by the structures in the PDB. Thus, we sought to identify other putative extant fold switchers with only one solved conformation. To do this, we identified two characteristic features of our \~{}100 extant fold-switching proteins, incorrect secondary structure predictions and likely independent folding cooperativity, and searched the PDB for other proteins with similar features. Reassuringly, this method identified dozens of other proteins in the literature with indication of a structural change but only one solved conformation in the PDB. Thus, we used it to estimate that 0.5-4\% of PDB proteins switch folds. These results demonstrate that extant fold-switching proteins are likely more common than the PDB reflects, which has implications for cell biology, genomics, and human health.

}, issn = {1091-6490}, doi = {10.1073/pnas.1800168115}, author = {Porter, Lauren L and Looger, Loren L} } @article {49129, title = {Fabricating optical-quality glass surfaces to study macrophage fusion.}, journal = {Journal of Visualized Experiments : JoVE}, year = {2018}, month = {2018 Mar 14}, abstract = {

Visualizing the formation of multinucleated giant cells (MGCs) from living specimens has been challenging due to the fact that most live imaging techniques require propagation of light through glass, but on glass macrophage fusion is a rare event. This protocol presents the fabrication of several optical-quality glass surfaces where adsorption of compounds containing long-chain hydrocarbons transforms glass into a fusogenic surface. First, preparation of clean glass surfaces as starting material for surface modification is described. Second, a method is provided for the adsorption of compounds containing long-chain hydrocarbons to convert non-fusogenic glass into a fusogenic substrate. Third, this protocol describes fabrication of surface micropatterns that promote a high degree of spatiotemporal control over MGC formation. Finally, fabricating glass bottom dishes is described. Examples of use of this in vitro cell system as a model to study macrophage fusion and MGC formation are shown.

}, issn = {1940-087X}, doi = {10.3791/56866}, author = {Faust, James J and Christenson, Wayne and Doudrick, Kyle and Heddleston, John and Chew, Teng-Leong and Lampe, Marko and Balabiyev, Arnat and Ros, Robert and Ugarova, Tatiana P} } @article {65770, title = {Fluorogenic Protein-Based Strategies for Detection, Actuation, and Sensing}, journal = {BioEssays}, volume = {40}, year = {2018}, month = {08/2018}, pages = {1800118}, abstract = {

Fluorescence imaging has become an indispensable tool in cell and molecular biology. GFP-like fluorescent proteins have revolutionized fluorescence microscopy, giving experimenters exquisite control over the localization and specificity of tagged constructs. However, these systems present certain drawbacks and as such, alternative systems based on a fluorogenic interaction between a chromophore and a protein have been developed. While these systems are initially designed as fluorescent labels, they also present new opportunities for the development of novel labeling and detection strategies. This review focuses on new labeling protocols, actuation methods, and biosensors based on fluorogenic protein systems. This review presents recently developed fluorogenic protein-based systems made of a protein tag incorporating an external chromophore. Beyond addressing some limitations of classical fluorescent proteins, these unique systems present characteristics than can be used to creatively push the limits of biological imaging, in particular for the development of new labeling protocols, actuation methods and biosensors.

}, issn = {0265-9247}, doi = {10.1002/bies.201800118}, url = {https://onlinelibrary-wiley-com.accesdistant.sorbonne-universite.fr/doi/pdf/10.1002/bies.201800118}, author = {Gautier, Arnaud and Tebo, Alison G.} } @article {49324, title = {Fluorogenic structure activity library pinpoints molecular variations in substrate specificity of structurally homologous esterases.}, journal = {The Journal of Biological Chemistry}, volume = {293}, year = {2018}, month = {2018 Jul 13}, pages = {13851-62}, abstract = {

Cellular esterases catalyze many essential biological functions by performing hydrolysis reactions on diverse substrates. The promiscuity of esterases complicates assignment of their substrate preferences and biological functions. To identify universal factors controlling esterase substrate recognition, we designed a 32-member structure-activity relationship (SAR) library of fluorogenic ester substrates and used this library to systematically interrogate esterase preference for chain length, branching patterns, and polarity to differentiate common classes of esterase substrates. Two structurally homologous bacterial esterases were screened against this library, refining their previously broad overlapping substrate specificity. esterase ybfF displayed a preference for γ-position thioethers and ethers, whereas Rv0045c from displayed a preference for branched substrates with and without thioethers. We determined that this substrate differentiation was partially controlled by individual substrate selectivity residues Tyr119 in ybfF and His187 in Rv0045c; reciprocal substitution of these residues shifted each esterase{\textquoteright}s substrate preference. This work demonstrates that the selectivity of esterases is tuned based on transition state stabilization, identifies thioethers as an underutilized functional group for esterase substrates, and provides a rapid method for differentiating structural isozymes. This SAR library could have multi-faceted future applications including in vivo imaging, biocatalyst screening, molecular fingerprinting, and inhibitor design.

}, issn = {1083-351X}, doi = {10.1074/jbc.RA118.003972}, author = {White, Alex and Koelper, Andrew and Russell, Arielle and Larsen, Erik M and Kim, Charles and Lavis, Luke D and Hoops, Geoffrey C and Johnson, R Jeremy} } @article {49032, title = {From electron crystallography of 2D crystals to MicroED of 3D crystals.}, journal = {Current Opinion in Colloid \& Interface Science }, volume = {34}, year = {2018}, month = {2018 Mar}, pages = {9-16}, abstract = {

Electron crystallography is widespread in material science applications, but for biological samples its use has been restricted to a handful of examples where two-dimensional (2D) crystals or helical samples were studied either by electron diffraction and/or imaging. Electron crystallography in cryoEM, was developed in the mid-1970s and used to solve the structure of several membrane proteins and some soluble proteins. In 2013, a new method for cryoEM was unveiled and named Micro-crystal Electron Diffraction, or MicroED, which is essentially three-dimensional (3D) electron crystallography of microscopic crystals. This method uses truly 3D crystals, that are about a billion times smaller than those typically used for X-ray crystallography, for electron diffraction studies. There are several important differences and some similarities between electron crystallography of 2D crystals and MicroED. In this review, we describe the development of these techniques, their similarities and differences, and offer our opinion of future directions in both fields.

}, doi = {10.1016/j.cocis.2018.01.010}, author = {Martynowycz, Michael W and Gonen, Tamir} } @article {49093, title = {Functional architecture of reward learning in mushroom body extrinsic neurons of larval Drosophila.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Mar 16}, pages = {1104}, abstract = {

The brain adaptively integrates present sensory input, past experience, and options for future action. The insect mushroom body exemplifies how a central brain structure brings about such integration. Here we use a combination of systematic single-cell labeling, connectomics, transgenic silencing, and activation experiments to study the mushroom body at single-cell resolution, focusing on the behavioral architecture of its input and output neurons (MBINs and MBONs), and of the mushroom body intrinsic APL neuron. Our results reveal the identity and morphology of almost all of these 44 neurons in stage 3 Drosophila larvae. Upon an initial screen, functional analyses focusing on the mushroom body medial lobe uncover sparse and specific functions of its dopaminergic MBINs, its MBONs, and of the GABAergic APL neuron across three behavioral tasks, namely odor preference, taste preference, and associative learning between odor and taste. Our results thus provide a cellular-resolution study case of how brains organize behavior.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-03130-1}, author = {Saumweber, Timo and Rohwedder, Astrid and Schleyer, Michael and Eichler, Katharina and Chen, Yi-chun and Aso, Yoshinori and Cardona, Albert and Eschbach, Claire and Kobler, Oliver and Voigt, Anne and Durairaja, Archana and Mancini, Nino and Zlatic, Marta and Truman, James W and Thum, Andreas S and Gerber, Bertram} } @article {49142, title = {Functional Imaging and Optogenetics in Drosophila.}, journal = {Genetics}, volume = {208}, year = {2018}, month = {2018 Apr}, pages = {1291-1309}, abstract = {

Understanding how activity patterns in specific neural circuits coordinate an animal{\textquoteright}s behavior remains a key area of neuroscience research. Genetic tools and a brain of tractable complexity make a premier model organism for these studies. Here, we review the wealth of reagents available to map and manipulate neuronal activity with light.

}, issn = {1943-2631}, doi = {10.1534/genetics.117.300228}, author = {Simpson, Julie H and Looger, Loren L} } @article {49509, title = {A GAL80 collection to inhibit GAL4 transgenes in olfactory sensory neurons.}, journal = {G3 (Bethesda, Md.)}, volume = {8}, year = {2018}, month = {2018 Nov 06}, pages = {3661-3668}, abstract = {

Fruit flies recognize hundreds of ecologically relevant odors and respond appropriately to them. The complexity, redundancy and interconnectedness of the olfactory machinery complicate efforts to pinpoint the functional contributions of any component neuron or receptor to behavior. Some contributions can only be elucidated in flies that carry multiple mutations and transgenes, but the production of such flies is currently labor-intensive and time-consuming. Here, we describe a set of transgenic flies that express the GAL80 in specific olfactory sensory neurons (). The GAL80s effectively and specifically subtract the activities of GAL4-driven transgenes that impart anatomical and physiological phenotypes. can allow researchers to efficiently activate only one or a few types of functional neurons in an otherwise nonfunctional olfactory background. Such experiments will improve our understanding of the mechanistic connections between odorant inputs and behavioral outputs at the resolution of only a few functional neurons.

}, issn = {2160-1836}, doi = {10.1534/g3.118.200569}, author = {Eliason, Jessica and Afify, Ali and Potter, Christopher and Matsumura, Lchiro} } @article {49573, title = {Gene flow mediates the role of sex chromosome meiotic drive during complex speciation.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Dec 13}, abstract = {

During speciation, sex chromosomes often accumulate interspecific genetic incompatibilities faster than the rest of the genome. The drive theory posits that sex chromosomes are susceptible to recurrent bouts of meiotic drive and suppression, causing the evolutionary build-up of divergent cryptic sex-linked drive systems and, incidentally, genetic incompatibilities. To assess the role of drive during speciation, we combine high-resolution genetic mapping of X-linked hybrid male sterility with population genomics analyses of divergence and recent gene flow between the fruitfly species, and . Our findings reveal a high density of genetic incompatibilities and a corresponding dearth of gene flow on the X chromosome. Surprisingly, we find that a known drive element recently migrated between species and, rather than contributing to interspecific divergence, caused a strong reduction in local sequence divergence, undermining the evolution of hybrid sterility. Gene flow can therefore mediate the effects of selfish genetic elements during speciation.

}, issn = {2050-084X}, doi = {10.7554/eLife.35468}, author = {Meiklejohn, Colin D and Landeen, Emily L and Gordon, Kathleen E and Rzatkiewicz, Thomas and Kingan, Sarah B and Geneva, Anthony J and Vedanayagam, Jeffrey P and Muirhead, Christina A and Garrigan, Daniel and Stern, David L and Presgraves, Daven C} } @article {49154, title = {Genetic dissection of neural circuits: a decade of progress}, journal = {Neuron}, volume = {98}, year = {2018}, month = {2018 Apr 18}, pages = {256-81}, abstract = {

Tremendous progress has been made since\ Neuron\ published our Primer on genetic dissection of neural circuits 10 years ago. Since then, cell-type-specific anatomical, neurophysiological, and perturbation studies have been carried out in a multitude of invertebrate and vertebrate organisms, linking neurons and circuits to behavioral functions. New methods allow systematic classification of cell types and provide genetic access to diverse neuronal types for studies of connectivity and neural coding during behavior. Here we evaluate key advances over the past decade and discuss future directions.

}, doi = {10.1016/j.neuron.2018.03.040}, author = {Luo, Liqun and Callaway, Edward M and Svoboda, Karel} } @article {49010, title = {A genetically encoded Ca2+ indicator based on circularly permutated sea anemone red fluorescent protein eqFP578.}, journal = {BMC Biology}, volume = {16}, year = {2018}, month = {2018 Jan 16}, pages = {9}, abstract = {

BACKGROUND: Genetically encoded calcium ion (Ca2+) indicators (GECIs) are indispensable tools for measuring Ca2+ dynamics and neuronal activities in vitro and in vivo. Red fluorescent protein (RFP)-based GECIs have inherent advantages relative to green fluorescent protein-based GECIs due to the longer wavelength light used for excitation. Longer wavelength light is associated with decreased phototoxicity and deeper penetration through tissue. Red GECI can also enable multicolor visualization with blue- or cyan-excitable fluorophores.

RESULTS: Here we report the development, structure, and validation of a new RFP-based GECI, K-GECO1, based on a circularly permutated RFP derived from the sea anemone Entacmaea quadricolor. We have characterized the performance of K-GECO1 in cultured HeLa cells, dissociated neurons, stem-cell-derived cardiomyocytes, organotypic brain slices, zebrafish spinal cord in vivo, and mouse brain in vivo.

CONCLUSION: K-GECO1 is the archetype of a new lineage of GECIs based on the RFP eqFP578 scaffold. It offers high sensitivity and fast kinetics, similar or better than those of current state-of-the-art indicators, with diminished lysosomal accumulation and minimal blue-light photoactivation. Further refinements of the K-GECO1 lineage could lead to further improved variants with overall performance that exceeds that of the most highly optimized red GECIs.

}, issn = {1741-7007}, doi = {10.1186/s12915-018-0480-0}, author = {Shen, Yi and Dana, Hod and Abdelfattah, Ahmed S and Patel, Ronak and Shea, Jamien and Molina, Rosana S and Rawal, Bijal and Rancic, Vladimir and Chang, Yu-Fen and Wu, Lanshi and Chen, Yingche and Qian, Yong and Wiens, Matthew D and Hambleton, Nathan and Ballanyi, Klaus and Hughes, Thomas E and Drobizhev, Mikhail and Kim, Douglas S and Koyama, Minoru and Schreiter, Eric R and Campbell, Robert E} } @article {49813, title = {High-performance GFP-based calcium indicators for imaging activity in neuronal populations and microcompartments.}, journal = {bioRxiv}, year = {2018}, month = {2018 Oct 3}, abstract = {

Calcium imaging with genetically encoded calcium indicators (GECIs) is routinely used to measure neural activity in intact nervous systems. GECIs are frequently used in one of two different modes: to track activity in large populations of neuronal cell bodies, or to follow dynamics in subcellular compartments such as axons, dendrites and individual synaptic compartments. Despite major advances, calcium imaging is still limited by the biophysical properties of existing GECIs, including affinity, signal-to-noise ratio, rise and decay kinetics, and dynamic range. Using structure-guided mutagenesis and neuron-based screening, we optimized the green fluorescent protein-based GECI GCaMP6 for different modes of in vivo imaging. The jGCaMP7 sensors provide improved detection of individual spikes (jGCaMP7s,f), imaging in neurites and neuropil (jGCaMP7b), and tracking large populations of neurons using 2-photon (jGCaMP7s,f) or wide-field (jGCaMP7c) imaging.

}, doi = {10.1101/434589}, author = {Dana, Hod and Sun, Yi and Mohar, Boaz and Hulse, Brad and Hasseman, Jeremy P and Tsegaye, Getahun and Tsang, Arthur and Wong, Allan and Patel, Ronak and Macklin, John J and Chen, Yang and Konnerth, Arthur and Jayaraman, Vivek and Looger, Loren L and Schreiter, Eric R and Svoboda, Karel and Kim, Douglas S} } @article {51794, title = {High-resolution transcriptional dissection of in vivo Atoh1-mediated hair cell conversion in mature cochleae identifies Isl1 as a co-reprogramming factor.}, journal = {PLoS Genetics}, volume = {14}, year = {2018}, month = {2018 07}, pages = {e1007552}, abstract = {

In vivo direct conversion of differentiated cells holds promise for regenerative medicine; however, improving the conversion efficiency and producing functional target cells remain challenging. Ectopic Atoh1 expression in non-sensory supporting cells (SCs) in mouse cochleae induces their partial conversion to hair cells (HCs) at low efficiency. Here, we performed single-cell RNA sequencing of whole mouse sensory epithelia harvested at multiple time points after conditional overexpression of Atoh1. Pseudotemporal ordering revealed that converted HCs (cHCs) are present along a conversion continuum that correlates with both endogenous and exogenous Atoh1 expression. Bulk sequencing of isolated cell populations and single-cell qPCR confirmed 51 transcription factors, including Isl1, are differentially expressed among cHCs, SCs and HCs. In transgenic mice, co-overexpression of Atoh1 and Isl1 enhanced the HC conversion efficiency. Together, our study shows how high-resolution transcriptional profiling of direct cell conversion can identify co-reprogramming factors required for efficient conversion.

}, keywords = {Animals, Animals, Newborn, Basic Helix-Loop-Helix Transcription Factors, Cellular Reprogramming, Gene Expression Profiling, Hair Cells, Auditory, LIM-Homeodomain Proteins, Mice, Mice, Inbred C57BL, Mice, Transgenic, Regeneration, Sequence Analysis, RNA, Single-Cell Analysis, Transcription Factors}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1007552}, author = {Yamashita, Tetsuji and Zheng, Fei and Finkelstein, David and Kellard, Zoe and Carter, Robert and Rosencrance, Celeste D and Sugino, Ken and Easton, John and Gawad, Charles and Zuo, Jian} } @conference {49317, title = {Honeybee detection and pose estimation using convolutional neural networks.}, booktitle = {RFIAP 2018}, year = {2018}, month = {2018 Jun 26}, abstract = {

The ability to automatize the analysis of video for monitoring animals and insects is of great interest for behavior science and ecology [1]. In particular, honeybees play a crucial role in agriculture as natural pollinators. However, recent studies has shown that phenomena such as colony collapse disorder are causing the loss of many colonies [2]. Due to the high number of interacting factors to explain these events, a multi-faceted analysis of the bees in their environment is required. We focus in our work in developing tools to help model and understand their behavior as individuals, in relation with the health and performance of the colony.

In this paper, we report the development of a new system for the detection, locali- zation and tracking of honeybee body parts from video on the entrance ramp of the colony. The proposed system builds on the recent advances in Convolutional Neu- ral Networks (CNN) for Human pose estimation and evaluates the suitability for the detection of honeybee pose as shown in Figure 1. This opens the door for novel animal behavior analysis systems that take advantage of the precise detection and tracking of the insect pose.\ 

}, url = {https://rfiap2018.ign.fr/sites/default/files/ARTICLES/RFIAP_2018/RFIAP_2018_Felipe_Honeybee.pdf}, author = {Rodriguez, Ivan F and Branson, Kristin M and Acuna, Edgar and Agosto-Rivera, Jose and Giray, Tugrul and Megret, Remi} } @article {49222, title = {Identification of a transporter complex responsible for the cytosolic entry of nitrogen-containing-bisphosphonates.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 May 10}, abstract = {

Nitrogen-containing-bisphosphonates (N-BPs) are a class of drugs widely prescribed to treat osteoporosis and other bone-related diseases. Although previous studies have established that N-BPs function by inhibiting the mevalonate pathway in osteoclasts, the mechanism by which N-BPs enter the cytosol from the extracellular space to reach their molecular target is not understood. Here we implemented a CRISPRi-mediated genome-wide screen and identified (solute carrier family 37 member A3) as a gene required for the action of N-BPs in mammalian cells. We observed that SLC37A3 forms a complex with ATRAID (all-trans retinoic acid-induced differentiation factor), a previously identified genetic target of N-BPs. SLC37A3 and ATRAID localize to lysosomes and are required for releasing N-BP molecules that have trafficked to lysosomes through fluid-phase endocytosis into the cytosol. Our results elucidate the route by which N-BPs are delivered to their molecular target, addressing a key aspect of the mechanism of action of N-BPs that may have significant clinical relevance.

}, issn = {2050-084X}, doi = {10.7554/eLife.36620}, author = {Yu, Zhou and Surface, Lauren E and Park, Chong Yon and Horlbeck, Max A and Wyant, Gregory A and Abu-Remaileh, Monther and Peterson, Timothy R and Sabatini, David M and Weissman, Jonathan S and O{\textquoteright}Shea, Erin K} } @article {49043, title = {Image co-localization - co-occurrence versus correlation.}, journal = {Journal of Cell Science}, volume = {131}, year = {2018}, month = {2018 Feb 08}, abstract = {

Fluorescence image co-localization analysis is widely utilized to suggest biomolecular interaction. However, there exists some confusion as to its correct implementation and interpretation. In reality, co-localization analysis consists of at least two distinct sets of methods, termed co-occurrence and correlation. Each approach has inherent and often contrasting strengths and weaknesses. Yet, neither one can be considered to always be preferable for any given application. Rather, each method is most appropriate for answering different types of biological question. This Review discusses the main factors affecting multicolor image co-occurrence and correlation analysis, while giving insight into the types of biological behavior that are better suited to one approach or the other. Further, the limits of pixel-based co-localization analysis are discussed in the context of increasingly popular super-resolution imaging techniques.

}, issn = {1477-9137}, doi = {10.1242/jcs.211847}, author = {Aaron, Jesse S and Taylor, Aaron B and Chew, Teng-Leong} } @article {49545, title = {Imaging cortical dynamics in GCaMP transgenic rats with a head-mounted widefield macroscope.}, journal = {Neuron}, year = {2018}, month = {2018 Oct 22}, abstract = {

Widefield imaging of calcium dynamics is an emerging method for mapping regional neural activity but is currently limited to restrained animals. Here we describe cScope, a head-mounted widefield macroscope\ developed to image large-scale cortical dynamics in rats during natural behavior. cScope provides a 7.8\ {\texttimes} 4\ mm field of view and dual illumination paths for both fluorescence and hemodynamic correction and can be fabricated at low cost using readily attainable components. We also report the development of Thy-1 transgenic rat strains with widespread neuronal expression of the calcium indicator GCaMP6f. We combined these two technologies to image large-scale calcium dynamics in the dorsal neocortex during a visual evidence accumulation\ task. Quantitative analysis of task-related dynamics revealed multiple regions having neural signals that encode behavioral choice and sensory evidence. Our results provide a new transgenic resource for calcium imaging in rats and extend the domain of head-mounted microscopes to larger-scale cortical dynamics.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2018.09.050}, author = {Scott, Benjamin B and Thiberge, Stephan Y and Guo, Caiying and Tervo, D Gowanlock R and Brody, Carlos D and Karpova, Alla Y and Tank, David W} } @article {49293, title = {Imaging dynamic and selective low-complexity domain interactions that control gene transcription.}, journal = {Science (New York, N.Y.)}, volume = {361}, year = {2018}, month = {2018 Jun 21}, pages = {eaar2555}, abstract = {

Many eukaryotic transcription factors (TFs) contain intrinsically disordered low-complexity domains (LCDs), but how they drive transactivation remains unclear. Here, live-cell single-molecule imaging reveals that TF-LCDs form local high-concentration interaction hubs at synthetic and endogenous genomic loci. TF-LCD hubs stabilize DNA binding, recruit RNA polymerase II (Pol II), and activate transcription. LCD-LCD interactions within hubs are highly dynamic, display selectivity with binding partners, and are differentially sensitive to disruption by hexanediols. Under physiological conditions, rapid and reversible LCD-LCD interactions occur between TFs and the Pol II machinery without detectable phase separation. Our findings reveal fundamental mechanisms underpinning transcriptional control and suggest a framework for developing single-molecule imaging screens for novel drugs targeting gene regulatory interactions implicated in disease.

}, issn = {1095-9203}, doi = {10.1126/science.aar2555}, author = {Chong, Shasha and Dugast-Darzacq, Claire and Liu, Zhe and Dong, Peng and Dailey, Gina M and Cattoglio, Claudia and Heckert, Alec and Banala, Sambashiva and Lavis, Luke and Darzacq, Xavier and Tjian, Robert} } @article {49245, title = {Imaging mRNA in vivo, from birth to death.}, journal = {Annual Review of Biophysics}, volume = {47}, year = {2018}, month = {2018 May 20}, pages = {85-106}, abstract = {

RNA is the fundamental information transfer system in the cell. The ability to follow single messenger RNAs (mRNAs) from transcription to degradation with fluorescent probes gives quantitative information about how the information is transferred from DNA to proteins. This review focuses on the latest technological developments in the field of single-mRNA detection and their usage to study gene expression in both fixed and live cells. By describing the application of these imaging tools, we follow the journey of mRNA from transcription to decay in single cells, with single-molecule resolution. We review current theoretical models for describing transcription and translation that were generated by single-molecule and single-cell studies. These methods provide a basis to study how single-molecule interactions generate phenotypes, fundamentally changing our understating of gene expression regulation.

}, issn = {1936-1238}, doi = {10.1146/annurev-biophys-070317-033037}, author = {Tutucci, Evelina and Livingston, Nathan M and Singer, Robert H and Wu, Bin} } @article {65769, title = {Improved Chemical-Genetic Fluorescent Markers for Live Cell Microscopy}, journal = {Biochemistry}, volume = {57}, year = {2018}, month = {11/2018}, pages = {5648 {\textendash} 5653}, abstract = {

Inducible chemical-genetic fluorescent markers are promising tools for live cell imaging requiring high spatiotemporal resolution and low background fluorescence. The fluorescence-activating and absorption shifting tag (FAST) was recently developed to form fluorescent molecular complexes with a family of small, synthetic fluorogenic chromophores (so-called fluorogens). Here, we use rational design to modify the binding pocket of the protein and screen for improved fluorescence performances with four different fluorogens. The introduction of a single mutation results in improvements in both quantum yield and dissociation constant with nearly all fluorogens tested. Our improved FAST (iFAST) allowed the generation of a tandem iFAST (td-iFAST) that forms green and red fluorescent reporters 1.6-fold and 2-fold brighter than EGFP and mCherry, respectively, while having a comparable size.

}, doi = {10.1021/acs.biochem.8b00649}, url = {https://pubs-acs-org.accesdistant.sorbonne-universite.fr/doi/pdf/10.1021/acs.biochem.8b00649}, author = {Tebo, Alison G and Pimenta, Frederico M and Zhang, Yu and Gautier, Arnaud} } @article {49494, title = {Improved methods for marking active neuron populations.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Oct 25}, pages = {4440}, abstract = {

Marking functionally distinct neuronal ensembles with high spatiotemporal resolution is a key challenge in systems neuroscience. We recently introduced CaMPARI, an engineered fluorescent protein whose green-to-red photoconversion depends on simultaneous light exposure and elevated calcium, which enabled marking active neuronal populations with single-cell and subsecond resolution. However, CaMPARI (CaMPARI1) has several drawbacks, including background photoconversion in low calcium, slow kinetics and reduced fluorescence after chemical fixation. In this work, we develop CaMPARI2, an improved sensor with brighter green and red fluorescence, faster calcium unbinding kinetics and decreased photoconversion in low calcium conditions. We demonstrate the improved performance of CaMPARI2 in mammalian neurons and in vivo in larval zebrafish brain and mouse visual cortex. Additionally, we herein develop an immunohistochemical detection method for specific labeling of the photoconverted red form of CaMPARI. The anti-CaMPARI-red antibody provides strong labeling that is selective for photoconverted CaMPARI in activated neurons in rodent brain tissue.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-06935-2}, author = {Moeyaert, Benjamien and Holt, Graham and Madangopal, Rajtarun and Perez-Alvarez, Alberto and Fearey, Brenna C and Trojanowski, Nicholas F and Ledderose, Julia and Zolnik, Timothy A and Das, Aniruddha and Patel, Davina and Brown, Timothy A and Sachdev, Robert N S and Eickholt, Britta J and Larkum, Matthew E and Turrigiano, Gina G and Dana, Hod and Gee, Christine E and Oertner, Thomas G and Hope, Bruce T and Schreiter, Eric R} } @article {49466, title = {In toto imaging and reconstruction of post-implantation mouse development at the single-cell level.}, journal = {Cell}, volume = {175}, year = {2018}, month = {2018 Oct 10}, pages = {859-876}, abstract = {

The mouse embryo has long been central to the study of mammalian development; however, elucidating the cell behaviors governing gastrulation and the formation of tissues and organs remains a fundamental challenge. A major obstacle is the lack of live imaging and image analysis technologies capable of systematically following cellular dynamics across the developing embryo. We developed a light-sheet microscope that adapts itself to the dramatic changes in size, shape, and optical properties of the post-implantation\ mouse embryo and captures its development from gastrulation to early organogenesis at\ the cellular level. We furthermore developed a computational framework for reconstructing long-term cell tracks, cell divisions, dynamic fate maps, and maps of tissue morphogenesis across the entire embryo. By jointly analyzing cellular dynamics in multiple embryos registered in space and time, we built a dynamic atlas of post-implantation mouse development that, together with our microscopy and computational methods, is provided as a resource.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2018.09.031}, author = {McDole, Katie and Guignard, Leo and Amat, Fernando and Berger, Andrew and Malandain, Gr{\'e}goire and Royer, Lo{\"\i}c A and Turaga, Srinivas C and Branson, Kristin and Keller, Philipp J} } @article {49367, title = {In vivo measurement of afferent activity with axon-specific calcium imaging.}, journal = {Nature Neuroscience}, year = {2018}, month = {2018 Aug 20}, abstract = {

In vivo calcium imaging from axons provides direct interrogation of afferent neural activity, informing the neural representations that a local circuit receives. Unlike in somata and dendrites, axonal recording of neural activity-both electrically and optically-has been difficult to achieve, thus preventing comprehensive understanding of neuronal circuit function. Here we developed an active transportation strategy to enrich GCaMP6, a genetically encoded calcium indicator, uniformly in axons with sufficient brightness, signal-to-noise ratio, and photostability to allow robust, structure-specific imaging of presynaptic activity in awake mice. Axon-targeted GCaMP6 enables frame-to-frame correlation for motion correction in axons and permits subcellular-resolution recording of axonal activity in previously inaccessible deep-brain areas. We used axon-targeted GCaMP6 to record layer-specific local afferents without contamination from somata or from intermingled dendrites in the cortex. We expect that axon-targeted GCaMP6 will facilitate new applications in investigating afferent signals relayed by genetically defined neuronal populations within and across specific brain regions.

}, issn = {1546-1726}, doi = {10.1038/s41593-018-0211-4}, author = {Broussard, Gerard Joey and Liang, Yajie and Fridman, Marina and Unger, Elizabeth K and Meng, Guanghan and Xiao, Xian and Ji, Na and Petreanu, Leopoldo and Tian, Lin} } @article {49369, title = {Inhibitory control of prefrontal cortex by the claustrum.}, journal = {Neuron}, volume = {99}, year = {2018}, month = {2018 Aug 07}, pages = {1029-39}, abstract = {

The claustrum is a small subcortical nucleus that has extensive excitatory connections with many cortical areas. While the anatomical connectivity from the claustrum to the cortex has been studied intensively, the physiological effect and underlying circuit mechanisms of claustrocortical communication remain elusive. Here we show that the claustrum provides strong, widespread, and long-lasting feedforward inhibition of the prefrontal cortex (PFC) sufficient to silence ongoing neural activity. This claustrocortical feedforward inhibition was predominantly mediated by interneurons containing neuropeptide Y, and to a lesser extent those containing parvalbumin. Therefore, in contrast to other long-range excitatory inputs to the PFC, the claustrocortical pathway is designed to provide overall inhibition of cortical activity. This unique circuit organization allows the claustrum to rapidly and powerfully suppress cortical networks and suggests a distinct role for the claustrum in regulating cognitive processes in prefrontal circuits.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2018.07.031}, author = {Jackson, Jesse and Karnani, Mahesh M and Zemelman, Boris V and Burdakov, Denis and Lee, Albert K} } @conference {49333, title = {Insights from Biology: low power circuits in the fruit fly.}, booktitle = {International Symposium on Low Power Electronics and Design}, year = {2018}, month = {2018 Jul 23-25}, publisher = {ACM}, organization = {ACM}, address = {Seattle, WA}, abstract = {

Fruit flies (Drosophila melanogaster) are small insects, with correspondingly small power budgets. Despite this, they perform sophisticated neural computations in real time. Careful study of these insects is revealing how some of these circuits work. Insights from these systems might be helpful in designing other low power circuits.

}, url = {https://dl.acm.org/citation.cfm?id=3241337}, author = {Scheffer, Louis K} } @article {49435, title = {Integration of parallel opposing memories underlies memory extinction.}, journal = {Cell}, volume = {175}, year = {2018}, month = {2018 Sep 06}, pages = {709-22}, abstract = {

Accurately predicting an outcome requires that animals learn supporting and conflicting evidence from sequential experience. In mammals and invertebrates, learned fear responses can be suppressed by experiencing predictive cues without punishment,\ a process called memory extinction. Here, we show that extinction of aversive memories in Drosophila requires specific dopaminergic neurons, which indicate that omission of punishment is remembered as a positive experience. Functional imaging revealed co-existence of intracellular calcium traces in different places in the mushroom body output neuron network for both the original aversive memory and a new appetitive extinction memory. Light and ultrastructural anatomy are consistent with parallel competing memories being combined within mushroom body output neurons that direct avoidance. Indeed, extinction-evoked plasticity in a pair of these neurons neutralizes the potentiated odor response imposed in the network by aversive learning. Therefore, flies track the accuracy of learned expectations by accumulating and integrating memories of conflicting events.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2018.08.021}, author = {Felsenberg, Johannes and Jacob, Pedro F and Walker, Thomas and Barnstedt, Oliver and Edmondson-Stait, Amelia J and Pleijzier, Markus W and Otto, Nils and Schlegel, Philipp and Sharifi, Nadiya and Perisse, Emmanuel and Smith, Carlas S and Lauritzen, J Scott and Costa, Marta and Jefferis, Gregory S X E and Bock, Davi D and Waddell, Scott} } @article {49094, title = {Integrative structure and functional anatomy of a nuclear pore complex.}, journal = {Nature}, volume = {555}, year = {2018}, month = {2018 Mar 14}, pages = {475-82}, abstract = {

Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

}, issn = {1476-4687}, doi = {10.1038/nature26003}, author = {Kim, Seung Joong and Fernandez-Martinez, Javier and Nudelman, Ilona and Shi, Yi and Zhang, Wenzhu and Raveh, Barak and Herricks, Thurston and Slaughter, Brian D and Hogan, Joanna A and Upla, Paula and Chemmama, Ilan E and Pellarin, Riccardo and Echeverria, Ignacia and Shivaraju, Manjunatha and Chaudhury, Azraa S and Wang, Junjie and Williams, Rosemary and Unruh, Jay R and Greenberg, Charles H and Jacobs, Erica Y and Yu, Zhiheng and de la Cruz, M Jason and Mironska, Roxana and Stokes, David L and Aitchison, John D and Jarrold, Martin F and Gerton, Jennifer L and Ludtke, Steven J and Akey, Christopher W and Chait, Brian T and Sali, Andrej and Rout, Michael P} } @article {49059, title = {Integrative whole-brain neuroscience in larval zebrafish.}, journal = {Current Opinion in Neurobiology}, volume = {50}, year = {2018}, month = {2018 Feb 24}, pages = {136-145}, abstract = {

Due to their small size and transparency, zebrafish larvae are amenable to a range of fluorescence microscopy techniques. With the development of sensitive genetically encoded calcium indicators, this has extended to the whole-brain imaging of neural activity with cellular resolution. This technique has been used to study brain-wide population dynamics accompanying sensory processing and sensorimotor transformations, and has spurred the development of innovative closed-loop behavioral paradigms in which stimulus-response relationships can be studied. More recently, microscopes have been developed that allow whole-brain calcium imaging in freely swimming and behaving larvae. In this review, we highlight the technologies underlying whole-brain functional imaging in zebrafish, provide examples of the sensory and motor processes that have been studied with this technique, and discuss the need to merge data from whole-brain functional imaging studies with neurochemical and anatomical information to develop holistic models of functional neural circuits.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2018.02.004}, author = {Vanwalleghem, Gilles C and Ahrens, Misha B and Scott, Ethan K} } @article {49451, title = {Integrin-mediated attachment of the blastoderm to the vitelline envelope impacts gastrulation of insects.}, journal = {bioRxiv}, year = {2018}, month = {2018 Oct 2}, abstract = {

During gastrulation, physical forces reshape the simple embryonic tissue to form a complex body plan of multicellular organisms. These forces often cause large-scale asymmetric movements of the embryonic tissue. In many embryos, the tissue undergoing gastrulation movements is surrounded by a rigid protective shell. While it is well recognized that gastrulation movements depend on forces generated by tissue-intrinsic contractility, it is not known if interactions between the tissue and the protective shell provide additional forces that impact gastrulation. Here we show that a particular part of the blastoderm tissue of the red flour beetle Tribolium castaneum tightly adheres in a temporally coordinated manner to the vitelline envelope surrounding the embryo. This attachment generates an additional force that counteracts the tissue-intrinsic contractile forces to create asymmetric tissue movements. Furthermore, this localized attachment is mediated by a specific integrin, and its knock-down leads to a gastrulation phenotype consistent with complete loss of attachment. Moreover, analysis of another integrin in the fruit fly Drosophila melanogaster suggests that gastrulation in this organism also relies on adhesion between the blastoderm and the vitelline. Together, our findings reveal a conserved mechanism whereby the spatiotemporal pattern of tissue adhesion to the vitelline envelope provides controllable counter-forces that shape gastrulation movements in insects.

}, doi = {10.1101/421701}, author = {Muenster, Stefan and Jain, Akanksha and Mietke, Alexander and Pavlopoulos, Anastasios and Grill, Stephan W and Tomancak, Pavel} } @article {49314, title = {Interacting organelles.}, journal = {Current Opinion in Cell Biology}, volume = {53}, year = {2018}, month = {2018 Aug}, pages = {84-91}, abstract = {

Eukaryotic cells are organized into membrane-bound organelles. These organelles communicate with one another through vesicular trafficking pathways and membrane contact sites (MCSs). MCSs are sites of close apposition between two or more organelles that play diverse roles in the exchange of metabolites, lipids and proteins. Organelle interactions at MCSs also are important for organelle division and biogenesis. For example, the division of several organelles, including mitochondria and endosomes, seem to be regulated by contacts with the endoplasmic reticulum (ER). Moreover, the biogenesis of autophagosomes and peroxisomes involves contributions from the ER and multiple other cellular compartments. Thus, organelle-organelle interactions allow cells to alter the shape and activities of their membrane-bound compartments, allowing them to cope with different developmental and environmental conditions.

}, doi = {10.1016/j.ceb.2018.06.003}, author = {Cohen, Sarah and Valm, Alex M and Lippincott-Schwartz, Jennifer} } @article {65091, title = {Interleukin 2 modulates thymic-derived regulatory T cell epigenetic landscape.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Dec 18}, pages = {5368}, abstract = {

Foxp3CD4 regulatory T (T) cells are essential for preventing fatal autoimmunity and safeguard immune homeostasis in vivo. While expression of the transcription factor Foxp3 and IL-2 signals are both required for the development and function of T cells, the commitment to the T cell lineage occurs during thymic selection upon T cell receptor (TCR) triggering, and precedes the expression of Foxp3. Whether signals beside TCR contribute to establish T cell epigenetic and functional identity is still unknown. Here, using a mouse model with reduced IL-2 signaling, we show that IL-2 regulates the positioning of the pioneer factor SATB1 in CD4 thymocytes and controls genome wide chromatin accessibility of thymic-derived T cells. We also show that T cells receiving only low IL-2 signals can suppress endogenous but not WT autoreactive T cell responses in vitro and in vivo. Our findings have broad implications for potential therapeutic strategies to reprogram T cells in vivo.

}, keywords = {Animals, Autoimmunity, Cell Differentiation, Cellular Reprogramming, Disease Models, Animal, Epigenesis, Genetic, Female, Forkhead Transcription Factors, HEK293 Cells, Humans, Interleukin-2, Interleukin-2 Receptor alpha Subunit, Listeriosis, Male, Matrix Attachment Region Binding Proteins, Mice, Mice, Inbred C57BL, Mice, Transgenic, Signal Transduction, T-Lymphocytes, Regulatory, Thymocytes, Thymus Gland}, issn = {2041-1723}, doi = {10.1038/s41467-018-07806-6}, author = {Chorro, Laurent and Suzuki, Masako and Chin, Shu Shien and Williams, Tere M and Snapp, Erik L and Odagiu, Livia and Labrecque, Nathalie and Lauvau, Gr{\'e}goire} } @article {49343, title = {Inverse-response Ca2+ indicators for optogenetic visualization of neuronal inhibition.}, journal = {Scientific Reports}, volume = {8}, year = {2018}, month = {2018 Aug 06}, pages = {11758}, abstract = {

We have developed a series of yellow genetically encoded Ca indicators for optical imaging (Y-GECOs) with inverted responses to Ca and apparent dissociation constants (K{\textquoteright}) ranging from 25 to 2400 nM. To demonstrate the utility of this affinity series of Ca indicators, we expressed the four highest affinity variants (K{\textquoteright}s = 25, 63, 121, and 190 nM) in the Drosophila medulla intrinsic neuron Mi1. Hyperpolarization of Mi1 by optogenetic stimulation of the laminar monopolar neuron L1 produced a decrease in intracellular Ca in layers 8-10, and a corresponding increase in Y-GECO fluorescence. These experiments revealed that lower K{\textquoteright} was associated with greater increases in fluorescence, but longer delays to reach the maximum signal change due to slower off-rate kinetics.

}, issn = {2045-2322}, doi = {10.1038/s41598-018-30080-x}, author = {Zhao, Yufeng and Bushey, Daniel and Zhao, Yongxin and Schreiter, Eric R and Harrison, D Jed and Wong, Allan M and Campbell, Robert E} } @article {49177, title = {Joint deformable registration of large EM image volumes: a matrix solver approach.}, journal = {arXiv}, year = {2018}, month = {2018 Apr 26}, abstract = {

Large electron microscopy image datasets for connectomics are typically composed of thousands to millions of partially overlapping two-dimensional images (tiles), which must be registered into a coherent volume prior to further analysis. A common registration strategy is to find matching features between neighboring and overlapping image pairs, followed by a numerical estimation of optimal image deformation using a so-called solver program.\ 
Existing solvers are inadequate for large data volumes, and inefficient for small-scale image registration.\ 
In this work, an efficient and accurate matrix-based solver method is presented. A linear system is constructed that combines minimization of feature-pair square distances with explicit constraints in a regularization term. In absence of reliable priors for regularization, we show how to construct a rigid-model approximation to use as prior. The linear system is solved using available computer programs, whose performance on typical registration tasks we briefly compare, and to which future scale-up is delegated. Our method is applied to the joint alignment of 2.67 million images, with more than 200 million point-pairs and has been used for successfully aligning the first full adult fruit fly brain.

}, url = {https://arxiv.org/abs/1804.10019}, author = {Khairy, Khaled and Denisov, Gennady and Saalfeld, Stephan} } @article {49143, title = {Juvenile hormone reveals mosaic developmental programs in the metamorphosing optic lobe of Drosophila melanogaster.}, journal = {Biology Open}, year = {2018}, month = {2018 Apr 04}, abstract = {

The development of the adult optic lobe (OL) of is directed by a wave of ingrowth of the photoreceptors over a two day period at the outset of metamorphosis which is accompanied by the appearance of the pupal-specific transcription factor Broad-Z3 (Br-Z3) and expression of early drivers in OL neurons. During this time, there are pulses of ecdysteroids that time the metamorphic events. At the outset, the transient appearance of juvenile hormone (JH) prevents precocious development of the OL caused by the ecdysteroid peak that initiates pupariation, but the artificial maintenance of JH after this time misdirects subsequent development. Axon ingrowth, Br-Z3 appearance and the expression of early drivers were unaffected, but aspects of later development such as the dendritic expansion of the lamina monopolar neurons and the expression of late drivers were suppressed. This effect of the exogenous JH mimic (JHM) pyriproxifen is lost by 24 hr after pupariation. Part of this effect of JHM is due to its suppression of the appearance of ecdysone receptor EcR-B1 that occurs after pupation and during early adult development.

}, issn = {2046-6390}, doi = {10.1242/bio.034025}, author = {Riddiford, Lynn M and Truman, James W and Nern, Aljoscha} } @article {64996, title = {Knock-in rats expressing Cre and Flp recombinases at the Parvalbumin locus.}, journal = {bioRxiv}, year = {2018}, month = {2018 Aug 07}, abstract = {

Rats have the ability to learn and perform sophisticated behavioral tasks, making them very useful for investigating neural circuit functions. In contrast to the extensive mouse genetic toolkit, the paucity of recombinase-expressing rat models has limited the ability to monitor and manipulate molecularly-defined neural populations in this species. Here we report the generation and validation of two knock-in rat strains expressing either\ Cre\ or\ Flp\ recombinase under the control of\ Parvalbumin (Pvalb), a gene expressed in the critical {\textquotedblleft}fast-spiking{\textquotedblright} subset of inhibitory interneurons (FSIs). These strains were generated with CRISPR-Cas9 gene editing and show highly specific and penetrant labeling of\ Pvalb-expressing neurons, as demonstrated by\ in situ\ hybridization and immunohistochemistry. We validated these models in both prefrontal cortex and striatum using both\ ex vivo\ and\ in vivo\ approaches, including whole-cell recording, optogenetics, extracellular physiology and photometry. Our results demonstrate the utility of these new transgenic models for a wide range of neuroscience experiments.

}, doi = {10.1101/386474}, author = {Jai Y. Yu and Jeffrey R. Pettibone and Caiying Guo and Shuqin Zhang and Thomas L. Saunders and Elizabeth D. Hughes and Wanda E. Filipiak and Michael G. Zeidler and Kevin J. Bender and Frederic Hopf and Clay N. Smyth and Viktor Kharazia and Anna Kiseleva and Thomas J. Davidson and Loren M. Frank and Joshua D. Berke} } @article {64995, title = {Lamellar junctions in the endolymphatic sac act as a relief valve to regulate inner ear pressure.}, journal = {eLife}, year = {2018}, month = {2018 Jun 19}, doi = {10.7554/eLife.37131}, author = {Ian A. Swinburne and Kishore R. Mosaliganti and Srigokul Upadhyayula and Tsung-Li Liu and David G. C. Hildebrand and Tony Y.-C. Tsai and Anzhi Chen and Ebaa Al-Obeidi and Anna K. Fass and Samir Malhotra and Florian Engert and Jeff W. Lichtman and Tom Kirchhausen and Sean G. Megason and Eric Betzig} } @article {49275, title = {Lamellar projections in the endolymphatic sac act as a relief valve to regulate inner ear pressure.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Jun 19}, abstract = {

The inner ear is a fluid-filled closed-epithelial structure whose function requires maintenance of an internal hydrostatic pressure and fluid composition. The endolymphatic sac (ES) is a dead-end epithelial tube connected to the inner ear whose function is unclear. ES defects can cause distended ear tissue, a pathology often seen in hearing and balance disorders. Using live imaging of zebrafish larvae, we reveal that the ES undergoes cycles of slow pressure-driven inflation followed by rapid deflation. Absence of these cycles in mutants leads to distended ear tissue. Using serial-section electron microscopy and adaptive optics lattice light-sheet microscopy, we find a pressure relief valve in the ES comprised of partially separated apical junctions and dynamic overlapping basal lamellae that separate under pressure to release fluid. We propose that this lmx1-dependent pressure relief valve is required to maintain fluid homeostasis in the inner ear and other fluid-filled cavities.

}, issn = {2050-084X}, doi = {10.7554/eLife.37131}, author = {Swinburne, Ian A and Mosaliganti, Kishore R and Upadhyayula, Srigokul and Liu, Tsung-Li and Hildebrand, David G C and Tsai, Tony Y-C and Chen, Anzhi and Al-Obeidi, Ebaa and Fass, Anna K and Malhotra, Samir and Engert, Florian and Lichtman, Jeff W and Kirchausen, Tomas and Betzig, Eric and Megason, Sean G} } @article {48937, title = {larvalign: Aligning gene expression patterns from the larval brain of Drosophila melanogaster.}, journal = {Neuroinformatics}, volume = {16}, year = {2018}, month = {2018 Jan 1}, pages = {65-80}, abstract = {

The larval brain of the fruit fly Drosophila melanogaster is a small, tractable model system for neuroscience. Genes for fluorescent marker proteins can be expressed in defined, spatially restricted neuron populations. Here, we introduce the methods for 1) generating a standard template of the larval central nervous system (CNS), 2) spatial mapping of expression patterns from different larvae into a reference space defined by the standard template. We provide a manually annotated gold standard that serves for evaluation of the registration framework involved in template generation and mapping. A method for registration quality assessment enables the automatic detection of registration errors, and a semi-automatic registration method allows one to correct registrations, which is a prerequisite for a high-quality, curated database of expression patterns. All computational methods are available within the larvalign software package: https://github.com/larvalign/larvalign/releases/tag/v1.0.

}, issn = {1559-0089}, doi = {10.1007/s12021-017-9349-6}, author = {Muenzing, Sascha E A and Strauch, Martin and Truman, James W and B{\"u}hler, Katja and Thum, Andreas S and Merhof, Dorit} } @article {49232, title = {Lineage-guided Notch-dependent gliogenesis by multi-potent progenitors.}, journal = {Development (Cambridge, England)}, year = {2018}, month = {2018 May 15}, abstract = {

Macroglial cells in the central nervous system exhibit regional specialization and carry out region-specific functions. Diverse glial cells arise from specific progenitors in specific spatiotemporal patterns. This raises an interesting possibility that there exist glial precursors with distinct developmental fates, which govern region-specific gliogenesis. Here we mapped the glial progeny produced by the type II neuroblasts, which, like vertebrate radial glia cells, yield both neurons and glia via intermediate neural progenitors (INPs). Distinct type II neuroblasts produce different characteristic sets of glia. A single INP can make both astrocyte-like and ensheathing glia, which co-occupy a relatively restrictive subdomain. Blocking apoptosis uncovers further lineage distinctions in the specification, proliferation, and survival of glial precursors. Both the switch from neurogenesis to gliogenesis and the subsequent glial expansion depend on Notch signaling. Taken together, lineage origins preconfigure the development of individual glial precursors with involvement of serial Notch actions in promoting gliogenesis.

}, issn = {1477-9129}, doi = {10.1242/dev.160127}, author = {Ren, Qingzhong and Awasaki, Takeshi and Wang, Yu-Chun and Huang, Yu-Fen and Lee, Tzumin} } @article {68435, title = {Linking neuronal lineage and wiring specificity.}, journal = {Neural Dev}, volume = {13}, year = {2018}, month = {04/2018}, pages = {5}, abstract = {

Brain function requires precise neural circuit assembly during development. Establishing a functional circuit involves multiple coordinated steps ranging from neural cell fate specification to proper matching between pre- and post-synaptic partners. How neuronal lineage and birth timing influence wiring specificity remains an open question. Recent findings suggest that the relationships between lineage, birth timing, and wiring specificity vary in different neuronal circuits. In this review, we summarize our current understanding of the cellular, molecular, and developmental mechanisms linking neuronal lineage and birth timing to wiring specificity in a few specific systems in Drosophila and mice, and review different methods employed to explore these mechanisms.

}, keywords = {Animals, Brain, Cell Lineage, Neural Pathways, Neurons}, issn = {1749-8104}, doi = {10.1186/s13064-018-0102-0}, author = {Li, Hongjie and Shuster, S Andrew and Li, Jiefu and Luo, Liqun} } @article {49473, title = {Long-Term Consolidation of Ensemble Neural Plasticity Patterns in Hippocampal Area CA1.}, journal = {Cell reports}, volume = {25}, year = {2018}, month = {2018 Oct 16}, pages = {640-650.e2}, abstract = {

Neural network remodeling underpins the ability to remember life experiences, but little is known about the long-term plasticity of neural populations. To study how the brain encodes episodic events, we used time-lapse two-photon microscopy and a fluorescent reporter of neural plasticity based on an enhanced form of the synaptic activity-responsive element (E-SARE) within the Arc promoter to track thousands of CA1 hippocampal pyramidal cells over weeks in mice that repeatedly encountered different environments. Each environment evokes characteristic patterns of ensemble neural plasticity, but with each encounter, the set of activated cells gradually evolves. After repeated exposures, the plasticity patterns evoked by an individual environment progressively stabilize. Compared with young adults, plasticity patterns in aged mice are less specific to individual environments and less stable across repeat experiences. Long-term consolidation of hippocampal plasticity patterns may support long-term memory formation, whereas weaker consolidation in aged subjects might reflect declining memory function.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2018.09.064}, author = {Attardo, Alessio and Lu, Ju and Kawashima, Takashi and Okuno, Hiroyuki and Fitzgerald, James E and Bito, Haruhiko and Schnitzer, Mark J} } @article {49124, title = {Low-dimensional and monotonic preparatory activity in mouse anterior lateral motor cortex.}, journal = {The Journal of Neuroscience : the official journal of the Society for Neuroscience}, volume = {38}, year = {2018}, month = {2018 Apr 25}, pages = {4163-85}, abstract = {

Neurons in multiple brain regions fire trains of action potentials anticipating specific movements, but this {\textquoteright}preparatory activity{\textquoteright} has not been systematically compared across behavioral tasks. We compared preparatory activity in auditory and tactile delayed-response tasks in male mice. Skilled, directional licking was the motor output. The anterior lateral motor cortex (ALM) is necessary for motor planning in both tasks. Multiple features of ALM preparatory activity during the delay epoch were similar across tasks. First, majority of neurons showed direction-selective activity and spatially intermingled neurons were selective for either movement direction. Second, many cells showed mixed coding of sensory stimulus and licking direction, with a bias toward licking direction. Third, delay activity was monotonic and low-dimensional. Fourth, pairs of neurons with similar direction selectivity showed high spike-count correlations. Our study forms the foundation to analyze the neural circuit mechanisms underlying preparatory activity in a genetically tractable model organism.Short-term memories link events separated in time. Neurons in frontal cortex fire trains of action potentials anticipating specific movements, often seconds before the movement. This {\textquoteright}preparatory activity{\textquoteright} has been observed in multiple brain regions, but has rarely been compared systematically across behavioral tasks in the same brain region. To identify common features of preparatory activity, we developed and compared preparatory activity in auditory and tactile delayed-response tasks in mice. The same cortical area is necessary for both tasks. Multiple features of preparatory activity, measured with high-density silicon probes, were similar across tasks. We find that preparatory activity is low-dimensional and monotonic. Our study forms the foundation to analyze the circuit mechanisms underlying preparatory activity in a genetically tractable model organism.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3152-17.2018}, author = {Inagaki, Hidehiko K and Inagaki, Miho and Romani, Sandro and Svoboda, Karel} } @article {49382, title = {Macropinosome formation by tent pole ruffling in macrophages.}, journal = {The Journal of Cell Biology}, volume = {217}, year = {2018}, month = {2018 Aug 27}, pages = {3873-85}, abstract = {

Pathogen-mediated activation of macrophages arms innate immune responses that include enhanced surface ruffling and macropinocytosis for environmental sampling and receptor internalization and signaling. Activation of macrophages with bacterial lipopolysaccharide (LPS) generates prominent dorsal ruffles, which are precursors for macropinosomes. Very rapid, high-resolution imaging of live macrophages with lattice light sheet microscopy (LLSM) reveals new features and actions of dorsal ruffles, which redefine the process of macropinosome formation and closure. We offer a new model in which ruffles are erected and supported by F-actin tent poles that cross over and twist to constrict the forming macropinosomes. This process allows for formation of large macropinosomes induced by LPS. We further describe the enrichment of active Rab13 on tent pole ruffles and show that CRISPR deletion of Rab13 results in aberrant tent pole ruffles and blocks the formation of large LPS-induced macropinosomes. Based on the exquisite temporal and spatial resolution of LLSM, we can redefine the ruffling and macropinosome processes that underpin innate immune responses.

}, issn = {1540-8140}, doi = {10.1083/jcb.201804137}, author = {Condon, Nicholas D and Heddleston, John M and Chew, Teng-Leong and Luo, Lin and McPherson, Peter S and Ioannou, Maria S and Hodgson, Louis and Stow, Jennifer L and Wall, Adam A} } @article {65768, title = {Macroscale fluorescence imaging against autofluorescence under ambient light}, journal = {Light: Science \& Applications}, year = {2018}, month = {11/2018}, pages = {1 {\textendash} 12}, abstract = {

Macroscale fluorescence imaging is increasingly used to observe biological samples. However, it may suffer from spectral interferences that originate from ambient light or autofluorescence of the sample or its support. In this manuscript, we built a simple and inexpensive fluorescence macroscope, which has been used to evaluate the performance of Speed OPIOM (Out of Phase Imaging after Optical Modulation), which is a reference-free dynamic contrast protocol, to selectively image reversibly photoswitchable fluorophores as labels against detrimental autofluorescence and ambient light. By tuning the intensity and radial frequency of the modulated illumination to the Speed OPIOM resonance and adopting a phase-sensitive detection scheme that ensures noise rejection, we enhanced the sensitivity and the signal-to-noise ratio for fluorescence detection in blot assays by factors of 50 and 10, respectively, over direct fluorescence observation under constant illumination. Then, we overcame the strong autofluorescence of growth media that are currently used in microbiology and realized multiplexed fluorescence observation of colonies of spectrally similar fluorescent bacteria with a unique configuration of excitation and emission wavelengths. Finally, we easily discriminated fluorescent labels from the autofluorescent and reflective background in labeled leaves, even under the interference of incident light at intensities that are comparable to sunlight. The proposed approach is expected to find multiple applications, from biological assays to outdoor observations, in fluorescence macroimaging.

}, doi = {10.1038/s41377-018-0098-6}, author = {Zhang, Ruikang and Chouket, Raja and Plamont, Marie-Aude and Kelemen, Zsolt and Espagne, Agathe and Tebo, Alison G and Gautier, Arnaud and Gissot, Lionel and Faure, Jean-Denis and Jullien, Ludovic and Croquette, Vincent and Saux, Thomas Le} } @article {49526, title = {Magnetocaloric materials as switchable high contrast ratio MRI labels.}, journal = {Magnetic Resonance in Medicine}, volume = {81}, year = {2018}, month = {2018 Nov 25}, pages = {2238-46}, abstract = {

PURPOSE: To develop switchable and tunable labels with high contrast ratio for MRI using magnetocaloric materials that have sharp first-order magnetic phase transitions at physiological temperatures and typical MRI magnetic field strengths.

METHODS: A prototypical magnetocaloric material iron-rhodium (FeRh) was prepared by melt mixing, high-temperature annealing, and ice-water quenching. Temperature- and magnetic field-dependent magnetization measurements of wire-cut FeRh samples were performed on a vibrating sample magnetometer. Temperature-dependent MRI of FeRh samples was performed on a 4.7T MRI.

RESULTS: Temperature-dependent MRI clearly demonstrated image contrast changes due to the sharp magnetic state transition of the FeRh samples in the MRI magnetic field (4.7T) and at a physiologically relevant temperature (~37{\textdegree}C).

CONCLUSION: A magnetocaloric material, FeRh, was demonstrated to act as a high contrast ratio switchable MRI contrast agent due to its sharp first-order magnetic phase transition in the DC magnetic field of MRI and at physiologically relevant temperatures. A wide range of magnetocaloric materials are available that can be tuned by materials science techniques to optimize their response under MRI-appropriate conditions and be controllably switched in situ with temperature, magnetic field, or a combination of both.

}, issn = {1522-2594}, doi = {10.1002/mrm.27615}, author = {Barbic, Mladen and Dodd, Stephen J and Morris, H Douglas and Dilley, Neil and Marcheschi, Barbara and Huston, Alan and Harris, Tim D and Koretsky, Alan P} } @article {49587, title = {Mapping Neurotransmitter Identity in the Whole-Mount Brain Using Multiplex High-Throughput Fluorescence Hybridization.}, journal = {Genetics}, volume = {211}, year = {2018}, month = {2018 Dec 18}, pages = {473-82}, abstract = {

Identifying the neurotransmitters used by specific neurons is a critical step in understanding the function of neural circuits. However, methods for the consistent and efficient detection of neurotransmitter markers remain limited. Fluorescence hybridization (FISH) enables direct labeling of type-specific mRNA in neurons. Recent advances in FISH allow this technique to be carried out in intact tissue samples such as whole-mount brains. Here, we present a FISH platform for high-throughput detection of eight common neurotransmitter phenotypes in brains. We greatly increase FISH throughput by processing samples mounted on coverslips and optimizing fluorophore choice for each probe to facilitate multiplexing. As application examples, we demonstrate cases of neurotransmitter co-expression, reveal neurotransmitter phenotypes of specific cell types and explore the onset of neurotransmitter expression in the developing optic lobe. Beyond neurotransmitter markers, our protocols can in principle be used for large scale FISH detection of any mRNA in whole-mount fly brains.

}, issn = {1943-2631}, doi = {10.1534/genetics.118.301749}, author = {Meissner, Geoffrey W and Nern, Aljoscha and Singer, Robert H and Wong, Allan M and Malkesman, Oz and Long, Xi} } @article {49347, title = {MDN brain descending neurons coordinately activate backward and inhibit forward locomotion.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Aug 02}, abstract = {

Command-like descending neurons can induce many behaviors, such as backward locomotion, escape, feeding, courtship, egg-laying, or grooming (we define {\textquoteright}command-like neuron{\textquoteright} as a neuron whose activation elicits or {\textquoteright}commands{\textquoteright} a specific behavior). In most animals it remains unknown how neural circuits switch between antagonistic behaviors: via top-down activation/inhibition of antagonistic circuits or via reciprocal inhibition between antagonistic circuits. Here we use genetic screens, intersectional genetics, circuit reconstruction by electron microscopy, and functional optogenetics to identify a bilateral pair of larval {\textquoteright}mooncrawler descending neurons{\textquoteright} (MDNs) with command-like ability to coordinately induce backward locomotion and block forward locomotion; the former by stimulating a backward-active premotor neuron, and the latter by disynaptic inhibition of a forward-specific premotor neuron. In contrast, direct monosynaptic reciprocal inhibition between forward and backward circuits was not observed. Thus, MDNs coordinate a transition between antagonistic larval locomotor behaviors. Interestingly, larval MDNs persist into adulthood, where they can trigger backward walking. Thus, MDNs induce backward locomotion in both limbless and limbed animals.

}, issn = {2050-084X}, doi = {10.7554/eLife.38554}, author = {Carreira-Rosario, Arnaldo and Zarin, Aref Arzan and Clark, Matthew Q and Manning, Laurina and Fetter, Richard D and Cardona, Albert and Doe, Chris Q} } @article {49051, title = {Measuring integrin conformational change on the cell surface with super-resolution microscopy.}, journal = {Cell Reports}, volume = {22}, year = {2018}, month = {2018 Feb 13}, pages = {1903-1912}, abstract = {

We use super-resolution interferometric photoactivation and localization microscopy (iPALM) and a constrained photoactivatable fluorescent protein integrin fusion to measure the displacement of the head of integrin lymphocyte function-associated 1 (LFA-1) resulting from integrin conformational change on the cell surface. We demonstrate that the distance of the LFA-1 head increases substantially between basal and ligand-engaged conformations, which can only be explained at the molecular level by integrin extension. We further demonstrate that one class of integrin antagonist maintains the bent conformation, while another antagonist class induces extension. Our molecular scale measurements on cell-surface LFA-1 are in excellent agreement with distances derived from crystallographic and electron microscopy structures of bent and extended integrins. Our distance measurements are also in excellent agreement with a previous model of LFA-1 bound to ICAM-1 derived from the orientation of LFA-1 on the cell surface measured using fluorescence polarization microscopy.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2018.01.062}, author = {Moore, Travis I and Aaron, Jesse and Chew, Teng-Leong and Springer, Timothy A} } @article {49153, title = {Measuring the global substrate specificity of mycobacterial serine hydrolases using a library of fluorogenic ester substrates.}, journal = {ACS Infectious Diseases}, volume = {4}, year = {2018}, month = {2018 Jun 8}, pages = {904-11}, abstract = {

Among the proteins required for lipid metabolism in Mycobacterium tuberculosis are a significant number of uncharacterized serine hydrolases, especially lipases and esterases. Using a streamlined synthetic method, a library of immolative fluorogenic ester substrates was expanded to better represent the natural lipidomic diversity of Mycobacterium. This expanded fluorogenic library was then used to rapidly characterize the global structure activity relationship (SAR) of mycobacterial serine hydrolases in M.\ smegmatis under different growth conditions. Confirmation of fluorogenic substrate activation by mycobacterial serine hydrolases was performed using nonspecific serine hydrolase inhibitors and reinforced the biological significance of the SAR. The hydrolases responsible for the global SAR were then assigned using gel-resolved activity measurements, and these assignments were used to rapidly identify the relative substrate specificity of previously uncharacterized mycobacterial hydrolases. These measurements provide a global SAR of mycobacterial hydrolase activity, a picture of cycling hydrolase activity, and a detailed substrate specificity profile for previously uncharacterized hydrolases.

}, issn = {2373-8227}, doi = {10.1021/acsinfecdis.7b00263}, author = {Bassett, Braden and Waibel, Brent and White, Alex and Hansen, Heather and Stephens, Dominique and Koelper, Andrew and Larsen, Erik M and Kim, Charles and Glanzer, Adam and Lavis, Luke D and Hoops, Geoffrey C and Johnson, R Jeremy} } @article {65030, title = {Membrane bending moduli of coexisting liquid phases containing transmembrane peptide.}, journal = {Biophys J}, volume = {114}, year = {2018}, month = {2018 May 08}, pages = {2152-2164}, abstract = {

A number of highly curved membranes in\ vivo, such as epithelial cell microvilli, have the relatively high sphingolipid content associated with "raft-like" composition. Given the much lower bending energy measured for bilayers with "nonraft" low sphingomyelin and low cholesterol content, observing high curvature for presumably more rigid compositions seems counterintuitive. To understand this behavior, we measured membrane rigidity by fluctuation analysis of giant unilamellar vesicles. We found that including a transmembrane helical GWALP peptide increases the membrane bending modulus of the liquid-disordered (Ld) phase. We observed this increase at both low-cholesterol fraction and higher, more physiological cholesterol fraction. We find that simplified, commonly used Ld and liquid-ordered (Lo) phases are not representative of those that coexist. When Ld and Lo phases coexist, GWALP peptide favors the Ld phase with a partition coefficient of 3-10 depending on mixture composition. In model membranes at high cholesterol fractions, Ld phases with GWALP have greater bending moduli than the Lo phase that would coexist.

}, keywords = {Amino Acid Sequence, Biomechanical Phenomena, Cell Membrane, Cholesterol, Mechanical Phenomena, Models, Molecular, Oligopeptides, Protein Conformation, alpha-Helical}, issn = {1542-0086}, doi = {10.1016/j.bpj.2018.03.026}, author = {Usery, Rebecca D and Enoki, Thais A and Wickramasinghe, Sanjula P and Nguyen, Vanessa P and Ackerman, David G and Greathouse, Denise V and Koeppe, Roger E and Barrera, Francisco N and Feigenson, Gerald W} } @article {49405, title = {MicroED structure of the NaK ion channel reveals a Na partition process into the selectivity filter.}, journal = {Communications Biology}, volume = {1}, year = {2018}, month = {2018}, pages = {38}, abstract = {

Sodium (Na) is a ubiquitous and important inorganic salt mediating many critical biological processes such as neuronal excitation, signaling, and facilitation of various transporters. The hydration states of Na are proposed to play critical roles in determining the conductance and the selectivity of Na channels, yet they are rarely captured by conventional structural biology means. Here we use the emerging cryo-electron microscopy (cryoEM) method micro-electron diffraction (MicroED) to study the structure of a prototypical tetrameric Na-conducting channel, NaK, to 2.5 {\r A} resolution from nano-crystals. Two new conformations at the external site of NaK are identified, allowing us to visualize a partially hydrated Na ion at the entrance of the channel pore. A process of dilation coupled with Na movement is identified leading to valuable insights into the mechanism of ion conduction and gating. This study lays the ground work for future studies using MicroED in membrane protein biophysics.

}, issn = {2399-3642}, doi = {10.1038/s42003-018-0040-8}, author = {Liu, Shian and Gonen, Tamir} } @article {49581, title = {MicroED structures of HIV-1 Gag CTD-SP1 reveal binding interactions with the maturation inhibitor bevirimat.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, year = {2018}, month = {2018 Dec 26}, pages = {13258-63}, abstract = {

HIV-1 protease (PR) cleavage of the Gag polyprotein triggers the assembly of mature, infectious particles. Final cleavage of Gag occurs at the junction helix between the capsid protein CA and the SP1 spacer peptide. Here we used MicroED to delineate the binding interactions of the maturation inhibitor bevirimat (BVM) using very thin frozen-hydrated, 3D microcrystals of a CTD-SP1 Gag construct with and without bound BVM. The 2.9-{\r A} MicroED structure revealed that a single BVM molecule stabilizes the six-helix bundle via both electrostatic interactions with the dimethylsuccinyl moiety and hydrophobic interactions with the pentacyclic triterpenoid ring. These results provide insight into the mechanism of action of BVM and related maturation inhibitors that will inform further drug discovery efforts. This study also demonstrates the capabilities of MicroED for structure-based drug design.

}, issn = {1091-6490}, doi = {10.1073/pnas.1806806115}, author = {Purdy, Michael D and Shi, Dan and Chrustowicz, Jakub and Hattne, Johan and Gonen, Tamir and Yeager, Mark} } @article {49085, title = {Model-free quantification and visualization of colocalization in fluorescence images.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, year = {2018}, month = {2018 Mar 13}, abstract = {

The spatial association between fluorescently tagged biomolecules in situ provides valuable insight into their biological relationship. Within the limits of diffraction, such association can be measured using either Pearson{\textquoteright}s Correlation Coefficient (PCC) or Spearman{\textquoteright}s Rank Coefficient (SRC), which are designed to measure linear and monotonic correlations, respectively. However, the relationship between real biological signals is often more complex than these measures assume, rendering their results difficult to interpret. Here, we have adapted methods from the field of information theory to measure the association between two probes{\textquoteright} concentrations based on their statistical dependence. Our approach is mathematically more general than PCC or SRC, making no assumptions about the type of relationship between the probes. We show that when applied to biological images, our measures provide more intuitive results that are also more robust to outliers and the presence of multiple relationships than PCC or SRC. We also devise a display technique to highlight regions in the input images where the probes{\textquoteright} association is higher versus lower. We expect that our methods will allow biologists to more accurately and robustly quantify and visualize the association between two probes in a pair of fluorescence images. {\textcopyright} 2018 International Society for Advancement of Cytometry.

}, issn = {1552-4930}, doi = {10.1002/cyto.a.23356}, author = {Taylor, Aaron B and Ioannou, Maria S and Aaron, Jesse and Chew, Teng-Leong} } @article {65766, title = {Modifying the Steric Properties in the Second Coordination Sphere of Designed Peptides Leads to Enhancement of Nitrite Reductase Activity}, journal = {Angewandte Chemie International Edition}, volume = {57}, year = {2018}, month = {01/2018}, pages = {3954 {\textendash} 3957}, abstract = {

Protein design is a useful strategy to interrogate the protein structure-function relationship. We demonstrate using a highly modular 3-stranded coiled coil (TRI-peptide system) that a functional type 2 copper center exhibiting copper nitrite reductase (NiR) activity exhibits the highest homogeneous catalytic efficiency under aqueous conditions for the reduction of nitrite to NO and H2O. Modification of the amino acids in the second coordination sphere of the copper center increases the nitrite reductase activity up to 75-fold compared to previously reported systems. We find also that steric bulk can be used to enforce a three-coordinate CuI in a site, which tends toward two-coordination with decreased steric bulk. This study demonstrates the importance of the second coordination sphere environment both for controlling metal-center ligation and enhancing the catalytic efficiency of metalloenzymes and their analogues.

}, doi = {10.1002/anie.201712757}, url = {https://onlinelibrary.wiley.com/doi/full/10.1002/anie.201712757}, author = {Koebke, Karl J and Yu, Fangting and Salerno, Elvin and Stappen, Casey Van and Tebo, Alison G and Penner-Hahn, James E and Pecoraro, Vincent L} } @article {49291, title = {Monitoring the effects of pharmacological reagents on mitochondrial morphology.}, journal = {Current Protocols in Cell Biology}, volume = {79}, year = {2018}, month = {2018 Jun}, pages = {e45}, abstract = {

This protocol describes how to apply appropriate pharmacological controls to induce mitochondrial fusion or fission in studies of mitochondria morphology for four different mammalian cell types, HepG2 human liver hepatocellular carcinoma cells, MCF7 human breast adenocarcinoma cells, HEK293 human embryonic kidney cells, and collagen sandwich culture of primary rat hepatocytes. The protocol provides methods of treating cells with these pharmacological controls, staining mitochondria with commercially available MitoTracker Green and TMRE dyes, and imaging the mitochondrial morphology in live cells using a confocal fluorescent microscope. It also describes the cell culture methods needed for this protocol. {\textcopyright} 2018 by John Wiley \& Sons, Inc.

}, issn = {1934-2616}, doi = {10.1002/cpcb.45}, author = {Fu, Dong and Lippincott-Schwartz, Jennifer} } @article {49257, title = {Motor control: three-dimensional metric of head movements in the mouse brain.}, journal = {Current Biology : CB}, volume = {28}, year = {2018}, month = {2018 Jun 04}, pages = {R660-R662}, abstract = {

Many forms of human and animal behavior involve head movements. A new study reveals the neural code for three-dimensional head movements in the midbrain of freely moving mice.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2018.04.079}, author = {Finkelstein, Arseny} } @article {49585, title = {Motor cortex is an input-driven dynamical system controlling dexterous movement.}, journal = {bioRxiv}, year = {2018}, month = {2018-12-14}, pages = {266320}, abstract = {

Skillful control of movement is central to our ability to sense and manipulate the world. A large body of work in nonhuman primates has demonstrated that motor cortex provides flexible, time-varying activity patterns that control the arm during reaching and grasping. Previous studies have suggested that these patterns are generated by strong local recurrent dynamics operating autonomously from inputs during movement execution. An alternative possibility is that motor cortex requires coordination with upstream brain regions throughout the entire movement in order to yield these patterns. Here, we developed an experimental preparation in the mouse to directly test these possibilities using optogenetics and electrophysiology during a skilled reach-to-grab-to-eat task. To validate this preparation, we first established that a specific, time-varying pattern of motor cortical activity was required to produce coordinated movement. Next, in order to disentangle the contribution of local recurrent motor cortical dynamics from external input, we optogenetically held the recurrent contribution constant, then observed how motor cortical activity recovered following the end of this perturbation. Both the neural responses and hand trajectory varied from trial to trial, and this variability reflected variability in external inputs. To directly probe the role of these inputs, we used optogenetics to perturb activity in the thalamus. Thalamic perturbation at the start of the trial prevented movement initiation, and perturbation at any stage of the movement prevented progression of the hand to the target; this demonstrates that input is required throughout the movement. By comparing motor cortical activity with and without thalamic perturbation, we were able to estimate the effects of external inputs on motor cortical population activity. Thus, unlike pattern-generating circuits that are local and autonomous, such as those in the spinal cord that generate left-right alternation during locomotion, the pattern generator for reaching and grasping is distributed across multiple, strongly-interacting brain regions.

}, doi = {10.1101/266320}, author = {Sauerbrei, Britton and Guo, Jian-Zhong and Mischiati, Matteo and Guo, Wendy and Kabra, Mayank and Verma, Nakul and Branson, Kristin M and Hantman, Adam W} } @article {49455, title = {moxMaple3: a photoswitchable fluorescent protein for PALM and protein highlighting in oxidizing cellular environments.}, journal = {Scientific Reports}, volume = {8}, year = {2018}, month = {2018 Oct 03}, pages = {14738}, abstract = {

The ability of fluorescent proteins (FPs) to fold robustly is fundamental to the autocatalytic formation of the chromophore. While the importance of the tertiary protein structure is well appreciated, the impact of individual amino acid mutations for FPs is often not intuitive and requires direct testing. In this study, we describe the engineering of a monomeric photoswitchable FP, moxMaple3, for use in oxidizing cellular environments, especially the eukaryotic secretory pathway. Surprisingly, a point mutation to replace a cysteine substantially improved the yield of correctly folded FP capable of chromophore formation, regardless of cellular environment. The improved folding of moxMaple3 increases the fraction of visibly tagged fusion proteins, as well as FP performance in PALM super-resolution microscopy, and thus makes moxMaple3 a robust monomeric FP choice for PALM and optical highlighting applications.

}, issn = {2045-2322}, doi = {10.1038/s41598-018-32955-5}, author = {Kaberniuk, Andrii A and Mohr, Manuel A and Verkhusha, Vladislav V and Snapp, Erik Lee} } @article {49370, title = {mTOR-dependent phosphorylation controls TFEB nuclear export.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Aug 17}, pages = {3312}, abstract = {

During starvation the transcriptional activation of catabolic processes is induced by the nuclear translocation and consequent activation of transcription factor EB (TFEB), a master modulator of autophagy and lysosomal biogenesis. However, how TFEB is inactivated upon nutrient refeeding is currently unknown. Here we show that TFEB subcellular localization is dynamically controlled by its continuous shuttling between the cytosol and the nucleus, with the nuclear export representing a limiting step. TFEB nuclear export is mediated by CRM1 and is modulated by nutrient availability via mTOR-dependent hierarchical multisite phosphorylation of serines S142 and S138, which are localized in proximity of a nuclear export signal (NES). Our data on TFEB nucleo-cytoplasmic shuttling suggest an unpredicted role of mTOR in nuclear export.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-05862-6}, author = {Napolitano, Gennaro and Esposito, Alessandra and Choi, Heejun and Matarese, Maria and Benedetti, Valerio and Di Malta, Chiara and Monfregola, Jlenia and Medina, Diego Luis and Lippincott-Schwartz, Jennifer and Ballabio, Andrea} } @conference {49417, title = {Multiple animals tracking in video using part affinity fields}, booktitle = {Visual observation and analysis of Vertebrate And Insect Behavior 2018}, year = {2018}, month = {2018 Aug 20}, abstract = {

In this work, we address the problem of pose detection and tracking of multiple individuals for the study of behaviour in insects and animals. Using a Deep Neural Network architecture, precise detection and association of the body parts can be performed. The models are learned based on user-annotated training videos, which gives flexibility to the approach. This is illustrated on two different animals: honeybees and mice, where very good performance in part recognition and association are observed despite the presence of multiple interacting individuals.

}, url = {http://homepages.inf.ed.ac.uk/rbf/VAIB18PAPERS/vaib18rodriguez.pdf}, author = {Rodriguez, Ivan F and Megret, Remi and Egnor, Roian and Branson, Kristin and Agosto, Jose L and Giray, Tugrul and Acuna, Edgar} } @article {65047, title = {Multiplicative updates for optimization problems with dynamics.}, journal = {IEEE Xplore}, year = {2018}, month = {2018 Apr 16}, abstract = {

We consider the problem of optimizing general convex objective functions with nonnegativity constraints. Using the Karush-Kuhn-Tucker (KKT) conditions for the nonnegativity constraints we will derive fast multiplicative update rules for several problems of interest in signal processing, including non-negative deconvolution, point-process smoothing, ML estimation for Poisson Observations, nonnegative least squares and nonnegative matrix factorization (NMF). Our algorithm can also account for temporal and spatial structure and regularization. We will analyze the performance of our algorithm on simultaneously recorded neuronal calcium imaging and electrophysiology data.

}, doi = {10.1109/ACSSC.2017.8335723}, author = {Abbas Kazemipour and Behtash Babadi and wu, min and Podgorski, Kaspar and Shaul Druckmann} } @article {49351, title = {Multispectral live-cell imaging.}, journal = {Current Protocols in Cell Biology}, volume = {79}, year = {2018}, month = {2018 Jun}, pages = {e46}, abstract = {

Fluorescent proteins and vital dyes are invaluable tools for studying dynamic processes within living cells. However, the ability to distinguish more than a few different fluorescent reporters in a single sample is limited by the spectral overlap of available fluorophores. Here, we present a protocol for imaging live cells labeled with six fluorophores simultaneously. A confocal microscope with a spectral detector is used to acquire images, and linear unmixing algorithms are applied to identify the fluorophores present in each pixel of the image. We describe the application of this method to visualize the dynamics of six different organelles, and to quantify the contacts between organelles. However, this method can be used to image any molecule amenable to tagging with a fluorescent probe. Thus, multispectral live-cell imaging is a powerful tool for systems-level analysis of cellular organization and dynamics. {\textcopyright} 2018 by John Wiley \& Sons, Inc.

}, issn = {1934-2616}, doi = {10.1002/cpcb.46}, author = {Cohen, Sarah and Valm, Alex M and Lippincott-Schwartz, Jennifer} } @article {49011, title = {Mutual inhibition of lateral inhibition: a network motif for an elementary computation in the brain.}, journal = {Current Opinion in Neurobiology}, volume = {49}, year = {2018}, month = {2018 Jan 16}, pages = {69-74}, abstract = {

A series of classical studies in non-human primates has revealed the neuronal activity patterns underlying decision-making. However, the circuit mechanisms for such patterns remain largely unknown. Recent detailed circuit analyses in simpler neural systems have started to reveal the connectivity patterns underlying analogous processes. Here we review a few of these systems that share a particular connectivity pattern, namely mutual inhibition of lateral inhibition. Close examination of these systems suggests that this recurring connectivity pattern ({\textquoteright}network motif{\textquoteright}) is a building block to enforce particular dynamics, which can be used not only for simple behavioral choice but also for more complex choices and other brain functions. Thus, a network motif provides an elementary computation that is not specific to a particular brain function and serves as an elementary building block in the brain.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2017.12.019}, author = {Koyama, Minoru and Pujala, Avinash} } @article {49527, title = {MYC induces a hybrid energetics program early in cell reprogramming.}, journal = {Stem Cell Reports}, volume = {11}, year = {2018}, month = {2018 Dec 11}, pages = {1479-92}, abstract = {

Cell reprogramming is thought to be associated with a full metabolic switch from an oxidative- to a glycolytic-based metabolism. However, neither the dynamics nor the factors controlling this metabolic switch are fully understood. By using cellular, biochemical, protein array, metabolomic, and respirometry analyses, we found that c-MYC establishes a robust bivalent energetics program early in cell reprogramming. Cells prone to undergo reprogramming exhibit high mitochondrial membrane potential and display a hybrid metabolism. We conclude that MYC proteins orchestrate a rewiring of somatic cell metabolism early in cell reprogramming, whereby somatic cells acquire the phenotypic plasticity necessary for their transition to pluripotency in response to either intrinsic or external cues.

}, issn = {2213-6711}, doi = {10.1016/j.stemcr.2018.10.018}, author = {Prieto, Javier and Seo, Arnold Y and Le{\'o}n, Marian and Santacatterina, Fulvio and Torresano, Laura and Palomino-Sch{\"a}tzlein, Martina and Gim{\'e}nez, Karen and Vallet-S{\'a}nchez, Azahara and Ponsoda, Xavier and Pineda-Lucena, Antonio and Cuezva, Jos{\'e} M and Lippincott-Schwartz, Jennifer and Torres, Josema} } @article {64997, title = {Neural circuit basis of aversive odour processing in drosophila from sensory input to descending output.}, journal = {bioRxiv}, year = {2018}, month = {2018 Aug 26}, abstract = {

Evolution has tuned the nervous system of most animals to produce stereotyped behavioural responses to ethologically relevant stimuli. For example, female\ Drosophila\ avoid laying eggs in the presence of geosmin, an odorant produced by toxic moulds. Using this system, we now identify third order olfactory neurons that are essential for an innate aversive behaviour. Connectomics data place these neurons in the context of a complete synaptic circuit from sensory input to descending output. We find multiple levels of valence-specific convergence, including a novel form of axo-axonic input onto second order neurons conveying another danger signal, the pheromone of parasitoid wasps. However we also observe a massive divergence as geosmin-responsive second order olfactory neurons connect with a diverse array of \~{}75 cell types. Our data suggest a transition from a labelled line organisation in the periphery to one in which olfactory information is mapped onto many different higher order populations with distinct behavioural significance.

}, doi = {10.1101/394403}, author = {Paavo Huoviala and Michael-John Dolan and Fiona M. Love and Shahar Frechter and Ruair{\'\i} J.V. Roberts and Zane Mitrevica and Philipp Schlegel and Alexander Shakeel Bates and Yoshinori Aso and Tiago Rodrigues and Hannah Cornwall and Marcus Stensmyr and Davi Bock and Gerald M. Rubin and Marta Costa and Gregory S.X.E. Jefferis} } @article {49116, title = {A Neural Circuit for the Suppression of Pain by a Competing Need State.}, journal = {Cell}, volume = {173}, year = {2018}, month = {2018 Mar 22}, pages = {140-52}, abstract = {

Hunger and pain are two competing signals that individuals must resolve to ensure survival. However, the neural processes that prioritize conflicting survival needs are poorly understood. We discovered that hunger attenuates behavioral responses and affective properties of inflammatory pain without altering acute\ nociceptive responses. This effect is centrally controlled, as activity in hunger-sensitive agouti-related protein (AgRP)-expressing neurons abrogates\ inflammatory pain. Systematic analysis of AgRP projection subpopulations revealed that the\ neural processing of hunger and inflammatory pain converge in the hindbrain parabrachial nucleus (PBN). Strikingly, activity in AgRP {\textrightarrow} PBN neurons blocked the behavioral response to inflammatory pain as effectively as hunger or analgesics. The anti-nociceptive effect of hunger is mediated by neuropeptide Y (NPY) signaling in the PBN. By investigating the intersection between hunger and pain, we have identified a neural circuit that mediates competing survival needs and uncovered NPY Y1 receptor signaling in the PBN as a target for pain suppression.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2018.02.057}, author = {Alhadeff, Amber L and Su, Zhenwei and Hernandez, Elen and Klima, Michelle L and Phillips, Sophie Z and Holland, Ruby A and Guo, Caiying and Hantman, Adam W and De Jonghe, Bart C and Betley, J Nicholas} } @article {49001, title = {Neural substrates of navigational decision-making in Drosophila larva anemotaxis.}, journal = {bioRxiv}, year = {2018}, month = {2018 Jan 08}, pages = {244608}, abstract = {

Small animals navigate in the environment as a function of varying sensory information in order to reach more favorable environmental conditions. To achieve this Drosophila larvae alternate periods of runs and turns in gradients of light, temperature, odors and CO2. While the sensory neurons that mediate the navigation behaviors in the different sensory gradients have been described, where and how are these navigational strategies are implemented in the central nervous system and controlled by neuronal circuit elements is not well known. Here we characterize for the first time the navigational strategies of Drosophila larvae in gradients of air-current speeds using high-throughput behavioral assays and quantitative behavioral analysis. We find that larvae extend runs when facing favorable conditions and increase turn rate when facing unfavorable direction, a strategy they use in other sensory modalities as well. By silencing the activity of individual neurons and very sparse expression patterns (2 or 3 neuron types), we further identify the sensory neurons and circuit elements in the ventral nerve cord and brain of the larva required for navigational decisions during anemotaxis. The phenotypes of these central neurons are consistent with a mechanism where the increase of the turning rate in unfavorable conditions and decrease in turning rate in favorable conditions are independently controlled.

}, doi = {10.1101/244608}, author = {Jovanic, Tihana and Truman, James W and Gershow, Marc and Zlatic, Marta} } @article {49337, title = {Neuroarchitecture of the Drosophila central complex: A catalog of nodulus and asymmetrical body neurons and a revision of the protocerebral bridge catalog.}, journal = {Journal of Comparative Neurology}, year = {2018}, month = {2018 Aug 7}, abstract = {

The central complex, a set of neuropils in the center of the insect brain, plays a crucial role in spatial aspects of sensory integration and motor control. Stereotyped neurons interconnect these neuropils with one another and with accessory structures. We screened over 5000 Drosophila melanogaster GAL4 lines for expression in two neuropils, the noduli (NO) of the central complex and the asymmetrical body (AB), and used multicolor stochastic labelling to analyze the morphology, polarity and organization of individual cells in a subset of the GAL4 lines that showed expression in these neuropils. We identified nine NO and three AB cell types and describe them here. The morphology of the NO neurons suggests that they receive input primarily in the lateral accessory lobe and send output to each of the six paired noduli. We demonstrate that the AB is a bilateral structure which exhibits asymmetry in size between the left and right bodies. We show that the AB neurons directly connect the AB to the central complex and accessory neuropils, that they target both the left and right ABs, and that one cell type preferentially innervates the right AB. We propose that the AB be considered a central complex neuropil in Drosophila. Finally, we present highly restricted GAL4 lines for most identified protocerebral bridge, NO and AB cell types. These lines, generated using the split-GAL4 method, will facilitate anatomical studies, behavioral assays, and physiological experiments.\ 

}, doi = {10.1002/cne.24512}, author = {Wolff, Tanya and Rubin, Gerald M} } @article {49528, title = {The neuronal basis of an illusory motion percept is explained by decorrelation of parallel motion pathways.}, journal = {Current Biology : CB}, volume = {28}, year = {2018}, month = {2018 Oct 31}, pages = {3748-78}, abstract = {

Both vertebrates and invertebrates perceive illusory motion, known as "reverse-phi," in visual stimuli that contain sequential luminance increments and decrements. However, increment (ON) and decrement (OFF) signals are initially processed by separate visual neurons, and parallel elementary motion detectors downstream respond selectively to the motion of light or dark edges, often termed ON- and OFF-edges. It remains unknown how and where ON and OFF signals combine to generate reverse-phi motion signals. Here, we show that each of Drosophila{\textquoteright}s elementary motion detectors encodes motion by combining both ON and OFF signals. Their pattern of responses reflects combinations of increments and decrements that co-occur in natural motion, serving to decorrelate their outputs. These results suggest that the general principle of signal decorrelation drives the functional specialization of parallel motion detection channels, including their selectivity for moving light or dark edges.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2018.10.007}, author = {Salazar-Gatzimas, Emilio and Agrochao, Margarida and Fitzgerald, James E and Clark, Damon A} } @article {49529, title = {Neuron-subtype-specific expression, interaction affinities, and specificity determinants of DIP/Dpr cell recognition proteins.}, journal = {Neuron}, volume = {100}, year = {2018}, month = {2018 Nov 12}, pages = {1385-1400}, abstract = {

Binding between DIP and Dpr neuronal recognition proteins has been proposed to regulate synaptic connections between lamina and medulla neurons in the Drosophila visual system. Each lamina neuron was previously shown to express many Dprs. Here, we demonstrate, by contrast, that their synaptic partners typically express one or two DIPs, with binding specificities matched to the lamina neuron-expressed Dprs. A deeper understanding of the molecular logic of DIP/Dpr interaction requires quantitative studies on the properties of these proteins. We thus generated a quantitative affinity-based DIP/Dpr interactome for all DIP/Dpr protein family members. This revealed a broad range of affinities and identified homophilic binding for some DIPs and some Dprs. These data, along with full-length ectodomain DIP/Dpr and DIP/DIP crystal structures, led to the identification of molecular determinants of DIP/Dpr specificity. This structural knowledge, along with a comprehensive set of quantitative binding affinities, provides new tools for functional studies in\ vivo.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2018.10.046}, author = {Cosmanescu, Filip and Katsamba, Phinikoula S and Sergeeva, Alina P and Ahlsen, Goran and Patel, Saurabh D and Brewer, Joshua J and Tan, Liming and Xu, Shuwa and Xiao, Qi and Nagarkar-Jaiswal, Sonal and Nern, Aljoscha and Bellen, Hugo J and Zipursky, S Lawrence and Honig, Barry and Shapiro, Lawrence} } @article {49095, title = {NeuroStorm: accelerating brain science discovery in the cloud.}, journal = {arXiv}, year = {2018}, month = {2018 Mar 09}, abstract = {

Neuroscientists are now able to acquire data at staggering rates across spatiotemporal scales. However, our ability to capitalize on existing datasets, tools, and intellectual capacities is hampered by technical challenges. The key barriers to accelerating scientific discovery correspond to the FAIR data principles: findability, global access to data, software interoperability, and reproducibility/re-usability. We conducted a hackathon dedicated to making strides in those steps. This manuscript is a technical report summarizing these achievements, and we hope serves as an example of the effectiveness of focused, deliberate hackathons towards the advancement of our quickly-evolving field.

}, url = {https://arxiv.org/abs/1803.03367}, author = {Kiar, Gregory and Anderson, Robert J and Baden, Alex and Badea, Alexandra and Bridgeford, Eric W and Champion, Andrew and Chandrashekar, Jayaram and Collman, Forrest and Duderstadt, Brandon and Evans, Alan C and Engert, Florian and Falk, Benjamin and Glatard, Tristan and Roncal, William Gray and Kennedy, David N and Maitlin-Shepard and Marren, Ryan A and Nnaemeka, Onyeka and Perlman, Eric and Seshamani, Sharmishtaas} } @article {68994, title = {Neutralizing Gatad2a-Chd4-Mbd3/NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency.}, journal = {Cell Stem Cell}, volume = {23}, year = {2018}, month = {09/2018}, pages = {412-425.e10}, abstract = {

Mbd3, a member of nucleosome remodeling and deacetylase (NuRD) co-repressor complex, was previously identified as an inhibitor for deterministic induced pluripotent stem cell (iPSC) reprogramming, where up to 100\% of donor cells successfully complete the process. NuRD can assume multiple mutually exclusive conformations, and it remains unclear whether this deterministic phenotype can be attributed to a specific Mbd3/NuRD subcomplex. Moreover, since complete ablation of Mbd3 blocks somatic cell proliferation, we aimed to explore functionally relevant alternative ways to neutralize Mbd3-dependent NuRD activity. We identify Gatad2a, a NuRD-specific subunit, whose complete deletion specifically disrupts Mbd3/NuRD repressive activity on the pluripotency circuitry during iPSC differentiation and reprogramming without ablating somatic cell proliferation. Inhibition of Gatad2a facilitates deterministic murine iPSC reprogramming within 8\ days. We validate a distinct molecular axis, Gatad2a-Chd4-Mbd3, within Mbd3/NuRD as being critical for blocking reestablishment of naive pluripotency and further highlight signaling-dependent and post-translational modifications of Mbd3/NuRD that influence its interactions and assembly.

}, keywords = {Animals, Cells, Cultured, DNA Helicases, DNA-Binding Proteins, Female, GATA Transcription Factors, Induced Pluripotent Stem Cells, Male, Mi-2 Nucleosome Remodeling and Deacetylase Complex, Mice, Mice, Inbred C57BL, Mice, Inbred CBA, Mice, Knockout, Mice, Transgenic, Transcription Factors}, issn = {1875-9777}, doi = {10.1016/j.stem.2018.07.004}, author = {Mor, Nofar and Rais, Yoach and Sheban, Daoud and Peles, Shani and Aguilera-Castrejon, Alejandro and Zviran, Asaf and Elinger, Dalia and Viukov, Sergey and Geula, Shay and Krupalnik, Vladislav and Zerbib, Mirie and Chomsky, Elad and Lasman, Lior and Shani, Tom and Bayerl, Jonathan and Gafni, Ohad and Hanna, Suhair and Buenrostro, Jason D and Hagai, Tzachi and Masika, Hagit and Vainorius, Gintautas and Bergman, Yehudit and Greenleaf, William J and Esteban, Miguel A and Elling, Ulrich and Levin, Yishai and Massarwa, Rada and Merbl, Yifat and Novershtern, Noa and Hanna, Jacob H} } @article {49532, title = {NeuTu: Software for Collaborative, Large-Scale, Segmentation-Based Connectome Reconstruction.}, journal = {Frontiers in Neural Circuits}, volume = {12}, year = {2018}, month = {2018}, pages = {101}, abstract = {

Reconstructing a connectome from an EM dataset often requires a large effort of proofreading automatically generated segmentations. While many tools exist to enable tracing or proofreading, recent advances in EM imaging and segmentation quality suggest new strategies and pose unique challenges for tool design to accelerate proofreading. Namely, we now have access to very large multi-TB EM datasets where (1) many segments are largely correct, (2) segments can be very large (several GigaVoxels), and where (3) several proofreaders and scientists are expected to collaborate simultaneously. In this paper, we introduce NeuTu as a solution to efficiently proofread large, high-quality segmentation in a collaborative setting. NeuTu is a client program of our high-performance, scalable image database called DVID so that it can easily be scaled up. Besides common features of typical proofreading software, NeuTu tames unprecedentedly large data with its distinguishing functions, including: (1) low-latency 3D visualization of large mutable segmentations; (2) interactive splitting of very large false merges with highly optimized semi-automatic segmentation; (3) intuitive user operations for investigating or marking interesting points in 3D visualization; (4) visualizing proofreading history of a segmentation; and (5) real-time collaborative proofreading with lock-based concurrency control. These unique features have allowed us to manage the workflow of proofreading a large dataset smoothly without dividing them into subsets as in other segmentation-based tools. Most importantly, NeuTu has enabled some of the largest connectome reconstructions as well as interesting discoveries in the fly brain.

}, issn = {1662-5110}, doi = {10.3389/fncir.2018.00101}, author = {Zhao, Ting and Olbris, Donald J and Yu, Yang and Plaza, Stephen M} } @article {65094, title = {New optical probes bring dopamine to light.}, journal = {Biochemistry}, volume = {57}, year = {2018}, month = {2018 Nov 13}, pages = {6379-6381}, abstract = {

Chemical signaling between neurons in the brain can be divided into two major categories: fast synaptic transmission and neuromodulation. Fast synaptic transmission, mediated by amino acids such as glutamate and GABA, occurs on millisecond time scales and results in the influx of ions through ligand-gated ion channels on postsynaptic neurons (Figure\ 1A). Electrophysiological and optical imaging tools, including genetically encoded voltage indicators, have enabled neuroscientists to link cause (neurotransmitter release) and effect (membrane polarization) of synaptic transmission in time and space. Unlike classical neurotransmitters, neuromodulators do not produce immediate electrical effects that excite or inhibit target neurons. Instead, neuromodulators tune the intrinsic or synaptic properties of neurons, most commonly through interaction with G-protein-coupled receptors (GPCRs) (Figure\ 1B). Neuromodulators can escape the synaptic cleft and diffuse broadly, allowing them to influence the activity of many neurons in a state-dependent manner. Therefore, the spatial component of neuromodulator flux is fundamentally important. However, the temporal and/or spatial limitations of techniques classically used to study neuromodulation, such as microdialysis and fast-scan cyclic voltammetry (FSCV), make it difficult to interpret how neuromodulator release affects the plasticity or function of target neuronal populations on a moment-to-moment basis. Therefore, tools that can detect neuromodulators with high spatiotemporal resolution are critical for understanding their impact on neural computations that control behavior in health and disease.

}, keywords = {Animals, Dopamine, Fluorescent Dyes, Humans, Light, Optical Imaging, Receptors, Dopamine}, issn = {1520-4995}, doi = {10.1021/acs.biochem.8b00883}, author = {Beyene, Abraham G and Delevich, Kristen and Yang, Sarah J and Landry, Markita P} } @article {49244, title = {Nicotinic cholinergic receptors in VTA glutamate neurons modulate excitatory transmission.}, journal = {Cell Reports}, volume = {23}, year = {2018}, month = {2018 May 22}, pages = {2236-2244}, abstract = {

Ventral tegmental area (VTA) glutamate neurons are important components of reward circuitry, but whether they are subject to cholinergic modulation is unknown. To study this, we used molecular, physiological, and photostimulation techniques to examine nicotinic acetylcholine receptors (nAChRs) in VTA glutamate neurons. Cells in the medial VTA, where glutamate neurons are enriched, are responsive to acetylcholine (ACh) released from cholinergic axons. VTA VGLUT2 neurons express mRNA and protein subunits known to comprise heteromeric nAChRs. Electrophysiology, coupled with two-photon microscopy and laser flash photolysis of photoactivatable nicotine, was used to demonstrate nAChR functional activity in the somatodendritic subcellular compartment of VTA VGLUT2 neurons. Finally, optogenetic isolation of intrinsic VTA glutamatergic microcircuits along with gene-editing techniques demonstrated that nicotine potently modulates excitatory transmission within the VTA via heteromeric nAChRs. These results indicate that VTA glutamate neurons are modulated by cholinergic mechanisms and participate in the cascade of physiological responses to nicotine exposure.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2018.04.062}, author = {Yan, Yijin and Peng, Can and Arvin, Matthew C and Jin, Xiao-Tao and Kim, Veronica J and Ramsey, Matthew D and Wang, Yong and Banala, Sambashiva and Wokosin, David L and McIntosh, J Michael and Lavis, Luke D and Drenan, Ryan M} } @article {49086, title = {Nociceptive interneurons control modular motor pathways to promote escape behavior in Drosophila.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Mar 12}, abstract = {

Rapid and efficient escape behaviors in response to noxious sensory stimuli are essential for protection and survival. Yet, how noxious stimuli are transformed to coordinated escape behaviors remains poorly understood. Inlarvae, noxious stimuli trigger sequential body bending and corkscrew-like rolling behavior. We identified a population of interneurons in the nerve cord of, termed Down-and-Back (DnB) neurons, that are activated by noxious heat, promote nociceptive behavior, and are required for robust escape responses to noxious stimuli. Electron microscopic circuit reconstruction shows that DnBs are targets of nociceptive and mechanosensory neurons, are directly presynaptic to pre-motor circuits, and link indirectly to Goro rolling command-like neurons. DnB activation promotes activity in Goro neurons, and coincident inactivation of Goro neurons prevents the rolling sequence but leaves intact body bending motor responses. Thus, activity from nociceptors to DnB interneurons coordinates modular elements of nociceptive escape behavior.

}, issn = {2050-084X}, doi = {10.7554/eLife.26016}, author = {Burgos, Anita and Honjo, Ken and Ohyama, Tomoko and Qian, Cheng Sam and Shin, Grace Ji-Eun and Gohl, Daryl M and Silies, Marion and Tracey, W Daniel and Zlatic, Marta and Cardona, Albert and Grueber, Wesley B} } @article {49457, title = {Noncanonical autophagy at ER exit sites regulates procollagen turnover.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, year = {2018}, month = {2018 Oct 04}, pages = {E10099-108}, abstract = {

Type I collagen is the main component of bone matrix and other connective tissues. Rerouting of its procollagen precursor to a degradative pathway is crucial for osteoblast survival in pathologies involving excessive intracellular buildup of procollagen that is improperly folded and/or trafficked. What cellular mechanisms underlie this rerouting remains unclear. To study these mechanisms, we employed live-cell imaging and correlative light and electron microscopy (CLEM) to examine procollagen trafficking both in wild-type mouse osteoblasts and osteoblasts expressing a bone pathology-causing mutant procollagen. We found that although most procollagen molecules successfully trafficked through the secretory pathway in these cells, a subpopulation did not. The latter molecules appeared in numerous dispersed puncta colocalizing with COPII subunits, autophagy markers and ubiquitin machinery, with more puncta seen in mutant procollagen-expressing cells. Blocking endoplasmic reticulum exit site (ERES) formation suppressed the number of these puncta, suggesting they formed after procollagen entry into ERESs. The punctate structures containing procollagen, COPII, and autophagic markers did not move toward the Golgi but instead were relatively immobile. They appeared to be quickly engulfed by nearby lysosomes through a bafilomycin-insensitive pathway. CLEM and fluorescence recovery after photobleaching experiments suggested engulfment occurred through a noncanonical form of autophagy resembling microautophagy of ERESs. Overall, our findings reveal that a subset of procollagen molecules is directed toward lysosomal degradation through an autophagic pathway originating at ERESs, providing a mechanism to remove excess procollagen from cells.

}, issn = {1091-6490}, doi = {10.1073/pnas.1814552115}, author = {Omari, Shakib and Makareeva, Elena and Roberts-Pilgrim, Anna and Mirigian, Lynn and Jarnik, Michal and Ott, Carolyn and Lippincott-Schwartz, Jennifer and Leikin, Sergey} } @article {49276, title = {A novel pyramidal cell type promotes sharp-wave synchronization in the hippocampus.}, journal = {Nature Neuroscience}, volume = {21}, year = {2018}, month = {2018 Jun 18}, pages = {985-95}, abstract = {

To support cognitive function, the CA3 region of the hippocampus performs computations involving attractor dynamics. Understanding how cellular and ensemble activities of CA3 neurons enable computation is critical for elucidating the neural correlates of cognition. Here we show that CA3 comprises not only classically described pyramid cells with thorny excrescences, but also includes previously unidentified {\textquoteright}athorny{\textquoteright} pyramid cells that lack mossy-fiber input. Moreover, the two neuron types have distinct morphological and physiological phenotypes and are differentially modulated by acetylcholine. To understand the contribution of these athorny pyramid neurons to circuit function, we measured cell-type-specific firing patterns during sharp-wave synchronization events in vivo and recapitulated these dynamics with an attractor network model comprising two principal cell types. Our data and simulations reveal a key role for athorny cell bursting in the initiation of sharp waves: transient network attractor states that signify the execution of pattern completion computations vital to cognitive function.

}, issn = {1546-1726}, doi = {10.1038/s41593-018-0172-7}, author = {Hunt, David L and Linaro, Daniele and Si, Bailu and Romani, Sandro and Spruston, Nelson} } @article {49176, title = {A novel sheet-like virus particle array is a hallmark of Zika virus infection.}, journal = {Emerging Microbes \& Infections}, volume = {7}, year = {2018}, month = {2018 Apr 25}, pages = {69}, abstract = {

Zika virus (ZIKV) is an emerging flavivirus that caused thousands of human infections in recent years. Compared to other human flaviviruses, ZIKV replication is not well understood. Using fluorescent, transmission electron, and focused ion beam-scanning electron microscopy, we examined ZIKV replication dynamics in Vero 76 cells and in the brains of infected laboratory mice. We observed the progressive development of a perinuclear flaviviral replication factory both in vitro and in vivo. In vitro, we illustrated the ZIKV lifecycle from particle cell entry to egress. ZIKV particles assembled and aggregated in an induced convoluted membrane structure and ZIKV strain-specific membranous vesicles. While most mature virus particles egressed via membrane budding, some particles also likely trafficked through late endosomes and egressed through membrane abscission. Interestingly, we consistently observed a novel sheet-like virus particle array consisting of a single layer of ZIKV particles. Our study further defines ZIKV replication and identifies a novel hallmark of ZIKV infection.

}, issn = {2222-1751}, doi = {10.1038/s41426-018-0071-8}, author = {Liu, Jun and Kline, Brandon A and Kenny, Tara A and Smith, Darci R and Soloveva, Veronica and Beitzel, Brett and Pang, Song and Lockett, Stephen and Hess, Harald F and Palacios, Gustavo and Kuhn, Jens H and Sun, Mei G and Zeng, Xiankun} } @article {49173, title = {Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms.}, journal = {Science (New York, N.Y.)}, volume = {360}, year = {2018}, month = {2018 Apr 20}, abstract = {

True physiological imaging of subcellular dynamics requires studying cells within their parent organisms, where all the environmental cues that drive gene expression, and hence the phenotypes that we actually observe, are present. A complete understanding also requires volumetric imaging of the cell and its surroundings at high spatiotemporal resolution, without inducing undue stress on either. We combined lattice light-sheet microscopy with adaptive optics to achieve, across large multicellular volumes, noninvasive aberration-free imaging of subcellular processes, including endocytosis, organelle remodeling during mitosis, and the migration of axons, immune cells, and metastatic cancer cells in vivo. The technology reveals the phenotypic diversity within cells across different organisms and developmental stages and may offer insights into how cells harness their intrinsic variability to adapt to different physiological environments.

}, issn = {1095-9203}, doi = {10.1126/science.aaq1392}, author = {Liu, Tsung-Li and Upadhyayula, Srigokul and Milkie, Daniel E and Singh, Ved and Wang, Kai and Swinburne, Ian A and Mosaliganti, Kishore R and Collins, Zach M and Hiscock, Tom W and Shea, Jamien and Kohrman, Abraham Q and Medwig, Taylor N and Dambournet, Daphne and Forster, Ryan and Cunniff, Brian and Ruan, Yuan and Yashiro, Hanako and Scholpp, Steffen and Meyerowitz, Elliot M and Hockemeyer, Dirk and Drubin, David G and Martin, Benjamin L and Matus, David Q and Koyama, Minoru and Megason, Sean G and Kirchhausen, Tom and Betzig, Eric} } @article {49141, title = {Odorant binding protein 69a connects social interaction to modulation of social responsiveness in Drosophila.}, journal = {PLoS Genetics}, volume = {14}, year = {2018}, month = {2018 Apr 09}, pages = {e1007328}, abstract = {

Living in a social environment requires the ability to respond to specific social stimuli and to incorporate information obtained from prior interactions into future ones. One of the mechanisms that facilitates social interaction is pheromone-based communication. In Drosophila melanogaster, the male-specific pheromone cis-vaccenyl acetate (cVA) elicits different responses in male and female flies, and functions to modulate behavior in a context and experience-dependent manner. Although it is the most studied pheromone in flies, the mechanisms that determine the complexity of the response, its intensity and final output with respect to social context, sex and prior interaction, are still not well understood. Here we explored the functional link between social interaction and pheromone-based communication and discovered an odorant binding protein that links social interaction to sex specific changes in cVA related responses. Odorant binding protein 69a (Obp69a) is expressed in auxiliary cells and secreted into the olfactory sensilla. Its expression is inversely regulated in male and female flies by social interactions: cVA exposure reduces its levels in male flies and increases its levels in female flies. Increasing or decreasing Obp69a levels by genetic means establishes a functional link between Obp69a levels and the extent of male aggression and female receptivity. We show that activation of cVA-sensing neurons is sufficeint to regulate Obp69a levels in the absence of cVA, and requires active neurotransmission between the sensory neuron to the second order olfactory neuron. The cross-talk between sensory neurons and non-neuronal auxiliary cells at the olfactory sensilla, represents an additional component in the machinery that promotes behavioral plasticity to the same sensory stimuli in male and female flies.

}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1007328}, author = {Bentzur, Assa and Shmueli, Anat and Omesi, Liora and Ryvkin, Julia and Knapp, Jon-Michael and Parnas, Moshe and Davis, Fred P and Shohat-Ophir, Galit} } @article {49235, title = {Of what use is connectomics? A personal perspective on the connectome.}, journal = {The Journal of Experimental Biology}, volume = {221}, year = {2018}, month = {2018 May 20}, abstract = {

The brain is a network of neurons and its biological output is behaviour. This is an exciting age, with a growing acknowledgement that the comprehensive compilation of synaptic circuits densely reconstructed in the brains of model species is now both technologically feasible and a scientifically enabling possibility in neurobiology, much as 30 years ago genomics was in molecular biology and genetics. Implemented by huge advances in electron microscope technology, especially focused ion beam-scanning electron microscope (FIB-SEM) milling (see Glossary), image capture and alignment, and computer-aided reconstruction of neuron morphologies, enormous progress has been made in the last decade in the detailed knowledge of the actual synaptic circuits formed by real neurons, in various brain regions of the fly It is useful to distinguish synaptic pathways that are major, with 100 or more presynaptic contacts, from those that are minor, with fewer than about 10; most neurites are both presynaptic and postsynaptic, and all synaptic sites have multiple postsynaptic dendrites. Work on has spearheaded these advances because cell numbers are manageable, and neuron classes are morphologically discrete and genetically identifiable, many confirmed by reporters. Recent advances are destined within the next few years to reveal the complete connectome in an adult fly, paralleling advances in the larval brain that offer the same prospect possibly within an even shorter time frame. The final amendment and validation of segmented bodies by human proof-readers remains the most time-consuming step, however. The value of a complete connectome in is that, by targeting to specific neurons transgenes that either silence or activate morphologically identified circuits, and then identifying the resulting behavioural outcome, we can determine the causal mechanism for behaviour from its loss or gain. More importantly, the connectome reveals hitherto unsuspected pathways, leading us to seek novel behaviours for these. Circuit information will eventually be required to understand how differences between brains underlie differences in behaviour, and especially to herald yet more advanced connectomic strategies for the vertebrate brain, with an eventual prospect of understanding cognitive disorders having a connectomic basis. Connectomes also help us to identify common synaptic circuits in different species and thus to reveal an evolutionary progression in candidate pathways.

}, issn = {1477-9145}, doi = {10.1242/jeb.164954}, author = {Meinertzhagen, Ian A} } @article {49115, title = {Opportunities and obstacles for deep learning in biology and medicine.}, journal = {Journal of The Royal Society Interface}, year = {2018}, month = {2018 Apr 4}, abstract = {

Deep learning describes a class of machine learning algorithms that are capable of combining raw inputs into layers of intermediate features. These algorithms have recently shown impressive results across a variety of domains. Biology and medicine are data-rich disciplines, but the data are complex and often ill-understood. Hence, deep learning techniques may be particularly well suited to solve problems of these fields. We examine applications of deep learning to a variety of biomedical problems{\textemdash}patient classification, fundamental biological processes and treatment of patients{\textemdash}and discuss whether deep learning will be able to transform these tasks or if the biomedical sphere poses unique challenges. Following from an extensive literature review, we find that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art. Even though improvements over previous baselines have been modest in general, the recent progress indicates that deep learning methods will provide valuable means for speeding up or aiding human investigation. Though progress has been made linking a specific neural network{\textquoteright}s prediction to input features, understanding how users should interpret these models to make testable hypotheses about the system under study remains an open challenge. Furthermore, the limited amount of labelled data for training presents problems in some domains, as do legal and privacy constraints on work with sensitive health records. Nonetheless, we foresee deep learning enabling changes at both bench and bedside with the potential to transform several areas of biology and medicine.

}, doi = {10.1098/rsif.2017.0387}, author = {Ching, Travers and Himmelstein, Daniel S and Beaulieu-Jones, Brett K and Kalinin, Alexandr A and Do, Brian T and Way, Gregory P and Ferrero, Enrico and Agapow, Paul-Michael and Zietz, Michael and Hoffman, Michael M and Xie, Wei and Rosen, Gail L and Lengerich, Benjamin J and Israeli, Johnny and Lanchantin, Jack and Woloszynek, Stephen and Carpenter, Anne E and Shrikumar, Avanti and Xu, Jinbo and Cofer, Evan M} } @article {49381, title = {Optical alignment device for two-photon microscopy.}, journal = {Biomedical Optics Express}, volume = {9}, year = {2018}, month = {2018 Aug 1}, pages = {3624-9}, abstract = {

Two-photon excitation fluorescence microscopy has revolutionized our understanding of brain structure and function through the high resolution and large penetration depth it offers. Investigating neural structures\ in vivo\ requires gaining optical access to the brain, which is typically achieved by replacing a part of the skull with one or several layers of cover glass windows. To compensate for the spherical aberrations caused by the presence of these layers of glass, collar-correction objectives are typically used. However, the efficiency of this correction has been shown to depend significantly on the tilt angle between the glass window surface and the optical axis of the imaging system. Here, we first expand these observations and characterize the effect of the tilt angle on the collected fluorescence signal with thicker windows (double cover slide) and compare these results with an objective devoid of collar-correction. Second, we present a simple optical alignment device designed to rapidly minimize the tilt angle\ in vivo\ and align the optical axis of the microscope perpendicularly to the glass window to an angle below 0.25{\textdegree}, thereby significantly improving the imaging quality. Finally, we describe a tilt-correction procedure for users in an\ in vivo\ setting, enabling the accurate alignment with a resolution of \<0.2{\textdegree} in only few iterations.

}, doi = {10.1364/BOE.9.003624}, author = {Gali{\~n}anes, Gregorio L and Marchand, Paul J and Turcotte, Raphael and Pellat, Sebastien and Ji, Na and Huber, Daniel} } @article {49366, title = {Optimization of fluorophores for chemical tagging and immunohistochemistry of Drosophila neurons.}, journal = {PLoS One}, volume = {13}, year = {2018}, month = {2018 Aug 15}, pages = {e0200759}, abstract = {

The use of genetically encoded {\textquoteright}self-labeling tags{\textquoteright} with chemical fluorophore ligands enables rapid labeling of specific cells in neural tissue. To improve the chemical tagging of neurons, we synthesized and evaluated new fluorophore ligands based on Cy, Janelia Fluor, Alexa Fluor, and ATTO dyes and tested these with recently improved Drosophila melanogaster transgenes. We found that tissue clearing and mounting in DPX substantially improves signal quality when combined with specific non-cyanine fluorophores. We compared and combined this labeling technique with standard immunohistochemistry in the Drosophila brain.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0200759}, author = {Meissner, Geoffrey W and Grimm, Jonathan B and Johnston, Rebecca M and Sutcliffe, Ben and Ng, Julian and Jefferis, Gregory S X E and Cachero, Sebastian and Lavis, Luke D and Malkesman, Oz} } @article {48976, title = {Optogenetic dissection of descending behavioral control in Drosophila.}, journal = {eLife}, year = {2018}, month = {2018}, pages = {e34275}, abstract = {

In most animals, the brain makes behavioral decisions that are transmitted by descending neurons to the nerve cord circuitry that produces behaviors. In insects, only a few descending neurons have been associated with specific behaviors. To explore how descending neurons control an insect{\textquoteright}s movements, we developed a novel method to systematically assay the behavioral effects of activating individual neurons on freely behaving terrestrial\ D. melanogaster. We calculated a two-dimensional representation of the entire behavior space explored by these flies and we associated descending neurons with specific behaviors by identifying regions of this space that were visited with increased frequency during optogenetic activation. Applying this approach across a large collection of descending neurons, we found that (1) activation of most of the descending neurons drove stereotyped behaviors, (2) in many cases multiple descending neurons activated similar behaviors, and (3) optogenetically-activated behaviors were often dependent on the behavioral state prior to activation.

}, doi = {10.7554/eLife.34275}, author = {Cande, Jessica and Namiki, Shigehiro and Qiu, Jirui and Korff, Wyatt and Card, Gwyneth M and Shaevitz, Joshua W and Stern, David L and Berman, Gordon J} } @article {49522, title = {Paring down to the essentials.}, journal = {Science (New York, N.Y.)}, volume = {362}, year = {2018}, month = {2018 Nov 23}, pages = {904}, issn = {1095-9203}, doi = {10.1126/science.aav6872}, author = {Wang, Tim} } @article {49002, title = {Persistent activity in a recurrent circuit underlies courtship memory in Drosophila.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Jan 11}, abstract = {

Recurrent connections are thought to be a common feature of the neural circuits that encode memories, but how memories are laid down in such circuits is not fully understood. Here we present evidence that courtship memory in Drosophila relies on the recurrent circuit between mushroom body gamma (MBg), M6 output, and aSP13 dopaminergic neurons. We demonstrate persistent neuronal activity of aSP13 neurons and show that it transiently potentiates synaptic transmission from MBγ\>M6 neurons. M6 neurons in turn provide input to aSP13 neurons, prolonging potentiation of MBγ\>M6 synapses over time periods that match short-term memory. These data support a model in which persistent aSP13 activity within a recurrent circuit lays the foundation for a short-term memory.

}, issn = {2050-084X}, doi = {10.7554/eLife.31425}, author = {Zhao, Xiaoliang and Lenek, Daniela and Dag, Ugur and Dickson, Barry and Keleman, Krystyna} } @article {49274, title = {Persistent sodium current mediates the steep voltage dependence of spatial coding in hippocampal pyramidal neurons.}, journal = {Neuron}, year = {2018}, month = {2018 Jun 05}, abstract = {

The mammalian hippocampus forms a cognitive map using neurons that fire according to an animal{\textquoteright}s position ("place cells") and many other behavioral and cognitive variables. The responses of these neurons are shaped by their presynaptic inputs and the nature of their postsynaptic integration. In CA1 pyramidal neurons, spatial responses in\ vivo exhibit a strikingly supralinear dependence on baseline membrane potential. The biophysical mechanisms underlying this nonlinear cellular computation are unknown. Here, through a combination of in\ vitro, in\ vivo, and in silico approaches, we show that persistent sodium current mediates the strong membrane potential dependence of place cell activity. This current operates at membrane potentials below the action potential threshold and over seconds-long timescales, mediating a powerful and rapidly reversible amplification of synaptic responses, which drives place cell firing. Thus, we identify a biophysical mechanism that shapes the coding properties of neurons composing the hippocampal cognitive map.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2018.05.025}, author = {Hsu, Ching-Lung and Zhao, Xinyu and Milstein, Aaron D and Spruston, Nelson} } @article {49121, title = {Photoactivatable drugs for nicotinic optopharmacology.}, journal = {Nature Methods}, volume = {15}, year = {2018}, month = {2018 Mar 26}, pages = {347-50}, abstract = {

Photoactivatable pharmacological agents have revolutionized neuroscience, but the palette of available compounds is limited. We describe a general method for caging tertiary amines by using a stable quaternary ammonium linkage that elicits a red shift in the activation wavelength. We prepared a photoactivatable nicotine (PA-Nic), uncageable via one- or two-photon excitation, that is useful to study nicotinic acetylcholine receptors (nAChRs) in different experimental preparations and spatiotemporal scales.

}, issn = {1548-7105}, doi = {10.1038/nmeth.4637}, author = {Banala, Sambashiva and Arvin, Matthew C and Bannon, Nicholas M and Jin, Xiao-Tao and Macklin, John J and Wang, Yong and Peng, Can and Zhao, Guiqing and Marshall, John J and Gee, Kyle R and Wokosin, David L and Kim, Veronica J and McIntosh, J Michael and Contractor, Anis and Lester, Henry A and Kozorovitskiy, Yevgenia and Drenan, Ryan M and Lavis, Luke D} } @article {49049, title = {Physical basis of amyloid fibril polymorphism.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Feb 16}, pages = {699}, abstract = {

Polymorphism is a key feature of amyloid fibril structures but it remains challenging to explain these variations for a particular sample. Here, we report electron cryomicroscopy-based reconstructions from different fibril morphologies formed by a peptide fragment from an amyloidogenic immunoglobulin light chain. The observed fibril morphologies vary in the number and cross-sectional arrangement of a structurally conserved building block. A comparison with the theoretically possible constellations reveals the experimentally observed spectrum of fibril morphologies to be governed by opposing sets of forces that primarily arise from the β-sheet twist, as well as peptide-peptide interactions within the fibril cross-section. Our results provide a framework for rationalizing and predicting the structure and polymorphism of cross-β fibrils, and suggest that a small number of physical parameters control the observed fibril architectures.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-03164-5}, author = {Close, William and Neumann, Matthias and Schmidt, Andreas and Hora, Manuel and Annamalai, Karthikeyan and Schmidt, Matthias and Reif, Bernd and Schmidt, Volker and Grigorieff, Nikolaus and F{\"a}ndrich, Marcus} } @conference {65885, title = {Point process latent variable models of larval zebrafish behavior}, booktitle = {NeurIPS}, year = {2018}, month = {12/2018}, abstract = {

A fundamental goal of systems neuroscience is to understand how neural activity gives rise to natural behavior. In order to achieve this goal, we must first build comprehensive models that offer quantitative descriptions of behavior. We develop a new class of probabilistic models to tackle this challenge in the study of larval zebrafish, an important model organism for neuroscience. Larval zebrafish locomote via sequences of punctate swim bouts--brief flicks of the tail--which are naturally modeled as a marked point process. However, these sequences of swim bouts belie a set of discrete and continuous internal states, latent variables that are not captured by standard point process models. We incorporate these variables as latent marks of a point process and explore various models for their dynamics. To infer the latent variables and fit the parameters of this model, we develop an amortized variational inference algorithm that targets the collapsed posterior distribution, analytically marginalizing out the discrete latent variables. With a dataset of over 120,000 swim bouts, we show that our models reveal interpretable discrete classes of swim bouts and continuous internal states like hunger that modulate their dynamics. These models are a major step toward understanding the natural behavioral program of the larval zebrafish and, ultimately, its neural underpinnings.

}, url = {http://papers.nips.cc/paper/8289-point-process-latent-variable-models-of-larval-zebrafish-behavior}, author = {Anuj Sharma and Robert Johnson and Florian Engert and Scott W. Linderman} } @article {49487, title = {A practical guide to adaptive light-sheet microscopy.}, journal = {Nature Protocols}, volume = {13}, year = {2018}, month = {2018 Oct 26}, pages = {2462{\textendash}2500}, abstract = {

We describe the implementation and use of an adaptive imaging framework for optimizing spatial resolution and signal strength in a light-sheet microscope. The framework, termed AutoPilot, comprises hardware and software modules for automatically measuring and compensating for mismatches between light-sheet and detection focal planes in living specimens. Our protocol enables researchers to introduce adaptive imaging capabilities in an existing light-sheet microscope or use our SiMView microscope blueprint to set up a new adaptive multiview light-sheet microscope. The protocol describes (i) the mechano-optical implementation of the adaptive imaging hardware, including technical drawings for all custom microscope components; (ii) the algorithms and software library for automated adaptive imaging, including the pseudocode and annotated source code for all software modules; and (iii) the execution of adaptive imaging experiments, as well as the configuration and practical use of the AutoPilot framework. Setup of the adaptive imaging hardware and software takes 1-2 weeks each. Previous experience with light-sheet microscopy and some familiarity with software engineering and building of optical instruments are recommended. Successful implementation of the protocol recovers near diffraction-limited performance in many parts of typical multicellular organisms studied with light-sheet microscopy, such as fruit fly and zebrafish embryos, for which resolution and signal strength are improved two- to fivefold.

}, issn = {1750-2799}, doi = {10.1038/s41596-018-0043-4}, author = {Royer, Lo{\"\i}c A and Lemon, William C and Chhetri, Raghav K and Keller, Philipp J} } @article {49012, title = {A preferred curvature-based continuum mechanics framework for modeling embryogenesis.}, journal = {Biophysical Journal}, volume = {114}, year = {2018}, month = {2018 Jan 23}, pages = {267-77}, abstract = {

Mechanics plays a key role in the development of higher organisms. However, understanding this relationship is complicated by the difficulty of modeling the link between local forces generated at the subcellular level and deformations observed at the tissue and whole-embryo levels. Here we propose an approach first developed for lipid bilayers and cell membranes, in which force-generation by cytoskeletal elements enters a continuum mechanics formulation for the full system in the form of local changes in preferred curvature. This allows us to express and solve the system using only tissue strains. Locations of preferred curvature are simply related to products of gene expression. A solution, in that context, means relaxing the system{\textquoteright}s mechanical energy to yield global morphogenetic predictions that accommodate a tendency toward the local preferred curvature, without a need to explicitly model force-generation mechanisms at the molecular level. Our computational framework, which we call SPHARM-MECH, extends a 3D spherical harmonics parameterization known as SPHARM to combine this level of abstraction with a sparse shape representation. The integration of these two principles allows computer simulations to be performed in three dimensions on highly complex shapes, gene expression patterns, and mechanical constraints. We demonstrate our approach by modeling mesoderm invagination in the fruit-fly embryo, where local forces generated by the acto-myosin meshwork in the region of the future mesoderm lead to formation of a ventral tissue fold. The process is accompanied by substantial changes in cell shape and long-range cell movements. Applying SPHARM-MECH to whole-embryo live imaging data acquired with light-sheet microscopy reveals significant correlation between calculated and observed tissue movements. Our analysis predicts the observed cell shape anisotropy on the ventral side of the embryo and suggests an active mechanical role of mesoderm invagination in supporting the onset of germ-band extension.

}, doi = {10.1016/j.bpj.2017.11.015}, author = {Khairy, Khaled and Lemon, William C and Amat, Fernando and Keller, Philipp J} } @article {65027, title = {Primed Conversion: The New Kid on the Block for Photoconversion.}, journal = {Chemistry}, volume = {24}, year = {2018}, month = {2018 Jun 12}, pages = {8268-8274}, abstract = {

In 2015, a novel way to convert photoconvertible fluorescent proteins was reported that uses the intercept of blue and far-red light instead of traditional violet or near-UV light illumination. This Minireview describes and contrasts this distinct two-step mechanism termed primed conversion with traditional photoconversion. We provide a comprehensive overview of what is known to date about primed conversion and focus on the molecular requirements for it to take place. We provide examples of its application to axially confined photoconversion in complex tissues as well as super-resolution microscopy. Further, we describe why and when it is useful, including its advantages and disadvantages, and give an insight into potential future development in the field.

}, issn = {1521-3765}, doi = {10.1002/chem.201705651}, author = {Mohr, Manuel Alexander and Pantazis, Periklis} } @article {49414, title = {Probing synaptic transmission and behavior in Drosophila with optogenetics: a laboratory exercise}, journal = {Journal of Undergraduate Neuroscience Education}, volume = {16}, year = {2018}, month = {2018 Summer}, pages = {A289-95}, abstract = {

Optogenetics is possibly the most revolutionary advance in neuroscience research techniques within the last decade. Here, we describe lab modules, presented at a workshop for undergraduate neuroscience educators, using optogenetic control of neurons in the fruit fly Drosophila melanogaster. Drosophila is a genetically accessible model system that combines behavioral and neurophysiological complexity, ease of use, and high research relevance. One lab module utilized two transgenic Drosophila strains, each activating specific circuits underlying startle behavior and backwards locomotion, respectively. The red-shifted channelrhodopsin, CsChrimson, was expressed in neurons sharing a common transcriptional profile, with the expression pattern further refined by the use of a Split GAL4 intersectional activation system. Another set of strains was used to investigate\ synaptic transmission at the larval neuromuscular junction. These expressed Channelrhodopsin 2 (ChR2) in glutamatergic neurons, including the motor neurons. The first strain expressed ChR2 in a wild type background, while the second contained the SNAP-25ts mutant allele, which confers heightened evoked potential amplitude and greatly increased spontaneous vesicle release frequency at the larval neuromuscular junction. These modules introduced educators and students to the use of optogenetic stimulation to control behavior and evoked release at a model synapse, and establish a basis for students to explore neurophysiology using this technique, through recapitulating classic experiments and conducting independent research.\ 

}, url = {http://www.funjournal.org/wp-content/uploads/2018/09/june-16-289.pdf?x91298}, author = {Vilinksy, Ilya and Hibbard, Karen L and Johnson Bruce R and Deitcher, David L} } @article {49122, title = {A proposed circuit computation in basal ganglia: History-dependent gain.}, journal = {Movement Disorders : official journal of the Movement Disorder Society}, year = {2018}, month = {2018 Mar 24}, abstract = {

In this Scientific Perspectives we first review the recent advances in our understanding of the functional architecture of basal ganglia circuits. Then we argue that these data can best be explained by a model in which basal ganglia act to control the gain of movement kinematics to shape performance based on prior experience, which we refer to as a history-dependent gain computation. Finally, we discuss how insights from the history-dependent gain model might translate from the bench to the bedside, primarily the implications for the design of adaptive deep brain stimulation. Thus, we explicate the key empirical and conceptual support for a normative, computational model with substantial explanatory power for the broad role of basal ganglia circuits in health and disease. {\textcopyright} 2018 The Authors. Movement Disorders published by Wiley Periodicals, Inc. on behalf of International Parkinson and Movement Disorder Society.

}, issn = {1531-8257}, doi = {10.1002/mds.27321}, author = {Yttri, Eric Allen and Dudman, Joshua Tate} } @article {68434, title = {Proximity labeling: spatially resolved proteomic mapping for neurobiology.}, journal = {Curr Opin Neurobiol}, volume = {50}, year = {2018}, month = {06/2018}, pages = {17-23}, abstract = {

Understanding signaling pathways in neuroscience requires high-resolution maps of the underlying protein networks. Proximity-dependent biotinylation with engineered enzymes, in combination with mass spectrometry-based quantitative proteomics, has emerged as a powerful method to dissect molecular interactions and the localizations of endogenous proteins. Recent applications to neuroscience have provided insights into the composition of sub-synaptic structures, including the synaptic cleft and inhibitory post-synaptic density. Here we compare the different enzymes and small-molecule probes for proximity labeling in the context of cultured neurons and tissue, review existing studies, and provide technical suggestions for the in vivo application of proximity labeling.

}, keywords = {Animals, Biotinylation, Humans, Neurobiology, Neuroimaging, Proteome, Proteomics}, issn = {1873-6882}, doi = {10.1016/j.conb.2017.10.015}, author = {Han, Shuo and Li, Jiefu and Ting, Alice Y} } @article {48941, title = {Reactive oxygen species regulate activity-dependent neuronal structural plasticity in Drosophila.}, journal = {eLife}, year = {2018}, month = {2018 Dec 12}, abstract = {

Neurons are inherently plastic, adjusting their structure, connectivity and excitability in response to changes in activity. How neurons sense changes in their activity level and then transduce these to structural changes remains to be fully elucidated. Working with the Drosophila larval locomotor network, we show that neurons use reactive oxygen species (ROS), metabolic byproducts, to monitor their activity. ROS signals are both necessary and sufficient for activity-dependent structural adjustments of both pre- and postsynaptic terminals and for network output, as measured by larval crawling behavior. We find the highly conserved Parkinsons disease-linked protein DJ-1b acts as a redox sensor in neurons where it regulates pre- and postsynaptic structural plasticity, in part via modulation of the PTEN-PI3Kinase pathway. Neuronal ROS thus play an important physiological role as second messengers required for neuronal and network tuning, whose dysregulation in the ageing brain and under neurodegenerative conditions may contribute to synaptic dysfunction.

}, doi = {10.7554/eLife.39393}, author = {Oswald, Matthew C W and Brooks, Paul S and Zwart, Maarten F and Mukherjee, Amrita and West, Ryan J H and Morarach, Khomgrit and Sweeney, Sean T and Landgraf, Matthias} } @article {49233, title = {Reinforcement signaling of punishment versus relief in fruit flies.}, journal = {Learning \& Memory (Cold Spring Harbor, N.Y.)}, volume = {25}, year = {2018}, month = {2018 Jun}, pages = {247-257}, abstract = {

Painful events establish opponent memories: cues that precede pain are remembered negatively, whereas cues that follow pain, thus coinciding with relief are recalled positively. How do individual reinforcement-signaling neurons contribute to this "timing-dependent valence-reversal?" We addressed this question using an optogenetic approach in the fruit fly. Two types of fly dopaminergic neuron, each comprising just one paired cell, indeed established learned avoidance of odors that preceded their photostimulation during training, and learned approach to odors that followed the photostimulation. This is in striking parallel to punishment versus relief memories reinforced by a real noxious event. For only one of these neuron types, both effects were strong enough for further analyses. Notably, interfering with dopamine biosynthesis in these neurons partially impaired the punishing effect, but not the relieving after-effect of their photostimulation. We discuss how this finding constraints existing computational models of punishment versus relief memories and introduce a new model, which also incorporates findings from mammals. Furthermore, whether using dopaminergic neuron photostimulation or a real noxious event, more prolonged punishment led to stronger relief. This parametric feature of relief may also apply to other animals and may explain particular aspects of related behavioral dysfunction in humans.

}, issn = {1549-5485}, doi = {10.1101/lm.047308.118}, author = {K{\"o}nig, Christian and Khalili, Afshin and Ganesan, Mathangi and Nishu, Amrita P and Garza, Alejandra P and Niewalda, Thomas and Gerber, Bertram and Aso, Yoshinori and Yarali, Ayse} } @article {49013, title = {Repetitive aggressive encounters generate a long-lasting internal state in Drosophila melanogaster males.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, year = {2018}, month = {2018 Jan 16}, pages = {1099-104}, abstract = {

Multiple studies have investigated the mechanisms of aggressive behavior in Drosophila; however, little is known about the effects of chronic fighting experience. Here, we investigated if repeated fighting encounters would induce an internal state that could affect the expression of subsequent behavior. We trained wild-type males to become winners or losers by repeatedly pairing them with hypoaggressive or hyperaggressive opponents, respectively. As described previously, we observed that chronic losers tend to lose subsequent fights, while chronic winners tend to win them. Olfactory conditioning experiments showed that winning is perceived as rewarding, while losing is perceived as aversive. Moreover, the effect of chronic fighting experience generalized to other behaviors, such as gap-crossing and courtship. We propose that in response to repeatedly winning or losing aggressive encounters, male flies form an internal state that displays persistence and generalization; fight outcomes can also have positive or negative valence. Furthermore, we show that the activities of the PPL1-γ1pedc dopaminergic neuron and the MBON-γ1pedc\>α/β mushroom body output neuron are required for aversion to an olfactory cue associated with losing fights.

}, issn = {1091-6490}, doi = {10.1073/pnas.1716612115}, author = {Kim, Yong-Kyu and Saver, Mathias and Simon, Jasper and Kent, Clement F and Shao, Lisha and Eddison, Mark and Agrawal, Pavan and Texada, Michael and Truman, James W and Heberlein, Ulrike} } @article {49497, title = {A resource for the antennal lobe provided by the connectome of glomerulus VA1v.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Nov 01}, abstract = {

Using FIB-SEM we report the entire synaptic connectome of glomerulus VA1v of the right antennal lobe in . Within the glomerulus we densely reconstructed all neurons, including hitherto elusive local interneurons. The -positive, sexually dimorphic VA1v included \>11,140 presynaptic sites with ~38,050 postsynaptic dendrites. These connected input olfactory receptor neurons (ORNs, 51 ipsilateral, 56 contralateral), output projection neurons (18 PNs), and local interneurons (56 of \>150 previously reported LNs). ORNs are predominantly presynaptic and PNs predominantly postsynaptic; newly reported LN circuits are largely an equal mixture and confer extensive synaptic reciprocity, except the newly reported LN2V with input from ORNs and outputs mostly to monoglomerular PNs, however. PNs were more numerous than previously reported from genetic screens, suggesting that the latter failed to reach saturation. We report a matrix of 192 bodies each having 50 connections; these form 88\% of the glomerulus{\textquoteright} pre/postsynaptic sites.

}, issn = {2050-084X}, doi = {10.7554/eLife.37550}, author = {Horne, Jane Anne and Langille, Carlie and McLin, Sari and Wiederman, Meagan and Lu, Zhiyuan and Xu, C Shan and Plaza, Stephen M and Scheffer, Louis K and Hess, Harald F and Meinertzhagen, Ian A} } @article {49060, title = {A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters.}, journal = {Nature Chemical Biology}, year = {2018}, month = {2018 Feb 26}, abstract = {

We developed a new way to engineer complex proteins toward multidimensional specifications using a simple, yet scalable, directed evolution strategy. By robotically picking mammalian cells that were identified, under a microscope, as expressing proteins that simultaneously exhibit several specific properties, we can screen hundreds of thousands of proteins in a library in just a few hours, evaluating each along multiple performance axes. To demonstrate the power of this approach, we created\ a genetically encoded fluorescent voltage indicator, simultaneously optimizing its\ brightness and membrane localization using our microscopy-guided cell-picking strategy. We produced the high-performance opsin-based fluorescent voltage reporter Archon1 and demonstrated its utility by imaging spiking and millivolt-scale subthreshold and synaptic activity in acute mouse brain slices and in larval zebrafish in vivo. We also measured postsynaptic responses downstream of optogenetically controlled neurons in C. elegans.

}, issn = {1552-4469}, doi = {10.1038/s41589-018-0004-9}, author = {Piatkevich, Kiryl D and Jung, Erica E and Straub, Christoph and Linghu, Changyang and Park, Demian and Suk, Ho-Jun and Hochbaum, Daniel R and Goodwin, Daniel and Pnevmatikakis, Eftychios and Pak, Nikita and Kawashima, Takashi and Yang, Chao-Tsung and Jeff L Rhoades and Shemesh, Or and Asano, Shoh and Yoon, Young-Gyu and Freifeld, Limor and Saulnier, Jessica L and Riegler, Clemens and Engert, Florian and Hughes, Thom and Drobizhev, Mikhail and Szabo, Balint and Ahrens, Misha B and Flavell, Steven W and Sabatini, Bernardo L and Boyden, Edward S} } @article {48997, title = {Robust model-based analysis of single-particle tracking experiments with Spot-On.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Jan 04}, abstract = {

Single-particle tracking (SPT) has become an important method to bridge biochemistry and cell biology since it allows direct observation of protein binding and diffusion dynamics in live cells. However, accurately inferring information from SPT studies is challenging due to biases in both data analysis and experimental design. To address analysis bias, we introduce {\textquoteright}Spot-On{\textquoteright}, an intuitive web-interface. Spot-On implements a kinetic modeling framework that accounts for known biases, including molecules moving out-of-focus, and robustly infers diffusion constants and subpopulations from pooled single-molecule trajectories. To minimize inherent experimental biases, we implement and validate stroboscopic photo-activation SPT (spaSPT), which minimizes motion-blur bias and tracking errors. We validate Spot-On using experimentally realistic simulations and show that Spot-On outperforms other methods. We then apply Spot-On to spaSPT data from live mammalian cells spanning a wide range of nuclear dynamics and demonstrate that Spot-On consistently and robustly infers subpopulation fractions and diffusion constants.

}, issn = {2050-084X}, doi = {10.7554/eLife.33125}, author = {Hansen, Anders S and Woringer, Maxime and Grimm, Jonathan B and Lavis, Luke D and Tjian, Robert and Darzacq, Xavier} } @article {49345, title = {Robustness of spike deconvolution for neuronal calcium imaging.}, journal = {The Journal of Neuroscience : the official journal of the Society for Neuroscience}, volume = {38}, year = {2018}, month = {2018 Aug 06}, pages = {7976-85}, abstract = {

Calcium imaging is a powerful method to record the activity of neural populations in many species, but inferring spike times from calcium signals is a challenging problem. We compared multiple approaches using multiple datasets with ground truth electrophysiology, and found that simple non-negative deconvolution (NND) outperformed all other algorithms on out-of-sample test data. We introduce a novel benchmark applicable to recordings without electrophysiological ground truth, based on the correlation of responses to two stimulus repeats, and used this to show that unconstrained NND also outperformed the other algorithms when run on "zoomed out" datasets of \~{}10,000 cell recordings from the visual cortex of mice of either sex. Finally, we show that NND-based methods match the performance of a supervised method based on convolutional neural networks, while avoiding some of the biases of such methods, and at much faster running times. We therefore recommend that spikes be inferred from calcium traces using simple NND, due to its simplicity, efficiency and accuracy.The experimental method that currently allows for recordings of the largest numbers of cells simultaneously is two-photon calcium imaging. However, use of this powerful method requires that neuronal firing times be inferred correctly from the large resulting datasets. Previous studies have claimed that complex supervised learning algorithms outperform simple deconvolution methods at this task. Unfortunately, these studies suffered from several problems and biases. When we repeated the analysis, using the same data and correcting these problems, we found that simpler spike inference methods perform better. Even more importantly, we found that supervised learning methods can introduce artifactual structure into spike trains, that can in turn lead to erroneous scientific conclusions. Of the algorithms we evaluated, we found that an extremely simple method performed best in all circumstances tested, was much faster to run, and was insensitive to parameter choices, making incorrect scientific conclusions much less likely.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3339-17.2018}, author = {Pachitariu, Marius and Stringer, Carsen and Harris, Kenneth D} } @article {48702, title = {The role of the serotonergic system in motor control.}, journal = {Neuroscience Research}, volume = {129}, year = {2018}, month = {2018 Apr}, pages = {32-9}, abstract = {

The serotonergic system in the vertebrate brain is implicated in various behaviors and diseases. Its involvement in motor control has been studied for over half a century, but efforts to build a unified model of its functions have been hampered due to the complexity of serotonergic neuromodulation. This review summarizes the anatomical structure of the serotonergic system, its afferent and efferent connections to other brain regions, and recent insights into the sensorimotor computations in the serotonergic system, and considers future research directions into the roles of serotonergic system in motor control.

}, doi = {10.1016/j.neures.2017.07.005}, author = {Kawashima, Takashi} } @article {68339, title = {The "sacral parasympathetic": ontogeny and anatomy of a myth.}, journal = {Clin Auton Res}, volume = {28}, year = {2018}, month = {2018 02}, pages = {13-21}, abstract = {

We recently defined genetic traits that distinguish sympathetic from parasympathetic neurons, both preganglionic and ganglionic (Espinosa-Medina et al., Science 354:893-897, 2016). By this set of criteria, we found that the sacral autonomic outflow is sympathetic, not parasympathetic as has been thought for more than a century. Proposing such a belated shift in perspective begs the question why the new criterion (cell types defined by their genetic make-up and dependencies) should be favored over the anatomical, physiological and pharmacological considerations of long ago that inspired the "parasympathetic" classification. After a brief reminder of the former, we expound the weaknesses of the latter and argue that the novel genetic definition helps integrating neglected anatomical and physiological observations and clearing the path for future research.

}, keywords = {Ganglia, Parasympathetic, Ganglia, Sympathetic, Humans, Sacrococcygeal Region, Spinal Cord}, issn = {1619-1560}, doi = {10.1007/s10286-017-0478-7}, author = {Espinosa-Medina, Isabel and Saha, Orthis and Boismoreau, Franck and Brunet, Jean-Fran{\c c}ois} } @article {49196, title = {Schaffer collateral inputs to CA1 excitatory and inhibitory neurons follow different connectivity rules.}, journal = {The Journal of Neuroscience : the official journal of the Society for Neuroscience}, volume = {38}, year = {2018}, month = {2018 May 04}, pages = {5140-52}, abstract = {

Neural circuits, governed by a complex interplay between excitatory and inhibitory neurons, are the substrate for information processing, and the organization of synaptic connectivity in neural network is an important determinant of circuit function. Here, we analyzed the fine structure of connectivity in hippocampal CA1 excitatory and inhibitory neurons innervated by Schaffer collaterals (SCs) using mGRASP in male mice. Our previous study revealed spatially structured synaptic connectivity between CA3-CA1 pyramidal cells (PCs). Surprisingly, parvalbumin-positive interneurons (PVs) showed a significantly more random pattern spatial structure. Notably, application of Peters{\textquoteright} Rule for synapse prediction by random overlap between axons and dendrites enhanced structured connectivity in PCs, but, by contrast, made the connectivity pattern in PVs more random. In addition, PCs in a deep sublayer of striatum pyramidale appeared more highly structured than PCs in superficial layers, and little or no sublayer specificity was found in PVs. Our results show that CA1 excitatory PCs and inhibitory PVs innervated by the same SC inputs follow different connectivity rules. The different organizations of fine scale structured connectivity in hippocampal excitatory and inhibitory neurons provide important insights into the development and functions of neural networks.Understanding how neural circuits generate behavior is one of the central goals of neuroscience. An important component of this endeavor is the mapping of fine-scale connection patterns that underlie, and help us infer, signal processing in the brain. Here, using our recently developed synapse detection technology (mGRASP and neuTube), we provide detailed profiles of synaptic connectivity in excitatory (CA1 pyramidal) and inhibitory (CA1 parvalbumin-positive) neurons innervated by the same presynaptic inputs (CA3 Schaffer collaterals). Our results reveal that these two types of CA1 neurons follow different connectivity patterns. Our new evidence for differently structured connectivity at a fine scale in hippocampal excitatory and inhibitory neurons provides a better understanding of hippocampal networks and will guide theoretical and experimental studies.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0155-18.2018}, author = {Kwon, Osung and Feng, Linqing and Druckmann, Shaul and Kim, Jinhyun} } @article {49258, title = {Science holds the key to unlocking economic success.}, year = {2018}, month = {2018 Jun 07}, abstract = {
The 2008 crisis should have led us to reshape how our economy works. But a decade on, what has really changed? The public knows that the same attitude that got us into the previous economic crisis will not bring us long-term prosperity, yet there is little vision from our leaders of what the future should look like. Our politicians are sleeping, yet have no dreams. To solve this, we must change emphasis from creating {\textquotedblleft}growth{\textquotedblright} to creating the future: the former is an inevitable product of the latter.
}, url = {https://www.telegraph.co.uk/business/2018/06/07/science-holds-key-unlocking-economic-success/}, author = {Phillips, James and Phillips, Matthew} } @article {49523, title = {Sensorimotor pathway controlling stopping behavior during chemotaxis in the larva.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Nov 22}, abstract = {

Sensory navigation results from coordinated transitions between distinct behavioral programs. During chemotaxis in the larva, the detection of positive odor gradients extends runs while negative gradients promote stops and turns. This algorithm represents a foundation for the control of sensory navigation across phyla. In the present work, we identified an olfactory descending neuron, PDM-DN, which plays a pivotal role in the organization of stops and turns in response to the detection of graded changes in odor concentrations. Artificial activation of this descending neuron induces deterministic stops followed by the initiation of turning maneuvers through head casts. Using electron microscopy, we reconstructed the main pathway that connects the PDM-DN neuron to the peripheral olfactory system and to the pre-motor circuit responsible for the actuation of forward peristalsis. Our results set the stage for a detailed mechanistic analysis of the sensorimotor conversion of graded olfactory inputs into action selection to perform goal-oriented navigation.

}, issn = {2050-084X}, doi = {10.7554/eLife.38740}, author = {Tastekin, Ibrahim and Khandelwal, Avinash and Tadres, David and Fessner, Nico D and Truman, James W and Zlatic, Marta and Cardona, Albert and Louis, Matthieu} } @article {64999, title = {A sequence-based approach for identifying protein fold switchers.}, journal = {bioRxiv}, year = {2018}, month = {2018 Nov 05}, abstract = {

Although most proteins conform to the classical one-structure/one-function paradigm, an increasing number of proteins with dual structures and functions are emerging. These fold-switching proteins remodel their secondary structures in response to cellular stimuli, fostering multi-functionality and tight cellular control. Accurate predictions of fold-switching proteins could both suggest underlying mechanisms for uncharacterized biological processes and reveal potential drug targets. Previously, we developed a prediction method for fold-switching proteins based on secondary structure predictions and structure-based thermodynamic calculations. Given the large number of genomic sequences without homologous experimentally characterized structures, however, we sought to predict fold-switching proteins from their sequences alone. To do this, we leveraged state-of-the-art secondary structure predictions, which require only amino acid sequences but are not currently designed to identify structural duality in proteins. Thus, we hypothesized that incorrect and inconsistent secondary structure predictions could be good initial predictors of fold-switching proteins. We found that secondary structure predictions of fold-switching proteins with solved structures are indeed less accurate than secondary structure predictions of non-fold-switching proteins with solved structures. These inaccuracies result largely from the conformations of fold-switching proteins that are underrepresented in the Protein Data Bank (PDB), and, consequently, the training sets of secondary structure predictors. Given that secondary structure predictions are homology-based, we hypothesized that decontextualizing the inaccurately-predicted regions of fold-switching proteins could weaken the homology relationships between these regions and their overpopulated structural representatives. Thus, we reran secondary structure predictions on these regions in isolation and found that they were significantly more inconsistent than in regions of non-fold-switching proteins. Thus, inconsistent secondary structure predictions can serve as a preliminary marker of fold switching. These findings have implications for genomics and the future development of secondary structure predictors.

}, doi = {10.1101/462606}, author = {Soumya Mishra and Loren L. Looger and Lauren L. Porter} } @article {49404, title = {Severing enzymes amplify microtubule arrays through lattice GTP-tubulin incorporation.}, journal = {Science (New York, N.Y.)}, volume = {361}, year = {2018}, month = {2018 Aug 24}, abstract = {

Spastin and katanin sever and destabilize microtubules. Paradoxically, despite their destructive activity they increase microtubule mass in vivo. We combined single-molecule total internal reflection fluorescence microscopy and electron microscopy to show that the elemental step in microtubule severing is the generation of nanoscale damage throughout the microtubule by active extraction of tubulin heterodimers. These damage sites are repaired spontaneously by guanosine triphosphate (GTP)-tubulin incorporation, which rejuvenates and stabilizes the microtubule shaft. Consequently, spastin and katanin increase microtubule rescue rates. Furthermore, newly severed ends emerge with a high density of GTP-tubulin that protects them against depolymerization. The stabilization of the newly severed plus ends and the higher rescue frequency synergize to amplify microtubule number and mass. Thus, severing enzymes regulate microtubule architecture and dynamics by promoting GTP-tubulin incorporation within the microtubule shaft.

}, issn = {1095-9203}, doi = {10.1126/science.aau1504}, author = {Vemu, Annapurna and Szczesna, Ewa and Zehr, Elena A and Spector, Jeffrey O and Grigorieff, Nikolaus and Deaconescu, Alexandra M and Roll-Mecak, Antonina} } @article {49495, title = {Shared and distinct transcriptomic cell types across neocortical areas.}, journal = {Nature}, volume = {563}, year = {2018}, month = {2018 Nov}, pages = {72-78}, abstract = {

The neocortex contains a multitude of cell types that are segregated into layers and functionally distinct areas. To investigate the diversity of cell types across the mouse neocortex, here we analysed 23,822 cells from two areas at distant poles of the mouse neocortex: the primary visual cortex and the anterior lateral motor cortex. We define 133 transcriptomic cell types by deep, single-cell RNA sequencing. Nearly all types of GABA (γ-aminobutyric acid)-containing neurons are shared across both areas, whereas most types of glutamatergic neurons were found in one of the two areas. By combining single-cell RNA sequencing and retrograde labelling, we match transcriptomic types of glutamatergic neurons to their long-range projection specificity. Our study establishes a combined transcriptomic and projectional taxonomy of cortical cell types from functionally distinct areas of the adult mouse cortex.

}, issn = {1476-4687}, doi = {10.1038/s41586-018-0654-5}, author = {Tasic, Bosiljka and Yao, Zizhen and Graybuck, Lucas T and Smith, Kimberly A and Nguyen, Thuc Nghi and Bertagnolli, Darren and Goldy, Jeff and Garren, Emma and Economo, Michael N and Viswanathan, Sarada and Penn, Osnat and Bakken, Trygve and Menon, Vilas and Miller, Jeremy and Fong, Olivia and Hirokawa, Karla E and Lathia, Kanan and Rimorin, Christine and Tieu, Michael and Larsen, Rachael and Casper, Tamara and Barkan, Eliza and Kroll, Matthew and Parry, Sheana and Shapovalova, Nadiya V and Hirschstein, Daniel and Pendergraft, Julie and Sullivan, Heather A and Kim, Tae Kyung and Szafer, Aaron and Dee, Nick and Groblewski, Peter and Wickersham, Ian and Cetin, Ali and Harris, Julie A and Levi, Boaz P and Sunkin, Susan M and Madisen, Linda and Daigle, Tanya L and Looger, Loren and Bernard, Amy and Phillips, John and Lein, Ed and Hawrylycz, Michael and Svoboda, Karel and Jones, Allan R and Koch, Christof and Zeng, Hongkui} } @article {48998, title = {Simple integration of fast excitation and offset, delayed inhibition computes directional selectivity in Drosophila.}, journal = {Nature Neuroscience}, volume = {21}, year = {2018}, month = {2018 Jan 08}, pages = {250-7}, abstract = {

A neuron that extracts directionally selective motion information from upstream signals lacking this selectivity must compare visual responses from spatially offset inputs. Distinguishing among prevailing algorithmic models for this computation requires measuring fast neuronal activity and inhibition. In the Drosophila melanogaster visual system, a fourth-order neuron-T4-is the first cell type in the ON pathway to exhibit directionally selective signals. Here we use in vivo whole-cell recordings of T4 to show that directional selectivity originates from simple integration of spatially offset fast excitatory and slow inhibitory inputs, resulting in a suppression of responses to the nonpreferred motion direction. We constructed a passive, conductance-based model of a T4 cell that accurately predicts the neuron{\textquoteright}s response to moving stimuli. These results connect the known circuit anatomy of the motion pathway to the algorithmic mechanism by which the direction of motion is computed.

}, issn = {1546-1726}, doi = {10.1038/s41593-017-0046-4}, author = {Gruntman, Eyal and Romani, Sandro and Reiser, Michael B} } @article {49046, title = {Single excitatory axons form clustered synapses onto CA1 pyramidal cell dendrites.}, journal = {Nature Neuroscience}, volume = {21}, year = {2018}, month = {2018 Mar}, pages = {353-63}, abstract = {

CA1 pyramidal neurons are a major output of the hippocampus and encode features of experience that constitute episodic memories. Feature-selective firing of these neurons results from the dendritic integration of inputs from multiple brain regions. While it is known that synchronous activation of spatially clustered inputs can contribute to firing through the generation of dendritic spikes, there is no established mechanism for spatiotemporal synaptic clustering. Here we show that single presynaptic axons form multiple, spatially clustered inputs onto the distal, but not proximal, dendrites of CA1 pyramidal neurons. These compound connections exhibit ultrastructural features indicative of strong synapses and occur much more commonly in entorhinal than in thalamic afferents. Computational simulations revealed that compound connections depolarize dendrites in a biophysically efficient manner, owing to their inherent spatiotemporal clustering. Our results suggest that distinct afferent projections use different connectivity motifs that differentially contribute to dendritic integration.

}, doi = {10.1038/s41593-018-0084-6}, author = {Bloss, Erik B and Cembrowski, Mark S and Karsh, Bill and Colonell, Jennifer and Fetter, Richard D and Spruston, Nelson} } @article {49221, title = {Single molecule fate of HIV-1 envelope reveals late-stage viral lattice incorporation.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 May 10}, pages = {1861}, abstract = {

Human immunodeficiency virus type 1 (HIV-1) assembly occurs on the inner leaflet of the host cell plasma membrane, incorporating the essential viral envelope glycoprotein (Env) within a budding lattice of HIV-1 Gag structural proteins. The mechanism by which Env incorporates into viral particles remains poorly understood. To determine the mechanism of recruitment of Env to assembly sites, we interrogate the subviral angular distribution of Env on cell-associated virus using multicolor, three-dimensional (3D) superresolution microscopy. We demonstrate that, in a manner dependent on cell type and on the long cytoplasmic tail of Env, the distribution of Env is biased toward the necks of cell-associated particles. We postulate that this neck-biased distribution is regulated by vesicular retention and steric complementarity of Env during independent Gag lattice formation.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-04220-w}, author = {Buttler, Carmen A and Pezeshkian, Nairi and Fernandez, Melissa V and Aaron, Jesse and Norman, Sofya and Freed, Eric O and Van Engelenburg, Schuyler B} } @article {68756, title = {Single Molecule RNA FISH (smFISH) in Whole-Mount Mouse Embryonic Organs}, journal = {Current Protocols in Cell Biology}, volume = {83}, year = {2018}, month = {11/2018}, pages = {e79}, abstract = {

Abstract Single molecule RNA fluorescence in situ hybridization (smFISH) has become the standard tool for high spatial resolution analysis of gene expression in the context of tissue organization. This article describes protocols to perform smFISH on whole-mount mouse embryonic organs, where tissue organization can be compared to RNA expression by co-immunostaining of known protein markers. An enzymatic labeling strategy is also introduced to produce low-cost smFISH probes. Important considerations and practical guidelines for imaging smFISH samples using fluorescence confocal microscopy are described. Finally, a suite of custom-written ImageJ macros is included with detailed instructions to enable semi-automated smFISH image analysis of both 2D and 3D images. {\textcopyright} 2018 by John Wiley \& Sons, Inc.

}, keywords = {co-immunostaining, enzymatic probe labeling, ImageJ macro quantification, smFISH}, doi = {https://doi.org/10.1002/cpcb.79}, url = {https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpcb.79}, author = {Wang, Shaohe} } @article {49485, title = {Social isolation-induced epigenetic and transcriptional changes in Drosophila dopaminergic neurons.}, journal = {bioRxiv}, year = {2018}, month = {2018 Oct 14}, abstract = {Epigenetic mechanisms play fundamental roles in brain function and behavior and stressors such as social isolation can alter animal behavior via epigenetic mechanisms. However, due to cellular heterogeneity, identifying cell-type-specific epigenetic changes in the brain is challenging. Here we report first use of a modified INTACT method in behavioral epigenetics of Drosophila: a method we call mini-INTACT. Using ChIP-seq on mini-INTACT purified dopaminergic nuclei, we identified epigenetic signatures in socially-isolated and socially-enriched Drosophila males. Social experience altered the epigenetic landscape in clusters of genes involved in transcription and neural function. Some of these alterations were predicted by expression changes of four transcription factors and the prevalence of their binding sites in several clusters. These transcription factors were previously identified as activity-regulated genes and their knockdown in dopaminergic neurons reduced the effects of social experience on sleep. Our work enables the use of Drosophila as a model for cell-type-specific behavioral epigenetics. }, doi = {10.1101/443226}, author = {Agrawal, Pavan and Chung, Phuong and Heberlein, Ulrike and Kent, Clement F} } @article {67288, title = {Specialized and spatially organized coding of sensory, motor, and cognitive variables in midbrain dopamine neurons}, journal = {bioRxiv}, year = {2018}, month = {10/2018}, abstract = {

There is increased appreciation that dopamine (DA) neurons in the midbrain respond not only to reward 1,2 and reward-predicting cues 1,3,4, but also to other variables such as distance to reward 5, movements 6{\textendash}11 and behavioral choices 12{\textendash}15. Based on these findings, a major open question is how the responses to these diverse variables are organized across the population of DA neurons. In other words, do individual DA neurons multiplex multiple variables, or are subsets of neurons specialized in encoding specific behavioral variables? The reason that this fundamental question has been difficult to resolve is that recordings from large populations of individual DA neurons have not been performed in a behavioral task with sufficient complexity to examine these diverse variables simultaneously. To address this gap, we used 2-photon calcium imaging through an implanted lens to record activity of \>300 midbrain DA neurons in the VTA during a complex decision-making task. As mice navigated in a virtual reality (VR) environment, DA neurons encoded an array of sensory, motor, and cognitive variables. These responses were functionally clustered, such that subpopulations of neurons transmitted information about a subset of behavioral variables, in addition to encoding reward. These functional clusters were spatially organized, such that neighboring neurons were more likely to be part of the same cluster. Taken together with the topography between DA neurons and their projections, this specialization and anatomical organization may aid downstream circuits in correctly interpreting the wide range of signals transmitted by DA neurons.

}, doi = {10.1101/456194}, url = {https://www.biorxiv.org/content/early/2018/10/29/456194}, author = {Engelhard, Ben and Finkelstein, Joel and Cox, Julia and Fleming, Weston and Jang, Hee Jae and Ornelas, Sharon and Koay, Sue Ann and Thiberge, Stephan and Daw, Nathaniel and Tank, David W. and Witten, Ilana B.} } @article {49418, title = {Speed dependent descending control of freezing behavior in Drosophila melanogaster.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Sep 12}, pages = {3697}, abstract = {

The most fundamental choice an animal has to make when it detects a threat is whether to freeze, reducing its chances of being noticed, or to flee to safety. Here we show that Drosophila melanogaster exposed to looming stimuli in a confined arena either freeze or flee. The probability of freezing versus fleeing is modulated by the fly{\textquoteright}s walking speed at the time of threat, demonstrating that freeze/flee decisions depend on behavioral state. We describe a pair of descending neurons crucially implicated in freezing. Genetic silencing of DNp09 descending neurons disrupts freezing yet does not prevent fleeing. Optogenetic activation of both DNp09 neurons induces running and freezing in a state-dependent manner. Our findings establish walking speed as a key factor in defensive response choices and reveal a pair of descending neurons as a critical component in the circuitry mediating selection and execution of freezing or fleeing behaviors.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-05875-1}, author = {Zacarias, Ricardo and Namiki, Shigehiro and Card, Gwyneth M and Vasconcelos, Maria Lu{\'\i}sa and Moita, Marta A} } @article {48984, title = {Stability, affinity and chromatic variants of the glutamate sensor iGluSnFR.}, journal = {Nature Methods}, volume = {15}, year = {2018}, month = {2018 Nov}, pages = {9386-9}, abstract = {

Single-wavelength fluorescent reporters allow visualization of specific neurotransmitters with high spatial and temporal resolution. We report variants of intensity-based glutamate-sensing fluorescent reporter (iGluSnFR) that are functionally brighter; detect submicromolar to millimolar amounts of glutamate; and have blue, cyan, green, or yellow emission profiles. These variants could be imaged in vivo in cases where original iGluSnFR was too dim, resolved glutamate transients in dendritic spines and axonal boutons, and allowed imaging at kilohertz rates.

}, doi = {10.1038/s41592-018-0171-3}, author = {Marvin, Jonathan S and Scholl, Benjamin and Wilson, Daniel E and Podgorski, Kaspar and Kazemipour, Abbas and Mueller, Johannes Alexander and Schoch-McGovern, Susanne and Wang, Samuel S-H and Quiroz, Francisco Jose Urra and Rebola, Nelson and Bao, Huan and Little, Justin P and Tkachuk, Ariana N and Hantman, Adam W and Chapman, Edwin R and Dietrich, Dirk and DiGregorio, David A and Fitzpatrick, David and Looger, Loren L} } @article {49584, title = {Stem cells repurpose proliferation to contain a breach in their niche barrier.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Dec 06}, abstract = {

Adult stem cells are responsible for life-long tissue maintenance. They reside in and interact with specialized tissue microenvironments (niches). Using murine hair follicle as a model, we show that when junctional perturbations in the niche disrupt barrier function, adjacent stem cells dramatically change their transcriptome independent of bacterial invasion and become capable of directly signaling to and recruiting immune cells. Additionally, these stem cells elevate cell cycle transcripts which reduce their quiescence threshold, enabling them to selectively proliferate within this microenvironment of immune distress cues. However, rather than mobilizing to fuel new tissue regeneration, these ectopically proliferative stem cells remain within their niche to contain the breach. Together, our findings expose a potential communication relay system that operates from the niche to the stem cells to the immune system and back. The repurposing of proliferation by these stem cells patch the breached barrier, stoke the immune response and restore niche integrity.

}, issn = {2050-084X}, doi = {10.7554/eLife.41661}, author = {Lay, Kenneth and Yuan, Shaopeng and Gur-Cohen, Shiri and Miao, Yuxuan and Han, Tianxiao and Naik, Shruti and Pasolli, H Amalia and Larsen, Samantha B and Fuchs, Elaine} } @article {68432, title = { Stepwise wiring of the Drosophila olfactory map requires specific Plexin B levels}, journal = {Elife}, volume = {7}, year = {2018}, month = {08/2018}, abstract = {

The precise assembly of a neural circuit involves many consecutive steps. The conflict between a limited number of wiring molecules and the complexity of the neural network impels each molecule to execute multiple functions at different steps. Here, we examined the cell-type specific distribution of endogenous levels of axon guidance receptor Plexin B (PlexB) in the developing antennal lobe, the first olfactory processing center in . We found that different classes of olfactory receptor neurons (ORNs) express PlexB at different levels in two wiring steps - axonal trajectory choice and subsequent target selection. In line with its temporally distinct patterns, the proper levels of PlexB control both steps in succession. Genetic interactions further revealed that the effect of high-level PlexB is antagonized by its canonical partner Sema2b. Thus, PlexB plays a multifaceted role in instructing the assembly of the olfactory circuit through temporally-regulated expression patterns and expression level-dependent effects.

}, keywords = {Animals, Arthropod Antennae, Axons, Drosophila melanogaster, Drosophila Proteins, Models, Biological, Nerve Tissue Proteins, Olfactory Receptor Neurons, Receptors, Cell Surface, Smell}, issn = {2050-084X}, doi = {10.7554/eLife.39088}, author = {Li, Jiefu and Guajardo, Ricardo and Xu, Chuanyun and Wu, Bing and Li, Hongjie and Li, Tongchao and Luginbuhl, David J and Xie, Xiaojun and Luo, Liqun} } @article {49448, title = {Strength of correlations in strongly recurrent neuronal networks.}, journal = {Physical Review X}, year = {2018}, month = {2018 Sep 17}, pages = {031072}, abstract = {

Spatiotemporal correlations in brain activity are functionally important and have been implicated in perception, learning and plasticity, exploratory behavior, and various aspects of cognition. Neurons in the cerebral cortex are strongly interacting. Their activity is temporally irregular and can exhibit substantial correlations. However, how the collective dynamics of highly recurrent and strongly interacting neurons can evolve into a state in which the activity of individual cells is highly irregular yet macroscopically correlated is an open question. Here, we develop a general theory that relates the strength of pairwise correlations to the anatomical features of networks of strongly coupled neurons. To this end, we investigate networks of binary units. When interactions are strong, the activity is irregular in a large region of parameter space. We find that despite the strong interactions, the correlations are generally very weak. Nevertheless, we identify architectural features, which if present, give rise to strong correlations without destroying the irregularity of the activity. For networks with such features, we determine how correlations scale with the network size and the number of connections. Our work shows the mechanism by which strong correlations can be consistent with highly irregular activity, two hallmarks of neuronal dynamics in the central nervous system.

}, doi = {10.1103/PhysRevX.8.031072}, author = {Darshan, Ran and van Vreeswijk, Carl and Hansel, David} } @article {49152, title = {Structural mechanism of functional modulation by gene splicing in NMDA receptors.}, journal = {Neuron}, volume = {98}, year = {2018}, month = {2018 Apr 10}, pages = {521-9}, abstract = {

Alternative gene splicing gives rise to N-methyl-D-aspartate (NMDA) receptor ion channels with defined functional properties and unique contributions to calcium signaling in a given chemical environment in the mammalian brain. Splice variants possessing the exon-5-encoded motif at the amino-terminal domain (ATD) of the GluN1 subunit are known to display robustly altered deactivation rates and pH sensitivity, but the underlying mechanism for this functional modification is largely unknown. Here, we show through cryoelectron microscopy (cryo-EM) that the presence of the exon 5 motif in GluN1 alters the local architecture of heterotetrameric GluN1-GluN2 NMDA receptors and creates contacts with the ligand-binding domains (LBDs) of the GluN1 and GluN2 subunits, which are absent in NMDA receptors lacking the exon 5 motif. The unique interactions established by the exon 5 motif are essential to the stability of the ATD/LBD and LBD/LBD interfaces that are critically involved in controlling proton sensitivity and deactivation.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2018.03.034}, author = {Regan, Michael C and Grant, Timothy and McDaniel, Miranda J and Karakas, Erkan and Zhang, Jing and Traynelis, Stephen F and Grigorieff, Nikolaus and Furukawa, Hiro} } @article {49057, title = {Structure of full-length human TRPM4.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, year = {2018}, month = {2018 Feb 20}, pages = {2377-82}, abstract = {

Transient receptor potential melastatin subfamily member 4 (TRPM4) is a widely distributed, calcium-activated, monovalent-selective cation channel. Mutations in human TRPM4 (hTRPM4) result in progressive familial heart block. Here, we report the electron cryomicroscopy structure of hTRPM4 in a closed, Na-bound, apo state at pH 7.5 to an overall resolution of 3.7 {\r A}. Five partially hydrated sodium ions are proposed to occupy the center of the conduction pore and the entrance to the coiled-coil domain. We identify an upper gate in the selectivity filter and a lower gate at the entrance to the cytoplasmic coiled-coil domain. Intramolecular interactions exist between the TRP domain and the S4-S5 linker, N-terminal domain, and N and C termini. Finally, we identify aromatic interactions via π-π bonds and cation-π bonds, glycosylation at an N-linked extracellular site, a pore-loop disulfide bond, and 24 lipid binding sites. We compare and contrast this structure with other TRP channels and discuss potential mechanisms of regulation and gating of human full-length TRPM4.

}, issn = {1091-6490}, doi = {10.1073/pnas.1722038115}, author = {Duan, Jingjing and Li, Zongli and Li, Jian and Santa-Cruz, Ana and Sanchez-Martinez, Silvia and Zhang, Jin and Clapham, David E} } @article {49574, title = {Structure of Plasmodium falciparum Rh5-CyRPA-Ripr invasion complex.}, journal = {Nature}, volume = {565}, year = {2018}, month = {2018 Dec 12}, pages = {118-21}, abstract = {

Plasmodium falciparum causes the severe form of malaria that has high levels of mortality in humans. Blood-stage merozoites of P. falciparum invade erythrocytes, and this requires interactions between multiple ligands from the parasite and receptors in hosts. These interactions include the binding of the Rh5-CyRPA-Ripr complex with the erythrocyte receptor basigin, which is an essential step for entry into human erythrocytes. Here we show that the Rh5-CyRPA-Ripr complex binds the erythrocyte cell line JK-1 significantly better than does Rh5 alone, and that this binding occurs through the insertion of Rh5 and Ripr into host membranes as a complex with high molecular weight. We report a cryo-electron microscopy structure of the Rh5-CyRPA-Ripr complex at subnanometre resolution, which reveals the organization of this essential invasion complex and the mode of interactions between members of the complex, and shows that CyRPA is a critical mediator of complex assembly. Our structure identifies blades 4-6 of the β-propeller of CyRPA as contact sites for Rh5 and Ripr. The limited contacts between Rh5-CyRPA and CyRPA-Ripr are consistent with the dissociation of Rh5 and Ripr from CyRPA for membrane insertion. A comparision of the crystal structure of Rh5-basigin with the cryo-electron microscopy structure of Rh5-CyRPA-Ripr suggests that Rh5 and Ripr are positioned parallel to the erythrocyte membrane before membrane insertion. This provides information on the function of this complex, and thereby provides insights into invasion by P. falciparum.

}, issn = {1476-4687}, doi = {10.1038/s41586-018-0779-6}, author = {Wong, Wilson and Huang, Rick and Menant, S{\'e}bastien and Hong, Chuan and Sandow, Jarrod J and Birkinshaw, Richard W and Healer, Julie and Hodder, Anthony N and Kanjee, Usheer and Tonkin, Christopher J and Heckmann, Denise and Soroka, Vladislav and S{\o}gaard, Teit Max Moscote and J{\o}rgensen, Thomas and Duraisingh, Manoj T and Czabotar, Peter E and de Jongh, Willem A and Tham, Wai-Hong and Webb, Andrew I and Yu, Zhiheng and Cowman, Alan F} } @article {49371, title = {Structure of the mammalian TRPM7, a magnesium channel required during embryonic development.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, year = {2018}, month = {2018 Aug 14}, pages = {E8201-10}, abstract = {

The transient receptor potential ion channel subfamily M, member 7 (TRPM7), is a ubiquitously expressed protein that is required for mouse embryonic development. TRPM7 contains both an ion channel and an α-kinase. The channel domain comprises a nonselective cation channel with notable permeability to Mg and Zn Here, we report the closed state structures of the mouse TRPM7 channel domain in three different ionic conditions to overall resolutions of 3.3, 3.7, and 4.1 {\r A}. The structures reveal key residues for an ion binding site in the selectivity filter, with proposed partially hydrated Mg ions occupying the center of the conduction pore. In high [Mg], a prominent external disulfide bond is found in the pore helix, which is essential for ion channel function. Our results provide a structural framework for understanding the TRPM1/3/6/7 subfamily and extend the knowledge base upon which to study the diversity and evolution of TRP channels.

}, issn = {1091-6490}, doi = {10.1073/pnas.1810719115}, author = {Duan, Jingjing and Li, Zongli and Li, Jian and Hulse, Raymond E and Santa-Cruz, Ana and Valinsky, William C and Abiria, Sunday A and Krapivinsky, Grigory and Zhang, Jin and Clapham, David E} } @article {49344, title = {Structure of the mouse TRPC4 ion channel.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Aug 06}, pages = {3102}, abstract = {

Members of the transient receptor potential (TRP) ion channels conduct cations into cells. They mediate functions ranging from neuronally mediated hot and cold sensation to intracellular organellar and primary ciliary signaling. Here we report a cryo-electron microscopy (cryo-EM) structure of TRPC4 in its unliganded (apo) state to an overall resolution of 3.3 {\r A}. The structure reveals a unique architecture with a long pore loop stabilized by a disulfide bond. Beyond the shared tetrameric six-transmembrane fold, the TRPC4 structure deviates from other TRP channels with a unique cytosolic domain. This unique cytosolic N-terminal domain forms extensive aromatic contacts with the TRP and the C-terminal domains. The comparison of our structure with other known TRP structures provides molecular insights into TRPC4 ion selectivity and extends our knowledge of the diversity and evolution of the TRP channels.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-05247-9}, author = {Duan, Jingjing and Li, Jian and Zeng, Bo and Chen, Gui-Lan and Peng, Xiaogang and Zhang, Yixing and Wang, Jianbin and Clapham, David E and Li, Zongli and Zhang, Jin} } @article {49014, title = {Structure-based inhibitors of tau aggregation.}, journal = {Nature Chemistry}, volume = {10}, year = {2018}, month = {2018 Feb}, pages = {170-176}, abstract = {

Aggregated tau protein is associated with over 20 neurological disorders, which include Alzheimer{\textquoteright}s disease. Previous work has shown that tau{\textquoteright}s sequence segments VQIINK and VQIVYK drive its aggregation, but inhibitors based on the structure of the VQIVYK segment only partially inhibit full-length tau aggregation and are ineffective at inhibiting seeding by full-length fibrils. Here we show that the VQIINK segment is the more powerful driver of tau aggregation. Two structures of this segment determined by the cryo-electron microscopy method micro-electron diffraction explain its dominant influence on tau aggregation. Of practical significance, the structures lead to the design of inhibitors that not only inhibit tau aggregation but also inhibit the ability of exogenous full-length tau fibrils to seed intracellular tau in HEK293 biosensor cells into amyloid. We also raise the possibility that the two VQIINK structures represent amyloid polymorphs of tau that may account for a subset of prion-like strains of tau.

}, issn = {1755-4349}, doi = {10.1038/nchem.2889}, author = {Seidler, P M and Boyer, D R and Rodriguez, J A and Sawaya, M R and Cascio, D and Murray, K and Gonen, T and Eisenberg, D S} } @article {49006, title = {Sub-{\r a}ngstr{\"o}m cryo-EM structure of a prion protofibril reveals a polar clasp.}, journal = {Nature Structural \& Molecular Biology}, year = {2018}, month = {2018 Jan 15}, abstract = {

The atomic structure of the infectious, protease-resistant, β-sheet-rich and fibrillar mammalian prion remains unknown. Through the cryo-EM method MicroED, we reveal the sub-{\r a}ngstr{\"o}m-resolution structure of a protofibril formed by a wild-type segment from the β2-α2 loop of the bank vole prion protein. The structure of this protofibril reveals a stabilizing network of hydrogen bonds that link polar zippers within a sheet, producing motifs we have named {\textquoteright}polar clasps{\textquoteright}.

}, issn = {1545-9985}, doi = {10.1038/s41594-017-0018-0}, author = {Gallagher-Jones, Marcus and Glynn, Calina and Boyer, David R and Martynowycz, Michael W and Hernandez, Evelyn and Miao, Jennifer and Zee, Chih-Te and Novikova, Irina V and Goldschmidt, Lukasz and McFarlane, Heather T and Helguera, Gustavo F and Evans, James E and Sawaya, Michael R and Cascio, Duilio and Eisenberg, David S and Gonen, Tamir and Rodriguez, Jose A} } @article {49492, title = {The subiculum is a patchwork of discrete subregions.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Oct 30}, abstract = {

In the hippocampus, the classical pyramidal cell type of the subiculum acts as a primary output, conveying hippocampal signals to a diverse suite of downstream regions. Accumulating evidence suggests that the subiculum pyramidal cell population may actually be comprised of discrete subclasses. Here, we investigated the extent and organizational principles governing pyramidal cell heterogeneity throughout the mouse subiculum. Using single-cell RNA-seq, we find that the subiculum pyramidal cell population can be deconstructed into eight separable subclasses. These subclasses were mapped onto abutting spatial domains, ultimately producing a complex laminar and columnar organization with heterogeneity across classical dorsal-ventral, proximal-distal, and superficial-deep axes. We further show that these transcriptomically defined subclasses correspond to differential protein products and can be associated with specific projection targets. This work deconstructs the complex landscape of subiculum pyramidal cells into spatially segregated subclasses that may be observed, controlled, and interpreted in future experiments.

}, issn = {2050-084X}, doi = {10.7554/eLife.37701}, author = {Cembrowski, Mark S and Wang, Lihua and Lemire, Andrew L and Copeland, Monique and DiLisio, Salvatore F and Clements, Jody and Spruston, Nelson} } @article {64998, title = {Superresolution architecture of pluripotency guarding adhesions.}, journal = {bioRxiv}, year = {2018}, month = {2018 Sep 19}, abstract = {

Human pluripotent stem cells (hPSC) can generate almost all adult cell lineages. While it is clear that key transcriptional programmes are important elements for maintaining pluripotency, the equally essential requirement for cell adhesion to specific extracellular matrix components remains poorly defined. Our recent observation that hPSC colonies form unusually large {\textquotedblleft}cornerstone{\textquotedblright} focal adhesions (FA), distinct from parental somatic cells, that are lost following differentiation, emphasises the potential of these atypical FA as gatekeepers of pluripotency. Here, using nanopatterns, we further demonstrate that physical restriction of adhesion size, in hPSC colonies, is sufficient to trigger differentiation. Using superresolution two-colour interfero-metric photo-activated localization microscopy (iPALM), we examined the three-dimensional architecture of these cornerstone adhesions and report vertical lamination of FA proteins with three main structural peculiarities: 1) integrin β5 and talin are present at high density, at the edges of cornerstone FA, adjacent to a vertical kank-rich protein wall. 2) Vinculin localises higher than expected with respect to the substrata and displays a head-above-tail orientation, and 3) surprisingly, actin and α-actinin are present in two discrete layers, a previously undescribed localisation for these proteins. Finally, we report that depletion of kanks diminishes FA patterning, and actin organisation within the colony, indicating a key role for kanks in hPSC colony architecture.

}, doi = {10.1101/402305}, author = {Aki Stubb and Camilo Guzm{\'a}n and Elisa N{\"a}rv{\"a} and Jesse Aaron and Teng-Leong Chew and Markku Saari and Mitro Miihkinen and Guillaume Jacquemet and Johanna Ivaska} } @article {49220, title = {Synaptic cleft segmentation in non-isotropic volume electron microscopy of the complete Drosophila brain.}, journal = {Medical Image Computing and Computer Assisted Intervention {\textendash} MICCAI 2018}, year = {2018}, month = {2018 Sep 26}, pages = {317-25}, abstract = {

Neural circuit reconstruction at single synapse resolution is increasingly recognized as crucially important to decipher the function of biological nervous systems. Volume electron microscopy in serial transmission or scanning mode has been demonstrated to provide the necessary resolution to segment or trace all neurites and to annotate all synaptic connections.\ 
Automatic annotation of synaptic connections has been done successfully in near isotropic electron microscopy of vertebrate model organisms. Results on non-isotropic data in insect models, however, are not yet on par with human annotation.\ 
We designed a new 3D-U-Net architecture to optimally represent isotropic fields of view in non-isotropic data. We used regression on a signed distance transform of manually annotated synaptic clefts of the CREMI challenge dataset to train this model and observed significant improvement over the state of the art.\ 
We developed open source software for optimized parallel prediction on very large volumetric datasets and applied our model to predict synaptic clefts in a 50 tera-voxels dataset of the complete Drosophila brain. Our model generalizes well to areas far away from where training data was available.

}, doi = {10.1007/978-3-030-00934-2_36}, author = {Heinrich, Larissa and Funke, Jan and Pape, Constantin and Nunez-Iglesias, Juan and Saalfeld, Stephan} } @article {49292, title = {Synaptic partner prediction from point annotations in insect brains.}, journal = {MICCAI 2018: Medical Image Computing and Computer Assisted Intervention}, year = {2018}, month = {2018 Sep 26}, abstract = {

High-throughput electron microscopy allows recording of lar- ge stacks of neural tissue with sufficient resolution to extract the wiring diagram of the underlying neural network. Current efforts to automate this process focus mainly on the segmentation of neurons. However, in order to recover a wiring diagram, synaptic partners need to be identi- fied as well. This is especially challenging in insect brains like Drosophila melanogaster, where one presynaptic site is associated with multiple post- synaptic elements. Here we propose a 3D U-Net architecture to directly identify pairs of voxels that are pre- and postsynaptic to each other. To that end, we formulate the problem of synaptic partner identification as a classification problem on long-range edges between voxels to encode both the presence of a synaptic pair and its direction. This formulation allows us to directly learn from synaptic point annotations instead of more ex- pensive voxel-based synaptic cleft or vesicle annotations. We evaluate our method on the MICCAI 2016 CREMI challenge and improve over the current state of the art, producing 3\% fewer errors than the next best method.

}, doi = {10.1007/978-3-030-00934-2_35}, author = {Buhmann, Julia and Krause, Renate and Lentini, Rodrigo Ceballos and Eckstein, Nils and Cook, Matthew and Turaga, Srinivas C and Funke, Jan} } @article {49050, title = {Synthetic and genetically encoded fluorescent neural activity indicators.}, journal = {Current Opinion in Neurobiology}, volume = {50}, year = {2018}, month = {2018 Feb 14}, pages = {101-108}, abstract = {

The ultimate goal of neuroscience is to relate the complex activity of cells and cell-networks to behavior and cognition. This requires tools and techniques to visualize neuronal activity. Fluorescence microscopy is an ideal tool to measure activity of cells in the brain due to the high sensitivity of the technique and the growing portfolio of optical hardware and fluorescent sensors. Here, we give a chemist{\textquoteright}s perspective on the recent progress of fluorescent activity indicators that enable the measurement of cellular events in the living brain. We discuss advances in both chemical and genetically encoded sensors and look forward to hybrid indicators, which incorporate synthetic organic dyes into genetically encoded protein constructs.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2018.01.003}, author = {Deo, Claire and Lavis, Luke D} } @article {49547, title = {Temporal control of Drosophila central nervous system development.}, journal = {Current Opinion in Neurobiology}, volume = {56}, year = {2018}, month = {2018 Nov 27}, pages = {24-32}, abstract = {

A complex nervous system requires precise numbers of various neuronal types produced with exquisite spatiotemporal control. This striking diversity is generated by a limited number of neural stem cells (NSC), where spatial and temporal patterning intersect. Drosophila is a genetically tractable model system that has significant advantages for studying stem cell biology and neuronal fate specification. Here we review the latest findings in the rich literature of temporal patterning of neuronal identity in the Drosophila central nervous system. Rapidly changing consecutive transcription factors expressed in NSCs specify short series of neurons with considerable differences. More slowly progressing changes are orchestrated by NSC intrinsic temporal factor gradients which integrate extrinsic signals to coordinate nervous system and organismal development.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2018.10.016}, author = {Miyares, Rosa Linda and Lee, Tzumin} } @article {49181, title = {Three-photon fluorescence microscopy with an axially elongated Bessel focus.}, journal = {Optics Letters}, volume = {43}, year = {2018}, month = {2018 Apr 15}, pages = {1914-1917}, abstract = {

Volumetric imaging tools that are simple to adopt, flexible, and robust are in high demand in the field of neuroscience, where the ability to image neurons and their networks with high spatiotemporal resolution is essential. Using an axially elongated focus approximating a Bessel beam, in combination with two-photon fluorescence microscopy, has proven successful at such an endeavor. Here, we demonstrate three-photon fluorescence imaging with an axially extended Bessel focus. We use an axicon-based module that allowed for the generation of Bessel foci of varying numerical apertures and axial lengths, and apply this volumetric imaging tool to image mouse brain slices and for in vivo imaging of the mouse brain.

}, issn = {1539-4794}, doi = {10.1364/OL.43.001914}, author = {Rodriguez, Cristina and Liang, Yajie and Lu, Rongwen and Ji, Na} } @article {49470, title = {Thy1 transgenic mice expressing the red fluorescent calcium indicator jRGECO1a for neuronal population imaging in vivo.}, journal = {PloS One}, volume = {13}, year = {2018}, month = {2018}, pages = {e0205444}, abstract = {

Calcium imaging is commonly used to measure the neural activity of large groups of neurons in mice. Genetically encoded calcium indicators (GECIs) can be delivered for this purpose using non-invasive genetic methods. Compared to viral gene transfer, transgenic targeting of GECIs provides stable long-term expression and obviates the need for invasive viral injections. Transgenic mice expressing the green GECI GCaMP6 are already widely used. Here we present the generation and characterization of transgenic mice expressing the sensitive red GECI jRGECO1a, driven by the Thy1 promoter. Four transgenic lines with different expression patterns showed sufficiently high expression for cellular in vivo imaging. We used two-photon microscopy to characterize visual responses of individual neurons in the visual cortex in vivo. The signal-to-noise ratio in transgenic mice was comparable to, or better than, mice transduced with adeno-associated virus. In addition, we show that Thy1-jRGECO1a transgenic mice are useful for transcranial population imaging and functional mapping using widefield fluorescence microscopy. We also demonstrate imaging of visual responses in retinal ganglion cells in vitro. Thy1-jRGECO1a transgenic mice are therefore a useful addition to the toolbox for imaging activity in intact neural networks.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0205444}, author = {Dana, Hod and Novak, Ondrej and Guardado-Montesino, Michael and Fransen, James W and Hu, Amy and Borghuis, Bart G and Guo, Caiying and Kim, Douglas S and Svoboda, Karel} } @article {49469, title = {The timing of action determines reward prediction signals in identified midbrain dopamine neurons.}, journal = {Nature Neuroscience}, volume = {21}, year = {2018}, month = {2018 Oct 15}, pages = {1563-73}, abstract = {

Animals adapt their behavior in response to informative sensory cues using multiple brain circuits. The activity of midbrain dopaminergic neurons is thought to convey a critical teaching signal: reward-prediction error. Although reward-prediction error signals are thought to be essential to learning, little is known about the dynamic changes in the activity of midbrain dopaminergic neurons as animals learn about novel sensory cues and appetitive rewards. Here we describe a large dataset of cell-attached recordings of identified dopaminergic neurons as naive mice learned a novel cue-reward association. During learning midbrain dopaminergic neuron activity results from the summation of sensory cue-related and movement initiation-related response components. These components are both a function of reward expectation yet they are dissociable. Learning produces an increasingly precise coordination of action initiation following sensory cues that results in apparent reward-prediction error correlates. Our data thus provide new insights into the circuit mechanisms that underlie a critical computation in a highly conserved learning circuit.

}, issn = {1546-1726}, doi = {10.1038/s41593-018-0245-7}, author = {Coddington, Luke T and Dudman, Joshua T} } @article {49456, title = {A toolbox for multiplexed super-resolution imaging of the E. coli nucleoid and membrane using novel PAINT labels.}, journal = {Scientific Reports}, volume = {8}, year = {2018}, month = {2018 Oct 03}, pages = {14768}, abstract = {

Maintenance of the bacterial homeostasis initially emanates from interactions between proteins and the bacterial nucleoid. Investigating their spatial correlation requires high spatial resolution, especially in tiny, highly confined and crowded bacterial cells. Here, we present super-resolution microscopy using a palette of fluorescent labels that bind transiently to either the membrane or the nucleoid of fixed E. coli cells. The presented labels are easily applicable, versatile and allow long-term single-molecule super-resolution imaging independent of photobleaching. The different spectral properties allow for multiplexed imaging in combination with other localisation-based super-resolution imaging techniques. As examples for applications, we demonstrate correlated super-resolution imaging of the bacterial nucleoid with the position of genetic loci, of nascent DNA in correlation to the entire nucleoid, and of the nucleoid of metabolically arrested cells. We furthermore show that DNA- and membrane-targeting labels can be combined with photoactivatable fluorescent proteins and visualise the nano-scale distribution of RNA polymerase relative to the nucleoid in drug-treated E. coli cells.

}, issn = {2045-2322}, doi = {10.1038/s41598-018-33052-3}, author = {Spahn, Christoph K and Glaesmann, Mathilda and Grimm, Jonathan B and Ayala, Anthony X and Lavis, Luke D and Heilemann, Mike} } @article {49510, title = {Tools for rapid high-resolution behavioral phenotyping of automatically isolated Drosophila.}, journal = {Cell Reports}, volume = {25}, year = {2018}, month = {2018 Nov 06}, pages = {1636-1649.e5}, abstract = {

Sparse manipulation of neuron excitability during free behavior is critical for identifying neural substrates of behavior. Genetic tools for precise neuronal manipulation exist in the fruit fly, Drosophila melanogaster, but behavioral tools are still lacking to identify potentially subtle phenotypes only detectible using high-throughput and high spatiotemporal resolution. We developed three assay components that can be used modularly to study natural and optogenetically induced behaviors. FlyGate automatically releases flies one at a time into an assay. FlyDetect tracks flies in real time, is robust to severe occlusions, and can be used to track appendages, such as the head. GlobeDisplay is a spherical projection system covering the fly{\textquoteright}s visual receptive field with a single projector. We demonstrate the utility of these components in an integrated system, FlyPEZ, by comprehensively modeling the input-output function for directional looming-evoked escape takeoffs and describing a millisecond-timescale phenotype from genetic silencing of a single visual projection neuron type.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2018.10.048}, author = {Williamson, W Ryan and Peek, Martin Y and Breads, Patrick and Coop, Brian and Card, Gwyneth M} } @article {49413, title = {Topographic precision in sensory and motor corticostriatal projections varies across cell type and cortical area.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Sep 03}, pages = {3549}, abstract = {

The striatum shows general topographic organization and regional differences in behavioral functions. How corticostriatal topography differs across cortical areas and cell types to support these distinct functions is unclear. This study contrasted corticostriatal projections from two layer 5 cell types, intratelencephalic (IT-type) and pyramidal tract (PT-type) neurons, using viral vectors expressing fluorescent reporters in Cre-driver mice. Corticostriatal projections from sensory and motor cortex are somatotopic, with a decreasing topographic specificity as injection sites move from sensory to motor and frontal areas. Topographic organization differs between IT-type and PT-type neurons, including injections in the same site, with IT-type neurons having higher topographic stereotypy than PT-type neurons. Furthermore, IT-type projections from interconnected cortical areas have stronger correlations in corticostriatal targeting than PT-type projections do. As predicted by a longstanding model, corticostriatal projections of interconnected cortical areas form parallel circuits in the basal ganglia.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-05780-7}, author = {Hooks, Bryan M and Papale, Andrew E and Paletzki, Ronald F and Feroze, Muhammad W and Eastwood, Brian S and Couey, Jonathan J and Winnubst, Johan and Chandrashekar, Jayaram and Gerfen, Charles R} } @article {49289, title = {A transgenic mouse for imaging activity-dependent dynamics of endogenous Arc mRNA in live neurons.}, journal = {Science Advances}, volume = {4}, year = {2018}, month = {2018 Jun}, pages = {eaar3448}, abstract = {

Localized translation plays a crucial role in synaptic plasticity and memory consolidation. However, it has not been possible to follow the dynamics of memory-associated mRNAs in living neurons in response to neuronal activity in real time. We have generated a novel mouse model where the endogenous Arc/Arg3.1 gene is tagged in its 3{\textquoteright} untranslated region with stem-loops that bind a bacteriophage PP7 coat protein (PCP), allowing visualization of individual mRNAs in real time. The physiological response of the tagged gene to neuronal activity is identical to endogenous Arc and reports the true dynamics of Arc mRNA from transcription to degradation. The transcription dynamics of Arc in cultured hippocampal neurons revealed two novel results: (i) A robust transcriptional burst with prolonged ON state occurs after stimulation, and (ii) transcription cycles continue even after initial stimulation is removed. The correlation of stimulation with Arc transcription and mRNA transport in individual neurons revealed that stimulus-induced Ca activity was necessary but not sufficient for triggering Arc transcription and that blocking neuronal activity did not affect the dendritic transport of newly synthesized Arc mRNAs. This mouse will provide an important reagent to investigate how individual neurons transduce activity into spatiotemporal regulation of gene expression at the synapse.

}, issn = {2375-2548}, doi = {10.1126/sciadv.aar3448}, author = {Das, Sulagna and Moon, Hyungseok C and Singer, Robert H and Park, Hye Yoon} } @article {49096, title = {Transport and sorting in the Golgi complex: multiple mechanisms sort diverse cargo.}, journal = {Current Opinion in Cell Biology}, volume = {50}, year = {2018}, month = {2018 Feb }, abstract = {

At the center of the secretory pathway, the Golgi complex ensures correct processing and sorting of cargos toward their final destination. Cargos are diverse in topology, function and destination. A remarkable feature of the Golgi complex is its ability to sort and process these diverse cargos destined for secretion, the cell surface, the lysosome, or retained within the secretory pathway. Just as these cargos are diverse so also are their sorting requirements and thus, their trafficking route. There is no one-size-fits-all sorting scheme in the Golgi. We propose a coexistence of models to reconcile these diverse needs. We review examples of differential sorting mediated by proteins and lipids. Additionally, we highlight recent technological developments that have potential to uncover new modes of transport.

}, doi = {10.1016/j.ceb.2018.03.002}, author = {Boncampain, Gaelle and Weigel, Aubrey V} } @article {49182, title = {Transvection Goes Live-Visualizing Enhancer-Promoter Communication between Chromosomes.}, journal = {Molecular Cell}, volume = {70}, year = {2018}, month = {2018 Apr 19}, pages = {195-196}, abstract = {

Lim et\ al. (2018) use live imaging in Drosophila embryos to show that enhancers can drive transcription from promoters on another chromosome when they are in close proximity. In addition, they show that multiple promoters can access the same enhancer without competition, potentially sharing a pool of factors in a transcriptional "hub."

}, issn = {1097-4164}, doi = {10.1016/j.molcel.2018.04.004}, author = {Tsai, Albert and Singer, Robert H and Crocker, Justin} } @article {49354, title = {Triggered cell-cell fusion assay for cytoplasmic and organelle intermixing studies.}, journal = {Current Protocols in Cell Biology}, volume = {81}, year = {2018}, month = {2018 Aug 13}, pages = {e61}, abstract = {

Different multicellular organisms undergo cell-cell fusion to form functional syncytia that support specialized functions necessary for proper development and survival. For years, monitoring the structural consequences of this process using live-cell imaging has been challenging due to the unpredictable timing of cell fusion events in tissue systems. Here we present a triggered vesicular stomatitis virus G-protein (VSV-G)-mediated cell-cell fusion assay that can be used to synchronize fusion between cells. This allows the study of cellular changes that occur during cell fusion. The process is induced using a fast wash of low pH isotonic buffer, promoting the fusion of plasma membranes of two or more adjacent cells within seconds. This approach is suitable for studying mixing of small cytoplasmic molecules between fusing cells as well as changes in organelle distribution and dynamics. {\textcopyright} 2018 by John Wiley \& Sons, Inc.

}, issn = {1934-2616}, doi = {10.1002/cpcb.61}, author = {Feliciano, Daniel and Nixon-Abell, Jonathon and Lippincott-Schwartz, Jennifer} } @article {65093, title = {Ultralarge modulation of fluorescence by neuromodulators in carbon nanotubes functionalized with self-assembled oligonucleotide rings.}, journal = {Nano Letters}, volume = {18}, year = {2018}, month = {2018 Nov 14}, pages = {6995-7003}, abstract = {

Noncovalent interactions between single-stranded DNA (ssDNA) oligonucleotides and single wall carbon nanotubes (SWNTs) have provided a unique class of tunable chemistries for a variety of applications. However, mechanistic insight into both the photophysical and intermolecular phenomena underlying their utility is lacking, which results in obligate heuristic approaches for producing ssDNA-SWNT based technologies. In this work, we present an ultrasensitive "turn-on" nanosensor for neuromodulators dopamine and norepinephrine with strong relative change in fluorescence intensity (Δ F/ F) of up to 3500\%, a signal appropriate for in vivo neuroimaging, and uncover the photophysical principles and intermolecular interactions that govern the molecular recognition and fluorescence modulation of this nanosensor synthesized from the spontaneous self-assembly of (GT) ssDNA rings on SWNTs. The fluorescence modulation of the ssDNA-SWNT conjugate is shown to exhibit remarkable sensitivity to the ssDNA sequence chemistry, length, and surface density, providing a set of parameters with which to tune nanosensor dynamic range, analyte selectivity\ and strength of fluorescence turn-on. We employ classical and quantum mechanical molecular dynamics simulations to rationalize our experimental findings. Calculations show that (GT) ssDNA form ordered rings around (9,4)\ SWNTs, inducing periodic surface potentials that modulate exciton recombination lifetimes. Further evidence is presented to elucidate how dopamine analyte binding modulates SWNT fluorescence. We discuss the implications of our findings for SWNT-based molecular imaging applications.

}, keywords = {Biosensing Techniques, DNA, Single-Stranded, Dopamine, Fluorescence, Nanotubes, Carbon, Neurotransmitter Agents, Norepinephrine, Oligonucleotides}, issn = {1530-6992}, doi = {10.1021/acs.nanolett.8b02937}, author = {Beyene, Abraham G and Alizadehmojarad, Ali A and Dorlhiac, Gabriel and Goh, Natalie and Streets, Aaron M and Kr{\'a}l, Petr and Vukovi{\'c}, Lela and Landry, Markita P} } @article {49386, title = {An unbiased template of the Drosophila brain and ventral nerve cord.}, journal = {bioRxiv}, year = {2018}, month = {2018 Jul 25}, abstract = {

The fruit fly Drosophila melanogaster is an important model organism for neuroscience with a wide array of genetic tools that enable the mapping of individuals neurons and neural subtypes. Brain templates are essential for comparative biological studies because they enable analyzing many individuals in a common reference space. Several central brain templates exist for Drosophila, but every one is either biased, uses sub-optimal tissue preparation, is imaged at low resolution, or does not account for artifacts. No publicly available Drosophila ventral nerve cord template currently exists. In this work, we created high-resolution templates of the Drosophila brain and ventral nerve cord using the best-available technologies for imaging, artifact correction, stitching, and template construction using groupwise registration. We evaluated our central brain template against the four most competitive, publicly available brain templates and demonstrate that ours enables more accurate registration with fewer local deformations in shorter time.

}, doi = {10.1101/376384}, author = {Bogovic, John A and Otsuna, Hideo and Heinrich, Larissa and Ito, Masayoshi and Jeter, Jennifer and Meissner, Geoffrey W and Nern, Aljoscha and Colonell, Jennifer and Malkesman, Oz and Saalfeld, Stephan} } @article {49120, title = {Unnecessary tension.}, journal = {Lab Animal}, volume = {47}, year = {2018}, month = {2018 Apr}, pages = {91}, issn = {1548-4475}, doi = {10.1038/s41684-018-0024-9}, author = {Cox, James D and Seltzer, Meghan J} } @article {48839, title = {Vision and locomotion shape the interactions between neuron types in mouse visual cortex.}, journal = {Neuron}, volume = {98}, year = {2018}, month = {2018 May 2}, pages = {602-15}, abstract = {

Cortical computation arises from the interaction of multiple neuronal\ types, including pyramidal (Pyr) cells and interneurons expressing Sst, Vip, or Pvalb. To study the circuit underlying such\ interactions, we imaged these four\ types\ of cells in\ mouse\ primary\ visual\ cortex(V1). Our recordings in darkness were consistent with a "disinhibitory" model in which\ locomotion\ activates Vip cells, thus inhibiting Sst cells and disinhibiting Pyr cells. However, the disinhibitory model failed when\ visual\ stimuli were present:\ locomotion\ increased Sst cell responses to large stimuli and Vip cell responses to small stimuli. A recurrent network model successfully predicted each cell type{\textquoteright}s activity from the measured activity of other\ types. Capturing the effects of\ locomotion, however, required allowing it to increase feedforward synaptic weights and modulate recurrent weights. This network model summarizes interneuron\ interactions\ and suggests that\ locomotion\ may alter cortical computation by changing effective synaptic connectivity.

}, doi = {https://doi.org/10.1101/058396}, author = {Dipoppa, Mario and Ranson, Adam and Krumin, Michael and Pachitariu, Marius and Carandini, Matteo and Harris, Kenneth D} } @article {49518, title = {Visual physiology of the layer 4 cortical circuit in silico.}, journal = {PLoS Computational Biology}, volume = {14}, year = {2018}, month = {2018 Nov 12}, pages = {e1006535}, abstract = {

Despite advances in experimental techniques and accumulation of large datasets concerning the composition and properties of the cortex, quantitative modeling of cortical circuits under in-vivo-like conditions remains challenging. Here we report and publicly release a biophysically detailed circuit model of layer 4 in the mouse primary visual cortex, receiving thalamo-cortical visual inputs. The 45,000-neuron model was subjected to a battery of visual stimuli, and results were compared to published work and new in vivo experiments. Simulations reproduced a variety of observations, including effects of optogenetic perturbations. Critical to the agreement between responses in silico and in vivo were the rules of functional synaptic connectivity between neurons. Interestingly, after extreme simplification the model still performed satisfactorily on many measurements, although quantitative agreement with experiments suffered. These results emphasize the importance of functional rules of cortical wiring and enable a next generation of data-driven models of in vivo neural activity and computations.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1006535}, author = {Arkhipov, Anton and Gouwens, Nathan W and Billeh, Yazan N and Gratiy, Sergey and Iyer, Ramakrishnan and Wei, Ziqiang and Xu, Zihao and Abbasi-Asl, Reza and Berg, Jim and Buice, Michael and Cain, Nicholas and da Costa, Nuno and de Vries, Saskia and Denman, Daniel and Durand, Severine and Feng, David and Jarsky, Tim and Lecoq, Jerome and Lee, Brian and Li, Lu and Mihalas, Stefan and Ocker, Gabriel K and Olsen, Shawn R and Reid, R Clay and Soler-Llavina, Gilberto and Sorensen, Staci A and Wang, Quanxin and Waters, Jack and Scanziani, Massimo and Koch, Christof} } @article {49331, title = {Visual projection neurons mediating directed courtship in Drosophila.}, journal = {Cell}, volume = {174}, year = {2018}, month = {2018 Jul 04}, pages = {607-21}, abstract = {

Many animals rely on vision to detect, locate, and track moving objects. In Drosophila courtship, males primarily use visual cues to orient toward and follow females and to select the ipsilateral wing for courtship song. Here, we show that the LC10 visual projection neurons convey essential visual information during courtship. Males with LC10 neurons silenced are unable to orient toward or maintain proximity to the female and do not predominantly use the ipsilateral wing when singing. LC10 neurons preferentially respond to small moving objects using an antagonistic motion-based center-surround mechanism. Unilateral activation of LC10 neurons recapitulates the orienting and ipsilateral wing extension normally elicited by females, and the potency with which LC10 induces wing extension is enhanced in a state of courtship arousal controlled by male-specific P1 neurons. These data suggest that LC10 is a major pathway relaying visual input to the courtship circuits in the male brain.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2018.06.020}, author = {Ribeiro, In{\^e}s M A and Drews, Michael and Bahl, Armin and Machacek, Christian and Borst, Alexander and Dickson, Barry J} } @article {49512, title = {Visualizing intracellular organelle and cytoskeletal interactions at nanoscale resolution on millisecond timescales. }, journal = {Cell}, volume = {175}, year = {2018}, month = {2018 Nov 15}, pages = {1430-42}, abstract = {In eukaryotic cells, organelles and the cytoskeleton undergo highly dynamic yet organized interactions capable of orchestrating complex cellular functions. Visualizing these interactions requires noninvasive, long-duration imaging of the intracellular environment at high spatiotemporal resolution and low background. To achieve these normally opposing goals, we developed grazing incidence structured illumination microscopy (GI-SIM) that is capable of imaging dynamic events near the basal cell cortex at 97-nm resolution and 266 frames/s over thousands of time points. We employed multi-color GI-SIM to characterize the fast dynamic interactions of diverse organelles and the cytoskeleton, shedding new light on the complex behaviors of these structures. Precise measurements of microtubule growth or shrinkage events helped distinguish among models of microtubule dynamic instability. Analysis of endoplasmic reticulum (ER) interactions with other organelles or microtubules uncovered new ER remodeling mechanisms, such as hitchhiking of the ER on motile organelles. Finally, ER-mitochondria contact sites were found to promote both mitochondrial fission and fusion.}, doi = {10.1016/j.cell.2018.09.057}, author = {Guo, Yuting and Li, Di and Zhang, Siwei and Yang, Yanrui and Liu, Jia-Jia and Wang, Xinyu and Liu, Chong and Milkie, Daniel E and Moore, Regan P and Tulu, U Serdar and Kiehart, Daniel P and Hu, Junjie and Lippincott-Schwartz, Jennifer and Betzig, Eric and Li, Dong} } @article {49022, title = {Visualizing transcription factor dynamics in living cells.}, journal = {The Journal of Cell Biology}, volume = {217}, year = {2018}, month = {2018 Jan 29}, pages = {1181-91}, abstract = {

The assembly of sequence-specific enhancer-binding transcription factors (TFs) at cis-regulatory elements in the genome has long been regarded as the fundamental mechanism driving cell type-specific gene expression. However, despite extensive biochemical, genetic, and genomic studies in the past three decades, our understanding of molecular mechanisms underlying enhancer-mediated gene regulation remains incomplete. Recent advances in imaging technologies now enable direct visualization of TF-driven regulatory events and transcriptional activities at the single-cell, single-molecule level. The ability to observe the remarkably dynamic behavior of individual TFs in live cells at high spatiotemporal resolution has begun to provide novel mechanistic insights and promises new advances in deciphering causal-functional relationships of TF targeting, genome organization, and gene activation. In this review, we review current transcription imaging techniques and summarize converging results from various lines of research that may instigate a revision of models to describe key features of eukaryotic gene regulation.

}, issn = {1540-8140}, doi = {10.1083/jcb.201710038}, author = {Liu, Zhe and Tjian, Robert} } @article {49058, title = {VPS4 is a dynamic component of the centrosome that regulates centrosome localization of γ-tubulin, centriolar satellite stability and ciliogenesis.}, journal = {Scientific Reports}, volume = {8}, year = {2018}, month = {2018 Feb 20}, pages = {3353}, abstract = {

The hexameric AAA ATPase VPS4 facilitates ESCRT III filament disassembly on diverse intracellular membranes. ESCRT III components and VPS4 have been localized to the ciliary transition zone and spindle poles and reported to affect centrosome duplication and spindle pole stability. How the canonical ESCRT pathway could mediate these events is unclear. We studied the association of VPS4 with centrosomes and found that GFP-VPS4 was a dynamic component of both mother and daughter centrioles. A mutant, VPS4, which can{\textquoteright}t hydrolyze ATP, was less dynamic and accumulated at centrosomes. Centrosome localization of the VPS4mutant, caused reduced γ-tubulin levels at centrosomes and consequently decreased microtubule growth and altered centrosome positioning. In addition, preventing VPS4 ATP hydrolysis nearly eliminated centriolar satellites and paused ciliogensis after formation of the ciliary vesicle. Zebrafish embryos injected with GFP-VPS4mRNA were less viable, exhibited developmental defects and had fewer cilia in Kupffer{\textquoteright}s vesicle. Surprisingly, ESCRT III proteins seldom localized to centrosomes and their depletion did not lead to these phenotypes. Our data support an ESCRT III-independent function for VPS4 at the centrosome and reveal that this evolutionary conserved AAA ATPase influences diverse centrosome functions and, as a result, global cellular architecture and development.

}, issn = {2045-2322}, doi = {10.1038/s41598-018-21491-x}, author = {Ott, Carolyn and Nachmias, Dikla and Adar, Shai and Jarnik, Michal and Sherman, Shachar and Birnbaum, Ramon Y and Lippincott-Schwartz, Jennifer and Elia, Natalie} } @article {49576, title = {Whole-cell, 3D and multi-color STED imaging with exchangeable fluorophores.}, journal = {Nano Letters}, volume = {19}, year = {2018}, month = {2018 Dec 10}, pages = {500-5}, abstract = {

We demonstrate STED microscopy of whole bacterial and eukaryotic cells using fluorogenic labels that reversibly bind to their target structure. A constant exchange of labels guarantees the removal of photobleached fluorophores and their replacement by intact fluorophores, thereby circumventing bleaching-related limitations of STED super-resolution imaging. We achieve a constant labeling density and demonstrate a fluorescence signal for long and theoretically unlimited acquisition times. Using this concept, we demonstrate whole-cell, 3D, multi-color and live cell STED microscopy.

}, issn = {1530-6992}, doi = {10.1021/acs.nanolett.8b04385}, author = {Spahn, Christoph and Grimm, Jonathan B and Lavis, Luke D and Lampe, Marko and Heilemann, Mike} } @article {49246, title = {The world of the identified or digital neuron.}, journal = {Journal of Neurogenetics}, year = {2018}, month = {2018 May 23}, pages = {1-6}, abstract = {

In general, neurons in insects and many other invertebrate groups are individually recognizable, enabling us to assign an index number to specific neurons in a manner which is rarely possible in a vertebrate brain. This endows many studies on insect nervous systems with the opportunity to document neurons with great precision, so that in favourable cases we can return to the same neuron or neuron type repeatedly so as to recognize many separate morphological classes. The visual system of the fly{\textquoteright}s compound eye particularly provides clear examples of the accuracy of neuron wiring, allowing numerical comparisons between representatives of the same cell type, and estimates of the accuracy of their wiring.

}, issn = {1563-5260}, doi = {10.1080/01677063.2018.1474214}, author = {Meinertzhagen, Ian A} } @article {48621, title = {3D Bayesian cluster analysis of super-resolution data reveals LAT recruitment to the T cell synapse.}, journal = {Scientific Reports}, volume = {7}, year = {2017}, month = {2017 Jun 22}, pages = {4077}, abstract = {

Single-molecule localisation microscopy (SMLM) allows the localisation of fluorophores with a precision of 10-30 nm, revealing the cell{\textquoteright}s nanoscale architecture at the molecular level. Recently, SMLM has been extended to 3D, providing a unique insight into cellular machinery. Although cluster analysis techniques have been developed for 2D SMLM data sets, few have been applied to 3D. This lack of quantification tools can be explained by the relative novelty of imaging techniques such as interferometric photo-activated localisation microscopy (iPALM). Also, existing methods that could be extended to 3D SMLM are usually subject to user defined analysis parameters, which remains a major drawback. Here, we present a new open source cluster analysis method for 3D SMLM data, free of user definable parameters, relying on a model-based Bayesian approach which takes full account of the individual localisation precisions in all three dimensions. The accuracy and reliability of the method is validated using simulated data sets. This tool is then deployed on novel experimental data as a proof of concept, illustrating the recruitment of LAT to the T-cell immunological synapse in data acquired by iPALM providing ~10 nm isotropic resolution.

}, issn = {2045-2322}, doi = {10.1038/s41598-017-04450-w}, author = {Griffi{\'e}, Juliette and Shlomovich, Leigh and Williamson, David J and Shannon, Michael and Aaron, Jesse and Khuon, Satya and L Burn, Garth and Boelen, Lies and Peters, Ruby and Cope, Andrew P and Cohen, Edward A K and Rubin-Delanchy, Patrick and Owen, Dylan M} } @article {48218, title = {Actin dynamics and competition for myosin monomer govern the sequential amplification of myosin filaments.}, journal = {Nature Cell Biology}, volume = {19}, year = {2017}, month = {2017 Jan 23}, pages = {85-93}, abstract = {

The cellular mechanisms governing non-muscle myosin II (NM2) filament assembly are largely unknown. Using EGFP-NM2A knock-in fibroblasts and multiple super-resolution imaging modalities, we characterized and quantified the sequential amplification of NM2 filaments within lamellae, wherein filaments emanating from single nucleation events continuously partition, forming filament clusters that populate large-scale actomyosin structures deeper in the cell. Individual partitioning events coincide spatially and temporally with the movements of diverging actin fibres, suppression of which inhibits partitioning. These and other data indicate that NM2A filaments are partitioned by the dynamic movements of actin fibres to which they are bound. Finally, we showed that partition frequency and filament growth rate in the lamella depend on MLCK, and that MLCK is competing with centrally active ROCK for a limiting pool of monomer with which to drive lamellar filament assembly. Together, our results provide new insights into the mechanism and spatio-temporal regulation of NM2 filament assembly in cells.

}, issn = {1476-4679}, doi = {10.1038/ncb3463}, author = {Beach, Jordan R and Bruun, Kyle S and Shao, Lin and Li, Dong and Swider, Zac and Remmert, Kirsten and Zhang, Yingfan and Conti, Mary A and Adelstein, Robert S and Rusan, Nasser M and Betzig, Eric and Hammer, John A} } @article {48843, title = {Actin-based protrusions of migrating neutrophils are intrinsically lamellar and facilitate direction changes.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Sep 26}, abstract = {

Leukocytes and other amoeboid cells change shape as they move, forming highly dynamic, actin-filled pseudopods. Although we understand much about the architecture and dynamics of thin lamellipodia made by slow-moving cells on flat surfaces, conventional light microscopy lacks the spatial and temporal resolution required to track complex pseudopods of cells moving in three dimensions. We therefore employed lattice light sheet microscopy to perform three-dimensional, time-lapse imaging of neutrophil-like HL-60 cells crawling through collagen matrices. To analyze three-dimensional pseudopods we: (i) developed fluorescent probe combinations that distinguish cortical actin from dynamic, pseudopod-forming actin networks, and (ii) adapted molecular visualization tools from structural biology to render and analyze complex cell surfaces. Surprisingly, three-dimensional pseudopods turn out to be composed of thin (\<0.75 {\textmu}m), flat sheets that sometimes interleave to form rosettes. Their laminar nature is not templated by an external surface, but likely reflects a linear arrangement of regulatory molecules. Although we find that Arp2/3-dependent pseudopods are dispensable for three-dimensional locomotion, their elimination dramatically decreases the frequency of cell turning, and pseudopod dynamics increase when cells change direction, highlighting the important role pseudopods play in pathfinding.

}, issn = {2050-084X}, doi = {10.7554/eLife.26990}, author = {Fritz-Laylin, Lillian K and Riel-Mehan, Megan and Chen, Bi-Chang and Lord, Samuel J and Goddard, Thomas D and Ferrin, Thomas E and Nicholson-Dykstra, Susan M and Higgs, Henry and Johnson, Graham T and Betzig, Eric and Mullins, R Dyche} } @article {48373, title = {Adaptive optical fluorescence microscopy.}, journal = {Nature Methods}, volume = {14}, year = {2017}, month = {2017 Mar 31}, pages = {374-380}, abstract = {

The past quarter century has witnessed rapid developments of fluorescence microscopy techniques that enable structural and functional imaging of biological specimens at unprecedented depth and resolution. The performance of these methods in multicellular organisms, however, is degraded by sample-induced optical aberrations. Here I review recent work on incorporating adaptive optics, a technology originally applied in astronomical telescopes to combat atmospheric aberrations, to improve image quality of fluorescence microscopy for biological imaging.

}, issn = {1548-7105}, doi = {10.1038/nmeth.4218}, author = {Ji, Na} } @article {48714, title = {Adaptive optical versus spherical aberration corrections for in vivo brain imaging.}, journal = {Biomedical Optics Express}, volume = {8}, year = {2017}, month = {2017 Aug}, pages = {3891-902}, abstract = {

Adjusting the objective correction collar is a widely used approach to correct spherical aberrations (SA) in optical microscopy. In this work, we characterized and compared its performance with adaptive optics in the context of\ in vivo\ brain imaging with two-photon fluorescence microscopy. We found that the presence of sample tilt had a deleterious effect on the performance of SA-only correction. At large tilt angles, adjusting the correction collar even worsened image quality. In contrast, adaptive optical correction always recovered optimal imaging performance regardless of sample tilt. The extent of improvement with adaptive optics was dependent on object size, with smaller objects having larger relative gains in signal intensity and image sharpness. These observations translate into a superior performance of adaptive optics for structural and functional brain imaging applications\ in vivo, as we confirmed experimentally.

}, doi = {10.1364/BOE.8.003891} } @article {49082, title = {Advances in neural engineering for rehabilitation.}, journal = {Behavioural Neurology}, volume = {2017}, year = {2017}, month = {2017}, pages = {9240921}, issn = {1875-8584}, doi = {10.1155/2017/9240921}, author = {Hu, Xiaoling and Zhao, Ting and Yao, Jun and Kuang, Yu and Yang, Yuan} } @article {48449, title = {An Amidase_3 domain-containing N-acetylmuramyl-L-alanine amidase is required for mycobacterial cell division.}, journal = {Scientific Reports}, volume = {7}, year = {2017}, month = {2017 Apr 25}, pages = {1140}, abstract = {

Mycobacteria possess a multi-layered cell wall that requires extensive remodelling during cell division. We investigated the role of an amidase_3 domain-containing N-acetylmuramyl-L-alanine amidase, a peptidoglycan remodelling enzyme implicated in cell division. We demonstrated that deletion of MSMEG_6281 (Ami1) in Mycobacterium smegmatis resulted in the formation of cellular chains, illustrative of cells that were unable to complete division. Suprisingly, viability in the Δami1 mutant was maintained through atypical lateral branching, the products of which proceeded to form viable daughter cells. We showed that these lateral buds resulted from mislocalization of DivIVA, a major determinant in facilitating polar elongation in mycobacterial cells. Failure of Δami1 mutant cells to separate also led to dysregulation of FtsZ ring bundling. Loss of Ami1 resulted in defects in septal peptidoglycan turnover with release of excess cell wall material from the septum or newly born cell poles. We noted signficant accumulation of 3-3 crosslinked muropeptides in the Δami1 mutant. We further demonstrated that deletion of ami1 leads to increased cell wall permeability and enhanced susceptiblity to cell wall targeting antibiotics. Collectively, these data provide novel insight on cell division in actinobacteria and highlights a new class of potential drug targets for mycobacterial diseases.

}, issn = {2045-2322}, doi = {10.1038/s41598-017-01184-7}, author = {Senzani, Sibusiso and Li, Dong and Bhaskar, Ashima and Ealand, Christopher and Chang, James and Rimal, Binayak and Liu, Chengyin and Joon Kim, Sung and Dhar, Neeraj and Kana, Bavesh} } @article {48415, title = {AMPK and vacuole-associated Atg14p orchestrate {\textmu}-lipophagy for energy production and long-term survival under glucose starvation.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Apr 10}, pages = {e21690}, abstract = {

Dietary restriction increases the longevity of many organisms but the cell signaling and organellar mechanisms underlying this capability are unclear. We demonstrate that to permit long-term survival in response to sudden glucose depletion, yeast cells activate lipid-droplet (LD) consumption through micro-lipophagy ({\textmu}-lipophagy), in which fat is metabolized as an alternative energy source. AMP-activated protein kinase (AMPK) activation triggered this pathway, which required Atg14p. More gradual glucose starvation, amino acid deprivation or rapamycin did not trigger {\textmu}-lipophagy and failed to provide the needed substitute energy source for long-term survival. During acute glucose restriction, activated AMPK was stabilized from degradation and interacted with Atg14p. This prompted Atg14p redistribution from ER exit sites onto liquid-ordered vacuole membrane domains, initiating {\textmu}-lipophagy. Our findings that activated AMPK and Atg14p are required to orchestrate {\textmu}-lipophagy for energy production in starved cells is relevant for studies on aging and evolutionary survival strategies of different organisms.

}, issn = {2050-084X}, doi = {10.7554/eLife.21690}, author = {Seo, Arnold Young and Lau, Pick-Wei and Feliciano, Daniel and Sengupta, Prabuddha and Le Gros, Mark A and Cinquin, Bertrand and Larabell, Carolyn A and Lippincott-Schwartz, Jennifer} } @article {48507, title = {Angular velocity integration in a fly heading circuit.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 May 22}, abstract = {

Many animals maintain an internal representation of their heading as they move through their surroundings. Such a compass representation was recently discovered in a neural population in the Drosophila melanogaster central complex, a brain region implicated in spatial navigation. Here, we use two-photon calcium imaging and electrophysiology in head-fixed walking flies to identify a different neural population that conjunctively encodes heading and angular velocity, and is excited selectively by turns in either the clockwise or counterclockwise direction. We show how these mirror-symmetric turn responses combine with the neurons{\textquoteright} connectivity to the compass neurons to create an elegant mechanism for updating the fly{\textquoteright}s heading representation when the animal turns in darkness. This mechanism, which employs recurrent loops with an angular shift, bears a resemblance to those proposed in theoretical models for rodent head direction cells. Our results provide a striking example of structure matching function for a broadly relevant computation.

}, issn = {2050-084X}, doi = {10.7554/eLife.23496}, author = {Turner-Evans, Daniel and Wegener, Stephanie and Rouault, Herv{\'e} and Franconville, Romain and Wolff, Tanya and Seelig, Johannes D and Druckmann, Shaul and Jayaraman, Vivek} } @article {67220, title = {Anisotropic EM Segmentation by 3D Affinity Learning and Agglomeration}, journal = {CoRR}, volume = {abs/1707.08935}, year = {2017}, abstract = {

The field of connectomics has recently produced neuron wiring diagrams from relatively large brain regions from multiple animals. Most of these neural reconstructions were computed from isotropic (e.g., FIBSEM) or near isotropic (e.g., SBEM) data. In spite of the remarkable progress on algorithms in recent years, automatic dense reconstruction from anisotropic data remains a challenge for the connectomics community. One significant hurdle in the segmentation of anisotropic data is the difficulty in generating a suitable initial over-segmentation. In this study, we present a segmentation method for anisotropic EM data that agglomerates a 3D over-segmentation computed from the 3D affinity prediction. A 3D U-net is trained to predict 3D affinities by the MALIS approach. Experiments on multiple datasets demonstrates the strength and robustness of the proposed method for anisotropic EM segmentation.

}, url = {https://arxiv.org/abs/1707.08935v2}, author = {Toufiq Parag and Fabian Tschopp and William Grisaitis and Srinivas C. Turaga and Xuewen Zhang and Brian Matejek and Lee Kamentsky and Jeff W. Lichtman and Hanspeter Pfister} } @article {65893, title = {Antibodies to biotin enable large-scale detection of biotinylation sites on proteins}, journal = {Nature Methods}, volume = {14}, year = {2017}, month = {Jan-12-2017}, pages = {1167 - 1170}, abstract = {

Although purification of biotinylated molecules is highly efficient, identifying specific sites of biotinylation remains challenging. We show that anti-biotin antibodies enable unprecedented enrichment of biotinylated peptides from complex peptide mixtures. Live-cell proximity labeling using APEX peroxidase followed by anti-biotin enrichment and mass spectrometry yielded over 1,600 biotinylation sites on hundreds of proteins, an increase of more than 30-fold in the number of biotinylation sites identified compared to streptavidin-based enrichment of proteins.

}, issn = {1548-7091}, doi = {10.1038/nmeth.4465}, url = {http://www.nature.com/articles/nmeth.4465http://www.nature.com/doifinder/10.1038/nmeth.4465http://www.nature.com/articles/nmeth.4465.pdfhttp://www.nature.com/articles/nmeth.4465.pdfhttp://www.nature.com/articles/nmeth.4465}, author = {Udeshi, Namrata D and Pedram, Kayvon and Svinkina, Tanya and Fereshetian, Shaunt and Myers, Samuel A and Aygun, Ozan and Krug, Karsten and Clauser, Karl and Ryan, Dominic and Ast, Tslil and Mootha, Vamsi K and Ting, Alice Y and Carr, Steven A} } @article {48534, title = {Applying systems-level spectral imaging and analysis to reveal the organelle interactome.}, journal = {Nature}, year = {2017}, month = {2017 May 24}, abstract = {

The organization of the eukaryotic cell into discrete membrane-bound organelles allows for the separation of incompatible biochemical processes, but the activities of these organelles must be coordinated. For example, lipid metabolism is distributed between the endoplasmic reticulum for lipid synthesis, lipid droplets for storage and transport, mitochondria and peroxisomes for β-oxidation, and lysosomes for lipid hydrolysis and recycling. It is increasingly recognized that organelle contacts have a vital role in diverse cellular functions. However, the spatial and temporal organization of organelles within the cell remains poorly characterized, as fluorescence imaging approaches are limited in the number of different labels that can be distinguished in a single image. Here we present a systems-level analysis of the organelle interactome using a multispectral image acquisition method that overcomes the challenge of spectral overlap in the fluorescent protein palette. We used confocal and lattice light sheet instrumentation and an imaging informatics pipeline of five steps to achieve mapping of organelle numbers, volumes, speeds, positions and dynamic inter-organelle contacts in live cells from a monkey fibroblast cell line. We describe the frequency and locality of two-, three-, four- and five-way interactions among six different membrane-bound organelles (endoplasmic reticulum, Golgi, lysosome, peroxisome, mitochondria and lipid droplet) and show how these relationships change over time. We demonstrate that each organelle has a characteristic distribution and dispersion pattern in three-dimensional space and that there is a reproducible pattern of contacts among the six organelles, that is affected by microtubule and cell nutrient status. These live-cell confocal and lattice light sheet spectral imaging approaches are applicable to any cell system expressing multiple fluorescent probes, whether in normal conditions or when cells are exposed to disturbances such as drugs, pathogens or stress. This methodology thus offers a powerful descriptive tool and can be used to develop hypotheses about cellular organization and dynamics.

}, issn = {1476-4687}, doi = {10.1038/nature22369}, author = {Valm, Alex M and Cohen, Sarah and Legant, Wesley R and Melunis, Justin and Hershberg, Uri and Wait, Eric and Cohen, Andrew R and Davidson, Michael W and Betzig, Eric and Lippincott-Schwartz, Jennifer} } @article {48156, title = {Atomic structures of fibrillar segments of hIAPP suggest tightly mated β-sheets are important for cytotoxicity.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Jan 03}, abstract = {

hIAPP fibrils are associated with Type-II Diabetes, but the link of hIAPP structure to islet cell death remains elusive. Here we observe that hIAPP fibrils are cytotoxic to cultured pancreatic β-cells, leading us to determine the structure and cytotoxicity of protein segments composing the amyloid spine of hIAPP. Using the cryoEM method MicroED, we discover that one segment, 19-29 S20G, forms pairs of β-sheets mated by a dry interface that share structural features with and are similarly cytotoxic to full-length hIAPP fibrils. In contrast, a second segment, 15-25 WT, forms non-toxic labile β-sheets. These segments possess different structures and cytotoxic effects, however, both can seed full-length hIAPP, and cause hIAPP to take on the cytotoxic and structural features of that segment. These results suggest that protein segment structures represent polymorphs of their parent protein and that segment 19-29 S20G may serve as a model for the toxic spine of hIAPP.

}, issn = {2050-084X}, doi = {10.7554/eLife.19273}, author = {Krotee, Pascal and Rodriguez, Jose A and Sawaya, Michael R and Cascio, Duilio and Reyes, Francis E and Shi, Dan and Hattne, Johan and Nannenga, Brent L and Oskarsson, Marie E and Philipp, Stephan and Griner, Sarah and Jiang, Lin and Glabe, Charles G and Westermark, Gunilla T and Gonen, Tamir and Eisenberg, David S} } @article {48265, title = {Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED.}, journal = {Nature Methods}, volume = {14}, year = {2017}, month = {2017 Feb 13}, pages = {399-402}, abstract = {

Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from pathologies that render them inappropriate for high-resolution structure determination. Here we show that fragmentation of large, imperfect crystals into microcrystals or nanocrystals can provide a simple path for high-resolution structure determination by the cryoEM method MicroED and potentially by serial femtosecond crystallography.

}, issn = {1548-7105}, doi = {10.1038/nmeth.4178}, author = {de la Cruz, M Jason and Hattne, Johan and Shi, Dan and Seidler, Paul and Rodriguez, Jose and Reyes, Francis E and Sawaya, Michael R and Cascio, Duilio and Weiss, Simon C and Kim, Sun Kyung and Hinck, Cynthia S and Hinck, Andrew P and Calero, Guillermo and Eisenberg, David and Gonen, Tamir} } @article {48266, title = {Axonal Endoplasmic Reticulum Ca(2+) Content Controls Release Probability in CNS Nerve Terminals.}, journal = {Neuron}, volume = {93}, year = {2017}, month = {2017 Jan 30}, pages = {867-81}, abstract = {

Although the endoplasmic reticulum (ER) extends throughout axons and axonal ER dysfunction is implicated in numerous neurological diseases, its role at nerve terminals is poorly understood. We developed novel genetically encoded ER-targeted low-affinity Ca(2+) indicators optimized for examining axonal ER Ca(2+). Our experiments revealed that presynaptic function is tightly controlled by ER Ca(2+) content. We found that neuronal activity drives net Ca(2+) uptake into presynaptic ER although this activity does not contribute significantly to shaping cytosolic Ca(2+) except during prolonged repetitive firing. In contrast, we found that axonal ER acts as an actuator of plasma membrane (PM) function: [Ca(2+)]ER controls STIM1 activation in presynaptic terminals, which results in the local modulation of presynaptic function, impacting activity-driven Ca(2+) entry and release probability. These experiments reveal a critical role of presynaptic ER in the control of neurotransmitter release and will help frame future investigations into the molecular basis of ER-driven neuronal disease states.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2017.01.010}, author = {de Juan-Sanz, Jaime and Holt, Graham T and Schreiter, Eric R and de Juan, Fernando and Kim, Douglas S and Ryan, Timothy A} } @article {48982, title = {Behavioral state modulates the ON visual motion pathway of Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, year = {2017}, month = {2017 Dec 18}, pages = {E102-11}, abstract = {

The behavioral state of an animal can dynamically modulate visual processing. In flies, the behavioral state is known to alter the temporal tuning of neurons that carry visual motion information into the central brain. However, where this modulation occurs and how it tunes the properties of this neural circuit are not well understood. Here, we show that the behavioral state alters the baseline activity levels and the temporal tuning of the first directionally selective neuron in the ON motion pathway (T4) as well as its primary input neurons (Mi1, Tm3, Mi4, Mi9). These effects are especially prominent in the inhibitory neuron Mi4, and we show that central octopaminergic neurons provide input to Mi4 and increase its excitability. We further show that octopamine neurons are required for sustained behavioral responses to fast-moving, but not slow-moving, visual stimuli in walking flies. These results indicate that behavioral-state modulation acts directly on the inputs to the directionally selective neurons and supports efficient neural coding of motion stimuli.

}, issn = {1091-6490}, doi = {10.1073/pnas.1703090115}, author = {Strother, James A and Wu, Shiuan-Tze and Rogers, Edward M and Eliason, Jessica L M and Wong, Allan M and Nern, Aljoscha and Reiser, Michael B} } @article {48785, title = {Behavioral time scale synaptic plasticity underlies CA1 place fields.}, journal = {Science (New York, N.Y.)}, volume = {357}, year = {2017}, month = {2017 Sep 08}, pages = {1033-1036}, abstract = {

Learning is primarily mediated by activity-dependent modifications of synaptic strength within neuronal circuits. We discovered that place fields in hippocampal area CA1 are produced by a synaptic potentiation notably different from Hebbian plasticity. Place fields could be produced in vivo in a single trial by potentiation of input that arrived seconds before and after complex spiking. The potentiated synaptic input was not initially coincident with action potentials or depolarization. This rule, named behavioral time scale synaptic plasticity, abruptly modifies inputs that were neither causal nor close in time to postsynaptic activation. In slices, five pairings of subthreshold presynaptic activity and calcium (Ca(2+)) plateau potentials produced a large potentiation with an asymmetric seconds-long time course. This plasticity efficiently stores entire behavioral sequences within synaptic weights to produce predictive place cell activity.

}, issn = {1095-9203}, doi = {10.1126/science.aan3846}, author = {Bittner, Katie C and Milstein, Aaron D and Grienberger, Christine and Romani, Sandro and Magee, Jeffrey C} } @article {48715, title = {Best practices for managing large CryoEM facilities.}, journal = {Journal of Structural Biology}, volume = {199}, year = {2017}, month = {2017-08-04}, pages = {225-36}, abstract = {

This paper provides an overview of the discussion and presentations from the Workshop on the Management of Large CryoEM Facilities held at the New York Structural Biology Center, New York, NY on February 6{\textendash}7, 2017. A major objective of the workshop was to discuss best practices for managing cryoEM facilities. The discussions were largely focused on supporting single-particle methods for cryoEM and topics included: user access, assessing projects, workflow, sample handling, microscopy, data management and processing, and user training.

}, doi = {10.1016/j.jsb.2017.07.011}, author = {Alewijnse, Bart and Ashton, Alun W and Chambers, Melissa G and Chen, Songye and Cheng, Anchi and Ebrahim, Mark and Eng, Edward T and Hagen, Wim JH and Koster, Abraham J and Lopez, Claudia S and Lukoyanova, Natalya and Ortega, Joaquin and Renault, Ludovic and Reyntjens, Steve and Rice, William J and Scapin, Giovanna and Schrijver, Raymond and Siebert, Alistair and Stagg, Scott M and et al} } @article {48977, title = {BIM for Facilities Management: Providing value at the Howard Hughes Medical Institute.}, journal = {Journal of the National Institute of Building Sciences}, volume = {5}, year = {2017}, month = {2017 Winter}, pages = {10-14}, abstract = {

While building information modeling (BIM) is widely embraced by the architectural, engineering and construction (AEC) industry, BIM adoption in facilities management (FM) is still relatively new and limited. BIM deliverables from design and construction generally do not fulfill FM needs unless they are clearly specified and carefully managed.

The Facilities Group responsible for the Janelia Research Campus of the Howard Hughes Medical Institute (HHMI) expects any BIM platform to provide value in operations and maintenance. Janelia{\textquoteright}s BIM vision goes beyond transferring BIM data to computerized maintenance management software (CMMS) and integrated workplace management system (IWMS) platforms. Instead, Janelia creates and maintains FM-capable BIM, utilizes the models to solve operational challenges and improves safety and efficiency in various ways,\ including engineering analysis for heating, ventilation and air conditioning (HVAC), electrical and plumbing; building automation systems (BAS) analysis; operational impact analysis; and BIM-aided operation safety.

}, author = {Wang, Grace and Philip, Mark and McKinley, Mark} } @article {48267, title = {A brainstem-spinal cord inhibitory circuit for mechanical pain modulation by GABA and Enkephalins.}, journal = {Neuron}, volume = {93}, year = {2017}, month = {2017 Jan 31}, pages = {822-39}, abstract = {

Pain thresholds are, in part, set as a function of emotional and internal states by descending modulation of nociceptive transmission in the spinal cord. Neurons of the rostral ventromedial medulla (RVM) are thought to critically contribute to this process; however, the neural circuits and synaptic mechanisms by which distinct populations of RVM neurons facilitate or diminish pain remain elusive. Here we used in\ vivo opto/chemogenetic manipulations and trans-synaptic tracing of genetically identified dorsal horn and RVM neurons to uncover an RVM-spinal cord-primary afferent circuit controlling pain thresholds. Unexpectedly, we found that RVM GABAergic neurons facilitate mechanical pain by inhibiting dorsal horn enkephalinergic/GABAergic interneurons. We further demonstrate that these interneurons gate sensory inputs and control pain through temporally coordinated enkephalin- and GABA-mediated presynaptic inhibition of somatosensory neurons. Our results uncover a descending disynaptic inhibitory circuit that facilitates mechanical pain, is engaged during stress, and could be targeted to establish higher pain thresholds.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2017.01.008}, author = {Fran{\c c}ois, Amaury and Low, Sarah A and Sypek, Elizabeth I and Christensen, Amelia J and Sotoudeh, Chaudy and Beier, Kevin T and Ramakrishnan, Charu and Ritola, Kimberly D and Sharif-Naeini, Reza and Deisseroth, Karl and Delp, Scott L and Malenka, Robert C and Luo, Liqun and Hantman, Adam W and Scherrer, Gr{\'e}gory} } @article {48645, title = {Building bridges between cellular and molecular structural biology.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Jul 06}, abstract = {

The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.

}, issn = {2050-084X}, doi = {10.7554/eLife.25835}, author = {Patwardhan, Ardan and Brandt, Robert and Butcher, Sarah J and Collinson, Lucy and Gault, David and Gr{\"u}newald, Kay and Hecksel, Corey and Huiskonen, Juha T and Iudin, Andrii and Jones, Martin L and Korir, Paul K and Koster, Abraham J and Lagerstedt, Ingvar and Lawson, Catherine L and Mastronarde, David and McCormick, Matthew and Parkinson, Helen and Rosenthal, Peter B and Saalfeld, Stephan and Saibil, Helen R and Sarntivijai, Sirarat and Solanes Valero, Irene and Subramaniam, Sriram and Swedlow, Jason R and Tudose, Ilinca and Winn, Martyn and Kleywegt, Gerard J} } @article {65894, title = {A bulky glycocalyx fosters metastasis formation by promoting G1 cell cycle progression}, journal = {eLife}, volume = {6}, year = {2017}, month = {Sep-12-2018}, abstract = {

Metastasis depends upon cancer cell growth and survival within the metastatic niche. Tumors which remodel their glycocalyces, by overexpressing bulky glycoproteins like mucins, exhibit a higher predisposition to metastasize, but the role of mucins in oncogenesis remains poorly understood. Here we report that a bulky glycocalyx promotes the expansion of disseminated tumor cells in vivo by fostering integrin adhesion assembly to permit G1 cell cycle progression. We engineered tumor cells to display glycocalyces of various thicknesses by coating them with synthetic mucin-mimetic glycopolymers. Cells adorned with longer glycopolymers showed increased metastatic potential, enhanced cell cycle progression, and greater levels of integrin-FAK mechanosignaling and Akt signaling in a syngeneic mouse model of metastasis. These effects were mirrored by expression of the ectodomain of cancer-associated mucin MUC1. These findings functionally link mucinous proteins with tumor aggression, and offer a new view of the cancer glycocalyx as a major driver of disease progression.

}, doi = {https://doi.org/10.7554/eLife.25752}, url = {https://elifesciences.org/articles/25752}, author = {Woods, Elliot C and Kai, FuiBoon and Barnes, J Matthew and Pedram, Kayvon and Pickup, Michael W and Hollander, Michael J and Weaver, Valerie M and Bertozzi, Carolyn R} } @article {48207, title = {Calcium-independent disruption of microtubule dynamics by nanosecond pulsed electric fields in U87 human glioblastoma cells}, year = {2017}, abstract = {

High powered, nanosecond duration, pulsed electric fields (nsPEF) cause cell death by a mechanism that is not fully understood and have been proposed as a targeted cancer therapy. Numerous chemotherapeutics work by disrupting microtubules. As microtubules are affected by electrical fields, this study looks at the possibility of disrupting them electrically with nsPEF. Human glioblastoma cells (U87-MG) treated with 100, 10 ns, 44 kV/cm pulses at a frequency of 10 Hz showed a breakdown of their interphase microtubule network that was accompanied by a reduction in the number of growing microtubules. This effect is temporally linked to loss of mitochondrial membrane potential and independent of cellular swelling and calcium influx, two factors that disrupt microtubule growth dynamics. Super-resolution microscopy revealed microtubule buckling and breaking as a result of nsPEF application, suggesting that nsPEF may act directly on microtubules.

}, author = {Lynn Carr and Sylvia M. Bardet and Ryan C. Burke and Delia Arnaud-Cormos and Philippe Leveque and Rodney P. O{\textquoteright}Connor} } @article {48647, title = {The candidate multi-cut for cell segmentation.}, journal = {2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018)}, year = {2017}, month = {2017 Jul 04}, abstract = {

Two successful approaches for the segmentation of biomedical images are (1) the selection of segment candidates from a merge-tree, and (2) the clustering of small superpixels by solving a Multi-Cut problem. In this paper, we introduce a model that unifies both approaches. Our model, the Candidate Multi-Cut (CMC), allows joint selection and clustering of segment candidates from a merge-tree. This way, we overcome the respective limitations of the individual methods: (1) the space of possible segmentations is not constrained to candidates of a merge-tree, and (2) the decision for clustering can be made on candidates larger than superpixels, using features over larger contexts. We solve the optimization problem of selecting and clustering of candidates using an integer linear program. On datasets of 2D light microscopy of cell populations and 3D electron microscopy of neurons, we show that our method generalizes well and generates more accurate segmentations than merge-tree or Multi-Cut methods alone.

}, doi = {10.1109/ISBI.2018.8363658}, author = {Funke, Jan and Zhang, Chong and Pietzsch, Tobias and Gonzalez Ballester, Miguel A and Saalfeld, Stephan} } @article {49003, title = {A canonical neural mechanism for behavioral variability.}, journal = {Nature Communications}, volume = {8}, year = {2017}, month = {2017 May 22}, pages = {15415}, abstract = {

The ability to generate variable movements is essential for learning and adjusting complex behaviours. This variability has been linked to the temporal irregularity of neuronal activity in the central nervous system. However, how neuronal irregularity actually translates into behavioural variability is unclear. Here we combine modelling, electrophysiological and behavioural studies to address this issue. We demonstrate that a model circuit comprising topographically organized and strongly recurrent neural networks can autonomously generate irregular motor behaviours. Simultaneous recordings of neurons in singing finches reveal that neural correlations increase across the circuit driving song variability, in agreement with the model predictions. Analysing behavioural data, we find remarkable similarities in the babbling statistics of 5-6-month-old human infants and juveniles from three songbird species and show that our model naturally accounts for these {\textquoteright}universal{\textquoteright} statistics.

}, issn = {2041-1723}, doi = {10.1038/ncomms15415}, author = {Darshan, Ran and Wood, William E and Peters, Susan and Leblois, Arthur and Hansel, David} } @article {48960, title = {Cell dynamics underlying oriented growth of the Drosophila wing imaginal disc.}, journal = {Development (Cambridge, England)}, volume = {144}, year = {2017}, month = {2017 Dec 01}, pages = {4406-4421}, abstract = {

Quantitative analysis of the dynamic cellular mechanisms shaping the Drosophila wing during its larval growth phase has been limited, impeding our ability to understand how morphogen patterns regulate tissue shape. Such analysis requires explants to be imaged under conditions that maintain both growth and patterning, as well as methods to quantify how much cellular behaviors change tissue shape. Here, we demonstrate a key requirement for the steroid hormone 20-hydroxyecdysone (20E) in the maintenance of numerous patterning systems in vivo and in explant culture. We find that low concentrations of 20E support prolonged proliferation in explanted wing discs in the absence of insulin, incidentally providing novel insight into the hormonal regulation of imaginal growth. We use 20E-containing media to observe growth directly and to apply recently developed methods for quantitatively decomposing tissue shape changes into cellular contributions. We discover that whereas cell divisions drive tissue expansion along one axis, their contribution to expansion along the orthogonal axis is cancelled by cell rearrangements and cell shape changes. This finding raises the possibility that anisotropic mechanical constraints contribute to growth orientation in the wing disc.

}, keywords = {Animals, Animals, Genetically Modified, Body Patterning, Cell Proliferation, Drosophila melanogaster, Ecdysterone, Gene Expression Profiling, Gene Expression Regulation, Developmental, Genes, Insect, Imaginal Discs, Insulin, Morphogenesis, Signal Transduction, Transcription, Genetic, Wings, Animal}, issn = {1477-9129}, doi = {10.1242/dev.155069}, author = {Dye, Natalie A and Popovi{\'c}, Marko and Spannl, Stephanie and Etournay, Rapha{\"e}l and Kainm{\"u}ller, Dagmar and Ghosh, Suhrid and Myers, Eugene W and J{\"u}licher, Frank and Eaton, Suzanne} } @article {48858, title = {Cell volume change through water efflux impacts cell stiffness and stem cell fate.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, year = {2017}, month = {2017 Sep 25}, pages = {E8618-27}, abstract = {

Cells alter their mechanical properties in response to their local microenvironment; this plays a role in determining cell function and can even influence stem cell fate. Here, we identify a robust and unified relationship between cell stiffness and cell volume. As a cell spreads on a substrate, its volume decreases, while its stiffness concomitantly increases. We find that both cortical and cytoplasmic cell stiffness scale with volume for numerous perturbations, including varying substrate stiffness, cell spread area, and external osmotic pressure. The reduction of cell volume is a result of water efflux, which leads to a corresponding increase in intracellular molecular crowding. Furthermore, we find that changes in cell volume, and hence stiffness, alter stem-cell differentiation, regardless of the method by which these are induced. These observations reveal a surprising, previously unidentified relationship between cell stiffness and cell volume that strongly influences cell biology.

}, issn = {1091-6490}, doi = {10.1073/pnas.1705179114}, author = {Guo, Ming and Pegoraro, Adrian F and Mao, Angelo and Zhou, Enhua H and Arany, Praveen R and Han, Yulong and Burnette, Dylan T and Jensen, Mikkel H and Kasza, Karen E and Moore, Jeffrey R and Mackintosh, Frederick C and Fredberg, Jeffrey J and Mooney, David J and Lippincott-Schwartz, Jennifer and Weitz, David A} } @article {68762, title = {Centrioles initiate cilia assembly but are dispensable for maturation and maintenance in C. elegans}, journal = {Journal of Cell Biology}, volume = {216}, year = {2017}, month = {04/2017}, pages = {1659-1671}, abstract = {

Cilia are cellular projections that assemble on centriole-derived basal bodies. While cilia assembly is absolutely dependent on centrioles, it is not known to what extent they contribute to downstream events. The nematode C. elegans provides a unique opportunity to address this question, as centrioles do not persist at the base of mature cilia. Using fluorescence microscopy and electron tomography, we find that centrioles degenerate early during ciliogenesis. The transition zone and axoneme are not completely formed at this time, indicating that cilia maturation does not depend on intact centrioles. The hydrolethalus syndrome protein HYLS-1 is the only centriolar protein known to remain at the base of mature cilia and is required for intraflagellar transport trafficking. Surprisingly, targeted degradation of HYLS-1 after initiation of ciliogenesis does not affect ciliary structures. Taken together, our results indicate that while centrioles are essential to initiate cilia formation, they are dispensable for cilia maturation and maintenance.

}, issn = {0021-9525}, doi = {10.1083/jcb.201610070}, url = {https://doi.org/10.1083/jcb.201610070}, author = {Serwas, Daniel and Su, Tiffany Y. and Roessler, Max and Wang, Shaohe and Dammermann, Alexander} } @article {48664, title = {Chemistry is dead. Long live chemistry!}, journal = {Biochemistry}, volume = {56}, year = {2017}, month = {2017 Jul 13}, pages = {5165-70}, abstract = {

Chemistry, once king of fluorescence microscopy, was usurped by the field of fluorescent proteins. The increased demands of modern microscopy techniques on the {\textquotedblleft}photon budget{\textquotedblright} requires better and brighter fluorophores. Here, we review the recent advances in biochemistry, protein engineering, and organic synthesis that have allowed a triumphant return of chemical dyes to modern biological imaging.

}, doi = {10.1021/acs.biochem.7b00529}, author = {Lavis, Luke D} } @article {48979, title = {Chemogenetic tools for causal cellular and neuronal biology.}, journal = {Physiological Reviews}, year = {2017}, month = {2017 Dec 12}, abstract = {

Chemogenetic technologies enable selective pharmacological control of specific cell populations. An increasing number of approaches have been developed that modulate different signaling pathways. Selective pharmacological control over G protein-coupled receptor signaling, ion channel conductances, protein association, protein stability, and small molecule targeting allows modulation of cellular processes in distinct cell types. Here, we review these chemogenetic technologies and instances of their applications in complex tissues in vivo and ex vivo.

}, doi = {10.1152/physrev.00009.2017}, author = {Atasoy, Deniz and Sternson, Scott M} } @article {48268, title = {Cilia-mediated Hedgehog signaling controls form and function in the mammalian larynx.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Feb 08}, abstract = {

Acoustic communication is fundamental to social interactions among animals, including humans. In fact, deficits in voice impair the quality of life for a large and diverse population of patients. Understanding the molecular genetic mechanisms of development and function in the vocal apparatus is thus an important challenge with relevance both to the basic biology of animal communication and to biomedicine. However, surprisingly little is known about the developmental biology of the mammalian larynx. Here, we used genetic fate mapping to chart the embryological origins of the tissues in the mouse larynx, and we describe the developmental etiology of laryngeal defects in mice with disruptions in cilia-mediated Hedgehog signaling. In addition, we show that mild laryngeal defects correlate with changes in the acoustic structure of vocalizations. Together, these data provide key new insights in the molecular genetics of form and function in the mammalian vocal apparatus.

}, issn = {2050-084X}, doi = {10.7554/eLife.19153}, author = {Tabler, Jacqueline M and Rigney, Maggie M and Berman, Gordon J and Gopalakrishnan, Swetha and Heude, Eglantine and Al-Lami, Hadeel Adel and Yannakoudakis, Basil Z and Fitch, Rebecca D and Carter, Christopher M and Vokes, Steven A and Liu, Karen J and Tajbakhsh, Shahragim and Egnor, Se Roian and Wallingford, John B} } @article {48764, title = {A circuit node that integrates convergent input from neuromodulatory and social behavior-promoting neurons to control aggression in Drosophila.}, journal = {Neuron}, volume = {95}, year = {2017}, month = {2017 Aug 30}, pages = {1112-1128.e7}, abstract = {

Diffuse neuromodulatory systems such as norepinephrine (NE) control brain-wide states such as arousal, but whether they control complex social behaviors more specifically is not clear. Octopamine (OA), the insect homolog of NE, is known to promote both arousal and aggression. We have performed a\ systematic, unbiased screen to identify OA receptor-expressing neurons (OARNs) that control aggression in Drosophila. Our results uncover a tiny population of male-specific aSP2 neurons that mediate a specific influence of OA on aggression, independent of any effect on arousal. Unexpectedly, these neurons receive convergent input from OA neurons and P1 neurons, a population of FruM(+) neurons that promotes male courtship behavior. Behavioral epistasis experiments suggest that aSP2 neurons may constitute an integration node at which OAergic neuromodulation can bias the output of P1 neurons to favor aggression over inter-male courtship. These results have potential implications for thinking about\ the role of related neuromodulatory systems in mammals.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2017.08.017}, author = {Watanabe, Kiichi and Chiu, Hui and Pfeiffer, Barret D and Wong, Allan M and Hoopfer, Eric D and Rubin, Gerald M and Anderson, David J} } @article {48751, title = {Circuits in the rodent brainstem that control whisking in concert with other orofacial motor actions.}, journal = {Neuroscience}, volume = {368}, year = {2017}, month = {2017 Aug 23}, pages = {152-70}, abstract = {

The world view of rodents is largely determined by sensation on two length scales. One is within the animal{\textquoteright}s peri-personal space. Sensorimotor control on this scale involves active movements of the nose, tongue, head, and vibrissa, along with sniffing to determine olfactory clues. The second scale involves the detection of more distant space through vision and audition; these detection processes also impact repositioning of the head, eyes, and ears. Here we focus on orofacial motor actions, primarily vibrissa-based touch but including nose twitching, head bobbing, and licking, that control sensation at short, peri-personal distances. The orofacial nuclei for control of the motor plants, as well as primary and secondary sensory nuclei associated with these motor actions, lie within the hindbrain. The current data support three themes: First, the position of the sensors is determined by the summation of two drive signals, i.e., a fast rhythmic component and an evolving orienting component. Second, the rhythmic component is coordinated across all orofacial motor actions and is phase-locked to sniffing as the animal explores. Reverse engineering reveals that the preB{\"o}tzinger inspiratory complex provides the reset to the relevant premotor oscillators. Third, direct feedback from somatosensory trigeminal nuclei can rapidly alter motion of the sensors. This feedback is disynaptic and can be tuned by high-level inputs. The elucidation of synergistic coordination of orofacial motor actions to form behaviors, beyond that of a common rhythmic component, represents a work in progress that encompasses feedback through the midbrain and forebrain as well as hindbrain areas.

}, issn = {1873-7544}, doi = {10.1016/j.neuroscience.2017.08.034}, author = {McElvain, Lauren E and Friedman, Beth and Karten, Harvey J and Svoboda, Karel and Wang, Fan and Desch{\^e}nes, Martin and Kleinfeld, David} } @article {68437, title = {Classifying Drosophila Olfactory Projection Neuron Subtypes by Single-Cell RNA Sequencing.}, journal = {Cell}, volume = {171}, year = {2017}, month = {11/2017}, pages = {1206-1220.e22}, abstract = {

The definition of neuronal type and how it relates to the transcriptome are open questions. Drosophila olfactory projection neurons (PNs) are among the best-characterized neuronal types: different PN classes target dendrites to distinct olfactory glomeruli, while PNs of the same class exhibit indistinguishable anatomical and physiological properties. Using single-cell RNA sequencing, we comprehensively characterized the transcriptomes of most PN classes and unequivocally mapped transcriptomes to specific olfactory function for six classes. Transcriptomes of\ closely related PN classes exhibit the largest differences during circuit assembly but become indistinguishable in adults, suggesting that neuronal subtype diversity peaks during development. Transcription factors and cell-surface molecules are the most differentially expressed genes between classes and are highly informative in encoding cell identity, enabling us to identify a new lineage-specific transcription factor that instructs PN dendrite targeting. These findings establish that neuronal transcriptomic identity corresponds with anatomical and physiological identity defined by connectivity and function.

}, keywords = {Animals, Brain, Cluster Analysis, Dendrites, Drosophila melanogaster, Gene Expression Profiling, Neurons, Olfactory Bulb, Organ Specificity, Pupa, Sequence Analysis, RNA, Single-Cell Analysis, Transcription Factors}, issn = {1097-4172}, doi = {10.1016/j.cell.2017.10.019}, author = {Li, Hongjie and Horns, Felix and Wu, Bing and Xie, Qijing and Li, Jiefu and Li, Tongchao and Luginbuhl, David J and Quake, Stephen R and Luo, Liqun} } @article {48980, title = {Clustering single cells: a review of approaches on high-and low-depth single-cell RNA-seq data.}, journal = {Briefings in Functional Genomics}, volume = {17}, year = {2017}, month = {2017 Dec 11}, pages = {240-45}, abstract = {

Advances in single-cell RNA-sequencing technology have resulted in a wealth of studies aiming to identify transcriptomic cell types in various biological systems. There are multiple experimental approaches to isolate and profile single cells, which provide different levels of cellular and tissue coverage. In addition, multiple computational strategies have been proposed to identify putative cell types from single-cell data. From a data generation perspective, recent single-cell studies can be classified into two groups: those that distribute reads shallowly over large numbers of cells and those that distribute reads more deeply over a smaller cell population. Although there are advantages to both approaches in terms of cellular and tissue coverage, it is unclear whether different computational cell type identification methods are better suited to one or the other experimental paradigm. This study reviews three cell type clustering algorithms, each representing one of three broad approaches, and finds that PCA-based algorithms appear most suited to low read depth data sets, whereas gene clustering-based and biclustering algorithms perform better on high read depth data sets. In addition, highly related cell classes are better distinguished by higher-depth data, given the same total number of reads; however, simultaneous discovery of distinct and similar types is better served by lower-depth, higher cell number data. Overall, this study suggests that the depth of profiling should be determined by initial assumptions about the diversity of cells in the population, and that the selection of clustering algorithm(s) is subsequently based on the depth of profiling will allow for better identification of putative transcriptomic cell types.

}, issn = {2041-2657}, doi = {10.1093/bfgp/elx044}, author = {Menon, Vilas} } @article {48809, title = {Cohesin can remain associated with chromosomes during DNA replication.}, journal = {Cell Reports}, volume = {20}, year = {2017}, month = {2017 Sep 19}, pages = {2749-55}, abstract = {

To ensure disjunction to opposite poles during anaphase, sister chromatids must be held together following DNA replication. This is mediated by cohesin, which is thought to entrap sister DNAs inside a tripartite ring composed of its Smc and kleisin (Scc1) subunits. How such structures are created during S phase is poorly understood, in particular whether they are derived from complexes that had entrapped DNAs prior to replication. To address this, we used selective photobleaching to determine whether cohesin associated with chromatin in G1 persists in\ situ after replication. We developed a non-fluorescent HaloTag ligand to discriminate the fluorescence recovery signal from labeling of newly synthesized Halo-tagged Scc1 protein (pulse-chase or pcFRAP). In cells where cohesin turnover is inactivated by deletion of WAPL, Scc1 can remain associated with chromatin throughout S phase. These findings suggest that cohesion might be generated by cohesin that is already bound to un-replicated DNA.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2017.08.092}, author = {Rhodes, James D P and Haarhuis, Judith H I and Grimm, Jonathan B and Rowland, Benjamin D and Lavis, Luke D and Nasmyth, Kim A} } @article {48991, title = {Common fibrillar spines of amyloid-β and human Islet Amyloid Polypeptide revealed by Micro Electron Diffraction and inhibitors developed using structure-based design.}, journal = {The Journal of Biological Chemistry}, volume = {293}, year = {2017}, month = {2017 Dec 27}, pages = {2888-902}, abstract = {

Amyloid-β (Aβ) and human islet amyloid polypeptide (hIAPP) aggregate to form amyloid fibrils that deposit in tissues, and are associated with Alzheimer{\textquoteright}s disease (AD) and Type-II Diabetes (T2D), respectively. Individuals with T2D have an increased risk of developing AD, and conversely, AD patients have an increased risk of developing T2D. Evidence suggests that this link between AD and T2D might originate from a structural similarity between aggregates of Aβ and hIAPP. Using the cryoEM method Micro-Electron Diffraction (MicroED) we determined the atomic structures of 11-residue segments from both Aβ and hIAPP, termed Aβ 24-34 WT and hIAPP 19-29 S20G, with 64\% sequence similarity. We observe a high degree of structural similarity between their backbone atoms (0.96 {\r A} RMSD). Moreover, fibrils of these segments induce amyloid formation through self- and cross-seeding. Furthermore, inhibitors designed for one segment show cross-efficacy for full-length Aβ and hIAPP and reduce cytotoxicity of both proteins, though by apparently blocking different cytotoxic mechanisms. The similarity of the atomic structures of Aβ 24-34 WT and hIAPP 19-29 S20G offers a molecular model for cross-seeding between Aβ and hIAPP.

}, issn = {1083-351X}, doi = {10.1074/jbc.M117.806109}, author = {Krotee, Pascal and Griner, Sarah L and Sawaya, Michael R and Cascio, Duilio and Rodriguez, Jose A and Shi, Dan and Philipp, Stephan and Murray, Kevin and Saelices, Lorena and Lee, Ji and Seidler, Paul and Glabe, Charles G and Jiang, Lin and Gonen, Tamir and Eisenberg, David S} } @article {48836, title = {Community-based benchmarking improves spike inference from two-photon calcium imaging data.}, journal = {PLoS Computational Biology}, volume = {14}, year = {2017}, month = {2018 May 21}, pages = {e1006157}, abstract = {

In recent years, two-photon calcium imaging has become a standard tool to probe the function of neural circuits and to study computations in neuronal populations. However, the acquired signal is only an indirect measurement of neural activity due to the comparatively slow dynamics of fluorescent calcium indicators. Different algorithms for estimating spike rates from noisy calcium measurements have been proposed in the past, but it is an open question how far performance can be improved. Here, we report the results of the spikefinder challenge, launched to catalyze the development of new spike rate inference algorithms through crowd-sourcing. We present ten of the submitted algorithms which show improved performance compared to previously evaluated methods. Interestingly, the top-performing algorithms are based on a wide range of principles from deep neural networks to generative models, yet provide highly correlated estimates of the neural activity. The competition shows that benchmark challenges can drive algorithmic developments in neuroscience.

}, doi = {10.1371/journal.pcbi.1006157}, author = {Berens, Philipp and Freeman, Jeremy and Deneux, Thomas and Chenkov, Nicolay and McColgan, Thomas and Speiser, Artur and Macke, Jakob H and Turaga, Srinivas C and Mineault, Patrick and Rupprecht, Peter and Gerhard, Stephan and Friedrich, Rainer W and Friedrich, Johannes and Paninski, Liam and Pachitariu, Marius and Harris, Kenneth D and Bolte, Ben and Machado, Timothy A and Ringach, Dario and etal} } @article {48720, title = {The complete connectome of a learning and memory centre in an insect brain.}, journal = {Nature}, volume = {548}, year = {2017}, month = {2017 Aug 09}, pages = {175-182}, abstract = {

Associating stimuli with positive or negative reinforcement is essential for survival, but a complete wiring diagram of a higher-order circuit supporting associative memory has not been previously available. Here we reconstruct one such circuit at synaptic resolution, the Drosophila larval mushroom body. We find that most Kenyon cells integrate random combinations of inputs but that a subset receives stereotyped inputs from single projection neurons. This organization maximizes performance of a model output neuron on a stimulus discrimination task. We also report a novel canonical circuit in each mushroom body compartment with previously unidentified connections: reciprocal Kenyon cell to modulatory neuron connections, modulatory neuron to output neuron connections, and a surprisingly high number of recurrent connections between Kenyon cells. Stereotyped connections found between output neurons could enhance the selection of learned behaviours. The complete circuit map of the mushroom body should guide future functional studies of this learning and memory centre.

}, issn = {1476-4687}, doi = {10.1038/nature23455}, author = {Eichler, Katharina and Li, Feng and Litwin-Kumar, Ashok and Park, Youngser and Andrade, Ingrid and Schneider-Mizell, Casey M and Saumweber, Timo and Huser, Annina and Eschbach, Claire and Gerber, Bertram and Fetter, Richard D and Truman, James W and Priebe, Carey E and Abbott, L F and Thum, Andreas S and Zlatic, Marta and Cardona, Albert} } @article {48436, title = {The comprehensive connectome of a neural substrate for {\textquoteright}ON{\textquoteright} motion detection in Drosophila.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Apr 22}, abstract = {

Analysing computations in neural circuits often uses simplified models because the actual neuronal implementation is not known. For example, a problem in vision, how the eye detects image motion, has long been analysed using Hassenstein-Reichardt (HR) detector or Barlow-Levick (BL) models. These both simulate motion detection well, but the exact neuronal circuits undertaking these tasks remain elusive. We reconstructed a comprehensive connectome of the circuits of Drosophila{\textquoteright}s motion-sensing T4 cells using a novel EM technique. We uncover complex T4 inputs and reveal that putative excitatory inputs cluster at T4{\textquoteright}s dendrite shafts, while inhibitory inputs localize to the bases. Consistent with our previous study, we reveal that Mi1 and Tm3 cells provide most synaptic contacts onto T4. We are, however, unable to reproduce the spatial offset between these cells reported previously. Our comprehensive connectome reveals complex circuits that include candidate anatomical substrates for both HR and BL types of motion detectors.

}, issn = {2050-084X}, doi = {10.7554/eLife.24394}, author = {Takemura, Shin-ya and Nern, Aljoscha and Chklovskii, Dmitri B and Scheffer, Louis K and Rubin, Gerald M and Meinertzhagen, Ian A} } @article {48488, title = {Confirmation of five novel susceptibility loci for systemic lupus erythematosus (SLE) and integrated network analysis of 82 SLE susceptibility loci.}, journal = {Human Molecular Genetics}, volume = {26}, year = {2017}, month = {2017 Mar 15}, pages = {1205-1216}, abstract = {

We recently identified ten novel SLE susceptibility loci in Asians and uncovered several additional suggestive loci requiring further validation. This study aimed to replicate five of these suggestive loci in a Han Chinese cohort from Hong Kong, followed by meta-analysis (11,656 cases and 23,968 controls) on previously reported Asian and European populations, and to perform bioinformatic analyses on all 82 reported SLE loci to identify shared regulatory signatures. We performed a battery of analyses for these five loci, as well as joint analyses on all 82 SLE loci. All five loci passed genome-wide significance: MYNN (rs10936599, Pmeta = 1.92 {\texttimes} 10-13, OR = 1.14), ATG16L2 (rs11235604, Pmeta = 8.87 {\texttimes} 10 -12, OR = 0.78), CCL22 (rs223881, Pmeta = 5.87 {\texttimes} 10-16, OR = 0.87), ANKS1A (rs2762340, Pmeta = 4.93 {\texttimes} 10-15, OR = 0.87) and RNASEH2C (rs1308020, Pmeta = 2.96 {\texttimes} 10-19, OR = 0.84) and co-located with annotated gene regulatory elements. The novel loci share genetic signatures with other reported SLE loci, including effects on gene expression, transcription factor binding, and epigenetic characteristics. Most (56\%) of the correlated (r2 \> 0.8) SNPs from the 82 SLE loci were implicated in differential expression (9.81 {\texttimes} 10-198 \< P \< 5 {\texttimes} 10-3) of cis-genes. Transcription factor binding sites for p53, MEF2A and E2F1 were significantly (P \< 0.05) over-represented in SLE loci, consistent with apoptosis playing a critical role in SLE. Enrichment analysis revealed common pathways, gene ontology, protein domains, and cell type-specific expression. In summary, we provide evidence of five novel SLE susceptibility loci. Integrated bioinformatics using all 82 loci revealed that SLE susceptibility loci share many gene regulatory features, suggestive of conserved mechanisms of SLE etiopathogenesis.

}, keywords = {Adaptor Proteins, Signal Transducing, Asian Continental Ancestry Group, Autophagy-Related Proteins, Chemokine CCL22, Gene Expression Regulation, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Humans, Kruppel-Like Transcription Factors, Lupus Erythematosus, Systemic, Polymorphism, Single Nucleotide, Ribonuclease H}, issn = {1460-2083}, doi = {10.1093/hmg/ddx026}, author = {Molineros, Julio E and Yang, Wanling and Zhou, Xu-Jie and Sun, Celi and Okada, Yukinori and Zhang, Huoru and Heng Chua, Kek and Lau, Yu-Lung and Kochi, Yuta and Suzuki, Akari and Yamamoto, Kazuhiko and Ma, Jianyang and Bang, So-Young and Lee, Hye-Soon and Kim, Kwangwoo and Bae, Sang-Cheol and Zhang, Hong and Shen, Nan and Looger, Loren L and Nath, Swapan K} } @article {48302, title = {Conformational states of a soluble, uncleaved HIV-1 envelope trimer.}, journal = {Journal of Virology}, volume = {91}, year = {2017}, month = {2017 Mar 01}, pages = {e00175-17}, abstract = {

HIV-1 envelope spike [Env; trimeric (gp160)3, cleaved to (gp120/gp41)3] induces membrane fusion, leading to viral entry. It is also the viral component targeted by neutralizing antibodies. Vaccine development requires production, in quantities suitable for clinical studies, of a recombinant form that resembles functional Env. HIV-1 gp140 trimers - the uncleaved ectodomains of (gp160)3 - from a few selected viral isolates adopt a compact conformation with many antigenic properties of native Env spikes. One is currently being evaluated in a clinical trial. We report here low-resolution (20{\r A}) cryoEM (electron cryomicroscopy) structures of this gp140 trimer, which adopts two principal conformations, one closed and the other slightly open. The former is indistinguishable at this resolution from those adopted by a stabilized, cleaved trimer (SOSIP) or by a membrane-bound Env trimer with truncated cytoplasmic tail (EnvΔCT). The latter conformation is closer to a partially open Env trimer than to the fully open conformation induced by CD4. These results show that a stable, uncleaved HIV-1 gp140 trimer has a compact structure close to that of native Env.IMPORTANCE Development of any HIV vaccine with a protein component (either prime or boost) requires production of a recombinant form to mimic the trimeric, functional HIV-1 envelope spike, in quantities suitable for clinical studies. Our understanding of the envelope structure has depended in part on a cleaved, soluble trimer, known as SOSIP.664, stabilized by several modifications including an engineered disulfide. This construct, difficult to produce in large quantities, has yet to induce better antibody responses than other envelope-based immunogens, even in animal models. The uncleaved ectodomain of the envelope protein, called gp140, has also been made as a soluble form to mimic the native Env present on the virion surface. Most HIV-1 gp140 preparations are not stable, however, and of inhomogeneous conformation. The results presented here show that gp140 preparations from suitable isolates can adopt a compact, native-like structure, supporting its use as a vaccine candidate.

}, issn = {1098-5514}, doi = {10.1128/JVI.00175-17}, author = {Liu, Yuhang and Pan, Junhua and Cai, Yongfei and Grigorieff, Nikolaus and Harrison, Stephen C and Chen, Bing} } @article {48658, title = {A connectome of a learning and memory center in the adult Drosophila brain.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Jul 18}, pages = {e26975}, abstract = {

Understanding memory formation, storage and retrieval requires knowledge of the underlying neuronal circuits. In\ Drosophila, the mushroom body (MB) is the major site of associative learning. We reconstructed the morphologies and synaptic connections of all 983 neurons within the three functional units, or compartments, that compose the adult MB{\textquoteright}s α lobe, using a dataset of isotropic 8-nm voxels collected by focused ion-beam milling scanning electron microscopy. We found that Kenyon cells (KCs), whose sparse activity encodes sensory information, each make multiple\ en passant\ synapses to MB output neurons (MBONs) in each compartment. Some MBONs have inputs from all KCs, while others differentially sample sensory modalities. Only six percent of KC\>MBON synapses receive a direct synapse from a dopaminergic neuron (DAN). We identified two unanticipated classes of synapses, KC\>DAN and DAN\>MBON. DAN activation produces a slow depolarization of the MBON in these DAN\>MBON synapses and can weaken memory recall.

}, doi = {10.7554/eLife.26975}, author = {Takemura, Shin-ya and Aso, Yoshinori and Hige, Toshihide and Wong, Allan M and Lu, Zhiyuan and Xu, C Shan and Rivlin, Patricia K and Hess, Harald F and Zhao, Ting and Parag, Toufiq and Berg, Stuart and Huang, Gary and Katz, William T and Olbris, Donald J and Plaza, Stephen M and Umayam, Lowell A and Aniceto, Roxanne and Chang, Lei-Ann and Lauchie, Shirley and et al} } @article {48728, title = {A consensus view of ESCRT-mediated Human Immunodeficiency Virus Type 1 abscission.}, journal = {Annual Review of Virology}, volume = {4}, year = {2017}, month = {2017 Jul 17}, pages = {309-25}, abstract = {

The strong dependence of retroviruses, such as human immunodeficiency virus type 1 (HIV-1), on host cell factors is no more apparent than when the endosomal sorting complex required for transport (ESCRT) machinery is purposely disengaged. The resulting potent inhibition of retrovirus release underscores the importance of understanding fundamental structure-function relationships at the ESCRT-HIV-1 interface. Recent studies utilizing advanced imaging technologies have helped clarify these relationships, overcoming hurdles to provide a range of potential models for ESCRT-mediated virus abscission. Here, we discuss these models in the context of prior work detailing ESCRT machinery and the HIV-1 release process. To provide a template for further refinement, we propose a new working model for ESCRT-mediated HIV-1 release that reconciles disparate and seemingly conflicting studies. Expected final online publication date for the Annual Review of Virology Volume 4 is September 29, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

}, issn = {2327-0578}, doi = {10.1146/annurev-virology-101416-041840}, author = {Lippincott-Schwartz, J and Freed, E O and van Engelenburg, S B} } @article {48888, title = {Conserved neural circuit structure across Drosophila larva development revealed by comparative connectomics.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Oct 23}, pages = {e29089}, abstract = {

During postembryonic development, the nervous system must adapt to a growing body. How changes in neuronal structure and connectivity contribute to the maintenance of appropriate circuit function remains unclear. In a previous paper (Schneider-Mizell et al., 2016), we measured the cellular neuroanatomy underlying synaptic connectivity in Drosophila. Here, we examined how neuronal morphology and connectivity change between 1st instar and 3rd instar larval stages using serial section electron microscopy. We reconstructed nociceptive circuits in a larva of each stage and found consistent topographically arranged connectivity between identified neurons. Five-fold increases in each size, number of terminal dendritic branches, and total number of synaptic inputs were accompanied by cell-type specific connectivity changes that preserved the fraction of total synaptic input associated with each presynaptic partner. We propose that precise patterns of structural growth act to conserve the computational function of a circuit, for example determining the location of a dangerous stimulus.

}, issn = {2050-084X}, doi = {10.7554/eLife.29089}, author = {Gerhard, Stephan and Andrade, Ingrid and Fetter, Richard D and Cardona, Albert and Schneider-Mizell, Casey M} } @article {48547, title = {Contacts between the endoplasmic reticulum and other membranes in neurons.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, year = {2017}, month = {2017 May 30}, pages = {E4859-67}, abstract = {

Close appositions between the membrane of the endoplasmic reticulum (ER) and other intracellular membranes have important functions in cell physiology. These include lipid homeostasis, regulation of Ca(2+) dynamics, and control of organelle biogenesis and dynamics. Although these membrane contacts have previously been observed in neurons, their distribution and abundance have not been systematically analyzed. Here, we have used focused ion beam-scanning electron microscopy to generate 3D reconstructions of intracellular organelles and their membrane appositions involving the ER (distance <=30 nm) in different neuronal compartments. ER-plasma membrane (PM) contacts were particularly abundant in cell bodies, with large, flat ER cisternae apposed to the PM, sometimes with a notably narrow lumen (thin ER). Smaller ER-PM contacts occurred throughout dendrites, axons, and in axon terminals. ER contacts with mitochondria were abundant in all compartments, with the ER often forming a network that embraced mitochondria. Small focal contacts were also observed with tubulovesicular structures, likely to be endosomes, and with sparse multivesicular bodies and lysosomes found in our reconstructions. Our study provides an anatomical reference for interpreting information about interorganelle communication in neurons emerging from functional and biochemical studies.

}, issn = {1091-6490}, doi = {10.1073/pnas.1701078114}, author = {Wu, Yumei and Whiteus, Christina and Xu, C Shan and Hayworth, Kenneth J and Weinberg, Richard J and Hess, Harald F and De Camilli, Pietro} } @article {48750, title = {Contractile actomyosin arcs promote the activation of primary mouse T cells in a ligand-dependent manner.}, journal = {PLoS One}, volume = {12}, year = {2017}, month = {2017}, pages = {e0183174}, abstract = {

Mechano-transduction is an emerging but still poorly understood component of T cell activation. Here we investigated the ligand-dependent contribution made by contractile actomyosin arcs populating the peripheral supramolecular activation cluster (pSMAC) region of the immunological synapse (IS) to T cell receptor (TCR) microcluster transport and proximal signaling in primary mouse T cells. Using super resolution microscopy, OT1-CD8+ mouse T cells, and two ovalbumin (OVA) peptides with different affinities for the TCR, we show that the generation of organized actomyosin arcs depends on ligand potency and the ability of myosin 2 to contract actin filaments. While weak ligands induce disorganized actomyosin arcs, strong ligands result in organized actomyosin arcs that correlate well with tension-sensitive CasL phosphorylation and the accumulation of ligands at the IS center. Blocking myosin 2 contractility greatly reduces the difference in the extent of Src and LAT phosphorylation observed between the strong and the weak ligand, arguing that myosin 2-dependent force generation within actin arcs contributes to ligand discrimination. Together, our data are consistent with the idea that actomyosin arcs in the pSMAC region of the IS promote a mechano-chemical feedback mechanism that amplifies the accumulation of critical signaling molecules at the IS.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0183174}, author = {Hong, Jinsung and Murugesan, Sricharan and Betzig, Eric and Hammer, John A} } @article {48729, title = {Cortical actin recovery at the immunological synapse leads to termination of lytic granule secretion in cytotoxic T lymphocytes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, year = {2017}, month = {2017 Aug 08}, pages = {E6585-94}, abstract = {

CD8(+) cytotoxic T lymphocytes (CTLs) eliminate virally infected cells through directed secretion of specialized lytic granules. Because a single CTL can kill multiple targets, degranulation must be tightly regulated. However, how CTLs regulate the termination of granule secretion remains unclear. Previous work demonstrated that centralized actin reduction at the immune synapse precedes degranulation. Using a combination of live confocal, total internal reflection fluorescence, and superresolution microscopy, we now show that, after granule fusion, actin recovers at the synapse and no further secretion is observed. Depolymerization of actin led to resumed granule secretion, suggesting that recovered actin acts as a barrier preventing sustained degranulation. Furthermore, RAB27a-deficient CTLs, which do not secrete cytotoxic granules, failed to recover actin at the synapse, suggesting that RAB27a-mediated granule secretion is required for actin recovery. Finally, we show that both actin clearance and recovery correlated with synaptic phosphatidylinositol 4,5-bisphosphate (PIP2) and that alterations in PIP2 at the immunological synapse regulate cortical actin in CTLs, providing a potential mechanism through which CTLs control cortical actin density. Our work provides insight into actin-related mechanisms regulating CTL secretion that may facilitate serial killing during immune responses.

}, issn = {1091-6490}, doi = {10.1073/pnas.1710751114}, author = {Ritter, Alex T and Kapnick, Senta M and Murugesan, Sricharan and Schwartzberg, Pamela L and Griffiths, Gillian M and Lippincott-Schwartz, Jennifer} } @article {48622, title = {Cryo-electron tomography reveals novel features of a viral RNA replication compartment.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Jun 27}, abstract = {

Positive-strand RNA viruses, the largest genetic class of viruses, include numerous important pathogens such as Zika virus. These viruses replicate their RNA genomes in novel, membrane-bounded mini-organelles, but the organization of viral proteins and RNAs in these compartments is largely unknown. We used cryo-electron tomography to reveal many previously unrecognized features of Flock house nodavirus (FHV) RNA replication compartments. These spherular invaginations of outer mitochondrial membranes are packed with electron-dense RNA fibrils and their volumes are closely correlated with RNA replication template length. Each spherule{\textquoteright}s necked aperture is crowned by a striking cupped ring structure containing multifunctional FHV RNA replication protein A. Subtomogram averaging of these crowns revealed twelve-fold symmetry, concentric flanking protrusions, and a central electron density. Many crowns were associated with long cytoplasmic fibrils, likely to be exported progeny RNA. These results provide new mechanistic insights into positive-strand RNA virus replication compartment structure, assembly, function and control.

}, issn = {2050-084X}, doi = {10.7554/eLife.25940}, author = {Ertel, Kenneth J and Benefield, Desir{\'e}e and Casta{\~n}o-Diez, Daniel and Pennington, Janice and Horswill, Mark and den Boon, Johan A and Otegui, Marisa and Ahlquist, Paul} } @article {48489, title = {CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface.}, journal = {Journal of Molecular Biology}, volume = {429}, year = {2017}, month = {2017 May 12}, pages = {1829-39}, abstract = {

Structure-based vaccine design depends on extensive structural analyses of antigen-antibody complexes. Single-particle electron cryomicroscopy (cryoEM) can circumvent some of the problems of x-ray crystallography as a pipeline for obtaining the required structures. We have examined the potential of single-particle cryoEM for determining the structure of influenza-virus hemagglutinin (HA):single-chain Fv (scFv) complexes, by studying a complex we failed to crystallize in pursuing an extended project of the human immune response to influenza vaccines. The result shows that a combination of cryoEM and molecular modeling can yield details of the antigen:antibody interface, although small variation in the twist of the rod-like HA trimer limited the overall resolution to about 4.5{\r A}. Comparison of principal 3D classes suggests ways to modify the HA trimer to overcome this limitation. A closely related antibody from the same donor did yield crystals when bound with the same HA, giving us an independent validation of the cryoEM results The two structures also augment our understanding of receptor-binding site recognition by antibodies that neutralize a wide range of influenza-virus variants.

}, issn = {1089-8638}, doi = {10.1016/j.jmb.2017.05.011}, author = {Liu, Yuhang and Pan, Junhua and Jenni, Simon and Raymond, Donald D and Caradonna, Tim and Do, Khoi T and Schmidt, Aaron G and Harrison, Stephen C and Grigorieff, Nikolaus} } @article {48607, title = {Cytoskeletal actin dynamics shape a ramifying actin network underpinning immunological synapse formation.}, journal = {Science Advances}, volume = {3}, year = {2017}, month = {2017 Jun 21}, pages = {e1603032}, abstract = {

T cell activation and especially trafficking of T cell receptor microclusters during immunological synapse formation are widely thought to rely on cytoskeletal remodeling. However, important details on the involvement of actin in the latter transport processes are missing. Using a suite of advanced optical microscopes to analyze resting and activated T cells, we show that, following contact formation with activating surfaces, these cells sequentially rearrange their cortical actin across the entire cell, creating a previously unreported ramifying actin network above the immunological synapse. This network shows all the characteristics of an inward-growing transportation network and its dynamics correlating with T cell receptor rearrangements. This actin reorganization is accompanied by an increase in the nanoscale actin meshwork size and the dynamic adjustment of the turnover times and filament lengths of two differently sized filamentous actin populations, wherein formin-mediated long actin filaments support a very flat and stiff contact at the immunological synapse interface. The initiation of immunological synapse formation, as highlighted by calcium release, requires markedly little contact with activating surfaces and no cytoskeletal rearrangements. Our work suggests that incipient signaling in T cells initiates global cytoskeletal rearrangements across the whole cell, including a stiffening process for possibly mechanically supporting contact formation at the immunological synapse interface as well as a central ramified transportation network apparently directed at the consolidation of the contact and the delivery of effector functions.

}, doi = {10.1126/sciadv.1603032}, author = {Fritzsche, Marco and Fernandes, Ricardo A and Chang, Veronica T and Colin-York, Huw and Clausen, Mathias P and Felce, James H and Galiani, Silvia and Erlenk{\"a}mper, Christoph and Santos, Ana M and Heddleston, John M and Pedroza-Pacheco, Isabela and Waithe, Dominic and de la Serna, Jorge Bernadino and Lagerholm, B Christoffer and Liu, Tsung-Li and Chew, Teng-Leong and Betzig, Eric and Davis, Simon J and Eggeling, Christian} } @article {48413, title = {Deconstructing behavioral neuropharmacology with cellular specificity.}, journal = {Science (New York, N.Y.)}, volume = {356}, year = {2017}, month = {2017 Apr 07}, abstract = {

Behavior has molecular, cellular, and circuit determinants. However, because many proteins are broadly expressed, their acute manipulation within defined cells has been difficult. Here, we combined the speed and molecular specificity of pharmacology with the cell type specificity of genetic tools. DART (drugs acutely restricted by tethering) is a technique that rapidly localizes drugs to the surface of defined cells, without prior modification of the native target. We first developed an AMPAR antagonist DART, with validation in cultured neuronal assays, in slices of mouse dorsal striatum, and in behaving mice. In parkinsonian animals, motor deficits were causally attributed to AMPARs in indirect spiny projection neurons (iSPNs) and to excess phasic firing of tonically active interneurons (TANs). Together, iSPNs and TANs (i.e., D2 cells) drove akinesia, whereas movement execution deficits reflected the ratio of AMPARs in D2 versus D1 cells. Finally, we designed a muscarinic antagonist DART in one iteration, demonstrating applicability of the method to diverse targets.

}, issn = {1095-9203}, doi = {10.1126/science.aaj2161}, author = {Shields, Brenda C and Kahuno, Elizabeth and Kim, Charles and Apostolides, Pierre F and Brown, Jennifer and Lindo, Sarah and Mensh, Brett D and Dudman, Joshua T and Lavis, Luke D and Tadross, Michael R} } @article {48602, title = {Deep learning for isotropic super-resolution from non-isotropic 3D electron microscopy.}, journal = {International Conference on Medical Image Computing and Computer-Assisted Intervention - MICCAI 2017. MICCAI 2017. Lecture Notes in Computer Science}, volume = {10434}, year = {2017}, month = {2017 Sept 4}, pages = {arXiv:1706.03142}, abstract = {

The most sophisticated existing methods to generate 3D isotropic super-resolution (SR) from non-isotropic electron microscopy (EM) are based on learned dictionaries. Unfortunately, none of the existing methods generate practically satisfying results. For 2D natural images, recently developed super-resolution methods that use deep learning have been shown to significantly outperform the previous state of the art. We have adapted one of the most successful architectures (FSRCNN) for 3D super-resolution, and compared its performance to a 3D U-Net architecture that has not been used previously to generate super-resolution. We trained both architectures on artificially downscaled isotropic ground truth from focused ion beam milling scanning EM (FIB-SEM) and tested the performance for various hyperparameter settings.

Our results indicate that both architectures can successfully generate 3D isotropic super-resolution from non-isotropic EM, with the U-Net performing consistently better. We propose several promising directions for practical application.

}, doi = {10.1007/978-3-319-66185-8_16}, author = {Heinrich, Larissa and Bogovic, John A and Saalfeld, Stephan} } @article {48419, title = {Defects in ER-endosome contacts impact lysosome function in hereditary spastic paraplegia.}, journal = {The Journal of Cell Biology}, volume = {216}, year = {2017}, month = {2017 Apr 07}, pages = {1337-55}, abstract = {

Contacts between endosomes and the endoplasmic reticulum (ER) promote endosomal tubule fission, but the mechanisms involved and consequences of tubule fission failure are incompletely understood. We found that interaction between the microtubule-severing enzyme spastin and the ESCRT protein IST1 at ER-endosome contacts drives endosomal tubule fission. Failure of fission caused defective sorting of mannose 6-phosphate receptor, with consequently disrupted lysosomal enzyme trafficking and abnormal lysosomal morphology, including in mouse primary neurons and human stem cell-derived neurons. Consistent with a role for ER-mediated endosomal tubule fission in lysosome function, similar lysosomal abnormalities were seen in cellular models lacking the WASH complex component strumpellin or the ER morphogen REEP1. Mutations in spastin, strumpellin, or REEP1 cause hereditary spastic paraplegia (HSP), a disease characterized by axonal degeneration. Our results implicate failure of the ER-endosome contact process in axonopathy and suggest that coupling of ER-mediated endosomal tubule fission to lysosome function links different classes of HSP proteins, previously considered functionally distinct, into a unifying pathway for axonal degeneration.

}, issn = {1540-8140}, doi = {10.1083/jcb.201609033}, author = {Allison, Rachel and Edgar, James R and Pearson, Guy and Rizo, Tania and Newton, Timothy and G{\"u}nther, Sven and Berner, Fiamma and Hague, Jennifer and Connell, James W and Winkler, J{\"u}rgen and Lippincott-Schwartz, Jennifer and Beetz, Christian and Winner, Beate and Reid, Evan} } @article {48648, title = {Desensitized D2 autoreceptors are resistant to trafficking.}, journal = {Scientific Reports}, volume = {7}, year = {2017}, month = {2017 Jun 29}, pages = {4379}, abstract = {

Dendritic release of dopamine activates dopamine D2 autoreceptors, which are inhibitory G protein-coupled receptors (GPCRs), to decrease the excitability of dopamine neurons. This study used tagged D2 receptors to identify the localization and distribution of these receptors in living midbrain dopamine neurons. GFP-tagged D2 receptors were found to be unevenly clustered on the soma and dendrites of dopamine neurons within the substantia nigra pars compacta (SNc). Physiological signaling and desensitization of the tagged receptors were not different from wild type receptors. Unexpectedly, upon desensitization the tagged D2 receptors were not internalized. When tagged D2 receptors were expressed in locus coeruleus neurons, a desensitizing protocol induced significant internalization. Likewise, when tagged {\textmu}-opioid receptors were expressed in dopamine neurons they too were internalized. The distribution and lack of agonist-induced internalization of D2 receptors on dopamine neurons indicate a purposefully regulated localization of these receptors.

}, issn = {2045-2322}, doi = {10.1038/s41598-017-04728-z}, author = {Robinson, Brooks G and Bunzow, James R and Grimm, Jonathan B and Lavis, Luke D and Dudman, Joshua T and Brown, Jennifer and Neve, Kim A and Williams, John T} } @article {48463, title = {Detachable glass microelectrodes for recording action potentials in active moving organs.}, journal = {American Journal of Physiology. Heart and Circulatory Physiology}, volume = {312}, year = {2017}, month = {2017 May 05}, pages = {H1248-59}, abstract = {

We describe new detachable floating glass micropipette electrode devices that provide targeted action potential recordings in active moving organs without requiring constant mechanical constraint or pharmacological inhibition of tissue motion. The technology is based on the concept of a glass micropipette electrode that is held firmly during cell targeting and intracellular insertion, after which a 100{\textmu}g glass microelectrode, a "microdevice", is gently released to remain within the moving organ. The microdevices provide long-term recordings of action potentials, even during millimeter-scale movement of tissue in which the device is embedded. We demonstrate two different glass micropipette electrode holding and detachment designs appropriate for the heart (sharp glass microdevices for cardiac myocytes in rats, guinea pigs and humans) and the brain (patch glass microdevices for neurons in rats). We explain how microdevices enable measurements of multiple cells within a moving organ that are typically difficult with other technologies. Using sharp microdevices, action potential duration (APD) was monitored continuously for 15 minutes in unconstrained perfused hearts during global ischemia-reperfusion, providing beat-to-beat measurements of changes in APD. Action potentials from neurons in the hippocampus of anaesthetized rats were measured with patch microdevices, which provided stable base potentials during long-term recordings. Our results demonstrate that detachable microdevices are an elegant and robust tool to record electrical activity with high temporal resolution and cellular level localization without disturbing the physiological working conditions of the organ.

}, issn = {1522-1539}, doi = {10.1152/ajpheart.00741.2016}, author = {Barbic, Mladen and Moreno, Angel and Harris, Timothy D and Kay, Matthew W} } @article {48511, title = {Development of photostable fluorophores for molecular imaging.}, journal = {Current Opinion in Chemical Biology}, volume = {39}, year = {2017}, month = {2017 May 22}, pages = {32-38}, abstract = {

Advances in fluorescence microscopy promise to unlock details of biological systems with high spatiotemporal precision. These new techniques also place a heavy demand on the {\textquoteright}photon budget{\textquoteright}-the number of photons one can extract from a sample. Improving the photostability of small molecule fluorophores using chemistry is a straightforward method for increasing the photon budget. Here, we review the (sometimes sparse) efforts to understand the mechanism of fluorophore photobleaching and recent advances to improve photostability through reducing the propensity for oxidation or through intramolecular triplet-state quenching. Our intent is to inspire a more thorough mechanistic investigation of photobleaching and the use of precise chemistry to improve fluorescent probes.

}, issn = {1879-0402}, doi = {10.1016/j.cbpa.2017.04.017}, author = {Zheng, Qinsi and Lavis, Luke D} } @article {65780, title = {Discovery of chemoautotrophic symbiosis in the giant shipworm Kuphus polythalamia (Bivalvia: Teredinidae) extends wooden-steps theory}, journal = {Proceedings of the National Academy of Sciences}, volume = {114}, year = {2017}, month = {05/2017}, pages = {E3652{\textendash}E3658}, abstract = {

Certain marine invertebrates harbor chemosynthetic bacterial symbionts, giving them the remarkable ability to consume inorganic chemicals such as hydrogen sulfide (H2S) rather than organic matter as food. These chemosynthetic animals are found near geochemical (e.g., hydrothermal vents) or biological (e.g., decaying wood or large animal carcasses) sources of H2S on the seafloor. Although many such symbioses have been discovered, little is known about how or where they originated. Here, we demonstrate a new chemosynthetic symbiosis in the giant teredinid bivalve (shipworm) Kuphus polythalamia and show that this symbiosis arose in a wood-eating ancestor via the displacement of ancestral cellulolytic symbionts by sulfur-oxidizing invaders. Here, wood served as an evolutionary stepping stone for a dramatic transition from heterotrophy to chemoautotrophy.The {\textquotedblleft}wooden-steps{\textquotedblright} hypothesis [Distel DL, et al. (2000) Nature 403:725{\textendash}726] proposed that large chemosynthetic mussels found at deep-sea hydrothermal vents descend from much smaller species associated with sunken wood and other organic deposits, and that the endosymbionts of these progenitors made use of hydrogen sulfide from biogenic sources (e.g., decaying wood) rather than from vent fluids. Here, we show that wood has served not only as a stepping stone between habitats but also as a bridge between heterotrophic and chemoautotrophic symbiosis for the giant mud-boring bivalve Kuphus polythalamia. This rare and enigmatic species, which achieves the greatest length of any extant bivalve, is the only described member of the wood-boring bivalve family Teredinidae (shipworms) that burrows in marine sediments rather than wood. We show that K. polythalamia harbors sulfur-oxidizing chemoautotrophic (thioautotrophic) bacteria instead of the cellulolytic symbionts that allow other shipworm species to consume wood as food. The characteristics of its symbionts, its phylogenetic position within Teredinidae, the reduction of its digestive system by comparison with other family members, and the loss of morphological features associated with wood digestion indicate that K. polythalamia is a chemoautotrophic bivalve descended from wood-feeding (xylotrophic) ancestors. This is an example in which a chemoautotrophic endosymbiosis arose by displacement of an ancestral heterotrophic symbiosis and a report of pure culture of a thioautotrophic endosymbiont.

}, issn = {0027-8424}, doi = {10.1073/pnas.1620470114}, url = {https://www.pnas.org/content/114/18/E3652}, author = {Distel, Daniel L. and Altamia, Marvin A. and Lin, Zhenjian and Shipway, J. Reuben and Han, Andrew and Forteza, Imelda and Antemano, Rowena and Limbaco, Ma. Gwen J. Pe{\~n}aflor and Tebo, Alison G. and Dechavez, Rande and Albano, Julie and Rosenberg, Gary and Concepcion, Gisela P. and Schmidt, Eric W. and Haygood, Margo G.} } @article {48786, title = {Dissection of the Drosophila neuropeptide F circuit using a high-throughput two-choice assay.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, year = {2017}, month = {2017 Sep 05}, pages = {e8091-9}, abstract = {

In their classic experiments, Olds and Milner showed that rats learn to lever press to receive an electric stimulus in specific brain regions. This led to the identification of mammalian reward centers. Our interest in defining the neuronal substrates of reward perception in the fruit fly Drosophila melanogaster prompted us to develop a simpler experimental approach wherein flies could implement behavior that induces self-stimulation of specific neurons in their brains. The high-throughput assay employs optogenetic activation of neurons when the fly occupies a specific area of a behavioral chamber, and the flies{\textquoteright} preferential occupation of this area reflects their choosing to experience optogenetic stimulation. Flies in which neuropeptide F (NPF) neurons are activated display preference for the illuminated side of the chamber. We show that optogenetic activation of NPF neuron is rewarding in olfactory conditioning experiments and that the preference for NPF neuron activation is dependent on NPF signaling. Finally, we identify a small subset of NPF-expressing neurons located in the dorsomedial posterior brain that are sufficient to elicit preference in our assay. This assay provides the means for carrying out unbiased screens to map reward neurons in flies.

}, issn = {1091-6490}, doi = {10.1073/pnas.1710552114}, author = {Shao, Lisha and Saver, Mathias and Chung, Phuong and Ren, Qingzhong and Lee, Tzumin and Kent, Clement F and Heberlein, Ulrike} } @article {48983, title = {Divergent connectivity of homologous command-like neurons mediates segment-specific touch responses in Drosophila.}, journal = {Neuron}, volume = {96}, year = {2017}, month = {2017 Dec 20}, pages = {1373-87}, abstract = {

Animals adaptively respond to a tactile stimulus by choosing an ethologically relevant behavior depending on the location of the stimuli. Here, we investigate how somatosensory inputs on different body segments are linked to distinct motor outputs in Drosophila larvae. Larvae escape by backward locomotion when touched on the head, while they crawl forward when touched on the tail. We identify a class of segmentally repeated second-order somatosensory interneurons, that we named Wave, whose activation in anterior and posterior segments elicit backward and forward locomotion, respectively. Anterior and posterior Wave neurons extend their dendrites in opposite directions to receive somatosensory inputs from the head and tail, respectively. Downstream of anterior Wave neurons, we identify premotor circuits including the neuron A03a5, which together with Wave, is necessary for the backward locomotion touch response. Thus, Wave neurons match their receptive field to appropriate motor programs by participating in different circuits in different segments.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2017.10.030}, author = {Takagi, Suguru and Cocanougher, Benjamin Thomas and Niki, Sawako and Miyamoto, Dohjin and Kohsaka, Hiroshi and Kazama, Hokto and Fetter, Richard Doty and Truman, James William and Zlatic, Marta and Cardona, Albert and Nose, Akinao} } @article {48416, title = {Diverse protocols for correlative super-resolution fluorescence imaging and electron microscopy of chemically fixed samples.}, journal = {Nature Protocols}, volume = {12}, year = {2017}, month = {2017 May}, pages = {916-946}, abstract = {

Our groups have recently developed related approaches for sample preparation for super-resolution imaging within endogenous cellular environments using correlative light and electron microscopy (CLEM). Four distinct techniques for preparing and acquiring super-resolution CLEM data sets for aldehyde-fixed specimens are provided, including Tokuyasu cryosectioning, whole-cell mount, cell unroofing and platinum replication, and resin embedding and sectioning. The choice of the best protocol for a given application depends on a number of criteria that are discussed in detail. Tokuyasu cryosectioning is relatively rapid but is limited to small, delicate specimens. Whole-cell mount has the simplest sample preparation but is restricted to surface structures. Cell unroofing and platinum replication creates high-contrast, 3D images of the cytoplasmic surface of the plasma membrane but is more challenging than whole-cell mount. Resin embedding permits serial sectioning of large samples but is limited to osmium-resistant probes, and is technically difficult. Expected results from these protocols include super-resolution localization (\~{}10-50 nm) of fluorescent targets within the context of electron microscopy ultrastructure, which can help address cell biological questions. These protocols can be completed in 2-7 d, are compatible with a number of super-resolution imaging protocols, and are broadly applicable across biology.

}, issn = {1750-2799}, doi = {10.1038/nprot.2017.017}, author = {Kopek, Benjamin G and Paez-Segala, Maria G and Shtengel, Gleb and Sochacki, Kem A and Sun, Mei G and Wang, Yalin and Xu, C Shan and Van Engelenburg, Schuyler B and Taraska, Justin W and Looger, Loren L and Hess, Harald F} } @article {48561, title = {Drosophila courtship conditioning as a measure of learning and memory.}, journal = {Journal of Visualized Experiments - Neuroscience }, year = {2017}, month = {2017-06-05}, pages = {e55808}, abstract = {

Many insights into the molecular mechanisms underlying learning and memory have been elucidated through the use of simple behavioral assays in model organisms such as the fruit fly,\ Drosophila melanogaster.\ Drosophila\ is useful for understanding the basic neurobiology underlying cognitive deficits resulting from mutations in genes associated with human cognitive disorders, such as intellectual disability (ID) and autism. This work describes a methodology for testing learning and memory using a classic paradigm in\ Drosophilaknown as courtship conditioning. Male flies\ court females using a distinct pattern of easily recognizable behaviors. Premated females are not receptive to mating and will reject the male{\textquoteright}s copulation attempts. In response to this rejection, male flies reduce their courtship behavior. This learned reduction in courtship behavior is measured over time, serving as an indicator of learning and memory. The basic numerical output of this assay is the courtship index (CI), which is defined as the percentage of time that a male spends courting during a 10 min interval. The learning index (LI) is the relative reduction of CI in flies that have been exposed to a premated female compared to na{\"\i}ve flies with no previous social encounters. For the statistical comparison of LIs between genotypes, a randomization test with bootstrapping is used. To illustrate how the assay can be used to address the role of a gene relating to learning and memory, the pan-neuronal knockdown of\ Dihydroxyacetone phosphate acyltransferase\ (Dhap-at) was characterized here. The human ortholog\ of\ Dhap-at,\ glyceronephosphate O-acyltransferase\ (GNPT), is involved in rhizomelic chondrodysplasia punctata type 2, an autosomal-recessive syndrome characterized by severe ID. Using the courtship conditioning assay, it was determined that Dhap-at is required for long-term memory, but not for short-term memory. This result serves as a basis for further investigation of the underlying molecular mechanisms.

}, doi = {10.3791/55808}, author = {Koemans, Tom S and Oppitz, Cornelia and Donders, Rogier AT and van Bokhoven, Hans and Schenck, Annette and Keleman, Krystyna and Kramer, Jamie M} } @article {65095, title = {Dual near-Infrared two-photon microscopy for deep-tissue dopamine nanosensor imaging.}, journal = {Advanced Functional Materials}, volume = {27}, year = {2017}, month = {2017 August 15}, pages = {1702112}, abstract = {

A key limitation for achieving deep imaging in biological structures lies in photon absorption and scattering leading to attenuation of fluorescence. In particular, neurotransmitter imaging is challenging in the biologically relevant context of the intact brain for which photons must traverse the cranium, skin, and bone. Thus, fluorescence imaging is limited to the surface cortical layers of the brain, only achievable with craniotomy. Herein, this study describes optimal excitation and emission wavelengths for through-cranium imaging, and demonstrates that near-infrared emissive nanosensors can be photoexcited using a two-photon 1560 nm excitation source. Dopamine-sensitive nanosensors can undergo two-photon excitation, and provide chirality-dependent responses selective for dopamine with fluorescent turn-on responses varying between 20\% and 350\%. The two-photon absorption cross-section and quantum yield of dopamine nanosensors are further calculated, and a two-photon power law relationship for the nanosensor excitation process is confirmed. Finally, the improved image quality of the nanosensors embedded 2-mm-deep into a brain-mimetic tissue phantom is shown, whereby one-photon excitation yields 42\% scattering, in contrast to 4\% scattering when the same object is imaged under two-photon excitation. The approach overcomes traditional limitations in deep-tissue fluorescence microscopy, and can enable neurotransmitter imaging in the biologically relevant milieu of the intact and living brain.

}, doi = {10.1002/adfm.v27.3910.1002/adfm.201702112}, url = {http://doi.wiley.com/10.1002/adfm.v27.39http://doi.wiley.com/10.1002/adfm.201702112https://onlinelibrary.wiley.com/doi/full/10.1002/adfm.201702112https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002\%2Fadfm.201702112}, author = {Bonis-O{\textquoteright}Donnell, Jackson T. Del and Page, Ralph H. and Beyene, Abraham G. and Tindall, Eric G. and McFarlane, Ian R. and Landry, Markita P.} } @article {68338, title = {Dual origin of enteric neurons in vagal Schwann cell precursors and the sympathetic neural crest}, journal = {Proceedings of the National Academy of Sciences}, volume = {114}, year = {2017}, month = {10/2017}, pages = {11980-11985}, abstract = {

Most of the enteric nervous system derives from the {\textquotedblleft}vagal{\textquotedblright} neural crest, lying at the level of somites 1{\textendash}7, which invades the digestive tract rostro-caudally from the foregut to the hindgut. Little is known about the initial phase of this colonization, which brings enteric precursors into the foregut. Here we show that the {\textquotedblleft}vagal crest{\textquotedblright} subsumes two populations of enteric precursors with contrasted origins, initial modes of migration, and destinations. Crest cells adjacent to somites 1 and 2 produce Schwann cell precursors that colonize the vagus nerve, which in turn guides them into the esophagus and stomach. Crest cells adjacent to somites 3{\textendash}7 belong to the crest streams contributing to sympathetic chains: they migrate ventrally, seed the sympathetic chains, and colonize the entire digestive tract thence. Accordingly, enteric ganglia, like sympathetic ones, are atrophic when deprived of signaling through the tyrosine kinase receptor ErbB3, while half of the esophageal ganglia require, like parasympathetic ones, the nerve-associated form of the ErbB3 ligand, Neuregulin-1. These dependencies might bear relevance to Hirschsprung disease, with which alleles of Neuregulin-1 are associated.

}, doi = {10.1073/pnas.1710308114}, url = {https://www.pnas.org/doi/abs/10.1073/pnas.1710308114}, author = {Isabel Espinosa-Medina and Ben Jevans and Franck Boismoreau and Zoubida Chettouh and Hideki Enomoto and Thomas M{\"u}ller and Carmen Birchmeier and Alan J. Burns and Jean-Fran{\c c}ois Brunet} } @article {48859, title = {A dynamic interplay of enhancer elements regulates Klf4 expression in na{\"\i}ve pluripotency.}, journal = {Genes \& Development}, volume = {31}, year = {2017}, month = {2017 Sep 01}, pages = {1795-1808}, abstract = {

Transcription factor (TF)-directed enhanceosome assembly constitutes a fundamental regulatory mechanism driving spatiotemporal gene expression programs during animal development. Despite decades of study, we know little about the dynamics or order of events animating TF assembly at cis-regulatory elements in living cells and the long-range molecular "dialog" between enhancers and promoters. Here, combining genetic, genomic, and imaging approaches, we characterize a complex long-range enhancer cluster governing Kr{\"u}ppel-like factor 4 (Klf4) expression in na{\"\i}ve pluripotency. Genome editing by CRISPR/Cas9 revealed that OCT4 and SOX2 safeguard an accessible chromatin neighborhood to assist the binding of other TFs/cofactors to the enhancer. Single-molecule live-cell imaging uncovered that two na{\"\i}ve pluripotency TFs, STAT3 and ESRRB, interrogate chromatin in a highly dynamic manner, in which SOX2 promotes ESRRB target search and chromatin-binding dynamics through a direct protein-tethering mechanism. Together, our results support a highly dynamic yet intrinsically ordered enhanceosome assembly to maintain the finely balanced transcription program underlying na{\"\i}ve pluripotency.

}, issn = {1549-5477}, doi = {10.1101/gad.303321.117}, author = {Xie, Liangqi and Torigoe, Sharon E and Xiao, Jifang and Mai, Daniel H and Li, Li and Davis, Fred P and Dong, Peng and Marie-Nelly, Herve and Grimm, Jonathan and Lavis, Luke and Darzacq, Xavier and Cattoglio, Claudia and Liu, Zhe and Tjian, Robert} } @article {48961, title = {Editorial overview: Making evolutionary sense of everything.}, journal = {Current Opinion in Genetics \& Development}, volume = {47}, year = {2017}, month = {2017 Dec}, pages = {iv-vi}, issn = {1879-0380}, doi = {10.1016/j.gde.2017.11.005}, author = {Stern, David L and Haag, Eric} } @article {48369, title = {Efficient method for whole-cell recording in freely moving rodents using ultraviolet-cured collar-based pipette stabilization.}, journal = {Cold Spring Harbor Protocols}, volume = {2017}, year = {2017}, month = {2017 Apr 03}, pages = {pdb.prot095810}, abstract = {

Whole-cell recording is a key technique for investigating synaptic and cellular mechanisms underlying various brain functions. However, because of its high sensitivity to mechanical disturbances, applying the whole-cell recording method to freely moving animals has been challenging. Here, we describe a technique for obtaining such recordings in freely moving, drug-free animals with a high success rate. This technique involves three major steps: obtaining a whole-cell recording from awake head-fixed animals, reliable and efficient stabilization of the pipette with respect to the animal{\textquoteright}s head using an ultraviolet (UV)-transparent collar and UV-cured adhesive, and rapid release of the animal from head fixation without loss of the recording. This technique has been successfully applied to obtain intracellular recordings from the hippocampus of freely moving rats and mice exploring a spatial environment, and should be generally applicable to other brain areas in animals engaged in a variety of natural behaviors.

}, issn = {1559-6095}, doi = {10.1101/pdb.prot095810}, author = {Lee, Doyun and Lee, Albert K} } @article {48192, title = {Electrophoresis of polar fluorescent tracers through the nerve sheath labels neuronal populations for anatomical and functional imaging.}, journal = {Scientific Reports}, volume = {7}, year = {2017}, month = {2017 Jan 13}, pages = {40433}, abstract = {

The delivery of tracers into populations of neurons is essential to visualize their anatomy and analyze their function. In some model systems genetically-targeted expression of fluorescent proteins is the method of choice; however, these genetic tools are not available for most organisms and alternative labeling methods are very limited. Here we describe a new method for neuronal labelling by electrophoretic dye delivery from a suction electrode directly through the neuronal sheath of nerves and ganglia in insects. Polar tracer molecules were delivered into the locust auditory nerve without destroying its function, simultaneously staining peripheral sensory structures and central axonal projections. Local neuron populations could be labelled directly through the surface of the brain, and in-vivo optical imaging of sound-evoked activity was achieved through the electrophoretic delivery of calcium indicators. The method provides a new tool for studying how stimuli are processed in peripheral and central sensory pathways and is a significant advance for the study of nervous systems in non-model organisms.

}, issn = {2045-2322}, doi = {10.1038/srep40433}, author = {Isaacson, Matthew D and Hedwig, Berthold} } @article {48414, title = {The emergence of directional selectivity in the visual motion pathway of Drosophila.}, journal = {Neuron}, volume = {94}, year = {2017}, month = {2017 Apr 05}, pages = {168-182.e10}, abstract = {

The perception of visual motion is critical for animal navigation, and flies are a prominent model system for exploring this neural computation. In Drosophila, the T4 cells of the medulla are directionally selective and necessary for ON motion behavioral responses. To examine the emergence of directional selectivity, we developed genetic driver lines for the neuron types with the most synapses onto T4 cells. Using calcium imaging, we found that these neuron types are not directionally selective and that selectivity arises in the T4 dendrites. By silencing each input neuron type, we identified which neurons are necessary for T4 directional selectivity and ON motion behavioral responses. We then determined the sign of the connections between these neurons and T4 cells using neuronal photoactivation. Our results indicate a computational architecture for motion detection that is a hybrid of classic theoretical models.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2017.03.010}, author = {Strother, James A and Wu, Shiuan-Tze and Wong, Allan M and Nern, Aljoscha and Rogers, Edward M and Le, Jasmine Q and Rubin, Gerald M and Reiser, Michael B} } @article {48994, title = {Emergence of reward expectation signals in identified dopamine neurons.}, journal = {bioRxiv}, year = {2017}, month = {2017 Dec 22}, abstract = {

Coherent control of purposive actions emerges from the coordination of multiple brain circuits during learning. Dissociable brain circuits and cell-types are thought to preferentially participate in distinct learning mechanisms. For example, the activity of midbrain dopamine (mDA) neurons is proposed to primarily, or even exclusively, reflect reward prediction error signals in well-trained animals. To study the specific contribution of individual circuits requires observing changes before tight functional coordination is achieved. However, little is known about the detailed timing of the emergence of reward-related representations in dopaminergic neurons. Here we recorded activity of identified dopaminergic neurons as naive mice learned a novel stimulus-reward association. We found that at early stages of learning mDA neuron activity reflected both external (sensory) and internal (action initiation) causes of reward expectation. The increasingly precise correlation of action initiation with sensory stimuli rather than an evaluation of outcomes governed mDA neuron activity. Thus, our data demonstrate that mDA neuron activity early in learning does not reflect errors, but is more akin to a Hebbian learning signal - providing new insight into a critical computation in a highly conserved, essential learning circuit.

}, doi = {10.1101/238881}, author = {Coddington, Luke T and Dudman, Joshua T} } @article {48490, title = {Enhanced FIB-SEM systems for large-volume 3D imaging.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 May 13}, abstract = {

Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) can automatically generate 3D images with superior z-axis resolution, yielding data that needs minimal image registration and related post-processing. Obstacles blocking wider adoption of FIB-SEM include slow imaging speed and lack of long-term system stability, which caps the maximum possible acquisition volume. Here we present techniques that accelerate image acquisition while greatly improving FIB-SEM reliability, allowing the system to operate for months and generating continuously imaged volumes \> 10(6) {\textmu}m(3). These volumes are large enough for connectomics, where the excellent z resolution can help in tracing of small neuronal processes and accelerate the tedious and time-consuming human proofreading effort. Even higher resolution can be achieved on smaller volumes. We present example data sets from mammalian neural tissue, Drosophila brain, and Chlamydomonas reinhardtii to illustrate the power of this novel high-resolution technique to address questions in both connectomics and cell biology.

}, issn = {2050-084X}, doi = {10.7554/eLife.25916}, author = {Xu, C Shan and Hayworth, Kenneth J and Lu, Zhiyuan and Grob, Patricia and Hassan, Ahmed M and Garc{\'\i}a-Cerd{\'a}n, Jos{\'e} G and Niyogi, Krishna K and Nogales, Eva and Weinberg, Richard J and Hess, Harald F} } @article {65018, title = {Ensemble cryo-EM elucidates the mechanism of translation fidelity.}, journal = {Nature}, volume = {546}, year = {2017}, month = {2017 Jun 01}, pages = {113-117}, abstract = {

Gene translation depends on accurate decoding of mRNA, the structural mechanism of which remains poorly understood. Ribosomes decode mRNA codons by selecting cognate aminoacyl-tRNAs delivered by elongation factor Tu (EF-Tu). Here we present high-resolution structural ensembles of ribosomes with cognate or near-cognate aminoacyl-tRNAs delivered by EF-Tu. Both cognate and near-cognate tRNA anticodons explore the aminoacyl-tRNA-binding site (A site) of an open 30S subunit, while inactive EF-Tu is separated from the 50S subunit. A transient conformation of decoding-centre nucleotide G530 stabilizes the cognate codon-anticodon helix, initiating step-wise {\textquoteright}latching{\textquoteright} of the decoding centre. The resulting closure of the 30S subunit docks EF-Tu at the sarcin-ricin loop of the 50S subunit, activating EF-Tu for GTP hydrolysis and enabling accommodation of the aminoacyl-tRNA. By contrast, near-cognate complexes fail to induce the G530 latch, thus favouring open 30S pre-accommodation intermediates with inactive EF-Tu. This work reveals long-sought structural differences between the pre-accommodation of cognate and near-cognate tRNAs that elucidate the mechanism of accurate decoding.

}, keywords = {Anticodon, Codon, Cryoelectron Microscopy, Escherichia coli, GTP Phosphohydrolases, Guanosine Triphosphate, Hydrolysis, Models, Molecular, Peptide Elongation Factor Tu, Protein Biosynthesis, Protein Domains, Ribosome Subunits, Ribosomes, RNA, Ribosomal, 16S, RNA, Transfer, Amino Acyl}, issn = {1476-4687}, doi = {10.1038/nature22397}, author = {Loveland, Anna B and Demo, Gabriel and Grigorieff, Nikolaus and Korostelev, Andrei A} } @article {48670, title = {Experience-dependent shaping of hippocampal CA1 intracellular activity in novel and familiar environments.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Jul 25}, abstract = {

The hippocampus is critical for producing stable representations of familiar spaces. How these representations arise is poorly understood, largely because changes to hippocampal inputs have not been measured during spatial learning. Here, using intracellular recording, we monitored inputs and plasticity-inducing complex spikes (CSs) in CA1 neurons while mice explored novel and familiar virtual environments. Inputs driving place field spiking increased in amplitude - often suddenly - during novel environment exploration. However, these increases were not sustained in familiar environments. Rather, the spatial tuning of inputs became increasingly similar across repeated traversals of the environment with experience - both within fields and throughout the whole environment. In novel environments, CSs were not necessary for place field formation. Our findings support a model in which initial inhomogeneities in inputs are amplified to produce robust place field activity, then plasticity refines this representation into one with less strongly modulated, but more stable, inputs for long-term storage.

}, issn = {2050-084X}, doi = {10.7554/eLife.23040}, author = {Cohen, Jeremy D and Bolstad, Mark and Lee, Albert K} } @article {48765, title = {Experimental and statistical reevaluation provides no evidence for Drosophila courtship song rhythms.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, year = {2017}, month = {2017 Aug 29}, pages = {9978-83}, abstract = {

From 1980 to 1992, a series of influential papers reported on the discovery, genetics, and evolution of a periodic cycling of the interval between Drosophila male courtship song pulses. The molecular mechanisms underlying this periodicity were never described. To reinitiate investigation of this phenomenon, we previously performed automated segmentation of songs but failed to detect the proposed rhythm [Arthur BJ, et al. (2013) BMC Biol 11:11; Stern DL (2014) BMC Biol 12:38]. Kyriacou et al. [Kyriacou CP, et al. (2017) Proc Natl Acad Sci USA 114:1970-1975] report that we failed to detect song rhythms because (i) our flies did not sing enough and (ii) our segmenter did not identify many of the song pulses. Kyriacou et al. manually annotated a subset of our recordings and reported that two strains displayed rhythms with genotype-specific periodicity, in agreement with their original reports. We cannot replicate this finding and show that the manually annotated data, the original automatically segmented data, and a new dataset provide no evidence for either the existence of song rhythms or song periodicity differences between genotypes. Furthermore, we have reexamined our methods and analysis and find that our automated segmentation method was not biased to prevent detection of putative song periodicity. We conclude that there is no evidence for the existence of Drosophila courtship song rhythms.

}, issn = {1091-6490}, doi = {10.1073/pnas.1707471114}, author = {Stern, David L and Clemens, Jan and Coen, Philip and Calhoun, Adam J and Hogenesch, John B and Arthur, Ben J and Murthy, Mala} } @article {48644, title = {Expression, purification, and contaminant detection for structural studies of Ralstonia metallidurance ClC protein rm1.}, journal = {PloS One}, volume = {12}, year = {2017}, month = {2017}, pages = {e0180163}, abstract = {

Single-particle electron cryo-microscopy (cryo-EM) has become a popular method for high-resolution study of the structural and functional properties of proteins. However, sufficient expression and purification of membrane proteins holds many challenges. We describe methods to overcome these obstacles using ClC-rm1, a prokaryotic chloride channel (ClC) family protein from Ralstonia metallidurans, overexpressed in Escherichia coli (E. coli) BL21(DE3) strain. Mass spectrometry and electron microscopy analyses of purified samples revealed multiple contaminants that can obfuscate results of subsequent high-resolution structural analysis. Here we describe the systematic optimization of sample preparation procedures, including expression systems, solubilization techniques, purification protocols, and contamination detection. We found that expressing ClC-rm1 in E. coli BL21(DE3) and using n-dodecyl-β-D-maltopyranoside as a detergent for solubilization and purification steps resulted in the highest quality samples of those we tested. However, although protein yield, sample stability, and the resolution of structural detail were improved following these changes, we still detected contaminants including Acriflavine resistant protein AcrB. AcrB was particularly difficult to remove as it co-purified with ClC-rm1 due to four intrinsic histidine residues at its C-terminus that bind to affinity resins. We were able to obtain properly folded pure ClC-rm1 by adding eGFP to the C-terminus and overexpressing the protein in the ΔacrB variant of the JW0451-2 E. coli strain.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0180163}, author = {Abeyrathne, Priyanka D and Grigorieff, Nikolaus} } @article {48710, title = {The extracellular metalloprotease AdamTS-A anchors neural lineages in place within and preserves the architecture of the central nervous system.}, journal = {Development (Cambridge, England)}, year = {2017}, month = {2017 Jul 31}, abstract = {

The extracellular matrix (ECM) regulates cell migration and sculpts organ shape. AdamTS proteins are extracellular metalloproteases known to modify ECM proteins and promote cell migration, but demonstrated roles for AdamTS proteins in regulating CNS structure and ensuring cell lineages remain fixed in place have not been uncovered. Using forward genetic approaches in Drosophila, we find that reduction of AdamTS-A function induces both the mass exodus of neural lineages out of the CNS and drastic perturbations to CNS structure. Expressed and active in surface glia, AdamTS-A acts in parallel to perlecan and in opposition to viking/collagen IV and βPS-integrin to keep CNS lineages rooted in place and to preserve the structural integrity of the CNS. viking/collagen IV and βPS-integrin are known to promote tissue stiffness and oppose the function of perlecan, which reduces tissue stiffness. Our work supports a model in which AdamTS-A anchors cells in place and preserves CNS architecture by reducing tissue stiffness.

}, issn = {1477-9129}, doi = {10.1242/dev.145854}, author = {Skeath, James B and Wilson, Beth A and Romero, Selena E and Snee, Mark J and Zhu, Yi and Lacin, Haluk} } @proceedings {48802, title = {Extracting low-dimensional dynamics from multiple large-scale neural population recordings by learning to predict correlations.}, year = {2017}, month = {2017 Dec 04}, abstract = {

A powerful approach for understanding neural population dynamics is to extract low-dimensional trajectories from population recordings using dimensionality reduction methods. Current approaches for dimensionality reduction on neural data are limited to single population recordings, and can not identify dynamics embedded across multiple measurements. We propose an approach for extracting low-dimensional dynamics from multiple, sequential recordings. Our algorithm scales to data comprising millions of observed dimensions, making it possible to access dynamics distributed across large populations or multiple brain areas. Building on subspace-identification approaches for dynamical systems, we perform parameter estimation by minimizing a moment-matching objective using a scalable stochastic gradient descent algorithm: The model is optimized to predict temporal covariations across neurons and across time. We show how this approach naturally handles missing data and multiple partial recordings, and can identify dynamics and predict correlations even in the presence of severe subsampling and small overlap between recordings. We demonstrate the effectiveness of the approach both on simulated data and a whole-brain larval zebrafish imaging dataset.\ 

}, url = {http://www.mackelab.org/pubs/Nonnenmacher_Turaga_NIPS_2017.pdf}, author = {Nonnenmacher, Marcel and Turaga, Srinivas C and Macke, Jakob H} } @article {48366, title = {Facilitating neuron-specific genetic manipulations in Drosophila using a split GAL4 repressor.}, journal = {Genetics}, volume = {206}, year = {2017}, month = {2017 Mar 31}, pages = {775-84}, abstract = {

Efforts to map neural circuits have been galvanized by the development of genetic technologies that permit the manipulation of targeted sets of neurons in the brains of freely behaving animals. The success of these efforts relies on the experimenter{\textquoteright}s ability to target arbitrarily small subsets of neurons for manipulation, but such specificity of targeting cannot routinely be achieved using existing methods. In Drosophila melanogaster, a widely used technique for refined cell-type specific manipulation is the Split GAL4 system, which augments the targeting specificity of the binary GAL4-UAS system by making GAL4 transcriptional activity contingent upon two enhancers, rather than one. To permit more refined targeting, we introduce here the "Killer Zipper" (KZip(+)), a suppressor that makes Split GAL4 targeting contingent upon a third enhancer. KZip(+) acts by disrupting both the formation and activity of Split GAL4 heterodimers, and we show how this added layer of control can be used to selectively remove unwanted cells from a Split GAL4 expression pattern or to subtract neurons of interest from a pattern to determine their requirement in generating a given phenotype. To facilitate application of the KZip(+) technology, we have developed a versatile set of LexAop-KZip(+) fly lines that can be used directly with the large number of LexA driver lines with known expression patterns. The Killer Zipper significantly sharpens the precision of neuronal genetic control available in Drosophila and may be extended to other organisms where Split GAL4-like systems are used.

}, issn = {1943-2631}, doi = {10.1534/genetics.116.199687}, author = {Dolan, Michael-John and Luan, Haojiang and Shropshire, William C and Sutcliffe, Ben and Cocanougher, Benjamin and Scott, Robert L and Frechter, Shahar and Zlatic, Marta and Jefferis, Gregory S X E and White, Benjamin H} } @proceedings {48805, title = {Fast amortized inference of neural activity from calcium imaging data with variational autoencoders.}, year = {2017}, month = {2017 Dec 04}, abstract = {

Calcium imaging permits optical measurement of neural activity. Since intracellular calcium concentration is an indirect measurement of neural activity, computational tools are necessary to infer the true underlying spiking activity from fluorescence measurements. Bayesian model inversion can be used to solve this problem, but typically requires either computationally expensive MCMC sampling, or faster but approximate maximum-a-posteriori optimization. Here, we introduce a flexible algorithmic framework for fast, efficient and accurate extraction of neural spikes from imaging data. Using the framework of variational autoencoders, we propose to amortize inference by training a deep neural network to perform model inversion efficiently. The recognition network is trained to produce samples from the posterior distribution over spike trains. Once trained, performing inference amounts to a fast single forward pass through the network, without the need for iterative optimization or sampling. We show that amortization can be applied flexibly to a wide range of nonlinear generative models and significantly improves upon the state of the art in computation time, while achieving competitive accuracy. Our framework is also able to represent posterior distributions over spike-trains. We demonstrate the generality of our method by proposing the first probabilistic approach for separating backpropagating action potentials from putative synaptic inputs in calcium imaging of dendritic spines.\ 

}, url = {http://www.mackelab.org/pubs/Speiser_NIPS_2017.pdf}, author = {Speiser, Artur and Yan, Jinyao and Archer, Evan and Buesing, Lars and Turaga, Srinivas C and Macke, Jakob H} } @article {48600, title = {Feature integration drives probabilistic behavior in the Drosophila escape response.}, journal = {Neuron}, volume = {94}, year = {2017}, month = {2017 Jun 21}, pages = {1190-204}, abstract = {

Animals rely on dedicated sensory circuits to extract and encode environmental features. How individual neurons integrate and translate these features into behavioral responses remains a major question. Here, we identify a visual\ projection neuron\ type that conveys predator approach information to the\ Drosophila\ giant fiber (GF) escape circuit. Genetic removal of this input during looming stimuli reveals that it encodes angular expansion velocity, whereas other input cell type(s) encode angular size. Motor program selection and timing emerge from\ linear\ integration of these two features within the GF. Linear integration improves size detection invariance over prior models and appropriately biases motor selection to rapid,\ GF-mediated\ escapes during fast looms. Our findings suggest\ feature integration, and motor control may occur as simultaneous operations within the same neuron and establish the\ Drosophila\ escape circuit as a model system in which these computations may be further dissected at the circuit level.

}, doi = {10.1016/j.neuron.2017.05.036}, author = {von Reyn, Catherine R and Nern, Aljoscha and Williamson, W Ryan and Breads, Patrick and Wu, Ming and Namiki, Shigehiro and Card, Gwyneth M} } @article {68439, title = {Fibroblast growth factor signaling instructs ensheathing glia wrapping of olfactory glomeruli.}, journal = {Proc Natl Acad Sci U S A}, volume = {114}, year = {2017}, month = {07/2017}, pages = {7505-7512}, abstract = {

The formation of complex but highly organized neural circuits requires interactions between neurons and glia. During the assembly of the olfactory circuit, 50 olfactory receptor neuron (ORN) classes and 50 projection neuron (PN) classes form synaptic connections in 50 glomerular compartments in the antennal lobe, each of which represents a discrete olfactory information-processing channel. Each compartment is separated from the adjacent compartments by membranous processes from ensheathing glia. Here we show that Thisbe, an FGF released from olfactory neurons, particularly from local interneurons, instructs ensheathing glia to wrap each glomerulus. The Heartless FGF receptor acts cell-autonomously in ensheathing glia to regulate process extension so as to insulate each neuropil compartment. Overexpressing Thisbe in ORNs or PNs causes overwrapping of the glomeruli their axons or dendrites target. Failure to establish the FGF-dependent glia structure disrupts precise ORN axon targeting and discrete glomerular formation.

}, keywords = {Animals, Animals, Genetically Modified, Axons, Drosophila, Drosophila Proteins, Fibroblast Growth Factors, Genotype, Microscopy, Confocal, Neuroglia, Neuropil, Olfactory Bulb, Olfactory Pathways, Olfactory Receptor Neurons, Signal Transduction}, issn = {1091-6490}, doi = {10.1073/pnas.1706533114}, author = {Wu, Bing and Li, Jiefu and Chou, Ya-Hui and Luginbuhl, David and Luo, Liqun} } @article {48204, title = {A fluorescent Hsp90 probe demonstrates the unique association between extracellular Hsp90 and malignancy in vivo.}, journal = {ACS chemical biology}, year = {2017}, month = {2017 Jan 19}, abstract = {

Extracellular expression of heat shock protein 90 (eHsp90) by tumor cells is correlated with malignancy. Development of small molecule probes that can detect eHsp90 in vivo may therefore have utility in the early detection of malignancy. We synthesized a cell impermeable far-red fluorophore-tagged Hsp90 inhibitor to target eHsp90 in vivo. High resolution confocal and lattice light sheet microscopy show that probe-bound eHsp90 accumulates in punctate structures on the plasma membrane of breast tumor cells and is actively internalized. The extent of internalization correlates with tumor cell aggressiveness, and this process can be induced in benign cells by over-expressing p110HER2. Whole body cryoslicing, imaging and histology of flank and spontaneous tumor-bearing mice strongly suggests that eHsp90 expression and internalization is a phenomenon unique to tumor cells in vivo and may provide an {\textquoteright}Achilles heel{\textquoteright} for the early diagnosis of metastatic disease and targeted drug delivery.

}, issn = {1554-8937}, doi = {10.1021/acschembio.7b00006}, author = {Crowe, Lauren B and Hughes, Philip F and Alcorta, David A and Osada, Takuya and Smith, Aaron P and Totzke, Juliane and Loiselle, David R and Lutz, Isaac D and Gargesha, Madhusudhana and Roy, Debasish and Roques, Jose and Darr, David and Lyerly, H Kim and Spector, Neil L and Haystead, Timothy Aj} } @article {65777, title = {Fluorogenic Labeling Strategies for Biological Imaging}, journal = {International Journal of Molecular Sciences}, volume = {18}, year = {2017}, month = {07/2017}, pages = {1473 {\textendash} 11}, abstract = {

The spatiotemporal fluorescence imaging of biological processes requires effective tools to label intracellular biomolecules in living systems. This review presents a brief overview of recent labeling strategies that permits one to make protein and RNA strongly fluorescent using synthetic fluorogenic probes. Genetically encoded tags selectively binding the exogenously applied molecules ensure high labeling selectivity, while high imaging contrast is achieved using fluorogenic chromophores that are fluorescent only when bound to their cognate tag, and are otherwise dark. Beyond avoiding the need for removal of unbound synthetic dyes, these approaches allow the development of sophisticated imaging assays, and open exciting prospects for advanced imaging, particularly for multiplexed imaging and super-resolution microscopy.

}, doi = {10.3390/ijms18071473}, url = {http://www.mdpi.com/1422-0067/18/7/1473}, author = {Li, Chenge and Tebo, Alison G. and Gautier, Arnaud} } @article {48935, title = {Fully integrated silicon probes for high-density recording of neural activity.}, journal = {Nature}, volume = {551}, year = {2017}, month = {2017 Nov 08}, pages = {232-236}, abstract = {

Sensory, motor and cognitive operations involve the coordinated action of large neuronal populations across multiple brain regions in both superficial and deep structures. Existing extracellular probes record neural activity with excellent spatial and temporal (sub-millisecond) resolution, but from only a few dozen neurons per shank. Optical Ca(2+) imaging offers more coverage but lacks the temporal resolution needed to distinguish individual spikes reliably and does not measure local field potentials. Until now, no technology compatible with use in unrestrained animals has combined high spatiotemporal resolution with large volume coverage. Here we design, fabricate and test a new silicon probe known as Neuropixels to meet this need. Each probe has 384 recording channels that can programmably address 960 complementary metal-oxide-semiconductor (CMOS) processing-compatible low-impedance TiN sites that tile a single 10-mm long, 70 {\texttimes} 20-μm cross-section shank. The 6 {\texttimes} 9-mm probe base is fabricated with the shank on a single chip. Voltage signals are filtered, amplified, multiplexed and digitized on the base, allowing the direct transmission of noise-free digital data from the probe. The combination of dense recording sites and high channel count yielded well-isolated spiking activity from hundreds of neurons per probe implanted in mice and rats. Using two probes, more than 700 well-isolated single neurons were recorded simultaneously from five brain structures in an awake mouse. The fully integrated functionality and small size of Neuropixels probes allowed large populations of neurons from several brain structures to be recorded in freely moving animals. This combination of high-performance electrode technology and scalable chip fabrication methods opens a path towards recording of brain-wide neural activity during behaviour.

}, issn = {1476-4687}, doi = {10.1038/nature24636}, author = {Jun, James J and Steinmetz, Nicholas A and Siegle, Joshua H and Denman, Daniel J and Bauza, Marius and Barbarits, Brian and Lee, Albert K and Anastassiou, Costas A and Andrei, Alexandru and Ayd{\i}n, {\c C}a{\u g}atay and Barbic, Mladen and Blanche, Timothy J and Bonin, Vincent and Couto, Jo{\~a}o and Dutta, Barundeb and Gratiy, Sergey L and Gutnisky, Diego A and H{\"a}usser, Michael and Karsh, Bill and Ledochowitsch, Peter and Lopez, Carolina Mora and Mitelut, Catalin and Musa, Silke and Okun, Michael and Pachitariu, Marius and Putzeys, Jan and Rich, P Dylan and Rossant, Cyrille and Sun, Wei-Lung and Svoboda, Karel and Carandini, Matteo and Harris, Kenneth D and Koch, Christof and O{\textquoteright}Keefe, John and Harris, Timothy D} } @article {48157, title = {A fully synthetic transcriptional platform for a multicellular eukaryote.}, journal = {Cell Reports}, volume = {18}, year = {2017}, month = {2017 Jan 03}, pages = {287-296}, abstract = {

Regions of genomic DNA called enhancers encode binding sites for transcription factor proteins. Binding of activators and repressors increase and reduce transcription, respectively, but it is not understood how combinations of activators and repressors generate precise patterns of transcription during development. Here, we explore this problem using\ a fully synthetic transcriptional platform in Drosophila consisting of engineered transcription factor gradients and artificial enhancers. We found that binding sites for a transcription factor that makes DNA accessible are required together with binding sites for transcriptional activators to produce a functional enhancer. Only in this context can changes in the number of activator binding sites mediate quantitative control of transcription. Using an engineered transcriptional repressor gradient, we demonstrate that overlapping repressor and activator binding sites provide more robust repression and sharper expression boundaries than non-overlapping sites. This may explain why this common motif is observed in many developmental enhancers.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2016.12.025}, author = {Crocker, Justin and Tsai, Albert and Stern, David L} } @article {48975, title = {The functional organization of descending sensory-motor pathways in Drosophila.}, journal = {eLife}, year = {2017}, month = {2018 Jun 26}, pages = {e34272}, abstract = {

In most animals, the brain controls the body via a set of descending neurons (DNs) that traverse the neck. DN activity activates, maintains or modulates locomotion and other behaviors. Individual DNs have been well-studied in species from insects to primates, but little is known about overall connectivity patterns across the DN population. We systematically investigated DN anatomy in\ Drosophila melanogaster\ and created over 100 transgenic lines targeting individual cell types. We identified roughly half of all\ Drosophila\ DNs and comprehensively map connectivity between sensory and motor neuropils in the brain and nerve cord, respectively. We find the nerve cord is a layered system of neuropils reflecting the fly{\textquoteright}s capability for two largely independent means of locomotion -- walking and flight -- using distinct sets of appendages. Our results reveal the basic functional map of descending pathways in flies and provide tools for systematic interrogation of neural circuits.

}, doi = {10.7554/eLife.34272}, author = {Namiki, Shigehiro and Dickinson, Michael H and Wong, Allan M and Korff, Wyatt and Card, Gwyneth M} } @article {48700, title = {Functional regulatory evolution outside of the minimal even-skipped stripe 2 enhancer.}, journal = {Development (Cambridge, England)}, year = {2017}, month = {2017 Jul 31}, abstract = {

Transcriptional enhancers are regions of DNA that drive precise patterns of gene expression. While many studies have elucidated how individual enhancers can evolve, most of this work has focused on what are called "minimal" enhancers, the smallest DNA regions that drive expression that approximates an aspect of native gene expression. Here we explore how the Drosophila erecta even-skipped (eve) locus has evolved by testing its activity in the divergent D. melanogaster genome. We found, as has been reported previously, that the D. erecta eve stripe 2 enhancer (eveS2) fails to drive appreciable expression in D. melanogaster (1). However, we found that a large transgene carrying the entire D. erecta eve locus drives normal eve expression, including in stripe 2. We performed a functional dissection of the region upstream of the D. erecta eveS2 region and found multiple Zelda motifs that are required for normal expression. Our results illustrate how sequences outside of minimal enhancer regions can evolve functionally through mechanisms other than changes in transcription factor binding sites that drive patterning.

}, issn = {1477-9129}, doi = {10.1242/dev.149427}, author = {Crocker, Justin and Stern, David L} } @article {48891, title = {A general method to fine-tune fluorophores for live-cell and in vivo imaging.}, journal = {Nature Methods}, volume = {14}, year = {2017}, month = {2017 Oct}, pages = {987-994}, abstract = {

Pushing the frontier of fluorescence microscopy requires the design of enhanced fluorophores with finely tuned properties. We recently discovered that incorporation of four-membered azetidine rings into classic fluorophore structures elicits substantial increases in brightness and photostability, resulting in the Janelia Fluor (JF) series of dyes. We refined and extended this strategy, finding that incorporation of 3-substituted azetidine groups allows rational tuning of the spectral and chemical properties of rhodamine dyes with unprecedented precision. This strategy allowed us to establish principles for fine-tuning the properties of fluorophores and to develop a palette of new fluorescent and fluorogenic labels with excitation ranging from blue to the far-red. Our results demonstrate the versatility of these new dyes in cells, tissues and animals.

}, keywords = {Animals, Brain, Cell Line, Coloring Agents, Drosophila, Image Processing, Computer-Assisted, Larva, Mice, Microscopy, Fluorescence, Photochemical Processes, Staining and Labeling}, issn = {1548-7105}, doi = {10.1038/nmeth.4403}, author = {Grimm, Jonathan B and Muthusamy, Anand K and Liang, Yajie and Brown, Timothy A and Lemon, William C and Patel, Ronak and Lu, Rongwen and Macklin, John J and Keller, Philipp J and Ji, Na and Lavis, Luke D} } @article {48733, title = {General synthetic method for Si-Fluoresceins and Si-Rhodamines.}, journal = {ACS Central Science}, volume = {3}, year = {2017}, month = {2017 Aug 09}, pages = {975-85}, abstract = {

The century-old fluoresceins and rhodamines persist as flexible scaffolds for fluorescent and fluorogenic compounds. Extensive exploration of these xanthene dyes has yielded general structure{\textendash}activity relationships where the development of new probes is limited only by imagination and organic chemistry. In particular, replacement of the xanthene oxygen with silicon has resulted in new red-shifted Si-fluoresceins and Si-rhodamines, whose high brightness and photostability enable advanced imaging experiments. Nevertheless, efforts to tune the chemical and spectral properties of these dyes have been hindered by difficult synthetic routes. Here, we report a general strategy for the efficient preparation of Si-fluoresceins and Si-rhodamines from readily synthesized bis(2-bromophenyl)silane intermediates. These dibromides undergo metal/bromide exchange to give bis-aryllithium or bis(aryl Grignard) intermediates, which can then add to anhydride or ester electrophiles to afford a variety of Si-xanthenes. This strategy enabled efficient (3{\textendash}5 step) syntheses of known and novel Si-fluoresceins, Si-rhodamines, and related dye structures. In particular, we discovered that previously inaccessible tetrafluorination of the bottom aryl ring of the Si-rhodamines resulted in dyes with improved visible absorbance in solution, and a convenient derivatization through fluoride-thiol substitution. This modular, divergent synthetic method will expand the palette of accessible xanthenoid dyes across the visible spectrum, thereby pushing further the frontiers of biological imaging.

}, doi = {10.1021/acscentsci.7b00247}, author = {Grimm, Jonathan B and Brown, Timothy A and Tkachuk, Ariana N and Lavis, Luke D} } @article {48698, title = {Genetic and neuronal mechanisms governing the sex-specific interaction between sleep and sexual behaviors in Drosophila.}, journal = {Nature Communications}, volume = {8}, year = {2017}, month = {2017 Jul 28}, pages = {154}, abstract = {

Animals execute one particular behavior among many others in a context-dependent manner, yet the mechanisms underlying such behavioral choice remain poorly understood. Here we studied how two fundamental behaviors, sex and sleep, interact at genetic and neuronal levels in Drosophila. We show that an increased need for sleep inhibits male sexual behavior by decreasing the activity of the male-specific P1 neurons that coexpress the sex determination genes fru (M) and dsx, but does not affect female sexual behavior. Further, we delineate a sex-specific neuronal circuit wherein the P1 neurons encoding increased courtship drive suppressed male sleep by forming mutually excitatory connections with the fru (M) -positive sleep-controlling DN1 neurons. In addition, we find that FRU(M) regulates male courtship and sleep through distinct neural substrates. These studies reveal the genetic and neuronal basis underlying the sex-specific interaction between sleep and sexual behaviors in Drosophila, and provide insights into how competing behaviors are co-regulated.Genes and circuits involved in sleep and sexual arousal have been extensively studied in Drosophila. Here the authors identify the sex determination genes fruitless and doublesex, and a sex-specific P1-DN1 neuronal feedback that governs the interaction between these competing behaviors.

}, issn = {2041-1723}, doi = {10.1038/s41467-017-00087-5}, author = {Chen, Dandan and Sitaraman, Divya and Chen, Nan and Jin, Xin and Han, Caihong and Chen, Jie and Sun, Mengshi and Baker, Bruce S and Nitabach, Michael N and Pan, Yufeng} } @article {48319, title = {Genetic and transgenic reagents for Drosophila simulans, D. mauritiana, D. yakuba, D. santomea and D. virilis.}, journal = {G3 (Bethesda, Md.)}, volume = {7}, year = {2017}, month = {2017 Mar 09}, pages = {1339-47}, abstract = {

Species of the Drosophila melanogaster species subgroup, including the species D. simulans, D. mauritiana, D. yakuba, and D. santomea, have long served as model systems for studying evolution. Studies in these species have been limited, however, by a paucity of genetic and transgenic reagents. Here we describe a collection of transgenic and genetic strains generated to facilitate genetic studies within and between these species. We have generated many strains of each species containing mapped piggyBac transposons including an enhanced yellow fluorescent protein gene expressed in the eyes and a phiC31 attP site-specific integration site. We have tested a subset of these lines for integration efficiency and reporter gene expression levels. We have also generated a smaller collection of other lines expressing other genetically encoded fluorescent molecules in the eyes and a number of other transgenic reagents that will be useful for functional studies in these species. In addition, we have mapped the insertion locations of 58 transposable elements in D. virilis that will be useful for genetic mapping studies.

}, issn = {2160-1836}, doi = {10.1534/g3.116.038885}, author = {Stern, David L and Crocker, Justin and Ding, Yun and Frankel, Nicol{\'a}s and Kappes, Gretchen and Kim, Elizabeth and Kuzmickas, Ryan and Lemire, Andrew and Mast, Joshua D and Picard, Serge} } @article {48845, title = {Genetic reagents for making split-GAL4 lines in Drosophila.}, journal = {Genetics }, volume = {209}, year = {2017}, month = {2018 March}, pages = {31-5}, abstract = {

The ability to reproducibly target expression of transgenes to small, defined subsets of cells is a key experimental tool for understanding many biological processes. The Drosophila nervous system contains thousands of distinct cell types and it has generally not been possible to limit expression to one or a few cell types when using a single segment of genomic DNA as an enhancer to drive expression. Intersectional methods, in which expression of the transgene only occurs where two different enhancers overlap in their expression patterns, can be used to achieve the desired specificity. This report describes a set of over 2,800 transgenic lines for use with the split-GAL4 intersectional method.

}, doi = {10.1101/197509}, author = {Dionne, Heather and Hibbard, Karen L and Cavallaro, Amanda and Kao, Jui-Chun and Rubin, Gerald M} } @article {48478, title = {Genetic tools to study juvenile hormone action in Drosophila.}, journal = {Scientific Reports}, volume = {7}, year = {2017}, month = {2017 May 18}, pages = {2132}, abstract = {

The insect juvenile hormone receptor is a basic helix-loop-helix (bHLH), Per-Arnt-Sim (PAS) domain protein, a novel type of hormone receptor. In higher flies like\ Drosophila, the ancestral receptor\ germ cell-expressed\ (gce) gene has duplicated to yield the paralog\ Methoprene-tolerant\ (Met). These paralogous receptors share redundant function during development but play unique roles in adults. Some aspects of JH function apparently require one receptor or the other. To provide a foundation for studying JH receptor function, we have recapitulated endogenous JH receptor expression with single cell resolution. Using Bacteria Artificial Chromosome (BAC) recombineering and a transgenic knock-in, we have generated a spatiotemporal expressional atlas of\ Metand\ gce\ throughout development. We demonstrate JH receptor expression in known JH target tissues, in which temporal expression corresponds with periods of hormone sensitivity. Larval expression largely supports the notion of functional redundancy. Furthermore, we provide the neuroanatomical distribution of JH receptors in both the larval and adult central nervous system, which will serve as a platform for future studies regarding JH action on insect behavior.

}, doi = {10.1038/s41598-017-02264-4}, author = {Baumann, Aaron A and Texada, Michael J and Chen, Hui-Min and Etheredge, Jack N and Miller, D L and Picard, Serge and Warner, Raechel D and Truman, James W and Riddiford, Lynn M} } @article {48732, title = {Genetically encoded biosensors.}, volume = {B2}, number = {14/350,199}, year = {2017}, month = {2017 Aug 01}, edition = {G01N 33/557 (20060101); G01N 33/58 (20060101); C07K 14/435 (20060101); C07K 14/245 (20060101); C07K 14/195 (20060101); G01N 33/68 (20060101)}, abstract = {

The present disclosure provides, inter alia, genetically encoded recombinant peptide biosensors comprising analyte-binding framework portions and signaling portions, wherein the signaling portions are present within the framework portions at sites or amino acid positions that undergo a conformational change upon interaction of the framework portion with an analyte.

}, url = {http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO2\&Sect2=HITOFF\&u=\%2Fnetahtml\%2FPTO\%2Fsearch-adv.htm\&r=2\&p=1\&f=G\&l=50\&d=PTXT\&S1=(\%22Howard+Hughes+medical\%22.ASNM.)\&OS=AN/\%22Howard+Hughes+medical\%22\&RS=AN/\%22Howard+Hughes+medical\%22}, author = {Marvin, Jonathan S and Looger, Loren L and Lee, Richard T and Schreiter, Eric R} } @article {68441, title = {A Genome-Scale Model of Simulates Mechanisms of Metabolic Diversity and Energy Conservation.}, journal = {mSystems}, volume = {2}, year = {2017}, month = {03/2017}, abstract = {

strain WP3 belongs to the group 1 branch of the genus and is a piezotolerant and psychrotolerant species isolated from the deep sea. In this study, a genome-scale model was constructed for WP3 using a combination of genome annotation, ortholog mapping, and physiological verification. The metabolic reconstruction contained 806 genes, 653 metabolites, and 922 reactions, including central metabolic functions that represented nonhomologous replacements between the group 1 and group 2 species. Metabolic simulations with the WP3 model demonstrated consistency with existing knowledge about the physiology of the organism. A comparison of model simulations with experimental measurements verified the predicted growth profiles under increasing concentrations of carbon sources. The WP3 model was applied to study mechanisms of anaerobic respiration through investigating energy conservation, redox balancing, and the generation of proton motive force. Despite being an obligate respiratory organism, WP3 was predicted to use substrate-level phosphorylation as the primary source of energy conservation under anaerobic conditions, a trait previously identified in other species. Further investigation of the ATP synthase activity revealed a positive correlation between the availability of reducing equivalents in the cell and the directionality of the ATP synthase reaction flux. Comparison of the WP3 model with an existing model of a group 2 species, MR-1, revealed that the WP3 model demonstrated greater flexibility in ATP production under the anaerobic conditions. Such flexibility could be advantageous to WP3 for its adaptation to fluctuating availability of organic carbon sources in the deep sea. The well-studied nature of the metabolic diversity of bacteria makes species from this genus a promising platform for investigating the evolution of carbon metabolism and energy conservation. The phylogeny is diverged into two major branches, referred to as group 1 and group 2. While the genotype-phenotype connections of group 2 species have been extensively studied with metabolic modeling, a genome-scale model has been missing for the group 1 species. The metabolic reconstruction of strain WP3 represented the first model for group 1 and the first model among piezotolerant and psychrotolerant deep-sea bacteria. The model brought insights into the mechanisms of energy conservation in WP3 under anaerobic conditions and highlighted its metabolic flexibility in using diverse carbon sources. Overall, the model opens up new opportunities for investigating energy conservation and metabolic adaptation, and it provides a prototype for systems-level modeling of other deep-sea microorganisms.

}, issn = {2379-5077}, doi = {10.1128/mSystems.00165-16}, author = {Dufault-Thompson, Keith and Jian, Huahua and Cheng, Ruixue and Li, Jiefu and Wang, Fengping and Zhang, Ying} } @article {48860, title = {Genomic probes.}, volume = {A1}, number = {US20170268035 }, year = {2017}, month = {2017 Sep 21}, edition = {C12Q 1/68 20060101 C12Q001/68; C12N 15/09 20060101 C12N015/09; C12P 19/34 20060101 C12P019/34; C07H 21/04 20060101 C07H021/04}, abstract = {Labeled probes, and methods of use thereof, comprise a Cas polypeptide conjugated to gRNA that is specific for target nucleic acid sequences, including genomic DNA sequences. The probes and methods can be used to label nucleic acid sequences without global DNA denaturation. The presently-disclosed subject matter meets some or all of the above identified needs, as will become evident to those of ordinary skill in the art after a study of information provided in this document.}, url = {http://appft.uspto.gov/netacgi/nph-Parser?Sect1=PTO1\&Sect2=HITOFF\&d=PG01\&p=1\&u=\%2Fnetahtml\%2FPTO\%2Fsrchnum.html\&r=1\&f=G\&l=50\&s1=\%2220170268035\%22.PGNR.\&OS=DN/20170268035\&RS=DN/20170268035}, author = {Singer, Robert H and Deng, Wulan and Lionnet, Timoth{\'e}e} } @article {48252, title = {The glia of the adult Drosophila nervous system.}, journal = {Glia}, volume = {65}, year = {2017}, month = {2017 Jan 30}, pages = {606-38}, abstract = {

Glia play crucial roles in the development and homeostasis of the nervous system. While the GLIA in the Drosophila embryo have been well characterized, their study in the adult nervous system has been limited. Here, we present a detailed description of the glia in the adult nervous system, based on the analysis of some 500 glial drivers we identified within a collection of synthetic GAL4 lines. We find that glia make up \~{}10\% of the cells in the nervous system and envelop all compartments of neurons (soma, dendrites, axons) as well as the nervous system as a whole. Our morphological analysis suggests a set of simple rules governing the morphogenesis of glia and their interactions with other cells. All glial subtypes minimize contact with their glial neighbors but maximize their contact with neurons and adapt their macromorphology and micromorphology to the neuronal entities they envelop. Finally, glial cells show no obvious spatial organization or registration with neuronal entities. Our detailed description of all glial subtypes and their regional specializations, together with the powerful genetic toolkit we provide, will facilitate the functional analysis of glia in the mature nervous system. GLIA 2017.

}, issn = {1098-1136}, doi = {10.1002/glia.23115}, author = {Kremer, Malte C and Jung, Christophe and Batelli, Sara and Rubin, Gerald M and Gaul, Ulrike} } @article {48374, title = {Heuristic rules underlying dragonfly prey selection and interception.}, journal = {Current Biology : CB}, volume = {27}, year = {2017}, month = {2017 Mar 28}, pages = {1124-37}, abstract = {

Animals use rules to initiate behaviors. Such rules are\ often described as triggers that determine when behavior begins. However, although less explored, these selection rules are also an opportunity to establish sensorimotor constraints that influence how the behavior ends. These constraints may be particularly significant in influencing success in prey capture. Here we explore this in dragonfly prey interception. We found that in the moments leading up to takeoff, perched dragonflies employ a series of sensorimotor rules that determine the time of takeoff and increase the probability of successful capture. First, the dragonfly makes a head saccade followed by smooth pursuit movements to orient its\ direction-of-gaze at potential prey. Second, the dragonfly assesses whether the prey{\textquoteright}s angular size and speed co-vary within a privileged range. Finally, the dragonfly times the moment of its takeoff to a prediction of when the prey will cross the zenith. Each of these processes serves a purpose. The angular size-speed criteria biases interception flights to catchable prey, while the head movements and the predictive takeoff ensure flights begin with the prey visually fixated and directly overhead-the key parameters that underlie interception steering. Prey that do not elicit takeoff generally fail at least one of the criterion, and the loss of prey fixation or overhead positioning during flight is strongly correlated with terminated flights. Thus from an abundance of potential targets, the dragonfly selects a stereotyped set of takeoff conditions based on the prey and body states most likely to end in successful capture.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2017.03.010}, author = {Lin, Huai-Ti and Leonardo, Anthony} } @article {65886, title = {Homeostatic plasticity shapes the visual system{\textquoteright}s first synapse}, journal = {Nature Communications}, volume = {8}, year = {2017}, month = {10/2017}, abstract = {

Vision in dim light depends on synapses between rods and rod bipolar cells (RBCs). Here, we find that these synapses exist in multiple configurations, in which single release sites of rods are apposed by one to three postsynaptic densities (PSDs). Single RBCs often form multiple PSDs with one rod; and neighboring RBCs share ~13\% of their inputs. Rod-RBC synapses develop while ~7\% of RBCs undergo programmed cell death (PCD). Although PCD is common throughout the nervous system, its influences on circuit development and function are not well understood. We generate mice in which ~53 and ~93\% of RBCs, respectively, are removed during development. In these mice, dendrites of the remaining RBCs expand in graded fashion independent of light-evoked input. As RBC dendrites expand, they form fewer multi-PSD contacts with rods. Electrophysiological recordings indicate that this homeostatic co-regulation of neurite and synapse development preserves retinal function in dim light.

}, doi = {10.1038/s41467-017-01332-7}, url = {http://www.nature.com/articles/s41467-017-01332-7http://www.nature.com/articles/s41467-017-01332-7.pdfhttp://www.nature.com/articles/s41467-017-01332-7.pdfhttp://www.nature.com/articles/s41467-017-01332-7}, author = {Johnson, Robert E. and Tien, Nai-Wen and Shen, Ning and Pearson, James T. and Soto, Florentina and Kerschensteiner, Daniel} } @article {48669, title = {How to make a worm twitch.}, journal = {Biophysical Journal}, volume = {112}, year = {2017}, month = {2017 May 09}, pages = {1737-1738}, issn = {1542-0086}, doi = {10.1016/j.bpj.2017.03.035}, author = {Keller, Philipp J} } @article {48318, title = {Imaging mRNA and protein interactions within neurons.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, year = {2017}, month = {2017 Mar 07}, pages = {E1875-E1884}, abstract = {

RNA-protein interactions are essential for proper gene expression regulation, particularly in neurons with unique spatial constraints. Currently, these interactions are defined biochemically, but a method is needed to evaluate them quantitatively within morphological context. Colocalization of two-color labels using wide-field microscopy is a method to infer these interactions. However, because of chromatic aberrations in the objective lens, this approach lacks the resolution to determine whether two molecules are physically in contact or simply nearby by chance. Here, we developed a robust super registration methodology that corrected the chromatic aberration across the entire image field to within 10 nm, which is capable of determining whether two molecules are physically interacting or simply in proximity by random chance. We applied this approach to image single-molecule FISH in combination with immunofluorescence (smFISH-IF) and determined whether the association between an mRNA and binding protein(s) within a neuron was significant or accidental. We evaluated several mRNA-binding proteins identified from RNA pulldown assays to determine which of these exhibit bona fide interactions. Surprisingly, many known mRNA-binding proteins did not bind the mRNA in situ, indicating that adventitious interactions are significant using existing technology. This method provides an ability to evaluate two-color registration compatible with the scale of molecular interactions.

}, issn = {1091-6490}, doi = {10.1073/pnas.1621440114}, author = {Eliscovich, Carolina and Shenoy, Shailesh M and Singer, Robert H} } @article {48939, title = {Immature HIV-1 lattice assembly dynamics are regulated by scaffolding from nucleic acid and the plasma membrane.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, year = {2017}, month = {2017 Nov 07}, pages = {E10056-65}, abstract = {

The packaging and budding of Gag polyprotein and viral RNA is a critical step in the HIV-1 life cycle. High-resolution structures of the Gag polyprotein have revealed that the capsid (CA) and spacer peptide 1 (SP1) domains contain important interfaces for Gag self-assembly. However, the molecular details of the multimerization process, especially in the presence of RNA and the cell membrane, have remained unclear. In this work, we investigate the mechanisms that work in concert between the polyproteins, RNA, and membrane to promote immature lattice growth. We develop a coarse-grained (CG) computational model that is derived from subnanometer resolution structural data. Our simulations recapitulate contiguous and hexameric lattice assembly driven only by weak anisotropic attractions at the helical CA-SP1 junction. Importantly, analysis from CG and single-particle tracking photoactivated localization (spt-PALM) trajectories indicates that viral RNA and the membrane are critical constituents that actively promote Gag multimerization through scaffolding, while overexpression of short competitor RNA can suppress assembly. We also find that the CA amino-terminal domain imparts intrinsic curvature to the Gag lattice. As a consequence, immature lattice growth appears to be coupled to the dynamics of spontaneous membrane deformation. Our findings elucidate a simple network of interactions that regulate the early stages of HIV-1 assembly and budding.

}, issn = {1091-6490}, doi = {10.1073/pnas.1706600114}, author = {Pak, Alexander J and Grime, John M A and Sengupta, Prabuddha and Chen, Antony K and Durumeric, Aleksander E P and Srivastava, Anand and Yeager, Mark and Briggs, John A G and Lippincott-Schwartz, Jennifer and Voth, Gregory A} } @article {48766, title = {Imp and Syp RNA-binding proteins govern decommissioning of Drosophila neural stem cells.}, journal = {Development (Cambridge, England)}, volume = {144}, year = {2017}, month = {2017 Aug 29}, pages = {3454-64}, abstract = {

The termination of the proliferation of Drosophila neural stem cells, also known as neuroblasts (NBs), requires a "decommissioning" phase that is controlled in a lineage-specific manner. Most NBs, with the exception of those of the Mushroom body (MB), are decommissioned by the ecdysone receptor and mediator complex causing them to shrink during metamorphosis, followed by nuclear accumulation of Prospero and cell cycle exit. Here, we demonstrate that the levels of Imp and Syp RNA-binding proteins regulate NB decommissioning. Descending Imp and ascending Syp expression have been shown to regulate neuronal temporal fate. We show that Imp levels decline slower in the MB than other central brain NBs. MB NBs continue to express Imp into pupation, and the presence of Imp prevents decommissioning partly by inhibiting the mediator complex. Late-larval induction of transgenic Imp prevents many non-MB NBs from decommissioning in early pupae. Moreover, the presence of abundant Syp in aged NBs permits Prospero accumulation that, in turn, promotes cell cycle exit. Together our results reveal that progeny temporal fate and progenitor decommissioning are co-regulated in protracted neuronal lineages.

}, issn = {1477-9129}, doi = {10.1242/dev.149500}, author = {Yang, Ching-Po and Samuels, Tamsin J and Huang, Yaling and Yang, Lu and Ish-Horowicz, David and Davis, Ilan and Lee, Tzumin} } @article {68995, title = {Improved Proliferative Capacity of NP-Like Cells Derived from Human Mesenchymal Stromal Cells and Neuronal Transdifferentiation by Small Molecules.}, journal = {Neurochem Res}, volume = {42}, year = {2017}, month = {02/2017}, pages = {415-427}, abstract = {

Neural progenitors (NP), found in fetal and adult brain, differentiate into neurons potentially able to be used in cell replacement therapies. This approach however, raises technical and ethical problems which limit their potential therapeutic use. Alternately, NPs can be obtained by transdifferentiation of non-neural somatic cells evading these difficulties. Human bone marrow mesenchymal stromal cells (MSCs) are suggested to transdifferentiate into NP-like cells, which however, have a low proliferation capacity. The present study demonstrates the requisite of cell adhesion for proliferation and survival of NP-like cells and re-evaluates some neuronal features after differentiation by standard procedures. Mature neuronal markers, though, were not detected by these procedures. A chemical differentiation approach was used in this study to convert MSCs-derived NP-like cells into neurons by using a cocktail of six molecules, CHIR99021, I-BET151, RepSox, DbcAMP, forskolin and Y-27632, defined after screening combinations of 22 small molecules. Direct transdifferentiation of MSCs into neuronal cells was obtained with the small molecule cocktail, without requiring the NP-like intermediate stage.

}, keywords = {Adolescent, Adult, Amides, Cell Proliferation, Cell Transdifferentiation, Cells, Cultured, Colforsin, Drug Combinations, Heterocyclic Compounds, 4 or More Rings, Humans, Male, Mesenchymal Stem Cells, Neural Stem Cells, Neurons, Pyridines, Young Adult}, issn = {1573-6903}, doi = {10.1007/s11064-016-2086-7}, author = {Aguilera-Castrejon, Alejandro and Pasantes-Morales, Herminia and Montesinos, Juan Jose and Cort{\'e}s-Medina, Lorena V and Castro-Manrreza, Marta E and Mayani, H{\'e}ctor and Ramos-Mandujano, Gerardo} } @article {48368, title = {In vivo patch-clamp recording in awake head-fixed rodents.}, journal = {Cold Spring Harbor Protocols}, volume = {2017}, year = {2017}, month = {2017 Apr 03}, pages = {pdb.prot095802}, abstract = {

Whole-cell recording has been used to measure and manipulate a neuron{\textquoteright}s spiking and subthreshold membrane potential, allowing assessment of the cell{\textquoteright}s inputs and outputs as well as its intrinsic membrane properties. This technique has also been combined with pharmacology and optogenetics as well as morphological reconstruction to address critical questions concerning neuronal integration, plasticity, and connectivity. This protocol describes a technique for obtaining whole-cell recordings in awake head-fixed animals, allowing such questions to be investigated within the context of an intact network and natural behavioral states. First, animals are habituated to sit quietly with their heads fixed in place. Then, a whole-cell recording is obtained using an efficient, blind patching protocol. We have successfully applied this technique to rats and mice.

}, issn = {1559-6095}, doi = {10.1101/pdb.prot095802}, author = {Lee, Doyun and Lee, Albert K} } @article {48253, title = {Inhibitory suppression of heterogeneously tuned excitation enhances spatial coding in CA1 place cells.}, journal = {Nature Neuroscience}, volume = {20}, year = {2017}, month = {2017 Jan 23}, pages = {417-26}, abstract = {

Place cells in the CA1 region of the hippocampus express location-specific firing despite receiving a steady barrage of heterogeneously tuned excitatory inputs that should compromise output dynamic range and timing. We examined the role of synaptic inhibition in countering the deleterious effects of off-target excitation. Intracellular recordings in behaving mice demonstrate that bimodal excitation drives place cells, while unimodal excitation drives weaker or no spatial tuning in interneurons. Optogenetic hyperpolarization of interneurons had spatially uniform effects on place cell membrane potential dynamics, substantially reducing spatial selectivity. These data and a computational model suggest that spatially uniform inhibitory conductance enhances rate coding in place cells by suppressing out-of-field excitation and by limiting dendritic amplification. Similarly, we observed that inhibitory suppression of phasic noise generated by out-of-field excitation enhances temporal coding by expanding the range of theta phase precession. Thus, spatially uniform inhibition allows proficient and flexible coding in hippocampal CA1 by suppressing heterogeneously tuned excitation.

}, issn = {1546-1726}, doi = {10.1038/nn.4486}, author = {Grienberger, Christine and Milstein, Aaron D and Bittner, Katie C and Romani, Sandro and Magee, Jeffrey C} } @article {48492, title = {Integrating Results across Methodologies Is Essential for Producing Robust Neuronal Taxonomies.}, journal = {Neuron}, volume = {94}, year = {2017}, month = {2017 May 17}, pages = {747-751.e1}, abstract = {

Elucidating the diversity and spatial organization of cell types in the brain is an essential goal of neuroscience, with many emerging technologies helping to advance this endeavor. Using a new in\ situ hybridization method that can measure the expression of hundreds of genes in a given mouse brain section (amplified seqFISH), Shah et\ al. (2016) describe a spatial organization of hippocampal cell types that differs from previous reports. In seeking to understand this discrepancy, we find that many of the barcoded genes used by seqFISH to characterize this spatial organization, when cross-validated by other sensitive methodologies, exhibit negligible expression in the hippocampus. Additionally, the results of Shah et\ al. (2016) do not recapitulate canonical cellular hierarchies and improperly classify major neuronal cell types. We suggest that, when describing the spatial organization of brain regions, cross-validation using multiple techniques should be used to yield robust and informative cellular classification. This Matters Arising paper is in response to Shah et\ al. (2016), published in Neuron. See also the response by Shah et\ al. (2017), published in this issue.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2017.04.023}, author = {Cembrowski, Mark S and Spruston, Nelson} } @article {48907, title = {Intercellular mRNA trafficking via membrane nanotube-like extensions in mammalian cells.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, year = {2017}, month = {2017 Oct 24}, pages = {E9873-E9882}, abstract = {

RNAs have been shown to undergo transfer between mammalian cells, although the mechanism behind this phenomenon and its overall importance to cell physiology is not well understood. Numerous publications have suggested that RNAs (microRNAs and incomplete mRNAs) undergo transfer via extracellular vesicles (e.g., exosomes). However, in contrast to a diffusion-based transfer mechanism, we find that full-length mRNAs undergo direct cell-cell transfer via cytoplasmic extensions characteristic of membrane nanotubes (mNTs), which connect donor and acceptor cells. By employing a simple coculture experimental model and using single-molecule imaging, we provide quantitative data showing that mRNAs are transferred between cells in contact. Examples of mRNAs that undergo transfer include those encoding GFP, mouse β-actin, and human Cyclin D1, BRCA1, MT2A, and HER2. We show that intercellular mRNA transfer occurs in all coculture models tested (e.g., between primary cells, immortalized cells, and in cocultures of immortalized human and murine cells). Rapid mRNA transfer is dependent upon actin but is independent of de novo protein synthesis and is modulated by stress conditions and gene-expression levels. Hence, this work supports the hypothesis that full-length mRNAs undergo transfer between cells through a refined structural connection. Importantly, unlike the transfer of miRNA or RNA fragments, this process of communication transfers genetic information that could potentially alter the acceptor cell proteome. This phenomenon may prove important for the proper development and functioning of tissues as well as for host-parasite or symbiotic interactions.

}, issn = {1091-6490}, doi = {10.1073/pnas.1706365114}, author = {Haimovich, Gal and Ecker, Christopher M and Dunagin, Margaret C and Eggan, Elliott and Raj, Arjun and Gerst, Jeffrey E and Singer, Robert H} } @article {65773, title = {Intramolecular Photogeneration of a Tyrosine Radical in a Designed Protein}, journal = {ChemPhotoChem}, volume = {1}, year = {2017}, month = {02/2017}, pages = {89 {\textendash} 92}, abstract = {

Long-distance biological electron transfer occurs through a hopping mechanism and often involves tyrosine as a high potential intermediate, for example in the early charge separation steps during photosynthesis. Protein design allows for the development of minimal systems to study the underlying principles of complex systems. Herein, we report the development of the first ruthenium-linked designed protein for the photogeneration of a tyrosine radical by intramolecular electron transfer.

}, doi = {10.1002/cptc.201600044}, url = {https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/cptc.201600044}, author = {Tebo, Alison G and Quaranta, Annamaria and Herrero, Christian and Pecoraro, Vincent L and Aukauloo, Ally} } @article {48643, title = {Ion Channels: History, Diversity, and Impact.}, journal = {Cold Spring Harbor Protocols}, volume = {2017}, year = {2017}, month = {2017 Jul 05}, pages = {pdb.top092288}, abstract = {

From patch-clamp techniques to recombinant DNA technologies, three-dimensional protein modeling, and optogenetics, diverse and sophisticated methods have been used to study ion channels and how they determine the electrical properties of cells.

}, issn = {1559-6095}, doi = {10.1101/pdb.top092288}, author = {Brenowitz, Stephan and Duguid, Ian and Kammermeier, Paul J} } @article {48434, title = {Live-cell super-resolution reveals F-Actin and plasma membrane dynamics at the T Cell synapse.}, journal = {Biophysical Journal}, volume = {112}, year = {2017}, month = {2017 Apr 25}, pages = {1703-13}, abstract = {

The cortical actin cytoskeleton has been shown to be critical for the reorganization and heterogeneity of plasma membrane components of many cells, including T\ cells. Building on previous studies at the T\ cell immunological synapse, we quantitatively assess the structure and dynamics of this meshwork using live-cell superresolution fluorescence microscopy and spatio-temporal image correlation spectroscopy. We show for the first time, to our knowledge, that not only does the dense actin cortex flow in a retrograde fashion toward the synapse center, but the plasma membrane itself shows similar behavior. Furthermore, using two-color, live-cell superresolution cross-correlation spectroscopy, we demonstrate that the two flows are correlated and, in addition, we show that coupling may extend to the outer leaflet of the plasma membrane by examining the flow of GPI-anchored proteins. Finally, we demonstrate that the actin flow is correlated with a third component,\ α-actinin, which upon CRISPR knockout led to reduced plasma membrane flow directionality despite increased actin flow velocity. We hypothesize that this apparent cytoskeletal-membrane coupling could provide a mechanism for driving the observed retrograde flow of signaling molecules such as the TCR, Lck, ZAP70, LAT, and SLP76.

}, doi = {10.1016/j.bpj.2017.01.038}, author = {Ashdown, George W and Burn, Garth L and Williamson, David J and Pandzic, Elvis and Peters, Ruby and Holden, Michael and Ewers, Helge and Shao, Lin and Wiseman, Paul W and Owen, Dylan M} } @article {68760, title = {Localized Lysosome Exocytosis Helps Breach Tissue Barriers}, journal = {Developmental Cell}, volume = {43}, year = {2017}, month = {11/2017}, pages = {377-378}, abstract = {

Cell invasion across basement membrane barriers is important in both normal development and cancer metastasis. In this issue of Developmental Cell, Naegeli et\ al. (2017) identify a mechanism for breaching basement membranes. Localized lysosome exocytosis fuels generation of large, invasive cellular protrusions that expand tiny basement membrane openings.

}, issn = {1534-5807}, doi = {https://doi.org/10.1016/j.devcel.2017.11.005}, url = {https://www.sciencedirect.com/science/article/pii/S1534580717309097}, author = {Shaohe Wang and Kenneth M. Yamada} } @article {48219, title = {Long-range self-organization of cytoskeletal myosin II filament stacks.}, journal = {Nature Cell Biology}, volume = {19}, year = {2017}, month = {2017 Jan 23}, pages = {133-41}, abstract = {

Although myosin II filaments are known to exist in non-muscle cells, their dynamics and organization are incompletely understood. Here, we combined structured illumination microscopy with pharmacological and genetic perturbations, to study the process of actomyosin cytoskeleton self-organization into arcs and stress fibres. A striking feature of the myosin II filament organization was their {\textquoteright}registered{\textquoteright} alignment into stacks, spanning up to several micrometres in the direction orthogonal to the parallel actin bundles. While turnover of individual myosin II filaments was fast (characteristic half-life time 60 s) and independent of actin filament turnover, the process of stack formation lasted a longer time (in the range of several minutes) and required myosin II contractility, as well as actin filament assembly/disassembly and crosslinking (dependent on formin Fmnl3, cofilin1 and α-actinin-4). Furthermore, myosin filament stack formation involved long-range movements of individual myosin filaments towards each other suggesting the existence of attractive forces between myosin II filaments. These forces, possibly transmitted via mechanical deformations of the intervening actin filament network, may in turn remodel the actomyosin cytoskeleton and drive its self-organization.

}, issn = {1476-4679}, doi = {10.1038/ncb3466}, author = {Hu, Shiqiong and Dasbiswas, Kinjal and Guo, Zhenhuan and Tee, Yee-Han and Thiagarajan, Visalatchi and Hersen, Pascal and Chew, Teng-Leong and Safran, Samuel A and Zaidel-Bar, Ronen and Bershadsky, Alexander D} } @article {48605, title = {Low-complexity domains adhere by reversible amyloid-like interactions between kinked β-sheets.}, journal = {bioRxiv}, year = {2017}, month = {2017 Jun 22}, abstract = {

Control of metabolism by compartmentation is a widespread feature of higher cells. Recent studies have focused on dynamic intracellular bodies such as stress granules, P-bodies, nucleoli, and metabolic puncta. These bodies appear as separate phases, some containing reversible, amyloid-like fibrils formed by interactions of low-complexity protein domains. Here we report five atomic structures of segments of low-complexity domains from granule-forming proteins, one determined to 1.1 {\r A} resolution by micro-electron diffraction. Four of these interacting protein segments show common characteristics, all in contrast to pathogenic amyloid: kinked peptide backbones, small surface areas of interaction, and predominate attractions between aromatic side-chains. By computationally threading the human proteome on three of our kinked structures, we identified hundreds of low-complexity segments potentially capable of forming such reversible interactions. These segments are found in proteins as diverse as RNA binders, nuclear pore proteins, keratins, and cornified envelope proteins, consistent with the capacity of cells to form a wide variety of dynamic intracellular bodies.

}, doi = {10.1101/153817}, author = {Hughes, Michael P and Sawaya, Michael R and Goldschmidt, Lukasz and Rodriguez, Jose A and Cascio, Duilio and Gonen, Tamir and Eisenberg, David S} } @article {48160, title = {Machine vision methods for analyzing social interactions.}, journal = {The Journal of Experimental Biology}, volume = {220}, year = {2017}, month = {2017 Jan 01}, pages = {25-34}, abstract = {

Recent developments in machine vision methods for automatic, quantitative analysis of social behavior have immensely improved both the scale and level of resolution with which we can dissect interactions between members of the same species. In this paper, we review these methods, with a particular focus on how biologists can apply them to their own work. We discuss several components of machine vision-based analyses: methods to record high-quality video for automated analyses, video-based tracking algorithms for estimating the positions of interacting animals, and machine learning methods for recognizing patterns of interactions. These methods are extremely general in their applicability, and we review a subset of successful applications of them to biological questions in several model systems with very different types of social behaviors.

}, issn = {1477-9145}, doi = {10.1242/jeb.142281}, author = {Robie, Alice A and Seagraves, Kelly M and Egnor, S E Roian and Branson, Kristin} } @article {48459, title = {Maintenance of persistent activity in a frontal thalamocortical loop.}, journal = {Nature}, volume = {545}, year = {2017}, month = {2017 May 03}, pages = {181-6}, abstract = {

Persistent neural activity maintains information that connects past and future events. Models of persistent activity often invoke reverberations within local cortical circuits, but long-range circuits could also contribute. Neurons in the mouse anterior lateral motor cortex (ALM) have been shown to have selective persistent activity that instructs future actions. The ALM is connected bidirectionally with parts of the thalamus, including the ventral medial and ventral anterior-lateral nuclei. We recorded spikes from the ALM and thalamus during tactile discrimination with a delayed directional response. Here we show that, similar to ALM neurons, thalamic neurons exhibited selective persistent delay activity that predicted movement direction. Unilateral photoinhibition of delay activity in the ALM or thalamus produced contralesional neglect. Photoinhibition of the thalamus caused a short-latency and near-complete collapse of ALM activity. Similarly, photoinhibition of the ALM diminished thalamic activity. Our results show that the thalamus is a circuit hub in motor preparation and suggest that persistent activity requires reciprocal excitation across multiple brain areas.

}, issn = {1476-4687}, doi = {10.1038/nature22324}, author = {Guo, Zengcai V and Inagaki, Hidehiko K and Daie, Kayvon and Druckmann, Shaul and Gerfen, Charles R and Svoboda, Karel} } @article {48493, title = {A map of anticipatory activity in mouse motor cortex.}, journal = {Neuron}, volume = {94}, year = {2017}, month = {2017 May 17}, pages = {866-879.e4}, abstract = {

Activity in the mouse anterior lateral motor cortex (ALM) instructs directional movements, often seconds before movement initiation. It is unknown whether this preparatory activity is localized to ALM or widely distributed within motor cortex. Here we imaged activity across motor cortex while mice performed a whisker-based object localization task with a delayed, directional licking response. During tactile sensation and the delay epoch, object location was represented in motor cortex areas that are medial and posterior relative to ALM, including vibrissal motor cortex. Preparatory activity appeared first in deep layers of ALM, seconds before the behavioral response, and remained localized to ALM until the behavioral response. Later, widely distributed neurons represented the outcome of the trial. Cortical area was more predictive of neuronal selectivity than laminar location or axonal projection target. Motor cortex therefore represents sensory, motor, and outcome information in a spatially organized manner.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2017.05.005}, author = {Chen, Tsai-Wen and Li, Nuo and Daie, Kayvon and Svoboda, Karel} } @article {48646, title = {Mapping the neural substrates of behavior.}, journal = {Cell}, volume = {170}, year = {2017}, month = {2017-07-13}, pages = {393-406}, abstract = {

Assigning behavioral functions to neural structures has long been a central goal in neuroscience and is a necessary first step toward a circuit-level understanding of how the brain generates behavior. Here, we map the neural substrates of locomotion and social behaviors for Drosophila melanogaster using automated machine-vision and machine-learning techniques. From videos of 400,000 flies, we quantified the behavioral effects of activating 2,204 genetically targeted populations of neurons. We combined a novel quantification of anatomy with our behavioral analysis to create brain-behavior correlation maps, which are shared as browsable web pages and interactive software. Based on these maps, we generated hypotheses of regions of the brain causally related to sensory processing, locomotor control, courtship, aggression, and sleep. Our maps directly specify genetic tools to target these regions, which we used to identify a small population of neurons with a role in the control of walking.

{\textbullet}We developed machine-vision methods to broadly and precisely quantify fly behavior{\textbullet}We measured effects of activating 2,204 genetically targeted neuronal populations{\textbullet}We created whole-brain maps of neural substrates of locomotor and social behaviors{\textbullet}We created resources for exploring our results and enabling further investigation

Machine-vision analyses of large behavior and neuroanatomy data reveal whole-brain maps of regions associated with numerous complex behaviors.

}, doi = {10.1016/j.cell.2017.06.032}, url = {http://dx.doi.org/10.1016/j.cell.2017.06.032}, author = {Robie, Alice A and Hirokawa, Jonathan and Edwards, Austin W and Umayam, Lowell A and Lee, Allen and Phillips, Mary L and Card, Gwyneth M and Korff, Wyatt and Rubin, Gerald M and Simpson, Julie H and Reiser, Michael B and Branson, Kristin M} } @article {48344, title = {Mechanism of ribosome rescue by ArfA and RF2.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Mar 16}, pages = {e23687}, abstract = {

ArfA rescues ribosomes stalled on truncated mRNAs by recruiting release factor RF2, which normally binds stop codons to catalyze peptide release. We report two 3.2-{\r A} resolution cryo-EM structures - determined from a single sample - of the 70S ribosome with ArfA{\textbullet}RF2 in the A site. In both states, the ArfA C-terminus occupies the mRNA tunnel downstream of the A site. One state contains a compact inactive RF2 conformation. Ordering of the ArfA N-terminus in the second state rearranges RF2 into an extended conformation that docks the catalytic GGQ motif into the peptidyl-transferase center. Our work thus reveals the structural dynamics of ribosome rescue. The structures demonstrate how ArfA "senses" the vacant mRNA tunnel and activates RF2 to mediate peptide release without a stop codon, allowing stalled ribosomes to be recycled.

}, issn = {2050-084X}, doi = {10.7554/eLife.23687}, author = {Demo, Gabriel and Svidritskiy, Egor and Madireddy, Rohini and Diaz-Avalos, Ruben and Grant, Timothy and Grigorieff, Nikolaus and Sousa, Duncan and Korostelev, Andrei A} } @article {48560, title = {Mechanisms underlying a thalamocortical transformation during active tactile sensation.}, journal = {PLoS Computational Biology}, volume = {13}, year = {2017}, month = {2017 Jun 07}, pages = {e1005576}, abstract = {

During active somatosensation, neural signals expected from movement of the sensors are suppressed in the cortex, whereas information related to touch is enhanced. This tactile suppression underlies low-noise encoding of relevant tactile features and the brain{\textquoteright}s ability to make fine tactile discriminations. Layer (L) 4 excitatory neurons in the barrel cortex, the major target of the somatosensory thalamus (VPM), respond to touch, but have low spike rates and low sensitivity to the movement of whiskers. Most neurons in VPM respond to touch and also show an increase in spike rate with whisker movement. Therefore, signals related to self-movement are suppressed in L4. Fast-spiking (FS) interneurons in L4 show similar dynamics to VPM neurons. Stimulation of halorhodopsin in FS interneurons causes a reduction in FS neuron activity and an increase in L4 excitatory neuron activity. This decrease of activity of L4 FS neurons contradicts the "paradoxical effect" predicted in networks stabilized by inhibition and in strongly-coupled networks. To explain these observations, we constructed a model of the L4 circuit, with connectivity constrained by in vitro measurements. The model explores the various synaptic conductance strengths for which L4 FS neurons actively suppress baseline and movement-related activity in layer 4 excitatory neurons. Feedforward inhibition, in concert with recurrent intracortical circuitry, produces tactile suppression. Synaptic delays in feedforward inhibition allow transmission of temporally brief volleys of activity associated with touch. Our model provides a mechanistic explanation of a behavior-related computation implemented by the thalamocortical circuit.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1005576}, author = {Gutnisky, Diego Adrian and Yu, Jianing and Hires, Samuel Andrew and To, Minh-Son and Bale, Michael and Svoboda, Karel and Golomb, David} } @article {48906, title = {Membrane dynamics and organelle biogenesis-lipid pipelines and vesicular carriers.}, journal = {BMC Biology}, volume = {15}, year = {2017}, month = {2017 Oct 31}, pages = {102}, abstract = {

Discoveries spanning several decades have pointed to vital membrane lipid trafficking pathways involving both vesicular and non-vesicular carriers. But the relative contributions for distinct membrane delivery pathways in cell growth and organelle biogenesis continue to be a puzzle. This is because lipids flow from many sources and across many paths via transport vesicles, non-vesicular transfer proteins, and dynamic interactions between organelles at membrane contact sites. This forum presents our latest understanding, appreciation, and queries regarding the lipid transport mechanisms necessary to drive membrane expansion during organelle biogenesis and cell growth.

}, issn = {1741-7007}, doi = {10.1186/s12915-017-0432-0}, author = {Stefan, Christopher J and Trimble, William S and Grinstein, Sergio and Drin, Guillaume and Reinisch, Karin and De Camilli, Pietro and Cohen, Sarah and Valm, Alex M and Lippincott-Schwartz, Jennifer and Levine, Tim P and Iaea, David B and Maxfield, Frederick R and Futter, Clare E and Eden, Emily R and Judith, Delphine and van Vliet, Alexander R and Agostinis, Patrizia and Tooze, Sharon A and Sugiura, Ayumu and McBride, Heidi M} } @article {48557, title = {Memory retrieval from first principles.}, journal = {Neuron}, volume = {94}, year = {2017}, month = {2017 Jun 07}, pages = {1027-1032}, abstract = {

The dilemma that neurotheorists face is that (1) detailed biophysical models that can be constrained by direct measurements, while being of great importance, offer no immediate insights into cognitive processes in the brain, and (2) high-level abstract cognitive models, on the other hand, while relevant for understanding behavior, are largely detached from neuronal processes and typically have many free, experimentally unconstrained parameters that have to be tuned to a particular data set and, hence, cannot be readily generalized to other experimental paradigms. In this contribution, we propose a set of "first principles" for neurally inspired cognitive modeling of memory retrieval that has no biologically unconstrained parameters and can be analyzed mathematically both at neuronal and cognitive levels. We apply this framework to the classical cognitive paradigm of free recall. We show that the resulting model accounts well for puzzling behavioral data on human participants and makes predictions that could potentially be tested with neurophysiological recording techniques.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2017.03.048}, author = {Katkov, M and Romani, S and Tsodyks, M} } @article {48558, title = {Mesoscale-duration activated states gate spiking in response to fast rises in membrane voltage in the awake brain.}, journal = {Journal of Neurophysiology}, volume = {118}, year = {2017}, month = {2017 May 31}, pages = {1270-91}, abstract = {

Seconds-scale network states, affecting many neurons within a network, modulate neural activity by complementing fast integration of neuron-specific inputs that arrive in the milliseconds before spiking. Non-rhythmic subthreshold dynamics at intermediate timescales, however, are less well-characterized. We found, using automated whole cell patch clamping in vivo, that spikes recorded in CA1 and barrel cortex in awake mice are often preceded not only by monotonic voltage rises lasting milliseconds, but also by more gradual (lasting 10s-100s of ms) depolarizations. The latter exert a gating function on spiking, in a fashion that depends on the gradual rise duration: the probability of spiking was higher for longer gradual rises, even controlling for the amplitude of the gradual rises. Barrel cortex double-autopatch recordings show that gradual rises are shared across some but not all neurons. The gradual rises may represent a new kind of state, intermediate both in timescale and in proportion of neurons participating, which gates a neuron{\textquoteright}s ability to respond to subsequent inputs.

}, issn = {1522-1598}, doi = {10.1152/jn.00116.2017}, author = {Singer, Annabelle C and Talei Franzesi, Giovanni and Kodandaramaiah, Suhasa B and Flores, Francisco J and Cohen, Jeremy D and Lee, Albert K and B{\"o}rgers, Christoph and Forest, Craig R and Kopell, Nancy J and Boyden, Edward S} } @article {48604, title = {A method to minimize condenser lens-induced hysteresis effects in a JEOL JEM-3200FSC microscope to enable stable cryoEM low-dose operations.}, journal = {bioRxiv}, year = {2017}, month = {2017 Jun 21}, abstract = {

Low dose imaging procedures are key for a successful cryoEM experiment (whether by electron cryotomography, single particle analysis, electron crystallography, or MicroED). We present a method to minimize magnetic hysteresis of the condenser lens system in the JEOL JEM-3200FSC transmission electron microscope (TEM) in order to maintain a stable optical axis for the beam path of low-dose imaging. The simple procedure involves independent voltage ramping of the CL1 and CL2 lenses immediately before switching to the focusing and exposure beam settings for data collection.

}, doi = {10.1101/153395}, author = {de la Cruz, Michael Jason and Martynowycz, Michael and Hattne, Johan and Shi, Dan and Gonen, Tamir} } @article {48617, title = {MicroED structure of Au146(p-MBA)57 at subatomic resolution reveals a twinned FCC cluster.}, journal = {Journal of Physical Chemistry Letters}, volume = {8}, year = {2017}, month = {2017 Oct 31}, pages = {arXiv:1706.07902 [physics.atm-clus]}, abstract = {

Solving the atomic structure of metallic clusters is fundamental to understanding their optical, electronic, and chemical properties. We report the structure of Au146(p-MBA)57\ at subatomic resolution (0.85 {\AA}) using electron diffraction (MicroED) and atomic resolution by X-ray diffraction. The 146 gold atoms may be decomposed into two constituent sets consisting of 119 core and 27 peripheral atoms. The core atoms are organized in a twinned FCC structure whereas the surface gold atoms follow a C2\ rotational symmetry about an axis bisecting the twinning plane. The protective layer of 57 p-MBAs fully encloses the cluster and comprises bridging, monomeric, and dimeric staple motifs. Au146(p-MBA)57\ is the largest cluster observed exhibiting a bulk-like FCC structure as well as the smallest gold particle exhibiting a stacking fault.

}, doi = {10.1021/acs.jpclett.7b02621}, url = {https://128.84.21.199/abs/1706.07902}, author = {Vergara, Sandra and Lukes, Dylan A and Martynowycz, Michael W and Santiago, Ulises and Plascencia-Villa, German and Weiss, Simon C and de la Cruz, Michael Jason and Black, David M and Alvarez, Marcos M and Lopez-Lozano, Xochitl and Barnes, Christopher O and Lin, Guowu and Weissker, Hans-Christian and Whetten, Robert L and Gonen, Tamir and Calero, Guillermo} } @article {48603, title = {MicroED structures from micrometer thick protein crystals.}, journal = {bioRxiv}, year = {2017}, month = {2017 Jun 20}, abstract = {

Theoretical calculations suggest that crystals exceeding 100 nm thickness are excluded by dynamical scattering from successful structure determination using microcrystal electron diffraction (MicroED). These calculations are at odds with experimental results where MicroED structures have been determined from significantly thicker crystals. Here we systematically evaluate the influence of thickness on the accuracy of MicroED intensities and the ability to determine structures from protein crystals one micrometer thick. To do so, we compare ab initio structures of a human prion protein segment determined from thin crystals to those determined from crystals up to one micrometer thick. We also compare molecular replacement solutions from crystals of varying thickness for a larger globular protein, proteinase K. Our results indicate that structures can be reliably determined from crystals at least an order of magnitude thicker than previously suggested by simulation, opening the possibility for an even broader range of MicroED experiments.

}, doi = {10.1101/152504}, author = {Martynowycz, Michael and Glynn, Calina and Miao, Jennifer and de la Cruz, Michael Jason and Hattne, Johan and Shi, Dan and Cascio, Duilio and Rodriguez, Jose and Gonen, Tamir} } @conference {67221, title = {Model-based Bayesian inference of neural activity and connectivity from all-optical interrogation of a neural circuit}, booktitle = {Advances in Neural Information Processing Systems}, year = {2017}, publisher = {Curran Associates, Inc.}, organization = {Curran Associates, Inc.}, abstract = {

Population activity measurement by calcium imaging can be combined with cellular resolution optogenetic activity perturbations to enable the mapping of neural connectivity in vivo. This requires accurate inference of perturbed and unperturbed neural activity from calcium imaging measurements, which are noisy and indirect, and can also be contaminated by photostimulation artifacts. We have developed a new fully Bayesian approach to jointly inferring spiking activity and neural connectivity from in vivo all-optical perturbation experiments. In contrast to standard approaches that perform spike inference and analysis in two separate maximum-likelihood phases, our joint model is able to propagate uncertainty in spike inference to the inference of connectivity and vice versa. We use the framework of variational autoencoders to model spiking activity using discrete latent variables, low-dimensional latent common input, and sparse spike-and-slab generalized linear coupling between neurons. Additionally, we model two properties of the optogenetic perturbation: off-target photostimulation and photostimulation transients. Using this model, we were able to fit models on 30 minutes of data in just 10 minutes. We performed an all-optical circuit mapping experiment in primary visual cortex of the awake mouse, and use our approach to predict neural connectivity between excitatory neurons in layer 2/3. Predicted connectivity is sparse and consistent with known correlations with stimulus tuning, spontaneous correlation and distance.

}, url = {https://discovery.ucl.ac.uk/id/eprint/10072143/}, author = {Aitchison, Laurence and Russell, Lloyd and Packer, Adam M and Yan, Jinyao and Castonguay, Philippe and H{\"a}usser, Michael and Turaga, Srinivas C}, editor = {I. Guyon and U. V. Luxburg and S. Bengio and H. Wallach and R. Fergus and S. Vishwanathan and R. Garnett} } @proceedings {48942, title = {Model-based Bayesian inference of neural activity and connectivity from all-optical interrogation of a neural circuit.}, year = {2017}, month = {2017 Dec 04}, abstract = {

Population activity measurement by calcium imaging can be combined with cellular resolution optogenetic activity perturbations to enable the mapping of neural connectivity in vivo. This requires accurate inference of perturbed and unperturbed neural activity from calcium imaging measurements, which are noisy and indirect, and can also be contaminated by photostimulation artifacts. We have developed a new fully Bayesian approach to jointly inferring spiking activity and neural connectivity from in vivo all-optical perturbation experiments. In contrast to standard approaches that perform spike inference and analysis in two separate maximum-likelihood phases, our joint model is able to propagate uncertainty in spike inference to the inference of connectivity and vice versa. We use the framework of variational autoencoders to model spiking activity using discrete latent variables, low-dimensional latent common input, and sparse spike-and-slab generalized linear coupling between neurons. Additionally, we model two properties of the optogenetic perturbation: off-target photostimulation and photostimulation transients. Our joint model includes at least two sets of discrete random variables; to avoid the dramatic slowdown typically caused by being unable to differentiate such variables, we introduce two strategies that have not, to our knowledge, been used with variational autoencoders. Using this model, we were able to fit models on 30 minutes of data in just 10 minutes. We performed an all-optical circuit mapping experiment in primary visual cortex of the awake mouse, and use our approach to predict neural connectivity between excitatory neurons in layer 2/3. Predicted connectivity is sparse and consistent with known correlations with stimulus tuning, spontaneous correlation and distance.

}, url = {https://papers.nips.cc/paper/6940-model-based-bayesian-inference-of-neural-activity-and-connectivity-from-all-optical-interrogation-of-a-neural-circuit}, author = {Aitchison, Laurence and Russell, Lloyd and Packer, Adam M and Yan, Jinyao and Castonguaye, Philippe and H{\"a}usser, Michael and Turaga, Srinivas C} } @article {48908, title = {Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres.}, journal = {Genes \& Development}, volume = {31}, year = {2017}, month = {2017 Oct 01}, pages = {1958-1972}, abstract = {

Histone CENP-A-containing nucleosomes play an important role in nucleating kinetochores at centromeres for chromosome segregation. However, the molecular mechanisms by which CENP-A nucleosomes engage with kinetochore proteins are not well understood. Here, we report the finding of a new function for the budding yeast Cse4/CENP-A histone-fold domain interacting with inner kinetochore protein Mif2/CENP-C. Strikingly, we also discovered that AT-rich centromere DNA has an important role for Mif2 recruitment. Mif2 contacts one side of the nucleosome dyad, engaging with both Cse4 residues and AT-rich nucleosomal DNA. Both interactions are directed by a contiguous DNA- and histone-binding domain (DHBD) harboring the conserved CENP-C motif, an AT hook, and RK clusters (clusters enriched for arginine-lysine residues). Human CENP-C has two related DHBDs that bind preferentially to DNA sequences of higher AT content. Our findings suggest that a DNA composition-based mechanism together with residues characteristic for the CENP-A histone variant contribute to the specification of centromere identity.

}, issn = {1549-5477}, doi = {10.1101/gad.304782.117}, author = {Xiao, Hua and Wang, Feng and Wisniewski, Jan and Shaytan, Alexey K and Ghirlando, Rodolfo and Fitzgerald, Peter C and Huang, Yingzi and Wei, Debbie and Li, Shipeng and Landsman, David and Panchenko, Anna R and Wu, Carl} } @article {48279, title = {Moonwalker descending neurons mediate visually evoked retreat in Drosophila.}, journal = {Current Biology : CB}, volume = {27}, year = {2017}, month = {2017 Mar 6}, pages = {766-71}, abstract = {

Insects, like most animals, tend to steer away from imminent threats [1-7]. Drosophila melanogaster, for example, generally initiate an escape take-off in response to a looming visual stimulus, mimicking a potential predator [8]. The escape response to a visual threat is, however, flexible [9-12] and can alternatively consist of walking backward away from the perceived threat [11], which may be a more effective response to ambush predators such as nymphal praying mantids [7]. Flexibility in escape behavior may also add an element of unpredictability that makes it difficult for predators to anticipate or learn the prey{\textquoteright}s likely response [3-6]. Whereas the fly{\textquoteright}s escape jump has been well studied [8, 9, 13-18], the neuronal underpinnings of evasive walking remain largely unexplored. We previously reported the identification of a cluster of descending neurons-the moonwalker descending neurons (MDNs)-the activity of which is necessary and sufficient to trigger backward walking [19], as well as a population of visual projection neurons-the lobula columnar 16 (LC16) cells-that respond to looming visual stimuli and elicit backward walking and turning [11]. Given the similarity of their activation phenotypes, we hypothesized that LC16 neurons induce backward walking via MDNs and that turning while walking backward might reflect asymmetric activation of the left and right MDNs. Here, we present data from functional imaging, behavioral epistasis, and unilateral activation experiments that support these hypotheses. We conclude that LC16 and MDNs are critical components of the neural circuit that transduces threatening visual stimuli into directional locomotor output.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2017.02.008}, author = {Sen, Rajyashree and Wu, Ming and Branson, Kristin and Robie, Alice and Rubin, Gerald M and Dickson, Barry J} } @article {48936, title = {A moving source of matrix components is essential for de novo basement membrane formation.}, journal = {Current Biology : CB}, volume = {27}, year = {2017}, month = {2017 Nov 02}, pages = {3526-34}, abstract = {

The basement membrane (BM) is a thin layer of extracellular matrix (ECM) beneath nearly all epithelial cell types that is critical for cellular and tissue function. It is composed of numerous components conserved among all bilaterians [1]; however, it is unknown how all of these components are generated and subsequently constructed to form a fully mature BM in the living animal. Although BM formation is thought to simply involve a process of self-assembly [2], this concept suffers from a number of logistical issues when considering its construction in\ vivo. First, incorporation of BM components appears to be hierarchical [3-5], yet it is unclear whether their production during embryogenesis must also be regulated in a temporal fashion. Second, many BM proteins are produced not only by the cells residing on the BM but also by surrounding cell types [6-9], and it is unclear how large, possibly insoluble protein complexes [10] are delivered into the matrix. Here we exploit our ability to live image and genetically dissect de novo BM formation during Drosophila development. This reveals that there is a temporal hierarchy of BM protein production that is essential for proper component incorporation. Furthermore, we show that BM components require secretion by migrating macrophages (hemocytes) during their developmental dispersal, which is critical for embryogenesis. Indeed, hemocyte migration is essential to deliver a subset of ECM components evenly throughout the embryo. This reveals that de novo BM construction requires a combination of both production and distribution logistics allowing for the timely delivery of core components.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2017.10.001}, author = {Matsubayashi, Yutaka and Louani, Adam and Dragu, Anca and S{\'a}nchez-S{\'a}nchez, Besaiz J and Serna-Morales, Eduardo and Yolland, Lawrence and Gyoergy, Attila and Vizcay, Gema and Fleck, Roland A and Heddleston, John M and Chew, Teng-Leong and Siekhaus, Daria E and Stramer, Brian M} } @article {48223, title = {moxDendra2: an inert photoswitchable protein for oxidizing environments.}, journal = {Chemical Communications}, volume = {53}, year = {2017}, month = {2017 Jan 19}, pages = {2106-9}, abstract = {

Fluorescent proteins (FPs) that can be optically highlighted enable PALM super-resolution microscopy and pulse-chase experiments of cellular molecules. Most FPs evolved in cytoplasmic environments either in the original source organism or in the cytoplasm of bacteria during the course of optimization for research applications. Consequently, many FPs may fold incorrectly in the chemically distinct environments in subcellular organelles. Here, we describe the first monomeric photoswitchable (from green to bright red) FP adapted for oxidizing environments.

}, doi = {10.1039/C6CC09997A}, author = {Kaberniuk, Andrii A and Morano, Nicholas C and Verkhusha, Vladislav V and Snapp, Erik Lee} } @article {48595, title = {mRNA quantification using single-molecule FISH in Drosophila embryos.}, journal = {Nature Protocols}, volume = {12}, year = {2017}, month = {2017 Jul}, pages = {1326-1348}, abstract = {

Spatial information is critical to the interrogation of developmental and tissue-level regulation of gene expression. However, this information is usually lost when global mRNA levels from tissues are measured using reverse transcriptase PCR, microarray analysis or high-throughput sequencing. By contrast, single-molecule fluorescence in situ hybridization (smFISH) preserves the spatial information of the cellular mRNA content with subcellular resolution within tissues. Here we describe an smFISH protocol that allows for the quantification of single mRNAs in Drosophila embryos, using commercially available smFISH probes (e.g., short fluorescently labeled DNA oligonucleotides) in combination with wide-field epifluorescence, confocal or instant structured illumination microscopy (iSIM, a super-resolution imaging approach) and a spot-detection algorithm. Fixed Drosophila embryos are hybridized in solution with a mixture of smFISH probes, mounted onto coverslips and imaged in 3D. Individual fluorescently labeled mRNAs are then localized within tissues and counted using spot-detection software to generate quantitative, spatially resolved gene expression data sets. With minimum guidance, a graduate student can successfully implement this protocol. The smFISH procedure described here can be completed in 4-5 d.

}, issn = {1750-2799}, doi = {10.1038/nprot.2017.030}, author = {Trcek, Tatjana and Lionnet, Timoth{\'e}e and Shroff, Hari and Lehmann, Ruth} } @article {48254, title = {Multicut brings automated neurite segmentation closer to human performance.}, journal = {Nature Methods}, volume = {14}, year = {2017}, month = {2017 Jan 31}, pages = {101-102}, issn = {1548-7105}, doi = {10.1038/nmeth.4151}, author = {Beier, Thorsten and Pape, Constantin and Rahaman, Nasim and Prange, Timo and Berg, Stuart and Bock, Davi D and Cardona, Albert and Knott, Graham W and Plaza, Stephen M and Scheffer, Louis K and Koethe, Ullrich and Kreshuk, Anna and Hamprecht, Fred A} } @article {48716, title = {Multi-scale approaches for high-speed imaging and analysis of large neural populations.}, journal = {PLoS Computational Biology}, volume = {13}, year = {2017}, month = {2017 Aug 03}, pages = {e1005685}, abstract = {

Progress in modern neuroscience critically depends on our ability to observe the activity of large neuronal populations with cellular spatial and high temporal resolution. However, two bottlenecks constrain efforts towards fast imaging of large populations. First, the resulting large video data is challenging to analyze. Second, there is an explicit tradeoff between imaging speed, signal-to-noise, and field of view: with current recording technology we cannot image very large neuronal populations with simultaneously high spatial and temporal resolution. Here we describe multi-scale approaches for alleviating both of these bottlenecks. First, we show that spatial and temporal decimation techniques based on simple local averaging provide order-of-magnitude speedups in spatiotemporally demixing calcium video data into estimates of single-cell neural activity. Second, once the shapes of individual neurons have been identified at fine scale (e.g., after an initial phase of conventional imaging with standard temporal and spatial resolution), we find that the spatial/temporal resolution tradeoff shifts dramatically: after demixing we can accurately recover denoised fluorescence traces and deconvolved neural activity of each individual neuron from coarse scale data that has been spatially decimated by an order of magnitude. This offers a cheap method for compressing this large video data, and also implies that it is possible to either speed up imaging significantly, or to "zoom out" by a corresponding factor to image order-of-magnitude larger neuronal populations with minimal loss in accuracy or temporal resolution.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1005685}, author = {Friedrich, Johannes and Yang, Weijian and Soudry, Daniel and Mu, Yu and Ahrens, Misha B and Yuste, Rafael and Peterka, Darcy S and Paninski, Liam} } @article {48278, title = {Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb.}, journal = {eLife}, volume = {7}, year = {2017}, month = {2018 Mar 29}, pages = {e34410}, abstract = {

During development, coordinated cell behaviors orchestrate tissue and organ morphogenesis. Detailed descriptions of cell lineages and behaviors provide a powerful framework to elucidate the mechanisms of morphogenesis. To study the cellular basis of limb development, we imaged transgenic fluorescently-labeled embryos from the crustacean Parhyale hawaiensis with multi-view light-sheet microscopy at high spatiotemporal resolution over several days of embryogenesis. The cell lineage of outgrowing thoracic limbs was reconstructed at single-cell resolution with new software called Massive Multi-view Tracker (MaMuT). In silico clonal analyses suggested that the early limb primordium becomes subdivided into anterior-posterior and dorsal-ventral compartments whose boundaries intersect at the distal tip of the growing limb. Limb-bud formation is associated with spatial modulation of cell proliferation, while limb elongation is also driven by preferential orientation of cell divisions along the proximal-distal growth axis. Cellular reconstructions were predictive of the expression patterns of limb development genes including the BMP morphogen Decapentaplegic.

}, doi = {10.7554/eLife.34410}, author = {Wolff, Carsten and Tinevez, Jean-Yves and Pietzsch, Tobias and Stamataki, Evangelia and Harich, Benjamin and Guignard, Leo and Preibisch, Stephan and Shorte, Spencer and Keller, Philipp J and Tomancak, Pavel and Pavlopoulos, Anastasios} } @article {48731, title = {Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation.}, journal = {Molecular Cell}, volume = {67}, year = {2017}, month = {2017 Jul 28}, pages = {566-78}, abstract = {

50 years ago, Vincent Allfrey and colleagues discovered that lymphocyte activation triggers massive acetylation of chromatin. However, the molecular mechanisms driving epigenetic accessibility are still unknown. We here show that stimulated lymphocytes decondense chromatin by three differentially regulated steps. First, chromatin is repositioned away from the nuclear periphery in response to global acetylation. Second, histone nanodomain clusters decompact into mononucleosome fibers through a mechanism that requires Myc and continual energy input. Single-molecule imaging shows that this step lowers transcription factor residence time and non-specific collisions during sampling for DNA targets. Third, chromatin interactions shift from long range to predominantly short range, and CTCF-mediated loops and contact domains double in numbers. This architectural change facilitates cognate promoter-enhancer contacts and also requires Myc and continual ATP production. Our results thus define the nature and transcriptional impact of chromatin decondensation and reveal an unexpected role for Myc in the establishment of nuclear topology in mammalian cells.

}, issn = {1097-4164}, doi = {10.1016/j.molcel.2017.07.013}, author = {Kieffer-Kwon, Kyong-Rim and Nimura, Keisuke and Rao, Suhas S P and Xu, Jianliang and Jung, Seolkyoung and Pekowska, Aleksandra and Dose, Marei and Stevens, Evan and Mathe, Ewy and Dong, Peng and Huang, Su-Chen and Ricci, Maria Aurelia and Baranello, Laura and Zheng, Ying and Ardori, Francesco Tomassoni and Resch, Wolfgang and Stavreva, Diana and Nelson, Steevenson and McAndrew, Michael and Casellas, Adriel and Finn, Elizabeth and Gregory, Charles and St Hilaire, Brian Glenn and Johnson, Steven M and Dubois, Wendy and Cosma, Maria Pia and Batchelor, Eric and Levens, David and Phair, Robert D and Misteli, Tom and Tessarollo, Lino and Hager, Gordon and Lakadamyali, Melike and Liu, Zhe and Floer, Monique and Shroff, Hari and Aiden, Erez Lieberman and Casellas, Rafael} } @article {49352, title = {Myosin VI facilitates connexin 43 gap junction accretion.}, journal = {Journal of Cell Science}, volume = {130}, year = {2017}, month = {2017 03 01}, pages = {827-840}, abstract = {

In this study, we demonstrate myosin VI enrichment at Cx43 (also known as GJA1)-containing gap junctions (GJs) in heart tissue, primary cardiomyocytes and cell culture models. In primary cardiac tissue and in fibroblasts from the myosin VI-null mouse as well as in tissue culture cells transfected with siRNA against myosin VI, we observe reduced GJ plaque size with a concomitant reduction in intercellular communication, as shown by fluorescence recovery after photobleaching (FRAP) and a new method of selective calcein administration. Analysis of the molecular role of myosin VI in Cx43 trafficking indicates that myosin VI is dispensable for the delivery of Cx43 to the cell surface and connexon movement in the plasma membrane. Furthermore, we cannot corroborate clathrin or Dab2 localization at gap junctions and we do not observe a function for the myosin-VI-Dab2 complex in clathrin-dependent endocytosis of annular gap junctions. Instead, we found that myosin VI was localized at the edge of Cx43 plaques by using total internal reflection fluorescence (TIRF) microscopy and use FRAP to identify a plaque accretion defect as the primary manifestation of myosin VI loss in Cx43 homeostasis. A fuller understanding of this derangement may explain the cardiomyopathy or gliosis associated with the loss of myosin VI.

}, keywords = {Amino Acid Motifs, Animals, Cell Communication, Cell Membrane, Cells, Cultured, Connexin 43, Embryo, Mammalian, Fibroblasts, Gap Junctions, Golgi Apparatus, Hela Cells, Humans, Mice, Models, Biological, Myocardium, Myocytes, Cardiac, Myosin Heavy Chains, Protein Domains, Protein Transport, Rats}, issn = {1477-9137}, doi = {10.1242/jcs.199083}, author = {Waxse, Bennett J and Sengupta, Prabuddha and Hesketh, Geoffrey G and Lippincott-Schwartz, Jennifer and Buss, Folma} } @article {48866, title = {Nanoscale visualization of biomineral formation in coral proto-polyps.}, journal = {Current Biology : CB}, volume = {27}, year = {2017}, month = {2017 Oct 11}, pages = {3191-6}, abstract = {

Calcium carbonate platforms produced by reef-building stony corals over geologic time are pervasive features around the world [1]; however, the mechanism by which these organisms produce the mineral is poorly understood (see review by [2]). It is generally assumed that stony corals precipitate calcium carbonate extracellularly as aragonite in a calcifying medium between the calicoblastic ectoderm and pre-existing skeleton, separated from the overlying seawater [2]. The calicoblastic ectoderm produces extracellular matrix (ECM) proteins, secreted to the calcifying medium [3-6], which appear to provide the nucleation, alteration, elongation, and inhibition mechanisms of the biomineral [7] and remain occluded and preserved in the skeleton [8-10]. Here we show in cell cultures of the stony coral Stylophora pistillata that calcium is concentrated in intracellular pockets that are subsequently exported from the cell where a nucleation process leads to the formation of extracellular aragonite crystals. Analysis of the growing crystals by lattice light-sheet microscopy suggests that the crystals elongate from the cells{\textquoteright} surfaces outward.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2017.09.012}, author = {Mass, Tali and Drake, Jeana L and Heddleston, John M and Falkowski, Paul G} } @article {48713, title = {Near-atomic resolution cryoelectron microscopy structure of the 30-fold homooligomeric SpoIIIAG channel essential to spore formation in Bacillus subtilis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, year = {2017}, month = {2017 Aug 07}, abstract = {

Bacterial sporulation allows starving cells to differentiate into metabolically dormant spores that can survive extreme conditions. Following asymmetric division, the mother cell engulfs the forespore, surrounding it with two bilayer membranes. During the engulfment process, an essential channel, the so-called feeding tube apparatus, is thought to cross both membranes to create a direct conduit between the mother cell and the forespore. At least nine proteins are required to create this channel, including SpoIIQ and SpoIIIAA-AH. Here, we present the near-atomic resolution structure of one of these proteins, SpoIIIAG, determined by single-particle cryo-EM. A 3D reconstruction revealed that SpoIIIAG assembles into a large and stable 30-fold symmetric complex with a unique mushroom-like architecture. The complex is collectively composed of three distinctive circular structures: a 60-stranded vertical β-barrel that forms a large inner channel encircled by two concentric rings, one β-mediated and the other formed by repeats of a ring-building motif (RBM) common to the architecture of various dual membrane secretion systems of distinct function. Our near-atomic resolution structure clearly shows that SpoIIIAG exhibits a unique and dramatic adaptation of the RBM fold with a unique β-triangle insertion that assembles into the prominent channel, the dimensions of which suggest the potential passage of large macromolecules between the mother cell and forespore during the feeding process. Indeed, mutation of residues located at key interfaces between monomers of this RBM resulted in severe defects both in vivo and in vitro, providing additional support for this unprecedented structure.

}, issn = {1091-6490}, doi = {10.1073/pnas.1704310114}, author = {Zeytuni, Natalie and Hong, Chuan and Flanagan, Kelly A and Worrall, Liam J and Theiltges, Kate A and Vuckovic, Marija and Huang, Rick K and Massoni, Shawn C and Camp, Amy H and Yu, Zhiheng and Strynadka, Natalie C} } @article {48417, title = {Near-infrared fluorescent protein iRFP713 as a reporter protein for optogenetic vectors, a transgenic Cre-reporter rat, and other neuronal studies.}, journal = {Journal of Neuroscience Methods}, volume = {284}, year = {2017}, month = {2017 Apr 02}, pages = {1-14}, abstract = {

BACKGROUND: The use of genetically-encoded fluorescent reporters is essential for the identification and observation of cells that express transgenic modulatory proteins. Near-infrared (NIR) fluorescent proteins have superior light penetration through biological tissue, but are not yet widely adopted.

NEW METHOD: Using the near-infrared fluorescent protein, iRFP713, improves the imaging resolution in thick tissue sections or the intact brain due to the reduced light-scattering at the longer, NIR wavelengths used to image the protein. Additionally, iRFP713 can be used to identify transgenic cells without photobleaching other fluorescent reporters or affecting opsin function. We have generated a set of adeno-associated vectors in which iRFP713 has been fused to optogenetic channels, and can be expressed constitutively or Cre-dependently.

RESULTS: iRFP713 is detectable when expressed in neurons both in vitro and in vivo without exogenously supplied chromophore biliverdin. Neuronally-expressed iRFP713 has similar properties to GFP-like fluorescent proteins, including the ability to be translationally fused to channelrhodopsin or halorhodopsin, however, it shows superior photostability compared to EYFP. Furthermore, electrophysiological recordings from iRFP713-labeled cells compared to cells labeled with mCherry suggest that iRFP713 cells are healthier and therefore more stable and reliable in an ex vivo preparation. Lastly, we have generated a transgenic rat that expresses iRFP713 in a Cre-dependent manner.

CONCLUSIONS: Overall, we have demonstrated that iRFP713 can be used as a reporter in neurons without the use of exogenous biliverdin, with minimal impact on viability and function thereby making it feasible to extend the capabilities for imaging genetically-tagged neurons in slices and in vivo.

}, issn = {1872-678X}, doi = {10.1016/j.jneumeth.2017.03.020}, author = {Richie, Christopher T and Whitaker, Leslie R and Whitaker, Keith W and Necarsulmer, Julie and Baldwin, Heather A and Zhang, Yajun and Fortuno, Lowella and Hinkle, Josh J and Koivula, Pyry and Henderson, Mark J and Sun, Wenzhi and Wang, Kai and Smith, Jeffrey C and Pickel, Jim and Ji, Na and Hope, Bruce T and Harvey, Brandon K} } @article {48919, title = {Network-size independent covering number bounds for deep networks.}, journal = {arXiv}, year = {2017}, month = {2017 Nov 02}, pages = {arXiv:1711.00753 }, abstract = {

We give a covering number bound for deep learning networks that is independent of the size of the network. The key for the simple analysis is that for linear classifiers, rotating the data doesn{\textquoteright}t affect the covering number. Thus, we can ignore the rotation part of each layer{\textquoteright}s linear transformation, and get the covering number bound by concentrating on the scaling part.

}, url = {https://arxiv.org/abs/1711.00753}, author = {Kabra, Mayank and Branson, Kristin M} } @article {48954, title = {Neural mechanisms of movement planning: motor cortex and beyond.}, journal = {Current Opinion in Neurobiology}, volume = {49}, year = {2017}, month = {2017 Nov 20}, pages = {33-41}, abstract = {

Neurons in motor cortex and connected brain regions fire in anticipation of specific movements, long before movement occurs. This neural activity reflects internal processes by which the brain plans and executes volitional movements. The study of motor planning offers an opportunity to understand how the structure and dynamics of neural circuits support persistent internal states and how these states influence behavior. Recent advances in large-scale neural recordings are beginning to decipher the relationship of the dynamics of populations of neurons during motor planning and movements. New behavioral tasks in rodents, together with quantified perturbations, link dynamics in specific nodes of neural circuits to behavior. These studies reveal a neural network distributed across multiple brain regions that collectively supports motor planning. We review recent advances and highlight areas where further work is needed to achieve a deeper understanding of the mechanisms underlying motor planning and related cognitive processes.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2017.10.023}, author = {Svoboda, Karel and Li, Nuo} } @article {48549, title = {Neural signatures of dynamic stimulus selection in Drosophila.}, journal = {Nature Neuroscience}, volume = {20}, year = {2017}, month = {2017 Jun 12}, pages = {1104-13}, abstract = {

Many animals orient using visual cues, but how a single cue is selected from among many is poorly understood. Here we show that Drosophila ring neurons{\textemdash}central brain neurons implicated in navigation{\textemdash}display visual stimulus selection. Using\ in vivo\ two-color two-photon imaging with genetically encoded calcium indicators, we demonstrate that individual ring neurons inherit simple-cell-like receptive fields from their upstream partners. Stimuli in the contralateral visual field suppressed responses to ipsilateral stimuli in both populations. Suppression strength depended on when and where the contralateral stimulus was presented, an effect stronger in ring neurons than in their upstream inputs. This history-dependent effect on the temporal structure of visual responses, which was well modeled by a simple biphasic filter, may determine how visual references are selected for the fly{\textquoteright}s internal compass. Our approach highlights how two-color calcium imaging can help identify and localize the origins of sensory transformations across synaptically connected neural populations.

}, doi = {10.1038/nn.4581}, author = {Sun, Yi and Nern, Aljoscha and Franconville, Romain and Dana, Hod and Schreiter, Eric R and Looger, Loren L and Svoboda, Karel and Kim, Douglas S and Hermundstad, Ann M and Jayaraman, Vivek} } @article {68438, title = {Neurobiology: A bitter-sweet symphony.}, journal = {Nature}, volume = {548}, year = {2017}, month = {08/2017}, pages = {285-287}, abstract = {

No abstract available.

}, keywords = {Humans, Neurobiology, Taste}, issn = {1476-4687}, doi = {10.1038/nature23537}, author = {Li, Jiefu and Luo, Liqun} } @article {48920, title = {Nuclear microenvironments modulate transcription from low-affinity enhancers.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Nov 02}, abstract = {

Transcription factors bind low-affinity DNA sequences for only short durations. It is not clear how brief, low-affinity interactions can drive efficient transcription. Here we report that the transcription factor Ultrabithorax (Ubx) utilizes low-affinity binding sites in the Drosophila melanogastershavenbaby (svb) locus and related enhancers in nuclear microenvironments of high Ubx concentrations. Related enhancers colocalize to the same microenvironments independently of their chromosomal location, suggesting that microenvironments are highly differentiated transcription domains. Manipulating the affinity of svb enhancers revealed an inverse relationship between enhancer affinity and Ubx concentration required for transcriptional activation. The Ubx cofactor, Homothorax (Hth), was co-enriched with Ubx near enhancers that require Hth, even though Ubx and Hth did not co-localize throughout the nucleus. Thus, microenvironments of high local transcription factor and cofactor concentrations could help low-affinity sites overcome their kinetic inefficiency. Mechanisms that generate these microenvironments could be a general feature of eukaryotic transcriptional regulation.

}, issn = {2050-084X}, doi = {10.7554/eLife.28975}, author = {Tsai, Albert and Muthusamy, Anand K and Alves, Mariana Rp and Lavis, Luke D and Singer, Robert H and Stern, David L and Crocker, Justin} } @article {48642, title = {The Ol1mpiad: concordance of behavioural faculties of stage 1 and stage 3 Drosophila larvae.}, journal = {The Journal of Experimental Biology}, volume = {220}, year = {2017}, month = {2017 Jul 01}, pages = {2452-2475}, abstract = {

Mapping brain function to brain structure is a fundamental task for neuroscience. For such an endeavour, the Drosophila larva is simple enough to be tractable, yet complex enough to be interesting. It features about 10,000 neurons and is capable of various taxes, kineses and Pavlovian conditioning. All its neurons are currently being mapped into a light-microscopical atlas, and Gal4 strains are being generated to experimentally access neurons one at a time. In addition, an electron microscopic reconstruction of its nervous system seems within reach. Notably, this electron microscope-based connectome is being drafted for a stage 1 larva - because stage 1 larvae are much smaller than stage 3 larvae. However, most behaviour analyses have been performed for stage 3 larvae because their larger size makes them easier to handle and observe. It is therefore warranted to either redo the electron microscopic reconstruction for a stage 3 larva or to survey the behavioural faculties of stage 1 larvae. We provide the latter. In a community-based approach we called the Ol1mpiad, we probed stage 1 Drosophila larvae for free locomotion, feeding, responsiveness to substrate vibration, gentle and nociceptive touch, burrowing, olfactory preference and thermotaxis, light avoidance, gustatory choice of various tastants plus odour-taste associative learning, as well as light/dark-electric shock associative learning. Quantitatively, stage 1 larvae show lower scores in most tasks, arguably because of their smaller size and lower speed. Qualitatively, however, stage 1 larvae perform strikingly similar to stage 3 larvae in almost all cases. These results bolster confidence in mapping brain structure and behaviour across developmental stages.

}, issn = {1477-9145}, doi = {10.1242/jeb.156646}, author = {Almeida-Carvalho, Maria J and Berh, Dimitri and Braun, Andreas and Chen, Yi-chun and Eichler, Katharina and Eschbach, Claire and Fritsch, Pauline M J and Gerber, Bertram and Hoyer, Nina and Jiang, Xiaoyi and Kleber, J{\"o}rg and Kl{\"a}mbt, Christian and K{\"o}nig, Christian and Louis, Matthieu and Michels, Birgit and Miroschnikow, Anton and Mirth, Christen and Miura, Daisuke and Niewalda, Thomas and Otto, Nils and Paisios, Emmanouil and Pankratz, Michael J and Petersen, Meike and Ramsperger, Noel and Randel, Nadine and Risse, Benjamin and Saumweber, Timo and Schlegel, Philipp and Schleyer, Michael and Soba, Peter and Sprecher, Simon G and Tanimura, Teiichi and Thum, Andreas S and Toshima, Naoko and Truman, Jim W and Yarali, Ayse and Zlatic, Marta} } @article {48649, title = {Opening a path to commercialization.}, journal = {Optics and Photonics News}, volume = {28}, year = {2017}, month = {2017 Jul 01}, pages = {42-9}, abstract = {

To smooth the academic-to-industry transition, one institution is experimenting with offering biomedical researchers pre-commercial open access to new optical imaging systems still under development. The approach, the authors of this case study suggest, can be a win on both sides.

}, doi = {10.1364/OPN.28.7.000042} } @article {48371, title = {Optical measurement of receptor tyrosine kinase oligomerization on live cells.}, journal = {Biochimica et Biophysica Acta (BBA) - Biomembranes}, volume = {1859}, year = {2017}, month = {2017 Apr 04}, pages = {1436-44}, abstract = {

Receptor tyrosine kinases (RTK) are important cell surface receptors that transduce extracellular signals across the plasma membrane. The traditional view of how these receptors function is that ligand binding to the extracellular domains acts as a master-switch that enables receptor monomers to dimerize and subsequently trans-phosphorylate each other on their intracellular domains. However, a growing body of evidence suggests that receptor oligomerization is not merely a consequence of ligand binding, but is instead part of a complex process responsible for regulation of receptor activation. Importantly, the oligomerization dynamics and subsequent activation of these receptors are affected by other cellular components, such as cytoskeletal machineries and cell membrane lipid characteristics. Thus receptor activation is not an isolated molecular event mediated by the ligand-receptor interaction, but instead involves orchestrated interactions between the receptors and other cellular components. Measuring receptor oligomerization dynamics on live cells can yield important insights into the characteristics of these interactions. Therefore, it is imperative to develop techniques that can probe receptor movements on the plasma membrane with optimal temporal and spatial resolutions. Various microscopic techniques have been used for this purpose. Optical techniques including single molecule tracking (SMT) and fluorescence correlation spectroscopy (FCS) measure receptor diffusion on live cells. Receptor-receptor interactions can also be assessed by detecting F{\"o}rster resonance energy transfer (FRET) between fluorescently-labeled receptors situated in close proximity or by counting the number of receptors within a diffraction limited fluorescence spot (stepwise bleaching). This review will describe recent developments of optical techniques that have been used to study receptor oligomerization on living cells. This article is part of a Special Issue entitled: Interactions between membrane receptors in cellular membranes edited by Kalina Hristova.

}, doi = {10.1016/j.bbamem.2017.03.026}, author = {Chung, Inhee} } @article {48799, title = {Optogenetic control with a photocleavable protein, PhoCl.}, journal = {Nature Methods}, volume = {14}, year = {2017}, month = {2017 Apr}, pages = {391-394}, abstract = {

To expand the range of experiments that are accessible with optogenetics, we developed a photocleavable protein (PhoCl) that spontaneously dissociates into two fragments after violet-light-induced cleavage of a specific bond in the protein backbone. We demonstrated that PhoCl can be used to engineer light-activatable Cre recombinase, Gal4 transcription factor, and a viral protease that in turn was used to activate opening of the large-pore ion channel Pannexin-1.

}, keywords = {Connexins, Directed Molecular Evolution, Green Fluorescent Proteins, HEK293 Cells, HSP90 Heat-Shock Proteins, Humans, Luminescent Proteins, Nerve Tissue Proteins, Nuclear Localization Signals, Optogenetics, Patch-Clamp Techniques, Photochemistry, Protein Engineering, Recombinant Proteins, Viral Nonstructural Proteins}, issn = {1548-7105}, doi = {10.1038/nmeth.4222}, author = {Zhang, Wei and Lohman, Alexander W and Zhuravlova, Yevgeniya and Lu, Xiaocen and Wiens, Matthew D and Hoi, Hiofan and Yaganoglu, Sine and Mohr, Manuel A and Kitova, Elena N and Klassen, John S and Pantazis, Periklis and Thompson, Roger J and Campbell, Robert E} } @article {48847, title = {Organization of the drosophila larval visual circuit.}, journal = {eLife}, year = {2017}, month = {2017 Aug 8}, pages = {e28387}, abstract = {

Visual systems transduce, process and transmit light-dependent environmental cues. Computation of visual features depends on photoreceptor neuron types (PR) present, organization of the eye and wiring of the underlying neural circuit. Here, we describe the circuit architecture of the visual system of\ Drosophila\ larvae by mapping the synaptic wiring diagram and neurotransmitters. By contacting different targets, the two larval PR-subtypes create two converging pathways potentially underlying the computation of ambient light intensity and temporal light changes already within this first visual processing center. Locally processed visual information then signals via dedicated projection interneurons to higher brain areas including the lateral horn and mushroom body. The stratified structure of the larval optic neuropil (LON) suggests common organizational principles with the adult fly and vertebrate visual systems. The complete synaptic wiring diagram of the LON paves the way to understanding how circuits with reduced numerical complexity control wide ranges of behaviors.

}, doi = {10.7554/eLife.28387}, author = {Larderet, Ivan and Fritsch, Pauline M J and Gendre, Nanae and Neagu-Maier, G Larisa and Fetter, Richard D and Schneider-Mizell, Casey M and Truman, James W and Zlatic, Marta and Cardona, Albert and Sprecher, Simon G} } @article {68763, title = {Patterned cell and matrix dynamics in branching morphogenesis}, journal = {Journal of Cell Biology}, volume = {216}, year = {2017}, month = {02/2017}, pages = {559-570}, abstract = {

Many embryonic organs undergo branching morphogenesis to maximize their functional epithelial surface area. Branching morphogenesis requires the coordinated interplay of multiple types of cells with the extracellular matrix (ECM). During branching morphogenesis, new branches form by {\textquotedblleft}budding{\textquotedblright} or {\textquotedblleft}clefting.{\textquotedblright} Cell migration, proliferation, rearrangement, deformation, and ECM dynamics have varied roles in driving budding versus clefting in different organs. Elongation of the newly formed branch and final maturation of the tip involve cellular mechanisms that include cell elongation, intercalation, convergent extension, proliferation, and differentiation. New methodologies such as high-resolution live imaging, tension sensors, and force-mapping techniques are providing exciting new opportunities for future research into branching morphogenesis.

}, issn = {0021-9525}, doi = {10.1083/jcb.201610048}, url = {https://doi.org/10.1083/jcb.201610048}, author = {Wang, Shaohe and Sekiguchi, Rei and Daley, William P. and Yamada, Kenneth M.} } @article {48433, title = {Pavlovian conditioning of larval Drosophila: an illustrated, multilingual, hands-on manual for odor-taste associative learning in maggots.}, journal = {Frontiers in Behavioral Neuroscience}, volume = {11}, year = {2017}, month = {2017 Apr 19}, pages = {45}, abstract = {

Larval Drosophila offer a study case for behavioral neurogenetics that is simple enough to be experimentally tractable, yet complex enough to be worth the effort. We provide a detailed, hands-on manual for Pavlovian odor-reward learning in these animals. Given the versatility of Drosophila for genetic analyses, combined with the evolutionarily shared genetic heritage with humans, the paradigm has utility not only in behavioral neurogenetics and experimental psychology, but for translational biomedicine as well. Together with the upcoming total synaptic connectome of the Drosophila nervous system and the possibilities of single-cell-specific transgene expression, it offers enticing opportunities for research. Indeed, the paradigm has already been adopted by a number of labs and is robust enough to be used for teaching in classroom settings. This has given rise to a demand for a detailed, hands-on manual directed at newcomers and/or at laboratory novices, and this is what we here provide. The paradigm and the present manual have a unique set of features: {\textbullet} The paradigm is cheap, easy, and robust; {\textbullet} The manual is detailed enough for newcomers or laboratory novices; {\textbullet} It briefly covers the essential scientific context; {\textbullet} It includes sheets for scoring, data analysis, and display; {\textbullet} It is multilingual: in addition to an English version we provide German, French, Japanese, Spanish and Italian language versions as well. The present manual can thus foster science education at an earlier age and enable research by a broader community than has been the case to date.

}, doi = {10.3389/fnbeh.2017.00045}, author = {Michels, Birgit and Saumweber, Timo and Biernacki, Roland and Thur, Jeanette and Glasgow, Rupert DV and Schleyer, Michael and Chen, Yi-chun and Eschbach, Claire and Stocker, Reinhard F and Toshima, Naoko and Tanimura, Teiichi and Louis, Matthieu and Arias-Gil, Gonzalo and Marescotti, Manuela and Benfenati, Fabio and Gerber, Bertram} } @article {48535, title = {Perceptually accurate display of two greyscale images as a single colour image.}, journal = {Journal of Microscopy}, year = {2017}, month = {2017 May 30}, abstract = {

Life scientists often desire to display the signal from two different molecular probes as a single colour image, so as to convey information about the probes{\textquoteright} relative concentrations as well as their spatial corelationship. Traditionally, such colour images are created through a merge display, where each greyscale signal is assigned to different channels of an RGB colour image. However, human perception of colour and greyscale intensity is not equivalent. Thus, a merged image display conveys to the typical viewer only a subset of the absolute and relative intensity information present in and between two greyscale images. The Commission Internationale de l{\textquoteright}Eclairage L*a*b* colour space (CIELAB) has been designed to specify colours according to the perceptually defined quantities of hue (perceived colour) and luminosity (perceived brightness). Here, we use the CIELAB colour space to encode two dimensions of information about two greyscale images within these two perceptual dimensions of a single colour image. We term our method a Perceptually Uniform Projection display and show using biological image examples how these displays convey more information about two greyscale signals than comparable RGB colour space-based techniques.

}, issn = {1365-2818}, doi = {10.1111/jmi.12588}, author = {Taylor, A B and Ioannou, M S and Watanabe, T and Hahn, K and Chew, T-L} } @article {49452, title = {Pleiotropy in enhancer function is encoded through diverse genetic architectures.}, journal = {bioRxiv}, year = {2017}, month = {2017 Sep 14}, abstract = {

Developmental genes can have complex cis-regulatory regions, with multiple enhancers scattered across stretches of DNA spanning tens or hundreds of kilobases. Early work revealed remarkable modularity of enhancers, where distinct regions of DNA, bound by combinations of transcription factors, drive gene expression in defined spatio-temporal domains. Nevertheless, a few reports have shown that enhancer function may be required in multiple developmental stages, implying that regulatory elements can be pleiotropic. In these cases, it is not clear whether the pleiotropic enhancers employ the same transcription factor binding sites to drive expression at multiple developmental stages or whether enhancers function as chromatin scaffolds, where independent sets of transcription factor binding sites act at different stages. In this work we have studied the activity of the enhancers of the shavenbaby gene throughout D. melanogaster development. We found that all seven shavenbaby enhancers drive gene expression in multiple tissues and developmental stages at varying levels of redundancy. We have explored how this pleiotropy is encoded in two of these enhancers. In one enhancer, the same transcription factor binding sites contribute to embryonic and pupal expression, whereas for a second enhancer, these roles are largely encoded by distinct transcription factor binding sites. Our data suggest that enhancer pleiotropy might be a common feature of cis-regulatory regions of developmental genes and that this pleiotropy can be encoded through multiple genetic architectures.

}, doi = {10.1101/188532}, author = {Preger-Ben Noon, Ella and Sabar{\'\i}s, Gonzalo and Ortiz, Daniela M and Sager, Jonathan and Liebowitz, Anna and Stern, David L and Frankel, Nicol{\'a}s} } @article {67286, title = {Predictive Coding of Novel versus Familiar Stimuli in the Primary Visual Cortex}, journal = {bioRxiv}, year = {2017}, month = {10/2017}, abstract = {

To explore theories of predictive coding, we presented mice with repeated sequences of images with novel images sparsely substituted. Under these conditions, mice could be rapidly trained to lick in response to a novel image, demonstrating a high level of performance on the first day of testing. Using 2-photon calcium imaging to record from layer 2/3 neurons in the primary visual cortex, we found that novel images evoked excess activity in the majority of neurons. When a new stimulus sequence was repeatedly presented, a majority of neurons had similarly elevated activity for the first few presentations, which then decayed to almost zero activity. The decay time of these transient responses was not fixed, but instead scaled with the length of the stimulus sequence. However, at the same time, we also found a small fraction of the neurons within the population (\~2\%) that continued to respond strongly and periodically to the repeated stimulus. Decoding analysis demonstrated that both the transient and sustained responses encoded information about stimulus identity. We conclude that the layer 2/3 population uses a two-channel predictive code: a dense transient code for novel stimuli and a sparse sustained code for familiar stimuli. These results extend and unify existing theories about the nature of predictive neural codes.

}, doi = {10.1101/197608}, url = {https://www.biorxiv.org/content/early/2017/10/03/197608}, author = {Homann, Jan and Koay, Sue Ann and Glidden, Alistair M. and Tank, David W. and Berry, Michael J.} } @article {48418, title = {PreMosa: Extracting 2D surfaces from 3D microscopy mosaics.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, year = {2017}, month = {2017 Apr 05}, pages = {2563-9}, abstract = {

Motivation: A significant focus of biological research is to understand the development, organization and function of tissues. A particularly productive area of study is on single layer epithelial tissues in which the adherence junctions of cells form a 2D manifold that is fluorescently labeled. Given the size of the tissue, a microscope must collect a mosaic of overlapping 3D stacks encompassing the stained surface. Downstream interpretation is greatly simplified by preprocessing such a dataset as follows: (a) extracting and mapping the stained manifold in each stack into a single 2D projection plane, (b) correcting uneven illumination artifacts, (c) stitching the mosaic planes into a single, large 2D image, and (d) adjusting the contrast.

Results: We have developed PreMosa, an efficient, fully automatic pipeline to perform the four preprocessing tasks above resulting in a single 2D image of the stained manifold across which contrast is optimized and illumination is even. Notable features are as follows. First, the 2D projection step employs a specially developed algorithm that actually finds the manifold in the stack based on maximizing contrast, intensity and smoothness. Second, the projection step comes first, implying all subsequent tasks are more rapidly solved in 2D. And last, the mosaic melding employs an algorithm that globally adjusts contrasts amongst the 2D tiles so as to produce a seamless, high-contrast image. We conclude with an evaluation using ground-truth datasets and present results on datasets from Drosophila melanogaster wings and Schmidtae mediterranea ciliary components.

Availability: PreMosa is available under https://cblasse.github.io/premosa.

Contact: blasse@mpi-cbg.de, myers@mpi-cbg.de.

}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btx195}, author = {Blasse, Corinna and Saalfeld, Stephan and Etournay, Rapha{\"e}l and Sagner, Andreas and Eaton, Suzanne and Myers, Eugene W} } @article {48992, title = {Protein-templated gold nanoparticle synthesis: protein organization, controlled gold sequestration, and unexpected reaction products.}, journal = {Dalton Transactions (Cambridge, England : 2003)}, volume = {46}, year = {2017}, month = {2017 Dec 21}, pages = {16465-16473}, abstract = {

Emerging applications that exploit the properties of nanoparticles for biotechnology require that the nanoparticles be biocompatible or support biological recognition. These types of particles can be produced through syntheses that involve biologically relevant molecules (proteins or natural extracts, for example). Many of the protocols that rely on these molecules are performed without a clear understanding of the mechanism by which the materials are produced. We have investigated a previously described reaction in which gold nanoparticles are produced from the reaction of chloroauric acid and proteins in solution. We find that modifications to the starting conditions can alter the product from the expected solution-suspended colloids to a product where colloids are formed within a solid, fibrous protein structure. We have interrogated this synthesis, exploiting the change in products to better understand this reaction. We have evaluated the kinetics and products for 7 different proteins over a range of concentrations and temperatures. The key factor that controls the synthetic outcome (colloid or fiber) is the concentration of the protein relative to the gold concentration. We find that the observed fibrous structures are more likely to form at low protein concentrations and when hydrophilic proteins are used. An analysis of the reaction kinetics shows that AuNP formation occurs faster at lower protein (fiber-forming) concentrations than at higher protein (colloid-forming) concentrations. These results contradict traditional expectations for reaction kinetics and protein-fiber formation and are instructive of the manner in which proteins template gold nanoparticle production.

}, issn = {1477-9234}, doi = {10.1039/c7dt03275g}, author = {Hart, Cassidy and Abuladel, Nouf and Bee, Madeleine and Kreider, Megan C and CVitan, Alexander C and Esson, Moira M and Farag, Andrew and Ibeh, Trisha and Kalivas, Eleni N and Larco, Daniel-Mario and Walker Long, Andrew and Lymperopoulos, Loukas and Mendel, Zachary and Miles, Nancy and Zareba, Carly M and Schwabacher, James C and Slucher, Helen and Vinals, Javier and Heddleston, John M and Li, Wenyue and Fox, Douglas M and Hartings, Matthew R} } @article {48542, title = {A protocol demonstrating 60 different Drosophila behaviors in one assay.}, journal = {Journal of Undergraduate Neuroscience Education (JUNE)}, volume = {15}, year = {2017}, month = {2017 Spring}, pages = {A110-6}, abstract = {

The fruit fly Drosophila melanogaster performs many behaviors, from simple motor actions to complex social interactions, that are of interest to neurobiologists studying how the brain controls behavior. Here, an undergraduate laboratory exercise uses cutting-edge methods to activate sets of neurons thermogenetically, triggering 60 different behaviors. Students learn how to recognize this large repertoire of behaviors from 16 fly strains that are publicly available, and from a large set of training videos provided here. A full protocol, timeline and handouts are included. Instructors need not have any experience working with flies. Student feedback is reported; in our experience, students are fascinated and highly engaged by watching animals perform such a broad array of behaviors. This exercise teaches fly husbandry and crossing, careful scientific observation, and principles of behavioral screening.

}, url = {http://www.funjournal.org/wp-content/uploads/2017/01/june-15-110.pdf}, author = {McKellar, Claire E and Wyttenbach, Robert A} } @article {48803, title = {Q\&A: The brain under a mesoscope: the forest and the trees.}, journal = {BMC Biology}, volume = {15}, year = {2017}, month = {2017 Sep 14}, pages = {82}, abstract = {

Neurons relevant to a particular behavior are often widely dispersed across the brain. To record activity in groups of individual neurons that might be distributed across large distances, neuroscientists and optical engineers have been developing a new type of microscope called a mesoscope. Mesoscopes have high spatial resolution and a large field of view. This Q\&A will discuss this exciting new technology, highlighting a particular instrument, the two-photon random access mesoscope (2pRAM).

}, issn = {1741-7007}, doi = {10.1186/s12915-017-0426-y}, author = {Sofroniew, Nicholas James} } @article {48343, title = {Quantifying transcription factor binding dynamics at the single-molecule level in live cells.}, journal = {Methods (San Diego, Calif.)}, year = {2017}, month = {2017 Mar 15}, abstract = {

Progressive, technological achievements in the quantitative fluorescence microscopy field are allowing researches from many different areas to start unraveling the dynamic intricacies of biological processes inside living cells. From super-resolution microscopy techniques to tracking of individual proteins, fluorescence microscopy is changing our perspective on how the cell works. Fortunately, a growing number of research groups are exploring single-molecule studies in living cells. However, no clear consensus exists on several key aspects of the technique such as image acquisition conditions, or analysis of the obtained data. Here, we describe a detailed approach to perform single-molecule tracking (SMT) of transcription factors in living cells to obtain key binding characteristics, namely their residence time and bound fractions. We discuss different types of fluorophores, labeling density, microscope, cameras, data acquisition, and data analysis. Using the glucocorticoid receptor as a model transcription factor, we compared alternate tags (GFP, mEOS, HaloTag, SNAP-tag, CLIP-tag) for potential multicolor applications. We also examine different methods to extract the dissociation rates and compare them with simulated data. Finally, we discuss several challenges that this exciting technique still faces.

}, issn = {1095-9130}, doi = {10.1016/j.ymeth.2017.03.014}, author = {Presman, Diego M and Ball, David A and Paakinaho, Ville and Grimm, Jonathan B and Lavis, Luke D and Karpova, Tatiana S and Hager, Gordon L} } @article {48559, title = {Quantitative mRNA imaging throughout the entire Drosophila brain.}, journal = {Nature Methods}, volume = {14}, year = {2017}, month = {2017 Jun 05}, pages = {703-6}, abstract = {

We describe a fluorescence in situ hybridization method that permits detection of the localization and abundance of single mRNAs (smFISH) in cleared whole-mount adult Drosophila brains. The approach is rapid and multiplexable and does not require molecular amplification; it allows facile quantification of mRNA expression with subcellular resolution on a standard confocal microscope. We further demonstrate single-mRNA detection across the entire brain using a custom Bessel beam structured illumination microscope (BB-SIM).

}, issn = {1548-7105}, doi = {10.1038/nmeth.4309}, author = {Long, Xi and Colonell, Jennifer and Wong, Allan M and Singer, Robert H and Lionnet, Timoth{\'e}e} } @article {48677, title = {Raphe circuits on the menu.}, journal = {Cell}, volume = {170}, year = {2017}, month = {2017 Jul 27}, pages = {409-10}, abstract = {

The dorsal raphe nucleus (DRN) is an important brain area for body-weight regulation. In this issue of\ Cell, Nectow et\ al. uncover cell-type-specific neural circuitry and pharmacology for appetite control within the DRN.

}, doi = {10.1016/j.cell.2017.07.017}, author = {Yang, Hui and Sternson, Scott M} } @article {48650, title = {Rational engineering of photoconvertible fluorescent proteins for dual-color fluorescence nanoscopy enabled by a triplet-state mechanism of primed conversion.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {56}, year = {2017}, month = {2017 Jun 29}, pages = {11628-33}, abstract = {

Green-to-red photoconvertible fluorescent proteins (pcFPs) are powerful tools for super-resolution localization microscopy and protein tagging. Recently, they have been found to undergo efficient photoconversion not only by the traditional 400-nm illumination but also by an alternative method termed primed conversion, employing dual wavelength illumination with blue and far-red/near-infrared light. Primed conversion has been reported only for Dendra2 and its mechanism has remained elusive. Here, we uncover the molecular mechanism of primed conversion by reporting the intermediate "primed" state to be a triplet dark state formed by intersystem crossing. We show that formation of this state can be influenced by the introduction of serine or threonine at sequence position 69 (Eos notation) and use this knowledge to create "pr"- (for primed convertible) variants of most known green-to-red pcFPs.

}, issn = {1521-3773}, doi = {10.1002/anie.201706121}, author = {Mohr, Manuel Alexander and Kobitski, Andrei Yu and Sabater, Lluc Rullan and Nienhaus, Karin and Obara, Christopher John and Lippincott-Schwartz, Jennifer and Nienhaus, Gerd Ulrich and Pantazis, Periklis} } @article {48220, title = {Real-time spike sorting platform for high-density extracellular probes with ground-truth validation and drift correction.}, journal = {bioRxiv}, year = {2017}, month = {2017 Jan 19}, abstract = {

Electrical recordings from a large array of electrodes give us access to neural population activity with single-cell, single-spike resolution. These recordings contain extracellular spikes which must be correctly detected and assigned to individual neurons. Despite numerous spike-sorting techniques developed in the past, a lack of high-quality ground-truth datasets hinders the validation of spike-sorting approaches. Furthermore, existing approaches requiring manual corrections are not scalable for hours of recordings exceeding 100 channels. To address these issues, we built a comprehensive spike-sorting pipeline that performs reliably under noise and probe drift by incorporating a channel-covariance feature and a clustering based on fast density-peak finding. We validated performance of our workflow using multiple ground-truth datasets that recently became available. Our software scales linearly and processes a 1000-channel recording in real-time using a single workstation. Accurate, real-time spike sorting from large recording arrays will enable more precise control of closed-loop feedback experiments and brain-computer interfaces.

}, doi = {10.1101/101030}, author = {Jun, James Jaeyoon and Mitelut, Catalin and Lai, Chongxi and Gratiy, Sergey and Anastassiou, Costas and Harris, Timothy D} } @inbook {48701, title = {Recent progress in the 3D reconstruction of Drosophila neural circuits.}, booktitle = {Decoding Neural Circuit Structure and Function}, year = {2017}, pages = {63-89}, publisher = {Springer}, organization = {Springer}, abstract = {

The brain of fruit fly Drosophila melanogaster has been used as a model system for functional analysis of neuronal circuits, including connectomics research, due to its modest size (~700\ μm) and availability of abundant molecular genetics tools for visualizing neurons. Three-dimensional (3D) reconstruction of high-resolution images of neurons or circuits visualized with appropriate methods is a critical step for obtaining information such as morphology and connectivity patterns of neuronal circuits. In this chapter, we introduce methods for generating 3D reconstructed images with data acquired from confocal laser scanning microscopy (CLSM) or electron microscopy (EM) to analyze neuronal circuits found in the central nervous system (CNS) of the fruit fly. Comparisons of different algorithms and strategies for reconstructing neuronal circuits, using actual studies as references, will be discussed within this chapter.

}, doi = {10.1007/978-3-319-57363-2_3}, author = {Shinomiya, Kazunori and Ito, Masayoshi} } @article {48494, title = {Representations of Novelty and Familiarity in a Mushroom Body Compartment.}, journal = {Cell}, volume = {169}, year = {2017}, month = {2017 May 09}, pages = {956-69}, abstract = {

Animals exhibit a behavioral response to novel sensory stimuli about which they have no prior knowledge. We have examined the neural and behavioral correlates of novelty and familiarity in the olfactory system of Drosophila. Novel odors elicit strong activity in output neurons (MBONs) of the α{\textquoteright}3 compartment of the mushroom body that is rapidly suppressed upon repeated exposure to the same odor. This transition in neural activity upon familiarization requires odor-evoked activity in the dopaminergic neuron innervating this compartment. Moreover, exposure of a fly to novel odors evokes an alerting response that can also be elicited by optogenetic activation of α{\textquoteright}3 MBONs. Silencing these MBONs eliminates the alerting behavior. These data suggest that the α{\textquoteright}3 compartment plays a causal role in the behavioral response to novel and familiar stimuli as a consequence of dopamine-mediated plasticity at the Kenyon cell-MBONα{\textquoteright}3 synapse.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2017.04.028}, author = {Hattori, Daisuke and Aso, Yoshinori and Swartz, Kurtis J and Rubin, Gerald M and Abbott, L F and Axel, Richard} } @article {48462, title = {Ring attractor dynamics in the Drosophila central brain.}, journal = {Science (New York, N.Y.)}, volume = {356}, year = {2017}, month = {2017 May 04}, pages = {849-53}, abstract = {

Ring attractors are a class of recurrent networks hypothesized to underlie the representation of heading direction. Such network structures, schematized as a ring of neurons whose connectivity depends on their heading preferences, can sustain a bump-like activity pattern whose location can be updated by continuous shifts along either turn direction. We recently reported that a population of fly neurons represents the animal{\textquoteright}s heading via bump-like activity dynamics. We combined two-photon calcium imaging in head-fixed flying flies with optogenetics to overwrite the existing population representation with an artificial one, which was then maintained by the circuit with naturalistic dynamics. A network with local excitation and global inhibition enforces this unique and persistent heading representation. Ring attractor networks have long been invoked in theoretical work; our study provides physiological evidence of their existence and functional architecture.

}, issn = {1095-9203}, doi = {10.1126/science.aal4835}, author = {Kim, Sung S and Rouault, Herv{\'e} and Druckmann, Shaul and Jayaraman, Vivek} } @article {48303, title = {RNP transport in cell biology: the long and winding road.}, journal = {Current Opinion in Cell Biology}, volume = {45}, year = {2017}, month = {2017 Feb 28}, pages = {38-46}, abstract = {

Regulation of gene expression is key determinant to cell structure and function. RNA localization, where specific mRNAs are transported to subcellular regions and then translated, is highly conserved in eukaryotes ranging from yeast to extremely specialized and polarized cells such as neurons. Messenger RNA and associated proteins (mRNP) move from the site of transcription in the nucleus to their final destination in the cytoplasm both passively through diffusion and actively via directed transport. Dysfunction of RNA localization, transport and translation machinery can lead to pathology. Single-molecule live-cell imaging techniques have revealed unique features of this journey with unprecedented resolution. In this review, we highlight key recent findings that have been made using these approaches and possible implications for spatial control of gene function.

}, issn = {1879-0410}, doi = {10.1016/j.ceb.2017.02.008}, author = {Eliscovich, Carolina and Singer, Robert H} } @article {48837, title = {Robustness of spike deconvolution for calcium imaging of neural spiking.}, journal = {bioRxiv}, year = {2017}, month = {2017 Jun 27}, pages = {156786}, abstract = {

Calcium imaging is a powerful method to record the activity of neural populations, but inferring spike times from calcium signals is a challenging problem. We compared multiple approaches using multiple datasets with ground truth electrophysiology, and found that simple non-negative deconvolution (NND) outperformed all other algorithms. We introduce a novel benchmark applicable to recordings without electrophysiological ground truth, based on the correlation of responses to two stimulus repeats, and used this to show that unconstrained NND also outperformed the other algorithms when run on {\textquoteright}zoomed out{\textquoteright} datasets of ~10,000 cell recordings. Finally, we show that NND-based methods match the performance of a supervised method based on convolutional neural networks, while avoiding some of the biases of such methods, and at much faster running times. We therefore recommend that spikes be inferred from calcium traces using simple NND, due to its simplicity, efficiency and accuracy.

}, doi = {https://doi.org/10.1101/156786}, author = {Pachitariu, Marius and Stringer, Carsen and Harris, Kenneth D} } @article {48787, title = {The role of disulfide bond replacements in analogues of the tarantula toxin ProTx-II and their effects on inhibition of the voltage-gated sodium ion channel Nav1.7.}, journal = {Journal of the American Chemical Society}, volume = {139}, year = {2017}, month = {2017 Sep 07}, pages = {13063-75}, abstract = {

Spider venom toxins, such as Protoxin-II (ProTx-II), have recently received much attention as selective Nav1.7 channel blockers, with potential to be developed as leads for the treatment of chronic nocioceptive pain. ProTx-II is a 30-amino acid peptide with three disulfide bonds that has been reported to adopt a well-defined inhibitory cystine knot (ICK) scaffold structure. Potential drawbacks with such peptides include poor pharmacodynamics and potential scrambling of the disulfide bonds in vivo. In order to address these issues, in the present study we report the solid-phase synthesis of lanthionine-bridged analogues of ProTx-II, in which one of the three disulfide bridges is replaced with a thioether linkage, and evaluate the biological properties of these analogues. We have also investigated the folding and disulfide bridging patterns arising from different methods of oxidation of the linear peptide precursor. Finally, we report the X-ray crystal structure of ProTx-II to atomic resolution; to our knowledge this is the first crystal structure of an ICK spider venom peptide not bound to a substrate.

}, issn = {1520-5126}, doi = {10.1021/jacs.7b06506}, author = {Wright, Zo{\"e} V F and McCarthy, Stephen and Dickman, Rachael and Reyes, Francis E and Sanchez-Martinez, Silvia and Cryar, Adam and Kilford, Ian and Hall, Adrian and Takle, Andrew K and Topf, Maya and Gonen, Tamir and Thalassinos, Konstantinos and Tabor, Alethea B} } @article {48269, title = {Self-organizing actin patterns shape membrane architecture but not cell mechanics.}, journal = {Nature Communications}, volume = {8}, year = {2017}, month = {2017 Feb 13}, pages = {14347}, abstract = {

Cell-free studies have demonstrated how collective action of actin-associated proteins can organize actin filaments into dynamic patterns, such as vortices, asters and stars. Using complementary microscopic techniques, we here show evidence of such self-organization of the actin cortex in living HeLa cells. During cell adhesion, an active multistage process naturally leads to pattern transitions from actin vortices over stars into asters. This process is primarily driven by Arp2/3 complex nucleation, but not by myosin motors, which is in contrast to what has been theoretically predicted and observed in vitro. Concomitant measurements of mechanics and plasma membrane fluidity demonstrate that changes in actin patterning alter membrane architecture but occur functionally independent of macroscopic cortex elasticity. Consequently, tuning the activity of the Arp2/3 complex to alter filament assembly may thus be a mechanism allowing cells to adjust their membrane architecture without affecting their macroscopic mechanical properties.

}, issn = {2041-1723}, doi = {10.1038/ncomms14347}, author = {Fritzsche, M and Li, D and Colin-York, H and Chang, V T and Moeendarbary, E and Felce, J H and Sezgin, E and Charras, G and Betzig, E and Eggeling, C} } @article {48495, title = {Semiparametric spectral modeling of the Drosophila connectome.}, journal = {arXiv}, year = {2017}, month = {2017 May 9}, pages = {1705.03297}, abstract = {

We present semiparametric spectral modeling of the complete larval Drosophila mushroom body connectome. Motivated by a thorough exploratory data analysis of the network via Gaussian mixture modeling (GMM) in the adjacency spectral embedding (ASE) representation space, we introduce the latent structure model (LSM) for network modeling and inference. LSM is a generalization of the stochastic block model (SBM) and a special case of the random dot product graph (RDPG) latent position model, and is amenable to semiparametric GMM in the ASE representation space. The resulting connectome code derived via semiparametric GMM composed with ASE captures latent connectome structure and elucidates biologically relevant neuronal properties.

}, url = {https://arxiv.org/abs/1705.03297}, author = {Priebe, Carey E. and Park, Youngser and Tang, Minh and Athreya, Avanti and Lyzinski, Vince and Vogelstein, Joshua T and Qin, Yichen and Cocanougher, Benjamin and Eichler, Katharina and Zlatic, Marta and Cardona, Albert} } @article {48938, title = {Semisynthetic fluorescent pH sensors for imaging exocytosis and endocytosis.}, journal = {Nature Communications}, volume = {8}, year = {2017}, month = {2017 Nov 10}, pages = {1412}, abstract = {

The GFP-based superecliptic pHluorin (SEP) enables detection of exocytosis and endocytosis, but its performance has not been duplicated in red fluorescent protein scaffolds. Here we describe "semisynthetic" pH-sensitive protein conjugates with organic fluorophores, carbofluorescein, and Virginia Orange that match the properties of SEP. Conjugation to genetically encoded self-labeling tags or antibodies allows visualization of both exocytosis and endocytosis, constituting new bright sensors for these key steps of synaptic transmission.

}, issn = {2041-1723}, doi = {10.1038/s41467-017-01752-5}, author = {Martineau, Magalie and Somasundaram, Agila and Grimm, Jonathan B and Gruber, Todd D and Choquet, Daniel and Taraska, Justin W and Lavis, Luke D and Perrais, David} } @article {48372, title = {Sensorimotor neuroscience: motor precision meets vision.}, journal = {Current Biology : CB}, volume = {27}, year = {2017}, month = {2017 Apr 03}, pages = {R261-R263}, abstract = {

Visual motion sensing neurons in the fly also encode a range of behavior-related signals. These nonvisual inputs appear to be used to correct some of the challenges of visually guided locomotion.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2017.02.047}, author = {Longden, Kit D and Huston, Stephen J and Reiser, Michael B} } @article {48458, title = {Shaping development by stochasticity and dynamics in gene regulation.}, journal = {Open Biology}, volume = {7}, year = {2017}, month = {2017 May}, abstract = {

Animal development is orchestrated by spatio-temporal gene expression programmes that drive precise lineage commitment, proliferation and migration events at the single-cell level, collectively leading to large-scale morphological change and functional specification in the whole organism. Efforts over decades have uncovered two {\textquoteright}seemingly contradictory{\textquoteright} mechanisms in gene regulation governing these intricate processes: (i) stochasticity at individual gene regulatory steps in single cells and (ii) highly coordinated gene expression dynamics in the embryo. Here we discuss how these two layers of regulation arise from the molecular and the systems level, and how they might interplay to determine cell fate and to control the complex body plan. We also review recent technological advancements that enable quantitative analysis of gene regulation dynamics at single-cell, single-molecule resolution. These approaches outline next-generation experiments to decipher general principles bridging gaps between molecular dynamics in single cells and robust gene regulations in the embryo.

}, issn = {2046-2441}, doi = {10.1098/rsob.170030}, author = {Dong, Peng and Liu, Zhe} } @article {48807, title = {Simulating extracted connectomes.}, journal = {bioRxiv}, year = {2017}, month = {2017 Aug 17}, abstract = {

Connectomes derived from volume EM imaging of the brain can generate detailed physical models of every neuron, and simulators such as NEURON or GENESIS are designed to work with such models. In principal, combining these technologies, plus transmitter and channel models, should allow detailed and accurate simulation of real neural circuits. Here we experiment with this combination, using a well-studied system (motion detection in Drosophila. Since simulation requires both the physical geometry (which we have) and the models of the synapses (which are not currently available), we built approximate synapses corresponding to their known and estimated function. Once we did so, we reproduced direction selectivity in T4 cells, one of the main functions of this neural circuit. This verified the basic functionality of both extraction and simulations, and provided a biologically relevant computation we could use in further experiments. We then compared models with different degrees of physical realism, from full detailed models down to models consisting of a single node, to examine the tradeoff of simulation resources required versus accuracy achieved. Our results show that much simpler models may be adequate, at least in the case of medulla neurons in Drosophila. Such models can be easily derived from fully detailed models, and result in simulations that are much smaller, much faster, and accurate enough for many purposes. Biologically, we show that a lumped neuron model reproduces the main motion detector operation, confirming the result of Gruntman, that dendritic compution is not required for this function.

}, doi = {10.1101/177113}, author = {Gornet, Jonathan and Scheffer, Louis K} } @article {48788, title = {Simultaneous activation of parallel sensory pathways promotes a grooming sequence in Drosophila.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Sep 09}, abstract = {

A central model that describes how behavioral sequences are produced features a neural architecture that readies different movements simultaneously, and a mechanism where prioritized suppression between the movements determines their sequential performance. We previously described a model whereby suppression drives a Drosophila grooming sequence that is induced by simultaneous activation of different sensory pathways that each elicit a distinct movement (Seeds et al. 2014). Here, we confirm this model using transgenic expression to identify and optogenetically activate sensory neurons that elicit specific grooming movements. Simultaneous activation of different sensory pathways elicits a grooming sequence that resembles the naturally induced sequence. Moreover, the sequence proceeds after the sensory excitation is terminated, indicating that a persistent trace of this excitation induces the next grooming movement once the previous one is performed. This reveals a mechanism whereby parallel sensory inputs can be integrated and stored to elicit a delayed and sequential grooming response.

}, issn = {2050-084X}, doi = {10.7554/eLife.28804}, author = {Hampel, Stefanie and McKellar, Claire E and Simpson, Julie H and Seeds, Andrew M} } @article {69340, title = {Single-Neuron Gene Expression Analysis Using the Maxwell{\textregistered} 16 LEV System in the Neural Systems and Behavior Course}, journal = {bioRxiv}, year = {2017}, month = {2017 Feb 10}, abstract = {

Gene expression analysis from single cells has become increasingly prominent across biological disciplines; thus, it is important to train students in these approaches. Here, we present an experimental and analysis pipeline that we developed for the Neural Systems \& Behavior (NS\&B) course at Marine Biological Laboratory. Our approach used the Maxwell{\textregistered} 16 LEV simplyRNA Tissue Kit and GoTaq{\textregistered} 2-Step RT-qPCR System for gene expression analysis from single neurons of the crustacean stomatogastric ganglion, a model system to study the generation of rhythmic motor patterns. We used double-stranded RNA to knockdown expression of a putative neuromodulator-activated sodium channel. We then examined the electrophysiological responses to known neuromodulators and confirmed that the response was reduced. Finally, we measured how mRNA levels of several ion channel genes changed in response. Our results provide new insights into the neural mechanisms underlying the generation and modulation of rhythmic motor patterns.

}, doi = {10.1101/107342}, url = {https://www.biorxiv.org/content/early/2017/02/10/107342}, author = {Rayna M. Harris and Adriane G. Otopalik and Colin J. Smith and Dirk Bucher and Jorge Golowasch and Hans A. Hofmann} } @article {48460, title = {Single-protein detection in crowded molecular environments in cryo-EM images.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 May 03}, abstract = {

We present an approach to study macromolecular assemblies by detecting component proteins{\textquoteright} characteristic high-resolution projection patterns, calculated from their known 3D structures, in single electron cryo-micrographs. Our method detects single apoferritin molecules in vitreous ice with high specificity and determines their orientation and location precisely. Simulations show that high spatial-frequency information and-in the presence of protein background-a whitening filter are essential for optimal detection, in particular for images taken far from focus. Experimentally, we could detect small viral RNA polymerase molecules, distributed randomly among binding locations, inside rotavirus particles. Based on the currently attainable image quality, we estimate a threshold for detection that is 150 kDa in ice and 300 kDa in 100 nm thick samples of dense biological material.

}, issn = {2050-084X}, doi = {10.7554/eLife.25648}, author = {Rickgauer, J Peter and Grigorieff, Nikolaus and Denk, Winfried} } @article {69341, title = {Sloppy morphological tuning in identified neurons of the crustacean stomatogastric ganglion}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Feb 8}, pages = {e22352}, abstract = {

Neuronal physiology depends on a neuron{\textquoteright}s ion channel composition and unique morphology. Variable ion channel compositions can produce similar neuronal physiologies across animals. Less is known regarding the morphological precision required to produce reliable neuronal physiology. Theoretical studies suggest that moraphology is tightly tuned to minimize wiring and conduction delay of synaptic events. We utilize high-resolution confocal microscopy and custom computational tools to characterize the morphologies of four neuron types in the stomatogastric ganglion (STG) of the crab \textitCancer borealis. Macroscopic branching patterns and fine cable properties are variable within and across neuron types. We compare these neuronal structures to synthetic minimal spanning neurite trees constrained by a wiring cost equation and find that STG neurons do not adhere to prevailing hypotheses regarding wiring optimization principles. In this highly modulated and oscillating circuit, neuronal structures appear to be governed by a space-filling mechanism that outweighs the cost of inefficient wiring.

}, keywords = {cancer borealis, dendritic tree, neuronal morphology, optimization principles, wiring cost}, issn = {2050-084X}, doi = {10.7554/eLife.22352}, url = {https://doi.org/10.7554/eLife.22352}, author = {Otopalik, Adriane G and Goeritz, Marie L and Sutton, Alexander C and Brookings, Ted and Guerini, Cosmo and Marder, Eve}, editor = {Calabrese, Ronald L} } @article {48159, title = {Solution of the structure of a calmodulin-peptide complex in a novel configuration from a variably twinned data set.}, journal = {Acta Crystallographica. Section D, Structural Biology}, volume = {73}, year = {2017}, month = {2017 Jan 01}, pages = {22-31}, abstract = {

Structure determination of conformationally variable proteins can prove challenging even when many possible molecular-replacement (MR) search models of high sequence similarity are available. Calmodulin (CaM) is perhaps the best-studied archetype of these flexible proteins: while there are currently \~{}450 structures of significant sequence similarity available in the Protein Data Bank (PDB), novel conformations of CaM and complexes thereof continue to be reported. Here, the details of the solution of a novel peptide-CaM complex structure by MR are presented, in which only one MR solution of marginal quality was found despite the use of 120 different search models, an exclusivity enhanced by the presence of a high degree of hemihedral twinning (overall refined twin fraction = 0.43). Ambiguities in the initial MR electron-density maps were overcome by using MR-SAD: phases from the MR partial model were used to identify weak anomalous scatterers (calcium, sulfur and chloride), which were in turn used to improve the phases, automatically rebuild the structure and resolve sequence ambiguities. Retrospective analysis of consecutive wedges of the original data sets showed twin fractions ranging from 0.32 to 0.55, suggesting that the data sets were variably twinned. Despite these idiosyncrasies and obstacles, the data themselves and the final model were of high quality and indeed showed a novel, nearly right-angled conformation of the bound peptide.

}, issn = {2059-7983}, doi = {10.1107/S2059798316019318}, author = {Keller, Jacob Pearson} } @article {48509, title = {Spatial Memory: Mice Quickly Learn a Safe Haven.}, journal = {Current Biology : CB}, volume = {27}, year = {2017}, month = {2017 May 22}, pages = {R388-R390}, abstract = {

New work on innate escape behavior shows that mice spontaneously form a spatially precise memory of the location of shelter, which is laid down quickly and updated continuously.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2017.04.007}, author = {Egnor, S E Roian} } @article {48009, title = {A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs.}, journal = {Nature Methods}, volume = {14}, year = {2017}, month = {2017 Jan 31}, pages = {45-8}, abstract = {

Many functional RNAs have an evolutionarily conserved secondary structure. Conservation of RNA base pairing induces pairwise covariations in sequence alignments. We developed a computational method, R-scape (RNA Structural Covariation Above Phylogenetic Expectation), that quantitatively tests whether covariation analysis supports the presence of a conserved RNA secondary structure. R-scape analysis finds no statistically significant support for proposed secondary structures of the long noncoding RNAs HOTAIR, SRA, and Xist.

}, author = {Rivas, Elena and Clements, Jody and Eddy, Sean R.} } @article {48435, title = {Stem cell-intrinsic, seven-up-triggered temporal factor gradients diversify intermediate neural progenitors.}, journal = {Current Biology : CB}, volume = {27}, year = {2017}, month = {2017 Apr 10}, pages = {1303-13}, abstract = {

Building a sizable, complex brain requires both cellular expansion and diversification. One mechanism to achieve these goals is production of multiple transiently amplifying intermediate neural progenitors (INPs) from a single neural stem cell. Like mammalian neural stem cells, Drosophila type II neuroblasts utilize INPs to produce neurons and glia. Within a given lineage, the consecutively born INPs produce morphologically distinct progeny, presumably due to differential inheritance of temporal factors. To uncover the underlying temporal fating mechanisms, we profiled type II neuroblasts{\textquoteright} transcriptome across time. Our results reveal opposing temporal gradients of Imp and Syp RNA-binding proteins (descending and ascending, respectively). Maintaining high Imp throughout serial INP production expands the number of neurons and glia with early temporal fate at the expense of cells with late fate. Conversely, precocious upregulation of Syp reduces the number of cells with early fate. Furthermore, we reveal that the transcription factor Seven-up initiates progression of the Imp/Syp gradients. Interestingly, neuroblasts that maintain initial Imp/Syp levels can still yield progeny with a small range of early fates. We therefore propose that the Seven-up-initiated Imp/Syp gradients create coarse temporal windows within type II neuroblasts to pattern INPs, which subsequently undergo fine-tuned subtemporal patterning.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2017.03.047}, author = {Ren, Qingzhong and Yang, Ching-Po and Liu, Zhiyong and Sugino, Ken and Mok, Kent and He, Yisheng and Ito, Masayoshi and Nern, Aljoscha and Otsuna, Hideo and Lee, Tzumin} } @conference {67293, title = {Stochastic filtering of two-photon imaging using reweighted l1}, booktitle = {2017 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)}, year = {2017}, month = {03/2017}, publisher = {IEEE}, organization = {IEEE}, address = {New Orleans, LA}, abstract = {
Two-photon (TP) calcium imaging is an important imaging modality in neuroscience, allowing for large-scale recording of neural activity in awake, behaving animals at behavior-relevant timescales. Interpretation of TP data requires the accurate extraction of temporal neural activity traces, which can be accomplished via manual or automated methods. In this work we seek to improve the accuracy of both manual and automated TP microscopy demixing methods by introducing a denoising algorithm based on a statistical model of TP data which includes spatial contiguity, sparse activity and Poisson observations. Our method leverages recent developments in stochastic filtering of structured signals based on Laplacian-scale mixture models (LSMs) to model the neural activity in TP data as a set of spatially correlated sparse variables. We apply our method on TP images taken from the visual cortex of an awake, behaving mouse, and demonstrate improved neural activity demixing over current pre-processing techniques.
}, doi = {10.1109/ICASSP.2017.7952314}, url = {https://ieeexplore.ieee.org/abstract/document/7952314}, author = {Charles, Adam S. and Song, Alexander and Koay, Sue Ann and Tank, David W. and Pillow, Jonathan W.} } @article {48346, title = {Stochastic protein labeling enables long-term single molecule observation in vivo.}, journal = {bioRxiv}, year = {2017}, month = {2017 Mar 13}, abstract = {Our ability to unambiguously image and track individual molecules in live cells is limited by packing of multiple copies of labeled molecules within the resolution limit. Here we devise a universal genetic strategy to precisely control protein copy number in a cell. This system has a dynamic titration range of more than 10,000 fold, enabling sparse labeling of proteins expressed at widely different levels. Combined with fluorescence signal amplification tags, this system extends the duration of automated single-molecule tracking by 2 orders of magnitude. We demonstrate long-term imaging of synaptic vesicle dynamics in cultured neurons as well as in live zebrafish. We found that axon initial segment utilizes a waterfall mechanism gating synaptic vesicle transport polarity by promoting anterograde transport processivity. Long-time observation also reveals that transcription factor Sox2 samples clustered binding sites in spatially-restricted sub-nuclear regions, suggesting that topological structures in the nucleus shape local gene activities by a sequestering mechanism. This strategy thus greatly expands the spatiotemporal length scales of live-cell single-molecule measurements for a quantitative understanding of complex control of molecular dynamics in vivo.}, doi = {10.1101/116186}, author = {Liu, Hui and Dong, Peng and Ioannou, Maria S and Li, Li and Shea, Jamien and Pasolli, H Amalia and Grimm, Jonathan B and Rivlin, Patricia K and Lavis, Luke D and Koyama, Minoru and Liu, Zhe} } @article {65096, title = {Stochastic simulation of dopamine neuromodulation for implementation of fluorescent neurochemical probes in the striatal extracellular space.}, journal = {ACS Chemical Neuroscience}, volume = {8}, year = {2017}, month = {2017 Oct 18}, pages = {2275-2289}, abstract = {

Imaging the dynamic behavior of neuromodulatory neurotransmitters in the extracelluar space that arise from individual quantal release events would constitute a major advance in neurochemical imaging. Spatial and temporal resolution of these highly stochastic neuromodulatory events requires concurrent advances in the chemical development of optical nanosensors selective for neuromodulators in concert with advances in imaging methodologies to capture millisecond neurotransmitter release. Herein, we develop and implement a stochastic model to describe dopamine dynamics in the extracellular space (ECS) of the brain dorsal striatum to guide the design and implementation of fluorescent neurochemical probes that record neurotransmitter dynamics in the ECS. Our model is developed from first-principles and simulates release, diffusion, and reuptake of dopamine in a 3D simulation volume of striatal tissue. We find that in vivo imaging of neuromodulation requires simultaneous optimization of dopamine nanosensor reversibility and sensitivity: dopamine imaging in the striatum or nucleus accumbens requires nanosensors with an optimal dopamine dissociation constant (K) of 1 μM, whereas Ks above 10 μM are required for dopamine imaging in the prefrontal cortex. Furthermore, as a result of the probabilistic nature of dopamine terminal activity in the striatum, our model reveals that imaging frame rates of 20 Hz are optimal for recording temporally resolved dopamine release events. Our work provides a modeling platform to probe how complex neuromodulatory processes can be studied with fluorescent nanosensors and enables direct evaluation of nanosensor chemistry and imaging hardware parameters. Our stochastic model is generic for evaluating fluorescent neurotransmission probes, and is broadly applicable to the design of other neurotransmitter fluorophores and their optimization for implementation in vivo.

}, keywords = {Animals, Corpus Striatum, Dopamine, Extracellular Space, Fluorescent Dyes, Neurotransmitter Agents, Prefrontal Cortex, Synaptic Transmission}, issn = {1948-7193}, doi = {10.1021/acschemneuro.7b00193}, author = {Beyene, Abraham G and McFarlane, Ian R and Pinals, Rebecca L and Landry, Markita P} } @article {48945, title = {Structural basis of bacterial transcription activation.}, journal = {Science (New York, N.Y.)}, volume = {358}, year = {2017}, month = {2017 Nov 17}, pages = {947-951}, abstract = {

In bacteria, the activation of gene transcription at many promoters is simple and only involves a single activator. The cyclic adenosine 3{\textquoteright},5{\textquoteright}-monophosphate receptor protein (CAP), a classic activator, is able to activate transcription independently through two different mechanisms. Understanding the class I mechanism requires an intact transcription activation complex (TAC) structure at a high resolution. Here we report a high-resolution cryo-electron microscopy structure of an intact Escherichia coli class I TAC containing a CAP dimer, a σ(70)-RNA polymerase (RNAP) holoenzyme, a complete class I CAP-dependent promoter DNA, and a de novo synthesized RNA oligonucleotide. The structure shows how CAP wraps the upstream DNA and how the interactions recruit RNAP. Our study provides a structural basis for understanding how activators activate transcription through the class I recruitment mechanism.

}, issn = {1095-9203}, doi = {10.1126/science.aao1923}, author = {Liu, Bin and Hong, Chuan and Huang, Rick K and Yu, Zhiheng and Steitz, Thomas A} } @article {48699, title = {Structure and topology around the cleavage site regulate post-translational cleavage of the HIV-1 gp160 signal peptide.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Jul 28}, abstract = {

Like all other secretory proteins, the HIV-1 envelope glycoprotein gp160, is targeted to the endoplasmic reticulum (ER) by its signal peptide during synthesis. Proper gp160 folding in the ER requires core glycosylation, disulfide-bond formation and proline isomerization. Signal-peptide cleavage occurs only late after gp160 chain termination and is dependent on folding of the soluble subunit gp120 to a near-native conformation. We here detail the mechanism by which co-translational signal-peptide cleavage is prevented. Conserved residues from the signal peptide and residues downstream of the canonical cleavage site form an extended alpha-helix in the ER membrane that covers the cleavage site, thus preventing cleavage. A point mutation in the signal peptide breaks the alpha helix allowing co-translational cleavage. We demonstrate that postponed cleavage of gp160 enhances functional folding of the molecule. The change to early cleavage results in decreased viral fitness compared to wild-type HIV.

}, issn = {2050-084X}, doi = {10.7554/eLife.26067}, author = {Snapp, Erik Lee and McCaul, Nicholas and Quandte, Matthias and Cabartova, Zuzana and Bontjer, Ilja and K{\"a}llgren, Carolina and Nilsson, IngMarie and Land, Aafke and von Heijne, Gunnar and Sanders, Rogier W and Braakman, Ineke} } @article {48865, title = {Structure of RNA polymerase bound to ribosomal 30S subunit.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Oct 13}, abstract = {

In bacteria, mRNA transcription and translation are coupled to coordinate optimal gene expression and maintain genome stability. Coupling is thought to involve direct interactions between RNA polymerase (RNAP) and the translational machinery. We present cryo-EM structures of E. coli RNAP core bound to the small ribosomal 30S subunit. The complex is stable under cell-like ionic conditions, consistent with functional interaction between RNAP and the 30S subunit. The RNA exit tunnel of RNAP aligns with the Shine-Dalgarno-binding site of the 30S subunit. Ribosomal protein S1 forms a wall of the tunnel between RNAP and the 30S subunit, consistent with its role in directing mRNAs onto the ribosome. The nucleic-acid-binding cleft of RNAP samples distinct conformations, suggesting different functional states during transcription-translation coupling. The architecture of the 30S{\textbullet}RNAP complex provides a structural basis for co-localization of the transcriptional and translational machineries, and inform future mechanistic studies of coupled transcription and translation.

}, issn = {2050-084X}, doi = {10.7554/eLife.28560}, author = {Demo, Gabriel and Rasouly, Aviram and Vasilyev, Nikita and Svetlov, Vladimir and Loveland, Anna B and Diaz-Avalos, Ruben and Grigorieff, Nikolaus and Nudler, Evgeny and Korostelev, Andrei A} } @article {48958, title = {Structure-based inhibitors of tau aggregation.}, journal = {Nature Chemistry}, year = {2017}, month = {2017 Nov 20}, abstract = {

Aggregated tau protein is associated with over 20 neurological disorders, which include Alzheimer{\textquoteright}s disease. Previous work has shown that tau{\textquoteright}s sequence segments VQIINK and VQIVYK drive its aggregation, but inhibitors based on the structure of the VQIVYK segment only partially inhibit full-length tau aggregation and are ineffective at inhibiting seeding by full-length fibrils. Here we show that the VQIINK segment is the more powerful driver of tau aggregation. Two structures of this segment determined by the cryo-electron microscopy method micro-electron diffraction explain its dominant influence on tau aggregation. Of practical significance, the structures lead to the design of inhibitors that not only inhibit tau aggregation but also inhibit the ability of exogenous full-length tau fibrils to seed intracellular tau in HEK293 biosensor cells into amyloid. We also raise the possibility that the two VQIINK structures represent amyloid polymorphs of tau that may account for a subset of prion-like strains of tau.

}, doi = {10.1038/nchem.2889}, author = {Seidler, P M and Boyer, D R and Rodriguez, J A and Sawaya, Michael R and Cascio, Duilio and Murray, K and Gonen, Tamir and Eisenberg, David S} } @article {48840, title = {Suite2p: beyond 10,000 neurons with standard two-photon microscopy.}, journal = {bioRxiv}, year = {2017}, month = {2017 Jul 20}, pages = {061507}, abstract = {

Two-photon microscopy of calcium-dependent sensors has enabled unprecedented recordings from vast populations of neurons. While the sensors and microscopes have matured over several generations of development, computational methods to process the resulting movies remain inefficient and can give results that are hard to interpret. Here we introduce Suite2p: a fast, accurate and complete pipeline that registers raw movies, detects active cells, extracts their calcium traces and infers their spike times. Suite2p runs on standard workstations, operates faster than real time, and recovers ~2 times more cells than the previous state-of-the-art method. Its low computational load allows routine detection of ~10,000 cells simultaneously with standard two-photon resonant-scanning microscopes. Recordings at this scale promise to reveal the fine structure of activity in large populations of neurons or large populations of subcellular structures such as synaptic boutons.

}, doi = {https://doi.org/10.1101/061507}, author = {Pachitariu, Marius and Stringer, Carsen and Dipoppa, Mario and Schr{\"o}der, Sylvia and Rossi, L Federico and Dalgleish, Henry and Carandini, Matteo and Harris, Kenneth D} } @article {48804, title = {Synthesis of Janelia Fluor HaloTag and SNAP-Tag Ligands and Their Use in Cellular Imaging Experiments.}, journal = {Methods in Molecular Biology (Clifton, N.J.)}, volume = {1663}, year = {2017}, month = {2017}, pages = {179-188}, abstract = {

The development of genetically encoded self-labeling protein tags such as the HaloTag and SNAP-tag has expanded the utility of chemical dyes in microscopy. Intracellular labeling using these systems requires small, cell-permeable dyes with high brightness and photostability. We recently discovered a general method to improve the properties of classic fluorophores by replacing N,N-dimethylamino groups with four-membered azetidine rings to create the "Janelia Fluor" dyes. Here, we describe the synthesis of the HaloTag and SNAP-tag ligands of Janelia Fluor 549 and Janelia Fluor 646 as well as standard labeling protocols for use in ensemble and single-molecule cellular imaging.

}, issn = {1940-6029}, doi = {10.1007/978-1-4939-7265-4_15}, author = {Grimm, Jonathan B and Brown, Timothy A and English, Brian P and Lionnet, Timoth{\'e}e and Lavis, Luke D} } @article {48657, title = {A systematic nomenclature for the Drosophila ventral nervous system.}, journal = {bioRxiv}, year = {2017}, month = {2017 Apr 26}, abstract = {

Insect nervous systems are proven and powerful model systems for neuroscience research with wide relevance in biology and medicine. However, descriptions of insect brains have suffered from a lack of a complete and uniform nomenclature. Recognising this problem the Insect Brain Name Working Group produced the first agreed hierarchical nomenclature system for the adult insect brain, using Drosophila melanogaster as the reference framework, with other insect taxa considered to ensure greater consistency and expandability (Ito et al., 2014). Ito et al. (2014) purposely focused on the gnathal regions that account for approximately 50\% of the adult CNS. We extend this nomenclature system to the sub-gnathal regions of the adult Drosophila nervous system to provide a nomenclature of the so-called ventral nervous system (VNS), which includes the thoracic and abdominal neuromeres that was not included in the original work and contains the neurons that play critical roles underpinning most fly behaviours.

}, doi = {10.1101/122952}, author = {Court, Robert Christopher and Armstrong, James Douglas and Borner, Jana and Card, Gwyneth M and Costa, Marta and Dickinson, Michael H and Duch, Carsten and Korff, Wyatt and Mann, Richard S and Merritt, David and Murphey, Rodney K and Namiki, Shigehiro and Seeds, Andrew M and Shepherd, David and Shirangi, Troy R and Simpson, Julie H and Truman, James W and Tuthill, John C and Williams, Darren W} } @article {48623, title = {Taking the measure of MicroED.}, journal = {Current Opinion in Structural Biology}, volume = {46}, year = {2017}, month = {2017 Jun 22}, pages = {79-86}, abstract = {

It is now possible to routinely determine atomic resolution structures by electron cryo-microscopy (cryoEM), facilitated in part by the method known as micro electron-diffraction (MicroED). Since its initial demonstration in 2013, MicroED has helped determine a variety of protein structures ranging in molecular weight from a few hundred Daltons to several hundred thousand Daltons. Some of these structures were novel while others were previously known. The resolutions of structures obtained thus far by MicroED range from 3.2{\r A} to 1.0{\r A}, with most better than 2.5{\r A}. Crystals of various sizes and shapes, with different space group symmetries, and with a range of solvent content have all been studied by MicroED. The wide range of crystals explored to date presents the community with a landscape of opportunity for structure determination from nano crystals. Here we summarize the lessons we have learned during the first few years of MicroED, and from our attempts at the first ab initio structure determined by the method. We re-evaluate theoretical considerations in choosing the appropriate crystals for MicroED and for extracting the most meaning out of measured data. With more laboratories worldwide adopting the technique, we speculate what the first decade might hold for MicroED.

}, issn = {1879-033X}, doi = {10.1016/j.sbi.2017.06.004}, author = {Rodriguez, Jose A and Eisenberg, David S and Gonen, Tamir} } @inbook {47793, title = {Targeted manipulation of neuronal activity in behaving adult flies.}, booktitle = {Decoding Neural Circuit Structure and Function}, year = {2017}, month = {2016 Aug 15}, pages = {191-222}, abstract = {

The ability to control the activity of specific neurons in freely behaving animals provides an effective way to probe the contributions of neural circuits to behavior. Wide interest in studying principles of neural circuit function using the fruit fly\ Drosophila melanogaster\ has fueled the construction of an extensive transgenic toolkit for performing such neural manipulations. Here we describe approaches for using these tools to manipulate the activity of specific neurons and assess how those manipulations impact the behavior of flies. We also describe methods for examining connectivity among multiple neurons that together form a neural circuit controlling a specific behavior. This work provides a resource for researchers interested in examining how neurons and neural circuits contribute to the rich repertoire of behaviors performed by flies.

}, doi = {10.1007/978-3-319-57363-2_7}, author = {Hampel, Stefanie and Seeds, Andrew M} } @article {48420, title = {Teaching old dyes new tricks: biological probes built from fluoresceins and rhodamines.}, journal = {Annual Review of Biochemistry}, volume = {86}, year = {2017}, month = {2017 Apr 07}, pages = {825-43}, abstract = {

Small-molecule fluorophores, such as fluorescein and rhodamine derivatives, are critical tools in modern biochemical and biological research. The field of chemical dyes is old; colored molecules were first discovered in the 1800s, and the fluorescein and rhodamine scaffolds have been known for over a century. Nevertheless, there has been a renaissance in using these dyes to create tools for biochemistry and biology. The application of modern chemistry, biochemistry, molecular genetics, and optical physics to these old structures enables and drives the development of novel, sophisticated fluorescent dyes. This critical review focuses on an important example of chemical biology-the melding of old and new chemical knowledge-leading to useful molecules for advanced biochemical and biological experiments. Expected final online publication date for the Annual Review of Biochemistry Volume 86 is June 20, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

}, issn = {1545-4509}, doi = {10.1146/annurev-biochem-061516-044839}, author = {Lavis, Luke D} } @article {48193, title = {TED: A Tolerant Edit Distance for segmentation evaluation.}, journal = {Methods}, volume = {115}, year = {2017}, month = {2017 Jan 17}, pages = {119-27}, abstract = {

In this paper, we present a novel error measure to compare a computer-generated segmentation of images or volumes against ground truth. This measure, which we call Tolerant Edit Distance (TED), is motivated by two observations that we usually encounter in biomedical image processing: (1) Some errors, like small boundary shifts, are tolerable in practice. Which errors are tolerable is application dependent and should be explicitly expressible in the measure. (2) Non-tolerable errors have to be corrected manually. The effort needed to do so should be reflected by the error measure. Our measure is the minimal weighted sum of split and merge operations to apply to one segmentation such that it resembles another segmentation within specified tolerance bounds. This is in contrast to other commonly used measures like Rand index or variation of information, which integrate small, but tolerable, differences. Additionally, the TED provides intuitive numbers and allows the localization and classification of errors in images or volumes. We demonstrate the applicability of the TED on 3D segmentations of neurons in electron microscopy images where topological correctness is arguable more important than exact boundary locations. Furthermore, we show that the TED is not just limited to evaluation tasks. We use it as the loss function in a max-margin learning framework to find parameters of an automatic neuron segmentation algorithm. We show that training to minimize the TED, i.e., to minimize crucial errors, leads to higher segmentation accuracy compared to other learning methods.

}, doi = {10.1016/j.ymeth.2016.12.013}, author = {Funke, Jan and Klein, Jonas and Moreno-Noguer, Francesc and Cardona, Albert and Cook, Matthew} } @article {48533, title = {Theta-paced flickering between place-cell maps in the hippocampus: A model based on short-term synaptic plasticity.}, journal = {Hippocampus}, volume = {27}, year = {2017}, month = {2017 May 30}, pages = {959-70}, abstract = {

Hippocampal place cells represent different environments with distinct neural activity patterns. Following an abrupt switch between two familiar configurations of visual cues defining two environments, the hippocampal neural activity pattern switches almost immediately to the corresponding representation. Surprisingly, during a transient period following the switch to the new environment, occasional fast transitions of activity patterns between the representations (flickering) were observed (Jezek et al. 2011). Here we show that an attractor neural network model of place cells with connections endowed with short-term synaptic plasticity can account for this phenomenon. A memory trace of the recent history of network activity is maintained in the state of the synapses, allowing the network to temporarily reactivate the representation of the previous environment in the absence of the corresponding sensory cues. The model predicts that the number of flickering events depends on the amplitude of the ongoing theta rhythm and the distance between the current position of the animal and its position at the time of cue switching. We test these predictions with new analysis of experimental data. These results suggest a potential role of short-term synaptic plasticity in recruiting the activity of different cell assemblies and in shaping hippocampal activity of behaving animals. This article is protected by copyright. All rights reserved.

}, issn = {1098-1063}, doi = {10.1002/hipo.22743}, author = {Mark, Shirley and Romani, Sandro and Jezek, Karel and Tsodyks, Misha} } @article {48624, title = {Three dimensional reconstruction of energy stores for jumping in planthoppers and froghoppers from confocal laser scanning microscopy.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Jun 21}, abstract = {

Jumping in planthopper and froghopper insects is propelled by a catapult-like mechanism requiring mechanical storage of energy and its quick release to accelerate the hind legs rapidly. To understand the functional biomechanics involved in these challenging movements, the internal skeleton, tendons and muscles involved were reconstructed in 3-D from confocal scans in unprecedented detail. Energy to power jumping was generated by slow contractions of hind leg depressor muscles and then stored by bending specialised elements of the thoracic skeleton that are composites of the rubbery protein resilin sandwiched between layers of harder cuticle with air-filled tunnels reducing mass. The images showed that the lever arm of the power-producing muscle changed in magnitude during jumping, but at all joint angles would cause depression, suggesting a mechanism by which the stored energy is released. This methodological approach illuminates how miniaturized components interact and function in complex and rapid movements of small animals.

}, issn = {2050-084X}, doi = {10.7554/eLife.23824}, author = {Siwanowicz, Igor and Burrows, Malcolm} } @article {48512, title = {Time-accuracy tradeoffs in kernel prediction: controlling prediction quality.}, journal = {Journal of Machine Learning Research}, volume = {18}, year = {2017}, month = {2017 Apr 1 }, pages = {1-29}, abstract = {

Kernel regression or classification (also referred to as weighted ε-NN methods in Machine Learning) are appealing for their simplicity and therefore ubiquitous in data analysis. How- ever, practical implementations of kernel regression or classification consist of quantizing or sub-sampling data for improving time efficiency, often at the cost of prediction quality. While such tradeoffs are necessary in practice, their statistical implications are generally not well understood, hence practical implementations come with few performance guaran- tees. In particular, it is unclear whether it is possible to maintain the statistical accuracy of kernel prediction{\textemdash}crucial in some applications{\textemdash}while improving prediction time.

The present work provides guiding principles for combining kernel prediction with data- quantization so as to guarantee good tradeoffs between prediction time and accuracy, and in particular so as to approximately maintain the good accuracy of vanilla kernel prediction.

Furthermore, our tradeoff guarantees are worked out explicitly in terms of a tuning parameter which acts as a knob that favors either time or accuracy depending on practical needs. On one end of the knob, prediction time is of the same order as that of single-nearest- neighbor prediction (which is statistically inconsistent) while maintaining consistency; on the other end of the knob, the prediction risk is nearly minimax-optimal (in terms of the original data size) while still reducing time complexity. The analysis thus reveals the interaction between the data-quantization approach and the kernel prediction method, and most importantly gives explicit control of the tradeoff to the practitioner rather than fixing the tradeoff in advance or leaving it opaque.

The theoretical results are validated on data from a range of real-world application domains; in particular we demonstrate that the theoretical knob performs as expected.\ 

}, url = {http://jmlr.org/papers/volume18/16-538/16-538.pdf}, author = {Kpotufe, Samory and Verma, Nakul} } @article {68761, title = {A toolkit for GFP-mediated tissue-specific protein degradation in C. elegans}, journal = {Development}, volume = {144}, year = {2017}, month = {07/2017}, pages = {2694-2701}, abstract = {

Proteins that are essential for embryo production, cell division and early embryonic events are frequently reused later in embryogenesis, during organismal development or in the adult. Examining protein function across these different biological contexts requires tissue-specific perturbation. Here, we describe a method that uses expression of a fusion between a GFP-targeting nanobody and a SOCS-box containing ubiquitin ligase adaptor to target GFP-tagged proteins for degradation. When combined with endogenous locus GFP tagging by CRISPR-Cas9 or with rescue of a null mutant with a GFP fusion, this approach enables routine and efficient tissue-specific protein ablation. We show that this approach works in multiple tissues {\textendash} the epidermis, intestine, body wall muscle, ciliated sensory neurons and touch receptor neurons {\textendash} where it recapitulates expected loss-of-function mutant phenotypes. The transgene toolkit and the strain set described here will complement existing approaches to enable routine analysis of the tissue-specific roles of C. elegans proteins.

}, issn = {0950-1991}, doi = {10.1242/dev.150094}, url = {https://doi.org/10.1242/dev.150094}, author = {Wang, Shaohe and Tang, Ngang Heok and Lara-Gonzalez, Pablo and Zhao, Zhiling and Cheerambathur, Dhanya K. and Prevo, Bram and Chisholm, Andrew D. and Desai, Arshad and Oegema, Karen} } @article {48985, title = {A topographic axis of transcriptional identity in thalamus.}, journal = {bioRxiv}, year = {2017}, month = {2017 Dec 31}, pages = {241315}, abstract = {

A fundamental goal in neuroscience is to uncover common principles by which different modalities of information are processed. In the mammalian brain, thalamus acts as the essential hub for forebrain circuits handling inputs from sensory, motor, limbic, and cognitive pathways. Whether thalamus imposes common transformations on each of these modalities is unknown. Molecular characterization offers a principled approach to revealing the organization of thalamus. Using near-comprehensive and projection-specific transcriptomic sequencing, we found that almost all thalamic nuclei fit into one of three profiles. These profiles lie on a single axis of genetic variance which is aligned with the mediolateral spatial axis of thalamus. Genes defining this axis of variance include receptors and ion channels, providing a systematic diversification of input/output transformations across the topography of thalamus. Single cell transcriptional profiling revealed graded heterogeneity within individual thalamic nuclei, demonstrating that a spectrum of cell types and potentially diverse input/output transforms exist within a given thalamic nucleus. Together, our data argue for an archetypal organization of pathways serving diverse input modalities, and provides a comprehensive organizational scheme for thalamus.

}, doi = {10.1101/241315}, author = {Phillips, James W and Schulman, Anton and Hara, Erina and Liu, Chenghao and Shields, Brenda C and Korff, Wyatt and Lemire, Andrew and Dudman, Joshua T and Nelson, Sacha B and Hantman, Adam W} } @article {48921, title = {Topological and modality-specific representation of somatosensory information in the fly brain.}, journal = {Science (New York, N.Y.)}, volume = {358}, year = {2017}, month = {2017 11 03}, pages = {615-623}, abstract = {

Insects and mammals share similarities of neural organization underlying the perception of odors, taste, vision, sound, and gravity. We observed that insect somatosensation also corresponds to that of mammals. In Drosophila, the projections of all the somatosensory neuron types to the insect{\textquoteright}s equivalent of the spinal cord segregated into modality-specific layers comparable to those in mammals. Some sensory neurons innervate the ventral brain directly to form modality-specific and topological somatosensory maps. Ascending interneurons with dendrites in matching layers of the nerve cord send axons that converge to respective brain regions. Pathways arising from leg somatosensory neurons encode distinct qualities of leg movement information and play different roles in ground detection. Establishment of the ground pattern and genetic tools for neuronal manipulation should provide the basis for elucidating the mechanisms underlying somatosensation.

}, issn = {1095-9203}, doi = {10.1126/science.aan4428}, author = {Tsubouchi, Asako and Yano, Tomoko and Yokoyama, Takeshi K and Murtin, Chlo{\'e} and Otsuna, Hideo and Ito, Kei} } @article {48367, title = {Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, year = {2017}, month = {2017 Mar 29}, pages = {2424-6}, abstract = {

Summary: State-of-the-art light and electron microscopes are capable of acquiring large image datasets, but quantitatively evaluating the data often involves manually annotating structures of interest. This processis time-consuming and often a major bottleneck in the evaluation pipeline. To overcome this problem, we have introduced the Trainable Weka Segmentation (TWS), a machine learning tool that leveragesa limited number of manual annotations in order to train a classifier and segment the remaining dataautomatically. In addition, TWS can provide unsupervised segmentation learning schemes (clustering) and can be customized to employ user-designed image features or classifiers.

Availability and Implementation: TWS is distributed as open-source software as part of the Fiji image processing distribution of ImageJ at http://imagej.net/Trainable_Weka_Segmentation.

Contact: ignacio.arganda@ehu.eus.

Supplementary information: Supplementary data are available at Bioinformatics online.

}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btx180}, author = {Arganda-Carreras, Ignacio and Kaynig, Verena and Rueden, Curtis and Eliceiri, Kevin W and Schindelin, Johannes and Cardona, Albert and Seung, H Sebastian} } @article {48934, title = {Ultra-selective looming detection from radial motion opponency.}, journal = {Nature}, volume = {551}, year = {2017}, month = {2017 Nov 08}, pages = {237-241}, abstract = {

Nervous systems combine lower-level sensory signals to detect higher-order stimulus features critical to survival, such as the visual looming motion created by an imminent collision or approaching predator. Looming-sensitive neurons have been identified in diverse animal species. Different large-scale visual features such as looming often share local cues, which means loom-detecting neurons face the challenge of rejecting confounding stimuli. Here we report the discovery of an ultra-selective looming detecting neuron, lobula plate/lobula columnar, type II (LPLC2) in Drosophila, and show how its selectivity is established by radial motion opponency. In the fly visual system, directionally selective small-field neurons called T4 and T5 form a spatial map in the lobula plate, where they each terminate in one of four retinotopic layers, such that each layer responds to motion in a different cardinal direction. Single-cell anatomical analysis reveals that each arm of the LPLC2 cross-shaped primary dendrites ramifies in one of these layers and extends along that layer{\textquoteright}s preferred motion direction. In vivo calcium imaging demonstrates that, as their shape predicts, individual LPLC2 neurons respond strongly to outward motion emanating from the centre of the neuron{\textquoteright}s receptive field. Each dendritic arm also receives local inhibitory inputs directionally selective for inward motion opposing the excitation. This radial motion opponency generates a balance of excitation and inhibition that makes LPLC2 non-responsive to related patterns of motion such as contraction, wide-field rotation or luminance change. As a population, LPLC2 neurons densely cover visual space and terminate onto the giant fibre descending neurons, which drive the jump muscle motor neuron to trigger an escape take off. Our findings provide a mechanistic description of the selective feature detection that flies use to discern and escape looming threats.

}, issn = {1476-4687}, doi = {10.1038/nature24626}, author = {Klapoetke, Nathan C and Nern, Aljoscha and Peek, Martin Y and Rogers, Edward M and Breads, Patrick and Rubin, Gerald M and Reiser, Michael B and Card, Gwyneth M} } @article {48513, title = {Unraveling cell-to-cell signaling networks with chemical biology.}, journal = {Nature Chemical Biology}, volume = {13}, year = {2017}, month = {2017 May 17}, pages = {564-568}, issn = {1552-4469}, doi = {10.1038/nchembio.2391}, author = {Gartner, Zev J and Prescher, Jennifer A and Lavis, Luke D} } @article {48280, title = {A variant Sp1 (R218Q) transcription factor might enhance HbF expression in β(0) -thalassaemia homozygotes.}, journal = {British Journal of Haematology}, volume = {180}, year = {2017}, month = {2017 Feb 27}, pages = {755-7}, issn = {1365-2141}, doi = {10.1111/bjh.14445}, author = {Jiang, Zhihua and Luo, Hong-Yuan and Farrell, John J and Zhang, Zhengjian and Schulz, Vincent P and Albarawi, Dilan and Steinberg, Martin H and Al-Allawi, Nasir A S and Gallagher, Patrick G and Forget, Bernard G and Chui, David H K} } @article {48304, title = {Video-rate volumetric functional imaging of the brain at synaptic resolution.}, journal = {Nature Neuroscience}, volume = {20}, year = {2017}, month = {2017 Feb 27}, pages = {620-8}, abstract = {

Neurons and neural networks often extend hundreds of micrometers in three dimensions. Capturing the calcium transients associated with their activity requires volume imaging methods with subsecond temporal resolution. Such speed is a challenge for conventional two-photon laser-scanning microscopy, because it depends on serial focal scanning in 3D and indicators with limited brightness. Here we present an optical module that is easily integrated into standard two-photon laser-scanning microscopes to generate an axially elongated Bessel focus, which when scanned in 2D turns frame rate into volume rate. We demonstrated the power of this approach in enabling discoveries for neurobiology by imaging the calcium dynamics of volumes of neurons and synapses in fruit flies, zebrafish larvae, mice and ferrets in vivo. Calcium signals in objects as small as dendritic spines could be resolved at video rates, provided that the samples were sparsely labeled to limit overlap in their axially projected images.

}, issn = {1546-1726}, doi = {10.1038/nn.4516}, author = {Lu, Rongwen and Sun, Wenzhi and Liang, Yajie and Kerlin, Aaron and Bierfeld, Jens and Seelig, Johannes D and Wilson, Daniel E and Scholl, Benjamin and Mohar, Boaz and Tanimoto, Masashi and Koyama, Minoru and Fitzpatrick, David and Orger, Michael B and Ji, Na} } @article {48838, title = {Visual motion computation in recurrent neural networks.}, journal = {bioRxiv}, year = {2017}, month = {2017 Jan 09}, pages = {099101}, abstract = {

Populations of neurons in primary visual cortex (V1) transform direct thalamic inputs into a cortical representation which acquires new spatio-temporal properties. One of these properties, motion selectivity, has not been strongly tied to putative neural mechanisms, and its origins remain poorly understood. Here we propose that motion selectivity is acquired through the recurrent mechanisms of a network of strongly connected neurons. We first show that a bank of V1 spatiotemporal receptive fields can be generated accurately by a network which receives only instantaneous inputs from the retina. The temporal structure of the receptive fields is generated by the long timescale dynamics associated with the high magnitude eigenvalues of the recurrent connectivity matrix. When these eigenvalues have complex parts, they generate receptive fields that are inseparable in time and space, such as those tuned to motion direction. We also show that the recurrent connectivity patterns can be learnt directly from the statistics of natural movies using a temporally-asymmetric Hebbian learning rule. Probed with drifting grating stimuli and moving bars, neurons in the model show patterns of responses analogous to those of direction-selective simple cells in primary visual cortex. These computations are enabled by a specific pattern of recurrent connections, that can be tested by combining connectome reconstructions with functional recordings.

}, doi = {https://doi.org/10.1101/099101}, author = {Pachitariu, Marius and Sahani, Maneesh} } @article {48496, title = {Visualizing dynamic microvillar search and stabilization during ligand detection by T cells.}, journal = {Science (New York, N.Y.)}, volume = {356}, year = {2017}, month = {2017 May 12}, abstract = {

During immune surveillance, T cells survey the surface of antigen-presenting cells. In searching for peptide-loaded major histocompatibility complexes (pMHCs), they must solve a classic trade-off between speed and sensitivity. It has long been supposed that microvilli on T cells act as sensory organs to enable search, but their strategy has been unknown. We used lattice light-sheet and quantum dot-enabled synaptic contact mapping microscopy to show that anomalous diffusion and fractal organization of microvilli survey the majority of opposing surfaces within 1 minute. Individual dwell times were long enough to discriminate pMHC half-lives and T cell receptor (TCR) accumulation selectively stabilized microvilli. Stabilization was independent of tyrosine kinase signaling and the actin cytoskeleton, suggesting selection for avid TCR microclusters. This work defines the efficient cellular search process against which ligand detection takes place.

}, issn = {1095-9203}, doi = {10.1126/science.aal3118}, author = {Cai, En and Marchuk, Kyle and Beemiller, Peter and Beppler, Casey and Rubashkin, Matthew G and Weaver, Valerie M and G{\'e}rard, Audrey and Liu, Tsung-Li and Chen, Bi-Chang and Betzig, Eric and Bartumeus, Frederic and Krummel, Matthew F} } @article {48752, title = {Visualizing long-term single-molecule dynamics in vivo by stochastic protein labeling.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, year = {2017}, month = {2017 Jan 09}, pages = {343-8}, abstract = {

Our ability to unambiguously image and track individual molecules in live cells is limited by packing of multiple copies of labeled molecules within the resolution limit. Here we devise a universal genetic strategy to precisely control copy number of fluorescently labeled molecules in a cell. This system has a dynamic titration range of \>10,000 fold, enabling sparse labeling of proteins expressed at different abundance levels. Combined with photostable labels, this system extends the duration of automated single-molecule tracking by 2 orders of magnitude. We demonstrate long-term imaging of synaptic vesicle dynamics in cultured neurons as well as in intact\ zebrafish. We found axon initial segment utilizes a "waterfall" mechanism gating synaptic vesicle transport polarity by promoting anterograde transport processivity. Long-time observation also reveals that transcription factor hops between clustered binding sites in spatially-restricted sub-nuclear regions, suggesting that topological structures in the nucleus shape local gene activities by a sequestering mechanism. This strategy thus greatly expands the spatiotemporal length scales of live-cell single-molecule measurements, enabling new experiments to quantitatively understand complex control of molecular dynamics\ in vivo.

}, doi = {10.1073/pnas.1713895115}, author = {Liu, Hui and Dong, Peng and Ioannou, Maria S and Li, Li and Shea, Jamien and Pasolli, H Amalia and Grimm, Jonathan B and Rivlin, Patricia K and Lavis, Luke D and Koyama, Minoru and Liu, Zhe} } @article {48730, title = {Volume imaging.}, volume = {B2}, number = {14/452,181}, year = {2017}, month = {2017 Aug 01}, edition = {G01J 4/00 (20060101); G02B 21/00 (20060101); G02B 21/36 (20060101)}, abstract = {

A system for a laser-scanning microscope includes an optical element configured to transmit light in a first direction onto a first beam path and to reflect light in a second direction to a second beam path that is different from the first beam path; a reflector on the first beam path; and a lens including a variable focal length, the lens positioned on the first beam path. The lens and reflector are positioned relative to each other to cause light transmitted by the optical element to pass through the lens a plurality of times and in a different direction each time. In some implementations, the system also can include a feedback system that receives a signal that represents an amount of focusing of the lens, and changes the focal length of the lens based on the received signal.

}, url = {http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO2\&Sect2=HITOFF\&u=\%2Fnetahtml\%2FPTO\%2Fsearch-adv.htm\&r=1\&p=1\&f=G\&l=50\&d=PTXT\&S1=(\%22Howard+Hughes+medical\%22.ASNM.)\&OS=AN/\%22Howard+Hughes+medical\%22\&RS=AN/\%22Howard+Hughes+medical\%22}, author = {Cui, Meng and Kong, Lingjie} } @article {67282, title = {Volumetric two-photon imaging of neurons using stereoscopy (vTwINS)}, journal = {Nature Methods}, volume = {14}, year = {2017}, month = {03/2017}, pages = {420 - 426}, abstract = {

Two-photon laser scanning microscopy of calcium dynamics using fluorescent indicators is a widely used imaging method for large-scale recording of neural activity\ in vivo. Here, we introduce volumetric two-photon imaging of neurons using stereoscopy (vTwINS), a volumetric calcium imaging method that uses an elongated, V-shaped point spread function to image a 3D brain volume. Single neurons project to spatially displaced {\textquoteright}image pairs{\textquoteright} in the resulting 2D image, and the separation distance between projections is proportional to depth in the volume. To demix the fluorescence time series of individual neurons, we introduce a modified orthogonal matching pursuit algorithm that also infers source locations within the 3D volume. We illustrated vTwINS by imaging neural population activity in the mouse primary visual cortex and hippocampus. Our results demonstrated that vTwINS provides an effective method for volumetric two-photon calcium imaging that increases the number of neurons recorded while maintaining a high frame rate.

}, issn = {1548-7091}, doi = {10.1038/nmeth.4226}, url = {http://www.nature.com/articles/nmeth.4226http://www.nature.com/articles/nmeth.4226.pdfhttp://www.nature.com/articles/nmeth.4226.pdfhttp://www.nature.com/articles/nmeth.4226}, author = {Song, Alexander and Charles, Adam S and Koay, Sue Ann and Gauthier, Jeff L and Thiberge, Stephan Y and Pillow, Jonathan W and Tank, David W} } @article {48461, title = {What can tiny mushrooms in fruit flies tell us about learning and memory?}, journal = {Neuroscience Research}, volume = {129}, year = {2017}, month = {2017 May 05}, pages = {8-16}, abstract = {

Nervous systems have evolved to translate external stimuli into appropriate behavioral responses. In an ever-changing environment, flexible adjustment of behavioral choice by experience-dependent learning is essential for the animal{\textquoteright}s survival. Associative learning is a simple form of learning that is widely observed from worms to humans. To understand the whole process of learning, we need to know how sensory information is represented and transformed in the brain, how it is changed by experience, and how the changes are reflected on motor output. To tackle these questions, studying numerically simple invertebrate nervous systems has a great advantage. In this review, I will feature the Pavlovian olfactory learning in the fruit fly, Drosophila melanogaster. The mushroom body is a key brain area for the olfactory learning in this organism. Recently, comprehensive anatomical information and the genetic tool sets were made available for the mushroom body circuit. This greatly accelerated the physiological understanding of the learning process. One of the key findings was dopamine-induced long-term synaptic plasticity that can alter the representations of stimulus valence. I will mostly focus on the new studies within these few years and discuss what we can possibly learn about the vertebrate systems from this model organism.

}, issn = {1872-8111}, doi = {10.1016/j.neures.2017.05.002}, author = {Hige, Toshihide} } @article {69342, title = {When complex neuronal structures may not matter}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Feb 6}, pages = {e23508}, abstract = {

Much work has explored animal-to-animal variability and compensation in ion channel expression. Yet, little is known regarding the physiological consequences of morphological variability. We quantify animal-to-animal variability in cable lengths (CV = 0.4) and branching patterns in the Gastric Mill (GM) neuron, an identified neuron type with highly-conserved physiological properties in the crustacean stomatogastric ganglion (STG) of \textitCancer borealis. We examined passive GM electrotonic structure by measuring the amplitudes and apparent reversal potentials (E\textsubscriptrevs) of inhibitory responses evoked with focal glutamate photo-uncaging in the presence of TTX. Apparent E\textsubscriptrevs were relatively invariant across sites (mean CV {\textpm} SD = 0.04 {\textpm} 0.01; 7{\textendash}20 sites in each of 10 neurons), which ranged between 100{\textendash}800 {\textmu}m from the somatic recording site. Thus, GM neurons are remarkably electrotonically compact (estimated λ \> 1.5 mm). Electrotonically compact structures, in consort with graded transmission, provide an elegant solution to observed morphological variability in the STG.

}, keywords = {electrotonus, morphology, Stomatogastric ganglion, variability, \textitCancer borealis}, issn = {2050-084X}, doi = {10.7554/eLife.23508}, url = {https://doi.org/10.7554/eLife.23508}, author = {Otopalik, Adriane G and Sutton, Alexander C and Banghart, Matthew and Marder, Eve}, editor = {Raman, Indira M} } @article {48497, title = {Whole-brain serial-section electron microscopy in larval zebrafish.}, journal = {Nature}, volume = {545}, year = {2017}, month = {2017 May 18}, pages = {345-349}, abstract = {

High-resolution serial-section electron microscopy (ssEM) makes it possible to investigate the dense meshwork of axons, dendrites, and synapses that form neuronal circuits. However, the imaging scale required to comprehensively reconstruct these structures is more than ten orders of magnitude smaller than the spatial extents occupied by networks of interconnected neurons, some of which span nearly the entire brain. Difficulties in generating and handling data for large volumes at nanoscale resolution have thus restricted vertebrate studies to fragments of circuits. These efforts were recently transformed by advances in computing, sample handling, and imaging techniques, but high-resolution examination of entire brains remains a challenge. Here, we present ssEM data for the complete brain of a larval zebrafish (Danio rerio) at 5.5 days post-fertilization. Our approach utilizes multiple rounds of targeted imaging at different scales to reduce acquisition time and data management requirements. The resulting dataset can be analysed to reconstruct neuronal processes, permitting us to survey all myelinated axons (the projectome). These reconstructions enable precise investigations of neuronal morphology, which reveal remarkable bilateral symmetry in myelinated reticulospinal and lateral line afferent axons. We further set the stage for whole-brain structure-function comparisons by co-registering functional reference atlases and in vivo two-photon fluorescence microscopy data from the same specimen. All obtained images and reconstructions are provided as an open-access resource.

}, issn = {1476-4687}, doi = {10.1038/nature22356}, author = {Hildebrand, David Grant Colburn and Cicconet, Marcelo and Torres, Russel Miguel and Choi, Woohyuk and Quan, Tran Minh and Moon, Jungmin and Wetzel, Arthur Willis and Scott Champion, Andrew and Graham, Brett Jesse and Randlett, Owen and Plummer, George Scott and Portugues, Ruben and Bianco, Isaac Henry and Saalfeld, Stephan and Baden, Alexander David and Lillaney, Kunal and Burns, Randal and Vogelstein, Joshua Tzvi and Schier, Alexander Franz and Lee, Wei-Chung Allen and Jeong, Won-Ki and Lichtman, Jeff William and Engert, Florian} } @article {48370, title = {Whole-cell recording in the awake brain.}, journal = {Cold Spring Harbor Protocols}, volume = {2017}, year = {2017}, month = {2017 Apr 03}, pages = {pdb.top087304}, abstract = {

Intracellular recording is an essential technique for investigating cellular mechanisms underlying complex brain functions. Despite the high sensitivity of the technique to mechanical disturbances, intracellular recording has been applied to awake, behaving, and even freely moving, animals. Here we summarize recent advances in these methods and their application to the measurement and manipulation of membrane potential dynamics for understanding neuronal computations in behaving animals.

}, issn = {1559-6095}, doi = {10.1101/pdb.top087304}, author = {Lee, Doyun and Lee, Albert K} } @article {48217, title = {Wiring the Drosophila brain with individually tailored neural lineages.}, journal = {Current Biology : CB}, volume = {27}, year = {2017}, month = {2017 Jan 23}, pages = {R77-R82}, abstract = {

A complex brain consists of multiple intricate neural networks assembled from distinct sets of input and output neurons as well as region-specific local interneurons. Within a given anatomical set, there exist diverse neuronal types that can vary in morphology, neural physiology, and modes of neurotransmission. The genetic programs that guide specification of neuronal types during neurogenesis preconfigure the brain. This is best demonstrated in the Drosophila central brain, which is composed of \~{}100 pairs of individually tailored neuronal lineages. Each neuronal lineage (the neurons/glia produced from a single stem cell) can contain multiple morphological classes of neurons that can consist of many analogous neuronal types. The detailed patterns of neuronal diversification are lineage-specific and can differ drastically even among neighboring neuronal lineages. Furthermore, the interrelationships between neuronal lineages and neural networks are complex. These phenomena underscore the importance of tracking all neuronal lineages in understanding brain development and evolution.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2016.12.026}, author = {Lee, Tzumin} } @article {48305, title = {Zyxin regulates endothelial von Willebrand factor secretion by reorganizing actin filaments around exocytic granules.}, journal = {Nature Communications}, volume = {8}, year = {2017}, month = {2017 Mar 03}, pages = {14639}, abstract = {

Endothelial exocytosis of Weibel-Palade body (WPB) is one of the first lines of defence against vascular injury. However, the mechanisms that control WPB exocytosis in the final stages (including the docking, priming and fusion of granules) are poorly understood. Here we show that the focal adhesion protein zyxin is crucial in this process. Zyxin downregulation inhibits the secretion of von Willebrand factor (VWF), the most abundant cargo in WPBs, from human primary endothelial cells (ECs) induced by cAMP agonists. Zyxin-deficient mice exhibit impaired epinephrine-stimulated VWF release, prolonged bleeding time and thrombosis, largely due to defective endothelial secretion of VWF. Using live-cell super-resolution microscopy, we visualize previously unappreciated reorganization of pre-existing actin filaments around WPBs before fusion, dependent on zyxin and an interaction with the actin crosslinker α-actinin. Our findings identify zyxin as a physiological regulator of endothelial exocytosis through reorganizing local actin network in the final stage of exocytosis.

}, issn = {2041-1723}, doi = {10.1038/ncomms14639}, author = {Han, Xiaofan and Li, Pin and Yang, Zhenghao and Huang, Xiaoshuai and Wei, Guoqin and Sun, Yujie and Kang, Xuya and Hu, Xueting and Deng, Qiuping and Chen, Liangyi and He, Aibin and Huo, Yingqing and Li, Dong and Betzig, Eric and Luo, Jincai} } @article {47875, title = {Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, year = {2016}, month = {2016 Oct 04}, pages = {11232-6}, abstract = {

Electrons, because of their strong interaction with matter, produce high-resolution diffraction patterns from tiny 3D crystals only a few hundred nanometers thick in a frozen-hydrated state. This discovery offers the prospect of facile structure determination of complex biological macromolecules, which cannot be coaxed to form crystals large enough for conventional crystallography or cannot easily be produced in sufficient quantities. Two potential obstacles stand in the way. The first is a phenomenon known as dynamical scattering, in which multiple scattering events scramble the recorded electron diffraction intensities so that they are no longer informative of the crystallized molecule. The second obstacle is the lack of a proven means of de novo phase determination, as is required if the molecule crystallized is insufficiently similar to one that has been previously determined. We show with four structures of the amyloid core of the Sup35 prion protein that, if the diffraction resolution is high enough, sufficiently accurate phases can be obtained by direct methods with the cryo-EM method microelectron diffraction (MicroED), just as in X-ray diffraction. The success of these four experiments dispels the concern that dynamical scattering is an obstacle to ab initio phasing by MicroED and suggests that structures of novel macromolecules can also be determined by direct methods.

}, issn = {1091-6490}, doi = {10.1073/pnas.1606287113}, author = {Sawaya, Michael R and Rodriguez, Jose and Cascio, Duilio and Collazo, Michael J and Shi, Dan and Reyes, Francis E and Hattne, Johan and Gonen, Tamir and Eisenberg, David S} } @article {47711, title = {Accurate design of megadalton-scale two-component icosahedral protein complexes.}, journal = {Science (New York, N.Y.)}, volume = {353}, year = {2016}, month = {2016 Jul 22}, pages = {389-94}, abstract = {

Nature provides many examples of self- and co-assembling protein-based molecular machines, including icosahedral protein cages that serve as scaffolds, enzymes, and compartments for essential biochemical reactions and icosahedral virus capsids, which encapsidate and protect viral genomes and mediate entry into host cells. Inspired by these natural materials, we report the computational design and experimental characterization of co-assembling, two-component, 120-subunit icosahedral protein nanostructures with molecular weights (1.8 to 2.8 megadaltons) and dimensions (24 to 40 nanometers in diameter) comparable to those of small viral capsids. Electron microscopy, small-angle x-ray scattering, and x-ray crystallography show that 10 designs spanning three distinct icosahedral architectures form materials closely matching the design models. In vitro assembly of icosahedral complexes from independently purified components occurs rapidly, at rates comparable to those of viral capsids, and enables controlled packaging of molecular cargo through charge complementarity. The ability to design megadalton-scale materials with atomic-level accuracy and controllable assembly opens the door to a new generation of genetically programmable protein-based molecular machines.

}, issn = {1095-9203}, doi = {10.1126/science.aaf8818}, author = {Bale, Jacob B and Gonen, Shane and Liu, Yuxi and Sheffler, William and Ellis, Daniel and Thomas, Chantz and Cascio, Duilio and Yeates, Todd O and Gonen, Tamir and King, Neil P and Baker, David} } @article {47509, title = {Activation of NMDA receptors and the mechanism of inhibition by ifenprodil.}, journal = {Nature}, volume = {534}, year = {2016}, month = {2016 Jun 2}, pages = {63-8}, abstract = {

The physiology of N-methyl-d-aspartate (NMDA) receptors is fundamental to brain development and function. NMDA receptors are ionotropic glutamate receptors that function as heterotetramers composed mainly of GluN1 and GluN2 subunits. Activation of NMDA receptors requires binding of neurotransmitter agonists to a ligand-binding domain (LBD) and structural rearrangement of an amino-terminal domain (ATD). Recent crystal structures of GluN1-GluN2B NMDA receptors bound to agonists and an allosteric inhibitor, ifenprodil, represent the allosterically inhibited state. However, how the ATD and LBD move to activate the NMDA receptor ion channel remains unclear. Here we applied X-ray crystallography, single-particle electron cryomicroscopy and electrophysiology to rat NMDA receptors to show that, in the absence of ifenprodil, the bi-lobed structure of GluN2 ATD adopts an open conformation accompanied by rearrangement of the GluN1-GluN2 ATD heterodimeric interface, altering subunit orientation in the ATD and LBD and forming an active receptor conformation that gates the ion channel.

}, issn = {1476-4687}, doi = {10.1038/nature17679}, author = {Tajima, Nami and Karakas, Erkan and Grant, Timothy and Simorowski, Noriko and Diaz-Avalos, Ruben and Grigorieff, Nikolaus and Furukawa, Hiro} } @article {48468, title = {Active dendritic properties and local inhibitory input enable selectivity for object motion in mouse superior colliculus neurons.}, journal = {The Journal of Neuroscience : the Official Journal of the Society for Neuroscience}, volume = {36}, year = {2016}, month = {2016 Aug 31}, pages = {9111-23}, abstract = {

UNLABELLED: Neurons respond to specific features of sensory stimuli. In the visual system, for example, some neurons respond to motion of small but not large objects, whereas other neurons prefer motion of the entire visual field. Separate neurons respond equally to local and global motion but selectively to additional features of visual stimuli. How and where does response selectivity emerge? Here, we show that wide-field (WF) cells in retino-recipient layers of the mouse superior colliculus (SC) respond selectively to small moving objects. Moreover, we identify two mechanisms that contribute to this selectivity. First, we show that input restricted to a small portion of the broad dendritic arbor of WF cells is sufficient to trigger dendritic spikes that reliably propagate to the soma/axon. In vivo whole-cell recordings reveal that nearly every action potential evoked by visual stimuli has characteristics of spikes initiated in dendrites. Second, inhibitory input from a different class of SC neuron, horizontal cells, constrains the range of stimuli to which WF cells respond. Horizontal cells respond preferentially to the sudden appearance or rapid movement of large stimuli. Optogenetic reduction of their activity reduces movement selectivity and broadens size tuning in WF cells by increasing the relative strength of responses to stimuli that appear suddenly or cover a large region of space. Therefore, strongly propagating dendritic spikes enable small stimuli to drive spike output in WF cells and local inhibition helps restrict responses to stimuli that are both small and moving.

SIGNIFICANCE STATEMENT: How do neurons respond selectively to some sensory stimuli but not others? In the visual system, a particularly relevant stimulus feature is object motion, which often reveals other animals. Here, we show how specific cells in the superior colliculus, one synapse downstream of the retina, respond selectively to object motion. These wide-field (WF) cells respond strongly to small objects that move slowly anywhere through a large region of space, but not to stationary objects or full-field motion. Action potential initiation in dendrites enables small stimuli to trigger visual responses and inhibitory input from cells that prefer large, suddenly appearing, or quickly moving stimuli restricts responses of WF cells to objects that are small and moving.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0645-16.2016}, author = {Gale, Samuel D and Murphy, Gabe J} } @article {47260, title = {Adaptive and background-aware GAL4 expression enhancement of co-registered confocal microscopy images.}, journal = {Neuroinformatics}, volume = {14}, year = {2016}, month = {2016 Jan 7}, pages = {221-33}, abstract = {

GAL4 gene expression imaging using confocal microscopy is a common and powerful technique used to study the nervous system of a model organism such as Drosophila melanogaster. Recent research projects focused on high throughput screenings of thousands of different driver lines, resulting in large image databases. The amount of data generated makes manual assessment tedious or even impossible. The first and most important step in any automatic image processing and data extraction pipeline is to enhance areas with relevant signal. However, data acquired via high throughput imaging tends to be less then ideal for this task, often showing high amounts of background signal. Furthermore, neuronal structures and in particular thin and elongated projections with a weak staining signal are easily lost. In this paper we present a method for enhancing the relevant signal by utilizing a Hessian-based filter to augment thin and weak tube-like structures in the image. To get optimal results, we present a novel adaptive background-aware enhancement filter parametrized with the local background intensity, which is estimated based on a common background model. We also integrate recent research on adaptive image enhancement into our approach, allowing us to propose an effective solution for known problems present in confocal microscopy images. We provide an evaluation based on annotated image data and compare our results against current state-of-the-art algorithms. The results show that our algorithm clearly outperforms the existing solutions.

}, issn = {1559-0089}, doi = {10.1007/s12021-015-9289-y}, author = {Trapp, Martin and Schulze, Florian and Novikov, Alexey A and Tirian, Laszlo and J Dickson, Barry and B{\"u}hler, Katja} } @article {47987, title = {Adaptive light-sheet microscopy for long-term, high-resolution imaging in living organisms.}, journal = {Nature Biotechnology}, volume = {34}, year = {2016}, month = {2016 Oct 31}, pages = {1267-78}, abstract = {

Optimal image quality in light-sheet microscopy requires a perfect overlap between the illuminating light sheet and the focal plane of the detection objective. However, mismatches between the light-sheet and detection planes are common owing to the spatiotemporally varying optical properties of living specimens. Here we present the AutoPilot framework, an automated method for spatiotemporally adaptive imaging that integrates (i) a multi-view light-sheet microscope capable of digitally translating and rotating light-sheet and detection planes in three dimensions and (ii) a computational method that continuously optimizes spatial resolution across the specimen volume in real time. We demonstrate long-term adaptive imaging of entire developing zebrafish (Danio rerio) and Drosophila melanogaster embryos and perform adaptive whole-brain functional imaging in larval zebrafish. Our method improves spatial resolution and signal strength two to five-fold, recovers cellular and sub-cellular structures in many regions that are not resolved by non-adaptive imaging, adapts to spatiotemporal dynamics of genetically encoded fluorescent markers and robustly optimizes imaging performance during large-scale morphogenetic changes in living organisms.

}, issn = {1546-1696}, doi = {10.1038/nbt.3708}, author = {Royer, Lo{\"\i}c A and Lemon, William C and Chhetri, Raghav K and Wan, Yinan and Coleman, Michael and Myers, Eugene W and Keller, Philipp J} } @article {47894, title = {Adult mouse cortical cell taxonomy revealed by single cell transcriptomics.}, journal = {Nature neuroscience}, volume = {19}, year = {2016}, month = {2016 Feb}, pages = {335-46}, abstract = {

Nervous systems are composed of various cell types, but the extent of cell type diversity is poorly understood. We constructed a cellular taxonomy of one cortical region, primary visual cortex, in adult mice on the basis of single-cell RNA sequencing. We identified 49 transcriptomic cell types, including 23 GABAergic, 19 glutamatergic and 7 non-neuronal types. We also analyzed cell type-specific mRNA processing and characterized genetic access to these transcriptomic types by many transgenic Cre lines. Finally, we found that some of our transcriptomic cell types displayed specific and differential electrophysiological and axon projection properties, thereby confirming that the single-cell transcriptomic signatures can be associated with specific cellular properties.

}, keywords = {Animals, Cell Line, Cerebral Cortex, Classification, gamma-Aminobutyric Acid, Gene Library, Genetic Markers, Glutamic Acid, Interneurons, Male, Mice, Mice, Inbred C57BL, Mice, Transgenic, Neurons, RNA, Sequence Analysis, RNA, Transcriptome, Visual Cortex}, issn = {1546-1726}, doi = {10.1038/nn.4216}, author = {Tasic, Bosiljka and Menon, Vilas and Nguyen, Thuc Nghi and Kim, Tae Kyung and Jarsky, Tim and Yao, Zizhen and Levi, Boaz and Gray, Lucas T and Sorensen, Staci A and Dolbeare, Tim and Bertagnolli, Darren and Goldy, Jeff and Shapovalova, Nadiya and Parry, Sheana and Lee, Changkyu and Smith, Kimberly and Bernard, Amy and Madisen, Linda and Sunkin, Susan M and Hawrylycz, Michael and Koch, Christof and Zeng, Hongkui} } @article {48068, title = {All-optical functional synaptic connectivity mapping in acute brain slices using CaMPARI.}, journal = {The Journal of Physiology}, volume = {595}, year = {2016}, month = {2017 Mar 01}, pages = {1465-77}, abstract = {

The calcium-modulated photoactivatable ratiometric integrator CaMPARI (Fosque et\ al., 2015) facilitates the study of neural circuits by permanently marking cells active during user-specified temporal windows. Permanent marking enables measurement of signals from large swathes of tissue and easy correlation of activity with other structural or functional labels. One potential application of CaMPARI is labeling neurons postsynaptic to specific populations targeted for optogenetic stimulation, giving rise to all-optical functional connectivity mapping. Here, we characterized the response of CaMPARI to several common types of neuronal calcium signals in mouse acute cortical brain slices. Our experiments show that CaMPARI is effectively converted by both action potentials and sub-threshold synaptic inputs, and that conversion level is correlated to synaptic strength. Importantly, we found that conversion rate can be tuned: it is linearly related to light intensity. At low photoconversion light levels CaMPARI offers a wide dynamic range due to slower conversion rate; at high light levels conversion is more rapid and more sensitive to activity. Finally, we employed CaMPARI and optogenetics for functional circuit mapping in ex vivo acute brain slices, which preserve in vivo-like connectivity of axon terminals. With a single light source, we stimulated channelrhodopsin-2-expressing long-range posteromedial (POm) thalamic axon terminals in cortex and induced CaMPARI conversion in recipient cortical neurons. We found that POm stimulation triggers robust photoconversion of layer 5 cortical neurons and weaker conversion of layer 2/3 neurons. Thus, CaMPARI enables network-wide, tunable, all-optical functional circuit mapping that captures supra- and sub-threshold depolarization. This article is protected by copyright. All rights reserved.

}, issn = {1469-7793}, doi = {10.1113/JP273116}, author = {Zolnik, Timothy A and Sha, Fern and Johenning, Friedrich and Schreiter, Eric R and Looger, Loren L and Larkum, Matthew E and Sachdev, Robert N S} } @article {47994, title = {AMPK activation prevents and reverses drug-induced mitochondrial and hepatocyte injury by promoting mitochondrial fusion and function.}, journal = {PLoS One}, volume = {11}, year = {2016}, month = {2016 Oct 31}, pages = {e0165638}, abstract = {

Mitochondrial damage is the major factor underlying drug-induced liver disease but whether conditions that thwart mitochondrial injury can prevent or reverse drug-induced liver damage is unclear. A key molecule regulating mitochondria quality control is AMP activated kinase (AMPK). When activated, AMPK causes mitochondria to elongate/fuse and proliferate, with mitochondria now producing more ATP and less reactive oxygen species. Autophagy is also triggered, a process capable of removing damaged/defective mitochondria. To explore whether AMPK activation could potentially prevent or reverse the effects of drug-induced mitochondrial and hepatocellular damage, we added an AMPK activator to collagen sandwich cultures of rat and human hepatocytes exposed to the hepatotoxic drugs, acetaminophen or diclofenac. In the absence of AMPK activation, the drugs caused hepatocytes to lose polarized morphology and have significantly decreased ATP levels and viability. At the subcellular level, mitochondria underwent fragmentation and had decreased membrane potential due to decreased expression of the mitochondrial fusion proteins Mfn1, 2 and/or Opa1. Adding AICAR, a specific AMPK activator, at the time of drug exposure prevented and reversed these effects. The mitochondria became highly fused and ATP production increased, and hepatocytes maintained polarized morphology. In exploring the mechanism responsible for this preventive and reversal effect, we found that AMPK activation prevented drug-mediated decreases in Mfn1, 2 and Opa1. AMPK activation also stimulated autophagy/mitophagy, most significantly in acetaminophen-treated cells. These results suggest that activation of AMPK prevents/reverses drug-induced mitochondrial and hepatocellular damage through regulation of mitochondrial fusion and autophagy, making it a potentially valuable approach for treatment of drug-induced liver injury.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0165638}, author = {Kang, Sun Woo Sophie and Haydar, Ghada and Taniane, Caitlin and Farrell, Geoffrey and Arias, Irwin M and Lippincott-Schwartz, Jennifer and Fu, Dong} } @article {47421, title = {Astrocytic glutamate transport regulates a Drosophila CNS synapse that lacks astrocyte ensheathment.}, journal = {The Journal of Comparative Neurology}, volume = {524}, year = {2016}, month = {2016 Apr 12}, pages = {1979-98}, abstract = {

Anatomical, molecular, and physiological interactions between astrocytes and neuronal synapses regulate information processing in the brain. The fruit fly Drosophila melanogaster has become a valuable experimental system for genetic manipulation of the nervous system and has enormous potential for elucidating mechanisms that mediate neuron-glia interactions. Here, we show the first electrophysiological recordings from Drosophila astrocytes and characterize their spatial and physiological relationship with particular synapses. Astrocyte intrinsic properties were found to be strongly analogous to those of vertebrate astrocytes, including a passive current-voltage relationship, low membrane resistance, high capacitance, and dye-coupling to local astrocytes. Responses to optogenetic stimulation of glutamatergic pre-motor neurons were correlated directly with anatomy using serial electron microscopy reconstructions of homologous identified neurons and surrounding astrocytic processes. Robust bidirectional communication was present: neuronal activation triggered astrocytic glutamate transport via Eaat1, and blocking Eaat1 extended glutamatergic interneuron-evoked inhibitory post-synaptic currents in motor neurons. The neuronal synapses were always located within a micron of an astrocytic process, but none were ensheathed by those processes. Thus, fly astrocytes can modulate fast synaptic transmission via neurotransmitter transport within these anatomical parameters. This article is protected by copyright. All rights reserved.

}, issn = {1096-9861}, doi = {10.1002/cne.24016}, author = {MacNamee, Sarah E and Liu, Kendra E and Gerhard, Stephan and Tran, Cathy T and Fetter, Richard D and Cardona, Albert and Tolbert, Leslie P and Oland, Lynne A} } @article {47730, title = {Atomic resolution structure determination by the cryo-EM method MicroED.}, journal = {Protein Science : a Publication of the Protein Society}, volume = {26}, year = {2016}, month = {2016 Jul 25}, pages = {8-15}, abstract = {

The electron cryo-microscopy (cryoEM) method MicroED has been rapidly developing. In this review we highlight some of the key steps in MicroED from crystal analysis to structure determination. We compare and contrast MicroED and the latest X-ray based diffraction method the X-ray free electron laser (XFEL). Strengths and shortcomings of both MicroED and XFEL are discussed. Finally, all current MicroED structures are tabulated with a view to the future. This article is protected by copyright. All rights reserved.

}, issn = {1469-896X}, doi = {10.1002/pro.2989}, author = {Liu, Shian and Hattne, Johan and Reyes, Francis E and Sanchez-Martinez, Silvia and de la Cruz, M Jason and Shi, D and Gonen, T} } @article {48163, title = {Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos.}, journal = {Development (Cambridge, England)}, volume = {143}, year = {2016}, month = {2016 Feb 01}, pages = {540-6}, abstract = {

Analysis of differential gene expression is crucial for the study of cell fate and behavior during embryonic development. However, automated methods for the sensitive detection and quantification of RNAs at cellular resolution in embryos are lacking. With the advent of single-molecule fluorescence in situ hybridization (smFISH), gene expression can be analyzed at single-molecule resolution. However, the limited availability of protocols for smFISH in embryos and the lack of efficient image analysis pipelines have hampered quantification at the (sub)cellular level in complex samples such as tissues and embryos. Here, we present a protocol for smFISH on zebrafish embryo sections in combination with an image analysis pipeline for automated transcript detection and cell segmentation. We use this strategy to quantify gene expression differences between different cell types and identify differences in subcellular transcript localization between genes. The combination of our smFISH protocol and custom-made, freely available, analysis pipeline will enable researchers to fully exploit the benefits of quantitative transcript analysis at cellular and subcellular resolution in tissues and embryos.

}, keywords = {Animals, Automation, Cell Membrane, Embryo, Nonmammalian, Gene Expression Regulation, Developmental, In Situ Hybridization, Fluorescence, RNA, RNA, Messenger, Subcellular Fractions, Transcription, Genetic, Zebrafish}, issn = {1477-9129}, doi = {10.1242/dev.128918}, author = {Stapel, L Carine and Lombardot, Benoit and Broaddus, Coleman and Kainmueller, Dagmar and Jug, Florian and Myers, Eugene W and Vastenhouw, Nadine L} } @article {47300, title = {Axonal filtering allows reliable output during dendritic plateau-driven complex spiking in CA1 neurons.}, journal = {Neuron}, volume = {89}, year = {2016}, month = {2016 Feb 17}, pages = {770-783}, abstract = {

In CA1 pyramidal neurons, correlated inputs trigger dendritic plateau potentials that drive neuronal plasticity and firing rate modulation. Given the strong electrotonic coupling between soma and axon, the \>25\ mV depolarization associated with the plateau could propagate through the axon to influence action potential initiation, propagation, and neurotransmitter release. We examined this issue in brain slices, awake mice, and a computational model. Despite profoundly inactivating somatic and proximal axon Na(+) channels, plateaus evoked action potentials that recovered to full amplitude in the distal axon (\>150\ μm) and triggered neurotransmitter release similar to regular spiking. This effect was due to strong attenuation of plateau depolarizations by axonal K(+) channels, allowing full axon repolarization and Na(+) channel deinactivation. High-pass filtering of dendritic plateaus by axonal K(+) channels should thus enable accurate transmission of gain-modulated firing rates, allowing neuronal firing to be efficiently read out by downstream regions as a simple rate code.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.12.040}, author = {Apostolides, Pierre F and Milstein, Aaron D and Grienberger, Christine and Bittner, Katie C and Magee, Jeffrey C} } @article {47393, title = {The basal ganglia: from motor commands to the control of vigor.}, journal = {Current Opinion in Neurobiology}, volume = {37}, year = {2016}, month = {2016 Mar 21}, pages = {158-66}, abstract = {

Vertebrates are remarkable for their ability to select and execute goal-directed actions: motor skills critical for thriving in complex, competitive environments. A key aspect of a motor skill is the ability to execute its component movements over a range of speeds, amplitudes and frequencies (vigor). Recent work has indicated that a subcortical circuit, the basal ganglia, is a critical determinant of movement vigor in rodents and primates. We propose that the basal ganglia evolved from a circuit that in lower vertebrates and some mammals is sufficient to directly command simple or stereotyped movements to one that indirectly controls the vigor of goal-directed movements. The implications of a dual role of the basal ganglia in the control of vigor and response to reward are also discussed.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2016.02.005}, author = {Dudman, Joshua T and Krakauer, John W} } @article {47850, title = {Behavioural integration of auditory and antennal stimulation during phonotaxis in the field cricket Gryllus bimaculatus (DeGeer).}, journal = {The Journal of Experimental Biology}, volume = {219}, year = {2016}, month = {2016 Sep 8}, pages = {3575-86}, abstract = {

Animals need to flexibly respond to stimuli from their environment without compromising behavioural consistency. For example, female crickets orienting toward a conspecific male{\textquoteright}s calling song in search of a mating partner need to stay responsive to other signals that provide information about obstacles and predators. Here, we investigate how spontaneously walking crickets and crickets engaging in acoustically guided goal-directed navigation, i.e. phonotaxis, respond to mechanosensory stimuli detected by their long antennae. We monitored walking behaviour of female crickets on a trackball during lateral antennal stimulation, which was achieved by moving a wire mesh transiently into reach of one antenna. During antennal stimulation alone, females reduced their walking speed, oriented toward the object and actively explored it with antennal movements. Additionally, some crickets initially turned away from the approaching object. Females responded in a similar way when the antennal stimulus was presented during ongoing phonotaxis: forward velocity was reduced and phonotactic steering was suppressed while the females turned toward and explored the object. Further, rapid steering bouts to individual chirps, typical for female phonotaxis, no longer occurred.Our data reveals that in this experimental situation antennal stimulation overrides phonotaxis for extended time periods. Phonotaxis in natural environments, which require the integration of multiple sensory cues, may therefore be more variable than phonotaxis measured under ideal laboratory conditions. Combining this new behavioural paradigm with neurophysiological methods will show where the sensory-motor integration of antennal and acoustic stimulation occurs and how this is achieved on a mechanistic level.

}, issn = {1477-9145}, doi = {10.1242/jeb.141606}, author = {Haberkern, Hannah and Hedwig, Berthold} } @article {47975, title = {Bessel beam plane illumination microscope.}, volume = {B2}, number = {US 14/215,912}, year = {2016}, month = {2016 Sep 20}, edition = {G02B27/09, G02B21/06, G02B21/00, G02B21/36}, abstract = {

A microscope has a light source for generating a light beam having a wavelength, λ, and beam-forming optics configured for receiving the light beam and generating a Bessel-like beam that is directed into a sample. The beam-forming optics include an excitation objective having an axis oriented in a first direction. Imaging optics are configured for receiving light from a position within the sample that is illuminated by the Bessel-like beam and for imaging the received light on a detector. The imaging optics include a detection objective having an axis oriented in a second direction that is non-parallel to the first direction. A detector is configured for detecting signal light received by the imaging optics, and an aperture mask is positioned.

}, author = {Betzig, Eric} } @article {47463, title = {Brain derived neurotrophic factor differentially modulates excitability of two classes of hippocampal output neurons.}, journal = {Journal of Neurophysiology}, volume = {116}, year = {2016}, month = {2016 May 4}, pages = {466-71}, abstract = {

Brain-derived neurotrophic factor (BDNF) plays an important role in hippocampus-dependent learning and memory. Canonically, this has been ascribed to an enhancing effect on neuronal excitability and synaptic plasticity in the CA1 region. However, it is the pyramidal neurons in the subiculum that form the primary efferent pathways conveying hippocampal information to other areas of the brain, and yet the effect of BDNF on these neurons has remained unexplored. We present new data that BDNF regulates neuronal excitability and cellular plasticity in a much more complex manner than previously suggested. Subicular pyramidal neurons can be divided into two major classes, which have different electrophysiological and morphological properties, different requirements for the induction of plasticity and different extra-hippocampal projections. We found that BDNF increases excitability in one class of subicular pyramidal neurons, yet decreases excitability of the other class. Further, while endogenous BDNF was necessary for the induction of synaptic plasticity in both cell types, BDNF enhanced intrinsic plasticity in one class of pyramidal neurons, yet suppressed intrinsic plasticity in the other. Taken together, these data suggest a novel role for BDNF signaling, as it appears to dynamically and bidirectionally regulate the output of hippocampal information to different regions of the brain.

}, issn = {1522-1598}, doi = {10.1152/jn.00186.2016}, author = {Graves, Austin R and Moore, Shannon J and Spruston, Nelson and Tryba, Andrew Kieran and Kaczorowski, Catherine C} } @article {47550, title = {Brain heating induced by near infrared lasers during multi-photon microscopy.}, journal = {Journal of Neurophysiology}, volume = {116}, year = {2016}, month = {2016 Jun 8}, pages = {1012-23}, abstract = {

Two-photon imaging and optogenetic stimulation rely on high illumination powers, particularly for state-of-the-art applications that target deeper structures, achieve faster measurements, or probe larger brain areas. However, little information is available on heating and resulting damage induced by high-power illumination in the brain. Here we used thermocouple probes and quantum dot nanothermometers to measure temperature changes induced by two-photon microscopy in the neocortex of awake and anaesthetized mice. We characterized heating as a function of wavelength, exposure time, and distance from the center of illumination. Although total power is highest near the surface of the brain, heating was most severe hundreds of microns below the focal plane, due to heat dissipation through the cranial window. Continuous illumination of a 1mm2 area produced a peak temperature increase of approximately 1.8{\textdegree}C/100mW. Continuous illumination with powers above 250 mW induced lasting damage, detected with immunohistochemistry against Iba1, GFAP, heat shock proteins, and activated Caspase-3. Higher powers were usable in experiments with limited duty ratios, suggesting an approach to mitigate damage in high-power microscopy experiments.

}, issn = {1522-1598}, doi = {10.1152/jn.00275.2016}, author = {Podgorski, Kaspar and Ranganathan, Gayathri Nattar} } @article {47380, title = {Brain-wide mapping of neural activity controlling zebrafish exploratory locomotion.}, journal = {eLife}, year = {2016}, month = {2016 Mar 22}, abstract = {

In the absence of salient sensory cues to guide behavior, animals must still execute sequences of motor actions in order to forage and explore. How such successive motor actions are coordinated to form global locomotion trajectories is unknown. We mapped the structure of larval zebrafish swim trajectories in homogeneous environments and found that trajectories were characterized by alternating sequences of repeated turns to the left and to the right. Using whole-brain light-sheet imaging, we identified activity relating to the behavior in specific neural populations that we termed the anterior rhombencephalic turning region (ARTR). ARTR perturbations biased swim direction and reduced the dependence of turn direction on turn history, indicating that the ARTR is part of a network generating the temporal correlations in turn direction. We also find suggestive evidence for ARTR mutual inhibition and ARTR projections to premotor neurons. Finally, simulations suggest the observed turn sequences may underlie efficient exploration of local environments.

}, doi = {10.7554/eLife.12741}, url = {http://dx.doi.org/10.7554/eLife.12741}, author = {Dunn, Timothy W. and Mu, Yu and Narayan, Sujatha and Randlett, Owen and Naumann, Eva A. and Yang, Chao-Tsung and Schier, Alexander F. and Freeman, Jeremy and Engert, Florian and Ahrens, Misha B.} } @article {47527, title = {A bright cyan-excitable orange fluorescent protein facilitates dual-emission microscopy and enhances bioluminescence imaging in vivo.}, journal = {Nature Biotechnology}, volume = {34}, year = {2016}, month = {2016 May 30}, pages = {760-7}, abstract = {

Orange-red fluorescent proteins (FPs) are widely used in biomedical research for multiplexed epifluorescence microscopy with GFP-based probes, but their different excitation requirements make multiplexing with new advanced microscopy methods difficult. Separately, orange-red FPs are useful for deep-tissue imaging in mammals owing to the relative tissue transmissibility of orange-red light, but their dependence on illumination limits their sensitivity as reporters in deep tissues. Here we describe CyOFP1, a bright, engineered, orange-red FP that is excitable by cyan light. We show that CyOFP1 enables single-excitation multiplexed imaging with GFP-based probes in single-photon and two-photon microscopy, including time-lapse imaging in light-sheet systems. CyOFP1 also serves as an efficient acceptor for resonance energy transfer from the highly catalytic blue-emitting luciferase NanoLuc. An optimized fusion of CyOFP1 and NanoLuc, called Antares, functions as a highly sensitive bioluminescent reporter in vivo, producing substantially brighter signals from deep tissues than firefly luciferase and other bioluminescent proteins.

}, issn = {1546-1696}, doi = {10.1038/nbt.3550}, author = {Chu, Jun and Oh, Younghee and Sens, Alex and Ataie, Niloufar and Dana, Hod and Macklin, John J and Laviv, Tal and Welf, Erik S and Dean, Kevin M and Zhang, Feijie and Kim, Benjamin B and Tang, Clement Tran and Hu, Michelle and Baird, Michelle A and Davidson, Michael W and Kay, Mark A and Fiolka, Reto and Yasuda, Ryohei and Kim, Douglas S and Ng, Ho-Leung and Lin, Michael Z} } @article {47729, title = {Bright photoactivatable fluorophores for single-molecule imaging.}, journal = {Nature Methods}, volume = {13}, year = {2016}, month = {2016 Oct 24}, pages = {985-8}, abstract = {

Small molecule fluorophores are important tools for advanced imaging experiments. The development of self-labeling protein tags such as the HaloTag and SNAP-tag has expanded the utility of chemical dyes in live-cell microscopy. We recently described a general method for improving the brightness and photostability of small, cell-permeable fluorophores, resulting in the novel azetidine-containing "Janelia Fluor" (JF) dyes. Here, we refine and extend the utility of the JF dyes by synthesizing photoactivatable derivatives that are compatible with live cell labeling strategies. These compounds retain the superior brightness of the JF dyes once activated, but their facile photoactivation also enables improved single-particle tracking and localization microscopy experiments.

}, doi = {10.1038/nmeth.4034}, author = {Lavis, Luke D and Grimm, Jonathan B and English, Brian P and Choi, Heejin and Muthusamy, Anand K and Mehl, Brian P and Dong, Peng and Brown, Timothy A and Lippincott-Schwartz, Jennifer and Liu, Zhe and Lionnet, Timoth{\'e}e} } @article {47299, title = {Calcium imaging of neural circuits with extended depth-of-field light-sheet microscopy.}, journal = {Optics Letters}, volume = {41}, year = {2016}, month = {2016 Feb 17}, pages = {855-8}, abstract = {

Increasing the volumetric imaging speed of light-sheet microscopy will improve its ability to detect fast changes in neural activity. Here, a system is introduced for brain-wide imaging of neural activity in the larval zebrafish by coupling structured illumination with cubic phase extended depth-of-field (EDoF) pupil encoding. This microscope enables faster light-sheet imaging and facilitates arbitrary plane scanning{\textemdash}removing constraints on acquisition speed, alignment tolerances, and physical motion near the sample. The usefulness of this method is demonstrated by performing multi-plane calcium imaging in the fish brain with a\ 416{\texttimes}832{\texttimes}160 μm\ field of view at 33\ Hz. The optomotor response behavior of the zebrafish is monitored at high speeds, and time-locked correlations of neuronal activity are resolved across its brain.

}, doi = {10.1364/OL.41.000855}, author = {Quirin, Sean and Vladimirov, Nikita and Yang, Chao-Tsung and Peterka, Darcy S and Yuste, Rafael and Ahrens, Misha B} } @article {47849, title = {Cell class-lineage analysis reveals sexually dimorphic lineage compositions in the Drosophila brain.}, journal = {Current Biology : CB}, volume = {26}, year = {2016}, month = {2016 Sep 08}, pages = {2583-93}, abstract = {

The morphology and physiology of neurons are directed by developmental decisions made within their lines of descent from single stem cells. Distinct stem cells may produce neurons having shared properties that define their cell class, such as the type of secreted neurotransmitter. The relationship between cell class and lineage is complex. Here we developed the transgenic cell class-lineage intersection (CLIn) system to assign cells of a particular class to specific lineages within the Drosophila brain. CLIn also enables birth-order analysis and genetic manipulation of particular cell classes arising from particular lineages. We demonstrated the power of CLIn in the context of the eight central brain type II lineages, which produce highly diverse progeny through intermediate neural progenitors. We mapped 18 dopaminergic neurons from three distinct clusters to six type\ II lineages that show lineage-characteristic neurite trajectories. In addition, morphologically distinct dopaminergic neurons are produced within a given lineage, and they arise in an invariant sequence. We also identified type II lineages that produce doublesex- and fruitless-expressing neurons and examined whether female-specific apoptosis in these lineages accounts for the lower number of these neurons in the female brain. Blocking apoptosis in these lineages resulted in more cells in both sexes with males still carrying more cells than females. This argues that sex-specific stem cell fate together with differential progeny apoptosis contribute to the final sexual dimorphism.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2016.07.086}, author = {Ren, Qingzhong and Awasaki, Takeshi and Huang, Yu-Fen and Liu, Zhiyong and Lee, Tzumin} } @article {47968, title = {Central brain circuitry for color-vision-modulated behaviors.}, journal = {Current Biology : CB}, volume = {26}, year = {2016}, month = {2016 Oct 24}, pages = {R981-8}, abstract = {

Color is famous for not existing in the external world: our brains create the perception of color from the spatial and temporal patterns of the wavelength and intensity of light. For an intangible quality, we have detailed knowledge of its origins and consequences. Much is known about the organization and evolution of the first phases of color processing, the filtering of light in the eye and processing in the retina, and about the final phases, the roles of color in behavior and natural selection. To understand how color processing in the central brain has evolved, we need well-defined pathways or circuitry where we can gauge how color contributes to the computations involved in specific behaviors. Examples of such pathways or circuitry that are dedicated to processing color cues are rare, despite the separation of color and luminance pathways early in the visual system of many species, and despite the traditional definition of color as being independent of luminance. This minireview presents examples in which color vision contributes to behaviors dominated by other visual modalities, examples that are not part of the canon of color vision circuitry. The pathways and circuitry process a range of chromatic properties of objects and their illumination, and are taken from a variety of species. By considering how color processing complements luminance processing, rather than being independent of it, we gain an additional way to account for the diversity of color coding in the central brain, its consequences for specific behaviors and ultimately the evolution of color vision.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2016.07.071}, author = {Longden, Kit D} } @article {48297, title = {The ciliary marginal zone of the zebrafish retina: clonal and time-lapse analysis of a continuously growing tissue.}, journal = {Development (Cambridge, England)}, volume = {143}, year = {2016}, month = {2016 Apr 01}, pages = {1099-107}, abstract = {

Clonal analysis is helping us understand the dynamics of cell replacement in homeostatic adult tissues (Simons and Clevers, 2011). Such an analysis, however, has not yet been achieved for continuously growing adult tissues, but is essential if we wish to understand the architecture of adult organs. The retinas of lower vertebrates grow throughout life from retinal stem cells (RSCs) and retinal progenitor cells (RPCs) at the rim of the retina, called the ciliary marginal zone (CMZ). Here, we show that RSCs reside in a niche at the extreme periphery of the CMZ and divide asymmetrically along a radial (peripheral to central) axis, leaving one daughter in the peripheral RSC niche and the other more central where it becomes an RPC. We also show that RPCs of the CMZ have clonal sizes and compositions that are statistically similar to progenitor cells of the embryonic retina and fit the same stochastic model of proliferation. These results link embryonic and postembryonic cell behaviour, and help to explain the constancy of tissue architecture that has been generated over a lifetime.

}, keywords = {Animals, Animals, Genetically Modified, Cell Differentiation, Cell Division, Cell Proliferation, Gene Expression Regulation, Developmental, Retina, Stem Cells, Zebrafish}, issn = {1477-9129}, doi = {10.1242/dev.133314}, author = {Wan, Yinan and Almeida, Alexandra D and Rulands, Steffen and Chalour, Naima and Muresan, Leila and Wu, Yunmin and Simons, Benjamin D and He, Jie and Harris, William A} } @article {47324, title = {A circuit mechanism for the propagation of waves of muscle contraction in Drosophila.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Feb 18}, abstract = {

Animals move by adaptively coordinating the sequential activation of muscles. The circuit mechanisms underlying coordinated locomotion are poorly understood. Here, we report on a novel circuit for propagation of waves of muscle contraction, using the peristaltic locomotion of Drosophila larvae as a model system. We found an intersegmental chain of synaptically connected neurons, alternating excitatory and inhibitory, necessary for wave propagation and active in phase with the wave. The excitatory neurons (A27h) are premotor and necessary only for forward locomotion, and are modulated by stretch receptors and descending inputs. The inhibitory neurons (GDL) are necessary for both forward and backward locomotion, suggestive of different yet coupled central pattern generators, and its inhibition is necessary for wave propagation. The circuit structure and functional imaging indicated that the commands to contract one segment promote the relaxation of the next segment, revealing a mechanism for wave propagation in peristaltic locomotion.

}, issn = {2050-084X}, doi = {10.7554/eLife.13253}, author = {Fushiki, Akira and Zwart, Maarten F and Kohsaka, Hiroshi and Fetter, Richard D and Cardona, Albert and Nose, Akinao} } @article {65008, title = {A circuit motif in the zebrafish hindbrain for a two alternative behavioral choice to turn left or right.}, journal = {Elife}, volume = {5}, year = {2016}, month = {2016 08 09}, abstract = {

Animals collect sensory information from the world and make adaptive choices about how to respond to it. Here, we reveal a network motif in the brain for one of the most fundamental behavioral choices made by bilaterally symmetric animals: whether to respond to a sensory stimulus by moving to the left or to the right. We define network connectivity in the hindbrain important for the lateralized escape behavior of zebrafish and then test the role of neurons by using laser ablations and behavioral studies. Key inhibitory neurons in the circuit lie in a column of morphologically similar cells that is one of a series of such columns that form a developmental and functional ground plan for building hindbrain networks. Repetition within the columns of the network motif we defined may therefore lie at the foundation of other lateralized behavioral choices.

}, keywords = {Action Potentials, Animals, Animals, Genetically Modified, Behavior, Animal, Choice Behavior, Laser Therapy, Locomotion, Neural Pathways, Neurons, Patch-Clamp Techniques, Perception, Rhombencephalon, Zebrafish}, issn = {2050-084X}, doi = {10.7554/eLife.16808}, author = {Koyama, Minoru and Minale, Francesca and Shum, Jennifer and Nishimura, Nozomi and Schaffer, Chris B and Fetcho, Joseph R} } @article {47422, title = {The collection of MicroED data for macromolecular crystallography.}, journal = {Nature Protocols}, volume = {11}, year = {2016}, month = {2016 May}, pages = {895-904}, abstract = {

The formation of large, well-ordered crystals for crystallographic experiments remains a crucial bottleneck to the structural understanding of many important biological systems. To help alleviate this problem in crystallography, we have developed the MicroED method for the collection of electron diffraction data from 3D microcrystals and nanocrystals of radiation-sensitive biological material. In this approach, liquid solutions containing protein microcrystals are deposited on carbon-coated electron microscopy grids and are vitrified by plunging them into liquid ethane. MicroED data are collected for each selected crystal using cryo-electron microscopy, in which the crystal is diffracted using very few electrons as the stage is continuously rotated. This protocol gives advice on how to identify microcrystals by light microscopy or by negative-stain electron microscopy in samples obtained from standard protein crystallization experiments. The protocol also includes information about custom-designed equipment for controlling crystal rotation and software for recording experimental parameters in diffraction image metadata. Identifying microcrystals, preparing samples and setting up the microscope for diffraction data collection take approximately half an hour for each step. Screening microcrystals for quality diffraction takes roughly an hour, and the collection of a single data set is \~{}10 min in duration. Complete data sets and resulting high-resolution structures can be obtained from a single crystal or by merging data from multiple crystals.

}, issn = {1750-2799}, doi = {10.1038/nprot.2016.046}, author = {Shi, Dan and Nannenga, Brent L and de la Cruz, M Jason and Liu, Jinyang and Sawtelle, Steven and Calero, Guillermo and Reyes, Francis E and Hattne, Johan and Gonen, Tamir} } @article {65034, title = {Comment on "A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme".}, journal = {Science}, volume = {353}, year = {2016}, month = {2016 Jul 22}, pages = {358}, abstract = {

Watanabe et al (Reports, 12 April 2013, p. 195) study the yeast SWR1/SWR-C complex responsible for depositing the histone variant H2A.Z by replacing nucleosomal H2A with H2A.Z. They report that reversal of H2A.Z replacement is mediated by SWR1 and related INO80 on an H2A.Z nucleosome carrying H3K56Q. Using multiple assays and reaction conditions, we find no evidence of such reversal of H2A.Z exchange.

}, keywords = {Adenosine Triphosphatases, Chromatin Assembly and Disassembly, Histones, Multienzyme Complexes, Nucleosomes, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins}, issn = {1095-9203}, doi = {10.1126/science.aad5921}, author = {Wang, Feng and Ranjan, Anand and Wei, Debbie and Wu, Carl} } @article {47932, title = {Comparative approaches to escape.}, journal = {Current Opinion in Neurobiology}, volume = {41}, year = {2016}, month = {2016 Oct 3}, pages = {167-173}, abstract = {

Neural circuits mediating visually evoked escape behaviors are promising systems in which to dissect the neural basis of behavior. Behavioral responses to predator-like looming stimuli, and their underlying neural computations, are remarkably similar across species. Recently, genetic tools have been applied in this classical paradigm, revealing novel non-cortical pathways that connect loom processing to defensive behaviors in mammals and demonstrating that loom encoding models from locusts also fit vertebrate neural responses. In both invertebrates and vertebrates, relative spike-timing in descending pathways is a mechanism for escape behavior choice. Current findings suggest that experimentally tractable systems, such as Drosophila, may be applicable models for sensorimotor processing and persistent states in higher organisms.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2016.09.012}, author = {Peek, Martin Y and Card, Gwyneth M} } @article {47935, title = {Competitive disinhibition mediates behavioral choice and sequences in Drosophila.}, journal = {Cell}, volume = {167}, year = {2016}, month = {2016 Oct 5}, pages = {858-70}, abstract = {

Even a simple sensory stimulus can elicit distinct innate behaviors and sequences. During sensorimotor decisions, competitive interactions among neurons that promote distinct behaviors must ensure the selection and maintenance of one behavior, while suppressing others. The circuit implementation of these competitive interactions is still an open question. By combining comprehensive electron microscopy reconstruction of inhibitory interneuron networks, modeling, electrophysiology, and behavioral studies, we determined the circuit mechanisms that\ contribute to the Drosophila larval sensorimotor decision to startle, explore, or perform a sequence of the two in response to a mechanosensory stimulus. Together, these studies reveal that, early in sensory processing, (1) reciprocally connected feedforward inhibitory interneurons implement behavioral choice, (2) local feedback disinhibition provides positive feedback that consolidates and maintains the chosen behavior, and (3) lateral disinhibition promotes sequence transitions. The combination of these interconnected circuit motifs can implement both behavior selection and the serial organization of behaviors into a sequence.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2016.09.009}, author = {Jovanic, Tihana and Schneider-Mizell, Casey M and Shao, Mei and Masson, Jean-Baptiste and Denisov, Gennady and Fetter, Richard D and Mensh, Brett D and Truman, James W and Cardona, Albert and Zlatic, Marta} } @article {47559, title = {Complicating connectomes: Electrical coupling creates parallel pathways and degenerate circuit mechanisms.}, journal = {Developmental Neurobiology}, year = {2016}, month = {2016 Jun 17}, abstract = {

Electrical coupling in circuits can produce non-intuitive circuit dynamics, as seen in both experimental work from the crustacean stomatogastric ganglion and in computational models inspired by the connectivity in this preparation. Ambiguities in interpreting the results of electrophysiological recordings can arise if sets of pre- or postsynaptic neurons are electrically coupled, or if the electrical coupling exhibits some specificity (e.g. rectifying, or voltage-dependent). Even in small circuits, electrical coupling can produce parallel pathways that can allow information to travel by monosynaptic and/or polysynaptic pathways. Consequently, similar changes in circuit dynamics can arise from entirely different underlying mechanisms. When neurons are coupled both chemically and electrically, modifying the relative strengths of the two interactions provides a mechanism for flexibility in circuit outputs. This, together with neuromodulation of gap junctions and coupled neurons is important both in developing and adult circuits. This article is protected by copyright. All rights reserved.

}, issn = {1932-846X}, doi = {10.1002/dneu.22410}, author = {Marder, Eve and Gutierrez, Gabrielle and Nusbaum, Michael P} } @article {47563, title = {Complicating connectomes: Electrical coupling creates parallel pathways and degenerate circuit mechanisms.}, journal = {Developmental Neurobiology}, year = {2016}, month = {2016 Jun 17}, abstract = {

Electrical coupling in circuits can produce non-intuitive circuit dynamics, as seen in both experimental work from the crustacean stomatogastric ganglion and in computational models inspired by the connectivity in this preparation. Ambiguities in interpreting the results of electrophysiological recordings can arise if sets of pre- or postsynaptic neurons are electrically coupled, or if the electrical coupling exhibits some specificity (e.g. rectifying, or voltage-dependent). Even in small circuits, electrical coupling can produce parallel pathways that can allow information to travel by monosynaptic and/or polysynaptic pathways. Consequently, similar changes in circuit dynamics can arise from entirely different underlying mechanisms. When neurons are coupled both chemically and electrically, modifying the relative strengths of the two interactions provides a mechanism for flexibility in circuit outputs. This, together with neuromodulation of gap junctions and coupled neurons is important both in developing and adult circuits. This article is protected by copyright. All rights reserved.

}, issn = {1932-846X}, doi = {10.1002/dneu.22410}, author = {Marder, Eve and Gutierrez, Gabrielle and Nusbaum, Michael P} } @article {47433, title = {Computational Analysis of Behavior.}, journal = {Annual Review of Neuroscience}, volume = {39}, year = {2016}, month = {2016 Apr 18}, pages = {217-36}, abstract = {

In this review, we discuss the emerging field of computational behavioral analysis-the use of modern methods from computer science and engineering to quantitatively measure animal behavior. We discuss aspects of experiment design important to both obtaining biologically relevant behavioral data and enabling the use of machine vision and learning techniques for automation. These two goals are often in conflict. Restraining or restricting the environment of the animal can simplify automatic behavior quantification, but it can also degrade the quality or alter important aspects of behavior. To enable biologists to design experiments to obtain better behavioral measurements, and computer scientists to pinpoint fruitful directions for algorithm improvement, we review known effects of artificial manipulation of the animal on behavior. We also review machine vision and learning techniques for tracking, feature extraction, automated behavior classification, and automated behavior discovery, the assumptions they make, and the types of data they work best with. Expected final online publication date for the Annual Review of Neuroscience Volume 39 is July 08, 2016. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.

}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-070815-013845}, author = {Egnor, S E Roian and Branson, Kristin} } @article {47600, title = {Connectome studies on Drosophila: a short perspective on a tiny brain.}, journal = {Journal of Neurogenetics}, volume = {30}, year = {2016}, month = {2016 Jun}, pages = {62-8}, abstract = {

The brain is a network of neurons, one that generates behaviour, and knowing the former is crucial to understanding the latter. Identifying the exact network of synaptic connections, or connectome, of the fly{\textquoteright}s central nervous system is now a major objective in Drosophila neurobiology, one that has been initiated in several laboratories, especially the Janelia Research Campus of the Howard Hughes Medical Institute. Progress is most advanced in the optic neuropiles of the visual system. The effort to derive a connectome from these and other neuropile regions is proceeding by various methods of electron microscopy, especially focused-ion beam milling scanning electron microscopy, and relies upon - but is to be carefully distinguished from - published light microscopic methods that reveal the projections of genetically labelled cell types. The latter reveal those neurons that come into close proximity and are therefore candidate synaptic partners. Synaptic partnerships are not in fact reliably revealed by such candidate pairs, anatomical connections often revealing unexpected pathways. Synaptic partnerships identified from ultrastructural features provide a strong heuristic basis to interpret not only functional interactions between identified neurons, but also a powerful means to predict such interactions, and suggest functional pathways not readily predicted from existing experimental evidence. The analysis of circuit function may proceed cell by cell, by examining the behavioural outcome of either interrupting or restoring function to any one element in an anatomically defined circuit, but can be foiled by degeneracy in pathway elements. Circuit information can also be used to identify and analyse circuit motifs, and their role in higher-order network properties. These attempts in Drosophila anticipate parallel attempts in other systems, notably the inner plexiform layer of the vertebrate retina, and augment the one complete connectome already available to us, that available for 30 years in the nematode Caenorhabditis elegans.

}, issn = {1563-5260}, doi = {10.3109/01677063.2016.1166224}, author = {Meinertzhagen, Ian A} } @article {47259, title = {The contribution of ultrasonic vocalizations to mouse courtship.}, journal = {Current Opinion in Neurobiology}, volume = {38}, year = {2016}, month = {2016 Jan 11}, pages = {1-5}, abstract = {

Vocalizations transmit information to social partners, and mice use these signals to exchange information during courtship. Ultrasonic vocalizations from adult males are tightly associated with their interactions with females, and vary as a function of male quality. Work in the last decade has established that the spectrotemporal features of male vocalizations are not learned, but that female attention toward specific vocal features is modified by social experience. Additionally, progress has been made on elucidating how mouse vocalizations are encoded in the auditory system, and on the olfactory circuits that trigger their production. Together these findings provide us with important insights into how vocal communication can contribute to social interactions.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2015.12.009}, author = {Egnor, Se Roian and Seagraves, Kelly M} } @conference {48179, title = {Convexity shape constraints for image segmentation.}, booktitle = {IEEE Conference on Computer Vision and Pattern Recognition (CVPR)}, year = {2016}, month = {2016 Jun 27}, publisher = {IEEE}, organization = {IEEE}, address = {Las Vegas, NV}, abstract = {

Segmenting an image into multiple components is a central task in computer vision. In many practical scenarios, prior knowledge about plausible components is available. Incorporating such prior knowledge into models and algorithms for image segmentation is highly desirable, yet can be non-trivial. In this work, we introduce a new approach that allows, for the first time, to constrain some or all components of a segmentation to have convex shapes. Specifically, we extend the Minimum Cost Multicut Problem by a class of constraints that enforce convexity. To solve instances of this NP-hard integer linear program to optimality, we separate the proposed constraints in the branch-and-cut loop of a state-of-the-art ILP solver. Results on photographs and micrographs demonstrate the effectiveness of the approach as well as its advantages over the state-of-the-art heuristic.

}, doi = {10.1109/CVPR.2016.50}, author = {Royer, Lo{\"\i}c A and Richmond, David L and Rother, Carsten and Andres, Bjoern and Kainmueller, Dagmar} } @article {47506, title = {Cryo-EM reveals the steric zipper structure of a light chain-derived amyloid fibril.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, year = {2016}, month = {2016 May 16}, pages = {6200-5}, abstract = {

Amyloid fibrils are proteinaceous aggregates associated with diseases in humans and animals. The fibrils are defined by intermolecular interactions between the fibril-forming polypeptide chains, but it has so far remained difficult to reveal the assembly of the peptide subunits in a full-scale fibril. Using electron cryomicroscopy (cryo-EM), we present a reconstruction of a fibril formed from the pathogenic core of an amyloidogenic immunoglobulin (Ig) light chain. The fibril density shows a lattice-like assembly of face-to-face packed peptide dimers that corresponds to the structure of steric zippers in peptide crystals. Interpretation of the density map with a molecular model enabled us to identify the intermolecular interactions between the peptides and rationalize the hierarchical structure of the fibril based on simple chemical principles.

}, issn = {1091-6490}, doi = {10.1073/pnas.1522282113}, author = {Schmidt, Andreas and Annamalai, Karthikeyan and Schmidt, Matthias and Grigorieff, Nikolaus and F{\"a}ndrich, Marcus} } @article {47353, title = {Data publication with the structural biology data grid supports live analysis.}, journal = {Nature Communications}, volume = {7}, year = {2016}, month = {2016 Mar 07}, pages = {10882}, abstract = {

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.

}, issn = {2041-1723}, doi = {10.1038/ncomms10882}, author = {Meyer, Peter A and Socias, Stephanie and Key, Jason and Ransey, Elizabeth and Tjon, Emily C and Buschiazzo, Alejandro and Lei, Ming and Botka, Chris and Withrow, James and Neau, David and Rajashankar, Kanagalaghatta and Anderson, Karen S and Baxter, Richard H and Blacklow, Stephen C and Boggon, Titus J and Bonvin, Alexandre M J J and Borek, Dominika and Brett, Tom J and Caflisch, Amedeo and Chang, Chung-I and Chazin, Walter J and Corbett, Kevin D and Cosgrove, Michael S and Crosson, Sean and Dhe-Paganon, Sirano and Di Cera, Enrico and Drennan, Catherine L and Eck, Michael J and Eichman, Brandt F and Fan, Qing R and Ferr{\'e}-D{\textquoteright}Amar{\'e}, Adrian R and Christopher Fromme, J and Garcia, K Christopher and Gaudet, Rachelle and Gong, Peng and Harrison, Stephen C and Heldwein, Ekaterina E and Jia, Zongchao and Keenan, Robert J and Kruse, Andrew C and Kvansakul, Marc and McLellan, Jason S and Modis, Yorgo and Nam, Yunsun and Otwinowski, Zbyszek and Pai, Emil F and Pereira, Pedro Jos{\'e} Barbosa and Petosa, Carlo and Raman, C S and Rapoport, Tom A and Roll-Mecak, Antonina and Rosen, Michael K and Rudenko, Gabby and Schlessinger, Joseph and Schwartz, Thomas U and Shamoo, Yousif and Sondermann, Holger and Tao, Yizhi J and Tolia, Niraj H and Tsodikov, Oleg V and Westover, Kenneth D and Wu, Hao and Foster, Ian and Fraser, James S and Maia, Filipe R N C and Gonen, Tamir and Kirchhausen, Tom and Diederichs, Kay and Crosas, Merc{\`e} and Sliz, Piotr} } @article {68443, title = {A Defensive Kicking Behavior in Response to Mechanical Stimuli Mediated by Drosophila Wing Margin Bristles.}, journal = {J Neurosci}, volume = {36}, year = {2016}, month = {11/2016}, pages = {11275-11282}, abstract = {

Mechanosensation, one of the fastest sensory modalities, mediates diverse behaviors including those pertinent for survival. It is important to understand how mechanical stimuli trigger defensive behaviors. Here, we report that Drosophila melanogaster adult flies exhibit a kicking response against invading parasitic mites over their wing margin with ultrafast speed and high spatial precision. Mechanical stimuli that mimic the mites{\textquoteright} movement evoke a similar kicking behavior. Further, we identified a TRPV channel, Nanchung, and a specific Nanchung-expressing neuron under each recurved bristle that forms an array along the wing margin as being essential sensory components for this behavior. Our electrophysiological recordings demonstrated that the mechanosensitivity of recurved bristles requires Nanchung and Nanchung-expressing neurons. Together, our results reveal a novel neural mechanism for innate defensive behavior through mechanosensation.

SIGNIFICANCE STATEMENT: We discovered a previously unknown function for recurved bristles on the Drosophila melanogaster wing. We found that when a mite (a parasitic pest for Drosophila) touches the wing margin, the fly initiates a swift and accurate kick to remove the mite. The fly head is dispensable for this behavior. Furthermore, we found that a TRPV channel, Nanchung, and a specific Nanchung-expressing neuron under each recurved bristle are essential for its mechanosensitivity and the kicking behavior. In addition, touching different regions of the wing margin elicits kicking directed precisely at the stimulated region. Our experiments suggest that recurved bristles allow the fly to sense the presence of objects by touch to initiate a defensive behavior (perhaps analogous to touch-evoked scratching; Akiyama et al., 2012).

}, keywords = {Animals, Avoidance Learning, Defense Mechanisms, Drosophila, Drosophila Proteins, Extremities, Mechanoreceptors, Mechanotransduction, Cellular, Physical Stimulation, Reflex, Sense Organs, Sensory Receptor Cells, Touch, Transient Receptor Potential Channels, Wings, Animal}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.1416-16.2016}, author = {Li, Jiefu and Zhang, Wei and Guo, Zhenhao and Wu, Sophia and Jan, Lily Yeh and Jan, Yuh-Nung} } @article {47508, title = {Design and synthesis of a calcium-sensitive photocage.}, journal = {Angewandte Chemie (International ed. in English)}, year = {2016}, month = {2016 May 24}, abstract = {

Photolabile protecting groups (or "photocages") enable precise spatiotemporal control of chemical functionality and facilitate advanced biological experiments. Extant photocages exhibit a simple input-output relationship, however, where application of light elicits a photochemical reaction irrespective of the environment. Herein, we refine and extend the concept of photolabile groups, synthesizing the first Ca(2+) -sensitive photocage. This system functions as a chemical coincidence detector, releasing small molecules only in the presence of both light and elevated [Ca(2+) ]. Caging a fluorophore with this ion-sensitive moiety yields an "ion integrator" that permanently marks cells undergoing high Ca(2+) flux during an illumination-defined time period. Our general design concept demonstrates a new class of light-sensitive material for cellular imaging, sensing, and targeted molecular delivery.

}, issn = {1521-3773}, doi = {10.1002/anie.201602941}, author = {Heckman, Laurel M and Grimm, Jonathan B and Schreiter, Eric R and Kim, Charles and Verdecia, Mark A and Shields, Brenda C and Lavis, Luke D} } @article {47562, title = {Design of a hyperstable 60-subunit protein icosahedron.}, journal = {Nature}, year = {2016}, month = {2016 Jun 15}, abstract = {

The icosahedron is the largest of the Platonic solids, and icosahedral protein structures are widely used in biological systems for packaging and transport. There has been considerable interest in repurposing such structures for applications ranging from targeted delivery to multivalent immunogen presentation. The ability to design proteins that self-assemble into precisely specified, highly ordered icosahedral structures would open the door to a new generation of protein containers with properties custom-tailored to specific applications. Here we describe the computational design of a 25-nanometre icosahedral nanocage that self-assembles from trimeric protein building blocks. The designed protein was produced in Escherichia coli, and found by electron microscopy to assemble into a homogenous population of icosahedral particles nearly identical to the design model. The particles are stable in 6.7 molar guanidine hydrochloride at up to 80 degrees Celsius, and undergo extremely abrupt, but reversible, disassembly between 2 molar and 2.25 molar guanidinium thiocyanate. The icosahedron is robust to genetic fusions: one or two copies of green fluorescent protein (GFP) can be fused to each of the 60 subunits to create highly fluorescent {\textquoteright}standard candles{\textquoteright} for use in light microscopy, and a designed protein pentamer can be placed in the centre of each of the 20 pentameric faces to modulate the size of the entrance/exit channels of the cage. Such robust and customizable nanocages should have considerable utility in targeted drug delivery, vaccine design and synthetic biology.

}, issn = {1476-4687}, doi = {10.1038/nature18010}, author = {Hsia, Yang and Bale, Jacob B and Gonen, Shane and Shi, Dan and Sheffler, William and Fong, Kimberly K and Nattermann, Una and Xu, Chunfu and Huang, Po-Ssu and Ravichandran, Rashmi and Yi, Sue and Davis, Trisha N and Gonen, Tamir and King, Neil P and Baker, David} } @article {47934, title = {A designer AAV variant permits efficient retrograde access to projection neurons.}, journal = {Neuron}, volume = {92}, year = {2016}, month = {2016 Oct 19}, pages = {372-82}, abstract = {

Efficient retrograde access to projection neurons for the delivery of sensors and effectors constitutes an important and enabling capability for neural circuit dissection. Such an approach would also be useful for gene therapy, including the treatment of neurodegenerative disorders characterized by pathological spread through functionally connected and highly distributed networks. Viral vectors, in particular, are powerful gene delivery vehicles for the nervous system, but all available tools suffer from inefficient retrograde transport or limited clinical potential. To address this need, we applied in\ vivo directed evolution to engineer potent retrograde functionality into the capsid of adeno-associated virus (AAV), a vector that has shown promise in neuroscience research and the clinic. A newly evolved variant, rAAV2-retro, permits robust retrograde access to projection neurons with efficiency comparable to classical synthetic retrograde tracers and enables sufficient sensor/effector expression for functional circuit interrogation and in\ vivo genome editing in targeted neuronal populations. VIDEO ABSTRACT.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2016.09.021}, author = {Tervo, D Gowanlock R and Hwang, Bum-Yeol and Viswanathan, Sarada and Gaj, Thomas and Lavzin, Maria and Ritola, Kimberly D and Lindo, Sarah and Michael, Susan and Kuleshova, Elena and Ojala, David and Huang, Cheng-Chiu and Gerfen, Charles R and Schiller, Jackie and Dudman, Joshua T and Hantman, Adam W and Looger, Loren L and Schaffer, David V and Karpova, Alla Y} } @article {48206, title = {Developmentally programmed germ cell remodelling by endodermal cell cannibalism.}, journal = {Nature Cell Biology}, volume = {18}, year = {2016}, month = {2016 Dec}, pages = {1302-10}, abstract = {

Primordial germ cells (PGCs) in many species associate intimately with endodermal cells, but the significance of such interactions is largely unexplored. Here, we show that Caenorhabditis elegans PGCs form lobes that are removed and digested by endodermal cells, dramatically altering PGC size and mitochondrial content. We demonstrate that endodermal cells do not scavenge lobes PGCs shed, but rather, actively remove lobes from the cell body. CED-10 (Rac)-induced actin, DYN-1 (dynamin) and LST-4 (SNX9) transiently surround lobe necks and are required within endodermal cells for lobe scission, suggesting that scission occurs through a mechanism resembling vesicle endocytosis. These findings reveal an unexpected role for endoderm in altering the contents of embryonic PGCs, and define a form of developmentally programmed cell remodelling involving intercellular cannibalism. Active roles for engulfing cells have been proposed in several neuronal remodelling events, suggesting that intercellular cannibalism may be a more widespread method used to shape cells than previously thought.

}, issn = {1476-4679}, doi = {10.1038/ncb3439}, author = {Abdu, Yusuff and Maniscalco, Chelsea and Heddleston, John M and Chew, Teng-Leong and Nance, Jeremy} } @article {47397, title = {The Dfam database of repetitive DNA families.}, journal = {Nucleic Acids Research}, volume = {44}, year = {2016}, month = {2016 Jan 4}, pages = {D81-9}, abstract = {

Repetitive DNA, especially that due to transposable elements (TEs), makes up a large fraction of many genomes. Dfam is an open access database of families of repetitive DNA elements, in which each family is represented by a multiple sequence alignment and a profile hidden Markov model (HMM). The initial release of Dfam, featured in the 2013 NAR Database Issue, contained 1143 families of repetitive elements found in humans, and was used to produce more than 100 Mb of additional annotation of TE-derived regions in the human genome, with improved speed. Here, we describe recent advances, most notably expansion to 4150 total families including a comprehensive set of known repeat families from four new organisms (mouse, zebrafish, fly and nematode). We describe improvements to coverage, and to our methods for identifying and reducing false annotation. We also describe updates to the website interface. The Dfam website has moved to http://dfam.org. Seed alignments, profile HMMs, hit lists and other underlying data are available for download.

}, issn = {1362-4962}, doi = {10.1093/nar/gkv1272}, author = {Hubley, Robert and Finn, Robert D and Clements, Jody and Eddy, Sean R and Jones, Thomas A and Bao, Weidong and Smit, Arian F A and Wheeler, Travis J} } @article {47434, title = {Direct neural pathways convey distinct visual information to Drosophila mushroom bodies.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Apr 15}, pages = {e14009}, abstract = {

Previously, we identified that visual and olfactory associative memories of Drosophila share the mushroom body (MB) circuits (Vogt et al. 2014). Despite well-characterized odor representations in the Drosophila MB, the MB circuit for visual information is totally unknown. Here we show that a small subset of MB Kenyon cells (KCs) selectively responds to visual but not olfactory stimulation. The dendrites of these atypical KCs form a ventral accessory calyx (vAC), distinct from the main calyx that receives olfactory input. We identified two types of visual projection neurons (VPNs) directly connecting the optic lobes and the vAC. Strikingly, these VPNs are differentially required for visual memories of color and brightness. The segregation of visual and olfactory domains in the MB allows independent processing of distinct sensory memories and may be a conserved form of sensory representations among insects.

}, issn = {2050-084X}, doi = {10.7554/eLife.14009}, author = {Vogt, Katrin and Aso, Yoshinori and Hige, Toshihide and Knapek, Stephan and Ichinose, Toshiharu and Friedrich, Anja B and Turner, Glenn C and Rubin, Gerald M and Tanimoto, Hiromu} } @booklet {67218, title = {Discovering Neuronal Cell Types and Their Gene Expression Profiles Using a Spatial Point Process Mixture Model}, year = {2016}, abstract = {

Cataloging the neuronal cell types that comprise circuitry of individual brain regions is a major goal of modern neuroscience and the BRAIN initiative. Single-cell RNA sequencing can now be used to measure the gene expression profiles of individual neurons and to categorize neurons based on their gene expression profiles. While the single-cell techniques are extremely powerful and hold great promise, they are currently still labor intensive, have a high cost per cell, and, most importantly, do not provide information on spatial distribution of cell types in specific regions of the brain. We propose a complementary approach that uses computational methods to infer the cell types and their gene expression profiles through analysis of brain-wide single-cell resolution in situ hybridization (ISH) imagery contained in the Allen Brain Atlas (ABA). We measure the spatial distribution of neurons labeled in the ISH image for each gene and model it as a spatial point process mixture, whose mixture weights are given by the cell types which express that gene. By fitting a point process mixture model jointly to the ISH images, we infer both the spatial point process distribution for each cell type and their gene expression profile. We validate our predictions of cell type-specific gene expression profiles using single cell RNA sequencing data, recently published for the mouse somatosensory cortex. Jointly with the gene expression profiles, cell features such as cell size, orientation, intensity and local density level are inferred per cell type.

}, author = {Furong Huang and Animashree Anandkumar and Christian Borgs and Jennifer Chayes and Ernest Fraenkel and Michael Hawrylycz and Ed Lein and Alessandro Ingrosso and Srinivas Turaga} } @article {48300, title = {Distinct subpopulations of FOXD1 stroma-derived cells regulate renal erythropoietin.}, journal = {The Journal of Clinical Investigation}, volume = {126}, year = {2016}, month = {2016 May 02}, pages = {1926-38}, abstract = {

Renal peritubular interstitial fibroblast-like cells are critical for adult erythropoiesis, as they are the main source of erythropoietin (EPO). Hypoxia-inducible factor 2 (HIF-2) controls EPO synthesis in the kidney and liver and is regulated by prolyl-4-hydroxylase domain (PHD) dioxygenases PHD1, PHD2, and PHD3, which function as cellular oxygen sensors. Renal interstitial cells with EPO-producing capacity are poorly characterized, and the role of the PHD/HIF-2 axis in renal EPO-producing cell (REPC) plasticity is unclear. Here we targeted the PHD/HIF-2/EPO axis in FOXD1 stroma-derived renal interstitial cells and examined the role of individual PHDs in REPC pool size regulation and renal EPO output. Renal interstitial cells with EPO-producing capacity were entirely derived from FOXD1-expressing stroma, and Phd2 inactivation alone induced renal Epo in a limited number of renal interstitial cells. EPO induction was submaximal, as hypoxia or pharmacologic PHD inhibition further increased the REPC fraction among Phd2-/- renal interstitial cells. Moreover, Phd1 and Phd3 were differentially expressed in renal interstitium, and heterozygous deficiency for Phd1 and Phd3 increased REPC numbers in Phd2-/- mice. We propose that FOXD1 lineage renal interstitial cells consist of distinct subpopulations that differ in their responsiveness to Phd2 inactivation and thus regulation of HIF-2 activity and EPO production under hypoxia or conditions of pharmacologic or genetic PHD inactivation.

}, issn = {1558-8238}, doi = {10.1172/JCI83551}, author = {Kobayashi, Hanako and Liu, Qingdu and Binns, Thomas C and Urrutia, Andres A and Davidoff, Olena and Kapitsinou, Pinelopi P and Pfaff, Andrew S and Olauson, Hannes and Wernerson, Annika and Fogo, Agnes B and Fong, Guo-Hua and Gross, Kenneth W and Haase, Volker H} } @article {47708, title = {Dopaminergic neurons write and update memories with cell-type-specific rules.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Jul 21}, pages = {e16135}, abstract = {

Associative learning is thought to involve parallel and distributed mechanisms of memory formation and storage. In Drosophila, the mushroom body (MB) is the major site of associative odor memory formation. Previously we described the anatomy of the adult MB and defined 20 types of dopaminergic neurons (DANs) that each innervate distinct MB compartments (Aso et al., 2014a; Aso et al., 2014b). Here we compare the properties of memories formed by optogenetic activation of individual DAN cell types. We found extensive differences in training requirements for memory formation, decay dynamics, storage capacity and flexibility to learn new associations. Even a single DAN cell type can either write or reduce an aversive memory, or write an appetitive memory, depending on when it is activated relative to odor delivery. Our results show that different learning rules are executed in seemingly parallel memory systems, providing multiple distinct circuit-based strategies to predict future events from past experiences.

}, issn = {2050-084X}, doi = {10.7554/eLife.16135}, author = {Aso, Yoshinori and Rubin, Gerald M} } @article {47553, title = {Doublesex regulates the connectivity of a neural circuit controlling Drosophila male courtship song.}, journal = {Developmental Cell}, volume = {37}, year = {2016}, month = {2016 Jun 20}, pages = {533-44}, abstract = {

It is unclear how regulatory genes establish neural circuits that compose sex-specific behaviors. The\ Drosophila melanogaster\ male courtship song provides a powerful model to study this problem. Courting males vibrate a wing to sing bouts of pulses and hums, called pulse and sine song, respectively. We report the discovery of male-specific thoracic interneurons{\textemdash}the TN1A neurons{\textemdash}that are required specifically for sine song. The TN1A neurons can drive the activity of a sex-non-specific wing motoneuron,\ hg1, which is also required for sine song. The male-specific connection between the TN1A neurons and the\ hg1\ motoneuron is regulated by the sexual differentiation gene\ doublesex. We find that\ doublesex\ is required in the TN1A neurons during development to increase the density of the TN1A arbors that interact with dendrites of the\ hg1motoneuron. Our findings demonstrate how a sexual differentiation gene can build a sex-specific circuit motif by modulating neuronal arborization.

{\textbullet}Doublesex-expressing TN1 neurons are necessary and sufficient for the male sine song{\textbullet}A subclass of TN1 neurons, TN1A, contributes to the sine song{\textbullet}TN1A neurons are functionally coupled to a sine song motoneuron,\ hg1{\textbullet}Doublesex\ regulates the connectivity between the TN1A and\ hg1\ neurons

It is unclear how developmental regulatory genes specify sex-specific behaviors. Shirangi et\ al. demonstrate that the\ Drosophila\ sexual differentiation gene\ doublesex\ encodes a sex-specific behavior{\textemdash}male song{\textemdash}by promoting the connectivity between the male-specific TN1A neurons and the sex-non-specific\ hg1\ neurons, which are required for production of the song.

}, doi = {10.1016/j.devcel.2016.05.012}, author = {Shirangi, Troy R and Wong, Allen M and Truman, James W and Stern, David L} } @article {47749, title = {Drosophila larval to pupal switch under nutrient stress requires IP3R/Ca(2+) signalling in glutamatergic interneurons.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Aug 5}, abstract = {

Neuronal circuits are known to integrate nutritional information, but the identity of the circuit components is not completely understood. Amino acids are a class of nutrients that are vital for the growth and function of an organism. Here, we report a neuronal circuit that allows Drosophila larvae to overcome amino acid deprivation and pupariate. We find that nutrient stress is sensed by the class IV multidendritic cholinergic neurons. Through live calcium imaging experiments, we show that these cholinergic stimuli are conveyed to glutamatergic neurons in the ventral ganglion through mAChR. We further show that IP3R-dependent calcium transients in the glutamatergic neurons convey this signal to downstream medial neurosecretory cells (mNSCs). The circuit ultimately converges at the ring gland and regulates expression of ecdysteroid biosynthetic genes. Activity in this circuit is thus likely to be an adaptation that provides a layer of regulation to help surpass nutritional stress during development.

}, issn = {2050-084X}, doi = {10.7554/eLife.17495}, author = {Jayakumar, Siddharth and Richhariya, Shlesha and Reddy, O Venkateswara and Texada, Michael J and Hasan, Gaiti} } @article {47394, title = {Dysfunctional calcium and glutamate signaling in striatal astrocytes from Huntington{\textquoteright}s Disease model mice.}, journal = {The Journal of Neuroscience : the official journal of the Society for Neuroscience}, volume = {36}, year = {2016}, month = {2016 Mar 23}, pages = {3453-70}, abstract = {

UNLABELLED: Astrocytes tile the entire CNS, but their functions within neural circuits in health and disease remain incompletely understood. We used genetically encoded Ca(2+)and glutamate indicators to explore the rules for astrocyte engagement in the corticostriatal circuit of adult wild-type (WT) and Huntington{\textquoteright}s disease (HD) model mice at ages not accompanied by overt astrogliosis (at approximately postnatal days 70-80). WT striatal astrocytes displayed extensive spontaneous Ca(2+)signals, but did not respond to cortical stimulation, implying that astrocytes were largely disengaged from cortical input in healthy tissue. In contrast, in HD model mice, spontaneous Ca(2+)signals were significantly reduced in frequency, duration, and amplitude, but astrocytes responded robustly to cortical stimulation with evoked Ca(2+)signals. These action-potential-dependent astrocyte Ca(2+)signals were mediated by neuronal glutamate release during cortical stimulation, accompanied by prolonged extracellular glutamate levels near astrocytes and tightly gated by Glt1 glutamate transporters. Moreover, dysfunctional Ca(2+)and glutamate signaling that was observed in HD model mice was largely, but not completely, rescued by astrocyte specific restoration of Kir4.1, emphasizing the important contributions of K(+)homeostatic mechanisms that are known to be reduced in HD model mice. Overall, our data show that astrocyte engagement in the corticostriatal circuit is markedly altered in HD. Such prodromal astrocyte dysfunctions may represent novel therapeutic targets in HD and other brain disorders.

SIGNIFICANCE STATEMENT: We report how early-onset astrocyte dysfunction without detectable astrogliosis drives disease-related processes in a mouse model of Huntington{\textquoteright}s disease (HD). The cellular mechanisms involve astrocyte homeostasis and signaling mediated by Kir4.1, Glt1, and Ca(2+) The data show that the rules for astrocyte engagement in a neuronal circuit are fundamentally altered in a brain disease caused by a known molecular defect and that fixing early homeostasis dysfunction remedies additional cellular deficits. Overall, our data suggest that key aspects of altered striatal function associated with HD may be triggered, at least in part, by dysfunctional astrocytes, thereby providing details of an emerging striatal microcircuit mechanism in HD. Such prodromal changes in astrocytes may represent novel therapeutic targets.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3693-15.2016}, author = {Jiang, Ruotian and Diaz-Castro, Blanca and Looger, Loren L and Khakh, Baljit S} } @article {47423, title = {Editorial overview: Neurobiology of cognitive behavior: Complexity of neural computation and cognition.}, journal = {Current Opinion in Neurobiology}, volume = {37}, year = {2016}, month = {2016 Mar 14}, pages = {v-viii}, issn = {1873-6882}, doi = {10.1016/j.conb.2016.03.003}, author = {Karpova, Alla and Kiani, Roozbeh} } @article {47710, title = {Editorial overview: Neurobiology of sex.}, journal = {Current Opinion in Neurobiology}, volume = {38}, year = {2016}, month = {2016 Jun}, pages = {A1-3}, issn = {1873-6882}, doi = {10.1016/j.conb.2016.06.001}, author = {Dulac, Catherine and Dickson, Barry J} } @article {47876, title = {Effect of magnetic nanoparticle shape on flux amplification in inductive coil magnetic resonance detection.}, journal = {Journal of Applied Physics}, year = {2016}, month = {2016 Sep 14}, pages = {104506-1-7}, abstract = {

We model and analyze the effect of particle shape on the signal amplification in inductive coil magnetic resonance\ detection\ using the reversible transverse\ magnetic susceptibility\ of oriented magnetic nanostructures. Utilizing the single magnetic domain Stoner-Wohlfarth model of uniform magnetization rotation, we reveal that different ellipsoidal particle shapes can have a pronounced effect on the magnetic flux enhancement in\ detection\ configurations typical of magnetic resonance settings. We compare and contrast the prolate ellipsoids, oblate ellipsoids, and exchange-biased spheres and show that the oblate ellipsoids and exchange-biased spheres have a significantly higher flux amplification effect than the prolate ellipsoids considered previously. In addition, oblate ellipsoids have a much broader polarizing\ magnetic fieldrange over which their transverse flux amplification is significant. We show the dependence of transverse flux amplification on magnetic resonance bias field and discuss the resulting signal-to-noise ratio of inductive magnetic resonance\ detection\ due to the magnetic\ nanoparticle-filled\ core of the magnetic resonance\ detection\ coil.

}, doi = {10.1063/1.4962451}, author = {Barbic, Mladen and El Bidweihy, Hatem} } @conference {47736, title = {Efficient convolutional neural networks for pixelwise classification on heterogeneous hardware systems.}, booktitle = { IEEE 13th International Symposium on Biomedical Imaging: From Nano to Macro}, year = {2016}, month = {2016 Jun 15}, address = {Clarion Congress Hotel in Prague Prague; Czech Republic}, abstract = {

With recent advances in high-throughput Electron Microscopy (EM) imaging it is now possible to image an entire nervous system of organisms like Drosophila melanogaster. One of the bottlenecks to reconstruct a connectome from these large volumes ({\oe} 100 TiB) is the pixel-wise prediction of membranes. The time it would typically take to process such a volume using a convolutional neural network (CNN) with a sliding window approach is in the order of years on a current GPU. With sliding windows, however, a lot of redundant computations are carried out. In this paper, we present an extension to the Caffe library to increase throughput by predicting many pixels at once. On a sliding window network successfully used for membrane classification, we show that our method achieves a speedup of up to 57{\texttimes}, maintaining identical prediction results.

}, isbn = {978-147992350-2}, doi = {10.1109/ISBI.2016.7493487}, author = {Tschopp, F and Martel, J N P and Turaga, Srinivas C and Cook, M and Funke, Jan} } @article {47386, title = {Emerging imaging and genomic tools for developmental systems biology.}, journal = {Developmental Cell}, volume = {36}, year = {2016}, month = {2016 Mar 21}, pages = {597-610}, abstract = {

Animal development is a complex and dynamic process orchestrated by exquisitely timed cell lineage commitment, divisions, migration, and morphological changes at the single-cell level. In the past decade, extensive genetic, stem cell, and genomic studies provided crucial insights into molecular underpinnings and the functional importance of genetic pathways governing various cellular differentiation processes. However, it is still largely unknown how the precise coordination of these pathways is achieved at the whole-organism level and how the highly regulated spatiotemporal choreography of development is established in turn. Here, we discuss the latest technological advances in imaging and single-cell genomics that hold great promise for advancing our understanding of this intricate process. We propose an integrated approach that combines such methods to quantitatively decipher in\ vivo cellular dynamic behaviors and their underlying molecular mechanisms at the systems level with single-cell, single-molecule resolution.

}, issn = {1878-1551}, doi = {10.1016/j.devcel.2016.02.016}, author = {Liu, Zhe and Keller, Philipp J} } @article {48132, title = {An empirical analysis of deep network loss surfaces.}, journal = {arXiv}, year = {2016}, month = {2016 Dec 13}, pages = {arXiv:1612.04010}, abstract = {

The training of deep neural networks is a high-dimension optimization problem with respect to the loss function of a model. Unfortunately, these functions are of high dimension and non-convex and hence difficult to characterize. In this paper, we empirically investigate the geometry of the loss functions for state-of-the-art networks with multiple stochastic optimization methods. We do this through several experiments that are visualized on polygons to understand how and when these stochastic optimization methods find minima.

}, url = {https://arxiv.org/pdf/1612.04010.pdf}, author = {Im, Daniel Jiwoong and Tao, Michael and Branson, Kristin} } @article {48042, title = {Engulfed cadherin fingers are polarized junctional structures between collectively migrating endothelial~cells.}, journal = {Nature Cell Biology}, volume = {18}, year = {2016}, month = {2016 Nov 14}, pages = {1311-23}, abstract = {

The development and maintenance of tissues requires collective cell movement, during which neighbouring cells coordinate the polarity of their migration machineries. Here, we ask how polarity signals are transmitted from one cell to another across symmetrical cadherin junctions, during collective migration. We demonstrate that collectively migrating endothelial cells have polarized VE-cadherin-rich membrane protrusions, {\textquoteleft}cadherin fingers{\textquoteright}, which leading cells extend from their rear and follower cells engulf at their front, thereby generating opposite membrane curvatures and asymmetric recruitment of curvature-sensing proteins. In follower cells, engulfment of cadherin fingers occurs along with the formation of a lamellipodia-like zone with low actomyosin contractility, and requires VE-cadherin/catenin complexes and Arp2/3-driven actin polymerization. Lateral accumulation of cadherin fingers in follower cells precedes turning, and increased actomyosin contractility can initiate cadherin finger extension as well as engulfment by a neighbouring cell, to promote follower behaviour. We propose that cadherin fingers serve as guidance cues that direct collective cell migration.

}, doi = {10.1038/ncb3438}, author = {Hayer, Arnold and Shao, Lin and Chung, Mingyu and Joubert, Lydia-Marie and Yang, Hee Won and Tsai, Feng-Chiao and Bisaria, Anjali and Betzig, Eric and Meyer, Tobias} } @article {47465, title = {Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 May 9}, abstract = {

Internal ribosome entry sites (IRESs) mediate cap-independent translation of viral mRNAs. Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the Taura syndrome virus IRES and translocase eEF2{\textbullet}GTP bound with sordarin. The structures suggest a trajectory of IRES translocation, required for translation initiation, and provide an unprecedented view of eEF2 dynamics. The IRES rearranges from extended to bent to extended conformations. This inchworm-like movement is coupled with ribosomal inter-subunit rotation and 40S head swivel. eEF2, attached to the 60S subunit, slides along the rotating 40S subunit to enter the A site. Its diphthamide-bearing tip at domain IV separates the tRNA-mRNA-like pseudoknot I (PKI) of the IRES from the decoding center. This unlocks 40S domains, facilitating head swivel and biasing IRES translocation via hitherto-elusive intermediates with PKI captured between the A and P sites. The structures suggest missing links in our understanding of tRNA translocation.

}, issn = {2050-084X}, doi = {10.7554/eLife.14874}, author = {Abeyrathne, Priyanka D and Koh, Cha San and Grant, Timothy and Grigorieff, Nikolaus and Korostelev, Andrei A} } @article {47412, title = {Epigenomic landscapes of retinal rods and cones.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Mar 07}, abstract = {

Rod and cone photoreceptors are highly similar in many respects but they have important functional and molecular differences. Here, we investigate genome-wide patterns of DNA methylation and chromatin accessibility in mouse rods and cones and correlate differences in these features with gene expression, histone marks, transcription factor binding, and DNA sequence motifs. Loss of NR2E3 in rods shifts their epigenomes to a more cone-like state. The data further reveal wide differences in DNA methylation between retinal photoreceptors and brain neurons. Surprisingly, we also find a substantial fraction of DNA hypo-methylated regions in adult rods that are not in active chromatin. Many of these regions exhibit hallmarks of regulatory regions that were active earlier in neuronal development, suggesting that these regions could remain undermethylated due to the highly compact chromatin in mature rods. This work defines the epigenomic landscapes of rods and cones, revealing features relevant to photoreceptor development and function.

}, issn = {2050-084X}, doi = {10.7554/eLife.11613}, author = {Mo, Alisa and Luo, Chongyuan and Davis, Fred P and Mukamel, Eran A and Henry, Gilbert L and Nery, Joseph R and Urich, Mark A and Picard, Serge and Lister, Ryan and Eddy, Sean R and Beer, Michael A and Ecker, Joseph R and Nathans, Jeremy} } @article {47688, title = {Evaluation of the Ser-His dipeptide, a putative catalyst of amide and ester hydrolysis.}, journal = {Organic Letters}, year = {2016}, month = {2016 Jul 11}, abstract = {

Efficient hydrolysis of amide bonds has long been a reaction of interest for organic chemists. The rate constants of proteases are unmatched by those of any synthetic catalyst. It has been proposed that a dipeptide containing serine and histidine is an effective catalyst of amide hydrolysis, based on an apparent ability to degrade a protein. The capacity of the Ser-His dipeptide to catalyze the hydrolysis of several discrete ester and amide substrates is investigated using previously described conditions. This dipeptide does not catalyze the hydrolysis of amide or unactivated ester groups in any of the substrates under the conditions evaluated.

}, issn = {1523-7052}, doi = {10.1021/acs.orglett.6b01279}, author = {MacDonald, Melissa J and Lavis, Luke D and Hilvert, Donald and Gellman, Samuel H} } @article {47510, title = {Evidence for an audience effect in mice: male social partners alter the male vocal response to female cues.}, journal = {The Journal of Experimental Biology}, volume = {219}, year = {2016}, month = {2016 May 15}, pages = {1437-48}, abstract = {

Mice (Mus musculus) form large and dynamic social groups and emit ultrasonic vocalizations in a variety of social contexts. Surprisingly, these vocalizations have been studied almost exclusively in the context of cues from only one social partner, despite the observation that in many social species the presence of additional listeners changes the structure of communication signals. Here, we show that male vocal behavior elicited by female odor is affected by the presence of a male audience - with changes in vocalization count, acoustic structure and syllable complexity. We further show that single sensory cues are not sufficient to elicit this audience effect, indicating that multiple cues may be necessary for an audience to be apparent. Together, these experiments reveal that some features of mouse vocal behavior are only expressed in more complex social situations, and introduce a powerful new assay for measuring detection of the presence of social partners in mice.

}, issn = {1477-9145}, doi = {10.1242/jeb.129361}, author = {Seagraves, Kelly M and Arthur, Ben J and Egnor, S E Roian} } @article {48043, title = {Evolved repression overcomes enhancer robustness.}, journal = {Developmental Cell}, volume = {39}, year = {2016}, month = {2016 Nov 10}, pages = {572-84}, abstract = {

Biological systems display extraordinary robustness. Robustness of transcriptional enhancers results mainly from clusters of binding sites for the same transcription factor, and it is not clear how robust enhancers can evolve loss of expression through point mutations. Here, we report the high-resolution functional dissection of a robust enhancer of the\ shavenbaby\ gene that has contributed to morphological evolution. We found that robustness is encoded by many binding sites for the transcriptional activator Arrowhead and that, during evolution, some of these activator sites were lost, weakening enhancer activity. Complete silencing of enhancer function, however, required evolution of a binding site for the spatially restricted potent repressor Abrupt. These findings illustrate that recruitment of\ repressor binding sites can overcome enhancer robustness and may minimize pleiotropic consequences of enhancer evolution. Recruitment of repression may be a general mode of evolution to break robust regulatory linkages.

}, doi = {10.1016/j.devcel.2016.10.010}, author = {Preger-Ben Noon, Ella and Davis, Fred P and Stern, David L} } @article {47601, title = {Falling apart.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016}, abstract = {

Destabilized nanobodies can be used to deliver fluorescent proteins and enzymes to specific targets inside cells.

}, issn = {2050-084X}, doi = {10.7554/eLife.18203}, author = {Marvin, Jonathan S and Looger, Loren L} } @conference {48832, title = {Fast and accurate spike sorting of high-channel count probes with KiloSort.}, booktitle = {Neural Information Processing Systems (NIPS 2016)}, year = {2016}, month = {2016 Dec 05}, address = {Barcelona, Spain}, abstract = {

New silicon technology is enabling large-scale electrophysiological recordings in vivo from hundreds to thousands of channels. Interpreting these recordings requires scalable and accurate automated methods for spike sorting, which should minimize the time required for manual curation of the results. Here we introduce KiloSort, a new integrated spike sorting framework that uses template matching both during spike detection and during spike clustering. KiloSort models the electrical voltage as a sum of template waveforms triggered on the spike times, which allows overlapping spikes to be identified and resolved. Unlike previous algorithms that compress the data with PCA, KiloSort operates on the raw data which allows it to construct a more accurate model of the waveforms. Processing times are faster than in previous algorithms thanks to batch-based optimization on GPUs. We compare KiloSort to an established algorithm and show favorable performance, at much reduced processing times. A novel post-clustering merging step based on the continuity of the templates further reduced substantially the number of manual operations required on this data, for the neurons with near-zero error rates, paving the way for fully automated spike sorting of multichannel electrode recordings.

}, url = {http://papers.nips.cc/paper/6326-fast-and-accurate-spike-sorting-of-high-channel-count-probes-with-kilosort}, author = {Pachitariu, Marius and Steinmetz, Nicholas A and Kadir, Shabnam N and Carandini, Matteo and Harris, Kenneth D} } @article {47485, title = {Flagellar membrane fusion and protein exchange in trypanosomes; a new form of cell-cell communication?}, journal = {F1000 Research}, volume = {5}, year = {2016}, month = {2016 Apr 14}, pages = {682}, abstract = {

Diverse structures facilitate direct exchange of proteins between cells, including plasmadesmata in plants and tunnelling nanotubes in bacteria and higher eukaryotes.\  Here we describe a new mechanism of protein transfer, flagellar membrane fusion, in the unicellular parasite\ Trypanosoma brucei. When fluorescently tagged trypanosomes were co-cultured, a small proportion of double-positive cells were observed. The formation of double-positive cells was dependent on the presence of extracellular calcium and was enhanced by placing cells in medium supplemented with fresh bovine serum. Time-lapse microscopy revealed that double-positive cells arose by bidirectional protein exchange in the absence of nuclear transfer.\  Furthermore, super-resolution microscopy showed that this process occurred in <=1 minute, the limit of temporal resolution in these experiments. Both cytoplasmic and membrane proteins could be transferred provided they gained access to the flagellum. Intriguingly, a component of the RNAi machinery (Argonaute) was able to move between cells, raising the possibility that small interfering RNAs are transported as cargo. Transmission electron microscopy showed that shared flagella contained two axonemes and two paraflagellar rods bounded by a single membrane. In some cases flagellar fusion was partial and interactions between cells were transient. In other cases fusion occurred along the entire length of the flagellum, was stable for several hours and might be irreversible. Fusion did not appear to be deleterious for cell function: paired cells were motile and could give rise to progeny while fused. The motile flagella of unicellular organisms are related to the sensory cilia of higher eukaryotes, raising the possibility that protein transfer between cells via cilia or flagella occurs more widely in nature.

}, doi = { 10.12688/f1000research.8249.1}, author = {Imhof, Simon and Fragoso, Cristina and Hemphill, Andrew and von Schubert, Conrad and Li, Dong and Legant, Wesley and Betzig, Eric} } @article {47768, title = {Flight of the dragonflies and damselflies.}, journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences}, volume = {371}, year = {2016}, month = {2016 Sep 26}, abstract = {

This work is a synthesis of our current understanding of the mechanics, aerodynamics and visually mediated control of dragonfly and damselfly flight, with the addition of new experimental and computational data in several key areas. These are: the diversity of dragonfly wing morphologies, the aerodynamics of gliding flight, force generation in flapping flight, aerodynamic efficiency, comparative flight performance and pursuit strategies during predatory and territorial flights. New data are set in context by brief reviews covering anatomy at several scales, insect aerodynamics, neuromechanics and behaviour. We achieve a new perspective by means of a diverse range of techniques, including laser-line mapping of wing topographies, computational fluid dynamics simulations of finely detailed wing geometries, quantitative imaging using particle image velocimetry of on-wing and wake flow patterns, classical aerodynamic theory, photography in the field, infrared motion capture and multi-camera optical tracking of free flight trajectories in laboratory environments. Our comprehensive approach enables a novel synthesis of datasets and subfields that integrates many aspects of flight from the neurobiology of the compound eye, through the aeromechanical interface with the surrounding fluid, to flight performance under cruising and higher-energy behavioural modes.This article is part of the themed issue {\textquoteright}Moving in a moving medium: new perspectives on flight{\textquoteright}.

}, issn = {1471-2970}, doi = {10.1098/rstb.2015.0389}, author = {Bomphrey, Richard J and Nakata, Toshiyuki and Henningsson, Per and Lin, Huai-Ti} } @inbook {48598, title = {Flow of information underlying a tactile decision in mice.}, booktitle = {Micro-, Meso- and Macro-Dynamics of the Brain}, year = {2016}, abstract = {

Motor planning allows us to conceive, plan, and initiate skilled motor behaviors. Motor planning involves activity distributed widely across the cortex. How this activity dynamically comes together to guide movement remains an unsolved problem. We study motor planning in mice performing a tactile decision behavior. Head-fixed mice discriminate object locations with their whiskers and report their choice by directional licking ({\textquotedblleft}lick left{\textquotedblright}/{\textquotedblleft}lick right{\textquotedblright}). A short-term memory component separates tactile {\textquotedblleft}sensation{\textquotedblright} and {\textquotedblleft}action{\textquotedblright} into distinct epochs. Using loss-of-function experiments, cell-type specific electrophysiology, and cellular imaging, we delineate when and how activity in specific brain areas and cell types drives motor planning in mice. Our results suggest that information flows serially from sensory to motor areas during motor planning. The motor cortex circuit maintains the motor plan during short-term memory and translates the motor plan into motor commands that drive the upcoming directional licking.

}, doi = {10.1007/978-3-319-28802-4_3}, author = {Li, Nuo and Guo, Zengcai V and Chen, Tsai-Wen and Svoboda, Karel} } @article {47697, title = {Forced chromatin looping raises fetal hemoglobin in adult sickle cells to higher levels than pharmacologic inducers.}, journal = {Blood}, year = {2016}, month = {2016 Jul 12}, abstract = {

Overcoming the silencing of the fetal γ-globin gene has been a long standing goal in the treatment of sickle cell disease (SCD). The major transcriptional enhancer of the β-globin locus, called LCR, dynamically interacts with the developmental stage-appropriate β-type globin genes via chromatin looping, a process requiring the protein Ldb1. In adult erythroid cells the LCR can be re-directed from the adult β- to the fetal γ-globin promoter by tethering Ldb1 to the human γ-globin promoter with custom designed zinc finger proteins (ZF-Ldb1), leading to reactivation of γ-globin gene expression. To compare this approach to pharmacological reactivation of fetal hemoglobin (HbF), hematopoietic cells from SCD patients were treated with a lentivirus expressing the ZF-Ldb1 or with chemical HbF inducers. The HbF increase in cells treated with ZF-Ldb1 was more than double of that observed with decitabine and pomalidomide; butyrate had an intermediate effect while tranylcypromine and hydroxyurea showed relatively low HbF reactivation. ZF-Ldb1 showed comparatively little toxicity, and reduced sickle Hb (HbS) synthesis as well as sickling of SCD erythroid cells under hypoxic conditions. The efficacy and low cytotoxicity of lentiviral-mediated ZF-Ldb1 gene transfer compared to the drug regimens support its therapeutic potential for the treatment of SCD.

}, issn = {1528-0020}, doi = {10.1182/blood-2016-01-691089}, author = {Breda, Laura and Motta, Irene and Lourenco, Silvia and Gemmo, Chiara and Deng, Wulan and Rupon, Jeremy W and Abdulmalik, Osheiza Y and Manwani, Deepa and Blobel, Gerd A and Rivella, Stefano} } @article {47993, title = {Formin-generated actomyosin arcs propel T cell receptor microcluster movement at the immune synapse.}, journal = {The Journal of Cell Biology}, volume = {215}, year = {2016}, month = {2016 Oct 31}, pages = {383-99}, abstract = {

Actin assembly and inward flow in the plane of the immunological synapse (IS) drives the centralization of T cell receptor microclusters (TCR MCs) and the integrin leukocyte functional antigen 1 (LFA-1). Using structured-illumination microscopy (SIM), we show that actin arcs populating the medial, lamella-like region of the IS arise from linear actin filaments generated by one or more formins present at the IS distal edge. After traversing the outer, Arp2/3-generated, lamellipodia-like region of the IS, these linear filaments are organized by myosin II into antiparallel concentric arcs. Three-dimensional SIM shows that active LFA-1 often aligns with arcs, whereas TCR MCs commonly reside between arcs, and total internal reflection fluorescence SIM shows TCR MCs being swept inward by arcs. Consistently, disrupting actin arc formation via formin inhibition results in less centralized TCR MCs, missegregated integrin clusters, decreased T-B cell adhesion, and diminished TCR signaling. Together, our results define the origin, organization, and functional significance of a major actomyosin contractile structure at the IS that directly propels TCR MC transport.

}, issn = {1540-8140}, doi = {10.1083/jcb.201603080}, author = {Murugesan, Sricharan and Hong, Jinsung and Yi, Jason and Li, Dong and Beach, Jordan R and Shao, Lin and Meinhardt, John and Madison, Grey and Wu, Xufeng and Betzig, Eric and Hammer, John A} } @article {47303, title = {Four individually identified paired dopamine neurons signal reward in larval Drosophila.}, journal = {Current Biology : CB}, year = {2016}, month = {2016 Feb 10}, abstract = {

Dopaminergic neurons serve multiple functions, including reinforcement processing during associative learning [1-12]. It is thus warranted to understand which dopaminergic neurons mediate which function. We study larval Drosophila, in which only approximately 120 of a total of 10,000 neurons are dopaminergic, as judged by the expression of tyrosine hydroxylase (TH), the rate-limiting enzyme of dopamine biosynthesis [5, 13]. Dopaminergic neurons mediating reinforcement in insect olfactory learning target the mushroom bodies, a higher-order "cortical" brain region [1-5, 11, 12, 14, 15]. We discover four previously undescribed paired neurons, the primary protocerebral anterior medial (pPAM) neurons. These neurons are TH positive and subdivide the medial lobe of the mushroom body into four distinct subunits. These pPAM neurons are acutely necessary for odor-sugar reward learning and require intact TH function in this process. However, they are dispensable for aversive learning and innate behavior toward the odors and sugars employed. Optogenetical activation of pPAM neurons is sufficient as a reward. Thus, the pPAM neurons convey a likely dopaminergic reward signal. In contrast, DL1 cluster neurons convey a corresponding punishment signal [5], suggesting a cellular division of labor to convey dopaminergic reward and punishment signals. On the level of individually identified neurons, this uncovers an organizational principle shared with adult Drosophila and mammals [1-4, 7, 9, 10] (but see [6]). The numerical simplicity and connectomic tractability of the larval nervous system [16-19] now offers a prospect for studying circuit principles of dopamine function at unprecedented resolution.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2016.01.012}, author = {Rohwedder, Astrid and Wenz, Nana L and Stehle, Bernhard and Huser, Annina and Yamagata, Nobuhiro and Zlatic, Marta and Truman, James W and Tanimoto, Hiromu and Saumweber, Timo and Gerber, Bertram and Thum, Andreas S} } @article {47549, title = {Frealign: an exploratory tool for single-particle cryo-EM.}, journal = {Methods in Enzymology}, year = {2016}, month = {2016 Jun 07}, abstract = {

Frealign is a software tool designed to process electron microscope images of single molecules and complexes to obtain reconstructions at the highest possible resolution. It provides a number of refinement parameters and options that allow users to tune their refinement to achieve specific goals, such as masking to classify selected regions within a particle, control over the refinement of specific alignment parameters to accommodate various data collection schemes, refinement of pseudosymmetric particles, and generation of initial maps. This chapter provides a general overview of Frealign functions and a more detailed guide to using Frealign in typical scenarios.

}, keywords = {High resolution; Refinement; Classification; Contrast transfer function; Masking; Asymmetry}, doi = {10.1016/bs.mie.2016.04.013}, author = {Grigorieff, Nikolaus} } @article {48386, title = {From Whole-Brain Data to Functional Circuit Models: The Zebrafish Optomotor Response.}, journal = {Cell}, volume = {167}, year = {2016}, month = {2016 11 03}, pages = {947-960.e20}, abstract = {

Detailed descriptions of brain-scale sensorimotor circuits underlying vertebrate behavior remain elusive. Recent advances in zebrafish neuroscience offer new opportunities to dissect such circuits via whole-brain imaging, behavioral analysis, functional perturbations, and network modeling. Here, we harness these tools to generate a brain-scale circuit\ model of the optomotor response, an orienting behavior evoked by visual motion. We show that such motion is processed by diverse neural response types distributed across multiple brain regions. To transform sensory input into action, these regions sequentially integrate eye- and direction-specific sensory streams, refine representations via interhemispheric inhibition, and demix locomotor instructions to independently drive turning and forward swimming. While experiments revealed many neural response types throughout the brain, modeling identified the dimensions of functional connectivity most critical for the behavior. We thus reveal how distributed neurons collaborate to generate behavior and illustrate a paradigm for distilling functional circuit models from whole-brain data.

}, keywords = {Animals, Brain, Feedback, Sensory, Neural Pathways, Neuroimaging, Neurons, Swimming, Visual Perception, Zebrafish}, issn = {1097-4172}, doi = {10.1016/j.cell.2016.10.019}, author = {Naumann, Eva A and Fitzgerald, James E and Dunn, Timothy W and Rihel, Jason and Sompolinsky, Haim and Engert, Florian} } @article {47924, title = {Fully-automatic synapse prediction and validation on a large data set.}, journal = {Frontiers in Neural Circuits}, volume = {12}, year = {2016}, month = {2018 Oct 29}, pages = {87}, abstract = {

Extracting a connectome from an electron microscopy (EM) data set requires identification of neurons and determination of synapses between neurons. As manual extraction of this information is very time-consuming, there has been extensive research effort to automatically segment the neurons to help guide and eventually replace manual tracing. Until recently, there has been comparatively less research on automatically detecting the actual synapses between neurons. This discrepancy can, in part, be attributed to several factors: obtaining neuronal shapes is a prerequisite first step in extracting a connectome, manual tracing is much more time-consuming than annotating synapses, and neuronal contact area can be used as a proxy for synapses in determining connections.
However, recent research has demonstrated that contact area alone is not a sufficient predictor of synaptic connection. Moreover, as segmentation has improved, we have observed that synapse annotation is consuming a more significant fraction of overall reconstruction time. This ratio will only get worse as segmentation improves, gating overall possible speed-up. Therefore, we address this problem by developing algorithms that automatically detect pre-synaptic neurons and their post-synaptic partners. In particular, pre-synaptic structures are detected using a Deep and Wide Multiscale Recursive Network, and post-synaptic partners are detected using a MLP with features conditioned on the local segmentation.
This work is novel because it requires minimal amount of training, leverages advances in image segmentation directly, and provides a complete solution for polyadic synapse detection. We further introduce novel metrics to evaluate our algorithm on connectomes of meaningful size. These metrics demonstrate that complete automatic prediction can be used to effectively characterize most connectivity correctly.

}, author = {Huang, Gary B. and Scheffer, Louis K and Plaza, Stephen M.} } @inbook {48432, title = {Functional and anatomical dissection of feeding circuits.}, booktitle = {Neuroendocrinology of Appetite}, year = {2016}, pages = {112-133}, abstract = {

This chapter reviews the application of new genetically encoded tools in feeding circuits that regulate appetite. Rapid activation and inhibition of agouti related peptide (AgRP) neurons conclusively established a causal role for rapid control of food intake. Chemogenetic activation of AgRP neurons using hM3Dq avoids the invasive protocols required for ChR2 activation. ChR2 distributes into axons, and selective optogenetic activation of AgRP neuron axon projection fields in distinct brain areas was used to examine their individual contribution to feeding behavior. Some of the brain areas targeted by AgRP neuron axon projections have been examined further for cell type specific control of appetite. Rodents with bed nucleus of stria terminalis (BNST) lesions show hyperphagia and obesity, indicating that reduced BNST output promotes feeding. pro-opiomelanocortin (POMC) neurons regulate feeding over longer timescales. parabrachial nucleus (PBN) neurons have a powerful inhibitory role on food intake, but their inhibition does not strongly elevate food intake.

}, doi = {10.1002/9781118839317.ch6}, author = {Atasoy, Deniz and Sternson, Scott M} } @article {47524, title = {Genetic and environmental control of neurodevelopmental robustness in Drosophila.}, journal = {PLoS One}, volume = {11}, year = {2016}, month = {2016 May 25}, pages = {e0155957}, abstract = {

Interindividual differences in neuronal wiring may contribute to behavioral individuality and affect susceptibility to neurological disorders. To investigate the causes and potential consequences of wiring variation in Drosophila melanogaster, we focused on a hemilineage of ventral nerve cord interneurons that exhibits morphological variability. We find that late-born subclasses of the 12A hemilineage are highly sensitive to genetic and environmental variation. Neurons in the second thoracic segment are particularly variable with regard to two developmental decisions, whereas its segmental homologs are more robust. This variability "hotspot" depends on Ultrabithorax expression in the 12A neurons, indicating variability is cell-intrinsic and under genetic control. 12A development is more variable and sensitive to temperature in long-established laboratory strains than in strains recently derived from the wild. Strains with a high frequency of one of the 12A variants also showed a high frequency of animals with delayed spontaneous flight initiation, whereas other wing-related behaviors did not show such a correlation and were thus not overtly affected by 12A variation. These results show that neurodevelopmental robustness is variable and under genetic control in Drosophila and suggest that the fly may serve as a model for identifying conserved gene pathways that stabilize wiring in stressful developmental environments. Moreover, some neuronal lineages are variation hotspots and thus may be more amenable to evolutionary change.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0155957}, author = {Mellert, David J and Williamson, W Ryan and Shirangi, Troy R and Card, Gwyneth M and Truman, James W} } @article {47726, title = {The genome of the crustacean Parhyale hawaiensis: a model for animal development, regeneration, immunity and lignocellulose digestion.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Nov 16}, pages = {e20062}, abstract = {

Parhyale hawaiensis is a blossoming model system for studies of developmental mechanisms and more recently adult regeneration. We have sequenced the genome allowing annotation of all key signaling pathways, small non-coding RNAs and transcription factors that will enhance ongoing functional studies. Parhayle is a member of the Malacostraca, which includes crustacean food crop species. We analysed the immunity related genes of Parhyale as an important comparative system for these species, where immunity related aquaculture problems have increased as farming has intensified. We also find that Parhyale and other species within Multicrustacea contain the enzyme sets necessary to perform lignocellulose digestion (wood eating), suggesting this ability may predate the diversification of this lineage. Our data provide an essential resource for further development of the Parhyale model. The first Malacostracan genome sequence will underpin ongoing comparative work in important food crop species and research investigating lignocellulose as energy source.

Publication first appeared in BioRxiv on August 2, 2016.\ http://dx.doi.org/10.1101/065789

}, doi = {10.7554/eLife.20062}, author = {Kao, Damian and Lai, Alvina G and Stamataki, Evangelia and Rosic, Silvana and Konstantinides, Nikolaos and Jarvis, Erin and Di Donfrancesco, Alessia and Pouchkina-Stantcheva, Natalia and Semon, Marie and Grillo, Marco and Bruce, Heather and Kumar, Suyash and Siwanowicz, Igor and Le, Andy and Lemire, Andrew and Extavour, Cassandra and Browne, William and Wolff, Carsten and Averof, Michalis and et al} } @article {47547, title = {GFP-aequorin protein sensor for ex~vivo and in~vivo imaging of Ca(2+) dynamics in high-Ca(2+) organelles.}, journal = {Cell Chemical Biology}, year = {2016}, month = {2016 Jun 1}, abstract = {

Proper functioning of organelles such as the ER or the Golgi apparatus requires luminal accumulation of Ca(2+) at high concentrations. Here we describe a\ ratiometric low-affinity Ca(2+) sensor of the GFP-aequorin protein (GAP) family optimized for measurements in high-Ca(2+) concentration environments. Transgenic animals expressing the ER-targeted sensor allowed monitoring of Ca(2+) signals inside the organelle. The use of the sensor was demonstrated under three experimental paradigms: (1) ER Ca(2+) oscillations in cultured astrocytes, (2) ex\ vivo functional mapping of cholinergic receptors triggering ER Ca(2+) release in acute hippocampal slices from transgenic mice, and (3) in\ vivo sarcoplasmic reticulum Ca(2+) dynamics in the muscle of transgenic flies. Our results provide proof of the suitability of the new biosensors to monitor Ca(2+) dynamics inside intracellular organelles under physiological conditions and open an avenue to explore complex Ca(2+) signaling in animal models of health and disease.

}, issn = {2451-9456}, doi = {10.1016/j.chembiol.2016.05.010}, author = {Navas-Navarro, Paloma and Rojo-Ruiz, Jonathan and Rodriguez-Prados, Macarena and Ganfornina, Mar{\'\i}a Dolores and Looger, Loren L and Alonso, Mar{\'\i}a Teresa and Garc{\'\i}a-Sancho, Javier} } @article {48094, title = {Global collaboration, learning from other fields.}, journal = {Neuron}, volume = {92}, year = {2016}, month = {2016 Nov 2}, pages = {561-563}, abstract = {

Neuroscience research is becoming increasingly more collaborative and interdisciplinary with partnerships between industry and academia and insights from fields beyond neuroscience. In the age of institutional initiatives and multi-investigator collaborations, scientists from around the world shared their perspectives on the effectiveness of large-scale collaborations versus single-lab, hypothesis-driven science.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2016.10.040} } @article {47967, title = {Glutamate-induced RNA localization and translation in neurons.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, year = {2016}, month = {2016 Sep 13}, abstract = {

Localization of mRNA is required for protein synthesis to occur within discrete intracellular compartments. Neurons represent an ideal system for studying the precision of mRNA trafficking because of their polarized structure and the need for synapse-specific targeting. To investigate this targeting, we derived a quantitative and analytical approach. Dendritic spines were stimulated by glutamate uncaging at a diffraction-limited spot, and the localization of single β-actin mRNAs was measured in space and time. Localization required NMDA receptor activity, a dynamic actin cytoskeleton, and the transacting RNA-binding protein, Zipcode-binding protein 1 (ZBP1). The ability of the mRNA to direct newly synthesized proteins to the site of localization was evaluated using a Halo-actin reporter so that RNA and protein were detected simultaneously. Newly synthesized Halo-actin was enriched at the site of stimulation, required NMDA receptor activity, and localized preferentially at the periphery of spines. This work demonstrates that synaptic activity can induce mRNA localization and local translation of β-actin where the new actin participates in stabilizing the expanding synapse in dendritic spines.

}, doi = {10.1073/pnas.1614267113}, author = {Yoon, Young J and Wu, Bin and Buxbaum, Adina R and Das, Sulagna and Tsai, Albert and English, Brian P and Grimm, Jonathan B and Lavis, Luke D and Singer, Robert H} } @article {47348, title = {High-density genotyping of immune-related loci identifies new SLE risk variants in individuals with Asian ancestry.}, journal = {Nature Genetics}, volume = {48}, year = {2016}, month = {2016 Mar}, pages = {323-30}, abstract = {

Systemic lupus erythematosus (SLE) has a strong but incompletely understood genetic architecture. We conducted an association study with replication in 4,478 SLE cases and 12,656 controls from six East Asian cohorts to identify new SLE susceptibility loci and better localize known loci. We identified ten new loci and confirmed 20 known loci with genome-wide significance. Among the new loci, the most significant locus was GTF2IRD1-GTF2I at 7q11.23 (rs73366469, Pmeta = 3.75 {\texttimes} 10(-117), odds ratio (OR) = 2.38), followed by DEF6, IL12B, TCF7, TERT, CD226, PCNXL3, RASGRP1, SYNGR1 and SIGLEC6. We identified the most likely functional variants at each locus by analyzing epigenetic marks and gene expression data. Ten candidate variants are known to alter gene expression in cis or in trans. Enrichment analysis highlights the importance of these loci in B cell and T cell biology. The new loci, together with previously known loci, increase the explained heritability of SLE to 24\%. The new loci share functional and ontological characteristics with previously reported loci and are possible drug targets for SLE therapeutics.

}, issn = {1546-1718}, doi = {10.1038/ng.3496}, author = {Sun, Celi and Molineros, Julio E and Looger, Loren L and Zhou, Xu-Jie and Kim, Kwangwoo and Okada, Yukinori and Ma, Jianyang and Qi, Yuan-Yuan and Kim-Howard, Xana and Motghare, Prasenjeet and Bhattarai, Krishna and Adler, Adam and Bang, So-Young and Lee, Hye-Soon and Kim, Tae-Hwan and Kang, Young Mo and Suh, Chang-Hee and Chung, Won Tae and Park, Yong-Beom and Choe, Jung-Yoon and Shim, Seung Cheol and Kochi, Yuta and Suzuki, Akari and Kubo, Michiaki and Sumida, Takayuki and Yamamoto, Kazuhiko and Lee, Shin-Seok and Kim, Young Jin and Han, Bok-Ghee and Dozmorov, Mikhail and Kaufman, Kenneth M and Wren, Jonathan D and Harley, John B and Shen, Nan and Chua, Kek Heng and Zhang, Hong and Bae, Sang-Cheol and Nath, Swapan K} } @article {47374, title = {High-density three-dimensional localization microscopy across large volumes.}, journal = {Nature Methods}, year = {2016}, month = {2016 Mar 7}, abstract = {

Extending three-dimensional (3D) single-molecule localization microscopy away from the coverslip and into thicker specimens will greatly broaden its biological utility. However, because of the limitations of both conventional imaging modalities and conventional labeling techniques, it is a challenge to localize molecules in three dimensions with high precision in such samples while simultaneously achieving the labeling densities required for high resolution of densely crowded structures. Here we combined lattice light-sheet microscopy with newly developed, freely diffusing, cell-permeable chemical probes with targeted affinity for DNA, intracellular membranes or the plasma membrane. We used this combination to perform high-localization precision, ultrahigh-labeling density, multicolor localization microscopy in samples up to 20 μm thick, including dividing cells and the neuromast organ of a zebrafish embryo. We also demonstrate super-resolution correlative imaging with protein-specific photoactivable fluorophores, providing a mutually compatible, single-platform alternative to correlative light-electron microscopy over large volumes.

}, issn = {1548-7105}, doi = {10.1038/nmeth.3797}, author = {Legant, Wesley R and Shao, Lin and Grimm, Jonathan B and Brown, Timothy A and Milkie, Daniel E and Avants, Brian B and Lavis, Luke D and Betzig, Eric} } @article {47811, title = {Highly photostable, reversibly photoswitchable fluorescent protein with high contrast ratio for live-cell superresolution microscopy.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, year = {2016}, month = {2016 Aug 25}, pages = {10364-9}, abstract = {

Two long-standing problems for superresolution (SR) fluorescence microscopy are high illumination intensity and long acquisition time, which significantly hamper its application for live-cell imaging. Reversibly photoswitchable fluorescent proteins (RSFPs) have made it possible to dramatically lower the illumination intensities in saturated depletion-based SR techniques, such as saturated depletion nonlinear structured illumination microscopy (NL-SIM) and reversible saturable optical fluorescence transition microscopy. The characteristics of RSFPs most critical for SR live-cell imaging include, first, the integrated fluorescence signal across each switching cycle, which depends upon the absorption cross-section, effective quantum yield, and characteristic switching time from the fluorescent "on" to "off" state; second, the fluorescence contrast ratio of on/off states; and third, the photostability under excitation and depletion. Up to now, the RSFPs of the Dronpa and rsEGFP (reversibly switchable EGFP) families have been exploited for SR imaging. However, their limited number of switching cycles, relatively low fluorescence signal, and poor contrast ratio under physiological conditions ultimately restrict their utility in time-lapse live-cell imaging and their ability to reach the desired resolution at a reasonable signal-to-noise ratio. Here, we present a truly monomeric RSFP, Skylan-NS, whose properties are optimized for the recently developed patterned activation NL-SIM, which enables low-intensity (\~{}100 W/cm(2)) live-cell SR imaging at \~{}60-nm resolution at subsecond acquisition times for tens of time points over broad field of view.

}, issn = {1091-6490}, doi = {10.1073/pnas.1611038113}, author = {Zhang, Xi and Zhang, Mingshu and Li, Dong and He, Wenting and Peng, Jianxin and Betzig, Eric and Xu, Pingyong} } @article {47558, title = {High-resolution macromolecular structure determination by MicroED, a cryo-EM method.}, journal = {Methods in Enzymology}, year = {2016}, month = {2016 Jun 16}, abstract = {

Microelectron diffraction (MicroED) is a new cryo-electron microscopy (cryo-EM) method capable of determining macromolecular structures at atomic resolution from vanishingly small 3D crystals. MicroED promises to solve atomic resolution structures from even the tiniest of crystals, less than a few hundred nanometers thick. MicroED complements frontier advances in crystallography and represents part of the rebirth of cryo-EM that is making macromolecular structure determination more accessible for all. Here we review the concept and practice of MicroED, for both the electron microscopist and crystallographer. Where other reviews have addressed specific details of the technique (Hattne et al., 2015,\ Shi et al., 2016\ and\ Shi et al., 2013), we aim to provide context and highlight important features that should be considered when performing a MicroED experiment.

}, keywords = {Electron; Diffraction; MicroED; Crystal; Protein; Crystallography; cryo-EM}, doi = {10.1016/bs.mie.2016.04.017}, author = {Rodriguez, J A and Gonen, Tamir} } @article {47526, title = {Hippocampal global remapping for different sensory modalities in flying bats.}, journal = {Nature Neuroscience}, volume = {19}, year = {2016}, month = {2016 May 30}, pages = {952-8}, abstract = {

Hippocampal place cells encode the animal{\textquoteright}s spatial position. However, it is unknown how different long-range sensory systems affect spatial representations. Here we alternated usage of vision and echolocation in Egyptian fruit bats while recording from single neurons in hippocampal areas CA1 and subiculum. Bats flew back and forth along a linear flight track, employing echolocation in darkness or vision in light. Hippocampal representations remapped between vision and echolocation via two kinds of remapping: subiculum neurons turned on or off, while CA1 neurons shifted their place fields. Interneurons also exhibited strong remapping. Finally, hippocampal place fields were sharper under vision than echolocation, matching the superior sensory resolution of vision over echolocation. Simulating several theoretical models of place-cells suggested that combining sensory information and path integration best explains the experimental sharpening data. In summary, here we show sensory-based global remapping in a mammal, suggesting that the hippocampus does not contain an abstract spatial map but rather a {\textquoteright}cognitive atlas{\textquoteright}, with multiple maps for different sensory modalities.

}, issn = {1546-1726}, doi = {10.1038/nn.4310}, author = {Geva-Sagiv, Maya and Romani, Sandro and Las, Liora and Ulanovsky, Nachum} } @article {47442, title = {Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016}, abstract = {

Clarifying gene expression in narrowly defined neuronal populations can provide insight into cellular identity, computation, and functionality. Here, we used next-generation RNA sequencing (RNA-seq) to produce a quantitative, whole genome characterization of gene expression for the major excitatory neuronal classes of the hippocampus; namely, granule cells and mossy cells of the dentate gyrus, and pyramidal cells of areas CA3, CA2, and CA1. Moreover, for the canonical cell classes of the trisynaptic loop, we profiled transcriptomes at both dorsal and ventral poles, producing a cell-class- and region-specific transcriptional description for these populations. This dataset clarifies the transcriptional properties and identities of lesser-known cell classes, and moreover reveals unexpected variation in the trisynaptic loop across the dorsal-ventral axis. We have created a public resource, Hipposeq (http://hipposeq.janelia.org), which provides analysis and visualization of these data and will act as a roadmap relating molecules to cells, circuits, and computation in the hippocampus.

}, issn = {2050-084X}, doi = {10.7554/eLife.14997}, author = {Cembrowski, Mark S and Wang, Lihua and Sugino, Ken and Shields, Brenda C and Spruston, Nelson} } @article {47883, title = {Hunger: The carrot and the stick.}, journal = {Molecular Metabolism}, volume = {5}, year = {2016}, month = {2016 Jan}, pages = {1-2}, issn = {2212-8778}, doi = {10.1016/j.molmet.2015.10.002}, author = {Sternson, Scott M} } @article {47728, title = {Identification of excitatory premotor interneurons which regulate local muscle contraction during Drosophila larval locomotion.}, journal = {Scientific Reports}, volume = {6}, year = {2016}, month = {2016}, pages = {30806}, abstract = {

We use Drosophila larval locomotion as a model to elucidate the working principles of motor circuits. Larval locomotion is generated by rhythmic and sequential contractions of body-wall muscles from the posterior to anterior segments, which in turn are regulated by motor neurons present in the corresponding neuromeres. Motor neurons are known to receive both excitatory and inhibitory inputs, combined action of which likely regulates patterned motor activity during locomotion. Although recent studies identified candidate inhibitory premotor interneurons, the identity of premotor interneurons that provide excitatory drive to motor neurons during locomotion remains unknown. In this study, we searched for and identified two putative excitatory premotor interneurons in this system, termed CLI1 and CLI2 (cholinergic lateral interneuron 1 and 2). These neurons were segmentally arrayed and activated sequentially from the posterior to anterior segments during peristalsis. Consistent with their being excitatory premotor interneurons, the CLIs formed GRASP- and ChAT-positive putative synapses with motoneurons and were active just prior to motoneuronal firing in each segment. Moreover, local activation of CLI1s induced contraction of muscles in the corresponding body segments. Taken together, our results suggest that the CLIs directly activate motoneurons sequentially along the segments during larval locomotion.

}, issn = {2045-2322}, doi = {10.1038/srep30806}, author = {Hasegawa, Eri and Truman, James W and Nose, Akinao} } @article {48008, title = {Illuminating the neuronal architecture underlying context in fear memory.}, journal = {Cell}, volume = {167}, year = {2016}, month = {2016 Nov 3}, pages = {888-9}, abstract = {

Context plays a foundational role in determining how to interpret potentially fear-producing stimuli, yet the precise neurobiological substrates of context are poorly understood. In this issue of Cell, Xu et\ al. elegantly show that parallel neuronal circuits are necessary for two distinct roles of context in fear conditioning.

}, author = {Cembrowski, Mark S and Spruston, N} } @article {48296, title = {Image-based correction of continuous and discontinuous non-planar axial distortion in serial section microscopy.}, journal = {Bioinformatics (Oxford, England)}, year = {2016}, month = {2016 Dec 23}, abstract = {

MOTIVATION: Serial section microscopy is an established method for detailed anatomy reconstruction of biological specimen. During the last decade, high resolution electron microscopy (EM) of serial sections has become the de-facto standard for reconstruction of neural connectivity at ever increasing scales (EM connectomics). In serial section microscopy, the axial dimension of the volume is sampled by physically removing thin sections from the embedded specimen and subsequently imaging either the block-face or the section series. This process has limited precision leading to inhomogeneous non-planar sampling of the axial dimension of the volume which, in turn, results in distorted image volumes. This includes that section series may be collected and imaged in unknown order.

RESULTS: We developed methods to identify and correct these distortions through image-based signal analysis without any additional physical apparatus or measurements. We demonstrate the efficacy of our methods in proof of principle experiments and application to real world problems.

AVAILABILITY AND IMPLEMENTATION: We made our work available as libraries for the ImageJ distribution Fiji and for deployment in a high performance parallel computing environment. Our sources are open and available at http://github.com/saalfeldlab/section-sort, http://github.com/saalfeldlab/z-spacing and http://github.com/saalfeldlab/z-spacing-spark CONTACT: : saalfelds@janelia.hhmi.orgSupplementary information: Supplementary data are available at Bioinformatics online.

}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btw794}, author = {Hanslovsky, Philipp and Bogovic, John A and Saalfeld, Stephan} } @article {47877, title = {Imaging far and wide.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Sep 23}, pages = {e21072}, abstract = {

A custom-built objective lens called the Mesolens allows relatively large biological specimens to be imaged with cellular resolution.

}, doi = {10.7554/eLife.18659}, author = {Chhetri, Raghav K and Keller, Philipp J} } @article {47812, title = {Improving data quality in neuronal population recordings.}, journal = {Nature Neuroscience}, volume = {19}, year = {2016}, month = {2016 Aug 26}, pages = {1165-74}, abstract = {

Understanding how the brain operates requires understanding how large sets of neurons function together. Modern recording technology makes it possible to simultaneously record the activity of hundreds of neurons, and technological developments will soon allow recording of thousands or tens of thousands. As with all experimental techniques, these methods are subject to confounds that complicate the interpretation of such recordings, and could lead to erroneous scientific conclusions. Here we discuss methods for assessing and improving the quality of data from these techniques and outline likely future directions in this field.

}, issn = {1546-1726}, doi = {10.1038/nn.4365}, author = {Harris, Kenneth D and Quiroga, Rodrigo Quian and Freeman, Jeremy and Smith, Spencer L} } @article {47548, title = {in vivo brain imaging with adaptive optical microscope.}, journal = {Conference on Lasers and Electro-Optics (CLEO): Applications and Technology}, year = {2016}, month = {2016 Jun }, pages = {AM40.1}, abstract = {

The diffraction limited resolution of two photon and confocal microscope can be recovered using adaptive optics to explore the detailed neuronal network in the brains of zebrafish and mouse in vivo.

}, doi = {10.1364/CLEO_AT.2016.AM4O.1}, author = {Wang, Kai and Sun, Wenzhi and Ji, Na and Betzig, Eric} } @article {47969, title = {Increased spatiotemporal resolution reveals highly dynamic dense tubular matrices in the peripheral ER.}, journal = {Science (New York, N.Y.)}, volume = {354}, year = {2016}, month = {2016 Oct 28}, pages = {433-46}, abstract = {

The endoplasmic reticulum (ER) is an expansive, membrane-enclosed organelle that plays crucial roles in numerous cellular functions. We used emerging superresolution imaging technologies to clarify the morphology and dynamics of the peripheral ER, which contacts and modulates most other intracellular organelles. Peripheral components of the ER have classically been described as comprising both tubules and flat sheets. We show that this system consists almost exclusively of tubules at varying densities, including structures that we term ER matrices. Conventional optical imaging technologies had led to misidentification of these structures as sheets because of the dense clustering of tubular junctions and a previously uncharacterized rapid form of ER motion. The existence of ER matrices explains previous confounding evidence that had indicated the occurrence of ER {\textquotedblleft}sheet{\textquotedblright} proliferation after overexpression of tubular junction{\textendash}forming proteins.

}, doi = {10.1126/science.aaf3928}, author = {Nixon-Abell, Jonathon and Obara, Christopher J and Weigel, Aubrey V and Li, Dong and Legant, Wesley R and Xu, CShan and Pasolli, H Amalia and Harvey, Kirsten and Hess, Harald F and Betzig, Eric and Blackstone, Craig and Lippincott-Schwartz, Jennifer} } @article {48842, title = {Inhibitory control of correlated intrinsic variability in cortical networks.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Dec 07}, abstract = {

Cortical networks exhibit intrinsic dynamics that drive coordinated, large-scale fluctuations across neuronal populations and create noise correlations that impact sensory coding. To investigate the network-level mechanisms that underlie these dynamics, we developed novel computational techniques to fit a deterministic spiking network model directly to multi-neuron recordings from different rodent species, sensory modalities, and behavioral states. The model generated correlated variability without external noise and accurately reproduced the diverse activity patterns in our recordings. Analysis of the model parameters suggested that differences in noise correlations across recordings were due primarily to differences in the strength of feedback inhibition. Further analysis of our recordings confirmed that putative inhibitory neurons were indeed more active during desynchronized cortical states with weak noise correlations. Our results demonstrate that network models with intrinsically-generated variability can accurately reproduce the activity patterns observed in multi-neuron recordings and suggest that inhibition modulates the interactions between intrinsic dynamics and sensory inputs to control the strength of noise correlations.

}, issn = {2050-084X}, doi = {10.7554/eLife.19695}, author = {Stringer, Carsen and Pachitariu, Marius and Steinmetz, Nicholas A and Okun, Michael and Bartho, Peter and Harris, Kenneth D and Sahani, Maneesh and Lesica, Nicholas A} } @article {65751, title = {Inhibitory control of correlated intrinsic variability in cortical networks}, journal = {Elife}, volume = {5}, year = {2016}, month = {12/2016}, pages = {e19695}, abstract = {

Cortical networks exhibit intrinsic dynamics that drive coordinated, large-scale fluctuations across neuronal populations and create noise correlations that impact sensory coding. To investigate the network-level mechanisms that underlie these dynamics, we developed novel computational techniques to fit a deterministic spiking network model directly to multi-neuron recordings from different rodent species, sensory modalities, and behavioral states. The model generated correlated variability without external noise and accurately reproduced the diverse activity patterns in our recordings. Analysis of the model parameters suggested that differences in noise correlations across recordings were due primarily to differences in the strength of feedback inhibition. Further analysis of our recordings confirmed that putative inhibitory neurons were indeed more active during desynchronized cortical states with weak noise correlations. Our results demonstrate that network models with intrinsically-generated variability can accurately reproduce the activity patterns observed in multi-neuron recordings and suggest that inhibition modulates the interactions between intrinsic dynamics and sensory inputs to control the strength of noise correlations.

}, doi = {https://doi.org/10.7554/eLife.19695}, author = {Stringer, Carsen and Pachitariu, Marius and Steinmetz, Nicholas A and Okun, Michael and Bartho, Peter and Harris, Kenneth D and Sahani, Maneesh and Lesica, Nicholas A} } @article {48990, title = {The insect central complex.}, journal = {Current Biology : CB}, volume = {26}, year = {2016}, month = {2016 Jun 06}, pages = {R453-7}, abstract = {

Hordes of tourists flock to Washington, D.C. every spring to see the cherry trees blossom. Once in the city, they must find their way to the Tidal Basin where the Japanese trees grow. Fortunately, a number of visual landmarks can help them to navigate. In 1910, the United States Congress passed The Height of Buildings Act, limiting the elevation of commercial and residential structures in D.C. to 130 feet. Thus, the 555-foot-tall Washington Monument often looms large against the horizon, serving as an anchor point to help set the tourists{\textquoteright} sense of direction. Once their heading is set, they can lose sight of the monument behind buildings or groups of tall Scandinavian visitors and still use their internal compass to navigate to the Basin. This compass keeps track of their paces and turns and updates their sense of where they are and where they need to go. Yet while their heading informs their actions, it does not dictate them. Tourists who have been to D.C. in the past can, for example, use remembered views to alter their routes to avoid crowds. On an even finer scale, their leg movements also depend on their current state - they might increase the frequency and length of their strides if hunger pangs compete with their desire to see cherry blossoms, for example. The way in which these disparate cues and motivations influence exploration is a neuroscience mystery across creatures large and small.

}, keywords = {Animals, Brain, Cues, Insecta, Spatial Navigation, Vision, Ocular}, issn = {1879-0445}, doi = {10.1016/j.cub.2016.04.006}, author = {Turner-Evans, Daniel B and Jayaraman, Vivek} } @article {48801, title = {Labeling cellular structures in vivo using confined primed conversion of photoconvertible fluorescent proteins.}, journal = {Nature Protocols}, volume = {11}, year = {2016}, month = {2016 Dec}, pages = {2419-2431}, abstract = {

The application of green-to-red photoconvertible fluorescent proteins (PCFPs) for in vivo studies in complex 3D tissue structures has remained limited because traditional near-UV photoconversion is not confined in the axial dimension, and photomodulation using axially confined, pulsed near-IR (NIR) lasers has proven inefficient. Confined primed conversion is a dual-wavelength continuous-wave (CW) illumination method that is capable of axially confined green-to-red photoconversion. Here we present a protocol to implement this technique with a commercial confocal laser-scanning microscope (CLSM); evaluate its performance on an in vitro setup; and apply primed conversion for in vivo labeling of single cells in developing zebrafish and mouse preimplantation embryos expressing the green-to-red photoconvertible protein Dendra2. The implementation requires a basic understanding of laser-scanning microscopy, and it can be performed within a single day once the required filter cube is manufactured.

}, keywords = {Animals, Light, Luminescent Proteins, Mice, Microscopy, Confocal, Staining and Labeling, Zebrafish}, issn = {1750-2799}, doi = {10.1038/nprot.2016.134}, author = {Mohr, Manuel Alexander and Argast, Paul and Pantazis, Periklis} } @article {47551, title = {A large field of view two-photon mesoscope with subcellular resolution for in vivo imaging.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Jun 14}, pages = {e14472}, abstract = {

Imaging is used to map activity across populations of neurons. Microscopes with cellular resolution have small (\<1 millimeter) fields of view and cannot simultaneously image activity distributed across multiple brain areas. Typical large field of view microscopes do not resolve single cells, especially in the axial dimension. We developed a 2-photon random access mesoscope (2p-RAM) that allows high-resolution imaging anywhere within a volume spanning multiple brain areas (∅ 5 mm x 1 mm cylinder). 2p-RAM resolution is near diffraction limited (lateral, 0.66 μm, axial 4.09 μm at the center; excitation wavelength = 970 nm; numerical aperture = 0.6) over a large range of excitation wavelengths. A fast three-dimensional scanning system allows efficient sampling of neural activity in arbitrary regions of interest across the entire imaging volume. We illustrate the use of the 2p-RAM by imaging neural activity in multiple, non-contiguous brain areas in transgenic mice expressing protein calcium sensors.

}, issn = {2050-084X}, doi = {10.7554/eLife.14472}, author = {Sofroniew, Nicholas James and Flickinger, Daniel and King, Jonathon and Svoboda, Karel} } @article {47599, title = {A large fraction of neocortical myelin ensheathes axons of local inhibitory neurons.}, journal = {eLife}, year = {2016}, month = {2016 Jul 6}, abstract = {

Myelin is best known for its role in increasing the conduction velocity and metabolic efficiency of long-range excitatory axons. Accordingly, the myelin observed in neocortical gray matter is thought to mostly ensheath excitatory axons connecting to subcortical regions and distant cortical areas. Using independent analyses of light and electron microscopy data from mouse neocortex, we show that a surprisingly large fraction of cortical myelin (half the myelin in layer 2/3 and a quarter in layer 4) ensheathes axons of inhibitory neurons, specifically of parvalbumin-positive basket cells. This myelin differs significantly from that of excitatory axons in distribution and protein composition. Myelin on inhibitory axons is unlikely to meaningfully hasten the arrival of spikes at their pre-synaptic terminals, due to the patchy distribution and short path-lengths observed. Our results thus highlight the need for exploring alternative roles for myelin in neocortical circuits.

}, doi = {10.7554/eLife.15784}, author = {Micheva, Kristina D and Wolman, Dylan and Mensh, Brett D and Pax, Elizabeth and Buchanan, JoAnn and Smith, Stephen J and Bock, Davi D} } @article {47925, title = {Large-scale electron microscopy image segmentation in spark.}, journal = {arXiv}, year = {2016}, month = {1 April 2016}, pages = {arXiv:1604.00385 }, abstract = {

The emerging field of connectomics aims to unlock the mysteries of the brain by understanding the connectivity between neurons. To map this connectivity, we acquire thousands of electron microscopy (EM) images with nanometer-scale resolution. After aligning these images, the resulting dataset has the potential to reveal the shapes of neurons and the synaptic connections between them. However, imaging the brain of even a tiny organism like the fruit fly yields terabytes of data. It can take years of manual effort to examine such image volumes and trace their neuronal connections. One solution is to apply image segmentation algorithms to help automate the tracing tasks. In this paper, we propose a novel strategy to apply such segmentation on very large datasets that exceed the capacity of a single machine. Our solution is robust to potential segmentation errors which could otherwise severely compromise the quality of the overall segmentation, for example those due to poor classifier generalizability or anomalies in the image dataset. We implement our algorithms in a Spark application which minimizes disk I/O, and apply them to a few large EM datasets, revealing both their effectiveness and scalability. We hope this work will encourage external contributions to EM segmentation by providing 1) a flexible plugin architecture that deploys easily on different cluster environments and 2) an in-memory representation of segmentation that could be conducive to new advances.

}, author = {Plaza, Stephen M and Berg, Stuart E.} } @article {47974, title = {Layer 4 fast-spiking interneurons filter thalamocortical signals during active somatosensation.}, journal = {Nature Neuroscience}, volume = {19}, year = {2016}, month = {2016 Oct 17}, pages = {1647-57}, abstract = {

We rely on movement to explore the environment, for example, by palpating an object. In somatosensory cortex, activity related to movement of digits or whiskers is suppressed, which could facilitate detection of touch. Movement-related suppression is generally assumed to involve corollary discharges. Here we uncovered a thalamocortical mechanism in which cortical fast-spiking interneurons, driven by sensory input, suppress movement-related activity in layer 4 (L4) excitatory neurons. In mice locating objects with their whiskers, neurons in the ventral posteromedial nucleus (VPM) fired in response to touch and whisker movement. Cortical L4 fast-spiking interneurons inherited these responses from VPM. In contrast, L4 excitatory neurons responded mainly to touch. Optogenetic experiments revealed that fast-spiking interneurons reduced movement-related spiking in excitatory neurons, enhancing selectivity for touch-related information during active tactile sensation. These observations suggest a fundamental computation performed by the thalamocortical circuit to accentuate salient tactile information.

}, issn = {1546-1726}, doi = {10.1038/nn.4412}, author = {Yu, Jianing and Gutnisky, Diego A and Hires, S Andrew and Svoboda, Karel} } @conference {48194, title = {Learning a metric for class-conditional KNN.}, booktitle = {International Joint Conference on Neural Networks, IJCNN 2016}, year = {2016}, month = {2016 Oct 31}, address = {Vancouver, British Columbia, Canada}, abstract = {

Na{\"\i}ve Bayes Nearest Neighbour (NBNN) is a simple and effective framework which addresses many of the pitfalls of K-Nearest Neighbour (KNN) classification. It has yielded competitive results on several computer vision benchmarks. Its central tenet is that during NN search, a query is not compared to every example in a database, ignoring class information. Instead, NN searches are performed within each class, generating a score per class. A key problem with NN techniques, including NBNN, is that they fail when the data representation does not capture perceptual (e.g. class-based) similarity. NBNN circumvents this by using independent engineered descriptors (e.g. SIFT). To extend its applicability outside of image-based domains, we propose to learn a metric which captures perceptual similarity. Similar to how Neighbourhood Components Analysis optimizes a differentiable form of KNN classification, we propose {\textquoteright}Class Conditional{\textquoteright} metric learning (CCML), which optimizes a soft form of the NBNN selection rule. Typical metric learning algorithms learn either a global or local metric. However, our proposed method can be adjusted to a particular level of locality by tuning a single parameter. An empirical evaluation on classification and retrieval tasks demonstrates that our proposed method clearly outperforms existing learned distance metrics across a variety of image and non-image datasets.

}, doi = {10.1109/IJCNN.2016.7727436}, author = {Im, Daniel Jiwoong and Taylor, Graham W} } @article {48005, title = {Learning recurrent representations for hierarchical behavior modeling.}, journal = {arXiv}, volume = {arXiv:1611.00094}, year = {2016}, month = {2016 Nov 1}, abstract = {

We propose a framework for detecting action patterns from motion sequences and modeling the sensory-motor relationship of animals, using a generative recurrent neural network. The network has a discriminative part (classifying actions) and a generative part (predicting motion), whose recurrent cells are laterally connected, allowing higher levels of the network to represent high level phenomena. We test our framework on two types of data, fruit fly behavior and online handwriting. Our results show that 1) taking advantage of unlabeled sequences, by predicting future motion, significantly improves action detection performance when training labels are scarce, 2) the network learns to represent high level phenomena such as writer identity and fly gender, without supervision, and 3) simulated motion trajectories, generated by treating motion prediction as input to the network, look realistic and may be used to qualitatively evaluate whether the model has learnt generative control rules.

}, author = {Eyjolfsdottir, Eyrun and Branson, Kristin and Yue, Yisong and Perona, Pietro} } @article {47937, title = {Light sheet microscopes: Novel imaging toolbox for visualizing life{\textquoteright}s processes.}, journal = {The International Journal of Biochemistry \& Cell Biology}, year = {2016}, month = {2016 Oct 7}, abstract = {

Capturing dynamic processes in live samples is a nontrivial task in biological imaging. Although fluorescence provides high specificity and contrast compared to other light microscopy techniques, the photophysical principles of this method can have a harmful effect on the sample. Current advances in light sheet microscopy have created a novel imaging toolbox that allows for rapid acquisition of high-resolution fluorescent images with minimal perturbation of the processes of interest. Each unique design has its own advantages and limitations. In this review, we describe several cutting edge light sheet microscopes and their optimal applications.

}, issn = {1878-5875}, doi = {10.1016/j.biocel.2016.10.002}, author = {Heddleston, John M and Chew, Teng-Leong} } @article {47399, title = {Lineage mapping identifies molecular and architectural similarities between the larval and adult Drosophila central nervous system.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016}, abstract = {

Neurogenesis in Drosophila occurs in two phases, embryonic and post-embryonic, in which the same set of neuroblasts give rise to the distinct larval and adult nervous systems, respectively. Here, we identified the embryonic neuroblast origin of the adult neuronal lineages in the ventral nervous system via lineage-specific GAL4 lines and molecular markers. Our lineage mapping revealed that neurons born late in the embryonic phase show axonal morphology and transcription factor profiles that are similar to the neurons born post-embryonically from the same neuroblast. Moreover, we identified three thorax-specific neuroblasts not previously characterized and show that HOX genes confine them to the thoracic segments. Two of these, NB2-3 and NB3-4, generate leg motor neurons. The other neuroblast is novel and appears to have arisen recently during insect evolution. Our findings provide a comprehensive view of neurogenesis and show how proliferation of individual neuroblasts is dictated by temporal and spatial cues.

}, issn = {2050-084X}, doi = {10.7554/eLife.13399}, author = {Lacin, Haluk and Truman, James W} } @article {48135, title = {Live cell single molecule-guided Bayesian localization super resolution microscopy.}, journal = {Cell Research}, year = {2016}, month = {2016 Dec 30}, issn = {1748-7838}, doi = {10.1038/cr.2015.160}, author = {Xu, Fan and Zhang, Mingshu and He, Wenting and Han, Renmin and Xue, Fudong and Liu, Zhiyong and Zhang, Fa and Lippincott-Schwartz, Jennifer and Xu, Pingyong} } @article {47933, title = {Live-cell single-molecule tracking reveals co-recognition of H3K27me3 and DNA targets polycomb Cbx7-PRC1 to chromatin.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Oct 10}, abstract = {

The Polycomb PRC1 plays essential roles in development and disease pathogenesis. Targeting of PRC1 to chromatin is thought to be mediated by the Cbx family proteins (Cbx2/4/6/7/8) binding to histone H3 with a K27me3 modification (H3K27me3). Despite this prevailing view, the molecular mechanisms of targeting remain poorly understood. Here, by combining live-cell single-molecule tracking (SMT) and genetic engineering, we reveal that H3K27me3 contributes significantly to the targeting of Cbx7 and Cbx8 to chromatin, but less to Cbx2, Cbx4, and Cbx6. Genetic disruption of the complex formation of PRC1 facilitates the targeting of Cbx7 to chromatin. Biochemical analyses uncover that the CD and AT-hook-like (ATL) motif of Cbx7 constitute a functional DNA-binding unit. Live-cell SMT of Cbx7 mutants demonstrates that Cbx7 is targeted to chromatin by co-recognizing of H3K27me3 and DNA. Our data suggest a novel hierarchical cooperation mechanism by which histone modifications and DNA coordinate to target chromatin regulatory complexes.

}, issn = {2050-084X}, doi = {10.7554/eLife.17667}, author = {Zhen, Chao Yu and Tatavosian, Roubina and Huynh, Thao Ngoc and Duc, Huy Nguyen and Das, Raibatak and Kokotovic, Marko and Grimm, Jonathan B and Lavis, Luke D and Lee, Jun and Mejia, Frances J and Li, Yang and Yao, Tingting and Ren, Xiaojun} } @article {48044, title = {Long distance projections of cortical pyramidal neurons.}, journal = {Journal of Neuroscience Research}, year = {2016}, month = {2016 Nov 12}, abstract = {

The neuronal circuits defined by the axonal projections of pyramidal neurons in the cerebral cortex are responsible for processing sensory and other information to plan and execute behavior. Subtypes of cortical pyramidal neurons are organized across layers, with those in different layers distinguished by their patterns of axonal projections and connectivity. For example, those in layers 2 and 3 project between cortical areas to integrate sensory and other information with motor areas; while those in layers 5 and 6 also integrate information between cortical areas, but also project to subcortical structures involved in the generation of behavior. Recent advances in neuroanatomical techniques allow one to target specific subtypes of cortical pyramidal neurons and label both their inputs and projections. Combining these methods with neurophysiological recording techniques and newly introduced atlases of the mouse brain provide the opportunity to achieve a detailed view of the organization of cerebral cortical circuits.

}, doi = {10.1002/jnr.23978}, author = {Gerfen, Charles R and Economo, Michael N and Chandrashekar, Jayaram} } @article {47565, title = {Macular telangiectasia type 1 managed with long-term aflibercept therapy.}, journal = {Ophthalmic Surgery, Lasers and Imaging Retina}, volume = {47}, year = {2016}, month = {2016 Jun}, pages = {593-5}, abstract = {

A 60-year-old man diagnosed with macular telangiectasia type 1 (MacTel 1) was treated for 3 years with monthly aflibercept (Eylea; Regeneron, Tarrytown, NY) and serially imaged with spectral-domain optical coherence tomography. When administered monthly, aflibercept appeared to have a beneficial effect on macular edema secondary to MacTel 1. Visual acuity preservation despite minimal chronic macular edema could be attributed to the lack of significant photoreceptor disruption.

}, doi = {10.3928/23258160-20160601-14}, author = {Kovach, Jaclyn L and Hess, Harald F and Rosenfeld, Philip J} } @article {47383, title = {A mammalian enhancer trap resource for discovering and manipulating neuronal cell types.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Mar 21}, abstract = {

There is a continuing need for driver strains to enable cell type-specific manipulation in the nervous system. Each cell type expresses a unique set of genes, and recapitulating expression of marker genes by BAC transgenesis or knock-in has generated useful transgenic mouse lines. However since genes are often expressed in many cell types, many of these lines have relatively broad expression patterns. We report an alternative transgenic approach capturing distal enhancers for more focused expression. We identified an enhancer trap probe often producing restricted reporter expression and developed efficient enhancer trap screening with the PiggyBac transposon. We established more than 200 lines and found many lines that label small subsets of neurons in brain substructures, including known and novel cell types. Images and other information about each line are available online (enhancertrap.bio.brandeis.edu).

}, issn = {2050-084X}, doi = {10.7554/eLife.13503}, author = {Shima, Yasuyuki and Sugino, Ken and Hempel, Chris and Shima, Masami and Taneja, Praveen and Bullis, James B and Mehta, Sonam and Lois, Carlos and Nelson, Sacha B} } @conference {48178, title = {Mapping auto-context decision forests to deep ConvNets for semantic segmentation.}, booktitle = {British Machine Vision Conference}, year = {2016}, month = {2016 Sep 19}, address = {York}, abstract = {

In this paper, we propose a mapping from the Auto-context model to a deep Convolutional Neural Network (ConvNet), bridging the gap be- tween these two models, and helping address the challenge of training ConvNets with limited training data.\ 

}, url = {http://www.bmva.org/bmvc/2016/abstracts.pdf}, author = {Richmond, David L and Kainmueller, Dagmar and Yang, Michael Y and Myers, Eugene W and Rother, Carsten} } @article {47398, title = {Mapping translation {\textquoteright}hot-spots{\textquoteright} in live cells by tracking single molecules of mRNA and ribosomes.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016}, abstract = {

Messenger RNA localization is important for cell motility by local protein translation. However, while single mRNAs can be imaged and their movements tracked in single cells, it has not yet been possible to determine whether these mRNAs are actively translating. Therefore, we imaged single β-actin mRNAs tagged with MS2 stem loops colocalizing with labeled ribosomes to determine when polysomes formed. A dataset of tracking information consisting of thousands of trajectories per cell demonstrated that mRNAs co-moving with ribosomes have significantly different diffusion properties from non-translating mRNAs that were exposed to translation inhibitors. These data indicate that ribosome load changes mRNA movement and therefore highly translating mRNAs move slower. Importantly, β-actin mRNA near focal adhesions exhibited sub-diffusive corralled movement characteristic of increased translation. This method can identify where ribosomes become engaged for local protein production and how spatial regulation of mRNA-protein interactions mediates cell directionality.

}, issn = {2050-084X}, doi = {10.7554/eLife.10415}, author = {Katz, Zachary B and English, Brian P and Lionnet, Timoth{\'e}e and Yoon, Young J and Monnier, Nilah and Ovryn, Ben and Bathe, Mark and Singer, Robert H} } @article {47992, title = {A mechanosensory circuit that mixes opponent channels to produce selectivity for complex stimulus features.}, journal = {Neuron}, volume = {92}, year = {2016}, month = {2016 Oct 27}, pages = {888-901}, abstract = {

Johnston{\textquoteright}s organ is the largest mechanosensory organ in\ Drosophila; it analyzes movements of the antenna due to sound, wind, gravity, and touch. Different Johnston{\textquoteright}s organ neurons (JONs) encode distinct stimulus features. Certain JONs respond in a sustained manner to steady displacements, and these JONs subdivide into opponent populations that prefer push or pull displacements. Here, we describe neurons in the brain (aPN3 neurons) that combine excitation and inhibition from push/pull JONs in different ratios. Consequently, different aPN3 neurons are sensitive to movement in different parts of the antenna{\textquoteright}s range, at different frequencies, or at different amplitude modulation rates. We use a model to show how the tuning of aPN3 neurons can arise from rectification and temporal filtering in JONs, followed by mixing of JON signals in different proportions. These results illustrate how several canonical neural circuit components{\textemdash}rectification, opponency, and filtering{\textemdash}can combine to produce selectivity for complex stimulus features.

}, doi = {10.1016/j.neuron.2016.09.059}, author = {Chang, Allison EB and Vaughan, Alexander G and Wilson, Rachel} } @article {47790, title = {Membrane dynamics of dividing cells imaged by lattice light-sheet microscopy.}, journal = {Molecular Biology of the Cell}, volume = {27}, year = {2016}, month = {2016 Aug 17}, pages = {3418-35}, abstract = {

Membrane remodeling is an essential part for transfer of components to and from the cell surface and membrane-bound organelles, and for changes in cell shape, particularly critical during cell division. Earlier analyses, based on classical optical live-cell imaging, mostly restricted by technical necessity to the attached bottom surface, showed persistent formation of endocytic clathrin pits and vesicles during mitosis. Taking advantage of the resolution, speed, and non-invasive illumination of the newly developed lattice light sheet fluorescence microscope, we reexamined their assembly dynamics over the entire cell surface and showed that clathrin pits form at a lower rate during late mitosis. Full-cell imaging measurements of cell surface area and volume throughout the cell cycle of single cells in culture and in zebrafish embryos showed that the total surface increased rapidly during the transition from telophase to cytokinesis, whereas cell volume increased slightly in metaphase and remained relatively constant during cytokinesis. These applications demonstrate the advantage of lattice light sheet microscopy and enable a new standard for imaging membrane dynamics in single cells and in multicellular assemblies.

}, issn = {1939-4586}, doi = {10.1091/mbc.E16-03-0164}, author = {Aguet, Fran{\c c}ois and Upadhyayula, Srigokul and Gaudin, Rapha{\"e}l and Chou, Yi-ying and Cocucci, Emanuele and He, Kangmin and Chen, Bi-Chang and Mosaliganti, Kishore and Pasham, Mithun and Skillern, Wesley and Legant, Wesley R and Liu, Tsung-Li and Findlay, Greg and Marino, Eric and Danuser, Gaudenz and Megason, Sean and Betzig, Eric and Kirchhausen, Tom} } @article {47966, title = {Memory elicited by courtship conditioning requires mushroom body neuronal subsets similar to those utilized in appetitive memory.}, journal = {PLoS One}, volume = {11}, year = {2016}, month = {2016 Oct 20}, pages = {e0164516}, abstract = {

An animal{\textquoteright}s ability to learn and to form memories is essential for its survival. The fruit fly has proven to be a valuable model system for studies of learning and memory. One learned behavior in fruit flies is courtship conditioning. In Drosophila courtship conditioning, male flies learn not to court females during training with an unreceptive female. He retains a memory of this training and for several hours decreases courtship when subsequently paired with any female. Courtship conditioning is a unique learning paradigm; it uses a positive-valence stimulus, a female fly, to teach a male to decrease an innate behavior, courtship of the female. As such, courtship conditioning is not clearly categorized as either appetitive or aversive conditioning. The mushroom body (MB) region in the fruit fly brain is important for several types of memory; however, the precise subsets of intrinsic and extrinsic MB neurons necessary for courtship conditioning are unknown. Here, we disrupted synaptic signaling by driving a shibirets effector in precise subsets of MB neurons, defined by a collection of split-GAL4 drivers. Out of 75 lines tested, 32 showed defects in courtship conditioning memory. Surprisingly, we did not have any hits in the γ lobe Kenyon cells, a region previously implicated in courtship conditioning memory. We did find that several γ lobe extrinsic neurons were necessary for courtship conditioning memory. Overall, our memory hits in the dopaminergic neurons (DANs) and the mushroom body output neurons were more consistent with results from appetitive memory assays than aversive memory assays. For example, protocerebral anterior medial DANs were necessary for courtship memory, similar to appetitive memory, while protocerebral posterior lateral 1 (PPL1) DANs, important for aversive memory, were not needed. Overall, our results indicate that the MB circuits necessary for courtship conditioning memory coincide with circuits necessary for appetitive memory.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0164516}, author = {Montague, Shelby A and Baker, Bruce S} } @article {47733, title = {Midbody remnant licenses primary cilia formation in epithelial cells.}, journal = {The Journal of Cell Biology}, volume = {214}, year = {2016}, month = {2016 Aug 1}, pages = {237-9}, abstract = {

Tethered midbody remnants dancing across apical microvilli, encountering the centrosome, and beckoning forth a cilium-who would have guessed this is how polarized epithelial cells coordinate the end of mitosis and the beginning of ciliogenesis? New evidence from Bernab{\'e}-Rubio et al. (2016. J. Cell Biol http://dx.doi.org/10.1083/jcb.201601020) supports this emerging model.

}, issn = {1540-8140}, doi = {10.1083/jcb.201607046}, author = {Ott, Carolyn M} } @article {47752, title = {MLlib: Machine learning in Apache Spark.}, journal = {Journal of Machine Learning Research}, volume = {17}, year = {2016}, month = {2016 Apr 01}, pages = {1-7}, abstract = {

Apache Spark is a popular open-source platform for large-scale data processing that is well-suited for iterative machine learning tasks. In this paper we present MLlib, Spark{\textquoteright}s open-source distributed machine learning library. MLlib provides efficient functionality for a wide range of learning settings and includes several underlying statistical, optimization, and linear algebra primitives. Shipped with Spark, MLlib supports several languages and provides a high-level API that leverages Spark{\textquoteright}s rich ecosystem to simplify the development of end-to-end machine learning pipelines. MLlib has experienced a rapid growth due to its vibrant open-source community of over 140 contributors, and includes extensive documentation to support further growth and to let users quickly get up to speed.\ 

}, url = {http://www.jmlr.org/papers/volume17/15-237/15-237.pdf}, author = {Meng, Xiangrui and Bradley, Joseph and Yavus, Burak and Sparks, Evan and Venkataraman, Shivaram and Liu, Davies and Freeman, Jeremy and Tsai, D B and Amde, Manish and Owen, Sean and Xin, Doris and Franklin, Michael J and Zadeh, Reza and Zaharia, Matei and Talwalkar, Ameet} } @article {47484, title = {Modeling truncated pixel values of faint reflections in MicroED images.}, journal = {Journal of Applied Crystallography}, volume = {49}, year = {2016}, month = {2016 May 11}, abstract = {

The weak pixel counts surrounding the Bragg spots in a diffraction image are important for establishing a model of the background underneath the peak and estimating the reliability of the integrated intensities. Under certain circumstances, particularly with equipment not optimized for low-intensity measurements, these pixel values may be corrupted by corrections applied to the raw image. This can lead to truncation of low pixel counts, resulting in anomalies in the integrated Bragg intensities, such as systematically higher signal-to-noise ratios. A correction for this effect can be approximated by a three-parameter lognormal distribution fitted to the weakly positive-valued pixels at similar scattering angles. The procedure is validated by the improved\ refinement\ of an atomic model against\ structure factor\ amplitudes derived from corrected micro-electron diffraction (MicroED) images.

}, doi = {10.1107/S1600576716007196}, author = {Hattne, Johan and Shi, Dan and de la Cruz, M Jason and Reyes, Francis E and Gonen, Tamir} } @article {47912, title = {Molecularly Defined Subplate Neurons Project Both to Thalamocortical Recipient Layers and Thalamus.}, journal = {Cerebral Cortex (New York, N.Y. : 1991)}, volume = {27}, year = {2016}, month = {2016 Sep 20}, pages = {4759-68}, abstract = {

In mammals, subplate neurons (SPNs) are among the first generated cortical neurons. While most SPNs exist only transiently during development, a number of SPNs persist among adult Layer 6b (L6b). During development, SPNs receive thalamic and intra-cortical input, and primarily project to Layer 4 (L4). SPNs are critical for the anatomical and functional development of thalamocortical connections and also pioneer corticothalamic projections. Since SPNs are heterogeneous, SPN subpopulations might serve different roles. Here, we investigate the connectivity of one subpopulation, complexin-3 (Cplx3)-positive SPNs (Cplx3-SPNs), in mouse whisker somatosensory (barrel) cortex (S1). We find that many Cplx3-SPNs survive into adulthood and become a subpopulation of L6b. Cplx3-SPNs axons project to thalamorecipient layers, that is, L4, 5a, and 1. The L4 projections are biased towards the septal regions between barrels in the second postnatal week. Thus, S1 Cplx3-SPN targets co-localize with the eventual projections of the medial posterior thalamic nucleus (POm). In addition to their cortical targets, Cplx3-SPNs also extend long-range axons to several thalamic nuclei, including POm. Thus, Cplx3-SPN/L6b neurons are associated with paralemniscal pathways and can potentially directly link thalamocortical and corticothalamic circuits. This suggests an additional key role for SPNs in the establishment and maintenance of thalamocortical processing.

}, issn = {1460-2199}, doi = {10.1093/cercor/bhw271}, author = {Viswanathan, Sarada and Sheikh, Aminah and Looger, Loren L and Kanold, Patrick O} } @article {47973, title = {Motion quantification during multi-photon functional imaging in behaving animals.}, journal = {Biomedical Optics Express}, volume = {7}, year = {2016}, month = {2016 Sep 1}, pages = {3686-3695}, abstract = {

Functional imaging in behaving animals is essential to understanding brain function. However, artifacts resulting from animal motion, including locomotion, can severely corrupt functional measurements. To dampen tissue motion, we designed a new optical window with minimal optical aberrations. Using the newly developed high-speed continuous volumetric imaging system based on an optical phase-locked ultrasound lens, we quantified motion of the cerebral cortex and hippocampal surface during two-photon functional imaging in behaving mice. We find that the out-of-plane motion is generally greater than the axial dimension of the point-spread-function during mouse locomotion, which indicates that high-speed continuous volumetric imaging is necessary to minimize motion artifacts.

}, doi = {10.1364/BOE.7.003686}, author = {Kong, Lingjie and Little, Justin P and Cui, Meng} } @article {47561, title = {Motor control of fly feeding.}, journal = {Journal of Neurogenetics}, volume = {30}, year = {2016}, month = {2016 Jun 16}, pages = {101-11}, abstract = {

Following considerable progress on the molecular and cellular basis of taste perception in fly sensory neurons, the time is now ripe to explore how taste information, integrated with hunger and satiety, undergo a sensorimotor transformation to lead to the motor actions of feeding behavior. I examine what is known of feeding circuitry in adult flies from more than 250 years of work in larger flies and from newer work in Drosophila. I review the anatomy of the proboscis, its muscles and their functions (where known), its motor neurons, interneurons known to receive taste inputs, interneurons that diverge from taste circuitry to provide information to other circuits, interneurons from other circuits that converge on feeding circuits, proprioceptors that influence the motor control of feeding, and sites of integration of hunger and satiety on feeding circuits. In spite of the several neuron types now known, a connected pathway from taste inputs to feeding motor outputs has yet to be found. We are on the threshold of an era where these individual components will be assembled into circuits, revealing how nervous system architecture leads to the control of behavior.

}, issn = {1563-5260}, doi = {10.1080/01677063.2016.1177047}, author = {McKellar, Claire E} } @article {47424, title = {Movement and structure of mitochondria in oligodendrocytes and their myelin sheaths.}, journal = {Glia}, volume = {64}, year = {2016}, month = {2016 May}, pages = {810-25}, abstract = {

Mitochondria play several crucial roles in the life of oligodendrocytes. During development of the myelin sheath they are essential providers of carbon skeletons and energy for lipid synthesis. During normal brain function their consumption of pyruvate will be a key determinant of how much lactate is available for oligodendrocytes to export to power axonal function. Finally, during calcium-overload induced pathology, as occurs in ischemia, mitochondria may buffer calcium or induce apoptosis. Despite their important functions, very little is known of the properties of oligodendrocyte mitochondria, and mitochondria have never been observed in the myelin sheaths. We have now used targeted expression of fluorescent mitochondrial markers to characterize the location and movement of mitochondria within oligodendrocytes. We show for the first time that mitochondria are able to enter and move within the myelin sheath. Within the myelin sheath the highest number of mitochondria was in the cytoplasmic ridges along the sheath. Mitochondria moved more slowly than in neurons and, in contrast to their behavior in neurons and astrocytes, their movement was increased rather than inhibited by glutamate activating NMDA receptors. By electron microscopy we show that myelin sheath mitochondria have a low surface area of cristae, which suggests a low ATP production. These data specify fundamental properties of the oxidative phosphorylation system in oligodendrocytes, the glial cells that enhance cognition by speeding action potential propagation and provide metabolic support to axons. GLIA 2016;64:810-825.

}, issn = {1098-1136}, doi = {10.1002/glia.22965}, author = {Rinholm, Johanne E and Vervaeke, Koen and Tadross, Michael R and Tkachuk, Ariana N and Kopek, Benjamin G and Brown, Timothy A and Bergersen, Linda H and Clayton, David A} } @article {47418, title = {Multifocus microscopy with precise color multi-phase diffractive optics applied in functional neuronal imaging.}, journal = {Biomedical Optics Express}, volume = {7}, year = {2016}, month = {2016 Feb 16}, pages = {855-69}, abstract = {

Multifocus microscopy (MFM) allows high-resolution instantaneous three-dimensional (3D) imaging and has been applied to study biological specimens ranging from single molecules inside cells nuclei to entire embryos. We here describe pattern designs and nanofabrication methods for diffractive optics that optimize the light-efficiency of the central optical component of MFM: the diffractive multifocus grating (MFG). We also implement a {\textquotedblleft}precise color{\textquotedblright} MFM layout with MFGs tailored to individual fluorophores in separate optical arms. The reported advancements enable faster and brighter volumetric time-lapse imaging of biological samples. In live microscopy applications, photon budget is a critical parameter and light-efficiency must be optimized to obtain the fastest possible frame rate while minimizing photodamage. We provide comprehensive descriptions and code for designing diffractive optical devices, and a detailed methods description for nanofabrication of devices. Theoretical efficiencies of reported designs is ≈90\% and we have obtained efficiencies of \> 80\% in MFGs of our own manufacture. We demonstrate the performance of a multi-phase MFG in 3D functional neuronal imaging in living\ C. elegans.

Additional authors include:

Xin Jin, Joan Pulupa, Christine Cho, Mustafa Mir, Mohamed El Beheiry, Xavier Darzacq, Marcelo Nollmann, Maxime Dahan, Carl Wu, Timoth{\'e}e Lionnet, J. Alexander Liddle, and Cornelia I. Bargmann

}, doi = {10.1364/BOE.7.000855}, author = {Abrahamsson, Sara and Ilic, Rob and Wisniewski, Jan and Mehl, Brian and Yu, Liya and Chen, Lei and Davanco, Marcelo and Oujedi, Laura and Fiche, Jean-Bernard and Hajj, Bassam} } @article {48299, title = {The multilayer connectome of Caenorhabditis elegans.}, journal = {PLoS Computational Biology}, volume = {12}, year = {2016}, month = {2016 Dec 16}, pages = {e1005283}, abstract = {

Connectomics has focused primarily on the mapping of synaptic links in the brain; yet it is well established that extrasynaptic volume transmission, especially via monoamines and neuropeptides, is also critical to brain function and occurs primarily outside the synaptic connectome. We have mapped the putative monoamine connections, as well as a subset of neuropeptide connections, in C. elegans based on new and published gene expression data. The monoamine and neuropeptide networks exhibit distinct topological properties, with the monoamine network displaying a highly disassortative star-like structure with a rich-club of interconnected broadcasting hubs, and the neuropeptide network showing a more recurrent, highly clustered topology. Despite the low degree of overlap between the extrasynaptic (or wireless) and synaptic (or wired) connectomes, we find highly significant multilink motifs of interaction, pinpointing locations in the network where aminergic and neuropeptide signalling modulate synaptic activity. Thus, the C. elegans connectome can be mapped as a multiplex network with synaptic, gap junction, and neuromodulator layers representing alternative modes of interaction between neurons. This provides a new topological plan for understanding how aminergic and peptidergic modulation of behaviour is achieved by specific motifs and loci of integration between hard-wired synaptic or junctional circuits and extrasynaptic signals wirelessly broadcast from a small number of modulatory neurons.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1005283}, author = {Bentley, Barry and Branicky, Robyn and Barnes, Christopher L and Chew, Yee Lian and Yemini, Eviatar and Bullmore, Edward T and V{\'e}rtes, Petra E and Schafer, William R} } @article {48131, title = {The nanoscale spatial organization of B cell receptors on IgM- and IgG-expressing human B cells.}, journal = {Molecular Biology of the Cell}, volume = {28}, year = {2016}, month = {2016 Dec 14}, pages = {511-23}, abstract = {

B cell activation is initiated by the binding of antigen to the B cell receptor (BCR). Here we used dSTORM super resolution imaging to characterize the nanoscale spatial organization of IgM and IgG BCRs on the surfaces of resting and antigen-activated human peripheral blood B cells. We provide insights into both the fundamental process of antigen-driven BCR clustering as well as differences in the spatial organization of IgM and IgG BCRs that may contribute to the characteristic differences in the responses of na{\"\i}ve and memory B cells to antigen. We provide evidence that although both IgM and IgG BCRs reside in highly heterogeneous protein islands that vary in both size and number of BCR single molecule localizations, both resting and activated B cells intrinsically maintain a high frequency of single isolated BCR localizations, which likely represent BCR monomers. IgG BCRs are more clustered than IgM BCRs on resting cells and form larger protein islands following antigen activation. Small dense BCR clusters likely formed via protein-protein interactions are present on the surface of resting cells and antigen activation induces these to come together to form less dense, larger islands, a process likely governed, at least in part, by protein-lipid interactions.

}, issn = {1939-4586}, doi = {10.1091/mbc.E16-06-0452}, author = {Lee, Jinmin and Sengupta, Prabuddha and Brzostowski, Joseph and Lippincott-Schwartz, Jennifer and Pierce, Susan K} } @article {47766, title = {Natural courtship song variation caused by an intronic retroelement in an ion channel gene.}, journal = {Nature}, year = {2016}, month = {2016 Aug 10}, abstract = {

Animal species display enormous variation for innate behaviours, but little is known about how this diversity arose. Here, using an unbiased genetic approach, we map a courtship song difference between wild isolates of Drosophila simulans and Drosophila mauritiana to a 966 base pair region within the slowpoke (slo) locus, which encodes a calcium-activated potassium channel. Using the reciprocal hemizygosity test, we confirm that slo is the causal locus and resolve the causal mutation to the evolutionarily recent insertion of a retroelement in a slo intron within D. simulans. Targeted deletion of this retroelement reverts the song phenotype and alters slo splicing. Like many ion channel genes, slo is expressed widely in the nervous system and influences a variety of behaviours; slo-null males sing little song with severely disrupted features. By contrast, the natural variant of slo alters a specific component of courtship song, illustrating that regulatory evolution of a highly pleiotropic ion channel gene can cause modular changes in behaviour.

}, issn = {1476-4687}, doi = {10.1038/nature19093}, author = {Ding, Yun and Berrocal, Augusto and Morita, Tomoko and Longden, Kit D and Stern, David L} } @article {48317, title = {A near atomic structure of the active human apoptosome.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Oct 04}, pages = {e17755}, abstract = {

In response to cell death signals, an active apoptosome is assembled from Apaf-1 and procaspase-9 (pc-9). Here we report a near atomic structure of the active human apoptosome determined by cryo-electron microscopy. The resulting model gives insights into cytochrome c binding, nucleotide exchange and conformational changes that drive assembly. During activation an acentric disk is formed on the central hub of the apoptosome. This disk contains four Apaf-1/pc-9 CARD pairs arranged in a shallow spiral with the fourth pc-9 CARD at lower occupancy. On average, Apaf-1 CARDs recruit 3 to 5 pc-9 molecules to the apoptosome and one catalytic domain may be parked on the hub, when an odd number of zymogens are bound. This suggests a stoichiometry of one or at most, two pc-9 dimers per active apoptosome. Thus, our structure provides a molecular framework to understand the role of the apoptosome in programmed cell death and disease.

}, issn = {2050-084X}, doi = {10.7554/eLife.17755}, author = {Cheng, Tat Cheung and Hong, Chuan and Akey, Ildik{\'o} V and Yuan, Shujun and Akey, Christopher W} } @article {48104, title = {A near-atomic structure of the dark apoptosome provides insight into assembly and activation.}, journal = {Structure (London, England : 1993)}, volume = {25}, year = {2016}, month = {2016 Nov 16}, pages = {40-52}, abstract = {

In Drosophila, the Apaf-1-related killer (Dark) forms an apoptosome that activates procaspases. To investigate function, we have determined a near-atomic structure of Dark double rings using cryo-electron microscopy. We then built a nearly complete model of the apoptosome that includes 7- and 8-blade β-propellers. We find that the preference for dATP during Dark assembly may be governed by Ser325, which is in close proximity to the 2{\textquoteright} carbon of the deoxyribose ring. Interestingly, β-propellers in V-shaped domains of the Dark apoptosome are more widely separated, relative to these features in the Apaf-1 apoptosome. This wider spacing may be responsible for the lack of cytochrome c binding to β-propellers in the Dark apoptosome. Our structure also highlights the roles of two loss-of-function mutations that may block Dark assembly. Finally, the improved model provides a framework to understand apical procaspase activation in the intrinsic cell death pathway.

}, issn = {1878-4186}, doi = {10.1016/j.str.2016.11.002}, author = {Cheng, Tat Cheung and Akey, Ildik{\'o} V and Yuan, Shujun and Yu, Zhiheng and Ludtke, Steven J and Akey, Christopher W} } @article {48128, title = {Near-atomic-resolution cryo-EM analysis of the Salmonella T3S injectisome basal body.}, journal = {Nature}, year = {2016}, month = {2016 Dec 14}, abstract = {

The type III secretion (T3S) injectisome is a specialized protein nanomachine that is critical for the pathogenicity of many Gram-negative bacteria, including purveyors of plague, typhoid fever, whooping cough, sexually transmitted infections and major nosocomial infections. This syringe-shaped 3.5-MDa macromolecular assembly spans both bacterial membranes and that of the infected host cell. The internal channel formed by the injectisome allows for the direct delivery of partially unfolded virulence effectors into the host cytoplasm. The structural foundation of the injectisome is the basal body, a molecular lock-nut structure composed predominantly of three proteins that form highly oligomerized concentric rings spanning the inner and outer membranes. Here we present the structure of the prototypical Salmonella enterica serovar Typhimurium pathogenicity island 1 basal body, determined using single-particle cryo-electron microscopy, with the inner-membrane-ring and outer-membrane-ring oligomers defined at 4.3 {\r A} and 3.6 {\r A} resolution, respectively. This work presents the first, to our knowledge, high-resolution structural characterization of the major components of the basal body in the assembled state, including that of the widespread class of outer-membrane portals known as secretins.

}, issn = {1476-4687}, doi = {10.1038/nature20576}, author = {Worrall, L J and Hong, C and Vuckovic, M and Deng, W and Bergeron, J R C and Majewski, D D and Huang, R K and Spreter, T and Finlay, B B and Yu, Z and Strynadka, N C J} } @article {47552, title = {Near-perfect synaptic integration by Nav1.7 in hypothalamic neurons regulates body weight.}, journal = {Cell}, volume = {165}, year = {2016}, month = {2016 Jun 16}, pages = {1749-61}, abstract = {

Neurons are well suited for computations on millisecond timescales, but some neuronal circuits set behavioral states over long time periods, such as those involved in energy homeostasis. We found that multiple types of hypothalamic neurons, including those that oppositely regulate body weight, are specialized as near-perfect synaptic integrators that summate inputs over extended timescales. Excitatory postsynaptic potentials (EPSPs) are greatly prolonged, outlasting the neuronal membrane time-constant up to 10-fold. This is due to the voltage-gated sodium channel Nav1.7 (Scn9a), previously associated with pain-sensation but not synaptic integration.\ Scn9a\ deletion in AGRP, POMC, or paraventricular hypothalamic neurons reduced EPSP duration, synaptic integration, and altered body weight in mice. In\ vivo whole-cell recordings in the hypothalamus confirmed near-perfect synaptic integration. These experiments show that integration of synaptic inputs over time by Nav1.7 is critical for body weight regulation and reveal a mechanism for synaptic control of circuits regulating long term homeostatic functions.

}, doi = {10.1016/j.cell.2016.05.019}, author = {Branco, Tiago and Tozer, Adam and Magnus, Christopher J and Sugino, Ken and Tanaka, Shinsuke and Lee, Albert K and Wood, John N and Sternson, Scott M} } @article {47564, title = {Neural circuits that drive startle behavior, with a focus on the Mauthner cells and spiral fiber neurons of fishes.}, journal = {Journal of Neurogenetics}, volume = {30}, year = {2016}, month = {2016 Jun}, pages = {89-100}, abstract = {

Startle behaviors are rapid, high-performance motor responses to threatening stimuli. Startle responses have been identified in a broad range of species across animal diversity. For investigations of neural circuit structure and function, these behaviors offer a number of benefits, including that they are driven by large and identifiable neurons and their neural control is simple in comparison to other behaviors. Among vertebrates, the best-known startle circuit is the Mauthner cell circuit of fishes. In recent years, genetic approaches in zebrafish have provided key tools for morphological and physiological dissection of circuits and greatly extended understanding of their architecture. Here we discuss the startle circuit of fishes, with a focus on the Mauthner cells and associated interneurons called spiral fiber neurons and we add new observations on hindbrain circuit organization. We also briefly review and compare startle circuits of several other taxa, paying particular attention to how movement direction is controlled.

}, issn = {1563-5260}, doi = {10.1080/01677063.2016.1182526}, author = {Hale, Melina E and Katz, Hilary R and Peek, Martin Y and Fremont, Rachel T} } @article {47283, title = {Neural circuits underlying visually evoked escapes in larval zebrafish.}, journal = {Neuron}, volume = {89}, year = {2016}, month = {2016 Feb 3}, pages = {613-628}, abstract = {

Escape behaviors deliver organisms away from imminent catastrophe. Here, we characterize behavioral responses of freely swimming larval zebrafish to\ looming visual stimuli simulating predators. We report that the visual system alone can recruit lateralized, rapid escape motor programs, similar to those elicited by mechanosensory modalities. Two-photon calcium imaging of retino-recipient midbrain regions isolated the optic tectum as an important center processing looming stimuli, with ensemble activity encoding the critical image size determining escape latency. Furthermore, we describe activity in retinal ganglion cell terminals and superficial inhibitory interneurons in the tectum during looming and propose a model for how temporal dynamics in tectal\ periventricular neurons might arise from computations between these two fundamental constituents. Finally, laser ablations of hindbrain circuitry confirmed that visual and mechanosensory modalities share the same premotor output network. We\ establish a circuit for the processing of aversive stimuli in the context of an innate visual behavior.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.12.021}, author = {Dunn, Timothy W and Gebhardt, Christoph and Naumann, Eva A and Riegler, Clemens and Ahrens, Misha B and Engert, Florian and Del Bene, Filippo} } @article {47965, title = {A new brain dopamine deficient Drosophila and its pharmacological and genetic rescue.}, journal = {Genes, Brain, and Behavior}, volume = {16}, year = {2016}, month = {2017 Mar.01 }, pages = {394-403}, abstract = {

Dopamine (DA) is a neurotransmitter with conserved behavioral roles between invertebrate and vertebrate animals. In addition to its neural functions, in insects DA is a critical substrate for cuticle pigmentation and hardening. Drosophila tyrosine hydroxylase (DTH) is the rate limiting enzyme for DA biosynthesis. Viable brain DA deficient flies were previously generated using tissue selective GAL4-UAS binary expression rescue of a DTH null mutation and these flies show specific behavioral impairments. To circumvent the limitations of rescue via binary expression, here we achieve rescue utilizing genomically integrated mutant DTH. As expected, our DA deficient flies have no detectable DTH or DA in the brain, and show reduced locomotor activity. This deficit can be rescued by L-DOPA/carbidopa feeding, similar to human Parkinson{\textquoteright}s disease treatment. Genetic rescue via GAL4/UAS-DTH was also successful, although this required the generation of a new UAS-DTH1 transgene devoid of most untranslated regions, since existing UAS-DTH transgenes express in the brain without a Gal4 driver via endogenous regulatory elements. A surprising finding of our newly constructed UAS-DTH1m is that it expresses DTH at an undetectable level when regulated by dopaminergic GAL4 drivers even when fully rescuing DA, indicating that DTH immunostaining is not necessarily a valid marker for DA expression. This finding necessitated optimizing DA immunohistochemistry, revealing details of DA innervation to the mushroom body and the central complex. When DA rescue is limited to specific DA neurons, DA does not diffuse beyond the DTH-expressing terminals, such that DA signaling can be limited to very specific brain regions.

}, issn = {1601-183X}, doi = {10.1111/gbb.12353}, author = {Cichewicz, Karol and Garren, Emma J and Adiele, Chika and Aso, Yoshinori and Wang, Zhang and Wu, Martin and Birman, Serge and Rubin, Gerald M and Hirsh, Jay} } @article {68765, title = {Non-centrosomal epidermal microtubules act in parallel to LET-502/ROCK to promote C. elegans elongation}, journal = {Development}, volume = {143}, year = {2016}, month = {01/2016}, pages = {160-173}, abstract = {

C. elegans embryonic elongation is a morphogenetic event driven by actomyosin contractility and muscle-induced tension transmitted through hemidesmosomes. A role for the microtubule cytoskeleton has also been proposed, but its contribution remains poorly characterized. Here, we investigate the organization of the non-centrosomal microtubule arrays present in the epidermis and assess their function in elongation. We show that the microtubule regulators γ-tubulin and NOCA-1 are recruited to hemidesmosomes and adherens junctions early in elongation. Several parallel approaches suggest that microtubule nucleation occurs from these sites. Disrupting the epidermal microtubule array by overexpressing the microtubule-severing protein Spastin or by inhibiting the C. elegans ninein homolog NOCA-1 in the epidermis mildly affected elongation. However, microtubules were essential for elongation when hemidesmosomes or the activity of the Rho kinase LET-502/ROCK were partially compromised. Imaging of junctional components and genetic analyses suggest that epidermal microtubules function together with Rho kinase to promote the transport of E-cadherin to adherens junctions and myotactin to hemidesmosomes. Our results indicate that the role of LET-502 in junctional remodeling is likely to be independent of its established function as a myosin II activator, but requires a microtubule-dependent pathway involving the syntaxin SYX-5. Hence, we propose that non-centrosomal microtubules organized by epidermal junctions contribute to elongation by transporting junction remodeling factors, rather than having a mechanical role.

}, issn = {0950-1991}, doi = {10.1242/dev.126615}, url = {https://doi.org/10.1242/dev.126615}, author = {Quintin, Sophie and Wang, Shahoe and Pontabry, Julien and Bender, Ambre and Robin, Fran{\c c}ois and Hyenne, Vincent and Landmann, Fr{\'e}d{\'e}ric and Gally, Christelle and Oegema, Karen and Labouesse, Michel} } @article {47727, title = {Non-insect crustacean models in developmental genetics including an encomium to Parhyale hawaiensis.}, journal = {Current Opinion in Genetics \& Development}, volume = {39}, year = {2016}, month = {2016 Jul 28}, pages = {149-156}, abstract = {

The impressive diversity of body plans, lifestyles and segmental specializations exhibited by crustaceans (barnacles, copepods, shrimps, crabs, lobsters and their kin) provides great material to address longstanding questions in evolutionary developmental biology. Recent advances in forward and reverse genetics and in imaging approaches applied in the amphipod Parhyale hawaiensis and other emerging crustacean model species have made it possible to probe the molecular and cellular basis of crustacean diversity. A number of biological and technical qualities like the slow tempo and holoblastic cleavage mode, the stereotypy of many cellular processes, the functional and morphological diversity of limbs along the body axis, and the availability of various experimental manipulations, have made Parhyale a powerful system to study normal development and regeneration.

}, issn = {1879-0380}, doi = {10.1016/j.gde.2016.07.004}, author = {Stamataki, Evangelia and Pavlopoulos, Anastasios} } @article {47468, title = {Opponent and bidirectional control of movement velocity in the basal ganglia.}, journal = {Nature}, year = {2016}, month = {2016 May 2}, abstract = {

For goal-directed behaviour it is critical that we can both select the appropriate action and learn to modify the underlying movements (for example, the pitch of a note or velocity of a reach) to improve outcomes. The basal ganglia are a critical nexus where circuits necessary for the production of behaviour, such as the neocortex and thalamus, are integrated with reward signalling to reinforce successful, purposive actions. The dorsal striatum, a major input structure of basal ganglia, is composed of two opponent pathways, direct and indirect, thought to select actions that elicit positive outcomes and suppress actions that do not, respectively. Activity-dependent plasticity modulated by reward is thought to be sufficient for selecting actions in the striatum. Although perturbations of basal ganglia function produce profound changes in movement, it remains unknown whether activity-dependent plasticity is sufficient to produce learned changes in movement kinematics, such as velocity. Here we use cell-type-specific stimulation in mice delivered in closed loop during movement to demonstrate that activity in either the direct or indirect pathway is sufficient to produce specific and sustained increases or decreases in velocity, without affecting action selection or motivation. These behavioural changes were a form of learning that accumulated over trials, persisted after the cessation of stimulation, and were abolished in the presence of dopamine antagonists. Our results reveal that the direct and indirect pathways can each bidirectionally control movement velocity, demonstrating unprecedented specificity and flexibility in the control of volition by the basal ganglia.

}, issn = {1476-4687}, doi = {10.1038/nature17639}, author = {Yttri, Eric A and Dudman, Joshua T} } @article {48096, title = {Opportunities for Technology and Tool Development.}, journal = {Neuron}, volume = {92}, year = {2016}, month = {2016 Nov 2}, pages = {564-566}, abstract = {

Major resources are now available to develop tools and technologies aimed at dissecting the circuitry and computations underlying behavior, unraveling the underpinnings of brain disorders, and understanding the neural substrates of cognition. Scientists from around the world shared their views around new tools and technologies to drive advances in neuroscience.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2016.10.042} } @article {47936, title = {The Oscillating Stimulus Transporter Assay, OSTA: Quantitative functional imaging of transporter protein activity in time and frequency domains.}, journal = {Molecular Cell}, volume = {64}, year = {2016}, month = {2016 Oct 6}, pages = {199-212}, abstract = {

Transmembrane transporter proteins allow the passage of essentially all biologically important molecules across the lipid membranes of cells and organelles and are therefore of central importance to all forms of life. Current methods of transporter measurement, however, are lacking in several dimensions. Herein, a method is presented in which oscillating stimuli are presented to transporter-expressing cells, and activity is measured through imaging the corresponding oscillating responses of intracellular fluorescent sensors. This approach yields continuous temporal readouts of transporter activity and can therefore be used to measure time-dependent responses to drugs and other stimuli. Because of the periodic nature of the response, temporal Fourier transforms can be used to identify and quantify regions of interest in the xy plane and to overcome noise. This technique, called the Oscillating Stimulus Transporter Assay (OSTA), should greatly facilitate both functional characterization of transporters as well as high-throughput screening of drugs for transporters of particular pathophysiological interest.

}, issn = {1097-4164}, doi = {10.1016/j.molcel.2016.09.001}, author = {Keller, Jacob P and Looger, Loren L} } @article {48118, title = {A plasma membrane template for macropinocytic cups.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Dec 13}, abstract = {

Macropinocytosis is a fundamental mechanism that allows cells to take up extracellular liquid into large vesicles. It critically depends on the formation of a ring of protrusive actin beneath the plasma membrane, which develops into the macropinocytic cup. We show that macropinocytic cups in Dictyostelium are organised around coincident intense patches of PIP3, active Ras and active Rac. These signalling patches are invariably associated with a ring of active SCAR/WAVE at their periphery, as are all examined structures based on PIP3 patches, including phagocytic cups and basal waves. Patch formation does not depend on the enclosing F-actin ring, and patches become enlarged when the RasGAP NF1 is mutated, showing that Ras plays an instructive role. New macropinocytic cups predominantly form by splitting from existing ones. We propose that cup-shaped plasma membrane structures form from self-organizing patches of active Ras/PIP3, which recruit a ring of actin nucleators to their periphery.

}, issn = {2050-084X}, doi = {10.7554/eLife.20085}, author = {Veltman, Douwe M and Williams, Thomas D and Bloomfield, Gareth and Chen, Bi-Chang and Betzig, Eric and Insall, Robert H and Kay, Robert R} } @article {47274, title = {A platform for brain-wide imaging and reconstruction of individual neurons.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Jan 20}, abstract = {

The structure of axonal arbors controls how signals from individual neurons are routed within the mammalian brain. However, the arbors of very few long-range projection neurons have been reconstructed in their entirety, as axons with diameters as small as 100 nm arborize in target regions dispersed over many millimeters of tissue. We introduce a platform for high-resolution, three-dimensional fluorescence imaging of complete tissue volumes that enables the visualization and reconstruction of long-range axonal arbors. This platform relies on a high-speed two-photon microscope integrated with a tissue vibratome and a suite of computational tools for large-scale image data. We demonstrate the power of this approach by reconstructing the axonal arbors of multiple neurons in the motor cortex across a single mouse brain.

}, issn = {2050-084X}, doi = {10.7554/eLife.10566}, author = {Economo, Michael N and Clack, Nathan G and Lavis, Luke D and Gerfen, Charles R and Svoboda, Karel and Myers, Eugene W and Chandrashekar, Jayaram} } @article {47305, title = {Postembryonic lineages of the Drosophila ventral nervous system: Neuroglian expression reveals the adult hemilineage associated fiber tracts in the adult thoracic neuromeres.}, journal = {The Journal of Comparative Neurology}, volume = {524}, year = {2016}, month = {2016 Feb 15}, pages = {2677-95}, abstract = {

During larval life most of the thoracic neuroblasts (NBs) in Drosophila undergo a second phase of neurogenesis to generate adult-specific neurons that remain in an immature, developmentally stalled state until pupation. Using a combination of MARCM and immunostaining with a neurotactin antibody Truman et al. (2004) identified 24 adult specific NB lineages within each thoracic hemineuromere of the larval ventral nervous system (VNS) but because the neurotactin labeling of lineage tracts disappearing early in metamorphosis they were unable extend the identification of the these lineages into the adult. Here we show that immunostaining with an antibody against the cell adhesion molecule Neuroglian reveals the same larval secondary lineage projections through metamorphosis and by identifying each neuroglian positive tract at selected stages we have traced the larval hemilineage tracts for all three thoracic neuromeres through metamorphosis into the adult. To validate tract identifications we used the genetic toolkit developed by Harris et al. (2015) to preserve hemilineage specific GAL4 expression patterns from larval into the adult stage. The immortalized expression proved a powerful confirmation of the analysis of the neuroglian scaffold. This work has enabled us to directly link the secondary, larval NB lineages to their adult counterparts. The data provide an anatomical framework that 1) makes it possible to assign most neurons to their parent lineage and 2) allows more precise definitions of the neuronal organization of the adult VNS based in developmental units/rules. This article is protected by copyright. All rights reserved.

}, issn = {1096-9861}, doi = {10.1002/cne.23988}, author = {Shepherd, David and Harris, Robin and Williams, Darren and Truman, James W} } @article {47731, title = {A practical guide to light sheet microscopy.}, journal = {Methods in Molecular Biology (Clifton, N.J.)}, volume = {1451}, year = {2016}, month = {2016}, pages = {321-31}, abstract = {

Light sheet fluorescence microscopy is an efficient method for imaging large volumes of biological tissue, including brains of larval zebrafish, at high spatial and fairly high temporal resolution with minimal phototoxicity.Here, we provide a practical guide for those who intend to build a light sheet microscope for fluorescence imaging in live larval zebrafish brains or other tissues.

}, issn = {1940-6029}, doi = {10.1007/978-1-4939-3771-4_22}, author = {Bennett, Davis V and Ahrens, Misha B} } @article {47382, title = {Practice makes perfect in memory recall.}, journal = {Learning \& Memory (Cold Spring Harbor, N.Y.)}, volume = {23}, year = {2016}, month = {2016 Apr}, pages = {169-73}, abstract = {

A large variability in performance is observed when participants recall briefly presented lists of words. The sources of such variability are not known. Our analysis of a large data set of free recall revealed a small fraction of participants that reached an extremely high performance, including many trials with the recall of complete lists. Moreover, some of them developed a number of consistent input-position-dependent recall strategies, in particular recalling words consecutively ("chaining") or in groups of consecutively presented words ("chunking"). The time course of acquisition and particular choice of positional grouping were variable among participants. Our results show that acquiring positional strategies plays a crucial role in improvement of recall performance.

}, issn = {1549-5485}, doi = {10.1101/lm.041178.115}, author = {Romani, Sandro and Katkov, Mikhail and Tsodyks, Misha} } @article {47410, title = {A primer on the Bayesian approach to high-density single-molecule trajectories analysis.}, journal = {Biophysical Journal}, volume = {110}, year = {2016}, month = {2016 Mar 29}, pages = {1209-15}, abstract = {

Tracking single molecules in living cells provides invaluable information on their environment and on the interactions that underlie their motion. New experimental techniques now permit the recording of large amounts of individual trajectories, enabling the implementation of advanced statistical tools for data analysis. In this primer, we present a Bayesian approach toward treating these data, and we discuss how it can be fruitfully employed to infer physical and biochemical parameters from single-molecule trajectories.

}, issn = {1542-0086}, doi = {10.1016/j.bpj.2016.01.018}, author = {El Beheiry, Mohamed and T{\"u}rkcan, Silvan and Richly, Maximilian U and Triller, Antoine and Alexandrou, Antigone and Dahan, Maxime and Masson, Jean-Baptiste} } @article {47602, title = {Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies.}, journal = {Nature Biotechnology}, volume = {34}, year = {2016}, month = {2016 Jul 4}, pages = {987-92}, abstract = {

Expansion microscopy (ExM) enables imaging of preserved specimens with nanoscale precision on diffraction-limited instead of specialized super-resolution microscopes. ExM works by physically separating fluorescent probes after anchoring them to a swellable gel. The first ExM method did not result in the retention of native proteins in the gel and relied on custom-made reagents that are not widely available. Here we describe protein retention ExM (proExM), a variant of ExM in which proteins are anchored to the swellable gel, allowing the use of conventional fluorescently labeled antibodies and streptavidin, and fluorescent proteins. We validated and demonstrated the utility of proExM for multicolor super-resolution (\~{}70 nm) imaging of cells and mammalian tissues on conventional microscopes.

}, issn = {1546-1696}, doi = {10.1038/nbt.3625}, author = {Tillberg, Paul and Chen, Fei and Piatkevich, Kiryl D and Zhao, Yongxin and Yu, Chih-Chieh Jay and English, Brian P and Gao, Linyi and Martorell, Anthony and Suk, Ho-Jun and Yoshida, Fumiaki and DeGennaro, Ellen M and Roossien, Douglas H and Gong, Guanyu and Seneviratne, Uthpala and Tannenbaum, Steven R and Desimone, Robert and Cai, Dawen and Boyden, Edward S} } @article {47419, title = {PSF engineering in multifocus microscopy for increased depth volumetric imaging.}, journal = {Biomedical Optics Express}, volume = {7}, year = {2016}, month = {2016 Feb 16}, pages = {726-31}, abstract = {

Imaging and localizing single molecules with high accuracy in a 3D volume is a challenging task. Here we combine multifocal microscopy, a recently developed volumetric imaging technique, with point spread function engineering to achieve an increased depth for single molecule imaging. Applications in 3D single molecule localization-based super-resolution imaging is shown over an axial depth of 4 {\textmu}m as well as for the tracking of diffusing beads in a fluid environment over 8 {\textmu}m.

}, doi = {10.1364/BOE.7.000726}, author = {Hajj, Bassam and El Beheiry, Mohamed and Dahan, Maxime} } @article {47062, title = {Quantitative neuroanatomy for connectomics in Drosophila.}, journal = {eLife}, year = {2016}, month = {2016 Mar 18}, pages = {e12059}, abstract = {

Neuronal circuit mapping using electron microscopy demands laborious proofreading or reconciliation of multiple independent reconstructions. Here, we describe new methods to apply quantitative arbor and network context to iteratively proofread and reconstruct circuits and create anatomically enriched wiring diagrams. We measured the morphological underpinnings of connectivity in new and existing reconstructions of\ Drosophila\ sensorimotor (larva) and visual (adult) systems. Synaptic inputs were preferentially located on numerous small, microtubule-free {\textquoteright}twigs{\textquoteright} which branch off a single microtubule-containing {\textquoteright}backbone{\textquoteright}. Omission of individual twigs accounted for 96\% of errors. However, the synapses of highly connected neurons were distributed across multiple twigs. Thus, the robustness of a strong connection to detailed twig anatomy was associated with robustness to reconstruction error. By comparing iterative reconstruction to the consensus of multiple reconstructions, we show that our method overcomes the need for redundant effort through the discovery and application of relationships between cellular neuroanatomy and synaptic connectivity.

}, doi = {10.7554/eLife.12059}, author = {Schneider-Mizell, Casey M. and Gerhard, Stephan and Longair, Mark and Kazimiers, Tom and Li, Feng and Zwart, Maarten and Champion, Andrew and Midgley, Frank and Fetter, Richard D and Saalfeld, Stephan and Cardona, Albert} } @article {47287, title = {Quantitatively predictable control of Drosophila transcriptional enhancers in vivo with engineered transcription factors.}, journal = {Nature Genetics}, year = {2016}, month = {2016 Feb 8}, abstract = {

Genes are regulated by transcription factors that bind to regions of genomic DNA called enhancers. Considerable effort is focused on identifying transcription factor binding sites, with the goal of predicting gene expression from DNA sequence. Despite this effort, general, predictive models of enhancer function are currently lacking. Here we combine quantitative models of enhancer function with manipulations using engineered transcription factors to examine the extent to which enhancer function can be controlled in a quantitatively predictable manner. Our models, which incorporate few free parameters, can accurately predict the contributions of ectopic transcription factor inputs. These models allow the predictable {\textquoteright}tuning{\textquoteright} of enhancers, providing a framework for the quantitative control of enhancers with engineered transcription factors.

}, issn = {1546-1718}, doi = {10.1038/ng.3509}, author = {Crocker, Justin and Ilsley, Garth R and Stern, David L} } @article {47537, title = {Rapid and semi-automated extraction of neuronal cell bodies and nuclei from electron microscopy image stacks.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1427}, year = {2016}, month = {2016}, pages = {277-90}, abstract = {

Connectomics-the study of how neurons wire together in the brain-is at the forefront of modern neuroscience research. However, many connectomics studies are limited by the time and precision needed to correctly segment large volumes of electron microscopy (EM) image data. We present here a semi-automated segmentation pipeline using freely available software that can significantly decrease segmentation time for extracting both nuclei and cell bodies from EM image volumes.

}, issn = {1940-6029}, doi = {10.1007/978-1-4939-3615-1_16}, author = {Holcomb, Paul S and Morehead, Michael and Doretto, Gianfranco and Chen, Peter and Berg, Stuart and Plaza, Stephen and Spirou, George} } @article {47938, title = {Rapid dynamics of general transcription factor TFIIB binding during preinitiation complex assembly revealed by single-molecule analysis.}, journal = {Genes and Development}, volume = {30}, year = {2016}, month = {2016 Sep 15}, pages = {2106-18}, abstract = {

Transcription of protein-encoding genes in eukaryotic cells requires the coordinated action of multiple general transcription factors (GTFs) and RNA polymerase II (Pol II). A {\textquotedblleft}step-wise{\textquotedblright} preinitiation complex (PIC) assembly model has been suggested based on conventional ensemble biochemical measurements, in which protein factors bind stably to the promoter DNA sequentially to build a functional PIC. However, recent dynamic measurements in live cells suggest that transcription factors mostly interact with chromatin DNA rather transiently. To gain a clearer dynamic picture of PIC assembly, we established an integrated in vitro single-molecule transcription platform reconstituted from highly purified human transcription factors and complemented it by live-cell imaging. Here we performed real-time measurements of the hierarchal promoter-specific binding of TFIID, TFIIA, and TFIIB. Surprisingly, we found that while promoter binding of TFIID and TFIIA is stable, promoter binding by TFIIB is highly transient and dynamic (with an average residence time of 1.5 sec). Stable TFIIB{\textendash}promoter association and progression beyond this apparent PIC assembly checkpoint control occurs only in the presence of Pol II{\textendash}TFIIF. This transient-to-stable transition of TFIIB-binding dynamics has gone undetected previously and underscores the advantages of single-molecule assays for revealing the dynamic nature of complex biological reactions.

}, doi = {10.1101/gad.285395.116}, author = {Zhang, Zhengjian and English, Brian P and Grimm, Jonathan B and Kazane, Stephanie A and Hu, Wenxin and Tsai, Albert and Inouye, Carla and You, Changjiang and Piehler, Jacob and Schultz, Peter G and Lavis, Luke D and Revyakin, Andrey and Tjian, Robert} } @article {48070, title = {Rationally subdividing the fly nervous system with versatile expression reagents.}, journal = {Journal of Neurogenetics}, volume = {30}, year = {2016}, month = {2016 Nov 15}, pages = {185-94}, abstract = {

The ability to image and manipulate specific cell populations in Drosophila enables the investigation of how neural circuits develop and coordinate appropriate motor behaviors. Gal4 lines give genetic access to many types of neurons, but the expression patterns of these reagents are often complex. Here, we present the generation and expression patterns of LexA lines based on the vesicular neurotransmitter transporters and Hox transcription factors. Intersections between these LexA lines and existing Gal4 collections provide a strategy for rationally subdividing complex expression patterns based on neurotransmitter or segmental identity.

}, issn = {1563-5260}, doi = {10.1080/01677063.2016.1248761}, author = {Simpson, J H} } @article {47741, title = {Real-time imaging of Huntingtin aggregates diverting target search and gene transcription.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Aug 03}, abstract = {

The presumptive altered dynamics of transient molecular interactions in vivo contributing to neurodegenerative diseases have remained elusive. Here, using single-molecule localization microscopy, we show that disease-inducing Huntingtin (mHtt) protein fragments display three distinct dynamic states in living cells - 1) fast diffusion, 2) dynamic clustering and 3) stable aggregation. Large, stable aggregates of mHtt exclude chromatin and form {\textquoteright}sticky{\textquoteright} decoy traps that impede target search processes of key regulators involved in neurological disorders. Functional domain mapping based on super-resolution imaging reveals an unexpected role of aromatic amino acids in promoting protein-mHtt aggregate interactions. Genome-wide expression analysis and numerical simulation experiments suggest mHtt aggregates reduce transcription factor target site sampling frequency and impair critical gene expression programs in striatal neurons. Together, our results provide insights into how mHtt dynamically forms aggregates and disrupts the finely-balanced gene control mechanisms in neuronal cells.

}, issn = {2050-084X}, doi = {10.7554/eLife.17056}, author = {Li, Li and Liu, Hui and Dong, Peng and Li, Dong and Legant, Wesley R and Grimm, Jonathan B and Lavis, Luke D and Betzig, Eric and Tjian, Robert and Liu, Zhe} } @article {47512, title = {Real-time quantification of single RNA translation dynamics in living cells.}, journal = {Science}, volume = {352}, year = {2016}, month = {2016 May 05}, pages = {1425-9}, abstract = {

Although mRNA translation is a fundamental biological process, it has never been imaged in real-time with single molecule precision in vivo. To achieve this, we developed Nascent Chain Tracking (NCT), a technique that uses multi-epitope tags and antibody-based fluorescent probes to quantify single mRNA protein synthesis dynamics. NCT reveals an elongation rate of ~10 amino acids per second, with initiation occurring stochastically every ~30 s. Polysomes contain ~1 ribosome every 200-900 nucleotides and are globular rather than elongated in shape. By developing multi-color probes, we show most polysomes act independently; however, a small fraction (~5\%) form complexes in which two distinct mRNAs can be translated simultaneously. The sensitivity and versatility of NCT make it a powerful new tool for quantifying mRNA translation kinetics.

}, doi = {10.1126/science.aaf0899}, author = {Morisaki, Tatsuya and Lyon, Kenneth and DeLuca, Keith F and DeLuca, Jennifer G and English, Brian P and Zhang, Zhengjian and Lavis, Luke D and Grimm, Jonathan B and Viswanathan, Sarada and Looger, Loren L} } @article {47267, title = {Real-time three-dimensional cell segmentation in large-scale microscopy data of developing embryos.}, journal = {Developmental Cell}, volume = {36}, year = {2016}, month = {2016 Jan 25}, pages = {225-40}, abstract = {

We present the Real-time Accurate Cell-shape Extractor (RACE), a high-throughput image analysis framework for automated three-dimensional cell segmentation in large-scale images. RACE is 55{\textendash}330 times faster and 2{\textendash}5 times more accurate than state-of-the-art methods. We demonstrate the generality of RACE by extracting cell-shape information from entire Drosophila, zebrafish, and mouse embryos imaged with confocal and light-sheet microscopes. Using RACE, we automatically reconstructed cellular-resolution tissue anisotropy maps across developing Drosophila embryos and quantified differences in cell-shape dynamics in wild-type and mutant embryos. We furthermore integrated RACE with our framework for automated cell lineaging and performed joint segmentation and cell tracking in entire Drosophila embryos. RACE processed these terabyte-sized datasets on a single computer within 1.4\ days. RACE is easy to use, as it requires adjustment of only three parameters, takes full advantage of state-of-the-art multi-core processors and graphics cards, and is available as open-source software for Windows, Linux, and Mac\ OS.

}, doi = {10.1016/j.devcel.2015.12.028}, author = {Stegmaier, Johannes and Amat, Fernando and Lemon, William C and McDole, Katie and Wan, Yinan and Teodoro, George and Mikut, Ralf and Keller, Philipp J} } @article {47440, title = {Repulsive cues combined with physical barriers and cell{\textendash}cell adhesion determine progenitor cell positioning during organogenesis}, journal = {Nature Communications}, volume = {7}, year = {2016}, month = {2016 Apr 18}, pages = {11288}, abstract = {

The precise positioning of organ progenitor cells constitutes an essential, yet poorly understood step during organogenesis. Using primordial germ cells that participate in gonad formation, we present the developmental mechanisms maintaining a motile progenitor cell population at the site where the organ develops. Employing high-resolution live-cell microscopy, we find that repulsive cues coupled with physical barriers confine the cells to the correct bilateral positions. This analysis revealed that cell polarity changes on interaction with the physical barrier and that the establishment of compact clusters involves increased cell-cell interaction time. Using particle-based simulations, we demonstrate the role of reflecting barriers, from which cells turn away on contact, and the importance of proper cell-cell adhesion level for maintaining the tight cell clusters and their correct positioning at the target region. The combination of these developmental and cellular mechanisms prevents organ fusion, controls organ positioning and is thus critical for its proper function.

}, doi = {10.1038/ncomms11288}, author = {Paksa, Azadeh and Bandemer, Jan and H{\"o}ckendorf, Burkhard and Razin, Nitzan and Tarbashevich, Katsiaryna and Minina, Sofia and Meyen, Dana and Gov, Nir S and Keller, Philipp J and Raz, Erez} } @article {65009, title = {Ribosome{\textbullet}RelA structures reveal the mechanism of stringent response activation.}, journal = {Elife}, volume = {5}, year = {2016}, month = {2016 07 19}, abstract = {

Stringent response is a conserved bacterial stress response underlying virulence and antibiotic resistance. RelA/SpoT-homolog proteins synthesize transcriptional modulators (p)ppGpp, allowing bacteria to adapt to stress. RelA is activated during amino-acid starvation, when cognate deacyl-tRNA binds to the ribosomal A (aminoacyl-tRNA) site. We report four cryo-EM structures of E. coli RelA bound to the 70S ribosome, in the absence and presence of deacyl-tRNA accommodating in the 30S A site. The boomerang-shaped RelA with a wingspan of more than 100 {\r A} wraps around the A/R (30S A-site/RelA-bound) tRNA. The CCA end of the A/R tRNA pins the central TGS domain against the 30S subunit, presenting the (p)ppGpp-synthetase domain near the 30S spur. The ribosome and A/R tRNA are captured in three conformations, revealing hitherto elusive states of tRNA engagement with the ribosomal decoding center. Decoding-center rearrangements are coupled with the step-wise 30S-subunit {\textquoteright}closure{\textquoteright}, providing insights into the dynamics of high-fidelity tRNA decoding.

}, keywords = {Cryoelectron Microscopy, Escherichia coli, Ligases, Protein Binding, Ribosomes, RNA, Transfer, Stress, Physiological}, issn = {2050-084X}, doi = {10.7554/eLife.17029}, author = {Loveland, Anna B and Bah, Eugene and Madireddy, Rohini and Zhang, Ying and Brilot, Axel F and Grigorieff, Nikolaus and Korostelev, Andrei A} } @article {47753, title = {RNA Polymerase II cluster dynamics predict mRNA output in living cells.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 May 03}, abstract = {

Protein clustering is a hallmark of genome regulation in mammalian cells. However, the dynamic molecular processes involved make it difficult to correlate clustering with functional consequences in vivo. We developed a live-cell super-resolution approach to uncover the correlation between mRNA synthesis and the dynamics of RNA Polymerase II (Pol II) clusters at a gene locus. For endogenous β-actin genes in mouse embryonic fibroblasts, we observe that short-lived (~8 s) Pol II clusters correlate with basal mRNA output. During serum stimulation, a stereotyped increase in Pol II cluster lifetime correlates with a proportionate increase in the number of mRNAs synthesized. Our findings suggest that transient clustering of Pol II may constitute a pre-transcriptional regulatory event that predictably modulates nascent mRNA output.

}, issn = {2050-084X}, doi = {10.7554/eLife.13617}, author = {Cho, Won-Ki and Jayanth, Namrata and English, Brian P and Inoue, Takuma and Andrews, J Owen and Conway, William and Grimm, Jonathan B and Spille, Jan-Hendrik and Lavis, Luke D and Lionnet, Timoth{\'e}e and Cisse, Ibrahim I} } @article {48069, title = {RNA-binding profiles of Drosophila CPEB proteins Orb and Orb2.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, year = {2016}, month = {2016 Oct 24}, abstract = {

Localized protein translation is critical in many biological contexts, particularly in highly polarized cells, such as neurons, to regulate gene expression in a spatiotemporal manner. The cytoplasmic polyadenylation element-binding (CPEB) family of RNA-binding proteins has emerged as a key regulator of mRNA transport and local translation required for early embryonic development, synaptic plasticity, and long-term memory (LTM). Drosophila Orb and Orb2 are single members of the CPEB1 and CPEB2 subfamilies of the CPEB proteins, respectively. At present, the identity of the mRNA targets they regulate is not fully known, and the binding specificity of the CPEB2 subfamily is a matter of debate. Using transcriptome-wide UV cross-linking and immunoprecipitation, we define the mRNA-binding sites and targets of Drosophila CPEBs. Both Orb and Orb2 bind linear cytoplasmic polyadenylation element-like sequences in the 3{\textquoteright} UTRs of largely overlapping target mRNAs, with Orb2 potentially having a broader specificity. Both proteins use their RNA-recognition motifs but not the Zinc-finger region for RNA binding. A subset of Orb2 targets is translationally regulated in cultured S2 cells and fly head extracts. Moreover, pan-neuronal RNAi knockdown of these targets suggests that a number of these targets are involved in LTM. Our results provide a comprehensive list of mRNA targets of the two CPEB proteins in Drosophila, thus providing insights into local protein synthesis involved in various biological processes, including LTM.

}, issn = {1091-6490}, doi = {10.1073/pnas.1603715113}, author = {Stepien, Barbara Krystyna and Oppitz, Cornelia and Gerlach, Daniel and Dag, Ugur and Novatchkova, Maria and Kr{\"u}ttner, Sebastian and Stark, Alexander and Keleman, Krystyna} } @article {47425, title = {Robust neuronal dynamics in premotor cortex during motor planning.}, journal = {Nature}, year = {2016}, month = {2016 Apr 13}, abstract = {

Neural activity maintains representations that bridge past and future events, often over many seconds. Network models can produce persistent and ramping activity, but the positive feedback that is critical for these slow dynamics can cause sensitivity to perturbations. Here we use electrophysiology and optogenetic perturbations in the mouse premotor cortex to probe the robustness of persistent neural representations during motor planning. We show that preparatory activity is remarkably robust to large-scale unilateral silencing: detailed neural dynamics that drive specific future movements were quickly and selectively restored by the network. Selectivity did not recover after bilateral silencing of the premotor cortex. Perturbations to one hemisphere are thus corrected by information from the other hemisphere. Corpus callosum bisections demonstrated that premotor cortex hemispheres can maintain preparatory activity independently. Redundancy across selectively coupled modules, as we observed in the premotor cortex, is a hallmark of robust control systems. Network models incorporating these principles show robustness that is consistent with data.

}, issn = {1476-4687}, doi = {10.1038/nature17643}, author = {Li, Nuo and Daie, Kayvon and Svoboda, Karel and Druckmann, Shaul} } @conference {47735, title = {Robust registration of calcium images by learned contrast synthesis.}, booktitle = {IEEE 13th International Symposium on Biomedical Imaging: From Nano to Macro}, year = {2016}, month = {2016 Jun 15}, address = {Clarion Congress Hotel in Prague Prague; Czech Republic}, abstract = {

Multi-modal image registration is a challenging task that is vital to fuse complementary signals for subsequent analyses. Despite much research into cost functions addressing this challenge, there exist cases in which these are ineffective. In this work, we show that (1) this is true for the registration of in-vivo Drosophila brain volumes visualizing genetically encoded calcium indicators to an nc82 atlas and (2) that machine learning based contrast synthesis can yield improvements. More specifically, the number of subjects for which the registration outright failed was greatly reduced (from 40\% to 15\%) by using a synthesized image.

}, isbn = {978-147992350-2}, doi = {10.1109/ISBI.2016.7493463}, author = {Bogovic, John A and Hanslovsky, Philipp and Wong, Allen M and Saalfeld, Stephan} } @article {68337, title = {The sacral autonomic outflow is sympathetic}, journal = {Science}, volume = {354}, year = {2016}, month = {11/2016}, pages = {893-897}, abstract = {

The autonomic nervous system regulates the function of internal organs such as the gut. The parasympathetic and sympathetic arms of this system tend to operate antagonistically. Espinosa-Medina et al. used anatomical and molecular analyses to reevaluate the assignment of neurons in the sacral autonomic nervous system (see the Perspective by Adameyko). Previously categorized as parasympathetic, these neurons are now identified as sympathetic. The results resolve a persistent confusion about how the two systems developed and open the avenue to more predictable outcomes in developing treatments targeted to the pelvic autonomic nervous system. Science, this issue p. 893; see also p. 833 Contrary to a century-old dogma, the pelvic nerves and ganglia do not belong to the parasympathetic nervous system but to the sympathetic one. A kinship between cranial and pelvic visceral nerves of vertebrates has been accepted for a century. Accordingly, sacral preganglionic neurons are considered parasympathetic, as are their targets in the pelvic ganglia that prominently control rectal, bladder, and genital functions. Here, we uncover 15 phenotypic and ontogenetic features that distinguish pre- and postganglionic neurons of the cranial parasympathetic outflow from those of the thoracolumbar sympathetic outflow in mice. By every single one, the sacral outflow is indistinguishable from the thoracolumbar outflow. Thus, the parasympathetic nervous system receives input from cranial nerves exclusively and the sympathetic nervous system from spinal nerves, thoracic to sacral inclusively. This simplified, bipartite architecture offers a new framework to understand pelvic neurophysiology as well as development and evolution of the autonomic nervous system.

}, doi = {10.1126/science.aah5454}, url = {https://www.science.org/doi/abs/10.1126/science.aah5454}, author = {I. Espinosa-Medina and O. Saha and F. Boismoreau and Z. Chettouh and F. Rossi and W. D. Richardson and J.-F. Brunet} } @article {47957, title = {Sampling Requirements for Stable Autoregressive Estimation}, journal = {CoRR}, volume = {abs/1605.01436}, year = {2016}, abstract = {

We consider the problem of estimating the parameters of a linear autoregressive model with sub-Gaussian innovations from a limited sequence of consecutive observations. Assuming that the parameters are compressible, we analyze the performance of the\ l1-regularized least squares as well as a greedy estimator of the parameters and characterize the sampling trade-offs required for stable recovery in the non-asymptotic regime. Our results extend those of compressed sensing for linear models where the covariates are i.i.d. and independent of the observation history to autoregressive processes with highly inter-dependent covariates. We also derive sufficient conditions on the sparsity level that guarantee the minimax optimality of the\ l1-regularized least squares estimate. Applying these techniques to simulated data as well as real-world datasets from crude oil prices and traffic speed data confirm our predicted theoretical performance gains in terms of estimation accuracy and model selection.

}, url = {http://arxiv.org/abs/1605.01436}, author = {Abbas Kazemipour and Sina Miran and Piya Pal and Behtash Babadi and Min Wu} } @article {47767, title = {Satb2 stations neurons along reflex arcs.}, journal = {Neuron}, volume = {91}, year = {2016}, month = {2016 Aug 17}, pages = {711-3}, abstract = {

The nociceptive flexor withdrawal reflex has an august place in the history of neuroscience. In this issue of\ Neuron, Hilde et\ al. (2016) advance our understanding of this reflex by characterizing the molecular identity and circuit connectivity of component interneurons. They assess how a DNA-binding factor Satb2 controls\ cell position, molecular identity, pre-and postsynaptic targeting, and function of a population of inhibitory sensory relay interneurons that serve to integrate both proprioceptive and nociceptive afferent information.

The nociceptive flexor withdrawal reflex has an august place in the history of neuroscience. In this issue of\ Neuron, Hilde et\ al. (2016) advance our understanding of this reflex by characterizing the molecular identity and circuit connectivity of component interneurons. They assess how a DNA-binding factor Satb2 controls cell position, molecular identity, pre-and postsynaptic targeting, and function of a population of inhibitory sensory relay interneurons that serve to integrate both proprioceptive and nociceptive afferent information.

}, doi = {10.1016/j.neuron.2016.08.005}, author = {Hantman, Adam W and Kaltschmidt, Julia A} } @article {47538, title = {A screen for constituents of motor control and decision making in Drosophila reveals visual distance-estimation neurons.}, journal = {Scientific Reports}, volume = {6}, year = {2016}, month = {2016}, pages = {27000}, abstract = {

Climbing over chasms larger than step size is vital to fruit flies, since foraging and mating are achieved while walking. Flies avoid futile climbing attempts by processing parallax-motion vision to estimate gap width. To identify neuronal substrates of climbing control, we screened a large collection of fly lines with temporarily inactivated neuronal populations in a novel high-throughput assay described here. The observed climbing phenotypes were classified; lines in each group are reported. Selected lines were further analysed by high-resolution video cinematography. One striking class of flies attempts to climb chasms of unsurmountable width; expression analysis guided us to C2 optic-lobe interneurons. Inactivation of C2 or the closely related C3 neurons with highly specific intersectional driver lines consistently reproduced hyperactive climbing whereas strong or weak artificial depolarization of C2/C3 neurons strongly or mildly decreased climbing frequency. Contrast-manipulation experiments support our conclusion that C2/C3 neurons are part of the distance-evaluation system.

}, issn = {2045-2322}, doi = {10.1038/srep27000}, author = {Triphan, Tilman and Nern, Aljoscha and Roberts, Sonia F and Korff, Wyatt and Naiman, Daniel Q and Strauss, Roland} } @article {47511, title = {Segmenting and Tracking Multiple Dividing Targets Using ilastik.}, journal = {Advances in anatomy, embryology, and cell biology}, volume = {219}, year = {2016}, month = {2016 May 21}, pages = {199-229}, abstract = {

Tracking crowded cells or other targets in biology is often a challenging task due to poor signal-to-noise ratio, mutual occlusion, large displacements, little discernibility, and the ability of cells to divide. We here present an open source implementation of conservation tracking (Schiegg et\ al., IEEE international conference on computer vision (ICCV). IEEE, New York, pp\ 2928-2935, 2013) in the ilastik software framework. This robust tracking-by-assignment algorithm explicitly makes allowance for false positive detections, undersegmentation, and cell division. We give an overview over the underlying algorithm and parameters, and explain the use for a light sheet microscopy sequence of a Drosophila embryo. Equipped with this knowledge, users will be able to track targets of interest in their own data.

}, issn = {0301-5556}, doi = {10.1007/978-3-319-28549-8_8}, author = {Haubold, Carsten and Schiegg, Martin and Kreshuk, Anna and Berg, Stuart and Koethe, Ullrich and Hamprecht, Fred A} } @article {47698, title = {Selective inhibition mediates the sequential recruitment of motor pools.}, journal = {Neuron}, volume = {91}, year = {2016}, month = {2016 Jul 12}, pages = {615-28}, abstract = {

Locomotor systems generate diverse motor patterns to produce the movements underlying behavior, requiring that motor neurons be recruited at various phases of the locomotor cycle. Reciprocal inhibition produces alternating motor patterns; however, the mechanisms that generate other phasic relationships between intrasegmental motor pools are unknown. Here, we investigate one such motor pattern in the Drosophila larva, using a multidisciplinary approach including electrophysiology and ssTEM-based circuit reconstruction. We find that two motor pools that are sequentially recruited during locomotion have identical excitable properties. In contrast, they receive input from divergent premotor circuits. We find that this motor pattern is not orchestrated by differential excitatory input but by a GABAergic interneuron acting as a delay line to the later-recruited motor pool. Our findings show how a motor pattern is generated as a function of the modular organization of locomotor networks through segregation of\ inhibition, a potentially general mechanism for sequential motor patterns.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2016.06.031}, author = {Zwart, Maarten F and Pulver, Stefan R and Truman, James W and Fushiki, Akira and Cardona, Albert and Landgraf, Matthias} } @article {48105, title = {Sensitive enhancement of vessel wall imaging with an endoesophageal Wireless Amplified NMR Detector (WAND).}, journal = {Magnetic Resonance in Medicine}, volume = {78}, year = {2016}, month = {2016 Dec 04}, pages = {2048-54}, abstract = {

PURPOSE: To improve the imaging quality of vessel walls with an endoesophageal Wireless Amplified NMR Detector (WAND).

METHODS: A cylindrically shaped double-frequency resonator has been constructed with a single metal wire that is self-connected by a pair of nonlinear capacitors. The double-frequency resonator can convert wirelessly provided pumping power into amplified MR signals. This compact design makes the detector easily insertable into a rodent esophagus.

RESULTS: The detector has good longitudinal and axial symmetry. Compared to an external surface coil, the WAND can enhance detection sensitivity by at least 5 times, even when the distance separation between the region of interest and the detector{\textquoteright}s cylindrical surface is twice the detector{\textquoteright}s own radius. Such detection capability enables us to observe vessel walls near the aortic arch and carotid bifurcation with elevated sensitivity.

CONCLUSION: A cylindrical MRI detector integrated with a wireless-powered amplifier has been developed as an endoesophageal detector to enhance detection sensitivity of vessel walls. This detector can greatly improve the imaging quality for vessel regions that are susceptible to atherosclerotic lesions. Magn Reson Med, 2016. {\textcopyright} 2016 International Society for Magnetic Resonance in Medicine.

}, issn = {1522-2594}, doi = {10.1002/mrm.26562}, author = {Zeng, Xianchun and Barbic, Mladen and Chen, Liangliang and Qian, Chunqi} } @article {47396, title = {Sensitive red protein calcium indicators for imaging neural activity.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Mar 24}, abstract = {

Genetically encoded calcium indicators (GECIs) allow measurement of activity in large populations of neurons and in small neuronal compartments, over times of milliseconds to months. Although GFP-based GECIs are widely used for in vivo neurophysiology, GECIs with red-shifted excitation and emission spectra have advantages for in vivo imaging because of reduced scattering and absorption in tissue, and a consequent reduction in phototoxicity. However, current red GECIs are inferior to the state-of-the-art GFP-based GCaMP6 indicators for detecting and quantifying neural activity. Here we present improved red GECIs based on mRuby (jRCaMP1a, b) and mApple (jRGECO1a), with sensitivity comparable to GCaMP6. We characterized the performance of the new red GECIs in cultured neurons and in mouse, Drosophila, zebrafish and C. elegans in vivo. Red GECIs facilitate deep-tissue imaging, dual-color imaging together with GFP-based reporters, and the use of optogenetics in combination with calcium imaging.

}, issn = {2050-084X}, doi = {10.7554/eLife.12727}, author = {Dana, Hod and Mohar, Boaz and Sun, Yi and Narayan, Sujatha and Gordus, Andrew and Hasseman, Jeremy P and Tsegaye, Getahun and Holt, Graham T and Hu, Amy and Walpita, Deepika and Patel, Ronak and Macklin, John J and Bargmann, Cornelia I and Ahrens, Misha B and Schreiter, Eric R and Jayaraman, Vivek and Looger, Loren L and Svoboda, Karel and Kim, Douglas S} } @article {47315, title = {Sequential ionic and conformational signaling by calcium channels drives neuronal gene expression.}, journal = {Science (New York, N.Y.)}, volume = {351}, year = {2016}, month = {2016 Feb 19}, pages = {863-7}, abstract = {

Voltage-gated CaV1.2 channels (L-type calcium channel α1C subunits) are critical mediators of transcription-dependent neural plasticity. Whether these channels signal via the influx of calcium ion (Ca2+), voltage-dependent conformational change (VΔC), or a combination of the two has thus far been equivocal. We fused CaV1.2 to a ligand-gated Ca2+-permeable channel, enabling independent control of localized Ca2+\ and VΔC signals. This revealed an unexpected dual requirement: Ca2+\ must first mobilize actin-bound Ca2+/calmodulin-dependent protein kinase II, freeing it for subsequent VΔC-mediated accumulation. Neither signal alone sufficed to activate transcription. Signal order was crucial: Efficiency peaked when Ca2+\ preceded VΔC by 10 to 20 seconds. CaV1.2 VΔC synergistically augmented signaling by\ N-methyl-D-aspartate receptors. Furthermore, VΔC mistuning correlated with autistic symptoms in Timothy syndrome. Thus, nonionic VΔC signaling is vital to the function of CaV1.2 in synaptic and neuropsychiatric processes.

}, doi = {10.1126/science.aad3647}, author = {Li, Boxing and Tadross, Michael R and Tsien, Richard W} } @article {47991, title = {The serotonergic system tracks the outcomes of actions to mediate short-term motor learning.}, journal = {Cell}, volume = {167}, year = {2016}, month = {2016 Oct 27}, pages = {933-46}, abstract = {

To execute accurate movements, animals must continuously adapt their behavior to changes in their\ bodies and environments. Animals can learn changes in the relationship between their locomotor commands and the resulting distance moved, then adjust command strength to achieve a desired travel distance. It is largely unknown which circuits implement this form of motor learning, or how. Using whole-brain neuronal imaging and circuit manipulations in larval zebrafish, we discovered that the serotonergic dorsal raphe nucleus (DRN) mediates short-term locomotor learning. Serotonergic DRN neurons respond phasically to swim-induced visual motion, but little to motion that is not self-generated. During prolonged exposure to a given motosensory gain, persistent DRN activity emerges that stores the learned efficacy of motor commands and adapts future locomotor drive for tens of seconds. The DRN{\textquoteright}s ability to track the effectiveness of motor intent may constitute a computational building block\ for the broader functions of the serotonergic system.

}, doi = {10.1016/j.cell.2016.09.055}, author = {Kawashima, Takashi and Zwart, Maarten F and Yang, Chao-Tsung and Mensh, Brett D and Ahrens, Misha B} } @article {47323, title = {Sex-specific regulation of Lgr3 in Drosophila neurons.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, year = {2016}, month = {2016 Feb 18}, abstract = {

The development of sexually dimorphic morphology and the potential for sexually dimorphic behavior in Drosophila are regulated by the Fruitless (Fru) and Doublesex (Dsx) transcription factors. Several direct targets of Dsx have been identified, but direct Fru targets have not been definitively identified. We show that Drosophila leucine-rich repeat G protein-coupled receptor 3 (Lgr3) is regulated by Fru and Dsx in separate populations of neurons. Lgr3 is a member of the relaxin-receptor family and a receptor for Dilp8, necessary for control of organ growth. Lgr3 expression in the anterior central brain of males is inhibited by the B isoform of Fru, whose DNA binding domain interacts with a short region of an Lgr3 intron. Fru A and C isoform mutants had no observed effect on Lgr3 expression. The female form of Dsx (Dsx(F)) separately up- and down-regulates Lgr3 expression in distinct neurons in the abdominal ganglion through female- and male-specific Lgr3 enhancers. Excitation of neural activity in the Dsx(F)-up-regulated abdominal ganglion neurons inhibits female receptivity, indicating the importance of these neurons for sexual behavior. Coordinated regulation of Lgr3 by Fru and Dsx marks a point of convergence of the two branches of the sex-determination hierarchy.

}, issn = {1091-6490}, doi = {10.1073/pnas.1600241113}, author = {Meissner, Geoffrey W and Luo, Shengzhan D and Dias, Brian G and Texada, Michael J and Baker, Bruce S} } @article {47487, title = {Shared and distinct retinal input to the mouse superior colliculus and dorsal lateral geniculate nucleus.}, journal = {Journal of Neurophysiology}, volume = {116}, year = {2016}, month = {2016 May 11}, pages = {602-10}, abstract = {

The mammalian retina conveys the vast majority of information about visual stimuli to two brain regions: the dorsal lateral geniculate nucleus (dLGN) and the superior colliculus (SC). The degree to which retinal ganglion cells (RGCs) send similar or distinct information to the two areas remains unclear despite the important constraints that different patterns of RGC input place on downstream visual processing. To resolve this ambiguity we injected a glycoprotein-deficient rabies virus coding for the expression of a fluorescent protein into the dLGN or SC; rabies virus labeled a smaller fraction of RGCs than lipophilic dyes like DiI but, crucially, did not label RGC axons of passage. ~80\% of the RGCs infected by rabies virus injected into the dLGN were co-labeled with DiI injected into the SC, suggesting that many dLGN-projecting RGCs also project to the SC. However, functional characterization of RGCs revealed that the SC receives input from several classes of RGCs that largely avoid the dLGN - in particular, RGCs in which (1) sustained changes in light intensity elicit transient changes in firing rate and/or (2) a small range of stimulus sizes or temporal fluctuations in light intensity elicit robust activity. Taken together, our results illustrate several unexpected asymmetries in the information that the mouse retina conveys to two major downstream targets and suggest that differences in the output of dLGN and SC neurons reflect, at least in part, differences in the functional properties of RGCs that innervate the SC but not the dLGN.

}, issn = {1522-1598}, doi = {10.1152/jn.00227.2016}, author = {Ellis, Erika M and Gauvain, Gregory and Sivyer, Benjamin and Murphy, Gabe J} } @article {47262, title = {Simultaneous denoising, deconvolution, and demixing of calcium imaging data.}, journal = {Neuron}, volume = {89}, year = {2016}, month = {2016 Jan 20}, pages = {285-99}, abstract = {

We present a modular approach for analyzing calcium imaging recordings of large neuronal ensembles. Our goal is to simultaneously identify the locations of the neurons, demix spatially overlapping components, and denoise and deconvolve the spiking activity from the slow dynamics of the calcium indicator. Our approach relies on a constrained nonnegative matrix factorization that expresses the spatiotemporal fluorescence activity as the product of a spatial matrix that encodes the spatial footprint of each neuron in the optical field and a temporal matrix that characterizes the calcium concentration of each neuron over time. This framework is combined with a novel constrained deconvolution approach that extracts estimates of neural activity from fluorescence traces, to create a spatiotemporal processing algorithm that requires minimal parameter tuning. We demonstrate the general applicability of our method by applying it to in\ vitro and in\ vivo multi-neuronal imaging data, whole-brain light-sheet imaging data, and dendritic imaging data.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.11.037}, author = {Pnevmatikakis, Eftychios A and Soudry, Daniel and Gao, Yuanjun and Machado, Timothy A and Merel, Josh and Pfau, David and Reardon, Thomas and Mu, Yu and Lacefield, Clay and Yang, Weijian and Ahrens, Misha and Bruno, Randy and Jessell, Thomas M and Peterka, Darcy S and Yuste, Rafael and Paninski, Liam} } @article {48800, title = {Single neuron morphology in vivo with confined primed conversion.}, journal = {Methods in Cell Biology}, volume = {133}, year = {2016}, month = {2016}, pages = {125-38}, abstract = {

Unraveling the structural organization of neurons can provide fundamental insights into brain function. However, visualizing neurite morphology in vivo remains difficult due to the high density and complexity of neural packing in the nervous system. Detailed analysis of neural morphology requires distinction of closely neighboring, highly intricate cellular structures such as neurites with high contrast. Green-to-red photoconvertible fluorescent proteins have become powerful tools to optically highlight molecular and cellular structures for developmental and cell biological studies. Yet, selective labeling of single cells of interest in vivo has been precluded due to inefficient photoconversion when using high intensity, pulsed, near-infrared laser sources that are commonly applied for achieving axially confined two-photon (2P) fluorescence excitation. Here we describe a novel optical mechanism, "confined primed conversion,"\ which employs continuous dual-wave illumination to achieve confined green-to-red photoconversion of single cells in live zebrafish embryos. Confined primed conversion exhibits wide applicability and this chapter specifically elaborates on employing this imaging modality to analyze neural morphology of optically targeted single neurons in the developing zebrafish brain.

}, keywords = {Animals, Brain, Embryo, Nonmammalian, Larva, Microscopy, Confocal, Neurites, Neurons, Single-Cell Analysis, Zebrafish}, issn = {0091-679X}, doi = {10.1016/bs.mcb.2015.12.005}, author = {Mohr, M A and Pantazis, P} } @article {47990, title = {Single-cell coding of sensory, spatial and numerical magnitudes in primate prefrontal, premotor and cingulate motor cortices.}, journal = {Experimental Brain Research}, volume = {234}, year = {2016}, month = {2016 Jan}, pages = {241-54}, abstract = {

The representation of magnitude information enables humans and animal species alike to successfully interact with the external environment. However, how various types of magnitudes are processed by single neurons to guide goal-directed behavior remains elusive. Here, we recorded single-cell activity from the dorsolateral prefrontal (PFC), dorsal premotor (PMd) and cingulate motor (CMA) cortices in monkeys discriminating discrete numerical (numerosity), continuous spatial (line length) and basic sensory (spatial frequency) stimuli. We found that almost exclusively PFC neurons represented the different magnitude types during sample presentation and working memory periods. The frequency of magnitude-selective cells in PMd and CMA did not exceed chance level. The proportion of PFC neurons selectively tuned to each of the three magnitude types were comparable. Magnitude coding was mainly dissociated at the single-neuron level, with individual neurons representing only one of the three tested magnitude types. Neuronal magnitude discriminability, coding strength and temporal evolution were comparable between magnitude types encoded by PFC neuron populations. Our data highlight the importance of PFC neurons in representing various magnitude categories. Such magnitude representations are based on largely distributed coding by single neurons that are anatomically intermingled within the same cortical area.

}, keywords = {Animals, Gyrus Cinguli, Judgment, Macaca mulatta, Male, Mathematical Concepts, Motor Cortex, Neurons, Patch-Clamp Techniques, Pattern Recognition, Visual, Prefrontal Cortex, Space Perception}, issn = {1432-1106}, doi = {10.1007/s00221-015-4449-8}, author = {Eiselt, Anne-Kathrin and Nieder, Andreas} } @article {68764, title = {A Small RNA-Catalytic Argonaute Pathway Tunes Germline Transcript Levels to Ensure Embryonic Divisions}, journal = {Cell}, volume = {165}, year = {2016}, month = {04/2016}, pages = {396-409}, abstract = {

Summary Multiple division cycles without growth are a characteristic feature of early embryogenesis. The female germline loads proteins and RNAs into oocytes to support these divisions, which lack many quality control mechanisms operating in somatic cells undergoing growth. Here, we describe a small RNA-Argonaute pathway that ensures early embryonic divisions in C.\ elegans by employing catalytic slicing activity to broadly tune, instead of silence, germline gene expression. Misregulation of one target, a kinesin-13 microtubule depolymerase, underlies a major phenotype associated with pathway loss. Tuning of target transcript levels is guided by the density of homologous small RNAs, whose generation must ultimately be related to target sequence. Thus, the tuning action of a small RNA-catalytic Argonaute pathway generates oocytes capable of supporting embryogenesis. We speculate that the specialized nature of germline chromatin led to the emergence of small RNA-catalytic Argonaute pathways in the female germline as a post-transcriptional control layer to optimize oocyte composition.

}, keywords = {22G RNA, Argonaute, Centromere, chromosome, CSR-1, embryogenesis, Fertility, germline, maternal load, Oogenesis, small RNA}, issn = {0092-8674}, doi = {https://doi.org/10.1016/j.cell.2016.02.040}, url = {https://www.sciencedirect.com/science/article/pii/S0092867416301908}, author = {Adina Gerson-Gurwitz and Shaohe Wang and Shashank Sathe and Rebecca Green and Gene~W. Yeo and Karen Oegema and Arshad Desai} } @article {47264, title = {The soft touch: low-affinity transcription factor binding sites in development and evolution.}, journal = {Current Topics in Developmental Biology}, year = {2016}, month = {2016 Jan 07}, abstract = {

Transcription factor proteins regulate gene expression by binding to specific DNA regions. Most studies of transcription factor binding sites have focused on the highest affinity sites for each factor. There is abundant evidence, however, that binding sites with a range of affinities, including very low affinities, are critical to gene regulation. Here, we present the theoretical and experimental evidence for the importance of low-affinity sites in gene regulation and development. We also discuss the implications of the widespread use of low-affinity sites in eukaryotic genomes for robustness, precision, specificity, and evolution of gene regulation.

}, doi = {10.1016/bs.ctdb.2015.11.018}, author = {Crocker, Justin and Preger-Ben Noon, Ella and Stern, David L} } @article {48116, title = {Sonic Hedgehog Pathway activation increases mitochondrial abundance and activity in hippocampal neurons.}, journal = {Molecular Biology of the Cell}, year = {2016}, month = {2016 Dec 08}, abstract = {

Mitochondria are essential organelles whose biogenesis, structure, and function are regulated by many signaling pathways. In this study we present evidence that, in hippocampal neurons, activation of the Sonic hedgehog (Shh) signaling pathway impacts multiple aspects of mitochondria. Mitochondrial mass was increased significantly in neurons treated with Shh. Using biochemical and fluorescence imaging analyses, we show that Shh signaling activity reduces mitochondrial fission and promotes mitochondrial elongation, at least in part, via suppression of the mitochondrial fission protein dynamin-like GTPase Drp1. Mitochondria from Shh-treated neurons were more electron-dense as revealed by electron microscopy, and had higher membrane potential and respiratory activity. We further show that Shh protects neurons against a variety of stresses, including the mitochondrial poison rotenone, amyloid β-peptide, hydrogen peroxide, and high levels of glutamate. Collectively, our data suggest a link between Shh pathway activity and the physiological properties of mitochondria in hippocampal neurons.

}, issn = {1939-4586}, doi = {10.1091/mbc.E16-07-0553}, author = {Yao, Pamela J and Manor, Uri and Petralia, Ronald S and Brose, Rebecca D and Wu, Ryan T Y and Ott, Carolyn and Wang, Ya-Xian and Charnoff, Ari and Lippincott-Schwartz, Jennifer and Mattson, Mark P} } @article {47278, title = {Spatial gene-expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons.}, journal = {Neuron}, year = {2016}, month = {2016 Jan 13}, abstract = {

Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types. This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but it may be further hampered by prominent within-class variability. Here, we considered a well-defined canonical neuronal population-hippocampal CA1 pyramidal cells (CA1 PCs)-and systematically examined the extent and spatial rules of transcriptional heterogeneity. Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences within CA1 along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous gene-expression gradients, producing a transcriptional profile consistent with a multifarious continuum of cells. This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.12.013}, author = {Cembrowski, Mark S and Bachman, Julia L and Wang, Lihua and Sugino, Ken and Shields, Brenda C and Spruston, Nelson} } @article {65891, title = {Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2}, journal = {Nature Protocols}, volume = {11}, year = {2016}, month = {Jan-03-2016}, pages = {456 - 475}, abstract = {

This protocol describes a method to obtain spatially resolved proteomic maps of specific compartments within living mammalian cells. An engineered peroxidase, APEX2, is genetically targeted to a cellular region of interest. Upon the addition of hydrogen peroxide for 1 min to cells preloaded with a biotin-phenol substrate, APEX2 generates biotin-phenoxyl radicals that covalently tag proximal endogenous proteins. Cells are then lysed, and biotinylated proteins are enriched with streptavidin beads and identified by mass spectrometry. We describe the generation of an appropriate APEX2 fusion construct, proteomic sample preparation, and mass spectrometric data acquisition and analysis. A two-state stable isotope labeling by amino acids in cell culture (SILAC) protocol is used for proteomic mapping of membrane-enclosed cellular compartments from which APEX2-generated biotin-phenoxyl radicals cannot escape. For mapping of open cellular regions, we instead use a {\textquoteright}ratiometric{\textquoteright} three-state SILAC protocol for high spatial specificity. Isotopic labeling of proteins takes 5{\textendash}7 cell doublings. Generation of the biotinylated proteomic sample takes 1 d, acquiring the mass spectrometric data takes 2{\textendash}5 d and analysis of the data to obtain the final proteomic list takes 1 week.

}, issn = {1754-2189}, doi = {10.1038/nprot.2016.018}, url = {http://www.nature.com/articles/nprot.2016.018http://www.nature.com/articles/nprot.2016.018.pdfhttp://www.nature.com/articles/nprot.2016.018.pdfhttp://www.nature.com/articles/nprot.2016.018}, author = {Hung, Victoria and Udeshi, Namrata D and Lam, Stephanie S and Loh, Ken H and Cox, Kurt J and Pedram, Kayvon and Carr, Steven A and Ting, Alice Y} } @article {47420, title = {Steroid receptors reprogram FoxA1 occupancy through dynamic chromatin transitions.}, journal = {Cell}, year = {2016}, month = {2016 Apr 6}, abstract = {

The estrogen receptor (ER), glucocorticoid receptor (GR), and forkhead box protein 1 (FoxA1) are significant factors in breast cancer progression. FoxA1 has been implicated in establishing ER-binding patterns though its unique ability to serve as a pioneer factor. However, the molecular interplay between ER, GR, and FoxA1 requires further investigation. Here we show that ER and GR both have the ability to alter the genomic distribution of the FoxA1 pioneer factor. Single-molecule tracking experiments in live cells reveal a highly dynamic interaction of FoxA1 with chromatin in\ vivo. Furthermore, the FoxA1 factor is not associated with detectable footprints at its binding sites throughout the genome. These findings support a model wherein interactions between transcription factors and pioneer factors are highly dynamic. Moreover, at a subset of genomic sites, the role of pioneer can be reversed, with the steroid receptors serving to enhance binding of FoxA1.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2016.02.067}, author = {Swinstead, Erin E and Miranda, Tina B and Paakinaho, Ville and Baek, Songjoon and Goldstein, Ido and Hawkins, Mary and Karpova, Tatiana S and Ball, David and Mazza, Davide and Lavis, Luke D and Grimm, Jonathan B and Morisaki, Tatsuya and Gr{\o}ntved, Lars and Presman, Diego M and Hager, Gordon L} } @article {48093, title = {Structure of a Holliday junction complex reveals mechanisms governing a highly regulated DNA transaction.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 May 25}, abstract = {

The molecular machinery responsible for DNA expression, recombination, and compaction has been difficult to visualize as functionally complete entities due to their combinatorial and structural complexity. We report here the structure of the intact functional assembly responsible for regulating and executing a site-specific DNA recombination reaction. The assembly is a 240-bp Holliday junction (HJ) bound specifically by 11 protein subunits. This higher-order complex is a key intermediate in the tightly regulated pathway for the excision of bacteriophage λ viral DNA out of the E. coli host chromosome, an extensively studied paradigmatic model system for the regulated rearrangement of DNA. Our results provide a structural basis for pre-existing data describing the excisive and integrative recombination pathways, and they help explain their regulation.

}, issn = {2050-084X}, doi = {10.7554/eLife.14313}, author = {Laxmikanthan, Gurunathan and Xu, Chen and Brilot, Axel F and Warren, David and Steele, Lindsay and Seah, Nicole and Tong, Wenjun and Grigorieff, Nikolaus and Landy, Arthur and Van Duyne, Gregory D} } @article {48117, title = {Structure of the transporter associated with antigen processing trapped by herpes simplex virus.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Dec 09}, abstract = {

The transporter associated with antigen processing (TAP) is an ATP-binding cassette (ABC) transporter essential to cellular immunity against viral infection. Some persistent viruses have evolved strategies to inhibit TAP so that they may go undetected by the immune system. The herpes simplex virus for example evades immune surveillance by blocking peptide transport with a small viral protein ICP47. In this study, we determined the structure of human TAP bound to ICP47 by electron cryo-microscopy (cryo-EM) to 4.0 {\r A}. The structure shows that ICP47 traps TAP in an inactive conformation distinct from the normal transport cycle. The specificity and potency of ICP47 inhibition result from contacts between the tip of the helical hairpin and the apex of the transmembrane cavity. This work provides a clear molecular description of immune evasion by a persistent virus. It also establishes the molecular structure of TAP to facilitate mechanistic studies of the antigen presentation process.

}, issn = {2050-084X}, doi = {10.7554/eLife.21829}, author = {Oldham, Michael L and Grigorieff, Nikolaus and Chen, Jue} } @article {47322, title = {Structured dendritic inhibition supports branch-selective integration in CA1 pyramidal cells.}, journal = {Neuron}, year = {2016}, month = {2016 Feb 18}, abstract = {

Neuronal circuit function is governed by precise patterns of connectivity between specialized groups of neurons. The diversity of GABAergic interneurons is a hallmark of cortical circuits, yet little is known about their targeting to individual postsynaptic dendrites. We examined synaptic connectivity between molecularly defined inhibitory interneurons and CA1 pyramidal cell dendrites using correlative light-electron microscopy and large-volume array tomography. We show that interneurons can be highly selective in their connectivity to specific dendritic branch types and, furthermore, exhibit precisely targeted connectivity to the origin or end of individual branches. Computational simulations indicate that the observed subcellular targeting enables control over the nonlinear integration of synaptic input or the initiation and backpropagation of action potentials in a branch-selective manner. Our results demonstrate that connectivity between interneurons and pyramidal cell dendrites is more precise and spatially segregated than previously appreciated, which may be a critical determinant of how inhibition shapes dendritic computation.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2016.01.029}, author = {Bloss, Erik B and Cembrowski, Mark S and Karsh, Bill and Colonell, Jennifer and Fetter, Richard D and Spruston, Nelson} } @article {47560, title = {Structured learning of assignment models for neuron reconstruction to minimize topological errors.}, journal = {IEEE 13th International Symposium on Biomedical Imaging (ISBI)}, year = {2016}, month = {2016 Ap 13}, pages = {607-11}, abstract = {

Structured learning provides a powerful framework for empirical risk minimization on the predictions of structured models. It allows end-to-end learning of model parameters to minimize an application specific loss function. This framework is particularly well suited for discrete optimization models that are used for neuron reconstruction from anisotropic electron microscopy (EM) volumes. However, current methods are still learning unary potentials by training a classifier that is agnostic about the model it is used in. We believe the reason for that lies in the difficulties of (1) finding a representative training sample, and (2) designing an application specific loss function that captures the quality of a proposed solution. In this paper, we show how to find a representative training sample from human generated ground truth, and propose a loss function that is suitable to minimize topological errors in the reconstruction. We compare different training methods on two challenging EM-datasets. Our structured learning approach shows consistently higher reconstruction accuracy than other current learning methods.

}, doi = {10.1109/ ISBI.2016.7493341}, author = {Funke, Jan and Klein, Jonas and Moreno-Noguer, Francesc and Cardona, Albert and Cook, Matthew} } @article {47292, title = {Studying small brains to understand the building blocks of cognition.}, journal = {Current Opinion in Neurobiology}, volume = {37}, year = {2016}, month = {2016 Jan 28}, pages = {59-65}, abstract = {

Cognition encompasses a range of higher-order mental processes, such as attention, working memory, and model-based decision-making. These processes are thought to involve the dynamic interaction of multiple central brain regions. A mechanistic understanding of such computations requires not only monitoring and manipulating specific neural populations during behavior, but also knowing the connectivity of the underlying circuitry. These goals are experimentally challenging in mammals, but are feasible in numerically simpler insect brains. In Drosophila melanogaster in particular, genetic tools enable precisely targeted physiology and optogenetics in actively behaving animals. In this article we discuss how these advantages are increasingly being leveraged to study abstract neural representations and sensorimotor computations that may be relevant for cognition in both insects and mammals.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2016.01.007}, author = {Haberkern, Hannah and Jayaraman, Vivek} } @article {47709, title = {Super-resolution spectroscopic microscopy via photon localization.}, journal = {Nature Communications}, volume = {7}, year = {2016}, month = {2016 Jul 25}, pages = {12290}, abstract = {

Traditional photon localization microscopy analyses only the spatial distributions of photons emitted by individual molecules to reconstruct super-resolution optical images. Unfortunately, however, the highly valuable spectroscopic information from these photons have been overlooked. Here we report a spectroscopic photon localization microscopy that is capable of capturing the inherent spectroscopic signatures of photons from individual stochastic radiation events. Spectroscopic photon localization microscopy achieved higher spatial resolution than traditional photon localization microscopy through spectral discrimination to identify the photons emitted from individual molecules. As a result, we resolved two fluorescent molecules, which were 15 nm apart, with the corresponding spatial resolution of 10 nm-a four-fold improvement over photon localization microscopy. Using spectroscopic photon localization microscopy, we further demonstrated simultaneous multi-colour super-resolution imaging of microtubules and mitochondria in COS-7 cells and showed that background autofluorescence can be identified through its distinct emission spectra.

}, issn = {2041-1723}, doi = {10.1038/ncomms12290}, author = {Dong, Biqin and Almassalha, Luay and Urban, Ben E and Nguyen, The-Quyen and Khuon, Satya and Chew, Teng-Leong and Backman, Vadim and Sun, Cheng and Zhang, Hao F} } @article {48045, title = {Synaptic transmission parallels neuromodulation in a central food-intake circuit.}, journal = {eLife}, year = {2016}, month = {2016 Nov 15}, abstract = {

NeuromedinU is a potent regulator of food intake and activity in mammals. In\ Drosophila, neurons producing the homologous neuropeptide hugin regulate feeding and locomotion in a similar manner. Here, we use EM-based reconstruction to generate the entire connectome of hugin-producing neurons in the\ Drosophila\ larval CNS. We demonstrate that hugin neurons use synaptic transmission in addition to peptidergic neuromodulation and identify acetylcholine as a key transmitter. Hugin neuropeptide and acetylcholine are both necessary for the regulatory effect on feeding. We further show that subtypes of hugin neurons connect chemosensory to endocrine system by combinations of synaptic and peptide-receptor connections. Targets include endocrine neurons producing DH44, a CRH-like peptide, and insulin-like peptides. Homologs of these peptides are likewise downstream of neuromedinU, revealing striking parallels in flies and mammals. We propose that hugin neurons are part of an ancient physiological control system that has been conserved at functional and molecular level.

}, doi = {10.7554/eLife.16799}, author = {Schlegel, Philipp and Texada, Michael J and Miroschnikow, Anton and Schoofs, Andreas and H{\"u}ckesfeld, Sebastian and Peters, Marc and Schneider-Mizell, Casey M and Lacin, Haluk and Li, Feng and Fetter, Richard D and Truman, James W and Cardona, Albert and Pankratz, Michael J} } @article {47916, title = {Synchronized excitability in a network enables generation of internal neuronal sequences.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Sep 28}, abstract = {

Hippocampal place field sequences are supported by sensory cues and network internal mechanisms. In contrast, sharp-wave (SPW) sequences, theta sequences and episode-field sequences are internally generated. The relationship of these sequences to memory is unclear. SPW sequences have been shown to support learning and have been assumed to also support episodic memory. Conversely, we demonstrate these SPW sequences were present even after episodic memory in trained rats was impaired and after other internal sequences - episode-field and theta sequences - were eliminated. SPW sequences did not support memory despite continuing to {\textquoteright}replay{\textquoteright} all task-related sequences - place-field and episode-field sequences. Sequence replay occurred selectively during a synchronous increase of population excitability -- SPWs. Similarly, theta sequences depended on the presence of repeated synchronized waves of excitability - theta oscillations. Thus, we suggest that either intermittent or rhythmic synchronized changes of excitability trigger sequential firing of neurons, which in turn supports learning and/or memory.

}, issn = {2050-084X}, doi = {10.7554/eLife.20697}, author = {Yingxue, Wang and Roth, Zachary and Pastalkova, Eva} } @article {47285, title = {Tagmentation-based mapping (tagmap) of mobile DNA genomic insertion sites.}, journal = {bioRxiv}, year = {2016}, month = {2016 Feb 2}, abstract = {

Multiple methods have been introduced over the past 30 years to identify the genomic insertion sites of transposable elements and other DNA elements that integrate into genomes. However, each of these methods suffer from limitations that can frustrate attempts to map multiple insertions in a single genome and to map insertions in genomes of high complexity that contain extensive repetitive DNA. I introduce a new method for transposon mapping that is simple to perform, can accurately map multiple insertions per genome, and generates long sequence reads that facilitate mapping to complex genomes. The method, called TagMap, for Tagmentation-based Mapping, relies on a modified Tn5 tagmentation protocol with a single tagmentation adaptor followed by PCR using primers specific to the tranposable element and the adaptor sequence. Several minor modifications to normal tagmentation reagents and protocols allow easy and rapid preparation of TagMap libraries. Short read sequencing starting from the adaptor sequence generates oriented reads that flank and are oriented toward the transposable element insertion site. The convergent orientation of adjacent reads at the insertion site allows straightforward prediction of the precise insertion site(s). A Linux shell script is provided to identify insertion sites from fastq files.

}, doi = {10.1101/037762} } @article {47813, title = {Technologies for imaging neural activity in large volumes.}, journal = {Nature Neuroscience}, volume = {19}, year = {2016}, month = {2016 Aug 26}, pages = {1154-64}, abstract = {

Neural circuitry has evolved to form distributed networks that act dynamically across large volumes. Conventional microscopy collects data from individual planes and cannot sample circuitry across large volumes at the temporal resolution relevant to neural circuit function and behaviors. Here we review emerging technologies for rapid volume imaging of neural circuitry. We focus on two critical challenges: the inertia of optical systems, which limits image speed, and aberrations, which restrict the image volume. Optical sampling time must be long enough to ensure high-fidelity measurements, but optimized sampling strategies and point-spread function engineering can facilitate rapid volume imaging of neural activity within this constraint. We also discuss new computational strategies for processing and analyzing volume imaging data of increasing size and complexity. Together, optical and computational advances are providing a broader view of neural circuit dynamics and helping elucidate how brain regions work in concert to support behavior.

}, issn = {1546-1726}, doi = {10.1038/nn.4358}, author = {Ji, Na and Freeman, Jeremy and Smith, Spencer L} } @article {47265, title = {Thalamus provides layer 4 of primary visual cortex with orientation- and direction-tuned inputs.}, journal = {Nature Neuroscience}, volume = {19}, year = {2016}, month = {2016 Feb}, pages = {308-15}, abstract = {

Understanding the functions of a brain region requires knowing the neural representations of its myriad inputs, local neurons and outputs. Primary visual cortex (V1) has long been thought to compute visual orientation from untuned thalamic inputs, but very few thalamic inputs have been measured in any mammal. We determined the response properties of ~28,000 thalamic boutons and ~4,000 cortical neurons in layers 1{\textendash}5 of awake mouse V1. Using adaptive optics that allows accurate measurement of bouton activity deep in cortex, we found that around half of the boutons in the main thalamorecipient L4 carried orientation-tuned information and that their orientation and direction biases were also dominant in the L4 neuron population, suggesting that these neurons may inherit their selectivity from tuned thalamic inputs. Cortical neurons in all layers exhibited sharper tuning than thalamic boutons and a greater diversity of preferred orientations. Our results provide data-rich constraints for refining mechanistic models of cortical computation.

}, doi = {10.1038/nn.4196}, author = {Sun, Wenzhi and Tan, Zhongchao and Mensh, Brett D and Ji, Na} } @article {48106, title = {Three pillars for the neural control of appetite.}, journal = {Annual Review of Physiology}, volume = {79}, year = {2016}, month = {2016 Nov 28}, pages = {401-23}, abstract = {

The neural control of appetite is important for understanding motivated behavior along with the present rising prevalence of obesity. Over the past several years, new tools for cell type-specific neuron activity monitoring and perturbation have enabled increasingly detailed analyses of the mechanisms underlying appetite-control systems. Three major neural circuits strongly and acutely influence appetite but with notably different characteristics. Although these circuits interact, they have distinct properties and thus appear to contribute to separate but interlinked processes influencing appetite, thereby forming three pillars of appetite control. Here, we summarize some of the key characteristics of appetite circuits that are emerging from recent work and synthesize the findings into a provisional framework that can guide future studies. Expected final online publication date for the Annual Review of Physiology Volume 79 is February 10, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

}, issn = {1545-1585}, doi = {10.1146/annurev-physiol-021115-104948}, author = {Sternson, Scott M and Eiselt, Anne-Kathrin} } @article {47913, title = {A timecourse analysis of systemic and gonadal effects of temperature on sexual development of the red-eared slider turtle Trachemys scripta elegans.}, journal = {Developmental Biology}, volume = {420}, year = {2016}, month = {2016 Dec 1 }, pages = {166-77}, abstract = {

Temperature dependent sex determination (TSD) is the process by which the environmental temperature experienced during embryogenesis influences the sex of an organism, as in the red-eared slider turtle Trachemys scripta elegans. In accord with current paradigms of vertebrate sex determination, temperature is believed to exert its effects on sexual development in T. scripta entirely within the middle third of development, when the gonad is forming. However, whether temperature regulates the transcriptome in T. scripta early embryos in a manner that could influence secondary sex characteristics or establish a pro-male or pro-female environment has not been investigated. In addition, apart from a handful of candidate genes, very little is known about potential similarities between the expression cascade during TSD and the genetic cascade that drives mammalian sex determination. Here, we conducted an unbiased transcriptome-wide analysis of the effects of male- and female-promoting temperatures on the turtle embryo prior to gonad formation, and on the gonad during the temperature sensitive period. We found sexually dimorphic expression reflecting differences in steroidogenic enzymes and brain development prior to gonad formation. Within the gonad, we mapped a cascade of differential expression similar to the genetic cascade established in mammals. Using a Hidden Markov Model based clustering approach, we identified groups of genes that show heterochronic shifts between M. musculus and T. scripta. We propose a model in which multiple factors influenced by temperature accumulate during early gonadogenesis, and converge on the antagonistic regulation of aromatase to canalize sex determination near the end of the temperature sensitive window of development.

}, issn = {1095-564X}, doi = {10.1016/j.ydbio.2016.09.018}, author = {Czerwinski, Michael and Natarajan, Anirudh and Barske, Lindsey and Looger, Loren L and Capel, Blanche} } @article {48007, title = {To the cloud! A grassroots proposal to accelerate brain science discovery.}, journal = {Neuron}, volume = {92}, year = {2016}, month = {2016 Nov 2}, pages = {622-7}, abstract = {

The revolution in neuroscientific data acquisition is creating an analysis challenge. We propose leveraging cloud-computing technologies to enable large-scale neurodata storing, exploring, analyzing, and modeling. This utility will empower scientists globally to generate and test theories of brain function and dysfunction.

}, author = {Neuro Cloud Consortium} } @article {47507, title = {Toll genes have an ancestral role in axis elongation.}, journal = {Current Biology : CB}, volume = {26}, year = {2016}, month = {2016 May 18}, pages = {1609-15}, abstract = {

One of the key morphogenetic processes used during development is the controlled intercalation of cells between their neighbors. This process has been co-opted into a range of developmental events, and it also underlies an event that occurs in each major group of bilaterians: elongation of the embryo along the anterior-posterior axis [1]. In Drosophila, a novel component of this process was recently discovered by Par{\'e} et\ al., who showed that three Toll genes function together to drive cell intercalation during germband extension [2]. This finding raises the question of whether this role of Toll genes is an evolutionary novelty of flies or a general mechanism of embryonic morphogenesis. Here we show that the Toll gene function in axis elongation is, in fact, widely conserved among arthropods. First, we functionally demonstrate that two Toll genes are required for cell intercalation in the beetle Tribolium castaneum. We then show that these genes belong to a previously undescribed Toll subfamily and that members of this subfamily exhibit striped expression (as seen in Tribolium and previously reported in Drosophila [3-5]) in embryos of six other arthropod species spanning the entire phylum. Last, we show that two of these Toll genes are required for normal morphogenesis during anterior-posterior embryo elongation in the spider Parasteatoda tepidariorum, a member of the most basally branching arthropod lineage. From our findings, we hypothesize that Toll genes had a morphogenetic function in embryo elongation in the last common ancestor of all arthropods, which existed over 550 million years ago.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2016.04.055}, author = {Benton, Matthew A and Pechmann, Matthias and Frey, Nadine and Stappert, Dominik and Conrads, Kai H and Chen, Yen-Ta and Stamataki, Evangelia and Pavlopoulos, Anastasios and Roth, Siegfried} } @article {47306, title = {Toward the neural implementation of structure learning.}, journal = {Current Opinion in Neurobiology}, volume = {37}, year = {2016}, month = {2016 Feb 11}, pages = {99-105}, abstract = {

Despite significant advances in neuroscience, the neural bases of intelligence remain poorly understood. Arguably the most elusive aspect of intelligence is the ability to make robust inferences that go far beyond one{\textquoteright}s experience. Animals categorize objects, learn to vocalize and may even estimate causal relationships - all in the face of data that is often ambiguous and sparse. Such inductive leaps are thought to result from the brain{\textquoteright}s ability to infer latent structure that governs the environment. However, we know little about the neural computations that underlie this ability. Recent advances in developing computational frameworks that can support efficient structure learning and inductive inference may provide insight into the underlying component processes and help pave the path for uncovering their neural implementation.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2016.01.014}, author = {Tervo, D Gowan and Tenenbaum, Joshua B and Gershman, Samuel J} } @article {47307, title = {Transcriptomes of lineage-specific Drosophila neuroblasts profiled by genetic targeting and robotic sorting.}, journal = {Development (Cambridge, England)}, volume = {143}, year = {2016}, month = {2016 Feb 1}, pages = {411-21}, abstract = {

A brain consists of numerous distinct neurons arising from a limited number of progenitors, called neuroblasts in Drosophila. Each neuroblast produces a specific neuronal lineage. To unravel the transcriptional networks that underlie the development of distinct neuroblast lineages, we marked and isolated lineage-specific neuroblasts for RNA sequencing. We labeled particular neuroblasts throughout neurogenesis by activating a conditional neuroblast driver in specific lineages using various intersection strategies. The targeted neuroblasts were efficiently recovered using a custom-built device for robotic single-cell picking. Transcriptome analysis of mushroom body, antennal lobe and type II neuroblasts compared with non-selective neuroblasts, neurons and glia revealed a rich repertoire of transcription factors expressed among neuroblasts in diverse patterns. Besides transcription factors that are likely to be pan-neuroblast, many transcription factors exist that are selectively enriched or repressed in certain neuroblasts. The unique combinations of transcription factors present in different neuroblasts may govern the diverse lineage-specific neuron fates.

}, issn = {1477-9129}, doi = {10.1242/dev.129163}, author = {Yang, Ching-Po and Fu, Chi-Cheng and Sugino, Ken and Liu, Zhiyong and Ren, Qingzhong and Liu, Ling-Yu and Yao, Xiaohao and Lee, Luke P and Lee, Tzumin} } @article {47521, title = {Translation dynamics of single mRNAs in live cells and neurons.}, journal = {Science (New York, N.Y.)}, volume = {352}, year = {2016}, month = {2016 May 05}, pages = {1430-5}, abstract = {

Translation is the fundamental biological process converting mRNA information into proteins. Single molecule imaging in live cells has illuminated the dynamics of RNA transcription; however, it is not yet applicable to translation. Here we report Single molecule Imaging of NAscent PeptideS (SINAPS) to assess translation in live cells. The approach provides direct readout of initiation, elongation, and location of translation. We show that mRNAs coding for endoplasmic reticulum (ER) proteins are translated when they encounter the ER membrane. Single molecule fluorescence recovery after photobleaching provides direct measurement of elongation speed (5 AA/s). In primary neurons mRNAs are translated in proximal dendrites but repressed in distal dendrites and display {\textquotedblleft}bursting{\textquotedblright} translation. This technology provides a tool to address the spatiotemporal translation mechanism of single mRNAs in living cells.

}, doi = {10.1126/science.aaf1084}, author = {Wu, Bin and Eliscovich, Carolina and Yoon, Young J and Singer, Robert H} } @article {68445, title = {Transmembrane channel-like (tmc) gene regulates Drosophila larval locomotion.}, journal = {Proc Natl Acad Sci U S A}, volume = {113}, year = {2016}, month = {06/2016}, pages = {7243-8}, abstract = {

Drosophila larval locomotion, which entails rhythmic body contractions, is controlled by sensory feedback from proprioceptors. The molecular mechanisms mediating this feedback are little understood. By using genetic knock-in and immunostaining, we found that the Drosophila melanogaster transmembrane channel-like (tmc) gene is expressed in the larval class I and class II dendritic arborization (da) neurons and bipolar dendrite (bd) neurons, both of which are known to provide sensory feedback for larval locomotion. Larvae with knockdown or loss of tmc function displayed reduced crawling speeds, increased head cast frequencies, and enhanced backward locomotion. Expressing Drosophila TMC or mammalian TMC1 and/or TMC2 in the tmc-positive neurons rescued these mutant phenotypes. Bending of the larval body activated the tmc-positive neurons, and in tmc mutants this bending response was impaired. This implicates TMC{\textquoteright}s roles in Drosophila proprioception and the sensory control of larval locomotion. It also provides evidence for a functional conservation between Drosophila and mammalian TMCs.

}, keywords = {Animals, Animals, Genetically Modified, Cell Line, Drosophila melanogaster, Drosophila Proteins, Larva, Locomotion, Membrane Proteins, Mutation, Neurons}, issn = {1091-6490}, doi = {10.1073/pnas.1606537113}, author = {Guo, Yanmeng and Wang, Yuping and Zhang, Wei and Meltzer, Shan and Zanini, Damiano and Yu, Yue and Li, Jiefu and Cheng, Tong and Guo, Zhenhao and Wang, Qingxiu and Jacobs, Julie S and Sharma, Yashoda and Eberl, Daniel F and G{\"o}pfert, Martin C and Jan, Lily Yeh and Jan, Yuh Nung and Wang, Zuoren} } @article {47525, title = {TRICK: A single-molecule method for imaging the first round of translation in living cells and animals.}, journal = {Methods in Enzymology}, volume = {572}, year = {2016}, month = {2016}, pages = {123-57}, abstract = {

The life of an mRNA is dynamic within a cell. The development of quantitative fluorescent microscopy techniques to image single molecules of RNA has allowed many aspects of the mRNA lifecycle to be directly observed in living cells. Recent advances in live-cell multicolor RNA imaging, however, have now made it possible to investigate RNA metabolism in greater detail. In this chapter, we present an overview of the design and implementation of the translating RNA imaging by coat protein knockoff RNA biosensor, which allows untranslated mRNAs to be distinguished from ones that have undergone a round of translation. The methods required for establishing this system in mammalian cell lines and Drosophila melanogaster oocytes are described here, but the principles may be applied to any experimental system.

}, issn = {1557-7988}, doi = {10.1016/bs.mie.2016.02.027}, author = {Halstead, J M and Wilbertz, J H and Wippich, F and Lionnet, T and Ephrussi, A and Chao, J A} } @article {47972, title = {An unsupervised method for quantifying the behavior of interacting individuals.}, journal = {Physical Biology}, volume = {14}, year = {2016}, month = {2017 Feb16}, pages = {1609.09345}, abstract = {

Behaviors involving the interaction of multiple individuals are complex and frequently crucial for an animal{\textquoteright}s survival. These interactions, ranging across sensory modalities, length scales, and time scales, are often subtle and difficult to characterize. Contextual effects on the frequency of behaviors become even more difficult to quantify when physical interaction between animals interferes with conventional data analysis, e.g. due to visual occlusion. We introduce a method for quantifying behavior in fruit fly interaction that combines high-throughput video acquisition and tracking of individuals with recent unsupervised methods for capturing an animal{\textquoteright}s entire behavioral repertoire. We find behavioral differences between solitary flies and those paired with an individual of the opposite sex, identifying specific behaviors that are affected by social and spatial context. Our pipeline allows for a comprehensive description of the interaction between two individuals using unsupervised machine learning methods, and will be used to answer questions about the depth of complexity and variance in fruit fly courtship.

}, doi = {10.1088/1478-3975/aa5c50}, url = {https://arxiv.org/abs/1609.09345v1}, author = {Klibaite, Ugne and Berman, Gordon J and Cande, Jessica and Stern, David L} } @article {47971, title = {V-1 regulates capping protein activity in vivo.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, year = {2016}, month = {2016 Oct 25}, pages = {E6610-9}, abstract = {

Capping Protein (CP) plays a central role in the creation of the Arp2/3-generated branched actin networks comprising lamellipodia and pseudopodia by virtue of its ability to cap the actin filament barbed end, which promotes Arp2/3-dependent filament nucleation and optimal branching. The highly conserved protein V-1/Myotrophin binds CP tightly in vitro to render it incapable of binding the barbed end. Here we addressed the physiological significance of this CP antagonist in Dictyostelium, which expresses a V-1 homolog that we show is very similar biochemically to mouse V-1. Consistent with previous studies of CP knockdown, overexpression of V-1 in Dictyostelium reduced the size of pseudopodia and the cortical content of Arp2/3 and induced the formation of filopodia. Importantly, these effects scaled positively with the degree of V-1 overexpression and were not seen with a V-1 mutant that cannot bind CP. V-1 is present in molar excess over CP, suggesting that it suppresses CP activity in the cytoplasm at steady state. Consistently, cells devoid of V-1, like cells overexpressing CP described previously, exhibited a significant decrease in cellular F-actin content. Moreover, V-1-null cells exhibited pronounced defects in macropinocytosis and chemotactic aggregation that were rescued by V-1, but not by the V-1 mutant. Together, these observations demonstrate that V-1 exerts significant influence in vivo on major actin-based processes via its ability to sequester CP. Finally, we present evidence that V-1{\textquoteright}s ability to sequester CP is regulated by phosphorylation, suggesting that cells may manipulate the level of active CP to tune their "actin phenotype."

}, issn = {1091-6490}, doi = {10.1073/pnas.1605350113}, author = {Jung, Goeh and Alexander, Christopher J and Wu, Xufeng S and Piszczek, Grzegorz and Chen, Bi-Chang and Betzig, Eric and Hammer, John A} } @article {47355, title = {Virginia Orange: A versatile, red-shifted fluorescein scaffold for single- and dual-input fluorogenic probes.}, journal = {Bioconjugate Chemistry}, volume = {27}, year = {2016}, month = {2016 Feb 17}, pages = {474-80}, abstract = {

Fluorogenic molecules are important tools for biological and biochemical research. The majority of fluorogenic compounds have a simple input-output relationship, where a single chemical input yields a fluorescent output. Development of new systems where multiple inputs converge to yield an optical signal could refine and extend fluorogenic compounds by allowing greater spatiotemporal control over the fluorescent signal. Here, we introduce a new red-shifted fluorescein derivative, Virginia Orange, as an exceptional scaffold for single- and dual-input fluorogenic molecules. Unlike fluorescein, installation of a single masking group on Virginia Orange is sufficient to fully suppress fluorescence, allowing preparation of fluorogenic enzyme substrates with rapid, single-hit kinetics. Virginia Orange can also be masked with two independent moieties; both of these masking groups must be removed to induce fluorescence. This allows facile construction of multi-input fluorogenic probes for sophisticated sensing regimes and genetic targeting of latent fluorophores to specific cellular populations.

}, issn = {1520-4812}, doi = {10.1021/acs.bioconjchem.5b00566}, author = {Grimm, Jonathan B and Gruber, Todd D and Ortiz, Gloria and Brown, Timothy A and Lavis, Luke D} } @article {48136, title = {Visual projection neurons in the Drosophila lobula link feature detection to distinct behavioral programs.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Dec 28}, abstract = {

Visual projection neurons (VPNs) provide an anatomical connection between early visual processing and higher brain regions. Here we characterize lobula columnar (LC) cells, a class of Drosophila VPNs that project to distinct central brain structures called optic glomeruli. We anatomically describe 22 different LC types and show that, for several types, optogenetic activation in freely moving flies evokes specific behaviors. The activation phenotypes of two LC types closely resemble natural avoidance behaviors triggered by a visual loom. In vivo two-photon calcium imaging reveals that these LC types respond to looming stimuli, while another type does not, but instead responds to the motion of a small object. Activation of LC neurons on only one side of the brain can result in attractive or aversive turning behaviors depending on the cell type. Our results indicate that LC neurons convey information on the presence and location of visual features relevant for specific behaviors.

}, issn = {2050-084X}, doi = {10.7554/eLife.21022}, author = {Wu, Ming and Nern, Aljoscha and Williamson, W Ryan and Morimoto, Mai M and Reiser, Michael B and Card, Gwyneth M and Rubin, Gerald M} } @article {47308, title = {Visualization and quantification for interactive analysis of neural connectivity in Drosophila.}, journal = {Computer Graphics Forum}, year = {2016}, month = {2016 Jan 28}, abstract = {

Neurobiologists investigate the brain of the common fruit fly\ Drosophila melanogaster\ to discover neural circuits and link them to complex behaviour. Formulating new hypotheses about connectivity requires potential connectivity information between individual neurons, indicated by overlaps of arborizations of two or more neurons. As the number of higher order overlaps (i.e. overlaps of three or more arborizations) increases exponentially with the number of neurons under investigation, visualization is impeded by clutter and quantification becomes a burden. Existing solutions are restricted to visual or quantitative analysis of pairwise overlaps, as they rely on precomputed overlap data. We present a novel tool that complements existing methods for potential connectivity exploration by providing for the first time the possibility to compute and visualize higher order arborization overlaps on the fly and to interactively explore this information in both its spatial anatomical context and on a quantitative level. Qualitative evaluation by neuroscientists and non-experts demonstrated the utility and usability of the tool.

}, doi = {10.1111/cgf.12792}, author = {Swoboda, N and Moosburner, J and Bruckner, S and Yu, JY and Dickson, Barry J and B{\"u}hler, Katja} } @article {47814, title = {Whole-animal imaging with high spatio-temporal resolution.}, journal = {Proceedings of SPIE}, volume = {9720}, year = {2016}, month = {2016 Jul 18}, pages = {97200R}, abstract = {

We developed isotropic multiview (IsoView) light-sheet microscopy in order to image fast cellular dynamics, such as cell movements in an entire developing embryo or neuronal activity throughput an entire brain or nervous system, with high resolution in all dimensions, high imaging speeds, good physical coverage and low photo-damage. To achieve high temporal resolution and high spatial resolution at the same time, IsoView microscopy rapidly images large specimens via simultaneous light-sheet illumination and fluorescence detection along four orthogonal directions. In a post-processing step, these four views are then combined by means of high-throughput multiview deconvolution to yield images with a system resolution of <= 450 nm in all three dimensions. Using IsoView microscopy, we performed whole-animal functional imaging of Drosophila embryos and larvae at a spatial resolution of 1.1-2.5 μm and at a temporal resolution of 2 Hz for up to 9 hours. We also performed whole-brain functional imaging in larval zebrafish and multicolor imaging of fast cellular dynamics across entire, gastrulating Drosophila embryos with isotropic, sub-cellular resolution. Compared with conventional (spatially anisotropic) light-sheet microscopy, IsoView microscopy improves spatial resolution at least sevenfold and decreases resolution anisotropy at least threefold. Compared with existing high-resolution light-sheet techniques, such as lattice lightsheet microscopy or diSPIM, IsoView microscopy effectively doubles the penetration depth and provides subsecond temporal resolution for specimens 400-fold larger than could previously be imaged.

}, isbn = {978-162841954-2}, issn = { 0277786X}, doi = {10.1117/12.2212564}, author = {Chhetri, Raghav and Amat, Fernando and Wan, Yinan and H{\"o}ckendorf, Burkhard and Lemon, William C and Keller, Philipp J} } @article {47486, title = {The wiring diagram of a glomerular olfactory system.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 May 13}, abstract = {

The sense of smell enables animals to react to long-distance cues according to learned and innate valences. Here, we have mapped with electron microscopy the complete wiring diagram of the Drosophila larval antennal lobe, an olfactory neuropil similar to the vertebrate olfactory bulb. We found a canonical circuit with uniglomerular projection neurons (uPNs) relaying gain-controlled ORN activity to the mushroom body and the lateral horn. A second, parallel circuit with multiglomerular projection neurons (mPNs) and hierarchically connected local neurons (LNs) selectively integrates multiple ORN signals already at the first synapse. LN-LN synaptic connections putatively implement a bistable gain control mechanism that either computes odor saliency through panglomerular inhibition, or allows some glomeruli to respond to faint aversive odors in the presence of strong appetitive odors. This complete wiring diagram will support experimental and theoretical studies towards bridging the gap between circuits and behavior.

}, issn = {2050-084X}, doi = {10.7554/eLife.14859}, author = {Berck, Matthew E and Khandelwal, Avinash and Claus, Lindsey and Hernandez-Nunez, Luis and Si, Guangwei and Tabone, Christopher J and Li, Feng and Truman, James W and Fetter, Richard D and Louis, Matthieu and Samuel, Aravinthan Dt and Cardona, Albert} } @article {47162, title = {The 2015 super-resolution microscopy roadmap.}, journal = {Journal of Physics D: Applied Physics}, volume = {48}, year = {2015}, month = {2015 Oct 14}, pages = {443001}, abstract = {

Far-field optical microscopy using focused light is an important tool in a number of scientific disciplines including chemical, (bio)physical and biomedical research, particularly with respect to the study of living cells and organisms. Unfortunately, the applicability of the optical microscope is limited, since the diffraction of light imposes limitations on the spatial resolution of the image. Consequently the details of, for example, cellular protein distributions, can be visualized only to a certain extent. Fortunately, recent years have witnessed the development of {\textquoteright}super-resolution{\textquoteright} far-field optical microscopy (nanoscopy) techniques such as stimulated emission depletion (STED), ground state depletion (GSD), reversible saturated optical (fluorescence) transitions (RESOLFT), photoactivation localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM), structured illumination microscopy (SIM) or saturated structured illumination microscopy (SSIM), all in one way or another addressing the problem of the limited spatial resolution of far-field optical microscopy. While SIM achieves a two-fold improvement in spatial resolution compared to conventional optical microscopy, STED, RESOLFT, PALM/STORM, or SSIM have all gone beyond, pushing the limits of optical image resolution to the nanometer scale. Consequently, all super-resolution techniques open new avenues of biomedical research. Because the field is so young, the potential capabilities of different super-resolution microscopy approaches have yet to be fully explored, and uncertainties remain when considering the best choice of methodology. Thus, even for experts, the road to the future is sometimes shrouded in mist. The super-resolution optical microscopy roadmap of\ Journal of Physics D: Applied Physicsaddresses this need for clarity. It provides guidance to the outstanding questions through a collection of short review articles from experts in the field, giving a thorough discussion on the concepts underlying super-resolution optical microscopy, the potential of different approaches, the importance of label optimization (such as reversible photoswitchable proteins) and applications in which these methods will have a significant impact.

}, doi = {10.1088/0022-3727/48/44/443001}, author = {Hell, Stefan W and Sahl, Steffen J and Bates, Mark and Zhuang, Xiaowei and Heintzmann, Rainer and Booth, Martin J and Bewersdorf, Joerg and Shtengel, Gleb and Hess, Harald F and Tinnefeld, Philip} } @article {46774, title = {Actin depletion initiates events leading to granule secretion at the immunological synapse.}, journal = {Immunity}, volume = {42}, year = {2015}, month = {2015 May 19}, pages = {864-76}, abstract = {

Cytotoxic T lymphocytes (CTLs) use polarized secretion to rapidly destroy virally infected and tumor cells. To understand the temporal relationships between key events leading to secretion, we used high-resolution 4D imaging. CTLs approached targets with actin-rich projections at the leading edge, creating an initially actin-enriched contact with rearward-flowing actin. Within 1\ min, cortical actin reduced across the synapse, T\ cell receptors (TCRs) clustered centrally to form the central supramolecular activation cluster (cSMAC), and centrosome polarization began. Granules clustered around the moving centrosome within 2.5\ min and reached the synapse after 6\ min. TCR-bearing intracellular vesicles were delivered to the cSMAC as the centrosome docked. We found that the centrosome and granules were delivered to an area of membrane with reduced cortical actin density and phospholipid PIP2. These data resolve the temporal order of events during synapse maturation in 4D and reveal a critical role for actin depletion in regulating secretion.

}, issn = {1097-4180}, doi = {10.1016/j.immuni.2015.04.013}, author = {Ritter, Alex T and Asano, Yukako and Stinchcombe, Jane C and Dieckmann, N M G and Chen, Bi-Chang and Gawden-Bone, C and van Engelenburg, Schuyler and Legant, Wesley and Gao, Liang and Davidson, Michael W and Betzig, Eric and Lippincott-Schwartz, Jennifer and Griffiths, Gillian M} } @article {46366, title = {Adenotrophic viviparity in tsetse flies: potential for population control and as an insect model for lactation.}, journal = {Annual Review of Entomology}, volume = {60}, year = {2015}, month = {2015 Jan 7}, pages = {351-71}, abstract = {

Tsetse flies (Glossina spp.), vectors of African trypanosomes, are distinguished by their specialized reproductive biology, defined by adenotrophic viviparity (maternal nourishment of progeny by glandular secretions followed by live birth). This trait has evolved infrequently among insects and requires unique reproductive mechanisms. A key event in Glossina reproduction involves the transition between periods of lactation and nonlactation (dry periods). Increased lipolysis, nutrient transfer to the milk gland, and milk-specific protein production characterize lactation, which terminates at the birth of the progeny and is followed by a period of involution. The dry stage coincides with embryogenesis of the progeny, during which lipid reserves accumulate in preparation for the next round of lactation. The obligate bacterial symbiont Wigglesworthia glossinidia is critical to tsetse reproduction and likely provides B vitamins required for metabolic processes underlying lactation and/or progeny development. Here we describe findings that utilized transcriptomics, physiological assays, and RNA interference-based functional analysis to understand different components of adenotrophic viviparity in tsetse flies.

}, issn = {1545-4487}, doi = {10.1146/annurev-ento-010814-020834}, author = {Benoit, Joshua B and Attardo, Geoffrey M and Baumann, Aaron A and Michalkova, Veronika and Aksoy, Serap} } @article {46525, title = {Age-dependent changes in intrinsic neuronal excitability in subiculum after status epilepticus.}, journal = {PLoS One}, volume = {10}, year = {2015}, month = {2015 Mar 16}, pages = {e0119411}, abstract = {

Kainic acid-induced status epilepticus (KA-SE) in mature rats results in the development of spontaneous recurrent seizures and a pattern of cell death resembling hippocampal sclerosis in patients with temporal lobe epilepsy. In contrast, KA-SE in young animals before postnatal day (P) 18 is less likely to cause cell death or epilepsy. To investigate whether changes in neuronal excitability occur in the subiculum after KA-SE, we examined the age-dependent effects of SE on the bursting neurons of subiculum, the major output region of the hippocampus. Patch-clamp recordings were used to monitor bursting in pyramidal neurons in the subiculum of rat hippocampal slices. Neurons were studied either one or 2-3 weeks following injection of KA or saline (control) in immature (P15) or more mature (P30) rats, which differ in their sensitivity to KA as well as the long-term sequelae of the KA-SE. A significantly greater proportion of subicular pyramidal neurons from P15 rats were strong-bursting neurons and showed increased frequency-dependent bursting compared to P30 animals. Frequency-dependent burst firing was enhanced in P30, but not in P15 rats following KA-SE. The enhancement of bursting induced by KA-SE in more mature rats suggests that the frequency-dependent limitation of repetitive burst firing, which normally occurs in the subiculum, is compromised following SE. These changes could facilitate the initiation of spontaneous recurrent seizures or their spread from the hippocampus to other parts of the brain.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0119411}, author = {Chung, Sungkwon and Spruston, Nelson and Koh, Sookyong} } @article {68446, title = {Ankyrin Repeats Convey Force to Gate the NOMPC Mechanotransduction Channel.}, journal = {Cell}, volume = {162}, year = {2015}, month = {09/2015}, pages = {1391-403}, abstract = {

How metazoan mechanotransduction channels sense mechanical stimuli is not well understood. The NOMPC channel in the transient receptor potential (TRP) family, a mechanotransduction channel for Drosophila touch sensation and hearing, contains 29 Ankyrin repeats (ARs) that associate with microtubules. These ARs have been postulated to act as a tether that conveys force to the channel. Here, we report that these N-terminal ARs form a cytoplasmic domain essential for NOMPC mechanogating in vitro, mechanosensitivity of touch receptor neurons in vivo, and touch-induced behaviors of Drosophila larvae. Duplicating the ARs elongates the filaments that tether NOMPC to microtubules in mechanosensory neurons. Moreover, microtubule association is required for NOMPC mechanogating. Importantly, transferring the NOMPC ARs to mechanoinsensitive voltage-gated potassium channels confers mechanosensitivity to the chimeric channels. These experiments strongly support a tether mechanism of mechanogating for the NOMPC channel, providing insights into the basis of mechanosensitivity of mechanotransduction channels.

}, keywords = {Animals, Drosophila, Drosophila Proteins, Kv1.2 Potassium Channel, Larva, Mechanotransduction, Cellular, Microtubules, Protein Structure, Tertiary, Touch, Transient Receptor Potential Channels}, issn = {1097-4172}, doi = {10.1016/j.cell.2015.08.024}, author = {Zhang, Wei and Cheng, Li E and Kittelmann, Maike and Li, Jiefu and Petkovic, Maja and Cheng, Tong and Jin, Peng and Guo, Zhenhao and G{\"o}pfert, Martin C and Jan, Lily Yeh and Jan, Yuh Nung} } @article {46505, title = {Applying superresolution localization-based microscopy to neurons.}, journal = {Synapse}, volume = {69}, year = {2015}, month = {2015 May}, pages = {283-94}, abstract = {

Proper brain function requires the precise localization of proteins and signaling molecules on a nanometer scale. The examination of molecular organization at this scale has been difficult in part because it is beyond the reach of conventional, diffraction-limited light microscopy. The recently developed method of superresolution, localization-based fluorescent microscopy (LBM), such as photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM), has demonstrated a resolving power at a 10 nm scale and is poised to become a vital tool in modern neuroscience research. Indeed, LBM has revealed previously unknown cellular architectures and organizational principles in neurons. Here, we discuss the principles of LBM, its current applications in neuroscience, and the challenges that must be met before its full potential is achieved. We also present the unpublished results of our own experiments to establish a sample preparation procedure for applying LBM to study brain tissue. Synapse, 69:283-294, 2015. {\textcopyright} 2015 Wiley Periodicals, Inc.

}, issn = {1098-2396}, doi = {10.1002/syn.21806}, author = {Zhong, Haining} } @article {47147, title = {Applying the brakes: when to stop eating.}, journal = {Neuron}, volume = {88}, year = {2015}, month = {2015 Nov 4}, pages = {440-1}, abstract = {

The nucleus accumbens regulates consummatory behaviors, such as eating. In this issue of Neuron, O{\textquoteright}Connor et\ al. (2015) identify dopamine receptor 1-expressing neurons that project to the lateral hypothalamus as mediating rapid control over feeding behavior.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.10.034}, author = {Betley, J Nicholas and Sternson, Scott M} } @article {65782, title = {Artificial metalloenzymes derived from three-helix bundles.}, journal = {Current Opinion in Chemical Biology}, volume = {25C}, year = {2015}, month = {01/2015}, pages = {65 {\textendash} 70}, abstract = {

Three-helix bundles and coiled-coil motifs are well-established de novo designed scaffolds that have been investigated for their metal-binding and catalytic properties. Satisfaction of the primary coordination sphere for a given metal is sufficient to introduce catalytic activity and a given structure may catalyze different reactions dependent on the identity of the incorporated metal. Here we describe recent contributions in the de novo design of metalloenzymes based on three-helix bundles and coiled-coil motifs, focusing on non-heme systems for hydrolytic and redox chemistry.

}, doi = {10.1016/j.cbpa.2014.12.034}, author = {Tebo, Alison G and Pecoraro, Vincent L} } @article {46530, title = {Asymmetric formation of coated pits on dorsal and ventral surfaces at the leading edge of motile cells and on protrusions of immobile cells.}, journal = {Molecular Biology of the Cell}, volume = {26}, year = {2015}, month = {2015 Apr 7}, pages = {2044-53}, abstract = {

Clathrin/AP2-coated vesicles are the principal endocytic carriers originating at the plasma membrane. In experiments reported here, we have used spinning disk confocal and lattice light sheet microscopy to study the assembly dynamics of coated pits on the dorsal and ventral membranes of migrating U373 glioblastoma cells stably expressing AP2-EGFP and on lateral protrusions from immobile SUM159 breast carcinoma cells, gene edited to express AP2-EGFP. On U373 cells, coated pits initiated on the dorsal membrane at the front of the lamellipodium, as well as at the approximate boundary between the lamellipodium and lamella, and continued to grow as they were swept back toward the cell body; coated pits were absent from the corresponding ventral membrane. We observed a similar dorsal/ventral asymmetry on membrane protrusions from SUM159 cells. Stationary-coated pits formed and budded on the remainder of the dorsal and ventral surfaces of both types of cells. These observations support a previously proposed model that invokes net membrane deposition at the leading edge due to an imbalance between the endocytic and exocytic membrane flow at the front of a migrating cell.

}, issn = {1939-4586}, doi = {10.1091/mbc.E15-01-0055}, author = {Kural, Comert and Akatay, Ahmet Ata and Gaudin, Rapha{\"e}l and Chen, Bi-Chang and Legant, Wesley R and Betzig, Eric and Kirchhausen, Tom} } @article {47086, title = {Automated cerebellar lobule segmentation with application to cerebellar structural analysis in cerebellar disease.}, journal = {NeuroImage}, volume = {127}, year = {2015}, month = {2015 Sep 23}, pages = {435-44}, abstract = {

The cerebellum plays an important role in both motor control and cognitive function. Cerebellar function is topographically organized and diseases that affect specific parts of the cerebellum are associated with specific patterns of symptoms. Accordingly, delineation and quantification of cerebellar sub-regions from magnetic resonance images are important in the study of cerebellar atrophy and associated functional losses. This paper describes an automated cerebellar lobule segmentation method based on a graph cut segmentation framework. Results from multi-atlas labeling and tissue classification contribute to the region terms in the graph cut energy function and boundary classification contributes to the boundary term in the energy function. A cerebellar parcellation is achieved by minimizing the energy function using the α-expansion technique. The proposed method was evaluated using a leave-one-out cross-validation on 15 subjects including both healthy controls and patients with cerebellar diseases. Based on reported Dice coefficients, the proposed method outperforms two state-of-the-art methods. The proposed method was then applied to 2(j) 77 subjects to study the region-specific cerebellar structural differences in three spinocerebellar ataxia (SCA) genetic subtypes. Quantitative analysis of the lobule volumes show distinct patterns of volume changes associated with different SCA subtypes consistent with known patterns of atrophy in these genetic subtypes.

}, issn = {1095-9572}, doi = {10.1016/j.neuroimage.2015.09.032}, author = {Yang, Zhen and Ye, Chuyang and Bogovic, John A and Carass, Aaron and Jedynak, Bruno M and Ying, Sarah H and Prince, Jerry L} } @article {46974, title = {Automatic adaptation to fast input changes in a time-invariant neural circuit.}, journal = {PLoS Computational Biology}, volume = {11}, year = {2015}, month = {2015 Aug 6}, pages = {e1004315}, doi = {10.1371/journal.pcbi.1004315}, author = {Bharioke, Arjun and Chklovskii, Dmitri B} } @article {47885, title = {Automatic estimation and correction of anisotropic magnification distortion in electron microscopes.}, journal = {Journal of Structural Biology}, volume = {192}, year = {2015}, month = {2015 Nov}, pages = {204-8}, abstract = {

We demonstrate a significant anisotropic magnification distortion, found on an FEI Titan Krios microscope and affecting magnifications commonly used for data acquisition on a Gatan K2 Summit detector. We describe a program (mag_distortion_estimate) to automatically estimate anisotropic magnification distortion from a set of images of a standard gold shadowed diffraction grating. We also describe a program (mag_distortion_correct) to correct for the estimated distortion in collected images. We demonstrate that the distortion present on the Titan Krios microscope limits the resolution of a set of rotavirus VP6 images to \~{}7 {\r A}, which increases to \~{}3 {\r A} following estimation and correction of the distortion. We also use a 70S ribosome sample to demonstrate that in addition to affecting resolution, magnification distortion can also interfere with the classification of heterogeneous data.

}, keywords = {Anisotropy, Cryoelectron Microscopy, Gold, Image Enhancement}, issn = {1095-8657}, doi = {10.1016/j.jsb.2015.08.006}, author = {Grant, Timothy and Grigorieff, Nikolaus} } @inbook {49450, title = {Basal ganglia: songbird models}, booktitle = {Encyclopedia of Computational Neuroscience}, year = {2015}, pages = {356-61}, abstract = {

Songbirds produce complex vocalizations, a behavior that depends on the ability of juveniles to imitate the song of an adult. Song learning relies on a specialized basal ganglia-thalamocortical loop. Several computational models have examined the role of this circuit in song learning, shedding light on the neurobiological mechanisms underlying sensorimotor learning.

}, author = {Leblois, Arthur and Darshan, Ran} } @article {46753, title = {Behavioral responses to a repetitive visual threat stimulus express a persistent state of defensive arousal in Drosophila}, journal = {Current Biology}, volume = {25}, year = {2015}, month = {2015 May 14}, pages = {1401-15}, abstract = {

The neural circuit mechanisms underlying emotion states remain poorly understood. Drosophila offers powerful genetic approaches for dissecting neural circuit function, but whether flies exhibit emotion-like behaviors has not been clear. We recently proposed that model organisms may express internal states displaying {\textquotedblleft}emotion primitives,{\textquotedblright} which are general characteristics common to different emotions, rather than specific anthropomorphic emotions such as {\textquotedblleft}fear{\textquotedblright} or {\textquotedblleft}anxiety.{\textquotedblright} These emotion primitives include scalability, persistence, valence, and generalization to multiple contexts. Here, we have applied this approach to determine whether flies{\textquoteright} defensive responses to moving overhead translational stimuli ({\textquotedblleft}shadows{\textquotedblright}) are purely reflexive or may express underlying emotion states. We describe a new behavioral assay in which flies confined in an enclosed arena are repeatedly exposed to an overhead translational stimulus. Repetitive stimuli promoted graded (scalable) and persistent increases in locomotor velocity and hopping, and occasional freezing. The stimulus also dispersed feeding flies from a food resource, suggesting both negative valence and context generalization. Strikingly, there was a significant delay before the flies returned to the food following stimulus-induced dispersal, suggestive of a slowly decaying internal defensive state. The length of this delay was increased when more stimuli were delivered for initial dispersal. These responses can be mathematically modeled by assuming an internal state that behaves as a leaky integrator of stimulus exposure. Our results suggest that flies{\textquoteright} responses to repetitive visual threat stimuli express an internal state exhibiting canonical emotion primitives, possibly analogous to fear in mammals. The mechanistic basis of this state can now be investigated in a genetically tractable insect species.

}, doi = {10.1016/j.cub.2015.03.058}, author = {Gibson, William T. and Gonzalez, Carlos R. and Fernandez, Conchi and Ramasamy, Lakshminarayanan and Tabachnik, Tanya and Du, Rebecca R. and Felsen, Panna D. and Maire, Michael M. and Perona, Pietro and Anderson, David J.} } @article {46817, title = {BigDataViewer: visualization and processing for large image data sets.}, journal = {Nature Methods}, volume = {12}, year = {2015}, month = {2015 May 28}, pages = {481-3}, issn = {1548-7105}, doi = {10.1038/nmeth.3392}, author = {Pietzsch, Tobias and Saalfeld, Stephan and Preibisch, Stephan and Tomancak, Pavel} } @article {46901, title = {BigNeuron: Large-scale 3D neuron reconstruction from optical microscopy images.}, journal = {Neuron}, volume = {87}, year = {2015}, month = {2015 Jul 15}, pages = {252-6}, abstract = {

Understanding the structure of single neurons is critical for understanding how they function within neural circuits. BigNeuron is a new community effort that combines modern bioimaging informatics, recent leaps in labeling and microscopy, and the widely recognized need for openness and standardization to provide a community resource for automated reconstruction of dendritic and axonal morphology of single neurons.

Understanding the structure of single neurons is critical for understanding how they function within neural circuits. BigNeuron is a new community effort that combines modern bioimaging informatics, recent leaps in labeling and microscopy, and the widely recognized need for openness and standardization to provide a community resource for automated reconstruction of dendritic and axonal morphology of single neurons.

}, doi = {10.1016/j.neuron.2015.06.036}, author = {Peng, Hanchuan and Hawrylycz, Michael and Roskams, Jane and Hill, Sean and Spruston, Nelson and Meijering, Erik and Ascoli, Giorgio A} } @article {46813, title = {BlastNeuron for automated comparison, retrieval and clustering of 3D neuron morphologies.}, journal = {Neuroinformatics}, volume = {13}, year = {2015}, month = {2015 Jun 3}, pages = {487-99}, abstract = {

Characterizing the identity and types of neurons in the brain, as well as their associated function, requires a means of quantifying and comparing 3D neuron morphology. Presently, neuron comparison methods are based on statistics from neuronal morphology such as size and number of branches, which are not fully suitable for detecting local similarities and differences in the detailed structure. We developed BlastNeuron to compare neurons in terms of their global appearance, detailed arborization patterns, and topological similarity. BlastNeuron first compares and clusters 3D neuron reconstructions based on global morphology features and moment invariants, independent of their orientations, sizes, level of reconstruction and other variations. Subsequently, BlastNeuron performs local alignment between any pair of retrieved neurons via a tree-topology driven dynamic programming method. A 3D correspondence map can thus be generated at the resolution of single reconstruction nodes. We applied BlastNeuron to three datasets: (1) 10,000+ neuron reconstructions from a public morphology database, (2) 681 newly and manually reconstructed neurons, and (3) neurons reconstructions produced using several independent reconstruction methods. Our approach was able to accurately and efficiently retrieve morphologically and functionally similar neuron structures from large morphology database, identify the local common structures, and find clusters of neurons that share similarities in both morphology and molecular profiles.

}, issn = {1559-0089}, doi = {10.1007/s12021-015-9272-7}, author = {Wan, Yinan and Long, Fuhui and Qu, Lei and Xiao, Hang and Hawrylycz, Michael and Myers, Eugene W and Peng, Hanchuan} } @article {47895, title = {Canonical genetic signatures of the adult human brain.}, journal = {Nature neuroscience}, volume = {18}, year = {2015}, month = {2015 Dec}, pages = {1832-44}, abstract = {

The structure and function of the human brain are highly stereotyped, implying a conserved molecular program responsible for its development, cellular structure and function. We applied a correlation-based metric called differential stability to assess reproducibility of gene expression patterning across 132 structures in six individual brains, revealing mesoscale genetic organization. The genes with the highest differential stability are highly biologically relevant, with enrichment for brain-related annotations, disease associations, drug targets and literature citations. Using genes with high differential stability, we identified 32 anatomically diverse and reproducible gene expression signatures, which represent distinct cell types, intracellular components and/or associations with neurodevelopmental and neurodegenerative disorders. Genes in neuron-associated compared to non-neuronal networks showed higher preservation between human and mouse; however, many diversely patterned genes displayed marked shifts in regulation between species. Finally, highly consistent transcriptional architecture in neocortex is correlated with resting state functional connectivity, suggesting a link between conserved gene expression and functionally relevant circuitry.

}, keywords = {Adult, Animals, Brain, Gene Regulatory Networks, Humans, Mice, Nerve Net, Transcriptome}, issn = {1546-1726}, doi = {10.1038/nn.4171}, author = {Hawrylycz, Michael and Miller, Jeremy A and Menon, Vilas and Feng, David and Dolbeare, Tim and Guillozet-Bongaarts, Angela L and Jegga, Anil G and Aronow, Bruce J and Lee, Chang-Kyu and Bernard, Amy and Glasser, Matthew F and Dierker, Donna L and Menche, J{\"o}rg and Szafer, Aaron and Collman, Forrest and Grange, Pascal and Berman, Kenneth A and Mihalas, Stefan and Yao, Zizhen and Stewart, Lance and Barab{\'a}si, Albert-L{\'a}szl{\'o} and Schulkin, Jay and Phillips, John and Ng, Lydia and Dang, Chinh and Haynor, David R and Jones, Allan and Van Essen, David C and Koch, Christof and Lein, Ed} } @article {47032, title = {CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015 Aug 31}, pages = {11870-5}, abstract = {

Direct visualization of genomic loci in the 3D nucleus is important for understanding the spatial organization of the genome and its association with gene expression. Various DNA FISH methods have been developed in the past decades, all involving denaturing dsDNA and hybridizing fluorescent nucleic acid probes. Here we report a novel approach that uses in vitro constituted nuclease-deficient clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated caspase 9 (Cas9) complexes as probes to label sequence-specific genomic loci fluorescently without global DNA denaturation (Cas9-mediated fluorescence in situ hybridization, CASFISH). Using fluorescently labeled nuclease-deficient Cas9 (dCas9) protein assembled with various single-guide RNA (sgRNA), we demonstrated rapid and robust labeling of repetitive DNA elements in pericentromere, centromere, G-rich telomere, and coding gene loci. Assembling dCas9 with an array of sgRNAs tiling arbitrary target loci, we were able to visualize nonrepetitive genomic sequences. The dCas9/sgRNA binary complex is stable and binds its target DNA with high affinity, allowing sequential or simultaneous probing of multiple targets. CASFISH assays using differently colored dCas9/sgRNA complexes allow multicolor labeling of target loci in cells. In addition, the CASFISH assay is remarkably rapid under optimal conditions and is applicable for detection in primary tissue sections. This rapid, robust, less disruptive, and cost-effective technology adds a valuable tool for basic research and genetic diagnosis.

}, issn = {1091-6490}, doi = {10.1073/pnas.1515692112}, author = {Deng, Wulan and Shi, Xinghua and Tjian, Robert and Lionnet, Timoth{\'e}e and Singer, Robert H} } @article {47015, title = {C/D box sRNA-guided 2{\textquoteright}-O-methylation patterns of archaeal rRNA molecules.}, journal = {BMC Genomics}, volume = {16}, year = {2015}, month = {2015 Aug 22}, pages = {632}, abstract = {

BACKGROUND: In archaea and eukaryotes, ribonucleoprotein complexes containing small C/D box s(no)RNAs use base pair complementarity to target specific sites within ribosomal RNA for 2{\textquoteright}-O-ribose methylation. These modifications aid in the folding and stabilization of nascent rRNA molecules and their assembly into ribosomal particles. The genomes of hyperthermophilic archaea encode large numbers of C/D box sRNA genes, suggesting an increased necessity for rRNA stabilization at extreme growth temperatures.

RESULTS: We have identified the complete sets of C/D box sRNAs from seven archaea using RNA-Seq methodology. In total, 489 C/D box sRNAs were identified, each containing two guide regions. A combination of computational and manual analyses predicts 719 guide interactions with 16S and 23S rRNA molecules. This first pan-archaeal description of guide sequences identifies (i) modified rRNA nucleotides that are frequently conserved between species and (ii) regions within rRNA that are hotspots for 2{\textquoteright}-O-methylation. Gene duplication, rearrangement, mutational drift and convergent evolution of sRNA genes and guide sequences were observed. In addition, several C/D box sRNAs were identified that use their two guides to target locations distant in the rRNA sequence but close in the secondary and tertiary structure. We propose that they act as RNA chaperones and facilitate complex folding events between distant sequences.

CONCLUSIONS: This pan-archaeal analysis of C/D box sRNA guide regions identified conserved patterns of rRNA 2{\textquoteright}-O-methylation in archaea. The interaction between the sRNP complexes and the nascent rRNA facilitates proper folding and the methyl modifications stabilize higher order rRNA structure within the assembled ribosome.

}, issn = {1471-2164}, doi = {10.1186/s12864-015-1839-z}, author = {Dennis, Patrick P and Tripp, Vanessa and Lui, Lauren and Lowe, Todd and Randau, Lennart} } @article {47057, title = {Cell type-specific pharmacology of NMDA receptors using masked MK801.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Sep 11}, abstract = {

N-Methyl-D-aspartate receptors (NMDA-Rs) are ion channels that are important for synaptic plasticity, which is involved in learning and drug addiction. We show enzymatic targeting of an NMDA-R antagonist, MK801, to a molecularly defined neuronal population with the cell-type-selectivity of genetic methods and the temporal control of pharmacology. We find that NMDA-Rs on dopamine neurons are necessary for cocaine-induced synaptic potentiation, demonstrating that cell type-specific pharmacology can be used to dissect signaling pathways within complex brain circuits.

}, issn = {2050-084X}, doi = {10.7554/eLife.10206}, author = {Yang, Yunlei and Lee, Peter and Sternson, Scott M} } @article {47033, title = {Cell type-specific transcriptomics of hypothalamic energy-sensing neuron responses to weight-loss.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Sep 2}, abstract = {

Molecular and cellular processes in neurons are critical for sensing and responding to energy deficit states, such as during weight-loss. AGRP neurons are a key hypothalamic population that is activated during energy deficit and increases appetite and weight-gain. Cell type-specific transcriptomics can be used to identify pathways that counteract weight-loss, and here we report high-quality gene expression profiles of AGRP neurons from well-fed and food-deprived young adult mice. For comparison, we also analyzed POMC neurons, an intermingled population that suppresses appetite and body weight. We find that AGRP neurons are considerably more sensitive to energy deficit than POMC neurons. Furthermore, we identify cell type-specific pathways involving endoplasmic reticulum-stress, circadian signaling, ion channels, neuropeptides, and receptors. Combined with methods to validate and manipulate these pathways, this resource greatly expands molecular insight into neuronal regulation of body weight, and may be useful for devising therapeutic strategies for obesity and eating disorders.

}, issn = {2050-084X}, doi = {10.7554/eLife.09800}, author = {Henry, Fredrick E and Sugino, Ken and Tozer, Adam and Branco, Tiago and Sternson, Scott M} } @article {46546, title = {Cellular levels of signaling factors are sensed by β-actin alleles to modulate transcriptional pulse intensity.}, journal = {Cell Reports}, volume = {11}, year = {2015}, month = {2015 Apr 7}, pages = {419-32}, abstract = {

The transcriptional response of β-actin to extra-cellular stimuli is a paradigm for transcription factor complex assembly and regulation. Serum induction leads to a precisely timed pulse of β-actin transcription in the cell population. Actin protein is proposed to be involved in this response, but it is not known whether cellular actin levels affect nuclear β-actin transcription. We perturbed the levels of key signaling factors and examined the effect on the induced transcriptional pulse by following endogenous β-actin alleles in single living cells. Lowering serum response factor (SRF) protein levels leads to loss of pulse integrity, whereas reducing actin protein levels reveals positive feedback regulation, resulting in elevated gene activation and a prolonged transcriptional response. Thus, transcriptional pulse fidelity requires regulated amounts of signaling proteins, and perturbations in factor levels eliminate the physiological response, resulting in either tuning down or exaggeration of the transcriptional pulse.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2015.03.039}, author = {Kalo, Alon and Kanter, Itamar and Shraga, Amit and Sheinberger, Jonathan and Tzemach, Hadar and Kinor, Noa and Singer, Robert H and Lionnet, Timoth{\'e}e and Shav-Tal, Yaron} } @article {46664, title = {A cellular resolution map of barrel cortex activity during tactile behavior.}, journal = {Neuron}, volume = {86}, year = {2015}, month = {2015 Apr 21}, pages = {783-99}, abstract = {

Comprehensive measurement of neural activity remains challenging due to the large numbers of neurons in each brain area. We used volumetric two-photon imaging in mice expressing GCaMP6s and nuclear red fluorescent proteins to sample activity in 75\% of superficial barrel cortex neurons across the relevant cortical columns, approximately 12,000 neurons per animal, during performance of a single whisker object localization task. Task-related activity peaked during object palpation. An encoding model\ related activity to behavioral variables. In the column corresponding to the spared whisker, 300 layer (L) 2/3 pyramidal neurons (17\%) each encoded touch and whisker movements. Touch representation declined by half in surrounding columns; whisker movement representation was unchanged. Following the emergence of stereotyped task-related movement, sensory representations showed no measurable plasticity. Touch direction was topographically organized, with distinct organization for passive and active touch. Our work reveals sparse and spatially intermingled representations of multiple tactile features.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.03.027}, author = {Peron, Simon P and Freeman, Jeremy and Iyer, Vijay and Guo, Caiying and Svoboda, Karel} } @article {47092, title = {Central neural circuitry mediating courtship song perception in male Drosophila.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Sep 21}, abstract = {

Animals use acoustic signals across a variety of social behaviors, particularly courtship. In Drosophila, song is detected by antennal mechanosensory neurons and further processed by second-order aPN1/aLN(al) neurons. However, little is known about the central pathways mediating courtship hearing. In this study, we identified a male-specific pathway for courtship hearing via third-order ventrolateral protocerebrum Projection Neuron 1 (vPN1) neurons and fourth-order pC1 neurons. Genetic inactivation of vPN1 or pC1 disrupts song-induced male-chaining behavior. Calcium imaging reveals that vPN1 responds preferentially to pulse song with long inter-pulse intervals (IPIs), while pC1 responses to pulse song closely match the behavioral chaining responses at different IPIs. Moreover, genetic activation of either vPN1 or pC1 induced courtship chaining, mimicking the behavioral response to song. These results outline the aPN1-vPN1-pC1 pathway as a labeled line for the processing and transformation of courtship song in males.

}, issn = {2050-084X}, doi = {10.7554/eLife.08477}, author = {Zhou, Chuan and Franconville, Romain and Vaughan, Alexander G and Robinett, Carmen C and Jayaraman, Vivek and Baker, Bruce S} } @article {47034, title = {Chemical perturbation of an intrinsically disordered region of TFIID distinguishes two modes of transcription initiation.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Aug 28}, abstract = {

Intrinsically disordered protein regions (IDRs) are peptide segments that fail to form stable 3-dimensional structures in the absence of partner proteins. They are abundant in eukaryotic proteomes and are often associated with human diseases, but their biological functions have been elusive to study. Here we report the identification of a tin(IV) oxochloride-derived cluster that binds an evolutionarily conserved IDR within the metazoan TFIID transcription complex. Binding arrests an isomerization of promoter-bound TFIID that is required for the engagement of Pol II during the first (de novo) round of transcription initiation. However, the specific chemical probe does not affect reinitiation, which requires the re-entry of Pol II, thus, mechanistically distinguishing these two modes of transcription initiation. This work also suggests a new avenue for targeting the elusive IDRs by harnessing certain features of metal-based complexes for mechanistic studies, and for the development of novel pharmaceutical interventions.

}, issn = {2050-084X}, doi = {10.7554/eLife.07777}, author = {Zhang, Zhengjian and Boskovic, Zarko and Hussain, Mahmud M and Hu, Wenxin and Inouye, Carla and Kim, Han-Je and Abole, A Katherine and Doud, Mary K and Lewis, Timothy A and Koehler, Angela N and Schreiber, Stuart L and Tjian, Robert} } @article {47124, title = {Clique topology reveals intrinsic geometric structure in neural correlations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015 Nov 3}, pages = {13455-60}, abstract = {

Detecting meaningful structure in neural activity and connectivity data is challenging in the presence of hidden nonlinearities, where traditional eigenvalue-based methods may be misleading. We introduce a novel approach to matrix analysis, called clique topology, that extracts features of the data invariant under nonlinear monotone transformations. These features can be used to detect both random and geometric structure, and depend only on the relative ordering of matrix entries. We then analyzed the activity of pyramidal neurons in rat hippocampus, recorded while the animal was exploring a 2D environment, and confirmed that our method is able to detect geometric organization using only the intrinsic pattern of neural correlations. Remarkably, we found similar results during nonspatial behaviors such as wheel running and rapid eye movement (REM) sleep. This suggests that the geometric structure of correlations is shaped by the underlying hippocampal circuits and is not merely a consequence of position coding. We propose that clique topology is a powerful new tool for matrix analysis in biological settings, where the relationship of observed quantities to more meaningful variables is often nonlinear and unknown.

}, issn = {1091-6490}, doi = {10.1073/pnas.1506407112}, author = {Giusti, Chad and Pastalkova, Eva and Curto, Carina and Itskov, Vladimir} } @article {47035, title = {Combinatorial DNA rearrangement facilitates the origin of new genes in ciliates.}, journal = {Genome Biology and Evolution}, volume = {7}, year = {2015}, month = {2015 Sep 2}, pages = {2859-70}, abstract = {

Programmed genome rearrangements in the unicellular eukaryote Oxytricha trifallax produce a transcriptionally active somatic nucleus from a copy of its germline nucleus during development. This process eliminates noncoding sequences that interrupt coding regions in the germline genome, and joins over 225,000 remaining DNA segments, some of which require inversion or complex permutation to build functional genes. This dynamic genomic organization permits some single DNA segments in the germline to contribute to multiple, distinct somatic genes via alternative processing. Like alternative mRNA splicing, the combinatorial assembly of DNA segments contributes to genetic variation and facilitates the evolution of new genes. In this study, we use comparative genomic analysis to demonstrate that the emergence of alternative DNA splicing is associated with the origin of new genes. Short duplications give rise to alternative gene segments that are spliced to the shared gene segments. Alternative gene segments evolve faster than shared, constitutive segments. Genes with shared segments frequently have different expression profiles, permitting functional divergence. This study reports alternative DNA splicing as a mechanism of new gene origination, illustrating how the process of programmed genome rearrangement gives rise to evolutionary innovation.

}, issn = {1759-6653}, doi = {10.1093/gbe/evv172}, author = {Chen, Xiao and Jung, Seolkyoung and Beh, Leslie Y and Eddy, Sean R and Landweber, Laura F} } @article {46940, title = {A common evolutionary origin for the ON- and OFF-edge motion detection pathways of the Drosophila visual system.}, journal = {Frontiers in Neural Circuits}, volume = {9}, year = {2015}, month = {2015}, pages = {33}, abstract = {

Synaptic circuits for identified behaviors in the Drosophila brain have typically been considered from either a developmental or functional perspective without reference to how the circuits might have been inherited from ancestral forms. For example, two candidate pathways for ON- and OFF-edge motion detection in the visual system act via circuits that use respectively either T4 or T5, two cell types of the fourth neuropil, or lobula plate (LOP), that exhibit narrow-field direction-selective responses and provide input to wide-field tangential neurons. T4 or T5 both have four subtypes that terminate one each in the four strata of the LOP. Representatives are reported in a wide range of Diptera, and both cell types exhibit various similarities in: (1) the morphology of their dendritic arbors; (2) their four morphological and functional subtypes; (3) their cholinergic profile in Drosophila; (4) their input from the pathways of L3 cells in the first neuropil, or lamina (LA), and by one of a pair of LA cells, L1 (to the T4 pathway) and L2 (to the T5 pathway); and (5) their innervation by a single, wide-field contralateral tangential neuron from the central brain. Progenitors of both also express the gene atonal early in their proliferation from the inner anlage of the developing optic lobe, being alone among many other cell type progeny to do so. Yet T4 receives input in the second neuropil, or medulla (ME), and T5 in the third neuropil or lobula (LO). Here we suggest that these two cell types were originally one, that their ancestral cell population duplicated and split to innervate separate ME and LO neuropils, and that a fiber crossing-the internal chiasma-arose between the two neuropils. The split most plausibly occurred, we suggest, with the formation of the LO as a new neuropil that formed when it separated from its ancestral neuropil to leave the ME, suggesting additionally that ME input neurons to T4 and T5 may also have had a common origin.

}, issn = {1662-5110}, doi = {10.3389/fncir.2015.00033}, author = {Shinomiya, Kazunori and Takemura, Shin-ya and Rivlin, Patricia K and Plaza, Stephen M and Scheffer, Louis K and Meinertzhagen, Ian A} } @article {46590, title = {Comprehensive imaging of cortical networks.}, journal = {Current Opinion in Neurobiology}, volume = {32}, year = {2015}, month = {2015 Apr 10}, pages = {115-123}, abstract = {

Neural computations are implemented by activity in spatially distributed neural circuits. Cellular imaging fills a unique niche in linking activity of specific types of neurons to behavior, over spatial scales spanning single neurons to entire brain regions, and temporal scales from milliseconds to months. Imaging may soon make it possible to track activity of all neurons in a brain region, such as a cortical column. We review recent methodological advances that facilitate optical imaging of neuronal populations in vivo, with an emphasis on calcium imaging using protein indicators in mice. We point out areas that are particularly ripe for future developments.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2015.03.016}, author = {Peron, Simon and Chen, Tsai-Wen and Svoboda, Karel} } @article {46900, title = {Confidence estimation as a stochastic process in a neurodynamical system of decision making.}, journal = {Journal of Neurophysiology}, volume = {114}, year = {2015}, month = {2015 Jul}, pages = {99-113}, abstract = {

Evaluation of confidence about one{\textquoteright}s knowledge is key to the brain{\textquoteright}s ability to monitor cognition. To investigate the neural mechanism of confidence assessment, we examined a biologically realistic spiking network model and found that it reproduced salient behavioral observations and single-neuron activity data from a monkey experiment designed to study confidence about a decision under uncertainty. Interestingly, the model predicts that changes of mind can occur in a mnemonic delay when confidence is low; the probability of changes of mind increases (decreases) with task difficulty in correct (error) trials. Furthermore, a so-called "hard-easy effect" observed in humans naturally emerges, i.e., behavior shows underconfidence (underestimation of correct rate) for easy or moderately difficult tasks and overconfidence (overestimation of correct rate) for very difficult tasks. Importantly, in the model, confidence is computed using a simple neural signal in individual trials, without explicit representation of probability functions. Therefore, even a concept of metacognition can be explained by sampling a stochastic neural activity pattern.

}, issn = {1522-1598}, doi = {10.1152/jn.00793.2014}, author = {Wei, Ziqiang and Wang, Xiao-Jing} } @article {46918, title = {Conjunctive input processing drives feature selectivity in hippocampal CA1 neurons.}, journal = {Nature Neuroscience}, year = {2015}, month = {2015 Jul 13}, abstract = {

Feature-selective firing allows networks to produce representations of the external and internal environments. Despite its importance, the mechanisms generating neuronal feature selectivity are incompletely understood. In many cortical microcircuits the integration of two functionally distinct inputs occurs nonlinearly through generation of active dendritic signals that drive burst firing and robust plasticity. To examine the role of this processing in feature selectivity, we recorded CA1 pyramidal neuron membrane potential and local field potential in mice running on a linear treadmill. We found that dendritic plateau potentials were produced by an interaction between properly timed input from entorhinal cortex and hippocampal CA3. These conjunctive signals positively modulated the firing of previously established place fields and rapidly induced new place field formation to produce feature selectivity in CA1 that is a function of both entorhinal cortex and CA3 input. Such selectivity could allow mixed network level representations that support context-dependent spatial maps.

}, issn = {1546-1726}, doi = {10.1038/nn.4062}, author = {Bittner, Katie C and Grienberger, Christine and Vaidya, Sachin P and Milstein, Aaron D and Macklin, John J and Suh, Junghyup and Tonegawa, Susumu and Magee, Jeffrey C} } @article {47056, title = {Connecting neural codes with behavior in the auditory system of Drosophila.}, journal = {Neuron}, volume = {87}, year = {2015}, month = {2015 Sep 9}, pages = {1332-43}, abstract = {

Brains are optimized for processing ethologically relevant sensory signals. However, few studies have characterized the neural coding mechanisms that underlie the transformation from natural sensory information to behavior. Here, we focus on acoustic communication in Drosophila melanogaster and use computational modeling to link natural courtship song, neuronal codes, and female behavioral responses to song. We show that melanogaster females are sensitive to long timescale song structure (on the order of tens of seconds). From intracellular recordings, we generate models that recapitulate neural responses to acoustic stimuli. We link these neural codes with female behavior by generating model neural responses to natural courtship song. Using a simple decoder, we predict female behavioral responses to the same song stimuli with high accuracy. Our modeling approach reveals how long timescale song features are represented by the Drosophila brain and how neural representations can be decoded to generate behavioral selectivity for acoustic communication signals.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.08.014}, author = {Clemens, Jan and Girardin, Cyrille C and Coen, Philip and Guan, Xiao-Juan and Dickson, Barry J and Murthy, Mala} } @article {46263, title = {Connectome of the fly visual circuitry.}, journal = {Microscopy}, volume = {64}, year = {2015}, month = {2015 Feb}, pages = {37-44}, abstract = {

Recent powerful tools for reconstructing connectomes using electron microscopy (EM) have made outstanding contributions to the field of neuroscience. As a prime example, the detection of visual motion is a classic problem of neural computation, yet our understanding of the exact mechanism has been frustrated by our incomplete knowledge of the relevant neurons and synapses. Recent connectomic studies have successfully identified the concrete neuronal circuit in the fly{\textquoteright}s visual system that computes the motion signals. This identification was greatly aided by the comprehensiveness of the EM reconstruction. Compared with light microscopy, which gives estimated connections from arbor overlap, EM gives unequivocal connections with precise synaptic counts. This paper reviews the recent study of connectomics in a brain of the fruit fly Drosophila and highlights how connectomes can provide a foundation for understanding the mechanism of neuronal functions by identifying the underlying neural circuits.

}, issn = {2050-5701}, doi = {10.1093/jmicro/dfu102}, author = {Takemura, Shin-ya} } @article {45854, title = {A consistent muscle activation strategy underlies crawling and swimming in Caenorhabditis elegans.}, journal = {Journal of the Royal Society Interface}, volume = {12}, year = {2015}, month = {2015 Jan 6}, pages = {20140963}, abstract = {

Although undulatory swimming is observed in many organisms, the neuromuscular basis for undulatory movement patterns is not well understood. To better understand the basis for the generation of these movement patterns, we studied muscle activity in the nematode Caenorhabditis elegans. Caenorhabditis elegans exhibits a range of locomotion patterns: in low viscosity fluids the undulation has a wavelength longer than the body and propagates rapidly, while in high viscosity fluids or on agar media the undulatory waves are shorter and slower. Theoretical treatment of observed behaviour has suggested a large change in force-posture relationships at different viscosities, but analysis of bend propagation suggests that short-range proprioceptive feedback is used to control and generate body bends. How muscles could be activated in a way consistent with both these results is unclear. We therefore combined automated worm tracking with calcium imaging to determine muscle activation strategy in a variety of external substrates. Remarkably, we observed that across locomotion patterns spanning a threefold change in wavelength, peak muscle activation occurs approximately 45{\textdegree} (1/8th of a cycle) ahead of peak midline curvature. Although the location of peak force is predicted to vary widely, the activation pattern is consistent with required force in a model incorporating putative length- and velocity-dependence of muscle strength. Furthermore, a linear combination of local curvature and velocity can match the pattern of activation. This suggests that proprioception can enable the worm to swim effectively while working within the limitations of muscle biomechanics and neural control.

}, issn = {1742-5662}, author = {Butler, Victoria J and Branicky, Robyn and Yemini, Eviatar and Liewald, Jana F and Gottschalk, Alexander and Kerr, Rex A and Chklovskii, Dmitri B and Schafer, William R} } @article {46370, title = {Constraints on the evolution of a doublesex target gene arising from doublesex{\textquoteright}s pleiotropic deployment.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015 Feb 24}, pages = {E852-61}, abstract = {

"Regulatory evolution," that is, changes in a gene{\textquoteright}s expression pattern through changes at its regulatory sequence, rather than changes at the coding sequence of the gene or changes of the upstream transcription factors, has been increasingly recognized as a pervasive evolution mechanism. Many somatic sexually dimorphic features of Drosophila melanogaster are the results of gene expression regulated by the doublesex (dsx) gene, which encodes sex-specific transcription factors (DSX(F) in females and DSX(M) in males). Rapid changes in such sexually dimorphic features are likely a result of changes at the regulatory sequence of the target genes. We focused on the Flavin-containing monooxygenase-2 (Fmo-2) gene, a likely direct dsx target, to elucidate how sexually dimorphic expression and its evolution are brought about. We found that dsx is deployed to regulate the Fmo-2 transcription both in the midgut and in fat body cells of the spermatheca (a female-specific tissue), through a canonical DSX-binding site in the Fmo-2 regulatory sequence. In the melanogaster group, Fmo-2 transcription in the midgut has evolved rapidly, in contrast to the conserved spermathecal transcription. We identified two cis-regulatory modules (CRM-p and CRM-d) that direct sexually monomorphic or dimorphic Fmo-2 transcription, respectively, in the midguts of these species. Changes of Fmo-2 transcription in the midgut from sexually dimorphic to sexually monomorphic in some species are caused by the loss of CRM-d function, but not the loss of the canonical DSX-binding site. Thus, conferring transcriptional regulation on a CRM level allows the regulation to evolve rapidly in one tissue while evading evolutionary constraints posed by other tissues.

}, issn = {1091-6490}, doi = {10.1073/pnas.1501192112}, author = {Luo, Shengzhan D and Baker, Bruce S} } @article {46890, title = {Continuous volumetric imaging via an optical phase-locked ultrasound lens.}, journal = {Nature Methods}, volume = {12}, year = {2015}, month = {2015-Jul 13}, pages = {759-62}, abstract = {

In vivo imaging at high spatiotemporal resolution is key to the understanding of complex biological systems. We integrated an optical phase-locked ultrasound lens into a two-photon fluorescence microscope and achieved microsecond-scale axial scanning, thus enabling volumetric imaging at tens of hertz. We applied this system to multicolor volumetric imaging of processes sensitive to motion artifacts, including calcium dynamics in behaving mouse brain and transient morphology changes and trafficking of immune cells.

}, doi = {10.1038/nmeth.3476}, author = {Kong, Lingjie and Tang, Jianyong and Little, Justin P and Yu, Yang and L{\"a}mmermann, Tim and Lin, Charles P and Germain, Ronald N and Cui, Meng} } @article {47214, title = {Control of sleep by dopaminergic inputs to the Drosophila mushroom body.}, journal = {Frontiers in Neural Circuits}, volume = {9}, year = {2015}, month = {2015 Nov 09}, pages = {73}, abstract = {

The Drosophila mushroom body (MB) is an associative learning network that is important for the control of sleep. We have recently identified particular intrinsic MB Kenyon cell (KC) classes that regulate sleep through synaptic activation of particular MB output neurons (MBONs) whose axons convey sleep control signals out of the MB to downstream target regions. Specifically, we found that sleep-promoting KCs increase sleep by preferentially activating cholinergic sleep-promoting MBONs, while wake-promoting KCs decrease sleep by preferentially activating glutamatergic wake-promoting MBONs. Here we use a combination of genetic and physiological approaches to identify wake-promoting dopaminergic neurons (DANs) that innervate the MB, and show that they activate wake-promoting MBONs. These studies reveal a dopaminergic sleep control mechanism that likely operates by modulation of KC-MBON microcircuits.

}, issn = {1662-5110}, doi = {10.3389/fncir.2015.00073}, author = {Sitaraman, Divya and Aso, Yoshinori and Rubin, Gerald M and Nitabach, Michael N} } @article {47901, title = {Correlated gene expression and target specificity demonstrate excitatory projection neuron diversity.}, journal = {Cerebral Cortex (New York, N.Y. : 1991)}, volume = {25}, year = {2015}, month = {2015 Feb}, pages = {433-49}, abstract = {

The neocortex contains diverse populations of excitatory neurons segregated by layer and further definable by their specific cortical and subcortical projection targets. The current study describes a systematic approach to identify molecular correlates of specific projection neuron classes in mouse primary somatosensory cortex (S1), using a combination of in situ hybridization (ISH) data mining, marker gene colocalization, and combined retrograde labeling with ISH for layer-specific marker genes. First, we identified a large set of genes with specificity for each cortical layer, and that display heterogeneous patterns within those layers. Using these genes as markers, we find extensive evidence for the covariation of gene expression and projection target specificity in layer 2/3, 5, and 6, with individual genes labeling neurons projecting to specific subsets of target structures. The combination of gene expression and target specificity imply a great diversity of projection neuron classes that is similar to or greater than that of GABAergic interneurons. The covariance of these 2 phenotypic modalities suggests that these classes are both discrete and genetically specified.

}, keywords = {Animals, Atlases as Topic, Data Mining, Gene Expression, In Situ Hybridization, Fluorescence, Male, Mice, Mice, Inbred C57BL, Neural Pathways, Neuronal Tract-Tracers, Neurons, Somatosensory Cortex}, issn = {1460-2199}, doi = {10.1093/cercor/bht243}, author = {Sorensen, Staci A and Bernard, Amy and Menon, Vilas and Royall, Joshua J and Glattfelder, Katie J and Desta, Tsega and Hirokawa, Karla and Mortrud, Marty and Miller, Jeremy A and Zeng, Hongkui and Hohmann, John G and Jones, Allan R and Lein, Ed S} } @article {47277, title = {Cortex commands the performance of skilled movement.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Dec 3}, abstract = {

Mammalian cerebral cortex is accepted as being critical for voluntary motor control, but what functions depend on cortex is still unclear. Here we used rapid, reversible optogenetic inhibition to test the role of cortex during a head-fixed task in which mice reach, grab, and eat a food pellet. Sudden cortical inhibition blocked initiation or froze execution of this skilled prehension behavior, but left untrained forelimb movements unaffected. Unexpectedly, kinematically normal prehension occurred immediately after cortical inhibition even during rest periods lacking cue and pellet. This {\textquoteright}rebound{\textquoteright} prehension was only evoked in trained and food-deprived animals, suggesting that a motivation-gated motor engram sufficient to evoke prehension is activated at inhibition{\textquoteright}s end. These results demonstrate the necessity and sufficiency of cortical activity for enacting a learned skill.

}, issn = {2050-084X}, doi = {10.7554/eLife.10774}, author = {Guo, Jian-Zhong and Graves, Austin R and Guo, Wendy W and Zheng, Jihong and Lee, Allen and Rodr{\'\i}guez-Gonz{\'a}lez, Juan and Li, Nuo and Macklin, John J and Phillips, James W and Mensh, Brett D and Branson, Kristin and Hantman, Adam W} } @article {47159, title = {Crowdsourcing the creation of image segmentation algorithms for connectomics.}, journal = {Frontiers in Neuroanatomy}, volume = {9}, year = {2015}, month = {2015 Nov 05}, pages = {142}, abstract = {

To stimulate progress in automating the reconstruction of neural circuits, we organized the first international challenge on 2D segmentation of electron microscopic (EM) images of the brain. Participants submitted boundary maps predicted for a test set of images, and were scored based on their agreement with a consensus of human expert annotations. The winning team had no prior experience with EM images, and employed a convolutional network. This {\textquotedblleft}deep learning{\textquotedblright} approach has since become accepted as a standard for segmentation of EM images. The challenge has continued to accept submissions, and the best so far has resulted from cooperation between two teams. The challenge has probably saturated, as algorithms cannot progress beyond limits set by ambiguities inherent in 2D scoring and the size of the test dataset. Retrospective evaluation of the challenge scoring system reveals that it was not sufficiently robust to variations in the widths of neurite borders. We propose a solution to this problem, which should be useful for a future 3D segmentation challenge.

}, doi = {10.3389/fnana.2015.00142}, author = {Arganda-Carreras, Ignacio and Turaga, Srinivas C and Berger, Daniel R and Ciresan, Dan and Giusti, Alessandro and Gambardella, Luca M and Schmidhuber, Juergen and Laptev, Dmitry and Dwivedi, Sarvesh and Buhmann, Joachim M} } @article {46998, title = {CTFFIND4: Fast and accurate defocus estimation from electron micrographs.}, journal = {Journal of Structural Biology}, volume = {192}, year = {2015}, month = {2015 Aug 13}, pages = {216-21}, abstract = {

CTFFIND is a widely-used program for the estimation of objective lens defocus parameters from transmission electron micrographs. Defocus parameters are estimated by fitting a model of the microscope{\textquoteright}s contrast transfer function (CTF) to an image{\textquoteright}s amplitude spectrum. Here we describe modifications to the algorithm which make it significantly faster and more suitable for use with images collected using modern technologies such as dose fractionation and phase plates. We show that this new version preserves the accuracy of the original algorithm while allowing for higher throughput. We also describe a measure of the quality of the fit as a function of spatial frequency and suggest this can be used to define the highest resolution at which CTF oscillations were successfully modeled.

}, issn = {1095-8657}, doi = {10.1016/j.jsb.2015.08.008}, author = {Rohou, Alexis and Grigorieff, Nikolaus} } @article {46380, title = {Data Exploration Toolkit for serial diffraction experiments.}, journal = {Acta Crystallographica Section D: Biological Crystallography}, volume = {71}, year = {2015}, month = {2015 Feb}, pages = {352-6}, abstract = {

Ultrafast diffraction at X-ray free-electron lasers (XFELs) has the potential to yield new insights into important biological systems that produce radiation-sensitive crystals. An unavoidable feature of the {\textquoteleft}diffraction before destruction{\textquoteright} nature of these experiments is that images are obtained from many distinct crystals and/or different regions of the same crystal. Combined with other sources of XFEL shot-to-shot variation, this introduces significant heterogeneity into the diffraction data, complicating processing and interpretation. To enable researchers to get the most from their collected data, a toolkit is presented that provides insights into the quality of, and the variation present in, serial crystallography data sets. These tools operate on the unmerged, partial intensity integration results from many individual crystals, and can be used on two levels: firstly to guide the experimental strategy during data collection, and secondly to help users make informed choices during data processing.

}, issn = {1399-0047}, doi = {10.1107/S1399004714025875}, author = {Zeldin, Oliver B and Brewster, Aaron S and Hattne, Johan and Uervirojnangkoorn, Monarin and Lyubimov, Artem Y and Zhou, Qiangjun and Zhao, Minglei and Weis, William I and Sauter, Nicholas K and Brunger, Axel T} } @article {47620, title = {Deacetylation of nuclear LC3 drives autophagy initiation under starvation.}, journal = {Molecular cell}, volume = {57}, year = {2015}, month = {2015 Feb 5}, pages = {456-66}, abstract = {

Shuttling of macromolecules between different cellular compartments helps regulate the timing and extent of different cellular activities. Here, we report that LC3, a key initiator of autophagy that cycles between the nucleus and cytoplasm, becomes selectively activated in the nucleus during starvation through deacetylation by the nuclear deacetylase Sirt1. Deacetylation of LC3 at K49 and K51 by Sirt1 allows LC3 to interact with the nuclear protein DOR and return to the cytoplasm with DOR, where it is able to bind Atg7 and other autophagy factors and undergo phosphatidylethanolamine conjugation to preautophagic membranes. The association of deacetylated LC3 with autophagic factors shifts LC3{\textquoteright}s distribution from the nucleus toward the cytoplasm. Thus, an acetylation-deacetylation cycle ensures that LC3 effectively redistributes in an activated form from nucleus to cytoplasm, where it plays a central role in autophagy to enable the cell to cope with the lack of external nutrients.

}, keywords = {Acetylation, Autophagy, Cell Nucleus, Cytoplasm, HEK293 Cells, Hela Cells, Humans, Lysine, Microscopy, Confocal, Microtubule-Associated Proteins, Sirtuin 1, Ubiquitin-Activating Enzymes}, issn = {1097-4164}, doi = {10.1016/j.molcel.2014.12.013}, author = {Huang, Rui and Xu, Yinfeng and Wan, Wei and Shou, Xin and Qian, Jiali and You, Zhiyuan and Liu, Bo and Chang, Chunmei and Zhou, Tianhua and Lippincott-Schwartz, Jennifer and Liu, Wei} } @article {46022, title = {Dendritic function in vivo.}, journal = {Trends in Neuroscience}, volume = {38}, year = {2015}, month = {2015 Jan}, pages = {45-54}, abstract = {

Dendrites are the predominant entry site for excitatory synaptic potentials in most types of central neurons. There is increasing evidence that dendrites are not just passive transmitting devices but play active roles in synaptic integration through linear and non-linear mechanisms. Frequently, excitatory synapses are formed on dendritic spines. In addition to relaying incoming electrical signals, spines can play important roles in modifying these signals through complex biochemical processes and, thereby, determine learning and memory formation. Here, we review recent advances in our understanding of the function of spines and dendrites in central mammalian neurons in vivo by focusing particularly on insights obtained from Ca(2+) imaging studies.

}, issn = {1878-108X}, doi = {10.1016/j.tins.2014.11.002}, author = {Grienberger, Christine and Chen, Xiaowei and Konnerth, Arthur} } @article {47178, title = {Dendritic integration: 60 years of progress.}, journal = {Nature Neuroscience}, volume = {18}, year = {2015}, month = {2015 Dec}, pages = {1713-21}, abstract = {

Understanding how individual neurons integrate the thousands of synaptic inputs they receive is critical to understanding how the brain works. Modeling studies in silico and experimental work in vitro, dating back more than half a century, have revealed that neurons can perform a variety of different passive and active forms of synaptic integration on their inputs. But how are synaptic inputs integrated in the intact brain? With the development of new techniques, this question has recently received substantial attention, with new findings suggesting that many of the forms of synaptic integration observed in vitro also occur in vivo, including in awake animals. Here we review six decades of progress, which collectively highlights the complex ways that single neurons integrate their inputs, emphasizing the critical role of dendrites in information processing in the brain.

}, issn = {1546-1726}, doi = {10.1038/nn.4157}, author = {Stuart, Greg J and Spruston, Nelson} } @article {47201, title = {Dendritic sodium spikes are required for long-term potentiation at distal synapses on hippocampal pyramidal neurons.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Aug 06}, abstract = {

Dendritic integration of synaptic inputs mediates rapid neural computation as well as longer-lasting plasticity. Several channel types can mediate dendritically initiated spikes (dSpikes), which may impact information processing and storage across multiple timescales; however, the roles of different channels in the rapid vs long-term effects of dSpikes are unknown. We show here that dSpikes mediated by Nav channels (blocked by a low concentration of TTX) are required for long-term potentiation (LTP) in the distal apical dendrites of hippocampal pyramidal neurons. Furthermore, imaging, simulations, and buffering experiments all support a model whereby fast Nav channel-mediated dSpikes (Na-dSpikes) contribute to LTP induction by promoting large, transient, localized increases in intracellular calcium concentration near the calcium-conducting pores of NMDAR and L-type Cav channels. Thus, in addition to contributing to rapid neural processing, Na-dSpikes are likely to contribute to memory formation via their role in long-lasting synaptic plasticity.

}, issn = {2050-084X}, doi = {10.7554/eLife.06414}, author = {Kim, Yujin and Hsu, Ching-Lung and Cembrowski, Mark S and Mensh, Brett D and Spruston, Nelson} } @article {46845, title = {Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces.}, journal = {Science}, volume = {348}, year = {2015}, month = {2015 Jun 19}, pages = {1365-8}, abstract = {

We describe a general approach to designing two-dimensional (2D) protein arrays mediated by noncovalent protein-protein interfaces. Protein homo-oligomers are placed into one of the seventeen 2D layer groups, the degrees of freedom of the lattice are sampled to identify configurations with shape-complementary interacting surfaces, and the interaction energy is minimized using sequence design calculations. We used the method to design proteins that self-assemble into layer groups P 3 2 1, P 4 21 2, and P 6. Projection maps of micrometer-scale arrays, assembled both in vitro and in vivo, are consistent with the design models and display the target layer group symmetry. Such programmable 2D protein lattices should enable new approaches to structure determination, sensing, and nanomaterial engineering.

}, doi = {10.1126/science.aaa9897 }, author = {Gonen, Shane and DiMaio, Frank and Gonen, Tamir and Baker, David} } @article {47215, title = {Direct in~vivo manipulation and imaging of calcium transients in neutrophils identify a critical role for leading-edge calcium flux.}, journal = {Cell Reports}, volume = {13}, year = {2015}, month = {2015 Dec 15}, pages = {2107-17}, abstract = {

Calcium signaling has long been associated with key events of immunity, including chemotaxis, phagocytosis, and activation. However, imaging and manipulation of calcium flux in motile immune cells in live animals remain challenging. Using light-sheet microscopy for in\ vivo calcium imaging in zebrafish, we observe characteristic patterns of calcium flux triggered by distinct events, including phagocytosis of pathogenic bacteria and migration of neutrophils toward inflammatory stimuli. In contrast to findings from ex\ vivo studies, we observe enriched calcium influx at the leading edge of migrating neutrophils. To directly manipulate calcium dynamics in\ vivo, we have developed transgenic lines with cell-specific expression of the mammalian TRPV1 channel, enabling ligand-gated, reversible, and spatiotemporal control of calcium influx. We find that controlled calcium influx can function to help define the neutrophil{\textquoteright}s leading edge. Cell-specific TRPV1 expression may have broad utility for precise control of calcium dynamics in other immune cell types and organisms.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2015.11.010}, author = {Beerman, Rebecca W and Matty, Molly A and Au, Gina G and Looger, Loren L and Choudhury, Kingshuk Roy and Keller, Philipp J and Tobin, David M} } @article {46849, title = {Direct wavefront sensing for high-resolution in vivo imaging in scattering tissue.}, journal = {Nature Communications}, volume = {6}, year = {2015}, month = {2015-Jun-15}, pages = {7276}, abstract = {

Adaptive optics by direct imaging of the wavefront distortions of a laser-induced guide star has long been used in astronomy, and more recently in microscopy to compensate for aberrations in transparent specimens. Here we extend this approach to tissues that strongly scatter visible light by exploiting the reduced scattering of near-infrared guide stars. The method enables in vivo two-photon morphological and functional imaging down to 700 μm inside the mouse brain.

}, issn = {2041-1723}, doi = {10.1038/ncomms8276}, author = {Wang, Kai and Sun, Wenzhi and Richie, Christopher T and Harvey, Brandon K and Betzig, Eric and Ji, Na} } @article {45979, title = {Distinct dopamine neurons mediate reward signals for short- and long-term memories.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015 Jan 13}, pages = {578-83}, abstract = {

Drosophila melanogaster can acquire a stable appetitive olfactory memory when the presentation of a sugar reward and an odor are paired. However, the neuronal mechanisms by which a single training induces long-term memory are poorly understood. Here we show that two distinct subsets of dopamine neurons in the fly brain signal reward for short-term (STM) and long-term memories (LTM). One subset induces memory that decays within several hours, whereas the other induces memory that gradually develops after training. They convey reward signals to spatially segregated synaptic domains of the mushroom body (MB), a potential site for convergence. Furthermore, we identified a single type of dopamine neuron that conveys the reward signal to restricted subdomains of the mushroom body lobes and induces long-term memory. Constant appetitive memory retention after a single training session thus comprises two memory components triggered by distinct dopamine neurons.

}, issn = {1091-6490}, doi = {10.1073/pnas.1421930112}, author = {Yamagata, Nobuhiro and Ichinose, Toshiharu and Aso, Yoshinori and Placais, Pierre-Yves and Friedrich, Anja B and Sima, Richard J and Preat, Thomas and Rubin, Gerald M and Tanimoto, Hiromu} } @article {46184, title = {Distribution and function of HCN channels in the apical dendritic tuft of neocortical pyramidal neurons.}, journal = {Journal of Neuroscience}, volume = {35}, year = {2015}, month = {2015 Jan 21}, pages = {1024-37}, abstract = {

The apical tuft is the most remote area of the dendritic tree of neocortical pyramidal neurons. Despite its distal location, the apical dendritic tuft of layer 5 pyramidal neurons receives substantial excitatory synaptic drive and actively processes corticocortical input during behavior. The properties of the voltage-activated ion channels that regulate synaptic integration in tuft dendrites have, however, not been thoroughly investigated. Here, we use electrophysiological and optical approaches to examine the subcellular distribution and function of hyperpolarization-activated cyclic nucleotide-gated nonselective cation (HCN) channels in rat layer 5B pyramidal neurons. Outside-out patch recordings demonstrated that the amplitude and properties of ensemble HCN channel activity were uniform in patches excised from distal apical dendritic trunk and tuft sites. Simultaneous apical dendritic tuft and trunk whole-cell current-clamp recordings revealed that the pharmacological blockade of HCN channels decreased voltage compartmentalization and enhanced the generation and spread of apical dendritic tuft and trunk regenerative activity. Furthermore, multisite two-photon glutamate uncaging demonstrated that HCN channels control the amplitude and duration of synaptically evoked regenerative activity in the distal apical dendritic tuft. In contrast, at proximal apical dendritic trunk and somatic recording sites, the blockade of HCN channels decreased excitability. Dynamic-clamp experiments revealed that these compartment-specific actions of HCN channels were heavily influenced by the local and distributed impact of the high density of HCN channels in the distal apical dendritic arbor. The properties and subcellular distribution pattern of HCN channels are therefore tuned to regulate the interaction between integration compartments in layer 5B pyramidal neurons.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2813-14.2015}, author = {Harnett, Mark T and Magee, Jeffrey C and Williams, Stephen R} } @article {47036, title = {Dopamine is required for the neural representation and control of movement vigor.}, journal = {Cell}, volume = {162}, year = {2015}, month = {2015 Sep 10}, pages = {1418-30}, abstract = {

Progressive depletion of midbrain dopamine neurons (PDD) is associated with deficits in the initiation, speed, and fluidity of voluntary movement. Models of\ basal ganglia function focus on initiation deficits; however, it is unclear how they account for deficits in the speed or amplitude of movement (vigor). Using an effort-based operant conditioning task for head-fixed mice, we discovered distinct functional classes of neurons in the dorsal striatum that represent movement vigor. Mice with PDD exhibited a progressive reduction in vigor, along with a selective impairment of its neural representation in striatum. Restoration of dopaminergic tone with a synthetic precursor ameliorated deficits in movement vigor and its neural representation, while suppression of striatal activity during movement was sufficient to reduce vigor. Thus, dopaminergic input to the dorsal striatum is indispensable for the emergence of striatal activity that mediates adaptive changes in movement vigor. These results suggest refined intervention strategies for Parkinson{\textquoteright}s disease.

}, doi = {10.1016/j.cell.2015.08.014}, author = {Panigrahi, Babita and Martin, Kathleen A and Li, Yi and Graves, Austin R and Vollmer, Alison and Olson, Lars and Mensh, Brett D and Karpova, Alla Y and Dudman, Joshua T} } @article {46773, title = {A dopamine-modulated neural circuit regulating aversive taste memory in Drosophila.}, journal = {Current Biology}, volume = {25}, year = {2015}, month = {2015 May 14}, pages = {1535-41}, abstract = {

Taste memories allow animals to modulate feeding behavior in accordance with past experience and avoid the consumption of potentially harmful food [1]. We have developed a single-fly taste memory assay to functionally interrogate the neural circuitry encoding taste memories [2]. Here, we screen a collection of Split-GAL4 lines that label small populations of neurons associated with the fly memory center-the mushroom bodies (MBs) [3]. Genetic silencing of PPL1 dopamine neurons disrupts conditioned, but not naive, feeding behavior, suggesting these neurons are selectively involved in the conditioned taste response. We identify two PPL1 subpopulations that innervate the MB α lobe and are essential for aversive taste memory. Thermogenetic activation of these dopamine neurons during training induces memory, indicating these neurons are sufficient for the reinforcing properties of bitter tastant to the MBs. Silencing of either the intrinsic MB neurons or the output neurons from the α lobe disrupts taste conditioning. Thermogenetic manipulation of these output neurons alters naive feeding response, suggesting that dopamine neurons modulate the threshold of response to appetitive tastants. Taken together, these findings detail a neural mechanism underlying the formation of taste memory and provide a functional model for dopamine-dependent plasticity in Drosophila.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2015.04.027}, author = {Masek, Pavel and Worden, Kurtresha and Aso, Yoshinori and Rubin, Gerald M and Keene, Alex C} } @article {46975, title = {Drosophila germ granules are structured and contain homotypic mRNA clusters.}, journal = {Nature Communications}, volume = {6}, year = {2015}, month = {2015 Aug 5}, pages = {7962}, abstract = {

Germ granules, specialized ribonucleoprotein particles, are a hallmark of all germ cells. In Drosophila, an estimated 200 mRNAs are enriched in the germ plasm, and some of these have important, often conserved roles in germ cell formation, specification, survival and migration. How mRNAs are spatially distributed within a germ granule and whether their position defines functional properties is unclear. Here we show, using single-molecule FISH and structured illumination microscopy, a super-resolution approach, that mRNAs are spatially organized within the granule whereas core germ plasm proteins are distributed evenly throughout the granule. Multiple copies of single mRNAs organize into {\textquoteright}homotypic clusters{\textquoteright} that occupy defined positions within the center or periphery of the granule. This organization, which is maintained during embryogenesis and independent of the translational or degradation activity of mRNAs, reveals new regulatory mechanisms for germ plasm mRNAs that may be applicable to other mRNA granules.

}, issn = {2041-1723}, doi = {10.1038/ncomms8962}, author = {Trcek, Tatjana and Grosch, Markus and York, Andrew and Shroff, Hari and Lionnet, Timoth{\'e}e and Lehmann, Ruth} } @article {47146, title = {Drosophila Lgr3 couples organ growth with maturation and ensures developmental stability.}, journal = {Current biology : CB}, volume = {25}, year = {2015}, month = {2015 Oct 19}, pages = {2723-9}, abstract = {

Early transplantation and grafting experiments suggest that body organs follow autonomous growth programs [1-3], therefore pointing to a need for coordination mechanisms to produce fit\ individuals with proper proportions. We recently\ identified Drosophila insulin-like peptide 8 (Dilp8) as a relaxin and insulin-like molecule secreted from growing tissues that plays a central role in coordinating growth between organs and coupling organ growth with animal maturation [4, 5]. Deciphering the function of Dilp8 in growth coordination relies on the identification of the receptor and tissues relaying Dilp8 signaling. We show here that the orphan receptor leucine-rich repeat-containing G protein-coupled receptor 3 (Lgr3), a member of the highly conserved family of relaxin family peptide receptors (RXFPs), mediates the checkpoint function of Dilp8 for entry into maturation. We functionally identify two Lgr3-positive neurons in each brain lobe that are required to induce a developmental delay upon overexpression of Dilp8. These neurons are located in the pars intercerebralis, an important neuroendocrine area in the brain, and make physical contacts with the PTTH neurons that ultimately control the\ production and release of the molting steroid ecdysone. Reducing Lgr3 levels in these neurons\ results in adult flies exhibiting increased fluctuating bilateral asymmetry, therefore recapitulating the phenotype of dilp8 mutants. Our work reveals a novel Dilp8/Lgr3 neuronal circuitry involved in a feedback mechanism that ensures coordination between organ growth and developmental transitions and prevents developmental variability.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2015.09.020}, author = {Colombani, Julien and Andersen, Ditte S and Boulan, Laura and Boone, Emilie and Romero, Nuria and Virolle, Virginie and Texada, Michael and L{\'e}opold, Pierre} } @article {46524, title = {Dual-channel circuit mapping reveals sensorimotor convergence in the primary motor cortex.}, journal = {The Journal of Neuroscience}, volume = {35}, year = {2015}, month = {2015 Mar 11}, pages = {4418-26}, abstract = {

Cortical cells integrate synaptic input from multiple sources, but how these different inputs are distributed across individual neurons is largely unknown. Differences in input might account for diverse responses in neighboring neurons during behavior. We present a strategy for comparing the strengths of multiple types of input onto the same neuron. We developed methods for independent dual-channel photostimulation of synaptic inputs using ChR2 together with ReaChR, a red-shifted channelrhodopsin. We used dual-channel photostimulation to probe convergence of sensory information in the mouse primary motor cortex. Input from somatosensory cortex and thalamus converges in individual neurons. Similarly, inputs from distinct somatotopic regions of the somatosensory cortex are integrated at the level of single motor cortex neurons. We next developed a ReaChR transgenic mouse under the control of both Flp- and Cre-recombinases that is an effective tool for circuit mapping. Our approach to dual-channel photostimulation enables quantitative comparison of the strengths of multiple pathways across all length scales of the brain.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3741-14.2015}, author = {Hooks, Bryan M and Lin, John Y and Guo, Caiying and Svoboda, Karel} } @article {46699, title = {Dynamic visualization of transcription and RNA subcellular localization in zebrafish.}, journal = {Development}, volume = {142}, year = {2015}, month = {2015 Apr 1}, pages = {1368-74}, abstract = {

Live imaging of transcription and RNA dynamics has been successful in cultured cells and tissues of vertebrates but is challenging to accomplish in vivo. The zebrafish offers important advantages to study these processes--optical transparency during embryogenesis, genetic tractability and rapid development. Therefore, to study transcription and RNA dynamics in an intact vertebrate organism, we have adapted the MS2 RNA-labeling system to zebrafish. By using this binary system to coexpress a fluorescent MS2 bacteriophage coat protein (MCP) and an RNA of interest tagged with multiple copies of the RNA hairpin MS2-binding site (MBS), live-cell imaging of RNA dynamics at single RNA molecule resolution has been achieved in other organisms. Here, using a Gateway-compatible MS2 labeling system, we generated stable transgenic zebrafish lines expressing MCP, validated the MBS-MCP interaction and applied the system to investigate zygotic genome activation (ZGA) and RNA localization in primordial germ cells (PGCs) in zebrafish. Although cleavage stage cells are initially transcriptionally silent, we detect transcription of MS2-tagged transcripts driven by the βactin promoter at \~{} 3-3.5 h post-fertilization, consistent with the previously reported ZGA. Furthermore, we show that MS2-tagged nanos3 3{\textquoteright}UTR transcripts localize to PGCs, where they are diffusely cytoplasmic and within larger cytoplasmic accumulations reminiscent of those displayed by endogenous nanos3. These tools provide a new avenue for live-cell imaging of RNA molecules in an intact vertebrate. Together with new techniques for targeted genome editing, this system will be a valuable tool to tag and study the dynamics of endogenous RNAs during zebrafish developmental processes.

}, issn = {1477-9129}, doi = {10.1242/dev.118968}, author = {Campbell, Philip D and Chao, Jeffrey A and Singer, Robert H and Marlow, Florence L} } @article {46835, title = {Dynamical feature extraction at the sensory periphery guides chemotaxis.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Jun 16}, abstract = {

Behavioral strategies employed for chemotaxis have been described across phyla, but the sensorimotor basis of this phenomenon has seldom been studied in naturalistic contexts. Here, we examine how signals experienced during free olfactory behaviors are processed by first-order olfactory sensory neurons (OSNs) of the Drosophila larva. We find that OSNs can act as differentiators that transiently normalize stimulus intensity-a property potentially derived from a combination of integral feedback and feed-forward regulation of olfactory transduction. In olfactory virtual reality experiments, we report that high activity levels of the OSN suppress turning, whereas low activity levels facilitate turning. Using a generalized linear model, we explain how peripheral encoding of olfactory stimuli modulates the probability of switching from a run to a turn. Our work clarifies the link between computations carried out at the sensory periphery and action selection underlying navigation in odor gradients.

}, issn = {2050-084X}, doi = {10.7554/eLife.06694}, author = {Schulze, Aljoscha and Gomez-Marin, Alex and Rajendran, Vani G and Lott, Gus and Musy, Marco and Ahammad, Parvez and Deogade, Ajinkya and Sharpe, James and Riedl, Julia and Jarriault, David and Trautman, Eric T and Werner, Christopher and Venkadesan, Madhusudhan and Druckmann, Shaul and Jayaraman, Vivek and Louis, Matthieu} } @article {47160, title = {Dynamics of CRISPR-Cas9 genome interrogation in living cells.}, journal = {Science (New York, N.Y.)}, volume = {350}, year = {2015}, month = {2015 Nov 13}, pages = {823-6}, abstract = {

The RNA-guided CRISPR-associated protein Cas9 is used for genome editing, transcriptional modulation, and live-cell imaging. Cas9-guide RNA complexes recognize and cleave double-stranded DNA sequences on the basis of 20-nucleotide RNA-DNA complementarity, but the mechanism of target searching in mammalian cells is unknown. Here, we use single-particle tracking to visualize diffusion and chromatin binding of Cas9 in living cells. We show that three-dimensional diffusion dominates Cas9 searching in vivo, and off-target binding events are, on average, short-lived (\<1 second). Searching is dependent on the local chromatin environment, with less sampling and slower movement within heterochromatin. These results reveal how the bacterial Cas9 protein interrogates mammalian genomes and navigates eukaryotic chromatin structure.

}, issn = {1095-9203}, doi = {10.1126/science.aac6572}, author = {Knight, Spencer C and Xie, Liangqi and Deng, Wulan and Guglielmi, Benjamin and Witkowsky, Lea B and Bosanac, Lana and Zhang, Elisa T and El Beheiry, Mohamed and Masson, Jean-Baptiste and Dahan, Maxime and Liu, Zhe and Doudna, Jennifer A and Tjian, Robert} } @article {46528, title = {Dynamics of ionic shifts in cortical spreading depression.}, journal = {Cerebral Cortex}, volume = {25}, year = {2015}, month = {2015 Apr 2}, pages = {4469-76}, abstract = {

Cortical spreading depression is a slowly propagating wave of near-complete depolarization of brain cells followed by temporary suppression of neuronal activity. Accumulating evidence indicates that cortical spreading depression underlies the migraine aura and that similar waves promote tissue damage in stroke, trauma, and hemorrhage. Cortical spreading depression is characterized by neuronal swelling, profound elevation of extracellular potassium and glutamate, multiphasic blood flow changes, and drop in tissue oxygen tension. The slow speed of the cortical spreading depression wave implies that it is mediated by diffusion of a chemical substance, yet the identity of this substance and the pathway it follows are unknown. Intercellular spread between gap junction-coupled neurons or glial cells and interstitial diffusion of K(+) or glutamate have been proposed. Here we use extracellular direct current potential recordings, K(+)-sensitive microelectrodes, and 2-photon imaging with ultrasensitive Ca(2+) and glutamate fluorescent probes to elucidate the spatiotemporal dynamics of ionic shifts associated with the propagation of cortical spreading depression in the visual cortex of adult living mice. Our data argue against intercellular spread of Ca(2+) carrying the cortical spreading depression wavefront and are in favor of interstitial K(+) diffusion, rather than glutamate diffusion, as the leading event in cortical spreading depression.

}, issn = {1460-2199}, doi = {10.1093/cercor/bhv054}, author = {Enger, Rune and Tang, Wannan and Vindedal, Gry Fluge and Jensen, Vidar and Johannes Helm, P and Sprengel, Rolf and Looger, Loren L and Nagelhus, Erlend A} } @article {47618, title = {Dynamin regulates metaphase furrow formation and plasma membrane compartmentalization in the syncytial Drosophila embryo.}, journal = {Biology open}, volume = {4}, year = {2015}, month = {2015}, pages = {301-11}, abstract = {

The successive nuclear division cycles in the syncytial Drosophila embryo are accompanied by ingression and regression of plasma membrane furrows, which surround individual nuclei at the embryo periphery, playing a central role in embryo compartmentalization prior to cellularization. Here, we demonstrate that cell cycle changes in dynamin localization and activity at the plasma membrane (PM) regulate metaphase furrow formation and PM organization in the syncytial embryo. Dynamin was localized on short PM furrows during interphase, mediating endocytosis of PM components. Dynamin redistributed off ingressed PM furrows in metaphase, correlating with stabilized PM components and the associated actin regulatory machinery on long furrows. Acute inhibition of dynamin in the temperature sensitive shibire mutant embryo resulted in morphogenetic consequences in the syncytial division cycle. These included inhibition of metaphase furrow ingression, randomization of proteins normally polarized to intercap PM and disruption of the diffusion barrier separating PM domains above nuclei. Based on these findings, we propose that cell cycle changes in dynamin orchestrate recruitment of actin regulatory machinery for PM furrow dynamics during the early mitotic cycles in the Drosophila embryo.

}, issn = {2046-6390}, doi = {10.1242/bio.20149936}, author = {Rikhy, Richa and Mavrakis, Manos and Lippincott-Schwartz, Jennifer} } @article {47467, title = {Early steps in primary cilium assembly require EHD1/EHD3-dependent ciliary vesicle formation.}, journal = {Nature Cell Biology}, volume = {17}, year = {2015}, month = {2015 Feb 16}, pages = {228-40}, abstract = {

Membrane association with mother centriole (M-centriole) distal appendages is critical for ciliogenesis initiation. How the Rab GTPase Rab11{\textendash}​Rab8\ cascade functions in early ciliary membrane assembly is unknown. Here, we show that the membrane shaping proteins ​EHD1\ and ​EHD3, in association with the Rab11{\textendash}​Rab8\ cascade, function in early ciliogenesis. ​EHD1\ and ​EHD3\ localize to preciliary membranes and the ciliary pocket. EHD-dependent membrane tubulation is essential for ciliary vesicle formation from smaller distal appendage vesicles (DAVs). Importantly, this step functions in M-centriole to basal body transformation and recruitment of transition zone proteins and ​IFT20. ​SNAP29, a SNARE membrane fusion regulator and ​EHD1-binding protein, is also required for DAV-mediated ciliary vesicle assembly. Interestingly, only after ciliary vesicle assembly is ​Rab8\ activated for ciliary growth. Our studies uncover molecular mechanisms informing a previously uncharacterized ciliogenesis step, whereby ​EHD1\ and ​EHD3\ reorganize the M-centriole and associated DAVs before coordinated ciliary membrane and axoneme growth.

}, issn = {1476-4679}, doi = {10.1038/ncb3109}, author = {Lu, Quanlong and Insinna, Christine and Ott, Carolyn and Stauffer, Jimmy and Pintado, Petra A and Rahajeng, Juliati and Baxa, Ulrich and Walia, Vijay and Cuenca, Adrian and Hwang, Yoo-Seok and Daar, Ira O and Lopes, Susana and Lippincott-Schwartz, Jennifer and Jackson, Peter K and Caplan, Steve and Westlake, Christopher J} } @article {46283, title = {Effects of long-term representations on free recall of unrelated words.}, journal = {Learning \& Memory}, volume = {22}, year = {2015}, month = {2015 Jan 15}, pages = {101-8}, abstract = {

Human memory stores vast amounts of information. Yet recalling this information is often challenging when specific cues are lacking. Here we consider an associative model of retrieval where each recalled item triggers the recall of the next item based on the similarity between their long-term neuronal representations. The model predicts that different items stored in memory have different probability to be recalled depending on the size of their representation. Moreover, items with high recall probability tend to be recalled earlier and suppress other items. We performed an analysis of a large data set on free recall and found a highly specific pattern of statistical dependencies predicted by the model, in particular negative correlations between the number of words recalled and their average recall probability. Taken together, experimental and modeling results presented here reveal complex interactions between memory items during recall that severely constrain recall capacity.

}, issn = {1549-5485}, doi = {10.1101/lm.035238.114}, author = {Katkov, Mikhail and Romani, Sandro and Tsodyks, Misha} } @proceedings {47837, title = {Efficient classifier training to minimize false merges in electron microscopy segmentation.}, year = {2015}, month = {2015}, pages = {657-65}, author = {Parag, Toufiq and Ciresan, Dan and Giusti, Alessandro} } @article {47082, title = {Efficient processing and analysis of large-scale light-sheet microscopy data.}, journal = {Nature Protocols}, volume = {10}, year = {2015}, month = {2015 Oct 2}, pages = {1679-96}, abstract = {

Light-sheet microscopy is a powerful method for imaging the development and function of complex biological systems at high spatiotemporal resolution and over long time scales. Such experiments typically generate terabytes of multidimensional image data, and thus they demand efficient computational solutions for data management, processing and analysis. We present protocols and software to tackle these steps, focusing on the imaging-based study of animal development. Our protocols facilitate (i) high-speed lossless data compression and content-based multiview image fusion optimized for multicore CPU architectures, reducing image data size 30{\textendash}500-fold; (ii) automated large-scale cell tracking and segmentation; and (iii) visualization, editing and annotation of multiterabyte image data and cell-lineage reconstructions with tens of millions of data points. These software modules are open source. They provide high data throughput using a single computer workstation and are readily applicable to a wide spectrum of biological model systems.

}, doi = {10.1038/nprot.2015.111}, author = {Amat, Fernando and H{\"o}ckendorf, Burkhard and Wan, Yinan and Lemon, William C and McDole, Katie and Keller, Philipp J} } @article {47263, title = {An emerging technology framework for the neurobiology of appetite.}, journal = {Cell Metabolism}, volume = {23}, year = {2015}, month = {2015 Dec 24}, pages = {234-53}, abstract = {

Advances in neuro-technology for mapping, manipulating, and monitoring molecularly defined cell types are rapidly advancing insight into neural circuits that regulate appetite. Here, we review these important tools and their applications in circuits that control food seeking and consumption. Technical capabilities provided by these tools establish a rigorous experimental framework for research into the neurobiology of hunger.

}, doi = {10.1016/j.cmet.2015.12.002}, author = {Sternson, Scott M and Atasoy, Deniz and Betley, J Nicholas and Henry, Fredrick E and Xu, Sheng-jin} } @article {47302, title = {Emotor control: computations underlying bodily resource allocation, emotions, and confidence.}, journal = {Dialogues in Clinical Neuroscience}, volume = {17}, year = {2015}, month = {2015 Dec}, pages = {391-401}, abstract = {

Emotional processes are central to behavior, yet their deeply subjective nature has been a challenge for neuroscientific study as well as for psychiatric diagnosis. Here we explore the relationships between subjective feelings and their underlying brain circuits from a computational perspective. We apply recent insights from systems neuroscience-approaching subjective behavior as the result of mental computations instantiated in the brain-to the study of emotions. We develop the hypothesis that emotions are the product of neural computations whose motor role is to reallocate bodily resources mostly gated by smooth muscles. This "emotor" control system is analagous to the more familiar motor control computations that coordinate skeletal muscle movements. To illustrate this framework, we review recent research on "confidence." Although familiar as a feeling, confidence is also an objective statistical quantity: an estimate of the probability that a hypothesis is correct. This model-based approach helped reveal the neural basis of decision confidence in mammals and provides a bridge to the subjective feeling of confidence in humans. These results have important implications for psychiatry, since disorders of confidence computations appear to contribute to a number of psychopathologies. More broadly, this computational approach to emotions resonates with the emerging view that psychiatric nosology may be best parameterized in terms of disorders of the cognitive computations underlying complex behavior.

}, issn = {1958-5969}, author = {Kepecs, Adam and Mensh, Brett D} } @article {46526, title = {Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Mar 17}, abstract = {

There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as the resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.

}, issn = {2050-084X}, doi = {10.7554/eLife.05421}, author = {Uervirojnangkoorn, Monarin and Zeldin, Oliver B and Lyubimov, Artem Y and Hattne, Johan and Brewster, Aaron S and Sauter, Nicholas K and Brunger, Axel T and Weis, William I} } @article {46471, title = {An enhanced gene targeting toolkit for Drosophila: golic+.}, journal = {Genetics}, volume = {199}, year = {2015}, month = {2015 Mar}, pages = {683-94}, abstract = {

Ends-out gene targeting allows seamless replacement of endogenous genes with engineered DNA fragments by homologous recombination, thus creating designer "genes" in the endogenous locus. Conventional gene targeting in Drosophila involves targeting with the preintegrated donor DNA in the larval primordial germ cells. Here we report G: ene targeting during O: ogenesis with L: ethality I: nhibitor and C: RISPR/Cas (Golic+), which improves on all major steps in such transgene-based gene targeting systems. First, donor DNA is integrated into precharacterized attP sites for efficient flip-out. Second, FLP, I-SceI, and Cas9 are specifically expressed in cystoblasts, which arise continuously from female germline stem cells, thereby providing a continual source of independent targeting events in each offspring. Third, a repressor-based lethality selection is implemented to facilitate screening for correct targeting events. Altogether, Golic+ realizes high-efficiency ends-out gene targeting in ovarian cystoblasts, which can be readily scaled up to achieve high-throughput genome editing.

}, issn = {1943-2631}, doi = {10.1534/genetics.114.173716}, author = {Chen, Hui-Min and Huang, Yaling and Pfeiffer, Barret D and Yao, Xiaohao and Lee, Tzumin} } @article {46852, title = {Epigenomic signatures of neuronal diversity in the mammalian brain.}, journal = {Neuron}, volume = {86}, year = {2015}, month = {2015 Jun 17}, pages = {1369-1384}, abstract = {

Neuronal diversity is essential for mammalian brain function but poses a challenge to molecular profiling. To address the need for tools that facilitate cell-type-specific epigenomic studies, we developed the first\ affinity purification approach to isolate nuclei from genetically defined cell types in a mammal. We\ combine this technique with next-generation sequencing to show that three subtypes of neocortical neurons have highly distinctive epigenomic landscapes. Over 200,000 regions differ in chromatin accessibility and DNA methylation signatures characteristic of gene regulatory regions. By footprinting and motif analyses, these regions are predicted to bind distinct cohorts of neuron subtype-specific transcription factors. Neuronal epigenomes reflect both past and present gene expression, with DNA hyper-methylation at developmentally critical genes appearing as a novel epigenomic signature in mature neurons. Taken together, our findings link the functional and transcriptional complexity of neurons to their underlying epigenomic diversity.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.05.018}, author = {Mo, Alisa and Mukamel, Eran A and Davis, Fred P and Luo, Chongyuan and Henry, Gilbert L and Picard, Serge and Urich, Mark A and Nery, Joseph R and Sejnowski, Terrence J and Lister, Ryan and Eddy, Sean R and Ecker, Joseph R and Nathans, Jeremy} } @article {47083, title = {Evaluation of super-resolution performance of the K2 electron-counting camera using 2D crystals of aquaporin-0.}, journal = {Journal of Structural Biology}, year = {2015}, month = {2015 Aug 28}, abstract = {

The K2 Summit camera was initially the only commercially available direct electron detection camera that was optimized for high-speed counting of primary electrons and was also the only one that implemented centroiding so that the resolution of the camera can be extended beyond the Nyquist limit set by the physical pixel size. In this study, we used well-characterized two-dimensional crystals of the membrane protein aquaporin-0 to characterize the performance of the camera below and beyond the physical Nyquist limit and to measure the influence of electron dose rate on image amplitudes and phases.

}, issn = {1095-8657}, doi = {10.1016/j.jsb.2015.08.015}, author = {Chiu, Po-Lin and Li, Xueming and Li, Zongli and Beckett, Brian and Brilot, Axel F and Grigorieff, Nikolaus and Agard, David A and Cheng, Yifan and Walz, Thomas} } @article {47135, title = {Even-Skipped(+) interneurons are core components of a sensorimotor circuit that maintains left-right symmetric muscle contraction amplitude.}, journal = {Neuron}, volume = {88}, year = {2015}, month = {2015 Oct 21}, pages = {314-29}, abstract = {

Bilaterally symmetric motor patterns-those in which left-right pairs of muscles contract synchronously and with equal amplitude (such as breathing, smiling,\ whisking, and locomotion)-are widespread throughout the animal kingdom. Yet, surprisingly little is known about the underlying neural circuits. We performed a thermogenetic screen to identify neurons required for bilaterally symmetric locomotion in Drosophila larvae and identified the evolutionarily conserved Even-skipped(+) interneurons (Eve/Evx). Activation or ablation of Eve(+) interneurons disrupted bilaterally symmetric muscle contraction amplitude, without affecting the timing of motor output. Eve(+) interneurons are not rhythmically active and thus function independently of the locomotor CPG. GCaMP6 calcium imaging of Eve(+) interneurons in freely moving larvae showed left-right asymmetric activation that correlated with larval behavior. TEM reconstruction of Eve(+) interneuron inputs and outputs showed that the Eve(+) interneurons are at the core of a sensorimotor circuit capable of detecting and modifying body wall muscle contraction.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.09.009}, author = {Heckscher, Ellie S and Zarin, Aref Arzan and Faumont, Serge and Clark, Matthew Q and Manning, Laurina and Fushiki, Akira and Schneider-Mizell, Casey M and Fetter, Richard D and Truman, James W and Zwart, Maarten F and Landgraf, Matthias and Cardona, Albert and Lockery, Shawn R and Doe, Chris Q} } @article {47055, title = {Evolving genital structures: A deep look at network co-option.}, journal = {Developmental Cell}, volume = {34}, year = {2015}, month = {2015 Sep 14}, pages = {485-6}, abstract = {

Novel body structures are often generated by the redeployment of ancestral components of the genome. In this issue of Developmental Cell, Glassford et\ al. (2015) present a thorough analysis of the co-option of a gene regulatory network in the origin of an evolutionary novelty.

}, issn = {1878-1551}, doi = {10.1016/j.devcel.2015.08.022}, author = {Preger-Ben Noon, Ella and Frankel, Nicol{\'a}s} } @article {47216, title = {Exocyst-dependent membrane addition is required for anaphase cell elongation and cytokinesis in Drosophila.}, journal = {PLoS Genetics}, volume = {11}, year = {2015}, month = {2015 Nov 03}, pages = {e1005632}, abstract = {

Mitotic and cytokinetic processes harness cell machinery to drive chromosomal segregation and the physical separation of dividing cells. Here, we investigate the functional requirements for exocyst complex function during cell division in vivo, and demonstrate a common mechanism that directs anaphase cell elongation and cleavage furrow progression during cell division. We show that onion rings (onr) and funnel cakes (fun) encode the Drosophila homologs of the Exo84 and Sec8 exocyst subunits, respectively. In onr and fun mutant cells, contractile ring proteins are recruited to the equatorial region of dividing spermatocytes. However, cytokinesis is disrupted early in furrow ingression, leading to cytokinesis failure. We use high temporal and spatial resolution confocal imaging with automated computational analysis to quantitatively compare wild-type versus onr and fun mutant cells. These results demonstrate that anaphase cell elongation is grossly disrupted in cells that are compromised in exocyst complex function. Additionally, we observe that the increase in cell surface area in wild type peaks a few minutes into cytokinesis, and that onr and fun mutant cells have a greatly reduced rate of surface area growth specifically during cell division. Analysis by transmission electron microscopy reveals a massive build-up of cytoplasmic astral membrane and loss of normal Golgi architecture in onr and fun spermatocytes, suggesting that exocyst complex is required for proper vesicular trafficking through these compartments. Moreover, recruitment of the small GTPase Rab11 and the PITP Giotto to the cleavage site depends on wild-type function of the exocyst subunits Exo84 and Sec8. Finally, we show that the exocyst subunit Sec5 coimmunoprecipitates with Rab11. Our results are consistent with the exocyst complex mediating an essential, coordinated increase in cell surface area that potentiates anaphase cell elongation and cleavage furrow ingression.

}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1005632}, author = {Giansanti, Maria Grazia and Vanderleest, Timothy E and Jewett, Cayla E and Sechi, Stefano and Frappaolo, Anna and Fabian, Lacramioara and Robinett, Carmen C and Brill, Julie A and Loerke, Dinah and Fuller, Margaret T and Blankenship, J Todd} } @article {48036, title = {Expansion microscopy.}, year = {2015}, abstract = {

In optical microscopy, fine structural details are resolved by using refraction to magnify images of a specimen. We discovered that by synthesizing a swellable polymer network within a specimen, it can be physically expanded, resulting in physical magnification. By covalently anchoring specific labels located within the specimen directly to the polymer network, labels spaced closer than the optical diffraction limit can be isotropically separated and optically resolved, a process we call expansion microscopy (ExM). Thus, this process can be used to perform scalable superresolution microscopy with diffraction-limited microscopes. We demonstrate ExM with apparent ~70-nanometer lateral resolution in both cultured cells and brain tissue, performing three-color superresolution imaging of ~107 cubic micrometers of the mouse hippocampus with a conventional confocal microscope.

}, author = {Fei Chen and Paul Tillberg and Edward Boyden} } @article {47020, title = {Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics.}, journal = {Science (New York, N.Y.)}, volume = {349}, year = {2015}, month = {2015 Aug 28}, abstract = {

Super-resolution fluorescence microscopy is distinct among nanoscale imaging tools in its ability to image protein dynamics in living cells. Structured illumination microscopy (SIM) stands out in this regard because of its high speed and low illumination intensities, but typically offers only a twofold resolution gain. We extended the resolution of live-cell SIM through two approaches: ultrahigh numerical aperture SIM at 84-nanometer lateral resolution for more than 100 multicolor frames, and nonlinear SIM with patterned activation at 45- to 62-nanometer resolution for approximately 20 to 40 frames. We applied these approaches to image dynamics near the plasma membrane of spatially resolved assemblies of clathrin and caveolin, Rab5a in early endosomes, and α-actinin, often in relationship to cortical actin. In addition, we examined mitochondria, actin, and the Golgi apparatus dynamics in three dimensions.

}, issn = {1095-9203}, doi = {10.1126/science.aab3500}, author = {Li, Dong and Shao, Lin and Chen, Bi-Chang and Zhang, Xi and Zhang, Mingshu and Moses, Brian and Milkie, Daniel E and Beach, Jordan R and Hammer, John A and Pasham, Mithun and Kirchhausen, Tomas and Baird, Michelle A and Davidson, Michael W and Xu, Pingyong and Betzig, Eric} } @article {47466, title = {Fatty acid trafficking in starved cells: regulation by lipid droplet lipolysis, autophagy, and mitochondrial fusion dynamics.}, journal = {Developmental Cell}, volume = {32}, year = {2015}, month = {2015 Mar 23}, pages = {678-92}, abstract = {

Fatty acids (FAs) provide cellular energy under starvation, yet how they mobilize and move into mitochondria in starved cells, driving oxidative respiration, is unclear. Here, we clarify this process by visualizing FA trafficking with a fluorescent FA probe. The labeled FA accumulated in lipid droplets (LDs) in well-fed cells but moved from LDs into mitochondria when cells were starved. Autophagy in starved cells replenished LDs with FAs, increasing LD number over time. Cytoplasmic lipases removed FAs from LDs, enabling their transfer into mitochondria. This required mitochondria to be highly fused and localized near LDs. When mitochondrial fusion was prevented in starved cells, FAs neither homogeneously distributed within mitochondria nor became efficiently metabolized. Instead, FAs reassociated with LDs and fluxed into neighboring cells. Thus, FAs engage in complex trafficking itineraries regulated by cytoplasmic lipases, autophagy, and mitochondrial fusion dynamics, ensuring maximum oxidative metabolism and avoidance of FA toxicity in starved cells.

}, keywords = {Animals, Autophagy, Biological Transport, Cell Line, Fatty Acids, Fibroblasts, Fluorescent Dyes, Lipase, Lipid Droplets, Lipid Metabolism, Lipolysis, Mice, Mitochondria, Mitochondrial Dynamics, Oxidation-Reduction, Respiration, Starvation}, issn = {1878-1551}, doi = {10.1016/j.devcel.2015.01.029}, author = {Rambold, Angelika S and Cohen, Sarah and Lippincott-Schwartz, Jennifer} } @article {46818, title = {Female mice ultrasonically interact with males during courtship displays.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 May 28}, pages = {e06203}, abstract = {

During courtship males attract females with elaborate behaviors. In mice, these displays include ultrasonic vocalizations. Ultrasonic courtship vocalizations were previously attributed to the courting male, despite evidence that both sexes produce virtually indistinguishable vocalizations. Because of this similarity, and the difficulty of assigning vocalizations to individuals, the vocal contribution of each individual during courtship is unknown. To address this question, we developed a microphone array system to localize vocalizations from socially interacting, individual adult mice. With this system, we show that female mice vocally interact with males during courtship. Males and females jointly increased their vocalization rates during chases. Furthermore, a female{\textquoteright}s participation in these vocal interactions may function as a signal that indicates a state of increased receptivity. Our results reveal a novel form of vocal communication during mouse courtship, and lay the groundwork for a mechanistic dissection of communication during social behavior.

}, issn = {2050-084X}, doi = {10.7554/eLife.06203}, author = {Neunuebel, Joshua P and Taylor, Adam L and Arthur, Ben J and Egnor, Se Roian} } @article {68482, title = {Fitness tradeoffs between spores and nonaggregating cells can explain the coexistence of diverse genotypes in cellular slime molds.}, journal = {Proc Natl Acad Sci U S A}, volume = {112}, year = {2015}, month = {03/2015}, pages = {2776-81}, abstract = {

Cellular slime molds, including the well-studied Dictyostelium discoideum, are amoebae whose life cycle includes both a single-cellular and a multicellular stage. To achieve the multicellular stage, individual amoebae aggregate upon starvation to form a fruiting body made of dead stalk cells and reproductive spores, a process that has been described in terms of cooperation and altruism. When amoebae aggregate they do not perfectly discriminate against nonkin, leading to chimeric fruiting bodies. Within chimeras, complex interactions among genotypes have been documented, which should theoretically reduce genetic diversity. This is however inconsistent with the great diversity of genotypes found in nature. Recent work has shown that a little-studied component of D. discoideum fitness--the loner cells that do not participate in the aggregation--can be selected for depending on environmental conditions and that, together with the spores, they could represent a bet-hedging strategy. We suggest that in all cellular slime molds the existence of loners could resolve the apparent diversity paradox in two ways. First, if loners are accounted for, then apparent genotypic skew in the spores of chimeras could simply be the result of different investments into spores versus loners. Second, in an ecosystem with multiple local environments differing in their food recovery characteristics and connected globally via weak-to-moderate dispersal, coexistence of multiple genotypes can occur. Finally, we argue that the loners make it impossible to define altruistic behavior, winners or losers, without a clear description of the ecology.

}, keywords = {Dictyostelium, Ecosystem, Life Cycle Stages, Spores, Protozoan}, issn = {1091-6490}, doi = {10.1073/pnas.1424242112}, author = {Tarnita, Corina E and Washburne, Alex and Martinez-Garcia, Ricardo and Sgro, Allyson E and Levin, Simon A} } @article {45844, title = {Fixation-resistant photoactivatable fluorescent proteins for CLEM.}, journal = {Nature Methods}, volume = {12}, year = {2015}, month = {2015 Mar}, pages = {215-8}, abstract = {

Fluorescent proteins facilitate a variety of imaging paradigms in live and fixed samples. However, they lose their fluorescence after heavy fixation, hindering applications such as correlative light and electron microscopy (CLEM). Here we report engineered variants of the photoconvertible Eos fluorescent protein that fluoresce and photoconvert normally in heavily fixed (0.5-1\% OsO4), plastic resin-embedded samples, enabling correlative super-resolution fluorescence imaging and high-quality electron microscopy.

}, issn = {1548-7105}, doi = {10.1038/nmeth.3225}, author = {Paez-Segala, Maria G and Sun, Mei G and Shtengel, Gleb and Viswanathan, Sarada and Baird, Michelle A and Macklin, John J and Patel, Ronak and Allen, John R and Howe, Elizabeth S and Piszczek, Grzegorz and Hess, Harald F and Davidson, Michael W and Wang, Yalin and Looger, Loren L} } @article {47179, title = {Free RNA polymerase in Escherichia coli.}, journal = {Biochimie}, volume = {119}, year = {2015}, month = {2015 Oct 19}, pages = {80-91}, abstract = {

The frequencies of transcription initiation of regulated and constitutive genes depend on the concentration of free RNA polymerase holoenzyme [Rf] near their promoters. Although RNA polymerase is largely confined to the nucleoid, it is difficult to determine absolute concentrations of [Rf] at particular locations within the nucleoid structure. However, relative concentrations of free RNA polymerase at different growth rates, [Rf]rel, can be estimated from the activities of constitutive promoters. Previous studies indicated that the rrnB P2 promoter is constitutive and that [Rf]rel in the vicinity of rrnB P2 increases with increasing growth rate. Recently it has become possible to directly visualize Rf in growing Escherichia coli cells. Here we examine some of the important issues relating to gene expression based on these new observations. We conclude that: (i) At a growth rate of 2 doublings/h, there are about 1000 free and 2350 non-specifically DNA-bound RNA polymerase molecules per average cell (12 and 28\%, respectively, of 8400 total) which are in rapid equilibrium. (ii) The reversibility of the non-specific binding generates more than 1000 free RNA polymerase molecules every second in the immediate vicinity of the DNA. Of these, most rebind non-specifically to the DNA within a few ms; the frequency of non-specific binding is at least two orders of magnitude greater than specific binding and transcript initiation. (iii) At a given amount of RNA polymerase per cell, [Rf] and the density of non-specifically DNA-bound RNA polymerase molecules along the DNA both vary reciprocally with the amount of DNA in the cell. (iv) At 2 doublings/h an E.\ coli cell contains, on the average, about 1 non-specifically bound RNA polymerase per 9\ kbp of DNA and 1 free RNA polymerase per 20\ kbp of DNA. However some DNA regions (i.e. near active rRNA operons) may have significantly higher than average [Rf].

}, issn = {1638-6183}, doi = {10.1016/j.biochi.2015.10.015}, author = {Patrick, Michael and Dennis, Patrick P and Ehrenberg, Mans and Bremer, Hans} } @article {46862, title = {From a meso- to micro-scale connectome: array tomography and mGRASP.}, journal = {Frontiers in Neuroanatomy}, volume = {9}, year = {2015}, month = {2015 Jun 04}, pages = {78}, abstract = {

Mapping mammalian synaptic connectivity has long been an important goal of neuroscience because knowing how neurons and brain areas are connected underpins an understanding of brain function. Meeting this goal requires advanced techniques with single synapse resolution and large-scale capacity, especially at multiple scales tethering the meso- and micro-scale connectome. Among several advanced LM-based connectome technologies, Array Tomography (AT) and mammalian GFP-Reconstitution Across Synaptic Partners (mGRASP) can provide relatively high-throughput mapping synaptic connectivity at multiple scales. AT- and mGRASP-assisted circuit mapping (ATing and mGRASPing), combined with techniques such as retrograde virus, brain clearing techniques, and activity indicators will help unlock the secrets of complex neural circuits. Here, we discuss these useful new tools to enable mapping of brain circuits at multiple scales, some functional implications of spatial synaptic distribution, and future challenges and directions of these endeavors.

}, issn = {1662-5129}, doi = {10.3389/fnana.2015.00078}, author = {Rah, Jong-Cheol and Feng, Linqing and Druckmann, Shaul and Lee, Hojin and Kim, Jinhyun} } @article {68481, title = {From intracellular signaling to population oscillations: bridging size- and time-scales in collective behavior.}, journal = {Mol Syst Biol}, volume = {11}, year = {2015}, month = {01/2015}, pages = {779}, abstract = {

Collective behavior in cellular populations is coordinated by biochemical signaling networks within individual cells. Connecting the dynamics of these intracellular networks to the population phenomena they control poses a considerable challenge because of network complexity and our limited knowledge of kinetic parameters. However, from physical systems, we know that behavioral changes in the individual constituents of a collectively behaving system occur in a limited number of well-defined classes, and these can be described using simple models. Here, we apply such an approach to the emergence of collective oscillations in cellular populations of the social amoeba Dictyostelium discoideum. Through direct tests of our model with quantitative in vivo measurements of single-cell and population signaling dynamics, we show how a simple model can effectively describe a complex molecular signaling network at multiple size and temporal scales. The model predicts novel noise-driven single-cell and population-level signaling phenomena that we then experimentally observe. Our results suggest that like physical systems, collective behavior in biology may be universal and described using simple mathematical models.

}, keywords = {Dictyostelium, Gene Expression Regulation, Image Processing, Computer-Assisted, Microfluidic Analytical Techniques, Molecular Dynamics Simulation, Signal Transduction}, issn = {1744-4292}, doi = {10.15252/msb.20145352}, author = {Sgro, Allyson E and Schwab, David J and Noorbakhsh, Javad and Mestler, Troy and Mehta, Pankaj and Gregor, Thomas} } @article {46267, title = {A general method to improve fluorophores for live-cell and single-molecule microscopy.}, journal = {Nature Methods}, volume = {12}, year = {2015}, month = {2015 Jan 19}, pages = {244-50}, abstract = {

Specific labeling of biomolecules with bright fluorophores is the keystone of fluorescence microscopy. Genetically encoded self-labeling tag proteins can be coupled to synthetic dyes inside living cells, resulting in brighter reporters than fluorescent proteins. Intracellular labeling using these techniques requires cell-permeable fluorescent ligands, however, limiting utility to a small number of classic fluorophores. Here we describe a simple structural modification that improves the brightness and photostability of dyes while preserving spectral properties and cell permeability. Inspired by molecular modeling, we replaced the N,N-dimethylamino substituents in tetramethylrhodamine with four-membered azetidine rings. This addition of two carbon atoms doubles the quantum efficiency and improves the photon yield of the dye in applications ranging from in vitro single-molecule measurements to super-resolution imaging. The novel substitution is generalizable, yielding a palette of chemical dyes with improved quantum efficiencies that spans the UV and visible range.

}, issn = {1548-7105}, doi = {10.1038/nmeth.3256}, author = {Grimm, Jonathan B and English, Brian P and Chen, Jiji and Slaughter, Joel P and Zhang, Zhengjian and Revyakin, Andrey and Patel, Ronak and Macklin, John J and Normanno, Davide and Singer, Robert H and Lionnet, Timoth{\'e}e and Lavis, Luke D} } @article {46549, title = {Generating customized transgene landing sites and multi-transgene arrays in Drosophila using phiC31 integrase.}, journal = {Genetics}, volume = {199}, year = {2015}, month = {2015 Apr}, pages = {919-34}, abstract = {

Transgenesis in numerous eukaryotes has been facilitated by the use of site-specific integrases to stably insert transgenes at predefined genomic positions (landing sites). However, the utility of integrase-mediated transgenesis in any system is constrained by the limited number and variable expression properties of available landing sites. By exploiting the nonstandard recombination activity exhibited by a phiC31 integrase mutant, we developed a rapid and inexpensive method for isolating landing sites that exhibit desired expression properties. Additionally, we devised a simple technique for constructing arrays of transgenes at a single landing site, thereby extending the utility of previously characterized landing sites. Using the fruit fly Drosophila melanogaster, we demonstrate the feasibility of these approaches by isolating new landing sites optimized to express transgenes in the nervous system and by building fluorescent reporter arrays at several landing sites. Because these strategies require the activity of only a single exogenous protein, we anticipate that they will be portable to species such as nonmodel organisms, in which genetic manipulation is more challenging, expediting the development of genetic resources in these systems.

}, issn = {1943-2631}, doi = {10.1534/genetics.114.173187}, author = {Knapp, Jon-Michael and Chung, Phuong and Simpson, Julie H} } @article {46535, title = {Genetic architecture and functional characterization of genes underlying the rapid diversification of male external genitalia between Drosophila simulans and Drosophila mauritiana.}, journal = {Genetics}, year = {2015}, month = {2015 Mar 16}, abstract = {

Male sexual characters are often among the first traits to diverge between closely related species and identifying the genetic basis of such changes can contribute to our understanding of their evolutionary history. However, little is known about the genetic architecture or the specific genes underlying the evolution of male genitalia. The morphology of the claspers, posterior lobes and anal plates exhibit striking differences between Drosophila mauritiana and Drosophila simulans. Using QTL and introgression-based high-resolution mapping, we identified several small regions on chromosome arms 3L and 3R that contribute to differences in these traits. However, we found that the loci underlying the evolution of clasper differences between these two species are independent from those that contribute to posterior lobe and anal plate divergence. Furthermore, while most of the loci affect each trait in the same direction and act additively, we also found evidence for epistasis between loci for clasper bristle number. In addition, we conducted an RNAi screen in D. melanogaster to investigate if positional and expression candidate genes located on chromosome 3L, are also involved in genital development. We found that six of these genes, including components of Wnt signaling and male-specific lethal 3 (msl3), regulate the development of genital traits consistent with the effects of the introgressed regions where they are located and that thus represent promising candidate genes for the evolution these traits.

}, issn = {1943-2631}, doi = {10.1534/genetics.114.174045}, author = {Tanaka, Kentaro M and Hopfen, Corinna and Herbert, Matthew R and Schl{\"o}tterer, Christian and Stern, David L and Masly, John P and McGregor, Alistair P and Nunes, Maria D S} } @article {47896, title = {Genome engineering of isogenic human ES cells to model autism disorders.}, journal = {Nucleic acids research}, volume = {43}, year = {2015}, month = {2015 May 26}, pages = {e65}, abstract = {

Isogenic pluripotent stem cells are critical tools for studying human neurological diseases by allowing one to study the effects of a mutation in a fixed genetic background. Of particular interest are the spectrum of autism disorders, some of which are monogenic such as Timothy syndrome (TS); others are multigenic such as the microdeletion and microduplication syndromes of the 16p11.2 chromosomal locus. Here, we report engineered human embryonic stem cell (hESC) lines for modeling these two disorders using locus-specific endonucleases to increase the efficiency of homology-directed repair (HDR). We developed a system to: (1) computationally identify unique transcription activator-like effector nuclease (TALEN) binding sites in the genome using a new software program, TALENSeek, (2) assemble the TALEN genes by combining golden gate cloning with modified constructs from the FLASH protocol, and (3) test the TALEN pairs in an amplification-based HDR assay that is more sensitive than the typical non-homologous end joining assay. We applied these methods to identify, construct, and test TALENs that were used with HDR donors in hESCs to generate an isogenic TS cell line in a scarless manner and to model the 16p11.2 copy number disorder without modifying genomic loci with high sequence similarity.

}, keywords = {Autistic Disorder, Binding Sites, Cell Engineering, Cell Line, Child Development Disorders, Pervasive, Deoxyribonucleases, Embryonic Stem Cells, Gene Targeting, Genome, Human, Humans, Long QT Syndrome, Models, Genetic, Recombinational DNA Repair, Software, Syndactyly}, issn = {1362-4962}, doi = {10.1093/nar/gkv164}, author = {Martinez, Refugio A and Stein, Jason L and Krostag, Anne-Rachel F and Nelson, Angelique M and Marken, John S and Menon, Vilas and May, Ryan C and Yao, Zizhen and Kaykas, Ajamete and Geschwind, Daniel H and Grimley, Joshua S} } @article {47014, title = {Genome-wide errant targeting by Hairy.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Aug 25}, abstract = {

Metazoan transcriptional repressors regulate chromatin through diverse histone modifications. Contributions of individual factors to the chromatin landscape in development is difficult to establish, as global surveys reflect multiple changes in regulators. Therefore, we studied the conserved Hairy/Enhancer of Split family repressor Hairy, analyzing histone marks and gene expression in Drosophila embryos. This long-range repressor mediates histone acetylation and methylation in large blocks, with highly context-specific effects on target genes. Most strikingly, Hairy exhibits biochemical activity on many loci that are uncoupled to changes in gene expression. Rather than representing inert binding sites, as suggested for many eukaryotic factors, many regions are targeted errantly by Hairy to modify the chromatin landscape. Our findings emphasize that identification of active cis-regulatory elements must extend beyond the survey of prototypical chromatin marks. We speculate that this errant activity may provide a path for creation of new regulatory elements, facilitating the evolution of novel transcriptional circuits.

}, issn = {2050-084X}, doi = {10.7554/eLife.06394}, author = {Kok, Kurtulus and Ay, Ahmet and Li, Li M and Arnosti, David N} } @article {46756, title = {Genomic signatures of evolutionary transitions from solitary to group living.}, journal = {Science}, year = {2015}, month = {2015 May 14}, abstract = {

The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown. We compared the genomes of ten bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings. First, many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity. Second, there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings. Third, though clearly independent in detail, these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements. Eusociality may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks.

}, issn = {1095-9203}, doi = {10.1126/science.aaa4788}, author = {Kapheim, Karen M and Pan, Hailin and Li, Cai and Salzberg, Steven L and Puiu, Daniela and Magoc, Tanja and Robertson, Hugh M and Hudson, Matthew E and Venkat, Aarti and Fischman, Brielle J and Hernandez, Alvaro and Yandell, Mark and Ence, Daniel and Holt, Carson and Yocum, George D and Kemp, William P and Bosch, Jordi and Waterhouse, Robert M and Zdobnov, Evgeny M and Stolle, Eckart and Kraus, F Bernhard and Helbing, Sophie and Moritz, Robin F A and Glastad, Karl M and Hunt, Brendan G and Goodisman, Michael A D and Hauser, Frank and Grimmelikhuijzen, Cornelis J P and Pinheiro, Daniel Guariz and Nunes, Francis Morais Franco and Soares, Michelle Prioli Miranda and Tanaka, {\'E}rica Donato and Sim{\~o}es, Zil{\'a} Luz Paulino and Hartfelder, Klaus and Evans, Jay D and Barribeau, Seth M and Johnson, Reed M and Massey, Jonathan H and Southey, Bruce R and Hasselmann, Martin and Hamacher, Daniel and Biewer, Matthias and Kent, Clement F and Zayed, Amro and Blatti, Charles and Sinha, Saurabh and Johnston, J Spencer and Hanrahan, Shawn J and Kocher, Sarah D and Wang, Jun and Robinson, Gene E and Zhang, Guojie} } @article {47084, title = {Green-to-red photoconversion of GCaMP.}, journal = {PLoS One}, volume = {10}, year = {2015}, month = {2015 Sep 18}, pages = {e0138127}, abstract = {

Genetically encoded calcium indicators (GECIs) permit imaging intracellular calcium transients. Among GECIs, the GFP-based GCaMPs are the most widely used because of their high sensitivity and rapid response to changes in intracellular calcium concentrations. Here we report that the fluorescence of GCaMPs-including GCaMP3, GCaMP5 and GCaMP6-can be converted from green to red following exposure to blue-green light (450-500 nm). This photoconversion occurs in both insect and mammalian cells and is enhanced in a low oxygen environment. The red fluorescent GCaMPs retained calcium responsiveness, albeit with reduced sensitivity. We identified several amino acid residues in GCaMP important for photoconversion and generated a GCaMP variant with increased photoconversion efficiency in cell culture. This light-induced spectral shift allows the ready labeling of specific, targeted sets of GCaMP-expressing cells for functional imaging in the red channel. Together, these findings indicate the potential for greater utility of existing GCaMP reagents, including transgenic animals.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0138127}, author = {Ai, Minrong and Mills, Holly and Kanai, Makoto and Lai, Jason and Deng, Jingjing and Schreiter, Eric and Looger, Loren and Neubert, Thomas and Suh, Greg} } @article {46973, title = {H2A histone-fold and DNA elements in nucleosome activate SWR1-mediated H2A.Z replacement in budding yeast.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Jun 27}, abstract = {

The histone variant H2A.Z is a universal mark of gene promoters, enhancers, and regulatory elements in eukaryotic chromatin. The chromatin remodeler SWR1 mediates site-specific incorporation of H2A.Z by a multi-step histone replacement reaction, evicting histone H2A-H2B from the canonical nucleosome and depositing the H2A.Z-H2B dimer. Binding of both substrates, the canonical nucleosome and the H2A.Z-H2B dimer, is essential for activation of SWR1. We found that SWR1 primarily recognizes key residues within the α2 helix in the histone-fold of nucleosomal histone H2A, a region not previously known to influence remodeler activity. Moreover, SWR1 interacts preferentially with nucleosomal DNA at superhelix location 2 on the nucleosome face distal to its linker-binding site. Our findings provide new molecular insights on recognition of the canonical nucleosome by a chromatin remodeler and have implications for ATP-driven mechanisms of histone eviction and deposition.

}, issn = {2050-084X}, doi = {10.7554/eLife.06845}, author = {Ranjan, Anand and Wang, Feng and Mizuguchi, Gaku and Wei, Debbie and Huang, Yingzi and Wu, Carl} } @article {47180, title = {Heterosynaptic plasticity underlies aversive olfactory learning in Drosophila}, journal = {Neuron}, volume = {88}, year = {2015}, month = {2015 Dec 2}, pages = {985-98}, abstract = {

Although associative learning has been localized to specific brain areas in many animals, identifying the underlying synaptic processes in vivo has been difficult. Here, we provide the first demonstration of long-term synaptic plasticity at the output site of the Drosophila mushroom body. Pairing an odor with activation of specific dopamine neurons induces both learning and odor-specific synaptic depression. The plasticity induction strictly depends on the temporal order of the two stimuli, replicating the logical requirement for associative learning. Furthermore, we reveal that dopamine action is confined to and distinct across different anatomical compartments of the mushroom body lobes. Finally, we find that overlap between sparse representations of different odors defines both stimulus specificity of the plasticity and generalizability of associative memories across odors. Thus, the plasticity we find here not only manifests important features of associative learning but also provides general insights into how a sparse sensory code is read out.

}, doi = {10.1016/j.neuron.2015.11.003}, author = {Hige, Toshihide and Aso, Yoshinori and Modi, Mehrab and Rubin, Gerald M and Turner, Glenn C} } @article {46895, title = {A high throughput (>90\%), large compensation range, single-prism femtosecond pulse compressor.}, journal = {arXiv}, year = {2015}, month = {2015 Jun 20}, pages = {arXiv:1306.5011 }, abstract = {

We demonstrate a high throughput, large compensation range, single-prism femtosecond pulse compressor, using a single prism and two roof mirrors. The compressor has zero angular dispersion, zero spatial dispersion, zero pulse-front tilt, and unity magnification. The high efficiency is achieved by adopting two roof mirrors as the retroreflectors. We experimentally achieved ~ -14500 fs2 group delay dispersion (GDD) with 30 cm of prism tip-roof mirror prism separation, and ~90.7\% system throughput with the current implementation. With better components, the throughput can be even higher.

}, url = {http://arxiv.org/abs/1306.5011}, author = {Kong, Lingjie and Cui, Meng} } @article {47128, title = {A higher order visual neuron tuned to the spatial amplitude spectra of natural scenes.}, journal = {Nature Communications}, volume = {6}, year = {2015}, month = {2015 Oct 06}, pages = {8522}, abstract = {

Animal sensory systems are optimally adapted to those features typically encountered in natural surrounds, thus allowing neurons with limited bandwidth to encode challengingly large input ranges. Natural scenes are not random, and peripheral visual systems in vertebrates and insects have evolved to respond efficiently to their typical spatial statistics. The mammalian visual cortex is also tuned to natural spatial statistics, but less is known about coding in higher order neurons in insects. To redress this we here record intracellularly from a higher order visual neuron in the hoverfly. We show that the cSIFE neuron, which is inhibited by stationary images, is maximally inhibited when the slope constant of the amplitude spectrum is close to the mean in natural scenes. The behavioural optomotor response is also strongest to images with naturalistic image statistics. Our results thus reveal a close coupling between the inherent statistics of natural scenes and higher order visual processing in insects.

}, issn = {2041-1723}, doi = {10.1038/ncomms9522}, author = {Dyakova, Olga and Lee, Yu-Jen and Longden, Kit D and Kiselev, Valerij G and Nordstr{\"o}m, Karin} } @article {46576, title = {High-performance probes for light and electron microscopy.}, journal = {Nature Methods}, volume = {12}, year = {2015}, month = {2015 Apr 27}, pages = {568-76}, abstract = {

We describe an engineered family of highly antigenic molecules based on GFP-like fluorescent proteins. These molecules contain numerous copies of peptide epitopes and simultaneously bind IgG antibodies at each location. These {\textquoteright}spaghetti monster{\textquoteright} fluorescent proteins (smFPs) distributed well in neurons, notably into small dendrites, spines and axons. smFP immunolabeling localized weakly expressed proteins not well resolved with traditional epitope tags. By varying epitope and scaffold, we generated a diverse family of mutually orthogonal antigens. In cultured neurons and mouse and fly brains, smFP probes allowed robust, orthogonal multicolor visualization of proteins, cell populations and neuropil. smFP variants complement existing tracers and greatly increase the number of simultaneous imaging channels, and they performed well in advanced preparations such as array tomography, super-resolution fluorescence imaging and electron microscopy. In living cells, the probes improved single-molecule image tracking and increased yield for RNA-seq. These probes facilitate new experiments in connectomics, transcriptomics and protein localization.

}, issn = {1548-7105}, doi = {10.1038/nmeth.3365}, author = {Viswanathan, Sarada and Williams, Megan E. and Bloss, Erik B. and Stasevich, Timothy J. and Speer, Colenso M. and Nern, Aljoscha and Pfeiffer, Barret D. and Hooks, Bryan M. and Li, Wei-Ping and English, Brian P. and Tian, Teresa and Henry, Gilbert L. and Macklin, John J. and Patel, Ronak and Gerfen, Charles R and Zhuang, Xiaowei and Wang, Yalin and Rubin, Gerald M and Looger, Loren L} } @article {46891, title = {High-resolution in vivo imaging of mouse brain through the intact skull.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015-Jul 13}, pages = {9236-41}, abstract = {

Multiphoton microscopy is the current method of choice for in vivo deep-tissue imaging. The long laser wavelength suffers less scattering, and the 3D-confined excitation permits the use of scattered signal light. However, the imaging depth is still limited because of the complex refractive index distribution of biological tissue, which scrambles the incident light and destroys the optical focus needed for high resolution imaging. Here, we demonstrate a wavefront-shaping scheme that allows clear imaging through extremely turbid biological tissue, such as the skull, over an extended corrected field of view (FOV). The complex wavefront correction is obtained and directly conjugated to the turbid layer in a noninvasive manner. Using this technique, we demonstrate in vivo submicron-resolution imaging of neural dendrites and microglia dynamics through the intact skulls of adult mice. This is the first observation, to our knowledge, of dynamic morphological changes of microglia through the intact skull, allowing truly noninvasive studies of microglial immune activities free from external perturbations.

}, keywords = {neuroimaging nonlinear microscopy wavefront shaping immunology adaptive optics}, doi = {10.1073/pnas.1505939112 }, url = {https://www.pnas.org/content/112/30/9236}, author = {Park, Jung-Hoon and Sun, Wei and Cui, Meng} } @article {46819, title = {High-resolution live imaging reveals axon-glia interactions during peripheral nerve injury and repair in zebrafish.}, journal = {Disease Models \& Mechanisms}, volume = {8}, year = {2015}, month = {2015 Jun 1}, pages = {553-64}, abstract = {

Neural damage is a devastating outcome of physical trauma. The glia are one of the main effectors of neuronal repair in the nervous system, but the dynamic interactions between peripheral neurons and Schwann cells during injury and regeneration remain incompletely characterized. Here, we combine laser microsurgery, genetic analysis, high-resolution intravital imaging and lattice light-sheet microscopy to study the interaction between Schwann cells and sensory neurons in a zebrafish model of neurotrauma. We found that chronic denervation by neuronal ablation leads to Schwann-cell death, whereas acute denervation by axonal severing does not affect the overall complexity and architecture of the glia. Neuronal-circuit regeneration begins when Schwann cells extend bridging processes to close the injury gap. Regenerating axons grow faster and directionally after the physiological clearing of distal debris by the Schwann cells. This might facilitate circuit repair by ensuring that axons are guided through unoccupied spaces within bands of B{\"u}ngner towards their original peripheral target. Accordingly, in the absence of Schwann cells, regenerating axons are misrouted, impairing the re-innervation of sensory organs. Our results indicate that regenerating axons use haptotaxis as a directional cue during the reconstitution of a neural circuit. These findings have implications for therapies aimed at neurorepair, which will benefit from preserving the architecture of the peripheral glia during periods of denervation.

}, issn = {1754-8411}, doi = {10.1242/dmm.018184}, author = {Xiao, Yan and Faucherre, Ad{\`e}le and Pola-Morell, Laura and Heddleston, John M and Liu, Tsung-Li and Chew, Teng-Leong and Sato, Fuminori and Sehara-Fujisawa, Atsuko and Kawakami, Koichi and L{\'o}pez-Schier, Hern{\'a}n} } @article {47145, title = {Histone H3 threonine phosphorylation regulates asymmetric histone inheritance in the Drosophila male germline.}, journal = {Cell}, volume = {163}, year = {2015}, month = {2015 Nov 5}, pages = {920-33}, abstract = {

A long-standing question concerns how stem cells maintain their identity through multiple divisions. Previously, we reported that pre-existing and newly synthesized histone H3 are asymmetrically distributed during Drosophila male germline stem cell (GSC) asymmetric division. Here, we show that phosphorylation at threonine 3 of H3 (H3T3P) distinguishes pre-existing versus newly synthesized H3. Converting T3 to the unphosphorylatable residue alanine (H3T3A) or to the phosphomimetic aspartate (H3T3D) disrupts asymmetric H3 inheritance. Expression of H3T3A or H3T3D specifically in early-stage germline also leads to cellular defects, including GSC loss and germline tumors. Finally, compromising the activity of the H3T3 kinase Haspin enhances the H3T3A but suppresses the H3T3D phenotypes. These studies demonstrate that H3T3P distinguishes sister chromatids enriched with distinct pools of H3 in order to coordinate asymmetric segregation of "old" H3 into GSCs and that tight regulation of H3T3 phosphorylation is required for male germline activity.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2015.10.002}, author = {Xie, Jing and Wooten, Matthew and Tran, Vuong and Chen, Bi-Chang and Pozmanter, Caitlin and Simbolon, Christine and Betzig, Eric and Chen, Xin} } @article {46742, title = {HMMER web server: 2015 update.}, journal = {Nucleic Acids Research}, year = {2015}, month = {2015 May 5}, abstract = {

The HMMER website, available at http://www.ebi.ac.uk/Tools/hmmer/, provides access to the protein homology search algorithms found in the HMMER software suite. Since the first release of the website in 2011, the search repertoire has been expanded to include the iterative search algorithm, jackhmmer. The continued growth of the target sequence databases means that traditional tabular representations of significant sequence hits can be overwhelming to the user. Consequently, additional ways of presenting homology search results have been developed, allowing them to be summarised according to taxonomic distribution or domain architecture. The taxonomy and domain architecture representations can be used in combination to filter the results according to the needs of a user. Searches can also be restricted prior to submission using a new taxonomic filter, which not only ensures that the results are specific to the requested taxonomic group, but also improves search performance. The repertoire of profile hidden Markov model libraries, which are used for annotation of query sequences with protein families and domains, has been expanded to include the libraries from CATH-Gene3D, PIRSF, Superfamily and TIGRFAMs. Finally, we discuss the relocation of the HMMER webserver to the European Bioinformatics Institute and the potential impact that this will have.

}, issn = {1362-4962}, doi = {10.1093/nar/gkv397}, author = {Finn, Robert D and Clements, Jody and Arndt, William and Miller, Benjamin L and Wheeler, Travis J and Schreiber, Fabian and Bateman, Alex and Eddy, Sean R} } @article {46480, title = {Homology searches for structural RNAs: from proof of principle to practical use.}, journal = {RNA}, volume = {21}, year = {2015}, month = {2015 Apr}, pages = {605-7}, issn = {1469-9001}, doi = {10.1261/rna.050484.115}, author = {Eddy, Sean R} } @article {46522, title = {Identification of genes that promote or inhibit olfactory memory formation in Drosophila.}, journal = {Genetics}, volume = {199}, year = {2015}, month = {2015 Apr}, pages = {1173-82}, abstract = {

Genetic screens in Drosophila melanogaster and other organisms have been pursued to filter the genome for genetic functions important for memory formation. Such screens have employed primarily chemical or transposon-mediated mutagenesis and have identified numerous mutants including classical memory mutants, dunce and rutabaga. Here, we report the results of a large screen using panneuronal RNAi expression to identify additional genes critical for memory formation. We identified \>500 genes that compromise memory when inhibited (low hits), either by disrupting the development and normal function of the adult animal or by participating in the neurophysiological mechanisms underlying memory formation. We also identified \>40 genes that enhance memory when inhibited (high hits). The dunce gene was identified as one of the low hits and further experiments were performed to map the effects of the dunce RNAi to the α/β and γ mushroom body neurons. Additional behavioral experiments suggest that dunce knockdown in the mushroom body neurons impairs memory without significantly affecting acquisition. We also characterized one high hit, sickie, to show that RNAi knockdown of this gene enhances memory through effects in dopaminergic neurons without apparent effects on acquisition. These studies further our understanding of two genes involved in memory formation, provide a valuable list of genes that impair memory that may be important for understanding the neurophysiology of memory or neurodevelopmental disorders, and offer a new resource of memory suppressor genes that will aid in understanding restraint mechanisms employed by the brain to optimize resources.

}, issn = {1943-2631}, doi = {10.1534/genetics.114.173575}, author = {Walkinshaw, Erica and Gai, Yunchao and Farkas, Caitlin and Richter, Daniel and Nicholas, Eric and Keleman, Krystyna and Davis, Ronald L} } @article {47037, title = {Identification of inhibitory premotor interneurons activated at a late phase in a motor cycle during Drosophila larval locomotion.}, journal = {PLoS One}, volume = {10}, year = {2015}, month = {2015 Sep 03}, pages = {e0136660}, abstract = {

Rhythmic motor patterns underlying many types of locomotion are thought to be produced by central pattern generators (CPGs). Our knowledge of how CPG networks generate motor patterns in complex nervous systems remains incomplete, despite decades of work in a variety of model organisms. Substrate borne locomotion in Drosophila larvae is driven by waves of muscular contraction that propagate through multiple body segments. We use the motor circuitry underlying crawling in larval Drosophila as a model to try to understand how segmentally coordinated rhythmic motor patterns are generated. Whereas muscles, motoneurons and sensory neurons have been well investigated in this system, far less is known about the identities and function of interneurons. Our recent study identified a class of glutamatergic premotor interneurons, PMSIs (period-positive median segmental interneurons), that regulate the speed of locomotion. Here, we report on the identification of a distinct class of glutamatergic premotor interneurons called Glutamatergic Ventro-Lateral Interneurons (GVLIs). We used calcium imaging to search for interneurons that show rhythmic activity and identified GVLIs as interneurons showing wave-like activity during peristalsis. Paired GVLIs were present in each abdominal segment A1-A7 and locally extended an axon towards a dorsal neuropile region, where they formed GRASP-positive putative synaptic contacts with motoneurons. The interneurons expressed vesicular glutamate transporter (vGluT) and thus likely secrete glutamate, a neurotransmitter known to inhibit motoneurons. These anatomical results suggest that GVLIs are premotor interneurons that locally inhibit motoneurons in the same segment. Consistent with this, optogenetic activation of GVLIs with the red-shifted channelrhodopsin, CsChrimson ceased ongoing peristalsis in crawling larvae. Simultaneous calcium imaging of the activity of GVLIs and motoneurons showed that GVLIs{\textquoteright} wave-like activity lagged behind that of motoneurons by several segments. Thus, GVLIs are activated when the front of a forward motor wave reaches the second or third anterior segment. We propose that GVLIs are part of the feedback inhibition system that terminates motor activity once the front of the motor wave proceeds to anterior segments.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0136660}, author = {Itakura, Yuki and Kohsaka, Hiroshi and Ohyama, Tomoko and Zlatic, Marta and Pulver, Stefan R and Nose, Akinao} } @article {47237, title = {Ig superfamily ligand and receptor pairs expressed in synaptic partners in Drosophila.}, journal = {Cell}, volume = {163}, year = {2015}, month = {2015 Dec 17}, pages = {1756-69}, abstract = {

Information processing relies on precise patterns of synapses between neurons. The cellular recognition mechanisms regulating this specificity are poorly understood. In the medulla of the Drosophila visual system, different neurons form synaptic connections in different layers. Here, we sought to identify candidate cell recognition molecules underlying this specificity. Using RNA sequencing (RNA-seq), we show that neurons with different synaptic specificities express unique combinations of mRNAs encoding hundreds of cell surface and secreted proteins. Using RNA-seq and protein tagging, we demonstrate that 21 paralogs of the Dpr family, a subclass of immunoglobulin (Ig)-domain containing proteins, are expressed in unique combinations in homologous neurons with different layer-specific synaptic connections. Dpr interacting proteins (DIPs), comprising nine paralogs of another subclass of Ig-containing proteins, are expressed in a complementary layer-specific fashion in a subset of synaptic partners. We propose that pairs of Dpr/DIP paralogs contribute to layer-specific patterns of synaptic connectivity.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2015.11.021}, author = {Tan, Liming and Zhang, Kelvin Xi and Pecot, Matthew Y and Nagarkar-Jaiswal, Sonal and Lee, Pei-Tseng and Takemura, Shin-ya and McEwen, Jason M and Nern, Aljoscha and Xu, Shuwa and Tadros, Wael and Chen, Zhenqing and Zinn, Kai and Bellen, Hugo J and Morey, Marta and Zipursky, S Lawrence} } @article {47161, title = {Imaging fictive locomotor patterns in larval Drosophila.}, journal = {Journal of Neurophysiology}, volume = {114}, year = {2015}, month = {2015 Nov 06}, pages = {2564-77}, abstract = {

We have established a preparation in larval Drosophila to monitor fictive locomotion simultaneously across abdominal and thoracic segments of the isolated CNS with genetically encoded Ca(2+) indicators. The Ca(2+) signals closely followed spiking activity measured electrophysiologically in nerve roots. Three motor patterns are analyzed. Two comprise waves of Ca(2+) signals that progress along the longitudinal body axis in a posterior-to-anterior or anterior-to-posterior direction. These waves had statistically indistinguishable intersegmental phase delays compared with segmental contractions during forward and backward crawling behavior, despite being \~{}10 times slower. During these waves, motor neurons of the dorsal longitudinal and transverse muscles were active in the same order as the muscle groups are recruited during crawling behavior. A third fictive motor pattern exhibits a left-right asymmetry across segments and bears similarities with turning behavior in intact larvae, occurring equally frequently and involving asymmetry in the same segments. Ablation of the segments in which forward and backward waves of Ca(2+) signals were normally initiated did not eliminate production of Ca(2+) waves. When the brain and subesophageal ganglion (SOG) were removed, the remaining ganglia retained the ability to produce both forward and backward waves of motor activity, although the speed and frequency of waves changed. Bilateral asymmetry of activity was reduced when the brain was removed and abolished when the SOG was removed. This work paves the way to studying the neural and genetic underpinnings of segmentally coordinated motor pattern generation in Drosophila with imaging techniques.

}, issn = {1522-1598}, doi = {10.1152/jn.00731.2015}, author = {Pulver, Stefan R and Bayley, Timothy G and Taylor, Adam L and Berni, Jimena and Bate, Michael and Hedwig, Berthold} } @article {46771, title = {Imaging live-cell dynamics and structure at the single-molecule level.}, journal = {Molecular Cell}, volume = {58}, year = {2015}, month = {2015 May 21}, pages = {644-59}, abstract = {

Observation of molecular processes inside living cells is fundamental to a quantitative understanding of how biological systems function. Specifically, decoding the complex behavior of single molecules enables us to measure kinetics, transport, and self-assembly at this fundamental level that is often veiled in ensemble experiments. In the past decade, rapid developments in fluorescence microscopy, fluorescence correlation spectroscopy, and fluorescent labeling techniques have enabled new experiments to investigate the robustness and stochasticity of diverse molecular mechanisms with high spatiotemporal resolution. This review discusses the concepts and strategies of structural and functional imaging in living cells at the single-molecule level with minimal perturbations to the specimen.

}, doi = {10.1016/j.molcel.2015.02.033}, author = {Liu, Zhe and Lavis, Luke D and Betzig, Eric} } @article {47127, title = {Imaging the neural basis of locomotion.}, journal = {Cell}, volume = {163}, year = {2015}, month = {2015 Oct 22}, pages = {541-2}, abstract = {

To investigate the fundamental question of how nervous systems encode, organize, and sequence behaviors, Kato et\ al. imaged neural activity with cellular resolution across the brain of the worm Caenorhabditis elegans. Locomotion behavior seems to be continuously represented by cyclical patterns of distributed neural activity that are present even in immobilized animals.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2015.10.014}, author = {Branson, Kristin and Freeman, Jeremy} } @article {47734, title = {Imaging transcription: past, present, and future.}, journal = {Cold Spring Harbor Symposia on Quantitative Biology}, volume = {80}, year = {2015}, month = {2015}, pages = {1-8}, abstract = {

Transcription, the first step of gene expression, is exquisitely regulated in higher eukaryotes to ensure correct development and homeostasis. Traditional biochemical, genetic, and genomic approaches have proved successful at identifying factors, regulatory sequences, and potential pathways that modulate transcription. However, they typically only provide snapshots or population averages of the highly dynamic, stochastic biochemical processes involved in transcriptional regulation. Single-molecule live-cell imaging has, therefore, emerged as a complementary approach capable of circumventing these limitations. By observing sequences of molecular events in real time as they occur in their native context, imaging has the power to derive cause-and-effect relationships and quantitative kinetics to build predictive models of transcription. Ongoing progress in fluorescence imaging technology has brought new microscopes and labeling technologies that now make it possible to visualize and quantify the transcription process with single-molecule resolution in living cells and animals. Here we provide an overview of the evolution and current state of transcription imaging technologies. We discuss some of the important concepts they uncovered and present possible future developments that might solve long-standing questions in transcriptional regulation.

}, issn = {1943-4456}, doi = {10.1101/sqb.2015.80.027201}, author = {Coleman, Robert A and Liu, Zhe and Darzacq, Xavier and Tjian, Robert and Singer, Robert H and Lionnet, Timoth{\'e}e} } @article {48389, title = {Impermanence of dendritic spines in live adult CA1 hippocampus.}, journal = {Nature}, volume = {523}, year = {2015}, month = {2015 Jul 30}, pages = {592-6}, abstract = {

The mammalian hippocampus is crucial for episodic memory formation and transiently retains information for about 3-4 weeks in adult mice and longer in humans. Although neuroscientists widely believe that neural synapses are elemental sites of information storage, there has been no direct evidence that hippocampal synapses persist for time intervals commensurate with the duration of hippocampal-dependent memory. Here we tested the prediction that the lifetimes of hippocampal synapses match the longevity of hippocampal memory. By using time-lapse two-photon microendoscopy in the CA1 hippocampal area of live mice, we monitored the turnover dynamics of the pyramidal neurons{\textquoteright} basal dendritic spines, postsynaptic structures whose turnover dynamics are thought to reflect those of excitatory synaptic connections. Strikingly, CA1 spine turnover dynamics differed sharply from those seen previously in the neocortex. Mathematical modelling revealed that the data best matched kinetic models with a single population of spines with a mean lifetime of approximately 1-2 weeks. This implies \~{}100\% turnover in \~{}2-3 times this interval, a near full erasure of the synaptic connectivity pattern. Although N-methyl-d-aspartate (NMDA) receptor blockade stabilizes spines in the neocortex, in CA1 it transiently increased the rate of spine loss and thus lowered spine density. These results reveal that adult neocortical and hippocampal pyramidal neurons have divergent patterns of spine regulation and quantitatively support the idea that the transience of hippocampal-dependent memory directly reflects the turnover dynamics of hippocampal synapses.

}, keywords = {Animals, CA1 Region, Hippocampal, Dendritic Spines, Endoscopy, Kinetics, Male, Memory, Episodic, Mice, Neocortex, Neuronal Plasticity, Photons, Pyramidal Cells, Receptors, N-Methyl-D-Aspartate, Synapses, Time Factors}, issn = {1476-4687}, doi = {10.1038/nature14467}, author = {Attardo, Alessio and Fitzgerald, James E and Schnitzer, Mark J} } @article {46701, title = {In the right place at the right time: visualizing and understanding mRNA localization.}, journal = {Nature Reviews Molecular Cell Biology}, volume = {16}, year = {2015}, month = {2015 Feb}, pages = {95-109}, abstract = {

The spatial regulation of protein translation is an efficient way to create functional and structural asymmetries in cells. Recent research has furthered our understanding of how individual cells spatially organize protein synthesis, by applying innovative technology to characterize the relationship between mRNAs and their regulatory proteins, single-mRNA trafficking dynamics, physiological effects of abrogating mRNA localization in vivo and for endogenous mRNA labelling. The implementation of new imaging technologies has yielded valuable information on mRNA localization, for example, by observing single molecules in tissues. The emerging movements and localization patterns of mRNAs in morphologically distinct unicellular organisms and in neurons have illuminated shared and specialized mechanisms of mRNA localization, and this information is complemented by transgenic and biochemical techniques that reveal the biological consequences of mRNA mislocalization.

}, keywords = {Animals, Biological Transport, Humans, Neurons, Protein Biosynthesis, Protein Transport, RNA, Messenger}, issn = {1471-0080}, doi = {10.1038/nrm3918}, author = {Buxbaum, Adina R and Haimovich, Gal and Singer, Robert H} } @article {46534, title = {In vivo neuroimaging through the highly scattering tissue via iterative multi-photon adaptive compensation technique.}, journal = {Optics Express}, volume = {23}, year = {2015}, month = {2015 Mar 9}, pages = {6145-50}, abstract = {

For in vivo deep tissue imaging, high order wavefront measurement and correction is needed for handling the severe wavefront distortion. Towards such a goal, we have developed the iterative multi-photon adaptive compensation technique (IMPACT). In this work, we explore using IMPACT to perform calcium imaging of neocortex through the intact skull of adult mice, and to image through the highly scattering white matter on the hippocampus surface.

}, issn = {1094-4087}, doi = {10.1364/OE.23.006145}, author = {Kong, Lingjie and Cui, Meng} } @article {46885, title = {InferenceMAP: mapping of single-molecule dynamics with Bayesian inference.}, journal = {Nature Methods}, volume = {12}, year = {2015}, month = {2015 Jun 30}, pages = {594-5}, issn = {1548-7105}, doi = {10.1038/nmeth.3441}, author = {Beheiry, Mohamed El and Dahan, Maxime and Masson, Jean-Baptiste} } @article {46929, title = {Inferring transient particle transport dynamics in live cells.}, journal = {Nature Methods}, volume = {12}, year = {2015}, month = {2015 Jul 20}, pages = {838-40}, abstract = {

Live-cell imaging and particle tracking provide rich information on mechanisms of intracellular transport. However, trajectory analysis procedures to infer complex transport dynamics involving stochastic switching between active transport and diffusive motion are lacking. We applied Bayesian model selection to hidden Markov modeling to infer transient transport states from trajectories of mRNA-protein complexes in live mouse hippocampal neurons and metaphase kinetochores in dividing human cells. The software is available at http://hmm-bayes.org/.

}, issn = {1548-7105}, doi = {10.1038/nmeth.3483}, author = {Monnier, Nilah and Barry, Zachary and Park, Hye Yoon and Su, Kuan-Chung and Katz, Zachary and English, Brian P and Dey, Arkajit and Pan, Keyao and Cheeseman, Iain M and Singer, Robert H and Bathe, Mark} } @article {47087, title = {Inhibitory gating of input comparison in the CA1 microcircuit.}, journal = {Neuron}, volume = {87}, year = {2015}, month = {2015 Sep 23}, pages = {1274-89}, abstract = {

Spatial and temporal features of synaptic inputs engage integration mechanisms on multiple scales, including presynaptic release sites, postsynaptic dendrites, and networks of inhibitory interneurons. Here we investigate how these mechanisms cooperate to filter synaptic input in hippocampal area CA1. Dendritic recordings from CA1 pyramidal neurons reveal that proximal inputs from CA3 as well as distal inputs from entorhinal cortex layer III (ECIII) sum sublinearly or linearly at low firing rates due to feedforward inhibition, but sum supralinearly at high firing rates due to synaptic facilitation, producing a high-pass filter. However, during ECIII and CA3 input comparison, supralinear dendritic integration is dynamically balanced by feedforward and\ feedback inhibition, resulting in suppression of dendritic complex spiking. We find that a particular subpopulation of CA1 interneurons expressing neuropeptide Y (NPY) contributes prominently to this dynamic filter by integrating both ECIII and CA3 input pathways and potently inhibiting CA1 pyramidal neuron dendrites.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.08.025}, author = {Milstein, Aaron D and Bloss, Erik B and Apostolides, Pierre F and Vaidya, Sachin P and Dilly, Geoffrey A and Zemelman, Boris V and Magee, Jeffrey C} } @article {47284, title = {The innate immune receptor PGRP-LC controls presynaptic homeostatic plasticity.}, journal = {Neuron}, volume = {88}, year = {2015}, month = {2015 Dec 16}, pages = {1157-64}, abstract = {

It is now appreciated that the brain is immunologically active. Highly conserved innate immune signaling responds to pathogen invasion and injury and promotes structural refinement of neural circuitry. However, it remains generally unknown whether innate immune signaling has a function during the day-to-day regulation of neural function in the absence of pathogens and irrespective of cellular damage or developmental change. Here we show that an innate immune receptor, a member of the peptidoglycan pattern recognition receptor family (PGRP-LC), is required for the induction and sustained expression of homeostatic synaptic plasticity. This receptor functions presynaptically, controlling the homeostatic modulation of the readily releasable pool of synaptic vesicles following inhibition of postsynaptic glutamate receptor function. Thus, PGRP-LC is a candidate receptor for retrograde, trans-synaptic signaling, a novel activity for innate immune signaling and the first known function of a PGRP-type receptor in the nervous system of any organism.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.10.049}, author = {Harris, Nathan and Braiser, Daniel J and Dickman, Dion K and Fetter, Richard D and Tong, Amy and Davis, Graeme W} } @conference {47229, title = {Interactive exemplar-based segmentation toolkit for biomedical image analysis.}, booktitle = {International Symposium on Biomedical Imaging}, year = {2015}, month = {2015 Apr}, abstract = {

In the field of biomedical imaging analysis on single-cell level, reliable and fast segmentation of the cell nuclei from the background on three-dimensional images is highly needed for the further analysis. In this work we propose an interactive cell segmentation toolkit that first establishes a set of exemplar regions from user input through an easy and intuitive interface in both 2D and 3D in real-time, then
extracts the shape and intensity features from those exemplars. Based on a local contrast-constrained region growing scheme, each connected component in the whole image would be filtered by the features from exemplars, forming an {\textquotedblleft}exemplar-matching{\textquotedblright} group which passed the filtering and would be part of the final segmentation result, and a {\textquotedblleft}non-exemplar-matching{\textquotedblright} group in which components
would be further segmented by the gradient vector field based algorithm. The results of the filtering process are visualized back to the user in near real-time, thus enhancing the experience in exemplar selecting and parameter tuning. The toolkit is distributed as a plugin within the open source Vaa3D system (http://vaa3d.org).

}, author = {Li, Xiang and Zhou, Zhi and Keller, Philipp J and Zeng, Hongkui and Liu, Tianming and Peng, Hanchuan} } @article {47619, title = {Intracellular and extracellular forces drive primary cilia movement.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015 Feb 3}, pages = {1410-5}, abstract = {

Primary cilia are ubiquitous, microtubule-based organelles that play diverse roles in sensory transduction in many eukaryotic cells. They interrogate the cellular environment through chemosensing, osmosensing, and mechanosensing using receptors and ion channels in the ciliary membrane. Little is known about the mechanical and structural properties of the cilium and how these properties contribute to ciliary perception. We probed the mechanical responses of primary cilia from kidney epithelial cells [Madin-Darby canine kidney-II (MDCK-II)], which sense fluid flow in renal ducts. We found that, on manipulation with an optical trap, cilia deflect by bending along their length and pivoting around an effective hinge located below the basal body. The calculated bending rigidity indicates weak microtubule doublet coupling. Primary cilia of MDCK cells lack interdoublet dynein motors. Nevertheless, we found that the organelles display active motility. 3D tracking showed correlated fluctuations of the cilium and basal body. These angular movements seemed random but were dependent on ATP and cytoplasmic myosin-II in the cell cortex. We conclude that force generation by the actin cytoskeleton surrounding the basal body results in active ciliary movement. We speculate that actin-driven ciliary movement might tune and calibrate ciliary sensory functions.

}, keywords = {Animals, Centrosome, Cilia, Dogs, Madin Darby Canine Kidney Cells, Microscopy, Electron, Movement}, issn = {1091-6490}, doi = {10.1073/pnas.1421845112}, author = {Battle, Christopher and Ott, Carolyn M and Burnette, Dylan T and Lippincott-Schwartz, Jennifer and Schmidt, Christoph F} } @article {46927, title = {Ketamine Inside Neurons?}, journal = {American Journal of Psychiatry}, volume = {172}, year = {2015}, month = {2015 Jul 17}, pages = {1064-6}, issn = {1535-7228}, doi = {10.1176/appi.ajp.2015.14121537}, author = {Lester, Henry A and Lavis, Luke D and Dougherty, Dennis A} } @article {46747, title = {Label-free spectroscopic detection of membrane potential using stimulated Raman scattering.}, journal = {Applied Physics Letters}, volume = {106}, year = {2015}, month = {2015 Apr 27}, pages = {173704}, abstract = {

Hyperspectral stimulated Raman scattering microscopy is deployed to measure single-membrane vibrational spectrum as a function of membrane potential. Using erythrocyte ghost as a model, quantitative correlation between transmembrane potential and Raman spectral profile was found. Specifically, the ratio between the area under Raman band at \~{}2930 cm-1 and that at \~{}2850 cm-1 increased by \~{}2.6 times when the potential across the erythrocyte ghost membrane varied from +10 mV to -10 mV. Our results show the feasibility of employing stimulated Raman scattering microscopy to probe the membrane potential without labeling.

}, doi = {10.1063/1.4919104}, author = {Liu, Bin and Lee, Hyeon Jeong and Zhang, Delong and Liao, Chien-Sheng and Ji, Na and Xia, Yuanqin and Cheng, Ji-Xin} } @article {46368, title = {Labeling of active neural circuits in vivo with designed calcium integrators.}, journal = {Science}, volume = {347}, year = {2015}, month = {2015 Feb 13}, pages = {755-60}, abstract = {

The identification of active neurons and circuits in vivo is a fundamental challenge in understanding the neural basis of behavior. Genetically encoded calcium (Ca(2+)) indicators (GECIs) enable quantitative monitoring of cellular-resolution activity during behavior. However, such indicators require online monitoring within a limited field of view. Alternatively, post hoc staining of immediate early genes (IEGs) indicates highly active cells within the entire brain, albeit with poor temporal resolution. We designed a fluorescent sensor, CaMPARI, that combines the genetic targetability and quantitative link to neural activity of GECIs with the permanent, large-scale labeling of IEGs, allowing a temporally precise "activity snapshot" of a large tissue volume. CaMPARI undergoes efficient and irreversible green-to-red conversion only when elevated intracellular Ca(2+) and experimenter-controlled illumination coincide. We demonstrate the utility of CaMPARI in freely moving larvae of zebrafish and flies, and in head-fixed mice and adult flies.

}, issn = {1095-9203}, doi = {10.1126/science.1260922}, author = {Fosque, Benjamin F and Sun, Yi and Dana, Hod and Yang, Chao-Tsung and Ohyama, Tomoko and Tadross, Michael R and Patel, Ronak and Zlatic, Marta and Kim, Douglas S and Ahrens, Misha B and Jayaraman, Vivek and Looger, Loren L and Schreiter, Eric R} } @article {46532, title = {Large-scale imaging in small brains.}, journal = {Current Opinion in Neurobiology}, volume = {32C}, year = {2015}, month = {2015 Jun 1}, pages = {78-86}, abstract = {

The dense connectivity in the brain means that one neuron{\textquoteright}s activity can influence many others. To observe this interconnected system comprehensively, an aspiration within neuroscience is to record from as many neurons as possible at the same time. There are two useful routes toward this goal: one is to expand the spatial extent of functional imaging techniques, and the second is to use animals with small brains. Here we review recent progress toward imaging many neurons and complete populations of identified neurons in small vertebrates and invertebrates.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2015.01.007}, author = {Ahrens, Misha B and Engert, Florian} } @article {48830, title = {Learning enhances sensory and multiple non-sensory representations in primary visual cortex.}, journal = {Neuron}, volume = {86}, year = {2015}, month = {2015 Jun 17}, pages = {1478-90}, abstract = {

We determined how learning modifies neural representations in primary visual cortex (V1) during acquisition of a visually guided behavioral task. We imaged the activity of the same layer 2/3 neuronal populations as mice learned to discriminate two visual patterns while running through a virtual corridor, where one pattern was rewarded. Improvements in behavioral performance were closely associated with increasingly distinguishable population-level representations of task-relevant stimuli, as a result of stabilization of existing and recruitment of new neurons selective for these stimuli. These effects correlated with the appearance of multiple task-dependent signals during learning: those that increased neuronal selectivity across the population when expert animals engaged in the task, and those reflecting anticipation or behavioral choices specifically in neuronal subsets preferring the rewarded stimulus. Therefore, learning engages diverse mechanisms that modify sensory and non-sensory representations in V1 to adjust its processing to task requirements and the behavioral relevance of visual stimuli.

}, keywords = {Animals, Calcium, Discrimination (Psychology), Female, Learning, Luminescent Proteins, Male, Mice, Mice, Inbred C57BL, Mice, Transgenic, Models, Neurological, Neurons, Nonlinear Dynamics, Optogenetics, Photic Stimulation, Sensory Receptor Cells, User-Computer Interface, Vision, Ocular, Visual Cortex}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.05.037}, author = {Poort, Jasper and Khan, Adil G and Pachitariu, Marius and Nemri, Abdellatif and Orsolic, Ivana and Krupic, Julija and Bauza, Marius and Sahani, Maneesh and Keller, Georg B and Mrsic-Flogel, Thomas D and Hofer, Sonja B} } @article {47744, title = {Learning: the good, the bad, and the fly.}, journal = {Neuron}, volume = {86}, year = {2015}, month = {2015 Apr 22}, pages = {343-5}, abstract = {

Olfactory memories can be very good-your mother{\textquoteright}s baking-or very bad-your father{\textquoteright}s cooking. We go through life forming these different associations with the smells we encounter. But what makes one association pleasant and another repulsive? Work in deep areas of the Drosophila brain has revealed the beginnings of an answer, as reported in this issue of Neuron by Owald et al. (2015).

}, keywords = {Animals, Appetitive Behavior, Dopaminergic Neurons, Drosophila, Mushroom Bodies, Smell}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.04.012}, author = {Hige, Toshihide and Turner, Glenn} } @article {45457, title = {Light sheet-based imaging and analysis of early embryogenesis in the fruit fly.}, journal = {Methods in Molecular Biology}, volume = {1189}, year = {2015}, month = {2015}, pages = {79-97}, abstract = {

The fruit fly is an excellent model system for investigating the sequence of epithelial tissue invaginations constituting the process of gastrulation. By combining recent advancements in light sheet fluorescence microscopy (LSFM) and image processing, the three-dimensional fly embryo morphology and relevant gene expression patterns can be accurately recorded throughout the entire process of embryogenesis. LSFM provides exceptionally high imaging speed, high signal-to-noise ratio, low level of photoinduced damage, and good optical penetration depth. This powerful combination of capabilities makes LSFM particularly suitable for live imaging of the fly embryo.The resulting high-information-content image data are subsequently processed to obtain the outlines of cells and cell nuclei, as well as the geometry of the whole embryo tissue by image segmentation. Furthermore, morphodynamics information is extracted by computationally tracking objects in the image. Towards that goal we describe the successful implementation of a fast fitting strategy of Gaussian mixture models.The data obtained by image processing is well-suited for hypothesis testing of the detailed biomechanics of the gastrulating embryo. Typically this involves constructing computational mechanics models that consist of an objective function providing an estimate of strain energy for a given morphological configuration of the tissue, and a numerical minimization mechanism of this energy, achieved by varying morphological parameters.In this chapter, we provide an overview of in vivo imaging of fruit fly embryos using LSFM, computational tools suitable for processing the resulting images, and examples of computational biomechanical simulations of fly embryo gastrulation.

}, issn = {1940-6029}, doi = {10.1007/978-1-4939-1164-6_6}, author = {Khairy, Khaled and Lemon, William C and Amat, Fernando and Keller, Philipp J} } @article {46985, title = {Lighting up genes in single cells at scale.}, journal = {Cell}, volume = {162}, year = {2015}, month = {2015 Aug 13}, pages = {705-7}, doi = {10.1016/j.cell.2015.07.052}, author = {Liu, Zhe} } @article {45847, title = {Low affinity binding site clusters confer Hox specificity and regulatory robustness.}, journal = {Cell}, volume = {160}, year = {2015}, month = {2015 Jan 15}, pages = {191-203}, abstract = {

In animals, Hox transcription factors define regional identity in distinct anatomical domains. How Hox genes encode this specificity is a paradox, because different Hox proteins bind with high affinity in\ vitro to similar DNA sequences. Here, we demonstrate that the Hox protein Ultrabithorax (Ubx) in complex with its cofactor Extradenticle (Exd) bound specifically to clusters of very low affinity sites in enhancers of the shavenbaby gene of Drosophila. These low affinity sites conferred specificity for Ubx binding in\ vivo, but multiple clustered sites were required for robust expression when embryos developed in\ variable environments. Although most individual Ubx binding sites are not evolutionarily conserved, the overall enhancer architecture-clusters of low affinity binding sites-is maintained and required for enhancer function. Natural selection therefore works at the level of the enhancer, requiring a particular density of low affinity Ubx sites to confer both specific and robust expression.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2014.11.041}, author = {Crocker, Justin and Abe, Namiko and Rinaldi, Lucrezia and McGregor, Alistair P and Frankel, Nicol{\'a}s and Wang, Shu and Alsawadi, Ahmad and Valenti, Philippe and Plaza, Serge and Payre, Fran{\c c}ois and Mann, Richard S and Stern, David L} } @article {47144, title = {A Low Affinity GCaMP3 Variant (GCaMPer) for Imaging the Endoplasmic Reticulum Calcium Store.}, journal = {PloS one}, volume = {10}, year = {2015}, month = {2015 Oct 09}, pages = {e0139273}, abstract = {

Endoplasmic reticulum calcium homeostasis is critical for cellular functions and is disrupted in diverse pathologies including neurodegeneration and cardiovascular disease. Owing to the high concentration of calcium within the ER, studying this subcellular compartment requires tools that are optimized for these conditions. To develop a single-fluorophore genetically encoded calcium indicator for this organelle, we targeted a low affinity variant of GCaMP3 to the ER lumen (GCaMPer (10.19)). A set of viral vectors was constructed to express GCaMPer in human neuroblastoma cells, rat primary cortical neurons, and human induced pluripotent stem cell-derived cardiomyocytes. We observed dynamic changes in GCaMPer (10.19) fluorescence in response to pharmacologic manipulations of the ER calcium store. Additionally, periodic calcium efflux from the ER was observed during spontaneous beating of cardiomyocytes. GCaMPer (10.19) has utility in imaging ER calcium in living cells and providing insight into luminal calcium dynamics under physiologic and pathologic states.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0139273}, author = {Henderson, Mark J and Baldwin, Heather A and Werley, Christopher A and Boccardo, Stefano and Whitaker, Leslie R and Yan, Xiaokang and Holt, Graham T and Schreiter, Eric R and Looger, Loren L and Cohen, Adam E and Kim, Douglas S and Harvey, Brandon K} } @article {46987, title = {Low-noise encoding of active touch by layer 4 in the somatosensory cortex.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Aug 6}, abstract = {

Cortical spike trains often appear noisy, with the timing and number of spikes varying across repetitions of stimuli. Spiking variability can arise from internal (behavioral state, unreliable neurons, or chaotic dynamics in neural circuits) and external (uncontrolled behavior or sensory stimuli) sources. The amount of irreducible internal noise in spike trains, an important constraint on models of cortical networks, has been difficult to estimate, since behavior and brain state must be precisely controlled or tracked. We recorded from excitatory barrel cortex neurons in layer 4 during active behavior, where mice control tactile input through learned whisker movements. Touch was the dominant sensorimotor feature, with \>70\% spikes occurring in millisecond timescale epochs after touch onset. The variance of touch responses was smaller than expected from Poisson processes, often reaching the theoretical minimum. Layer 4 spike trains thus reflect the millisecond-timescale structure of tactile input with little noise.

}, issn = {2050-084X}, doi = {10.7554/eLife.06619}, author = {Andrew Hires, Samuel and Gutnisky, Diego A and Yu, Jianing and O{\textquoteright}Connor, Daniel H and Svoboda, Karel} } @article {47238, title = {A major locus controls a genital shape difference involved in reproductive isolation between Drosophila yakuba and Drosophila santomea.}, journal = {G3 (Bethesda, Md.)}, volume = {5}, year = {2015}, month = {2015 Oct 28}, pages = {2893-901}, abstract = {

Rapid evolution of genitalia shape, a widespread phenomenon in animals with internal fertilization, offers the opportunity to dissect the genetic architecture of morphological evolution linked to sexual selection and speciation. Most quantitative trait loci (QTL) mapping studies of genitalia divergence have focused on Drosophila melanogaster and its three most closely related species, D. simulans, D. mauritiana, and D. sechellia, and have suggested that the genetic basis of genitalia evolution involves many loci. We report the first genetic study of male genitalia evolution between D. yakuba and D. santomea, two species of the D. melanogaster species subgroup. We focus on male ventral branches, which harm females during interspecific copulation. Using landmark-based geometric morphometrics, we characterized shape variation in parental species, F1 hybrids, and backcross progeny and show that the main axis of shape variation within the backcross population matches the interspecific variation between parental species. For genotyping, we developed a new molecular method to perform multiplexed shotgun genotyping (MSG), which allowed us to prepare genomic DNA libraries from 365 backcross individuals in a few days using little DNA. We detected only three QTL, one of which spans 2.7 Mb and exhibits a highly significant effect on shape variation that can be linked to the harmfulness of the ventral branches. We conclude that the genetic architecture of genitalia morphology divergence may not always be as complex as suggested by previous studies.

}, issn = {2160-1836}, doi = {10.1534/g3.115.023481}, author = {Peluffo, Alexandre E and Nuez, Isabelle and Debat, Vincent and Savisaar, Rosina and Stern, David L and Orgogozo, Virginie} } @article {47143, title = {Mapping nonlinear receptive field structure in primate retina at single cone resolution.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Oct 30}, abstract = {

The function of a neural circuit is shaped by the computations performed by its interneurons, which in many cases are not easily accessible to experimental investigation. Here, we elucidate the transformation of visual signals flowing from the input to the output of the primate retina, using a combination of large-scale multi-electrode recordings from an identified ganglion cell type, visual stimulation targeted at individual cone photoreceptors, and a hierarchical computational model. The results reveal nonlinear subunits in the circuity of OFF midget ganglion cells, which subserve high-resolution vision. The model explains light responses to a variety of stimuli more accurately than a linear model, including stimuli targeted to cones within and across subunits. The recovered model components are consistent with known anatomical organization of midget bipolar interneurons. These results reveal the spatial structure of linear and nonlinear encoding, at the resolution of single cells and at the scale of complete circuits.

}, issn = {2050-084X}, doi = {10.7554/eLife.05241}, author = {Freeman, Jeremy and Field, Greg D and Li, Peter H and Greschner, Martin and Gunning, Deborah E and Mathieson, Keith and Sher, Alexander and Litke, Alan M and Paninski, Liam and Simoncelli, Eero P and Chichilnisky, E J} } @article {46326, title = {Mapping social behavior-induced brain activation at cellular resolution in the mouse.}, journal = {Cell Reports}, volume = {10}, year = {2015}, month = {2015 Jan 13}, pages = {292-305}, abstract = {

Understanding how brain activation mediates behaviors is a central goal of systems neuroscience. Here, we apply an automated method for mapping brain activation in the mouse in order to probe how sex-specific social behaviors are represented in the male brain. Our method uses the immediate-early-gene c-fos, a marker of neuronal activation, visualized by serial two-photon tomography: the c-fos-GFP+ neurons are computationally detected, their distribution is registered to a reference brain and a brain atlas, and their numbers are analyzed by statistical tests. Our results reveal distinct and shared female and male interaction-evoked patterns of male brain activation representing sex discrimination and social recognition. We also identify brain regions whose degree of activity correlates to specific features of social behaviors and estimate the total numbers and the densities of activated neurons per brain areas. Our study opens the door to automated screening of behavior-evoked brain activation in the mouse.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2014.12.014}, author = {Kim, Yongsoo and Venkataraju, Kannan Umadevi and Pradhan, Kith and Mende, Carolin and Taranda, Julian and Turaga, Srinivas C and Arganda-Carreras, Ignacio and Ng, Lydia and Hawrylycz, Michael J and Rockland, Kathleen S and Seung, H Sebastian and Osten, Pavel} } @article {46815, title = {Measuring the optimal exposure for single particle cryo-EM using a 2.6 {\r A} reconstruction of rotavirus VP6.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 May 29}, pages = {10.7554}, abstract = {

Biological specimens suffer radiation damage when imaged in an electron microscope, ultimately limiting the attainable resolution. At a given resolution, an optimal exposure can be defined that maximizes the signal-to-noise ratio in the image. Using a 2.6 {\r A} resolution single particle cryo-EM reconstruction of rotavirus VP6, determined from movies recorded with a total exposure of 100 electrons/{\r A}(2), we obtained accurate measurements of optimal exposure values over a wide range of resolutions. At low and intermediate resolutions our measured values are considerably higher than obtained previously for crystalline specimens, indicating that both images and movies should be collected with higher exposures than are generally used. We demonstrate a method of using our optimal exposure values to filter movie frames, yielding images with improved contrast that lead to higher resolution reconstructions. This {\textquoteright}high-exposure{\textquoteright} technique should benefit cryo-EM work on all types of samples, especially those of relatively low molecular mass.

}, issn = {2050-084X}, doi = {10.7554/eLife.06980}, author = {Grant, Timothy and Grigorieff, Nikolaus} } @article {46881, title = {MicroED data collection and processing.}, journal = {Acta Crystallographica Section A: Foundations \& Advances}, volume = {71}, year = {2015}, month = {2015 Jul 01}, pages = {353-60}, abstract = {

MicroED, a method at the intersection of X-ray crystallography and electron cryo-microscopy, has rapidly progressed by exploiting advances in both fields and has already been successfully employed to determine the atomic structures of several proteins from sub-micron-sized, three-dimensional crystals. A major limiting factor in X-ray crystallography is the requirement for large and well ordered crystals. By permitting electron diffraction patterns to be collected from much smaller crystals, or even single well ordered domains of large crystals composed of several small mosaic blocks, MicroED has the potential to overcome the limiting size requirement and enable structural studies on difficult-to-crystallize samples. This communication details the steps for sample preparation, data collection and reduction necessary to obtain refined, high-resolution, three-dimensional models by MicroED, and presents some of its unique challenges.

}, issn = {2053-2733}, doi = {10.1107/S2053273315010669}, author = {Hattne, Johan and Reyes, Francis E and Nannenga, Brent L and Shi, Dan and de la Cruz, M Jason and Leslie, Andrew G W and Gonen, Tamir} } @article {48205, title = {Microtubule-dependent transport and dynamics of vimentin intermediate filaments.}, journal = {Molecular Biology of the Cell}, volume = {26}, year = {2015}, month = {2015 May 01}, pages = {1675-86}, abstract = {

We studied two aspects of vimentin intermediate filament dynamics-transport of filaments and subunit exchange. We observed transport of long filaments in the periphery of cells using live-cell structured illumination microscopy. We studied filament transport elsewhere in cells using a photoconvertible-vimentin probe and total internal reflection microscopy. We found that filaments were rapidly transported along linear tracks in both anterograde and retrograde directions. Filament transport was microtubule dependent but independent of microtubule polymerization and/or an interaction with the plus end-binding protein APC. We also studied subunit exchange in filaments by long-term imaging after photoconversion. We found that converted vimentin remained in small clusters along the length of filaments rather than redistributing uniformly throughout the network, even in cells that divided after photoconversion. These data show that vimentin filaments do not depolymerize into individual subunits; they recompose by severing and reannealing. Together these results show that vimentin filaments are very dynamic and that their transport is required for network maintenance.

}, keywords = {HEK293 Cells, Histone Deacetylase Inhibitors, Humans, Intermediate Filaments, Microtubules, Protein Multimerization, Protein Transport, Vimentin}, issn = {1939-4586}, doi = {10.1091/mbc.E14-09-1398}, author = {Hookway, Caroline and Ding, Liya and Davidson, Michael W and Rappoport, Joshua Z and Danuser, Gaudenz and Gelfand, Vladimir I} } @article {47239, title = {Minimally invasive microendoscopy system for in vivo functional imaging of deep nuclei in the mouse brain.}, journal = {Biomedical Optics Express}, volume = {6}, year = {2015}, month = {2015 Nov 1}, pages = {4546-56}, abstract = {

The ability to image neurons anywhere in the mammalian brain is a major goal of optical microscopy. Here we describe a minimally invasive microendoscopy system for studying the morphology and function of neurons at depth. Utilizing a guide cannula with an ultrathin wall, we demonstrated in vivo two-photon fluorescence imaging of deeply buried nuclei such as the striatum (2.5 mm depth), substantia nigra (4.4 mm depth) and lateral hypothalamus (5.0 mm depth) in mouse brain. We reported, for the first time, the observation of neuronal activity with subcellular resolution in the lateral hypothalamus and substantia nigra of head-fixed awake mice.

}, issn = {2156-7085}, doi = {10.1364/BOE.6.004546}, author = {Bocarsly, Miriam E and Jiang, Wan-Chen and Wang, Chen and Dudman, Joshua T and Ji, Na and Aponte, Yeka} } @article {48311, title = {Mitochondrial transcription factor A (TFAM) binds to RNA containing 4-way junctions and mitochondrial tRNA.}, journal = {PloS one}, volume = {10}, year = {2015}, month = {2015 nov 6}, pages = {e0142436}, abstract = {

Mitochondrial DNA (mtDNA) is maintained within nucleoprotein complexes known as nucleoids. These structures are highly condensed by the DNA packaging protein, mitochondrial Transcription Factor A (TFAM). Nucleoids also include RNA, RNA:DNA hybrids, and are associated with proteins involved with RNA processing and mitochondrial ribosome biogenesis. Here we characterize the ability of TFAM to bind various RNA containing substrates in order to determine their role in TFAM distribution and function within the nucleoid. We find that TFAM binds to RNA-containing 4-way junctions but does not bind appreciably to RNA hairpins, internal loops, or linear RNA:DNA hybrids. Therefore the RNA within nucleoids largely excludes TFAM, and its distribution is not grossly altered with removal of RNA. Within the cell, TFAM binds to mitochondrial tRNAs, consistent with our RNA 4-way junction data. Kinetic binding assays and RNase-insensitive TFAM distribution indicate that DNA remains the preferred substrate within the nucleoid. However, TFAM binds to tRNA with nanomolar affinity and these complexes are not rare. TFAM-immunoprecipitated tRNAs have processed ends, suggesting that binding is not specific to RNA precursors. The amount of each immunoprecipitated tRNA is not well correlated with tRNA celluar abundance, indicating unequal TFAM binding preferences. TFAM-mt-tRNA interaction suggests potentially new functions for this protein.

}, keywords = {Animals, DNA-Binding Proteins, High Mobility Group Proteins, Kinetics, Mice, Nucleic Acid Conformation, Protein Binding, RNA, RNA, Transfer, Surface Plasmon Resonance, Swiss 3T3 Cells}, issn = {1932-6203}, doi = {10.1371/journal.pone.0142436}, author = {Brown, Timothy A and Tkachuk, Ariana N and Clayton, David A} } @article {68480, title = {Modeling oscillations and spiral waves in Dictyostelium populations.}, journal = {Phys Rev E Stat Nonlin Soft Matter Phys}, volume = {91}, year = {2015}, month = {06/2015}, pages = {062711}, abstract = {

Unicellular organisms exhibit elaborate collective behaviors in response to environmental cues. These behaviors are controlled by complex biochemical networks within individual cells and coordinated through cell-to-cell communication. Describing these behaviors requires new mathematical models that can bridge scales-from biochemical networks within individual cells to spatially structured cellular populations. Here we present a family of "multiscale" models for the emergence of spiral waves in the social amoeba Dictyostelium discoideum. Our models exploit new experimental advances that allow for the direct measurement and manipulation of the small signaling molecule cyclic adenosine monophosphate (cAMP) used by Dictyostelium cells to coordinate behavior in cellular populations. Inspired by recent experiments, we model the Dictyostelium signaling network as an excitable system coupled to various preprocessing modules. We use this family of models to study spatially unstructured populations of "fixed" cells by constructing phase diagrams that relate the properties of population-level oscillations to parameters in the underlying biochemical network. We then briefly discuss an extension of our model that includes spatial structure and show how this naturally gives rise to spiral waves. Our models exhibit a wide range of novel phenomena. including a density-dependent frequency change, bistability, and dynamic death due to slow cAMP dynamics. Our modeling approach provides a powerful tool for bridging scales in modeling of Dictyostelium populations.

}, keywords = {Cyclic AMP, Dictyostelium, Extracellular Space, Kinetics, Models, Biological, Signal Transduction}, issn = {1550-2376}, doi = {10.1103/PhysRevE.91.062711}, author = {Noorbakhsh, Javad and Schwab, David J and Sgro, Allyson E and Gregor, Thomas and Mehta, Pankaj} } @article {46670, title = {Molecular dynamics simulations of the human glucose transporter GLUT1.}, journal = {PLoS One}, volume = {10}, year = {2015}, month = {2015 Apr 28}, pages = {e0125361}, abstract = {

Glucose transporters (GLUTs) provide a pathway for glucose transport across membranes. Human GLUTs are implicated in devastating diseases such as heart disease, hyper- and hypo-glycemia, type 2 diabetes and caner. The human GLUT1 has been recently crystalized in the inward-facing open conformation. However, there is no other structural information for other conformations. The X-ray structures of E. coli Xylose permease (XylE), a glucose transporter homolog, are available in multiple conformations with and without the substrates D-xylose and D-glucose. XylE has high sequence homology to human GLUT1 and key residues in the sugar-binding pocket are conserved. Here we construct a homology model for human GLUT1 based on the available XylE crystal structure in the partially occluded outward-facing conformation. A long unbiased all atom molecular dynamics simulation starting from the model can capture a new fully opened outward-facing conformation. Our investigation of molecular interactions at the interface between the transmembrane (TM) domains and the intracellular helices (ICH) domain in the outward- and inward-facing conformation supports that the ICH domain likely stabilizes the outward-facing conformation in GLUT1. Furthermore, inducing a conformational transition, our simulations manifest a global asymmetric rocker switch motion and detailed molecular interactions between the substrate and residues through the water-filled selective pore along a pathway from the extracellular to the intracellular side. The results presented here are consistent with previously published biochemical, mutagenesis and functional studies. Together, this study shed light on the structure and functional relationships of GLUT1 in multiple conformational states.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0125361}, author = {Park, Min-Sun} } @article {46823, title = {Molecular mechanism of vinculin activation and nanoscale spatial organization in focal adhesions.}, journal = {Nature Cell Biology}, volume = {17}, year = {2015}, month = {2015 Jun 8}, pages = {880-92}, abstract = {

Focal adhesions (FAs) link the extracellular matrix to the actin cytoskeleton to mediate cell adhesion, migration, mechanosensing and signalling. FAs have conserved nanoscale protein organization, suggesting that the position of proteins within FAs regulates their activity and function. Vinculin binds different FA proteins to mediate distinct cellular functions, but how vinculin{\textquoteright}s interactions are spatiotemporally organized within FAs is unknown. Using interferometric photoactivation localization super-resolution microscopy to assay vinculin nanoscale localization and a FRET biosensor to assay vinculin conformation, we found that upward repositioning within the FA during FA maturation facilitates vinculin activation and mechanical reinforcement of FAs. Inactive vinculin localizes to the lower integrin signalling layer in FAs by binding to phospho-paxillin. Talin binding activates vinculin and targets active vinculin higher in FAs where vinculin can engage retrograde actin flow. Thus, specific protein interactions are spatially segregated within FAs at the nanoscale to regulate vinculin activation and function.

}, issn = {1476-4679}, doi = {10.1038/ncb3180}, author = {Case, Lindsay B and Baird, Michelle A and Shtengel, Gleb and Campbell, Sharon L and Hess, Harald F and Davidson, Michael W and Waterman, Clare M} } @article {46307, title = {A motor cortex circuit for motor planning and movement}, journal = {Nature}, volume = {519}, year = {2015}, month = {2015 Feb 25}, pages = {51-6}, abstract = {

Activity in motor cortex predicts specific movements seconds before they occur, but how this preparatory activity relates to upcoming movements is obscure. We dissected the conversion of preparatory activity to movement within a structured motor cortex circuit. An anterior lateral region of the mouse cortex (a possible homologue of premotor cortex in primates) contains equal proportions of intermingled neurons predicting ipsi- or contralateral movements, yet unilateral inactivation of this cortical region during movement planning disrupts contralateral movements. Using cell-type-specific electrophysiology, cellular imaging and optogenetic perturbation, we show that layer 5 neurons projecting within the cortex have unbiased laterality. Activity with a contralateral population bias arises specifically in layer 5 neurons projecting to the brainstem, and only late during movement planning. These results reveal the transformation of distributed preparatory activity into movement commands within hierarchically organized cortical circuits.

}, doi = {10.1038/nature14178}, author = {Nuo Li and Tsai-Wen Chen and Zengcai V. Guo and Charles R. Gerfen and Karel Svoboda} } @article {46531, title = {A multi-layered protein network stabilizes the Escherichia coli FtsZ-ring and modulates constriction dynamics.}, journal = {PLoS Genetics}, volume = {11}, year = {2015}, month = {2015 Apr 07}, pages = {e1005128}, abstract = {

The prokaryotic tubulin homolog, FtsZ, forms a ring-like structure (FtsZ-ring) at midcell. The FtsZ-ring establishes the division plane and enables the assembly of the macromolecular division machinery (divisome). Although many molecular components of the divisome have been identified and their interactions extensively characterized, the spatial organization of these proteins within the divisome is unclear. Consequently, the physical mechanisms that drive divisome assembly, maintenance, and constriction remain elusive. Here we applied single-molecule based superresolution imaging, combined with genetic and biophysical investigations, to reveal the spatial organization of cellular structures formed by four important divisome proteins in E. coli: FtsZ, ZapA, ZapB and MatP. We show that these interacting proteins are arranged into a multi-layered protein network extending from the cell membrane to the chromosome, each with unique structural and dynamic properties. Further, we find that this protein network stabilizes the FtsZ-ring, and unexpectedly, slows down cell constriction, suggesting a new, unrecognized role for this network in bacterial cell division. Our results provide new insight into the structure and function of the divisome, and highlight the importance of coordinated cell constriction and chromosome segregation.

}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1005128}, author = {Buss, Jackson and Coltharp, Carla and Shtengel, Gleb and Yang, Xinxing and Hess, Harald and Xiao, Jie} } @article {46557, title = {A multilevel multimodal circuit enhances action selection in Drosophila.}, journal = {Nature}, volume = {520}, year = {2015}, month = {2015 Apr 20}, pages = {633-9}, abstract = {

Natural events present multiple types of sensory cues, each detected by a specialized sensory modality. Combining information from several modalities is essential for the selection of appropriate actions. Key to understanding multimodal computations is determining the structural patterns of multimodal convergence and how these patterns contribute to behaviour. Modalities could converge early, late or at multiple levels in the sensory processing hierarchy. Here we show that combining mechanosensory and nociceptive cues synergistically enhances the selection of the fastest mode of escape locomotion in Drosophila larvae. In an electron microscopy volume that spans the entire insect nervous system, we reconstructed the multisensory circuit supporting the synergy, spanning multiple levels of the sensory processing hierarchy. The wiring diagram revealed a complex multilevel multimodal convergence architecture. Using behavioural and physiological studies, we identified functionally connected circuit nodes that trigger the fastest locomotor mode, and others that facilitate it, and we provide evidence that multiple levels of multimodal integration contribute to escape mode selection. We propose that the multilevel multimodal convergence architecture may be a general feature of multisensory circuits enabling complex input{\textendash}output functions and selective tuning to ecologically relevant combinations of cues.

}, doi = {10.1038/nature14297}, author = {Ohyama, Tomoko and Schneider-Mizell, Casey M. and Fetter, Richard D. and Aleman, Javier Valdes and Franconville, Romain and Rivera-Alba, Marta and Mensh, Brett D. and Branson, Kristin M. and Simpson, Julie H. and Truman, James W. and Cardona, Albert and Zlatic, Marta} } @article {46527, title = {Myosin 18A coassembles with nonmuscle myosin 2 to form mixed bipolar filaments.}, journal = {Current Biology}, volume = {25}, year = {2015}, month = {2015 Mar 30}, pages = {942-8}, abstract = {

Class-18 myosins are most closely related to conventional class-2 nonmuscle myosins (NM2). Surprisingly, the purified head domains of Drosophila, mouse, and human myosin 18A (M18A) lack actin-activated ATPase activity and the ability to translocate actin filaments, suggesting that the functions of M18A in\ vivo do not depend on intrinsic motor activity. M18A has the longest coiled coil of any myosin outside of the class-2 myosins, suggesting that it might form bipolar filaments similar to conventional myosins. To address this possibility, we expressed and purified full-length mouse M18A using the baculovirus/Sf9 system. M18A did not form large bipolar filaments under any of the conditions tested. Instead, M18A formed an \~{}65-nm-long bipolar structure with two heads at each end. Importantly, when NM2 was polymerized in the presence of M18A, the two myosins formed mixed bipolar filaments, as evidenced by cosedimentation, electron microscopy, and single-molecule imaging. Moreover, super-resolution imaging of NM2 and M18A using fluorescently tagged proteins and immunostaining of endogenous proteins showed that NM2 and M18A are present together within individual filaments inside living cells. Together, our in\ vitro and live-cell imaging data argue strongly that M18A coassembles with NM2 into mixed bipolar filaments. M18A could regulate the biophysical properties of these filaments and, by virtue of its extra N- and C-terminal domains, determine the localization and/or molecular interactions of the filaments. Given the numerous, fundamental cellular and developmental roles attributed to NM2, our results have far-reaching biological implications.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2015.02.012}, author = {Billington, Neil and Beach, Jordan R and Heissler, Sarah M and Remmert, Kirsten and Guzik-Lendrum, Stephanie and Nagy, Attila and Takagi, Yasuharu and Shao, Lin and Li, Dong and Yang, Yi and Zhang, Yingfan and Barzik, Melanie and Betzig, Eric and Hammer, John A and Sellers, James R} } @article {68448, title = {NAD$^{+}$/NADH metabolism and NAD$^{+}$-dependent enzymes in cell death and ischemic brain injury: current advances and therapeutic implications.}, journal = {Curr Med Chem}, volume = {22}, year = {2015}, month = {2015}, pages = {1239-47}, abstract = {

NAD(+) and NADH play crucial roles in a variety of biological processes including energy metabolism, mitochondrial functions, and gene expression. Multiple studies have indicated that NAD(+) administration can profoundly decrease oxidative cell death as well as ischemic and traumatic brain injury, suggesting NAD(+) metabolism as a promising therapeutic target for cerebral ischemia and head injury. Cumulating evidence has suggested that NAD(+) can produce its protective effects by multiple mechanisms, including preventing mitochondrial alterations, enhancing energy metabolism, preventing virtually all forms of cell death including apoptosis, necrosis and autophagy, inhibiting inflammation, directly increasing antioxidation capacity of cells and tissues, and activating SIRT1. Increasing evidence has also suggested that NADH metabolism is a potential therapeutic target for treating several neurological disorders. A number of studies have further indicated that multiple NAD(+)-dependent enzymes such as sirtuins, polymerase(ADP-ribose) polymerases (PARPs) and CD38 mediate cell death and multiple biological processes. In this article, an overview of the recent findings regarding the roles of NAD(+)/NADH and NAD(+)-dependent enzymes in cell death and ischemic brain injury is provided. These findings have collectively indicated that NAD(+)/NADH and NAD(+)-dependent enzymes play fundamental roles in oxidative stress-induced cell death and ischemic brain injury, which may become promising therapeutic targets for brain ischemia and multiple other neurological disorders.

}, keywords = {ADP-ribosyl Cyclase 1, Animals, Brain Injuries, Brain Ischemia, Cell Death, Humans, NAD, Poly(ADP-ribose) Polymerases, Sirtuins}, issn = {1875-533X}, doi = {10.2174/0929867322666150209154420}, author = {Ma, Yingxin and Nie, Hui and Chen, Heyu and Li, Jiefu and Hong, Yunyi and Wang, Ban and Wang, Caixia and Zhang, Jie and Cao, Wei and Zhang, Mingchao and Xu, Yongning and Ding, Xianting and Yin, Shan Kai and Qu, Xinkai and Ying, Weihai} } @article {46894, title = {Neural circuit to integrate opposing motions in the visual field.}, journal = {Cell}, volume = {162}, year = {2015}, month = {2015 Jul 16}, pages = {351-62}, abstract = {

When navigating in their environment, animals use visual motion cues as feedback signals that are elicited by their own motion. Such signals are provided by wide-field neurons sampling motion directions at multiple image points as the animal maneuvers. Each one of these neurons responds selectively to a specific optic flow-field representing the spatial distribution of motion vectors on the retina. Here, we describe the discovery of a group of local, inhibitory interneurons in the fruit fly Drosophila key for filtering these cues. Using anatomy, molecular characterization, activity manipulation, and physiological recordings, we demonstrate that these interneurons convey direction-selective inhibition to wide-field neurons with opposite preferred direction and provide evidence for how their connectivity enables the computation required for integrating opposing motions. Our\ results indicate that, rather than sharpening directional selectivity per se, these circuit elements reduce noise by eliminating non-specific responses to complex visual information.
{\textbullet}Discovery of bi-stratified glutamatergic lobula plate-intrinsic (LPi) interneurons{\textbullet}LPi neurons provide visual null direction inhibition to wide-field tangential cells{\textbullet}Blocking LPi activity leads to target neurons responding to inadequate motion cues{\textbullet}Motion opponency thus increases flow-field selectivity
Newly identified inhibitory neurons are central to an integrative circuit that enables Drosophila to process visual cues with opposite motions generated during flight. The neurons are required to discriminate between distinct complex motion patterns, indicating that neural processing of opposing cues can yield outcomes beyond the simple sum of two inputs.

}, doi = {10.1016/j.cell.2015.06.035}, author = {Mauss, Alex S and Pankova, Katarina and Arenz, Alexander and Nern, Aljoscha and Rubin, Gerald M and Borst, Alexander} } @article {47354, title = {Neural coding in barrel cortex during whisker-guided locomotion.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Dec 23}, abstract = {

Animals seek out relevant information by moving through a dynamic world, but sensory systems are usually studied under highly constrained and passive conditions that may not probe important dimensions of the neural code. Here, we explored neural coding in the barrel cortex of head-fixed mice that tracked walls with their whiskers in tactile virtual reality. Optogenetic manipulations revealed that barrel cortex plays a role in wall-tracking. Closed-loop optogenetic control of layer 4 neurons can substitute for whisker-object contact to guide behavior resembling wall tracking. We measured neural activity using two-photon calcium imaging and extracellular recordings. Neurons were tuned to the distance between the animal snout and the contralateral wall, with monotonic, unimodal, and multimodal tuning curves. This rich representation of object location in the barrel cortex could not be predicted based on simple stimulus-response relationships involving individual whiskers and likely emerges within cortical circuits.

}, issn = {2050-084X}, doi = {10.7554/eLife.12559}, author = {Sofroniew, Nicholas James and Vlasov, Yurii A and Andrew Hires, Samuel and Freeman, Jeremy and Svoboda, Karel} } @article {48312, title = {Neural coding of perceived odor intensity.}, journal = {eNeuro}, volume = {2}, year = {2015}, month = {2015 Nov-Dec}, abstract = {

Stimulus intensity is a fundamental perceptual feature in all sensory systems. In olfaction, perceived odor intensity depends on at least two variables: odor concentration; and duration of the odor exposure or adaptation. To examine how neural activity at early stages of the olfactory system represents features relevant to intensity perception, we studied the responses of mitral/tufted cells (MTCs) while manipulating odor concentration and exposure duration. Temporal profiles of MTC responses to odors changed both as a function of concentration and with adaptation. However, despite the complexity of these responses, adaptation and concentration dependencies behaved similarly. These similarities were visualized by principal component analysis of average population responses and were quantified by discriminant analysis in a trial-by-trial manner. The qualitative functional dependencies of neuronal responses paralleled psychophysics results in humans. We suggest that temporal patterns of MTC responses in the olfactory bulb contribute to an internal perceptual variable: odor intensity.

}, keywords = {Adaptation, Physiological, Animals, Mice, Inbred C57BL, Neurons, Odorants, Olfactory Bulb, Perception, Smell}, issn = {2373-2822}, doi = {10.1523/ENEURO.0083-15.2015}, author = {Sirotin, Yevgeniy B and Shusterman, Roman and Rinberg, Dmitry} } @article {47038, title = {A neural command circuit for grooming movement control.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Sep 7}, abstract = {

Animals perform many stereotyped movements, but how nervous systems are organized for controlling specific movements remains unclear. Here we use anatomical, optogenetic, behavioral, and physiological techniques to identify a circuit in Drosophila melanogaster that can elicit stereotyped leg movements that groom the antennae. Mechanosensory chordotonal neurons detect displacements of the antennae and excite three different classes of functionally connected interneurons, which include two classes of brain interneurons and different parallel descending neurons. This multilayered circuit is organized such that neurons within each layer are sufficient to specifically elicit antennal grooming. However, we find differences in the durations of antennal grooming elicited by neurons in the different layers, suggesting that the circuit is organized to both command antennal grooming and control its duration. As similar features underlie stimulus-induced movements in other animals, we infer the possibility of a common circuit organization for movement control that can be dissected in Drosophila.

}, issn = {2050-084X}, doi = {10.7554/eLife.08758}, author = {Hampel, Stefanie and Franconville, Romain and Simpson, Julie H and Seeds, Andrew M} } @article {46694, title = {Neural dynamics for landmark orientation and angular path integration.}, journal = {Nature}, volume = {521}, year = {2015}, month = {2015 May 14}, pages = {186-191}, abstract = {

Many animals navigate using a combination of visual landmarks and path integration. In mammalian brains, head direction cells integrate these two streams of information by representing an animal{\textquoteright}s heading relative to landmarks, yet maintaining their directional tuning in darkness based on self-motion cues. Here we use two-photon calcium imaging in head-fixed Drosophila melanogaster walking on a ball in a virtual reality arena to demonstrate that landmark-based orientation and angular path integration are combined in the population responses of neurons whose dendrites tile the ellipsoid body, a toroidal structure in the centre of the fly brain. The neural population encodes the fly{\textquoteright}s azimuth relative to its environment, tracking visual landmarks when available and relying on self-motion cues in darkness. When both visual and self-motion cues are absent, a representation of the animal{\textquoteright}s orientation is maintained in this network through persistent activity, a potential substrate for short-term memory. Several features of the population dynamics of these neurons and their circular anatomical arrangement are suggestive of ring attractors, network structures that have been proposed to support the function of navigational brain circuits.

}, doi = {10.1038/nature14446}, author = {Seelig, Johannes D and Jayaraman, Vivek} } @article {47134, title = {Neural encoding of odors during active sampling and in turbulent plumes.}, journal = {Neuron}, volume = {88}, year = {2015}, month = {2015 Oct 21}, pages = {403-18}, abstract = {

Sensory inputs are often fluctuating and intermittent, yet animals reliably utilize them to direct behavior. Here we ask how natural stimulus fluctuations influence the dynamic neural encoding of odors. Using the locust olfactory system, we isolated two main causes of odor intermittency: chaotic odor plumes and active sampling behaviors. Despite their irregularity, chaotic odor plumes still drove dynamic neural response features including the synchronization, temporal patterning, and short-term plasticity of spiking in projection neurons, enabling classifier-based stimulus identification and activating downstream decoders (Kenyon cells). Locusts can also impose odor intermittency through active sampling movements with their unrestrained antennae. Odors triggered immediate, spatially targeted antennal scanning that, paradoxically, weakened individual neural responses. However, these frequent but weaker responses were highly informative about stimulus location. Thus, not only are odor-elicited dynamic neural responses compatible with natural stimulus fluctuations and important for stimulus identification, but locusts actively increase intermittency, possibly to improve stimulus localization.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.09.007}, author = {Huston, Stephen J and Stopfer, Mark and Cassenaer, Stijn and Aldworth, Zane N and Laurent, Gilles} } @article {47240, title = {Neural Network Model of Memory Retrieval.}, journal = {Frontiers in Computational Neuroscience}, volume = {9}, year = {2015}, month = {2015 Dec 17}, pages = {149}, abstract = {

Human memory can store large amount of information. Nevertheless, recalling is often a challenging task. In a classical free recall paradigm, where participants are asked to repeat a briefly presented list of words, people make mistakes for lists as short as 5 words. We present a model for memory retrieval based on a Hopfield neural network where transition between items are determined by similarities in their long-term memory representations. Meanfield analysis of the model reveals stable states of the network corresponding (1) to single memory representations and (2) intersection between memory representations. We show that oscillating feedback inhibition in the presence of noise induces transitions between these states triggering the retrieval of different memories. The network dynamics qualitatively predicts the distribution of time intervals required to recall new memory items observed in experiments. It shows that items having larger number of neurons in their representation are statistically easier to recall and reveals possible bottlenecks in our ability of retrieving memories. Overall, we propose a neural network model of information retrieval broadly compatible with experimental observations and is consistent with our recent graphical model (Romani et al., 2013).

}, issn = {1662-5188}, doi = {10.3389/fncom.2015.00149}, author = {Recanatesi, Stefano and Katkov, Mikhail and Romani, Sandro and Tsodyks, Misha} } @article {46189, title = {The neural representation of taste quality at the periphery.}, journal = {Nature}, volume = {517}, year = {2015}, month = {2015 Jan 15}, pages = {373-6}, abstract = {

The mammalian taste system is responsible for sensing and responding to the five basic taste qualities: sweet, sour, bitter, salty and umami. Previously, we showed that each taste is detected by dedicated taste receptor cells (TRCs) on the tongue and palate epithelium. To understand how TRCs transmit information to higher neural centres, we examined the tuning properties of large ensembles of neurons in the first neural station of the gustatory system. Here, we generated and characterized a collection of transgenic mice expressing a genetically encoded calcium indicator in central and peripheral neurons, and used a gradient refractive index microendoscope combined with high-resolution two-photon microscopy to image taste responses from ganglion neurons buried deep at the base of the brain. Our results reveal fine selectivity in the taste preference of ganglion neurons; demonstrate a strong match between TRCs in the tongue and the principal neural afferents relaying taste information to the brain; and expose the highly specific transfer of taste information between taste cells and the central nervous system.

}, keywords = {Animals, Calcium, Geniculate Ganglion, Mice, Mice, Transgenic, Neurons, Taste, Taste Buds, Taste Perception, Tongue}, issn = {1476-4687}, doi = {10.1038/nature13873}, author = {Barretto, Robert P J and Gillis-Smith, Sarah and Chandrashekar, Jayaram and Yarmolinsky, David A and Schnitzer, Mark J and Ryba, Nicholas J P and Zuker, Charles S} } @article {46481, title = {Neuroarchitecture and neuroanatomy of the Drosophila central complex: A GAL4-based dissection of protocerebral bridge neurons and circuits. (Front cover)}, journal = {The Journal of Comparative Neurology}, volume = {523}, year = {2015}, month = {2015 May 1}, pages = {Spc1 (Front Cover)}, abstract = {

Insects exhibit an elaborate repertoire of behaviors in response to environmental stimuli. The central complex plays a key role in combining various modalities of sensory information with an insect{\textquoteright}s internal state and past experience to select appropriate responses. Progress has been made in understanding the broad spectrum of outputs from the central complex neuropils and circuits involved in numerous behaviors. Many resident neurons have also been identified. However, the specific roles of these intricate structures and the functional connections between them remain largely obscure. Significant gains rely on obtaining a comprehensive catalog of the neurons and associated GAL4 lines that arborize within these brain regions, and on mapping neuronal pathways connecting these structures. To this end, small populations of neurons in the Drosophila melanogaster central complex were stochastically labeled using the multicolor flip-out technique and a catalog was created of the neurons, their morphologies, trajectories, relative arrangements, and corresponding GAL4 lines. This report focuses on one structure of the central complex, the protocerebral bridge, and identifies just 17 morphologically distinct cell types that arborize in this structure. This work also provides new insights into the anatomical structure of the four components of the central complex and its accessory neuropils. Most strikingly, we found that the protocerebral bridge contains 18 glomeruli, not 16, as previously believed. Revised wiring diagrams that take into account this updated architectural design are presented. This updated map of the Drosophila central complex will facilitate a deeper behavioral and physiological dissection of this sophisticated set of structures. J. Comp. Neurol. 523:997-1037, 2015. {\textcopyright} 2014 Wiley Periodicals, Inc.

}, issn = {1096-9861}, doi = {10.1002/cne.23773}, author = {Wolff, Tanya and Iyer, Nirmala A and Rubin, Gerald M} } @article {47158, title = {Neurodata without borders: creating a common data format for neurophysiology}, journal = {Neuron}, volume = {88}, year = {2015}, month = {2015 Nov 18}, pages = {629-34}, abstract = {

The Neurodata Without Borders (NWB) initiative promotes data standardization in neuroscience to increase research reproducibility and opportunities. In the first NWB pilot project, neurophysiologists and software developers produced a common data format for recordings and metadata of cellular electrophysiology and optical imaging experiments. The format specification, application programming interfaces, and sample datasets have been released.

}, doi = {10.1016/j.neuron.2015.10.025}, author = {Teeters, Jeffrey L and Godfrey, Keith and Young, Rob and Dang, Chinh and Friedsam, Claudia and Wark, Barry and Asari, Hiroki and Peron, Simon and Li, Nuo and Peyrache, Adrien} } @article {46926, title = {Neuron hemilineages provide the functional ground plan for the Drosophila ventral nervous system.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Jul 20}, abstract = {

Drosophila central neurons arise from neuroblasts that generate neurons in a pair-wise fashion, with the two daughters providing the basis for distinct A and B hemilineage groups. Thirty three postembryonically-born hemilineages contribute over 90\% of the neurons in each thoracic hemisegment. We devised genetic approaches to define the anatomy of most of these hemilineages and to assessed their functional roles using the heat-sensitive channel dTRPA1. The simplest hemilineages contained local interneurons and their activation caused tonic or phasic leg movements lacking interlimb coordination. The next level was hemilineages of similar projection cells that drove intersegmentally coordinated behaviors such as walking. The highest level involved hemilineages whose activation elicited complex behaviors such as takeoff. These activation phenotypes indicate that the hemilineages vary in their behavioral roles with some contributing to local networks for sensorimotor processing and others having higher order functions of coordinating these local networks into complex behavior.

}, issn = {2050-084X}, doi = {10.7554/eLife.04493}, author = {Harris, Robin M and Pfeiffer, Barret D and Rubin, Gerald M and Truman, James W} } @article {46972, title = {Neuronal representation of ultraviolet visual stimuli in mouse primary visual cortex.}, journal = {Scientific Reports}, volume = {5}, year = {2015}, month = {2015 Jul 29}, pages = {12597}, abstract = {

The mouse has become an important model for understanding the neural basis of visual perception. Although it has long been known that mouse lens transmits ultraviolet (UV) light and mouse opsins have absorption in the UV band, little is known about how UV visual information is processed in the mouse brain. Using a custom UV stimulation system and in vivo calcium imaging, we characterized the feature selectivity of layer 2/3 neurons in mouse primary visual cortex (V1). In adult mice, a comparable percentage of the neuronal population responds to UV and visible stimuli, with similar pattern selectivity and receptive field properties. In young mice, the orientation selectivity for UV stimuli increased steadily during development, but not direction selectivity. Our results suggest that, by expanding the spectral window through which the mouse can acquire visual information, UV sensitivity provides an important component for mouse vision.

}, issn = {2045-2322}, doi = {10.1038/srep12597}, author = {Tan, Zhongchao and Sun, Wenzhi and Chen, Tsai-Wen and Kim, Douglas and Ji, Na} } @article {46574, title = {Neurons for hunger and thirst transmit a negative-valence teaching signal.}, journal = {Nature}, volume = {521}, year = {2015}, month = {2015 Apr 27}, pages = {180-5}, abstract = {

Homeostasis is a biological principle for regulation of essential physiological parameters within a set range. Behavioural responses due to deviation from homeostasis are critical for survival, but motivational processes engaged by physiological need states are incompletely understood. We examined motivational characteristics of two separate neuron populations that regulate energy and fluid homeostasis by using cell-type-specific activity manipulations in mice. We found that starvation-sensitive AGRP neurons exhibit properties consistent with a negative-valence teaching signal. Mice avoided activation of AGRP neurons, indicating that AGRP neuron activity has negative valence. AGRP neuron inhibition conditioned preference for flavours and places. Correspondingly, deep-brain calcium imaging revealed that AGRP neuron activity rapidly reduced in response to food-related cues. Complementary experiments activating thirst-promoting neurons also conditioned avoidance. Therefore, these need-sensing neurons condition preference for environmental cues associated with nutrient or water ingestion, which is learned through reduction of negative-valence signals during restoration of homeostasis.

}, doi = {10.1038/nature14416}, author = {Betley, J Nicholas and Xu, Shengjin and Cao, Zhen Fang Huang and Gong, Rong and Magnus, Christopher J and Yu, Yang and Sternson, Scott M} } @article {46479, title = {Neuroscience: hot on the trail of temperature processing.}, journal = {Nature}, volume = {519}, year = {2015}, month = {2015 Mar 19}, pages = {296-7}, issn = {1476-4687}, doi = {10.1038/nature14209}, author = {Florence, T J and Reiser, Michael B} } @article {46799, title = {New insights and system designs for temporally focused multiphoton optogenetics. }, journal = {Proceedings of SPIE}, volume = {9329}, year = {2015}, month = {2015 Mar 5}, pages = {932928}, abstract = {

Temporal focusing (TF) multiphoton systems constitute a powerful solution for cellular resolution optogenetic stimulation and recording in three-dimensional, scattering tissue. Here, we address two fundamental aspects in the design of such systems: first, we examine the design of TF systems with specific optical sectioning by comparatively analyzing previously published results. Next, we develop a solution for obtaining TF in a flexible three-dimensional pattern of cellmatched focal spots. Our solution employs spatio-temporal focusing (SSTF) in a unique optical system design that can be integrated before essentially any multiphoton imaging or stimulation system.

}, doi = {10.1117/12.2078678}, author = {Mayblum, Tom and Schejter, Adi and Dana, Hod and Shoham, Shy} } @article {46504, title = {Next generation multilocus sequence typing (NGMLST) and the analytical software program MLSTEZ enable efficient, cost-effective, high-throughput, multilocus sequencing typing.}, journal = {Fungal Genetics and Biology}, volume = {75}, year = {2015}, month = {2015 Feb}, pages = {64-71}, abstract = {

Multilocus sequence typing (MLST) has become the preferred method for genotyping many biological species, and it is especially useful for analyzing haploid eukaryotes. MLST is rigorous, reproducible, and informative, and MLST genotyping has been shown to identify major phylogenetic clades, molecular groups, or subpopulations of a species, as well as individual strains or clones. MLST molecular types often correlate with important phenotypes. Conventional MLST involves the extraction of genomic DNA and the amplification by PCR of several conserved, unlinked gene sequences from a sample of isolates of the taxon under investigation. In some cases, as few as three loci are sufficient to yield definitive results. The amplicons are sequenced, aligned, and compared by phylogenetic methods to distinguish statistically significant differences among individuals and clades. Although MLST is simpler, faster, and less expensive than whole genome sequencing, it is more costly and time-consuming than less reliable genotyping methods (e.g. amplified fragment length polymorphisms). Here, we describe a new MLST method that uses next-generation sequencing, a multiplexing protocol, and appropriate analytical software to provide accurate, rapid, and economical MLST genotyping of 96 or more isolates in single assay. We demonstrate this methodology by genotyping isolates of the well-characterized, human pathogenic yeast Cryptococcus neoformans.

}, issn = {1096-0937}, doi = {10.1016/j.fgb.2015.01.005}, author = {Chen, Yuan and Frazzitta, Aubrey E and Litvintseva, Anastasia P and Fang, Charles and Mitchell, Thomas G and Springer, Deborah J and Ding, Yun and Yuan, George and Perfect, John R} } @article {68766, title = {NOCA-1 functions with γ-tubulin and in parallel to Patronin to assemble non-centrosomal microtubule arrays in \textitC. elegans}, journal = {eLife}, volume = {4}, year = {2015}, month = {09/2015}, pages = {e08649}, abstract = {

Non-centrosomal microtubule arrays assemble in differentiated tissues to perform mechanical and transport-based functions. In this study, we identify \textitCaenorhabditis elegans NOCA-1 as a protein with homology to vertebrate ninein. NOCA-1 contributes to the assembly of non-centrosomal microtubule arrays in multiple tissues. In the larval epidermis, NOCA-1 functions redundantly with the minus end protection factor Patronin/PTRN-1 to assemble a circumferential microtubule array essential for worm growth and morphogenesis. Controlled degradation of a γ-tubulin complex subunit in this tissue revealed that γ-tubulin acts with NOCA-1 in parallel to Patronin/PTRN-1. In the germline, NOCA-1 and γ-tubulin co-localize at the cell surface, and inhibiting either leads to a microtubule assembly defect. γ-tubulin targets independently of NOCA-1, but NOCA-1 targeting requires γ-tubulin when a non-essential putatively palmitoylated cysteine is mutated. These results show that NOCA-1 acts with γ-tubulin to assemble non-centrosomal arrays in multiple tissues and highlight functional overlap between the ninein and Patronin protein families.

}, keywords = {ninein, NOCA-1, non-centrosomal microtubule array, Patronin, PTRN-1}, issn = {2050-084X}, doi = {10.7554/eLife.08649}, url = {https://doi.org/10.7554/eLife.08649}, author = {Wang, Shaohe and Wu, Di and Quintin, Sophie and Green, Rebecca A and Cheerambathur, Dhanya K and Ochoa, Stacy D and Desai, Arshad and Oegema, Karen}, editor = {Akhmanova, Anna} } @article {48387, title = {Nonlinear circuits for naturalistic visual motion estimation.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Oct 24}, pages = {e09123}, abstract = {

Many animals use visual signals to estimate motion. Canonical models suppose that animals estimate motion by cross-correlating pairs of spatiotemporally separated visual signals, but recent experiments indicate that humans and flies perceive motion from higher-order correlations that signify motion in natural environments. Here we show how biologically plausible processing motifs in neural circuits could be tuned to extract this information. We emphasize how known aspects of Drosophila{\textquoteright}s visual circuitry could embody this tuning and predict fly behavior. We find that segregating motion signals into ON/OFF channels can enhance estimation accuracy by accounting for natural light/dark asymmetries. Furthermore, a diversity of inputs to motion detecting neurons can provide access to more complex higher-order correlations. Collectively, these results illustrate how non-canonical computations improve motion estimation with naturalistic inputs. This argues that the complexity of the fly{\textquoteright}s motion computations, implemented in its elaborate circuits, represents a valuable feature of its visual motion estimator.

}, keywords = {Animals, Drosophila, Locomotion, Models, Neurological, Motion Perception, Neurons, Visual Pathways}, issn = {2050-084X}, doi = {10.7554/eLife.09123}, author = {Fitzgerald, James E and Clark, Damon A} } @article {47016, title = {Novel behavioral paradigm reveals lower temporal limits on mouse olfactory decisions.}, journal = {The Journal of Neuroscience : the Official Journal of the Society for Neuroscience}, volume = {35}, year = {2015}, month = {2015 Aug 19}, pages = {11667-73}, abstract = {

UNLABELLED: Temporal limits on perceptual decisions set strict boundaries on the possible underlying neural computations. How odor information is encoded in the olfactory system is still poorly understood. Here, we sought to define the limit on the speed of olfactory processing. To achieve this, we trained mice to discriminate different odor concentrations in a novel behavioral setup with precise odor delivery synchronized to the sniffing cycle. Mice reported their choice by moving a horizontal treadmill with their front limbs. We found that mice reported discriminations of 75\% accuracy in 70-90 ms after odor inhalation. For a low concentration and nontrigeminal odorant, this time was 90-140 ms, showing that mice process odor information rapidly even in the absence of trigeminal stimulation. These response times establish, after accounting for odor transduction and motor delays, that olfactory processing can take tens of milliseconds. This study puts a strong limit on the underlying neural computations and suggests that the action potentials forming the neural basis for these decisions are fired in a few tens of milliseconds.

SIGNIFICANCE STATEMENT: Understanding how sensory information is processed requires different approaches that span multiple levels of investigation from genes to neurons to behavior. Limits on behavioral performance constrain the possible neural mechanisms responsible for specific computations. Using a novel behavioral paradigm, we established that mice can make decisions about odor intensity surprisingly fast. After accounting for sensory and motor delays, the limit on some olfactory neural computations can be as low as a few tens of milliseconds, which suggests that only the first action potentials across a population of neurons contribute to these computations.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4693-14.2015}, author = {Resulaj, Arbora and Rinberg, Dmitry} } @article {46925, title = {Nuclear accessibility of β-actin mRNA is measured by 3D single-molecule real-time tracking.}, journal = {Journal of Cell Biology}, volume = {209}, year = {2015}, month = {2015 May 25}, pages = {609-19}, abstract = {

Imaging single proteins or RNAs allows direct visualization of the inner workings of the cell. Typically, three-dimensional (3D) images are acquired by sequentially capturing a series of 2D sections. The time required to step through the sample often impedes imaging of large numbers of rapidly moving molecules. Here we applied multifocus microscopy (MFM) to instantaneously capture 3D single-molecule real-time images in live cells, visualizing cell nuclei at 10 volumes per second. We developed image analysis techniques to analyze messenger RNA (mRNA) diffusion in the entire volume of the nucleus. Combining MFM with precise registration between fluorescently labeled mRNA, nuclear pore complexes, and chromatin, we obtained globally optimal image alignment within 80-nm precision using transformation models. We show that β-actin mRNAs freely access the entire nucleus and fewer than 60\% of mRNAs are more than 0.5 {\textmu}m away from a nuclear pore, and we do so for the first time accounting for spatial inhomogeneity of nuclear organization.

}, issn = {1540-8140}, doi = {10.1083/jcb.201411032}, author = {Smith, Carlas S and Preibisch, Stephan and Joseph, Aviva and Abrahamsson, Sara and Rieger, Bernd and Myers, Eugene and Singer, Robert H and Grunwald, David} } @article {46506, title = {Numb is not a critical regulator of Notch-mediated cell fate decisions in the developing chick inner ear.}, journal = {Frontiers in Cellular Neuroscience}, volume = {9}, year = {2015}, month = {2015}, pages = {74}, abstract = {

The Notch signaling pathway controls differentiation of hair cells and supporting cells in the vertebrate inner ear. Here, we have investigated whether Numb, a known regulator of Notch activity in Drosophila, is involved in this process in the embryonic chick. The chicken homolog of Numb is expressed throughout the otocyst at early stages of development and is concentrated at the basal pole of the cells. It is asymmetrically allocated at some cell divisions, as in Drosophila, suggesting that it could act as a determinant inherited by one of the two daughter cells and favoring adoption of a hair-cell fate. To test the implication of Numb in hair cell fate decisions and the regulation of Notch signaling, we used different methods to overexpress Numb at different stages of inner ear development. We found that sustained or late Numb overexpression does not promote hair cell differentiation, and Numb does not prevent the reception of Notch signaling. Surprisingly, none of the Numb-overexpressing cells differentiated into hair cells, suggesting that high levels of Numb protein could interfere with intracellular processes essential for hair cell survival. However, when Numb was overexpressed early and more transiently during ear development, no effect on hair cell formation was seen. These results suggest that in the inner ear at least, Numb does not significantly repress Notch activity and that its asymmetric distribution in dividing precursor cells does not govern the choice between hair cell and supporting cell fates.

}, issn = {1662-5102}, doi = {10.3389/fncel.2015.00074}, author = {Eddison, Mark and Weber, Sara J and Ariza-McNaughton, Linda and Lewis, Julian and Daudet, Nicolas} } @article {46548, title = {Numerical study of multi-conjugate large area wavefront correction for deep tissue microscopy.}, journal = {Optics Express}, volume = {23}, year = {2015}, month = {2015 Mar 23}, pages = {7463-70}, abstract = {

Wavefront distortion fundamentally limits the achievable imaging depth and quality in thick tissue. Wavefront correction can help restore the diffraction limited focus albeit with a small field of view (FOV), which limits its imaging applications. In this work, we numerically investigate whether the multi-conjugate configuration, originally developed for astronomical adaptive optics, may increase the correction FOV in random turbid media. The results show that the multi-conjugate configuration can significantly improve the correction area compared to the widely adopted pupil plane correction. Even in the simple case of single-conjugation, it still outperforms the pupil plane correction. This study provides a guideline for designing the optimal wavefront correction system in deep tissue imaging.

}, issn = {1094-4087}, doi = {10.1364/OE.23.007463}, author = {Wu, Tsai-Wei and Cui, Meng} } @article {46816, title = {The nutrient-responsive hormone CCHamide-2 controls growth by regulating insulin-like peptides in the brain of Drosophila melanogaster.}, journal = {PLoS Genetics}, volume = {11}, year = {2015}, month = {2015 May}, pages = {e1005209}, abstract = {

The coordination of growth with nutritional status is essential for proper development and physiology. Nutritional information is mostly perceived by peripheral organs before being relayed to the brain, which modulates physiological responses. Hormonal signaling ensures this organ-to-organ communication, and the failure of endocrine regulation in humans can cause diseases including obesity and diabetes. In Drosophila melanogaster, the fat body (adipose tissue) has been suggested to play an important role in coupling growth with nutritional status. Here, we show that the peripheral tissue-derived peptide hormone CCHamide-2 (CCHa2) acts as a nutrient-dependent regulator of Drosophila insulin-like peptides (Dilps). A BAC-based transgenic reporter revealed strong expression of CCHa2 receptor (CCHa2-R) in insulin-producing cells (IPCs) in the brain. Calcium imaging of brain explants and IPC-specific CCHa2-R knockdown demonstrated that peripheral-tissue derived CCHa2 directly activates IPCs. Interestingly, genetic disruption of either CCHa2 or CCHa2-R caused almost identical defects in larval growth and developmental timing. Consistent with these phenotypes, the expression of dilp5, and the release of both Dilp2 and Dilp5, were severely reduced. Furthermore, transcription of CCHa2 is altered in response to nutritional levels, particularly of glucose. These findings demonstrate that CCHa2 and CCHa2-R form a direct link between peripheral tissues and the brain, and that this pathway is essential for the coordination of systemic growth with nutritional availability. A mammalian homologue of CCHa2-R, Bombesin receptor subtype-3 (Brs3), is an orphan receptor that is expressed in the islet β-cells; however, the role of Brs3 in insulin regulation remains elusive. Our genetic approach in Drosophila melanogaster provides the first evidence, to our knowledge, that bombesin receptor signaling with its endogenous ligand promotes insulin production.

}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1005209}, author = {Sano, Hiroko and Nakamura, Akira and Texada, Michael J and Truman, James W and Ishimoto, Hiroshi and Kamikouchi, Azusa and Nibu, Yutaka and Kume, Kazuhiko and Ida, Takanori and Kojima, Masayasu} } @article {46861, title = {Open source tools for large-scale neuroscience.}, journal = {Current Opinion in Neurobiology}, volume = {32}, year = {2015}, month = {2015 Jun}, pages = {156-63}, abstract = {

New technologies for monitoring and manipulating the nervous system promise exciting biology but pose challenges for analysis and computation. Solutions can be found in the form of modern approaches to distributed computing, machine learning, and interactive visualization. But embracing these new technologies will require a cultural shift: away from independent efforts and proprietary methods and toward an open source and collaborative neuroscience.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2015.04.002}, author = {Freeman, Jeremy} } @proceedings {65005, title = {An open-source VAA3D plugin for real-time 3D visualization of terabyte-sized volumetric images.}, year = {2015}, month = {2015 Apr 19}, abstract = {

Modern high-throughput bioimaging techniques pose the unprecedented challenge of exploring and analyzing the produced Terabyte-scale volumetric images directly in their 3D space. Without expensive virtual reality devices and/or parallel computing infrastructures, this becomes even more demanding and calls for new, more scalable tools that help exploring these very large 3D data also on common laptops and graphic hardware. To this end, we developed a plugin for the open-source, cross-platform Vaa3D system to extend its powerful 3D visualization and analysis capabilities to images of potentially unlimited size. When used with large volumetric images up to 2.5 Terabyte in size, Vaa3D-TeraFly exhibited real-time (subsecond) performance that scaled constantly on image size. The tool has been implemented in C++ with Qt and OpenGL and it is freely and publicly available both as open-source and as binary package along with the main Vaa3D distribution.

}, doi = {10.1109/ISBI.2015.7163925}, author = {Alessandro Bria and Giulio Iannello and Hanchuan Peng} } @article {47126, title = {Opposing intrinsic temporal gradients guide neural stem cell production of varied neuronal fates.}, journal = {Science (New York, N.Y.)}, volume = {350}, year = {2015}, month = {2015 Oct 16}, pages = {317-20}, abstract = {

Neural stem cells show age-dependent developmental potentials, as evidenced by their production of distinct neuron types at different developmental times. Drosophila neuroblasts produce long, stereotyped lineages of neurons. We searched for factors that could regulate neural temporal fate by RNA-sequencing lineage-specific neuroblasts at various developmental times. We found that two RNA-binding proteins, IGF-II mRNA-binding protein (Imp) and Syncrip (Syp), display opposing high-to-low and low-to-high temporal gradients with lineage-specific temporal dynamics. Imp and Syp promote early and late fates, respectively, in both a slowly progressing and a rapidly changing lineage. Imp and Syp control neuronal fates in the mushroom body lineages by regulating the temporal transcription factor Chinmo translation. Together, the opposing Imp/Syp gradients encode stem cell age, specifying multiple cell fates within a lineage.

}, issn = {1095-9203}, doi = {10.1126/science.aad1886}, author = {Liu, Zhiyong and Yang, Ching-Po and Sugino, Ken and Fu, Chi-Cheng and Liu, Ling-Yu and Yao, Xiaohao and Lee, Luke P and Lee, Tzumin} } @article {46745, title = {Optimized tools for multicolor stochastic labeling reveal diverse stereotyped cell arrangements in the fly visual system.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015 May 11}, pages = {E2967-76}, abstract = {

We describe the development and application of methods for high-throughput neuroanatomy in Drosophila using light microscopy. These tools enable efficient multicolor stochastic labeling of neurons at both low and high densities. Expression of multiple membrane-targeted and distinct epitope-tagged proteins is controlled both by a transcriptional driver and by stochastic, recombinase-mediated excision of transcription-terminating cassettes. This MultiColor FlpOut (MCFO) approach can be used to reveal cell shapes and relative cell positions and to track the progeny of precursor cells through development. Using two different recombinases, the number of cells labeled and the number of color combinations observed in those cells can be controlled separately. We demonstrate the utility of MCFO in a detailed study of diversity and variability of Distal medulla (Dm) neurons, multicolumnar local interneurons in the adult visual system. Similar to many brain regions, the medulla has a repetitive columnar structure that supports parallel information processing together with orthogonal layers of cell processes that enable communication between columns. We find that, within a medulla layer, processes of the cells of a given Dm neuron type form distinct patterns that reflect both the morphology of individual cells and the relative positions of their arbors. These stereotyped cell arrangements differ between cell types and can even differ for the processes of the same cell type in different medulla layers. This unexpected diversity of coverage patterns provides multiple independent ways of integrating visual information across the retinotopic columns and implies the existence of multiple developmental mechanisms that generate these distinct patterns.

}, issn = {1091-6490}, doi = {10.1073/pnas.1506763112}, author = {Nern, Aljoscha and Pfeiffer, Barret D and Rubin, Gerald M} } @article {47017, title = {Optogenetics: 10 years after ChR2 in neurons-views from the community.}, journal = {Nature Neuroscience}, volume = {18}, year = {2015}, month = {2015 Aug 26}, pages = {1202-12}, issn = {1546-1726}, doi = {10.1038/nn.4106}, author = {Adamantidis, Antoine and Arber, Silvia and Bains, Jaideep S and Bamberg, Ernst and Bonci, Antonello and Buzs{\'a}ki, Gy{\"o}rgy and Cardin, Jessica A and Costa, Rui M and Dan, Yang and Goda, Yukiko and Graybiel, Ann M and H{\"a}usser, Michael and Hegemann, Peter and Huguenard, John R and Insel, Thomas R and Janak, Patricia H and Johnston, Daniel and Josselyn, Sheena A and Koch, Christof and Kreitzer, Anatol C and L{\"u}scher, Christian and Malenka, Robert C and Miesenb{\"o}ck, Gero and Nagel, Georg and Roska, Botond and Schnitzer, Mark J and Shenoy, Krishna V and Soltesz, Ivan and Sternson, Scott M and Tsien, Richard W and Tsien, Roger Y and Turrigiano, Gina G and Tye, Kay M and Wilson, Rachel I} } @article {46924, title = {Oscillatory patterns in hippocampus under light and deep isoflurane anesthesia closely mirror prominent brain states in awake animals.}, journal = {Hippocampus}, volume = {26}, year = {2015}, month = {2015 Jul 18}, pages = {102-9}, abstract = {

The hippocampus exhibits a variety of distinct states of activity under different conditions. For instance the rhythmic patterns of activity orchestrated by the theta oscillation during running and REM sleep are markedly different from the large irregular activity (LIA) observed during awake resting and slow wave sleep. We found that under different levels of isoflurane anesthesia activity in the hippocampus of rats displays two distinct states which have several qualities that mirror the theta and LIA states. These data provide further evidence that the two states are intrinsic modes of the hippocampus; while also characterizing a preparation that could be useful for studying the natural activity states in hippocampus. This article is protected by copyright. All rights reserved.

}, issn = {1098-1063}, doi = {10.1002/hipo.22494}, author = {Lustig, Brian and Wang, Yingxue and Pastalkova, Eva} } @article {47304, title = {P1 interneurons promote a persistent internal state that enhances inter-male aggression in Drosophila.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Dec 29}, abstract = {

How brains are hardwired to produce aggressive behavior, and how aggression circuits are related to those that mediate courtship, is not well understood. A large-scale screen for aggression-promoting neurons in Drosophila identified several independent hits that enhanced both inter-male aggression and courtship. Genetic intersections revealed that 8-10 P1 interneurons, previously thought to exclusively control male courtship, were sufficient to promote fighting. Optogenetic experiments indicated that P1 activation could promote aggression at a threshold below that required for wing extension. P1 activation in the absence of wing extension triggered persistent aggression via an internal state that could endure for minutes. High-frequency P1 activation promoted wing extension and suppressed aggression during photostimulation, whereas aggression resumed and wing extension was inhibited following photostimulation offset. Thus, P1 neuron activation promotes a latent, internal state that facilitates aggression and courtship, and controls the overt expression of these social behaviors in a threshold-dependent, inverse manner.

}, issn = {2050-084X}, doi = {10.7554/eLife.11346}, author = {Hoopfer, Eric D and Jung, Yonil and Inagaki, Hidehiko K and Rubin, Gerald M and Anderson, David J} } @article {48313, title = {Peptide dimer structure in an Aβ(1-42) fibril visualized with cryo-EM.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015 Sep 22}, pages = {11858-63}, abstract = {

Alzheimer{\textquoteright}s disease (AD) is a fatal neurodegenerative disorder in humans and the main cause of dementia in aging societies. The disease is characterized by the aberrant formation of β-amyloid (Aβ) peptide oligomers and fibrils. These structures may damage the brain and give rise to cerebral amyloid angiopathy, neuronal dysfunction, and cellular toxicity. Although the connection between AD and Aβ fibrillation is extensively documented, much is still unknown about the formation of these Aβ aggregates and their structures at the molecular level. Here, we combined electron cryomicroscopy, 3D reconstruction, and integrative structural modeling methods to determine the molecular architecture of a fibril formed by Aβ(1-42), a particularly pathogenic variant of Aβ peptide. Our model reveals that the individual layers of the Aβ fibril are formed by peptide dimers with face-to-face packing. The two peptides forming the dimer possess identical tilde-shaped conformations and interact with each other by packing of their hydrophobic C-terminal β-strands. The peptide C termini are located close to the main fibril axis, where they produce a hydrophobic core and are surrounded by the structurally more flexible and charged segments of the peptide N termini. The observed molecular architecture is compatible with the general chemical properties of Aβ peptide and provides a structural basis for various biological observations that illuminate the molecular underpinnings of AD. Moreover, the structure provides direct evidence for a steric zipper within a fibril formed by full-length Aβ peptide.

}, keywords = {Amino Acid Sequence, Amyloid, Amyloid beta-Peptides, Cryoelectron Microscopy, Epitope Mapping, Image Processing, Computer-Assisted, Immunoglobulin Fab Fragments, Models, Molecular, Molecular Sequence Data, Peptide Fragments, Peptides, Protein Multimerization, Protein Structure, Secondary}, issn = {1091-6490}, doi = {10.1073/pnas.1503455112}, author = {Schmidt, Matthias and Rohou, Alexis and Lasker, Keren and Yadav, Jay K and Schiene-Fischer, Cordelia and F{\"a}ndrich, Marcus and Grigorieff, Nikolaus} } @article {47409, title = {Plasticity-driven individualization of olfactory coding in mushroom body output neurons.}, journal = {Nature}, volume = {526}, year = {2015}, month = {2015 Oct 8}, pages = {258-62}, abstract = {

Although all sensory circuits ascend to higher brain areas where stimuli are represented in sparse, stimulus-specific activity patterns, relatively little is known about sensory coding on the descending side of neural circuits, as a network converges. In insects, mushroom bodies have been an important model system for studying sparse coding in the olfactory system, where this format is important for accurate memory formation. In Drosophila, it has recently been shown that the 2,000 Kenyon cells of the mushroom body converge onto a population of only 34 mushroom body output neurons (MBONs), which fall into 21 anatomically distinct cell types. Here we provide the first, to our knowledge, comprehensive view of olfactory representations at the fourth layer of the circuit, where we find a clear transition in the principles of sensory coding. We show that MBON tuning curves are highly correlated with one another. This is in sharp contrast to the process of progressive decorrelation of tuning in the earlier layers of the circuit. Instead, at the population level, odour representations are reformatted so that positive and negative correlations arise between representations of different odours. At the single-cell level, we show that uniquely identifiable MBONs display profoundly different tuning across different animals, but that tuning of the same neuron across the two hemispheres of an individual fly was nearly identical. Thus, individualized coordination of tuning arises at this level of the olfactory circuit. Furthermore, we find that this individualization is an active process that requires a learning-related gene, rutabaga. Ultimately, neural circuits have to flexibly map highly stimulus-specific information in sparse layers onto a limited number of different motor outputs. The reformatting of sensory representations we observe here may mark the beginning of this sensory-motor transition in the olfactory system.

}, keywords = {Adenylyl Cyclases, Animals, Drosophila melanogaster, Drosophila Proteins, Female, Learning, Male, Mushroom Bodies, Mutation, Neuronal Plasticity, Neurons, Olfactory Pathways, Olfactory Perception, Psychomotor Performance}, issn = {1476-4687}, doi = {10.1038/nature15396}, author = {Hige, Toshihide and Aso, Yoshinori and Rubin, Gerald M and Turner, Glenn C} } @inbook {46570, title = {Population genomic and phylogenomic insights into the evolution of physiology and behaviour in social insects}, booktitle = {Advances in Insect Physiology}, number = {48}, year = {2015}, pages = {293{\textendash}324}, abstract = {

Genomics revolutionized the field of social insect research by providing powerful tools to understand the relationship between genes, physiology and behaviour of social insects. Notably, analysis of gene expression and methylation patterns in the different castes of insect colonies highlighted many genes that likely underlie caste-specific physiological and behavioural phenotypes. However, earlier studies of social insect genomes lacked an {\textquoteleft}evolutionary{\textquoteright} context.\ Out of the millions of DNA bases found in the genome of a social insect, which pieces were most important to fitness over the timescale of social evolution?\ Here, we review a burgeoning body of literature that utilizes between-species or within-species genomic comparisons to highlight the evolutionary forces that have shaped social insect genomes. These pioneering phylogenetic and population genomic studies provide a critically needed evolutionary context to social insect genomes and underscore the importance of adaptive changes in physiology and behaviour in social evolution.

}, doi = {10.1016/bs.aiip.2015.01.002}, author = {Kent, Clement F and Zayed, Amro} } @conference {47129, title = {Post-acquisition image based compensation for thickness variation in microscopy section series.}, booktitle = {IEEE 12th International Symposium on Biomedical Imaging (ISBI)}, year = {2015}, month = {2015 Jul 01}, abstract = {

Serial section Microscopy is an established method for volumetric anatomy reconstruction. Section series imaged with Electron Microscopy are currently vital for the reconstruction of the synaptic connectivity of entire animal brains such as that of Drosophila melanogaster. The process of removing ultrathin layers from a solid block containing the specimen, however, is a fragile procedure and has limited precision with respect to section thickness. We have developed a method to estimate the relative z-position of each individual section as a function of signal change across the section series. First experiments show promising results on both serial section Transmission Electron Microscopy (ssTEM) data and Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) series. We made our solution available as Open Source plugins for the TrakEM2 software and the ImageJ distribution Fiji.

}, doi = {10.1109/ISBI.2015.7163922}, author = {Hanslovsky, Philipp and Bogovic, John and Saalfeld, Stephan} } @article {46788, title = {Post-acquisition image based compensation for thickness variation in microscopy section series.}, journal = {IEEE International Symposium on Biomedical Imaging}, year = {2015}, month = {2014 Nov 25}, pages = {507-11}, abstract = {

Serial section Microscopy is an established method for volumetric anatomy reconstruction. Section series imaged with Electron Microscopy are currently vital for the reconstruction of the synaptic connectivity of entire animal brains such as that of Drosophila melanogaster. The process of removing ultrathin layers from a solid block containing the specimen, however, is a fragile procedure and has limited precision with respect to section thickness. We have developed a method to estimate the relative z-position of each individual section as a function of signal change across the section series. First experiments show promising results on both serial section Transmission Electron Microscopy (ssTEM) data and Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) series. We made our solution available as Open Source plugins for the TrakEM2 software and the ImageJ distribution Fiji.

}, url = {http://arxiv.org/abs/1411.6970}, author = {Hanslovsky, Philpp and Bogovic, John A and Saalfeld, Stephan} } @article {46571, title = {A primer to single-particle cryo-electron microscopy}, journal = {Cell }, volume = {161}, year = {2015}, month = {2015 Apr 23}, pages = {438-49}, chapter = {438-49}, abstract = {

Cryo-electron microscopy (cryo-EM) of single-particle specimens is used to determine the structure of proteins and macromolecular complexes without the need for crystals. Recent advances in detector technology and software algorithms now allow images of unprecedented quality to be recorded and structures to be determined at near-atomic resolution. However, compared with X-ray crystallography, cryo-EM is a young technique with distinct challenges. This primer explains the different steps and considerations involved in structure determination by single-particle cryo-EM to provide an overview for scientists wishing to understand more about this technique and the interpretation of data obtained with it, as well as a starting guide for new practitioners.

}, doi = {10.1016/j.cell.2015.03.050}, author = {Cheng, Yifan and Grigorieff, Nikolaus and Penczek, Pawel A and Walz, Thomas} } @article {46883, title = {Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher.}, journal = {Nature Communications}, volume = {6}, year = {2015}, month = {2015 Jul 7}, pages = {7357}, abstract = {

Many cellular functions rely on DNA-binding proteins finding and associating to specific sites in the genome. Yet the mechanisms underlying the target search remain poorly understood, especially in the case of the highly organized mammalian cell nucleus. Using as a model Tet repressors (TetRs) searching for a multi-array locus, we quantitatively analyse the search process in human cells with single-molecule tracking and single-cell protein-DNA association measurements. We find that TetRs explore the nucleus and reach their target by 3D diffusion interspersed with transient interactions with non-cognate sites, consistent with the facilitated diffusion model. Remarkably, nonspecific binding times are broadly distributed, underlining a lack of clear delimitation between specific and nonspecific interactions. However, the search kinetics is not determined by diffusive transport but by the low association rate to nonspecific sites. Altogether, our results provide a comprehensive view of the recruitment dynamics of proteins at specific loci in mammalian cells.

}, issn = {2041-1723}, doi = {10.1038/ncomms8357}, author = {Normanno, Davide and Boudarene, Lydia and Dugast-Darzacq, Claire and Chen, Jiji and Richter, Christian and Proux, Florence and B{\'e}nichou, Olivier and Voituriez, Rapha{\"e}l and Darzacq, Xavier and Dahan, Maxime} } @article {47616, title = {Profile of Eric Betzig, Stefan Hell, and W. E. Moerner, 2014 Nobel Laureates in Chemistry.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015 Mar 3}, pages = {2630-2}, issn = {1091-6490}, doi = {10.1073/pnas.1500784112}, author = {Lippincott-Schwartz, Jennifer} } @article {46658, title = {Projection-specific characteristics of retinal input to the brain.}, journal = {The Journal of Neuroscience}, volume = {35}, year = {2015}, month = {2015 Apr 22}, pages = {6575-83}, abstract = {

The brain receives information about the direction of object motion from several types of retinal ganglion cells (RGCs). On-Off direction-selective (DS) RGCs respond preferentially to stimuli moving quickly in one of four directions and provide a significant (but difficult to quantify) fraction of RGC input to the SC. On DS RGCs, in comparison, respond preferentially to stimuli moving slowly in one of three directions and are thought to only target retinorecipient nuclei comprising the accessory optic system, e.g., the medial terminal nucleus (MTN). To determine the fraction of SC-projecting RGCs that exhibit direction selectivity, and the specificity with which On-Off and On DS RGCs target retinorecipient areas, we performed optical and electrophysiological recordings from RGCs retrogradely labeled from the mouse SC and MTN. We found, surprisingly, that both On-Off and On DS RGCs innervate the SC; collectively they constitute nearly 40\% of SC-projecting RGCs. In comparison, only On DS RGCs project to the MTN. Subsequent experiments revealed that individual On DS RGCs innervate either the SC or MTN and exhibit robust projection-specific differences in somatodendritic morphology, cellular excitability, and light-evoked activity; several projection-specific differences in the output of On DS RGCs correspond closely to differences in excitatory synaptic input the cells receive. Our results reveal a robust projection of On DS RGCs to the SC, projection-specific differences in the response properties of On DS RGCs, and biophysical and synaptic mechanisms that underlie these functional differences.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4298-14.2015}, author = {Gauvain, Gregory and Murphy, Gabe J} } @article {47202, title = {Propagation of homeostatic sleep signals by segregated synaptic microcircuits of the Drosophila mushroom body.}, journal = {Current Biology : CB}, volume = {25}, year = {2015}, month = {2015 Nov 16}, pages = {2915-27}, abstract = {

The Drosophila mushroom body (MB) is a key associative memory center that has also been implicated in the control of sleep. However, the identity of MB neurons underlying homeostatic sleep regulation, as well as the types of sleep signals generated by specific classes of MB neurons, has remained poorly understood. We recently identified two MB output neuron (MBON) classes whose axons convey sleep control signals from the MB to converge in the same downstream target region: a cholinergic sleep-promoting MBON class and a glutamatergic wake-promoting MBON class. Here, we deploy a combination of neurogenetic, behavioral, and physiological approaches to identify and mechanistically dissect sleep-controlling circuits of the MB. Our studies reveal the existence of two segregated excitatory synaptic microcircuits that propagate homeostatic sleep information from different populations of intrinsic MB\ "Kenyon cells" (KCs) to specific sleep-regulating MBONs: sleep-promoting KCs increase sleep by preferentially activating the cholinergic MBONs, while wake-promoting KCs decrease sleep by preferentially activating the glutamatergic MBONs. Importantly, activity of the sleep-promoting MB microcircuit is increased by sleep deprivation and is necessary for homeostatic rebound sleep (i.e., the increased sleep that occurs after, and in compensation for, sleep lost during deprivation). These studies reveal for the first time specific functional connections between subsets of KCs and particular MBONs and establish the identity of synaptic microcircuits underlying transmission of homeostatic sleep signals in the MB.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2015.09.017}, author = {Sitaraman, Divya and Aso, Yoshinori and Jin, Xin and Chen, Nan and Felix, Mario and Rubin, Gerald M and Nitabach, Michael N} } @article {46497, title = {Proper migration and axon outgrowth of zebrafish cranial motoneuron subpopulations require the cell adhesion molecule MDGA2A.}, journal = {Biology Open}, volume = {4}, year = {2015}, month = {2015}, pages = {146-54}, abstract = {

The formation of functional neuronal circuits relies on accurate migration and proper axonal outgrowth of neuronal precursors. On the route to their targets migrating cells and growing axons depend on both, directional information from neurotropic cues and adhesive interactions mediated via extracellular matrix molecules or neighbouring cells. The inactivation of guidance cues or the interference with cell adhesion can cause severe defects in neuronal migration and axon guidance. In this study we have analyzed the function of the MAM domain containing glycosylphosphatidylinositol anchor 2A (MDGA2A) protein in zebrafish cranial motoneuron development. MDGA2A is prominently expressed in distinct clusters of cranial motoneurons, especially in the ones of the trigeminal and facial nerves. Analyses of MDGA2A knockdown embryos by light sheet and confocal microscopy revealed impaired migration and aberrant axonal outgrowth of these neurons; suggesting that adhesive interactions mediated by MDGA2A are required for the proper arrangement and outgrowth of cranial motoneuron subtypes.

}, issn = {2046-6390}, doi = {10.1242/bio.20148482}, author = {Ingold, Esther and Vom Berg-Maurer, Colette M and Burckhardt, Christoph J and Lehnherr, Andr{\'e} and Rieder, Philip and Keller, Philipp J and Stelzer, Ernst H and Greber, Urs F and Neuhauss, Stephan C F and Gesemann, Matthias} } @article {69344, title = {Quantitative Reevaluation of the Effects of Short- and Long-Term Removal of Descending Modulatory Inputs on the Pyloric Rhythm of the Crab, Cancer borealis }, journal = {eneuro}, volume = {2}, year = {2015}, month = {2015 Jan 14}, pages = {ENEURO.0058-14.2015}, abstract = {

The crustacean stomatogastric ganglion (STG) receives descending neuromodulatory inputs from three anterior ganglia: the paired commissural ganglia (CoGs), and the single esophageal ganglion (OG). In this paper, we provide the first detailed and quantitative analyses of the short- and long-term effects of removal of these descending inputs (decentralization) on the pyloric rhythm of the STG. Thirty minutes after decentralization, the mean frequency of the pyloric rhythm dropped from 1.20 Hz in control to 0.52 Hz. Whereas the relative phase of pyloric neuron activity was approximately constant across frequency in the controls, after decentralization this changed markedly. Nine control preparations kept for 5{\textendash}6 d\ in vitro\ maintained pyloric rhythm frequencies close to their initial values. Nineteen decentralized preparations kept for 5{\textendash}6 d dropped slightly in frequency from those seen at 30 min following decentralization, but then displayed stable activity over 6 d. Bouts of higher frequency activity were intermittently seen in both control and decentralized preparations, but the bouts began earlier and were more frequent in the decentralized preparations. Although the bouts may indicate that the removal of the modulatory inputs triggered changes in neuronal excitability, these changes did not produce obvious long-lasting changes in the frequency of the decentralized preparations.

}, doi = {10.1523/ENEURO.0058-14.2015}, url = {https://www.eneuro.org/lookup/doi/10.1523/ENEURO.0058-14.2015https://syndication.highwire.org/content/doi/10.1523/ENEURO.0058-14.2015}, author = {Hamood, Albert W. and Haddad, Sara A. and Otopalik, Adriane G. and Rosenbaum, Philipp and Marder, Eve} } @article {46499, title = {The Release 6 reference sequence of the Drosophila melanogaster genome.}, journal = {Genome Research}, volume = {25}, year = {2015}, month = {2015 Mar}, pages = {445-58}, abstract = {

Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy and middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. Further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.

}, issn = {1549-5469}, doi = {10.1101/gr.185579.114}, author = {Hoskins, Roger A and Carlson, Joseph W and Wan, Kenneth H and Park, Soo and Mendez, Ivonne and Galle, Samuel E and Booth, Benjamin W and Pfeiffer, Barret D and George, Reed A and Svirskas, Robert and Krzywinski, Martin and Schein, Jacqueline and Accardo, Maria Carmela and Damia, Elisabetta and Messina, Giovanni and Mendez-Lago, Maria and de Pablos, Beatriz and Demakova, Olga V and Andreyeva, Evgeniya N and Boldyreva, Lidiya V and Marra, Marco and Carvalho, A Bernardo and Dimitri, Patrizio and Villasante, Alfredo and Zhimulev, Igor F and Rubin, Gerald M and Karpen, Gary H and Celniker, Susan E} } @article {46698, title = {Reminiscences on my life with RNA: a self-indulgent perspective.}, journal = {RNA}, volume = {21}, year = {2015}, month = {2015 Apr}, pages = {508-9}, keywords = {Humans, Narration, RNA}, issn = {1469-9001}, doi = {10.1261/rna.050922.115}, author = {Singer, Robert H} } @article {46344, title = {Representing "stuff" in visual cortex.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015 Jan 27}, pages = {942-3}, issn = {1091-6490}, doi = {10.1073/pnas.1423496112}, author = {Ziemba, Corey M and Freeman, Jeremy} } @article {47182, title = {Reward signal in a recurrent circuit drives appetitive long-term memory formation.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Nov 18}, abstract = {

Dopamine signals reward in animal brains. A single presentation of a sugar reward to Drosophila activates distinct subsets of dopamine neurons that independently induce short- and long-term olfactory memories (STM and LTM, respectively). In this study, we show that a recurrent reward circuit underlies the formation and consolidation of LTM. This feedback circuit is composed of a single class of reward-signaling dopamine neurons (PAM-α1) projecting to a restricted region of the mushroom body (MB), and a specific MB output cell type, MBON-α1, whose dendrites arborize that same MB compartment. Both MBON-α1 and PAM-α1 neurons are required during the acquisition and consolidation of appetitive LTM. MBON-α1 additionally mediates the retrieval of LTM, which is dependent on the dopamine receptor signaling in the MB α/β neurons. Our results suggest that a reward signal transforms a nascent memory trace into a stable LTM using a feedback circuit at the cost of memory specificity.

}, issn = {2050-084X}, doi = {10.7554/eLife.10719}, author = {Ichinose, Toshiharu and Aso, Yoshinori and Yamagata, Nobuhiro and Abe, Ayako and Rubin, Gerald M and Tanimoto, Hiromu} } @article {46185, title = {Rfam 12.0: updates to the RNA families database.}, journal = {Nucleic Acids Research}, volume = {43}, year = {2015}, month = {2015 Jan 28}, pages = {D130-7}, abstract = {

The Rfam database (available at http://rfam.xfam.org) is a collection of non-coding RNA families represented by manually curated sequence alignments, consensus secondary structures and annotation gathered from corresponding Wikipedia, taxonomy and ontology resources. In this article, we detail updates and improvements to the Rfam data and website for the Rfam 12.0 release. We describe the upgrade of our search pipeline to use Infernal 1.1 and demonstrate its improved homology detection ability by comparison with the previous version. The new pipeline is easier for users to apply to their own data sets, and we illustrate its ability to annotate RNAs in genomic and metagenomic data sets of various sizes. Rfam has been expanded to include 260 new families, including the well-studied large subunit ribosomal RNA family, and for the first time includes information on short sequence- and structure-based RNA motifs present within families.

}, issn = {1362-4962}, doi = {10.1093/nar/gku1063}, author = {Nawrocki, Eric P and Burge, Sarah W and Bateman, Alex and Daub, Jennifer and Eberhardt, Ruth Y and Eddy, Sean R and Floden, Evan W and Gardner, Paul P and Jones, Thomas A and Tate, John and Finn, Robert D} } @article {69343, title = {Robust circuit rhythms in small circuits arise from variable circuit components and mechanisms}, journal = {Current Opinion in Neurobiology}, volume = {31}, year = {2015}, month = {2015 Apr 1}, pages = {156-163}, abstract = {

Small central pattern generating circuits found in invertebrates have significant advantages for the study of the circuit mechanisms that generate brain rhythms. Experimental and computational studies of small oscillatory circuits reveal that similar rhythms can arise from disparate mechanisms. Animal-to-animal variation in the properties of single neurons and synapses may underly robust circuit performance, and can be revealed by perturbations. Neuromodulation can produce altered circuit performance but also ensure reliable circuit function.

}, issn = {0959-4388}, doi = {https://doi.org/10.1016/j.conb.2014.10.012}, url = {https://www.sciencedirect.com/science/article/pii/S0959438814002128}, author = {Eve Marder and Marie L Goeritz and Adriane G Otopalik} } @article {47956, title = {Robust estimation of self-exciting point process models with application to neuronal modeling.}, journal = {CoRR}, volume = {abs/1507.03955}, year = {2015}, abstract = {

We consider the problem of estimating discrete selfexciting point process models from limited binary observations, where the history of the process serves as the covariate. We analyze the performance of two classes of estimators, namely the {\textquoteleft}1-regularized maximum likelihood and greedy estimators, for a canonical self-exciting point process and characterize the sampling tradeoffs required for stable recovery in the non-asymptotic regime. Our results extend those of compressed sensing for linear and generalized linear models with i.i.d. covariates to point processes with highly inter-dependent covariates. We further provide simulation studies as well as application to real spiking data from mouse{\textquoteright}s lateral geniculate nucleus and ferret{\textquoteright}s retinal ganglion cells which agree with our theoretical predictions.

}, url = {http://arxiv.org/abs/1507.03955}, author = {Abbas Kazemipour and Min Wu and Behtash Babadi} } @article {47203, title = {The role of motion extrapolation in amphibian prey capture.}, journal = {The Journal of Neuroscience : the official journal of the Society for Neuroscience}, volume = {35}, year = {2015}, month = {2015 Nov 18}, pages = {15430-41}, abstract = {

UNLABELLED: Sensorimotor delays decouple behaviors from the events that drive them. The brain compensates for these delays with predictive mechanisms, but the efficacy and timescale over which these mechanisms operate remain poorly understood. Here, we assess how prediction is used to compensate for prey movement that occurs during visuomotor processing. We obtained high-speed video records of freely moving, tongue-projecting salamanders catching walking prey, emulating natural foraging conditions. We found that tongue projections were preceded by a rapid head turn lasting \~{}130 ms. This motor lag, combined with the \~{}100 ms phototransduction delay at photopic light levels, gave a \~{}230 ms visuomotor response delay during which prey typically moved approximately one body length. Tongue projections, however, did not significantly lag prey position but were highly accurate instead. Angular errors in tongue projection accuracy were consistent with a linear extrapolation model that predicted prey position at the time of tongue contact using the average prey motion during a \~{}175 ms period one visual latency before the head movement. The model explained successful strikes where the tongue hit the fly, and unsuccessful strikes where the fly turned and the tongue hit a phantom location consistent with the fly{\textquoteright}s earlier trajectory. The model parameters, obtained from the data, agree with the temporal integration and latency of retinal responses proposed to contribute to motion extrapolation. These results show that the salamander predicts future prey position and that prediction significantly improves prey capture success over a broad range of prey speeds and light levels.

SIGNIFICANCE STATEMENT: Neural processing delays cause actions to lag behind the events that elicit them. To cope with these delays, the brain predicts what will happen in the future. While neural circuits in the retina and beyond have been suggested to participate in such predictions, few behaviors have been explored sufficiently to constrain circuit function. Here we show that salamanders aim their tongues by using extrapolation to estimate future prey position, thereby compensating for internal delays from both visual and motor processing. Predictions made just before a prey turn resulted in the tongue being projected to a position consistent with the prey{\textquoteright}s pre-turn trajectory. These results define the computations and operating regimen for neural circuits that predict target motion.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3189-15.2015}, author = {Borghuis, Bart G and Leonardo, Anthony} } @article {46743, title = {Role of the subesophageal zone in sensorimotor control of orientation in Drosophila larva.}, journal = {Current Biology}, volume = {25}, year = {2015}, month = {2015 May 6}, pages = {1448-60}, abstract = {

Chemotaxis is a powerful paradigm to investigate how nervous systems represent and integrate changes in sensory signals to direct navigational decisions. In the Drosophila melanogaster larva, chemotaxis mainly consists of an alternation of distinct behavioral modes: runs and directed turns. During locomotion, turns are triggered by the integration of temporal changes in the intensity of the stimulus. Upon completion of a turning maneuver, the direction of motion is typically realigned toward the odor gradient. While the anatomy of the peripheral olfactory circuits and the locomotor system of the larva are reasonably well documented, the neural circuits connecting the sensory neurons to the motor neurons remain unknown. We combined a loss-of-function behavioral screen with optogenetics-based clonal gain-of-function manipulations to identify neurons that are necessary and sufficient for the initiation of reorientation maneuvers in odor gradients. Our results indicate that a small subset of neurons residing in the subesophageal zone controls the rate of transition from runs to turns-a premotor function compatible with previous observations made in other invertebrates. After having shown that this function pertains to the processing of inputs from different sensory modalities (olfaction, vision, thermosensation), we conclude that the subesophageal zone operates as a general premotor center that regulates the selection of different behavioral programs based on the integration of sensory stimuli. The present analysis paves the way for a systematic investigation of the neural computations underlying action selection in a miniature brain amenable to genetic manipulations.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2015.04.016}, author = {Tastekin, Ibrahim and Riedl, Julia and Schilling-Kurz, Verena and Gomez-Marin, Alex and Truman, James W and Louis, Matthieu} } @proceedings {47288, title = {Sample complexity of learning Mahalanobis distance metrics.}, volume = {28}, year = {2015}, month = {2015-Jul }, address = {Montreal, Canada}, abstract = {

Metric learning seeks a transformation of the feature space that enhances prediction quality for a given task. In this work we provide PAC-style sample complexity rates for supervised metric learning. We give matching lower- and upper-bounds showing that sample complexity scales with the representation dimension when no assumptions are made about the underlying data distribution. In addition, by leveraging the structure of the data distribution, we provide rates fine-tuned to a specific notion of the intrinsic complexity of a given dataset, allowing us to relax the dependence on representation dimension. We show both theoretically and empirically that augmenting the metric learning optimization criterion with a simple norm-based regularization is important and can help adapt to a dataset{\textquoteright}s intrinsic complexity yielding better generalization, thus partly explaining the empirical success of similar\ regularizations\ reported in previous works.

}, keywords = {metric learning, sample complexity}, url = {https://papers.nips.cc/paper/5811-sample-complexity-of-learning-mahalanobis-distance-metrics}, author = {Verma, Nakul and Branson, Kristin M} } @article {47615, title = {Selective visualization of GLUT4 storage vesicles and associated Rab proteins using IRAP-pHluorin.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1298}, year = {2015}, month = {2015}, pages = {173-9}, abstract = {

Fluorescence microscopy and fluorescent protein (FP)-tagged GLUT4 molecule have been great tools to characterize GLUT4 localization and dynamics inside the cell. However, it was difficult to distinguish GLUT4 storage vesicles (GSVs) from other intracellular compartments containing GLUT4 in live cells. Here, we describe the use of IRAP-pHluorin and total internal reflection fluorescence (TIRF) microscopy to selectively visualize GSVs and Rab proteins that associate with GSVs. This assay is also valuable to further defining GSV identity by unraveling other GSV-associated proteins.

}, keywords = {3T3-L1 Cells, Adipocytes, Animals, Cattle, Cell Membrane, Cystinyl Aminopeptidase, Exocytosis, Glucose Transporter Type 4, Green Fluorescent Proteins, Image Processing, Computer-Assisted, Insulin, Mice, Microscopy, Fluorescence, rab GTP-Binding Proteins, Transfection}, issn = {1940-6029}, doi = {10.1007/978-1-4939-2569-8_14}, author = {Chen, Yu and Lippincott-Schwartz, Jennifer} } @article {46454, title = {A sensitive and robust enzyme kinetic experiment using microplates and fluorogenic ester substrates}, journal = {Journal of Chemical Education}, volume = {92}, year = {2015}, month = {2015 Feb}, pages = {385-8}, abstract = {

Enzyme kinetics measurements are a standard component of undergraduate biochemistry laboratories. The combination of serine hydrolases and fluorogenic enzyme substrates provides a rapid, sensitive, and general method for measuring enzyme kinetics in an undergraduate biochemistry laboratory. In this method, the kinetic activity of multiple protein variants is determined in parallel using a microplate reader, multichannel pipets, serial dilutions, and fluorogenic ester substrates. The utility of this methodology is illustrated by the measurement of differential enzyme activity in microplate volumes in triplicate with small protein samples and low activity enzyme variants. Enzyme kinetic measurements using fluorogenic substrates are, thus, adaptable for use with student-purified enzyme variants and for comparative enzyme kinetics studies. The rapid setup and analysis of these kinetic experiments not only provides advanced undergraduates with experience in a fundamental biochemical technique, but also provides the adaptability for use in inquiry-based laboratories.

}, issn = {0021-9584}, doi = {10.1021/ed500452f}, author = {Johnson, R. Jeremy and Hoops, Geoffrey C. and Savas, Christopher J. and Kartje, Zachary and Lavis, Luke D} } @article {46187, title = {Sensory determinants of behavioral dynamics in Drosophila thermotaxis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015 Jan 13}, pages = {E220-9}, abstract = {

Complex animal behaviors are built from dynamical relationships between sensory inputs, neuronal activity, and motor outputs in patterns with strategic value. Connecting these patterns illuminates how nervous systems compute behavior. Here, we study Drosophila larva navigation up temperature gradients toward preferred temperatures (positive thermotaxis). By tracking the movements of animals responding to fixed spatial temperature gradients or random temperature fluctuations, we calculate the sensitivity and dynamics of the conversion of thermosensory inputs into motor responses. We discover three thermosensory neurons in each dorsal organ ganglion (DOG) that are required for positive thermotaxis. Random optogenetic stimulation of the DOG thermosensory neurons evokes behavioral patterns that mimic the response to temperature variations. In vivo calcium and voltage imaging reveals that the DOG thermosensory neurons exhibit activity patterns with sensitivity and dynamics matched to the behavioral response. Temporal processing of temperature variations carried out by the DOG thermosensory neurons emerges in distinct motor responses during thermotaxis.

}, issn = {1091-6490}, doi = {10.1073/pnas.1416212112}, author = {Klein, Mason and Afonso, Bruno and Vonner, Ashley J and Hernandez-Nunez, Luis and Berck, Matthew and Tabone, Christopher J and Kane, Elizabeth A and Pieribone, Vincent A and Nitabach, Michael N and Cardona, Albert and Zlatic, Marta and Sprecher, Simon G and Gershow, Marc and Garrity, Paul A and Samuel, Aravinthan D T} } @article {46285, title = {Short-term plasticity based network model of place cells dynamics.}, journal = {Hippocampus}, volume = {25}, year = {2015}, month = {2015 Jan}, pages = {94-105}, abstract = {

Rodent hippocampus exhibits strikingly different regimes of population activity in different behavioral states. During locomotion, hippocampal activity oscillates at theta frequency (5-12 Hz) and cells fire at specific locations in the environment, the place fields. As the animal runs through a place field, spikes are emitted at progressively earlier phases of the theta cycles. During immobility, hippocampus exhibits sharp irregular bursts of activity, with occasional rapid orderly activation of place cells expressing a possible trajectory of the animal. The mechanisms underlying this rich repertoire of dynamics are still unclear. We developed a novel recurrent network model that accounts for the observed phenomena. We assume that the network stores a map of the environment in its recurrent connections, which are endowed with short-term synaptic depression. We show that the network dynamics exhibits two different regimes that are similar to the experimentally observed population activity states in the hippocampus. The operating regime can be solely controlled by external inputs. Our results suggest that short-term synaptic plasticity is a potential mechanism contributing to shape the population activity in hippocampus.

}, issn = {1098-1063}, doi = {10.1002/hipo.22355}, author = {Romani, Sandro and Tsodyks, Misha} } @article {46863, title = {Single molecules, cells, and super-resolution optics (Nobel Lecture).}, journal = {Angewandte Chemie (International Edition in English)}, year = {2015}, month = {2015 Jun 18}, abstract = {

The resolution of a microscope is determined by the diffraction limit in classical microscopy, whereby objects that are separated by half a wavelength can no longer be visually separated. To go below the diffraction limit required several tricks and discoveries. In his Nobel Lecture, E. Betzig describes the developments that have led to modern super high-resolution microscopy.

}, issn = {1521-3773}, doi = {10.1002/anie.201501003}, author = {Betzig, Eric} } @article {48315, title = {Single-molecule insights into mRNA dynamics in neurons.}, journal = {Trends in Cell Biology}, volume = {25}, year = {2015}, month = {2015 Aug}, pages = {468-75}, abstract = {

Targeting of mRNAs to neuronal dendrites and axons plays an integral role in intracellular signaling, development, and synaptic plasticity. Single-molecule imaging of mRNAs in neurons and brain tissue has led to enhanced understanding of mRNA dynamics. Here we discuss aspects of mRNA regulation as revealed by single-molecule detection, which has led to quantitative analyses of mRNA diversity, localization, transport, and translation. These exciting new discoveries propel our understanding of the life of an mRNA in a neuron and how its activity is regulated at the single-molecule level.

}, keywords = {Animals, Humans, In Situ Hybridization, Fluorescence, Intracellular Membranes, Neuronal Plasticity, Neurons, Protein Biosynthesis, RNA, Messenger, Signal Transduction}, issn = {1879-3088}, doi = {10.1016/j.tcb.2015.05.005}, author = {Buxbaum, Adina R and Yoon, Young J and Singer, Robert H and Park, Hye Yoon} } @article {46798, title = {Solving the third-shift problem in ic piracy with test-aware logic locking.}, journal = {IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems}, volume = {34}, year = {2015}, month = {2015 Jun}, pages = {961-71}, abstract = {

The increasing IC manufacturing cost encourages a business model where design houses outsource IC fabrication to remote foundries. Despite cost savings, this model exposes design houses to IC piracy as remote foundries can manufacture in excess to sell on the black market. Recent efforts in digital hardware security aim to thwart piracy by using XOR-based chip locking, cryptography, and active metering. To counter direct attacks and lower the exposure of unlocked circuits to the foundry, we introduce a multiplexor-based locking strategy that preserves test response allowing IC testing by an untrusted party before activation. We demonstrate a simple yet effective attack against a locked circuit that does not preserve test response, and validate the effectiveness of our locking strategy on IWLS 2005 benchmarks.

}, doi = {10.1109/TCAD.2015.2404876}, author = {Plaza, Stephen M and Markov, Igor L} } @article {46942, title = {A specific component of the evoked potential mirrors phasic dopamine neuron activity during conditioning.}, journal = {The Journal of Neuroscience : the official journal of the Society for Neuroscience}, volume = {35}, year = {2015}, month = {2015 Jul 22}, pages = {10451-9}, abstract = {

UNLABELLED: Midbrain dopamine (DA) neurons are thought to be a critical node in the circuitry that mediates reward learning. DA neurons receive diverse inputs from regions distributed throughout the neuraxis from frontal neocortex to the mesencephalon. While a great deal is known about changes in the activity of individual DA neurons during learning, much less is known about the functional changes in the microcircuits in which DA neurons are embedded. Here we used local field potentials recorded from the midbrain of behaving mice to show that the midbrain evoked potential (mEP) faithfully reflects the temporal and spatial structure of the phasic response of midbrain neuron populations during conditioning. By comparing the mEP to simultaneously recorded single units, we identified specific components of the mEP that corresponded to phasic DA and non-DA responses to salient stimuli. The DA component of the mEP emerged with the acquisition of a conditioned stimulus, was extinguished following changes in reinforcement contingency, and could be inhibited by pharmacological manipulations that attenuate the phasic responses of DA neurons. In contrast to single-unit recordings, the mEP permitted relatively dense sampling of the midbrain circuit during conditioning and thus could be used to reveal the spatiotemporal structure of multiple intermingled midbrain circuits. Finally, the mEP response was stable for months and thus provides a new approach to study long-term changes in the organization of ventral midbrain microcircuits during learning.

SIGNIFICANCE STATEMENT: Neurons that synthesize and release the neurotransmitter dopamine play a critical role in voluntary reward-seeking behavior. Much of our insight into the function of dopamine neurons comes from recordings of individual cells in behaving animals; however, it is notoriously difficult to record from dopamine neurons due to their sparsity and depth, as well as the presence of intermingled non-dopaminergic neurons. Here we show that much of the information that can be learned from recordings of individual dopamine and non-dopamine neurons is also revealed by changes in specific components of the local field potential. This technique provides an accessible measurement that could prove critical to our burgeoning understanding of the molecular, functional, and anatomical diversity of neuron populations in the midbrain.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4096-14.2015}, author = {Pan, Wei-Xing and Dudman, Joshua T} } @article {47085, title = {A specific E3 ligase/deubiquitinase pair modulates TBP protein levels during muscle differentiation.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015}, abstract = {

TFIID-a complex of TATA-binding protein (TBP) and TBP-associated factors (TAFs)-is a central component of the Pol II promoter recognition apparatus. Recent studies have revealed significant downregulation of TFIID subunits in terminally differentiated myocytes, hepatocytes and adipocytes. Here, we report that TBP protein levels are tightly regulated by the ubiquitin-proteasome system. Using an in vitro ubiquitination assay coupled with biochemical fractionation, we identified Huwe1 as an E3 ligase targeting TBP for K48-linked ubiquitination and proteasome-mediated degradation. Upregulation of Huwe1 expression during myogenesis induces TBP degradation and myotube differentiation. We found that Huwe1 activity on TBP is antagonized by the deubiquitinase USP10, which protects TBP from degradation. Thus, modulating the levels of both Huwe1 and USP10 appears to fine-tune the requisite degradation of TBP during myogenesis. Together, our study unmasks a previously unknown interplay between an E3 ligase and a deubiquitinating enzyme regulating TBP levels during cellular differentiation.

}, issn = {2050-084X}, doi = {10.7554/eLife.08536}, author = {Li, Li and Martinez, Silvia Sanchez and Hu, Wenxin and Liu, Zhe and Tjian, Robert} } @article {46700, title = {Specific interaction of KIF11 with ZBP1 regulates the transport of β-actin mRNA and cell motility.}, journal = {Journal of Cell Science}, volume = {128}, year = {2015}, month = {2015 Mar 1}, pages = {1001-10}, abstract = {

ZBP1-modulated localization of β-actin mRNA enables a cell to establish polarity and structural asymmetry. Although the mechanism of β-actin mRNA localization has been well established, the underlying mechanism of how a specific molecular motor contributes to the transport of the ZBP1 (also known as IGF2BP1) complex in non-neuronal cells remains elusive. In this study, we report the isolation and identification of KIF11, a microtubule motor, which physically interacts with ZBP1 and is a component of β-actin messenger ribonucleoprotein particles (mRNPs). We show that KIF11 colocalizes with the β-actin mRNA, and the ability of KIF11 to transport β-actin mRNA is dependent on ZBP1. We characterize the corresponding regions of ZBP1 and KIF11 that mediate the interaction of the two proteins in vitro and in vivo. Disruption of the in vivo interaction of KIF11 with ZBP1 delocalizes β-actin mRNA and affects cell migration. Our study reveals a molecular mechanism by which a particular microtubule motor mediates the transport of an mRNP through direct interaction with an mRNA-binding protein.

}, issn = {1477-9137}, doi = {10.1242/jcs.161679}, author = {Song, Tingting and Zheng, Yi and Wang, Yarong and Katz, Zachary and Liu, Xin and Chen, Shaoying and Singer, Robert H and Gu, Wei} } @article {48831, title = {State-dependent population coding in primary auditory cortex.}, journal = {The Journal of Neuroscience : the official journal of the Society for Neuroscience}, volume = {35}, year = {2015}, month = {2015 Feb 04}, pages = {2058-73}, abstract = {

Sensory function is mediated by interactions between external stimuli and intrinsic cortical dynamics that are evident in the modulation of evoked responses by cortical state. A number of recent studies across different modalities have demonstrated that the patterns of activity in neuronal populations can vary strongly between synchronized and desynchronized cortical states, i.e., in the presence or absence of intrinsically generated up and down states. Here we investigated the impact of cortical state on the population coding of tones and speech in the primary auditory cortex (A1) of gerbils, and found that responses were qualitatively different in synchronized and desynchronized cortical states. Activity in synchronized A1 was only weakly modulated by sensory input, and the spike patterns evoked by tones and speech were unreliable and constrained to a small range of patterns. In contrast, responses to tones and speech in desynchronized A1 were temporally precise and reliable across trials, and different speech tokens evoked diverse spike patterns with extremely weak noise correlations, allowing responses to be decoded with nearly perfect accuracy. Restricting the analysis of synchronized A1 to activity within up states yielded similar results, suggesting that up states are not equivalent to brief periods of desynchronization. These findings demonstrate that the representational capacity of A1 depends strongly on cortical state, and suggest that cortical state should be considered as an explicit variable in all studies of sensory processing.

}, keywords = {Animals, Auditory Cortex, Cortical Synchronization, Evoked Potentials, Auditory, Gerbillinae, Male, Neurons}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3318-14.2015}, author = {Pachitariu, Marius and Lyamzin, Dmitry R and Sahani, Maneesh and Lesica, Nicholas A} } @article {46379, title = {Stimulation-evoked Ca2+ signals in astrocytic processes at hippocampal CA3-CA1 synapses of adult mice are modulated by glutamate and ATP.}, journal = {The Journal of Neuroscience}, volume = {35}, year = {2015}, month = {2015 Feb 18}, pages = {3016-21}, abstract = {

To date, it has been difficult to reveal physiological Ca(2+) events occurring within the fine astrocytic processes of mature animals. The objective of the study was to explore whether neuronal activity evokes astrocytic Ca(2+) signals at glutamatergic synapses of adult mice. We stimulated the Schaffer collateral/commissural fibers in acute hippocampal slices from adult mice transduced with the genetically encoded Ca(2+) indicator GCaMP5E driven by the glial fibrillary acidic protein promoter. Two-photon imaging revealed global stimulation-evoked astrocytic Ca(2+) signals with distinct latencies, rise rates, and amplitudes in fine processes and somata. Specifically, the Ca(2+) signals in the processes were faster and of higher amplitude than those in the somata. A combination of P2 purinergic and group I/II metabotropic glutamate receptor (mGluR) antagonists reduced the amplitude of the Ca(2+) transients by 30-40\% in both astrocytic compartments. Blockage of the mGluRs alone only modestly reduced the magnitude of the stimulation-evoked Ca(2+) signals in processes and failed to affect the somatic Ca(2+) response. Local application of group I or I/II mGluR agonists or adenosine triphosphate (ATP) elicited global astrocytic Ca(2+) signals that mimicked the stimulation-evoked astrocytic Ca(2+) responses. We conclude that stimulation-evoked Ca(2+) signals in astrocytic processes at CA3-CA1 synapses of adult mice (1) differ from those in astrocytic somata and (2) are modulated by glutamate and ATP.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3319-14.2015}, author = {Tang, Wannan and Szokol, Karolina and Jensen, Vidar and Enger, Rune and Trivedi, Chintan A and Hvalby, {\O}ivind and Helm, P Johannes and Looger, Loren L and Sprengel, Rolf and Nagelhus, Erlend A} } @article {47133, title = {Stochastic electrotransport selectively enhances the transport of highly electromobile molecules.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015 Nov 2}, pages = {E6274-83}, abstract = {

Nondestructive chemical processing of porous samples such as fixed biological tissues typically relies on molecular diffusion. Diffusion into a porous structure is a slow process that significantly delays completion of chemical processing. Here, we present a novel electrokinetic method termed stochastic electrotransport for rapid nondestructive processing of porous samples. This method uses a rotational electric field to selectively disperse highly electromobile molecules throughout a porous sample without displacing the low-electromobility molecules that constitute the sample. Using computational models, we show that stochastic electrotransport can rapidly disperse electromobile molecules in a porous medium. We apply this method to completely clear mouse organs within 1{\textendash}3 days and to stain them with nuclear dyes, proteins, and antibodies within 1 day. Our results demonstrate the potential of stochastic electrotransport to process large and dense tissue samples that were previously infeasible in time when relying on diffusion.

}, doi = {10.1073/pnas.1510133112}, author = {Kim, Sung-Yon and Cho, Jae Hun and Murray, Evan and Bakh, Naveed and Choi, Heejin and Ohn, Kimberly and Ruelas, Luzdary and Hubbert, Austin and McCue, Meg and Vassallo, Sara L and Keller, Philipp J and Chung, Kwanghun} } @article {46886, title = {Structural basis for the antipolymer activity of Hb ζ22βsζ2βs2 trapped in a tense conformation.}, journal = {Journal of Molecular Structure}, volume = {1099}, year = {2015}, month = {2015 Nov}, pages = {99-107}, abstract = {

The phenotypical severity of sickle cell disease (SCD) can be mitigated by modifying mutant hemoglobin S (Hb S, Hb α2β2s) to contain embryonic ζ globin in place of adult α-globin subunits (Hb ζ2β2s). Crystallographical analyses of liganded Hb ζζ2β2s, though, demonstrate a tense (T-state) quaternary structure that paradoxically predicts its participation in--rather than its exclusion from--pathological deoxyHb S polymers. We resolved this structure-function conundrum by examining the effects of α\ {\textrightarrow}\ ζ exchange on the characteristics of specific amino acids that mediate sickle polymer assembly. Superposition analyses of the βs subunits of T-state deoxyHb α2β2s and T-state CO-liganded Hb ζ2β2s reveal significant displacements of both mutant βsVal6 and conserved β-chain contact residues, predicting weakening of corresponding polymer-stabilizing interactions. Similar comparisons of the α- and ζ-globin subunits implicate four amino acids that are either repositioned or undergo non-conservative substitution, abrogating critical polymer contacts. CO-Hb ζ2βs2 additionally exhibits a unique trimer-of-heterotetramers crystal packing that is sustained by novel intermolecular interactions involving the pathological βsVal6, contrasting sharply with the classical double-stranded packing of deoxyHb S. Finally, the unusually large buried solvent-accessible surface area for CO-Hb ζ2β2s suggests that it does not co-assemble with deoxyHb S in\ vivo \ . In sum, the antipolymer activities of Hb ζ2β2s appear to arise from both repositioning and replacement of specific α- and βs-chain residues, favoring an alternate T-state solution structure that is excluded from pathological deoxyHb S polymers. These data account for the antipolymer activity of Hb ζ2β2s, and recommend the utility of SCD therapeutics that capitalize on α-globin exchange strategies.

}, issn = {0022-2860}, doi = {10.1016/j.molstruc.2015.06.047}, author = {Safo, Martin K and Ko, Tzu-Ping and Schreiter, Eric R and Russell, J. Eric} } @article {47241, title = {Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Oct 06}, abstract = {

Adenosine triphosphate (ATP), the chemical energy currency of biology, is synthesized in eukaryotic cells primarily by the mitochondrial ATP synthase. ATP synthases operate by a rotary catalytic mechanism where proton translocation through the membrane-inserted FO region is coupled to ATP synthesis in the catalytic F1 region via rotation of a central rotor subcomplex. We report here single particle electron cryomicroscopy (cryo-EM) analysis of the bovine mitochondrial ATP synthase. Combining cryo-EM data with bioinformatic analysis allowed us to determine the fold of the a subunit, suggesting a proton translocation path through the FO region that involves both the a and b subunits. 3D classification of images revealed seven distinct states of the enzyme that show different modes of bending and twisting in the intact ATP synthase. Rotational fluctuations of the c8-ring within the FO region support a Brownian ratchet mechanism for proton-translocation-driven rotation in ATP synthases.

}, issn = {2050-084X}, doi = {10.7554/eLife.10180}, author = {Zhou, Anna and Rohou, Alexis and Schep, Daniel G and Bason, John V and Montgomery, Martin G and Walker, John E and Grigorieff, Nikolaus and Rubinstein, John L} } @article {46923, title = {Structure of a designed tetrahedral protein assembly variant engineered to have improved soluble expression.}, journal = {Protein Science}, volume = {24}, year = {2015}, month = {2015 Jul 15}, pages = {1695-701}, abstract = {

We recently reported the development of a computational method for the design of co-assembling, multi-component protein nanomaterials. While four such materials were validated at high-resolution by X-ray crystallography, low yield of soluble protein prevented X-ray structure determination of a fifth designed material, T33-09. Here we report the design and crystal structure of T33-31, a variant of T33-09 with improved soluble yield resulting from redesign efforts focused on mutating solvent-exposed side chains to charged amino acids. The structure is found to match the computational design model with atomic-level accuracy, providing further validation of the design approach and demonstrating a simple and potentially general means of improving the yield of designed protein nanomaterials. This article is protected by copyright. All rights reserved.

}, issn = {1469-896X}, doi = {10.1002/pro.2748}, author = {Bale, Jacob B and Park, Rachel U and Liu, Yuxi and Gonen, Shane and Gonen, Tamir and Cascio, Duilio and King, Neil P and Yeates, Todd O and Baker, David} } @article {48316, title = {Structure of the L protein of vesicular stomatitis virus from electron cryomicroscopy.}, journal = {Cell}, volume = {162}, year = {2015}, month = {2015 Jul 16}, pages = {314-27}, abstract = {

The large (L) proteins of non-segmented, negative-strand RNA viruses, a group that includes Ebola and rabies viruses, catalyze RNA-dependent RNA polymerization with viral ribonucleoprotein as template, a non-canonical sequence of capping and methylation reactions, and polyadenylation of viral messages. We have determined by electron cryomicroscopy the structure of the vesicular stomatitis virus (VSV) L protein. The density map, at a resolution of 3.8 {\r A}, has led to an atomic model for nearly all of the 2109-residue polypeptide chain, which comprises three enzymatic domains (RNA-dependent RNA polymerase [RdRp], polyribonucleotidyl transferase [PRNTase], and methyltransferase) and two structural domains. The RdRp resembles the corresponding enzymatic regions of dsRNA virus polymerases and influenza virus polymerase. A loop from the PRNTase (capping) domain projects into the catalytic site of the RdRp, where it appears to have the role of a priming loop and to couple product elongation to large-scale conformational changes in L.

}, keywords = {Cryoelectron Microscopy, DNA-Directed RNA Polymerases, Models, Molecular, Protein Structure, Tertiary, Sequence Homology, Amino Acid, Transcription, Genetic, Vesicular stomatitis Indiana virus, Viral Proteins}, issn = {1097-4172}, doi = {10.1016/j.cell.2015.06.018}, author = {Liang, Bo and Li, Zongli and Jenni, Simon and Rahmeh, Amal A and Morin, Benjamin M and Grant, Timothy and Grigorieff, Nikolaus and Harrison, Stephen C and Whelan, Sean P J} } @article {47031, title = {Structure of the toxic core of α-synuclein from invisible crystals.}, journal = {Nature}, volume = {525}, year = {2015}, month = {2015 Sep 9}, pages = {486-90}, abstract = {

The protein α-synuclein is the main component of Lewy bodies, the neuron-associated aggregates seen in Parkinson disease and other neurodegenerative pathologies. An 11-residue segment, which we term NACore, appears to be responsible for amyloid formation and cytotoxicity of human α-synuclein. Here we describe crystals of NACore that have dimensions smaller than the wavelength of visible light and thus are invisible by optical microscopy. As the crystals are thousands of times too small for structure determination by synchrotron X-ray diffraction, we use micro-electron diffraction to determine the structure at atomic resolution. The 1.4 {\r A} resolution structure demonstrates that this method can determine previously unknown protein structures and here yields, to our knowledge, the highest resolution achieved by any cryo-electron microscopy method to date. The structure exhibits protofibrils built of pairs of face-to-face β-sheets. X-ray fibre diffraction patterns show the similarity of NACore to toxic fibrils of full-length α-synuclein. The NACore structure, together with that of a second segment, inspires a model for most of the ordered portion of the toxic, full-length α-synuclein fibril, presenting opportunities for the design of inhibitors of α-synuclein fibrils.

}, issn = {1476-4687}, doi = {10.1038/nature15368}, author = {Rodriguez, Jose A and Ivanova, Magdalena I and Sawaya, Michael R and Cascio, Duilio and Reyes, Francis E and Shi, Dan and Sangwan, Smriti and Guenther, Elizabeth L and Johnson, Lisa M and Zhang, Meng and Jiang, Lin and Arbing, Mark A and Nannenga, Brent L and Hattne, Johan and Whitelegge, Julian and Brewster, Aaron S and Messerschmidt, Marc and Boutet, S{\'e}bastien and Sauter, Nicholas K and Gonen, Tamir and Eisenberg, David S} } @article {47039, title = {A subset of serotonergic neurons evokes hunger in adult Drosophila.}, journal = {Current Biology : CB}, volume = {25}, year = {2015}, month = {2015 Sep 2}, pages = {2435-40}, abstract = {

Hunger is a complex motivational state that drives multiple behaviors. The sensation of hunger is caused by an imbalance between energy intake and expenditure. One immediate response to hunger is increased food consumption. Hunger also modulates behaviors related to food seeking such as increased locomotion and enhanced sensory sensitivity in both insects [1-5] and vertebrates [6, 7]. In addition, hunger can promote the expression of food-associated memory [8, 9]. Although progress is being made [10], how hunger is represented in the brain and how it coordinates these behavioral responses is not fully understood in any system. Here, we use Drosophila melanogaster to identify neurons encoding hunger. We found a small group of neurons that, when activated, induced a fed fly to eat as though it were starved, suggesting that these neurons are downstream of the metabolic regulation of hunger. Artificially activating these neurons also promotes appetitive memory performance in sated flies, indicating that these neurons are not simply feeding command neurons but likely play a more general role in encoding hunger. We determined that the neurons relevant for the feeding effect are serotonergic and project broadly within the brain, suggesting a possible mechanism for how various responses to hunger are coordinated. These findings extend our\ understanding of the neural circuitry that drives feeding and enable future exploration of how state influences neural activity within this circuit.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2015.08.005}, author = {Albin, Stephanie D and Kaun, Karla R and Knapp, Jon-Michael and Chung, Phuong and Heberlein, Ulrike and Simpson, Julie H} } @article {47204, title = {Sweet and bitter taste in the brain of awake behaving animals.}, journal = {Nature}, volume = {527}, year = {2015}, month = {2015 Nov 26}, pages = {512-5}, abstract = {

Taste is responsible for evaluating the nutritious content of food, guiding essential appetitive behaviours, preventing the ingestion of toxic substances, and helping to ensure the maintenance of a healthy diet. Sweet and bitter are two of the most salient sensory percepts for humans and other animals; sweet taste allows the identification of energy-rich nutrients whereas bitter warns against the intake of potentially noxious chemicals. In mammals, information from taste receptor cells in the tongue is transmitted through multiple neural stations to the primary gustatory cortex in the brain. Recent imaging studies have shown that sweet and bitter are represented in the primary gustatory cortex by neurons organized in a spatial map, with each taste quality encoded by distinct cortical fields. Here we demonstrate that by manipulating the brain fields representing sweet and bitter taste we directly control an animal{\textquoteright}s internal representation, sensory perception, and behavioural actions. These results substantiate the segregation of taste qualities in the cortex, expose the innate nature of appetitive and aversive taste responses, and illustrate the ability of gustatory cortex to recapitulate complex behaviours in the absence of sensory input.

}, keywords = {Animals, Appetitive Behavior, Avoidance Learning, Brain Mapping, Cerebral Cortex, Discrimination (Psychology), Male, Mice, Mice, Inbred C57BL, Optogenetics, Stereotaxic Techniques, Taste, Taste Perception, Wakefulness}, issn = {1476-4687}, doi = {10.1038/nature15763}, author = {Peng, Yueqing and Gillis-Smith, Sarah and Jin, Hao and Tr{\"a}nkner, Dimitri and Ryba, Nicholas J P and Zuker, Charles S} } @article {47152, title = {Synaptic circuits and their variations within different columns in the visual system of Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015 Nov 3}, pages = {13711-6}, abstract = {

We reconstructed the synaptic circuits of seven columns in the second neuropil or medulla behind the fly{\textquoteright}s compound eye. These neurons embody some of the most stereotyped circuits in one of the most miniaturized of animal brains. The reconstructions allow us, for the first time to our knowledge, to study variations between circuits in the medulla{\textquoteright}s neighboring columns. This variation in the number of synapses and the types of their synaptic partners has previously been little addressed because methods that visualize multiple circuits have not resolved detailed connections, and existing connectomic studies, which can see such connections, have not so far examined multiple reconstructions of the same circuit. Here, we address the omission by comparing the circuits common to all seven columns to assess variation in their connection strengths and the resultant rates of several different and distinct types of connection error. Error rates reveal that, overall, \<1\% of contacts are not part of a consensus circuit, and we classify those contacts that supplement (E+) or are missing from it (E-). Autapses, in which the same cell is both presynaptic and postsynaptic at the same synapse, are occasionally seen; two cells in particular, Dm9 and Mi1, form >=20-fold more autapses than do other neurons. These results delimit the accuracy of developmental events that establish and normally maintain synaptic circuits with such precision, and thereby address the operation of such circuits. They also establish a precedent for error rates that will be required in the new science of connectomics.

}, issn = {1091-6490}, doi = {10.1073/pnas.1509820112}, author = {Takemura, Shin-ya and Xu, C Shan and Lu, Zhiyuan and Rivlin, Patricia K and Parag, Toufiq and Olbris, Donald J and Plaza, Stephen and Zhao, Ting and Katz, William T and Umayam, Lowell and Weaver, Charlotte and Hess, Harald F and Horne, Jane Anne and Nunez-Iglesias, Juan and Aniceto, Roxanne and Chang, Lei-Ann and Lauchie, Shirley and Nasca, Ashley and Ogundeyi, Omotara and Sigmund, Christopher and Takemura, Satoko and Tran, Julie and Langille, Carlie and Le Lacheur, Kelsey and McLin, Sari and Shinomiya, Aya and Chklovskii, Dmitri B and Meinertzhagen, Ian A and Scheffer, Louis K} } @article {46887, title = {Synaptic Orb2A bridges memory acquisition and late memory consolidation in Drosophila.}, journal = {Cell Reports}, volume = {11}, year = {2015}, month = {2015 Jun 30}, pages = {1953-65}, abstract = {

To adapt to an ever-changing environment, animals consolidate some, but not all, learning experiences to long-term memory. In mammals, long-term memory consolidation often involves neural pathway reactivation hours after memory acquisition. It is not known whether this delayed-reactivation schema is\ common across the animal kingdom or how information is stored during the delay period. Here, we show\ that, during courtship suppression learning, Drosophila exhibits delayed long-term memory consolidation. We also show that the same class of dopaminergic neurons engaged earlier in memory acquisition is also both necessary and sufficient for delayed long-term memory consolidation. Furthermore, we present evidence that, during learning, the translational regulator Orb2A tags specific synapses of mushroom body neurons for later consolidation. Consolidation involves the subsequent recruitment of Orb2B and the activity-dependent synthesis of CaMKII. Thus, our results provide evidence for the role of a neuromodulated, synapse-restricted molecule bridging memory acquisition and long-term memory consolidation in a learning animal.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2015.05.037}, author = {Kr{\"u}ttner, Sebastian and Traunm{\"u}ller, Lisa and Dag, Ugur and Jandrasits, Katharina and Stepien, Barbara and Iyer, Nirmala and Fradkin, Lee G and Noordermeer, Jasprina N and Mensh, Brett D and Keleman, Krystyna} } @article {46697, title = {Synonymous modification results in high-fidelity gene expression of repetitive protein and nucleotide sequences.}, journal = {Genes \& Development}, volume = {29}, year = {2015}, month = {2015 Apr 15}, pages = {876-86}, abstract = {

Repetitive nucleotide or amino acid sequences are often engineered into probes and biosensors to achieve functional readouts and robust signal amplification. However, these repeated sequences are notoriously prone to aberrant deletion and degradation, impacting the ability to correctly detect and interpret biological functions. Here, we introduce a facile and generalizable approach to solve this often unappreciated problem by modifying the nucleotide sequences of the target mRNA to make them nonrepetitive but still functional ("synonymous"). We first demonstrated the procedure by designing a cassette of synonymous MS2 RNA motifs and tandem coat proteins for RNA imaging and showed a dramatic improvement in signal and reproducibility in single-RNA detection in live cells. The same approach was extended to enhancing the stability of engineered fluorescent biosensors containing a fluorescent resonance energy transfer (FRET) pair of fluorescent proteins on which a great majority of systems thus far in the field are based. Using the synonymous modification to FRET biosensors, we achieved correct expression of full-length sensors, eliminating the aberrant truncation products that often were assumed to be due to nonspecific proteolytic cleavages. Importantly, the biological interpretations of the sensor are significantly different when a correct, full-length biosensor is expressed. Thus, we show here a useful and generally applicable method to maintain the integrity of expressed genes, critical for the correct interpretation of probe readouts.

}, issn = {1549-5477}, doi = {10.1101/gad.259358.115}, author = {Wu, Bin and Miskolci, Veronika and Sato, Hanae and Tutucci, Evelina and Kenworthy, Charles A and Donnelly, Sara K and Yoon, Young J and Cox, Dianne and Singer, Robert H and Hodgson, Louis} } @article {47242, title = {Synthesis of a far-red photoactivatable silicon-containing rhodamine for super-resolution microscopy.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {55}, year = {2015}, month = {2015 Dec 11}, pages = {1723-7}, abstract = {

The rhodamine system is a flexible framework for building small-molecule fluorescent probes. Changing N-substitution patterns and replacing the xanthene oxygen with a dimethylsilicon moiety can shift the absorption and fluorescence emission maxima of rhodamine dyes to longer wavelengths. Acylation of the rhodamine nitrogen atoms forces the molecule to adopt a nonfluorescent lactone form, providing a convenient method to make fluorogenic compounds. Herein, we take advantage of all of these structural manipulations and describe a novel photoactivatable fluorophore based on a Si-containing analogue of Q-rhodamine. This probe is the first example of a "caged" Si-rhodamine, exhibits higher photon counts compared to established localization microscopy dyes, and is sufficiently red-shifted to allow multicolor imaging. The dye is a useful label for super-resolution imaging and constitutes a new scaffold for far-red fluorogenic molecules.

}, issn = {1521-3773}, doi = {10.1002/anie.201509649}, author = {Grimm, Jonathan B and Klein, Teresa and Kopek, Benjamin G and Shtengel, Gleb and Hess, Harald F and Sauer, Markus and Lavis, Luke D} } @article {46787, title = {Systematic imaging reveals features and changing localization of mRNAs in Drosophila development.}, journal = {Elife}, volume = {4}, year = {2015}, month = {2015}, abstract = {

mRNA localization is critical for eukaryotic cells and affects numerous transcripts, yet how cells regulate distribution of many mRNAs to their subcellular destinations is still unknown. We combined transcriptomics and systematic imaging to determine the tissue-specific expression and subcellular distribution of 5862 mRNAs during Drosophila oogenesis. mRNA localization is widespread in the ovary and detectable in all of its cell types-the somatic epithelial, the nurse cells, and the oocyte. Genes defined by a common RNA localization share distinct gene features and differ in expression level, 3{\textquoteright}UTR length and sequence conservation from unlocalized mRNAs. Comparison of mRNA localizations in different contexts revealed that localization of individual mRNAs changes over time in the oocyte and between ovarian and embryonic cell types. This genome scale image-based resource (Dresden Ovary Table, DOT, http://tomancak-srv1.mpi-cbg.de/DOT/main.html) enables the transition from mechanistic dissection of singular mRNA localization events towards global understanding of how mRNAs transcribed in the nucleus distribute in cells.

}, issn = {2050-084X}, doi = {10.7554/eLife.05003}, author = {Jambor, Helena and Surendranath, Vineeth and Kalinka, Alex T and Mejstrik, Pavel and Saalfeld, Stephan and Tomancak, Pavel} } @article {45792, title = {Theta sequences are essential for internally generated hippocampal firing fields.}, journal = {Nature Neuroscience}, volume = {18}, year = {2015}, month = {2015 Feb}, pages = {282-8}, abstract = {

Sensory cue inputs and memory-related internal brain activities govern the firing of hippocampal neurons, but which specific firing patterns are induced by either of the two processes remains unclear. We found that sensory cues guided the firing of neurons in rats on a timescale of seconds and supported the formation of spatial firing fields. Independently of the sensory inputs, the memory-related network activity coordinated the firing of neurons not only on a second-long timescale, but also on a millisecond-long timescale, and was dependent on medial septum inputs. We propose a network mechanism that might coordinate this internally generated firing. Overall, we suggest that two independent mechanisms support the formation of spatial firing fields in hippocampus, but only the internally organized system supports short-timescale sequential firing and episodic memory.

}, issn = {1546-1726}, doi = {10.1038/nn.3904}, author = {Wang, Yingxue and Romani, Sandro and Lustig, Brian and Leonardo, Anthony and Pastalkova, Eva} } @article {47266, title = {A three-camera imaging microscope for high-speed single-molecule tracking and super-resolution imaging in living cells.}, journal = {Proceedings of SPIE}, volume = {9550}, year = {2015}, month = {2015 Aug 21}, pages = {955008 }, abstract = {

Our aim is to develop quantitative single-molecule assays to study when and where molecules are interacting inside living cells and where enzymes are active. To this end we present a three-camera imaging microscope for fast tracking of multiple interacting molecules simultaneously, with high spatiotemporal resolution. The system was designed around an ASI RAMM frame using three separate tube lenses and custom multi-band dichroics to allow for enhanced detection efficiency. The frame times of the three Andor iXon Ultra EMCCD cameras are hardware synchronized to the laser excitation pulses of the three excitation lasers, such that the fluorophores are effectively immobilized during frame acquisitions and do not yield detections that are motion-blurred. Stroboscopic illumination allows robust detection from even rapidly moving molecules while minimizing bleaching, and since snapshots can be spaced out with varying time intervals, stroboscopic illumination enables a direct comparison to be made between fast and slow molecules under identical light dosage. We have developed algorithms that accurately track and co-localize multiple interacting biomolecules. The three-color microscope combined with our co-movement algorithms have made it possible for instance to simultaneously image and track how the chromosome environment affects diffusion kinetics or determine how mRNAs diffuse during translation. Such multiplexed single-molecule measurements at a high spatiotemporal resolution inside living cells will provide a major tool for testing models relating molecular architecture and biological dynamics.

}, doi = {10.1117/12.2190246}, author = {English, Brian P and Singer, Robert H} } @article {47183, title = {Three-dimensional tracking of plus-tips by lattice light-sheet microscopy permits the quantification of microtubule growth trajectories within the mitotic apparatus.}, journal = {Journal of Biomedical Optics}, volume = {20}, year = {2015}, month = {2015 Oct 1}, pages = {101206}, issn = {1560-2281}, doi = {10.1117/1.JBO.20.10.101206}, author = {Yamashita, Norio and Morita, Masahiko and Legant, Wesley R and Chen, Bi-Chang and Betzig, Eric and Yokota, Hideo and Mimori-Kiyosue, Yuko} } @article {46369, title = {Tracking surface glycans on live cancer cells with single-molecule sensitivity.}, journal = {Angewandte Chemie International Edition English}, volume = {54}, year = {2015}, month = {2015 Feb 2}, pages = {1765-9}, abstract = {

Using a combination of metabolically labeled glycans, a bioorthogonal copper(I)-catalyzed azide-alkyne cycloaddition, and the controlled bleaching of fluorescent probes conjugated to azide- or alkyne-tagged glycans, a sufficiently low spatial density of dye-labeled glycans was achieved, enabling dynamic single-molecule tracking and super-resolution imaging of N-linked sialic acids and O-linked N-acetyl galactosamine (GalNAc) on the membrane of live cells. Analysis of the trajectories of these dye-labeled glycans in mammary cancer cells revealed constrained diffusion of both N- and O-linked glycans, which was interpreted as reflecting the mobility of the glycan rather than to be caused by transient immobilization owing to spatial inhomogeneities on the plasma membrane. Stochastic optical reconstruction microscopy (STORM) imaging revealed the structure of dynamic membrane nanotubes.

}, issn = {1521-3773}, doi = {10.1002/anie.201407976}, author = {Jiang, Hao and English, Brian P and Hazan, Rachel B and Wu, Peng and Ovryn, Ben} } @article {68447, title = {A transcriptional reporter of intracellular Ca(2+) in Drosophila.}, journal = {Nat Neurosci}, volume = {18}, year = {2015}, month = {06/2015}, pages = {917-25}, abstract = {

Intracellular Ca(2+) is a widely used neuronal activity indicator. Here we describe a transcriptional reporter of intracellular Ca(2+) (TRIC) in Drosophila that uses a binary expression system to report Ca(2+)-dependent interactions between calmodulin and its target peptide. We found that in vitro assays predicted in vivo properties of TRIC and that TRIC signals in sensory systems depend on neuronal activity. TRIC was able to quantitatively monitor neuronal responses that changed slowly, such as those of neuropeptide F-expressing neurons to sexual deprivation and neuroendocrine pars intercerebralis cells to food and arousal. Furthermore, TRIC-induced expression of a neuronal silencer in nutrient-activated cells enhanced stress resistance, providing a proof of principle that TRIC can be used for circuit manipulation. Thus, TRIC facilitates the monitoring and manipulation of neuronal activity, especially those reflecting slow changes in physiological states that are poorly captured by existing methods. TRIC{\textquoteright}s modular design should enable optimization and adaptation to other organisms.

}, keywords = {Animals, Calcium, Calcium Signaling, Cells, Cultured, Drosophila, Molecular Sequence Data, Mutagenesis, Neural Pathways, Olfactory Pathways, Optic Lobe, Nonmammalian, Stress, Psychological, Synaptic Transmission, Visual Pathways}, issn = {1546-1726}, doi = {10.1038/nn.4016}, author = {Gao, Xiaojing J and Riabinina, Olena and Li, Jiefu and Potter, Christopher J and Clandinin, Thomas R and Luo, Liqun} } @article {47025, title = {The transgenic RNAi project at Harvard Medical School: resources and validation.}, journal = {Genetics}, volume = {201}, year = {2015}, month = {2015 Aug 28}, pages = {843-52}, abstract = {

To facilitate large scale functional studies in Drosophila, the Drosophila Transgenic RNAi Project (TRiP) at Harvard Medical School (HMS) was established along with several goals: developing efficient vectors for RNAi that work in all tissues, generating a genome scale collection of RNAi stocks with input from the community, distributing the lines as they are generated through existing stock centers, validating as many lines as possible using RT-qPCR and phenotypic analyses, and developing tools and web resources for identifying RNAi lines and retrieving existing information on their quality. With these goals in mind, here we describe in detail the various tools we developed and the status of the collection, which is currently comprised of 11,491 lines and covering 71\% of Drosophila genes. Data on the characterization of the lines either by RT-qPCR or phenotype is available on a dedicated web site, the RNAi Stock Validation and Phenotypes Project (RSVP; www.flyrnai.org/RSVP.html), and stocks are available from three stock centers, the Bloomington Drosophila Stock Center (USA), National Institute of Genetics (Japan), and TsingHua Fly Center (China).

}, issn = {1943-2631}, doi = {10.1534/genetics.115.180208}, author = {Perkins, L A and Holderbaum, L and Tao, R and Hu, Y and Sopko, R and McCall, K and Yang-Zhou, D and Flockhart, I and Binari, R and Shim, H-S and Miller, A and Housden, A and Foos, M and Randkelv, S and Kelley, C and Namgyal, P and Villalta, C and Liu, L-P and Jiang, X and Huan-Huan, Q and Xia, W and Fujiyama, A and Toyoda, A and Ayers, K and Blum, A and Czech, B and Neumuller, R and Yan, D and Cavallaro, A and Hibbard, K and Hall, D and Cooley, L and Hannon, G J and Lehmann, R and Parks, A and Mohr, S E and Ueda, R and Kondo, S and Ni, J-Q and Perrimon, Norbert} } @article {46533, title = {Translation. An RNA biosensor for imaging the first round of translation from single cells to living animals.}, journal = {Science}, volume = {347}, year = {2015}, month = {2015 Mar 20}, pages = {1367-671}, abstract = {

Analysis of single molecules in living cells has provided quantitative insights into the kinetics of fundamental biological processes; however, the dynamics of messenger RNA (mRNA) translation have yet to be addressed. We have developed a fluorescence microscopy technique that reports on the first translation events of individual mRNA molecules. This allowed us to examine the spatiotemporal regulation of translation during normal growth and stress and during Drosophila oocyte development. We have shown that mRNAs are not translated in the nucleus but translate within minutes after export, that sequestration within P-bodies regulates translation, and that oskar mRNA is not translated until it reaches the posterior pole of the oocyte. This methodology provides a framework for studying initiation of protein synthesis on single mRNAs in living cells.

}, issn = {1095-9203}, doi = {10.1126/science.aaa3380}, author = {Halstead, James M and Lionnet, Timoth{\'e}e and Wilbertz, Johannes H and Wippich, Frank and Ephrussi, Anne and Singer, Robert H and Chao, Jeffrey A} } @article {46325, title = {Ultrastructurally smooth thick partitioning and volume stitching for large-scale connectomics.}, journal = {Nature Methods}, volume = {12}, year = {2015}, month = {2015 Feb 16}, pages = {319-22}, abstract = {

Focused-ion-beam scanning electron microscopy (FIB-SEM) has become an essential tool for studying neural tissue at resolutions below 10 nm {\texttimes} 10 nm {\texttimes} 10 nm, producing data sets optimized for automatic connectome tracing. We present a technical advance, ultrathick sectioning, which reliably subdivides embedded tissue samples into chunks (20 μm thick) optimally sized and mounted for efficient, parallel FIB-SEM imaging. These chunks are imaged separately and then {\textquoteright}volume stitched{\textquoteright} back together, producing a final three-dimensional data set suitable for connectome tracing.

}, issn = {1548-7105}, doi = {10.1038/nmeth.3292}, author = {Hayworth, Kenneth J and Xu, C Shan and Lu, Zhiyuan and Knott, Graham W and Fetter, Richard D and Tapia, Juan Carlos and Lichtman, Jeff W and Hess, Harald F} } @proceedings {46519, title = {Understanding classifier errors by examining influential neighbors.}, year = {2015}, month = {06/2015}, publisher = {IEEE}, address = {Boston, MA}, abstract = {

Modern supervised learning algorithms can learn very accurate and complex discriminating functions. But when these classifiers fail, this complexity can also be a drawback because there is no easy, intuitive way to diagnose why they are failing and remedy the problem. This important question has received little attention. To address this problem, we propose a novel method to analyze and understand a classifier{\textquoteright}s errors. Our method centers around a measure of how much influence a training example has on the classifier{\textquoteright}s prediction for a test example. To understand why a classifier is\ mispredicting\ the label of a given test example, the user can find and review the most influential training examples that caused this\ misprediction, allowing them to focus their attention on relevant areas of the data space. This will aid the user in determining if and how the training data is inconsistently labeled or lacking in diversity, or if the feature representation is insufficient. As computing the influence of each training example is computationally impractical, we propose a novel distance metric to approximate influence for boosting classifiers that is fast enough to be used interactively. We also show several novel use paradigms of our distance metric. Through experiments, we show that it can be used to find incorrectly or inconsistently labeled training examples, to find specific areas of the data space that need more training data, and to gain insight into which features are missing from the current representation.\ 

Code is available at\ https://github.com/kristinbranson/InfluentialNeighbors.

}, author = {Mayank Kabra and Alice A. Robie and Kristin Branson} } @article {65781, title = {Variable primary coordination environments of Cd(II) binding to three helix bundles provide a pathway for rapid metal exchange.}, journal = {Metallomics}, volume = {7}, year = {2015}, month = {10/2015}, pages = {1555 {\textendash} 1561}, abstract = {

Members of the ArsR/SmtB family of transcriptional repressors, such as CadC, regulate the intracellular levels of heavy metals like Cd(II), Hg(II), and Pb(II). These metal sensing proteins bind their target metals with high specificity and affinity, however, a lack of structural information about these proteins makes defining the coordination sphere of the target metal difficult. Lingering questions as to the identity of Cd(II) coordination in CadC are addressed via protein design techniques. Two designed peptides with tetrathiolate metal binding sites were prepared and characterized, revealing fast exchange between CdS3O and CdS4 coordination spheres. Correlation of (111m)Cd PAC spectroscopy and (113)Cd NMR spectroscopy suggests that Cd(II) coordinated to CadC is in fast exchange between CdS3O and CdS4 forms, which may provide a mechanism for rapid sensing of heavy metal contaminants by this regulatory protein.

}, doi = {10.1039/c5mt00228a}, author = {Tebo, Alison G and Hemmingsen, Lars and Pecoraro, Vincent L} } @article {46922, title = {Vinculin is required for cell polarization, migration, and extracellular matrix remodeling in 3D collagen.}, journal = {FASEB Journal}, volume = {29}, year = {2015}, month = {2015 Nov}, pages = {4555-67}, abstract = {

Vinculin is filamentous (F)-actin-binding protein enriched in integrin-based adhesions to the extracellular matrix (ECM). Whereas studies in 2-dimensional (2D) tissue culture models have suggested that vinculin negatively regulates cell migration by promoting cytoskeleton-ECM coupling to strengthen and stabilize adhesions, its role in regulating cell migration in more physiologic, 3-dimensional (3D) environments is unclear. To address the role of vinculin in 3D cell migration, we analyzed the morphodynamics, migration, and ECM remodeling of primary murine embryonic fibroblasts (MEFs) with cre/loxP-mediated vinculin gene disruption in 3D collagen I cultures. We found that vinculin promoted 3D cell migration by increasing directional persistence. Vinculin was necessary for persistent cell protrusion, cell elongation, and stable cell orientation in 3D collagen, but was dispensable for lamellipodia formation, suggesting that vinculin-mediated cell adhesion to the ECM is needed to convert actin-based cell protrusion into persistent cell shape change and migration. Consistent with this finding, vinculin was necessary for efficient traction force generation in 3D collagen without affecting myosin II activity and promoted 3D collagen fiber alignment and macroscopical gel contraction. Our results suggest that vinculin promotes directionally persistent cell migration and tension-dependent ECM remodeling in complex 3D environments by increasing cell-ECM adhesion and traction force generation.-Thievessen, I., Fakhri, N., Steinwachs, J., Kraus, V., McIsaac, R. S., Gao, L., Chen, B.-C., Baird, M. A., Davidson, M. W., Betzig, E., Oldenbourg, R., Waterman, C., M., Fabry, B. Vinculin is required for cell polarization, migration, and extracellular matrix remodeling in 3D collagen.

}, issn = {1530-6860}, doi = {10.1096/fj.14-268235}, author = {Thievessen, Ingo and Fakhri, Nikta and Steinwachs, Julian and Kraus, Viola and McIsaac, R Scott and Gao, Liang and Chen, Bi-Chang and Baird, Michelle A and Davidson, Michael W and Betzig, Eric and Oldenbourg, Rudolf and Waterman, Clare M and Fabry, Ben} } @article {46744, title = {Visualization and neuronal cell targeting during electrophysiological recordings facilitated by quantum dots.}, journal = {Proceedings of SPIE}, volume = {9305}, year = {2015}, month = {2015 Mar 10}, pages = {9305Y}, abstract = {

The simultaneous visualization, identification and targeting of neurons during patch clamp-mediated electrophysiological recordings is a basic technique in neuroscience, yet it is often complicated by the inability to visualize the pipette tip, particularly in deep brain tissue. Here we demonstrate a novel approach in which fluorescent quantum dot probes are used to coat pipettes prior to their use. The strong two-photon absorption cross sections of the quantum dots afford robust contrast at significantly deeper penetration depths than current methods allow. We demonstrate the utility of this technique in multiple recording formats both in vitro and in vivo where imaging of the pipettes is achieved at remarkable depths (up to 800 microns). Notably, minimal perturbation of cellular physiology is observed over the hours-long time course of neuronal recordings. We discuss our results within the context of the role that quantum dot nanoprobes may play in understanding neuronal cell physiology.

}, doi = {10.1117/12.2076934}, author = {Field, Lauren D and Andrasfalvy, Bertalan K and Gali{\~n}anes, Gregorio L and Huber, Daniel and Barbic, Mladen and Macklin, John J and Susumu, Kimihiro and Delehanty, James B and Huston, Alan L and Makara, Judit K and Medintz, Igor L} } @article {46020, title = {Visualizing whole-brain activity and development at the single-cell level using light-sheet microscopy.}, journal = {Neuron}, volume = {85}, year = {2015}, month = {2015 Feb 4}, pages = {462-83}, abstract = {

The nature of nervous system function and development is inherently global, since all components eventually influence one another. Networks communicate through dense synaptic, electric, and modulatory connections and develop through concurrent growth and interlinking of their neurons, processes, glia, and blood vessels. These factors drive the development of techniques capable of imaging neural signaling, anatomy, and developmental processes at ever-larger scales. Here, we discuss the nature of questions benefitting from large-scale imaging techniques and introduce recent applications. We focus on emerging light-sheet microscopy approaches, which are well suited for live imaging of large systems with high spatiotemporal resolution and over long periods of time. We also discuss computational methods suitable for extracting biological information from the resulting system-level image data sets. Together with new tools for reporting and manipulating neuronal activity and gene expression, these techniques promise new insights into the large-scale function and development of neural systems.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2014.12.039}, author = {Keller, Philipp J and Ahrens, Misha B} } @article {46314, title = {Whisking.}, journal = {Current Biology}, volume = {25}, year = {2015}, month = {2015 Feb 16}, pages = {R137-40}, abstract = {

Eyes may be {\textquoteright}the window to the soul{\textquoteright} in humans, but whiskers provide a better path to the inner lives of rodents. The brain has remarkable abilities to focus its limited resources on information that matters, while ignoring a cacophony of distractions. While inspecting a visual scene, primates foveate to multiple salient locations, for example mouths and eyes in images of people, and ignore the rest. Similar processes have now been observed and studied in rodents in the context of whisker-based tactile sensation. Rodents use their mechanosensitive whiskers for a diverse range of tactile behaviors such as navigation, object recognition and social interactions. These animals move their whiskers in a purposive manner to locations of interest. The shapes of whiskers, as well as their movements, are exquisitely adapted for tactile exploration in the dark tight burrows where many rodents live. By studying whisker movements during tactile behaviors, we can learn about the tactile information available to rodents through their whiskers and how rodents direct their attention. In this primer, we focus on how the whisker movements of rats and mice are providing clues about the logic of active sensation and the underlying neural mechanisms.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2015.01.008}, author = {Sofroniew, Nicholas J and Svoboda, Karel} } @inbook {47184, title = {Who is talking to whom: Synaptic partner detection in anisotropic volumes of insect brain.}, booktitle = {Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2015}, number = {9349}, year = {2015}, pages = {661-8}, abstract = {

Automated reconstruction of neural connectivity graphs from electron microscopy image stacks is an essential step towards large-scale neural circuit mapping. While significant progress has recently been made in automated segmentation of neurons and detection of synapses, the problem of synaptic partner assignment for polyadic (one-to-many) synapses, prevalent in the\ Drosophila\ brain, remains unsolved. In this contribution, we propose a method which automatically assigns pre- and postsynaptic roles to neurites adjacent to a synaptic site. The method constructs a probabilistic graphical model over potential synaptic partner pairs which includes factors to account for a high rate of one-to-many connections, as well as the possibility of the same neuron to be pre-synaptic in one synapse and post-synaptic in another. The algorithm has been validated on a publicly available stack of ssTEM images of\ Drosophila\ neural tissue and has been shown to reconstruct most of the synaptic relations correctly.

}, doi = {10.1007/978-3-319-24553-9_81}, author = {Kreshuk, Anna and Funke, Jan and Cardona, Albert and Hamprecht, Fred A} } @article {47116, title = {Whole-animal functional and developmental imaging with isotropic spatial resolution}, journal = {Nature Methods}, volume = {12}, year = {2015}, month = {2015 Oct 26}, pages = {1171-8}, abstract = {

Imaging fast cellular dynamics across large specimens requires high resolution in all dimensions, high imaging speeds, good physical coverage and low photo-damage. To meet these requirements, we developed isotropic multiview (IsoView) light-sheet microscopy, which rapidly images large specimens via simultaneous light-sheet illumination and fluorescence detection along four orthogonal directions. Combining these four views by means of high-throughput multiview deconvolution yields images with high resolution in all three dimensions. We demonstrate whole-animal functional imaging of Drosophila larvae at a spatial resolution of 1.1-2.5 μm and temporal resolution of 2 Hz for several hours. We also present spatially isotropic whole-brain functional imaging in Danio rerio larvae and spatially isotropic multicolor imaging of fast cellular dynamics across gastrulating Drosophila embryos. Compared with conventional light-sheet microscopy, IsoView microscopy improves spatial resolution at least sevenfold and decreases resolution anisotropy at least threefold. Compared with existing high-resolution light-sheet techniques, IsoView microscopy effectively doubles the penetration depth and provides subsecond temporal resolution for specimens 400-fold larger than could previously be imaged.

}, doi = {10.1038/nmeth.3632}, author = {Chhetri, Raghav K and Amat, Fernando and Wan, Yinan and H{\"o}ckendorf, Burkhard and Lemon, William C and Keller, Philipp J} } @article {48388, title = {Whole-brain activity mapping onto a zebrafish brain atlas.}, journal = {Nature methods}, volume = {12}, year = {2015}, month = {2015 Nov}, pages = {1039-46}, abstract = {

In order to localize the neural circuits involved in generating behaviors, it is necessary to assign activity onto anatomical maps of the nervous system. Using brain registration across hundreds of larval zebrafish, we have built an expandable open-source atlas containing molecular labels and definitions of anatomical regions, the Z-Brain. Using this platform and immunohistochemical detection of phosphorylated extracellular signal{\textendash}regulated kinase (ERK) as a readout of neural activity, we have developed a system to create and contextualize whole-brain maps of stimulus- and behavior-dependent neural activity. This mitogen-activated protein kinase (MAP)-mapping assay is technically simple, and data analysis is completely automated. Because MAP-mapping is performed on freely swimming fish, it is applicable to studies of nearly any stimulus or behavior. Here we demonstrate our high-throughput approach using pharmacological, visual and noxious stimuli, as well as hunting and feeding. The resultant maps outline hundreds of areas associated with behaviors.

}, keywords = {Algorithms, Animals, Automation, Behavior, Animal, Brain, Brain Mapping, Calcium, Extracellular Signal-Regulated MAP Kinases, Image Processing, Computer-Assisted, Immunohistochemistry, Microscopy, Confocal, Neurites, Neurons, Phosphorylation, Principal Component Analysis, Reproducibility of Results, Software, Swimming, Zebrafish}, issn = {1548-7105}, doi = {10.1038/nmeth.3581}, author = {Randlett, Owen and Wee, Caroline L and Naumann, Eva A and Nnaemeka, Onyeka and Schoppik, David and Fitzgerald, James E and Portugues, Ruben and Lacoste, Alix M B and Riegler, Clemens and Engert, Florian and Schier, Alexander F} } @article {46984, title = {Whole-central nervous system functional imaging in larval Drosophila.}, journal = {Nature Communications}, volume = {6}, year = {2015}, month = {2015 Aug 11}, pages = {7924}, abstract = {

Understanding how the brain works in tight concert with the rest of the central nervous system (CNS) hinges upon knowledge of coordinated activity patterns across the whole CNS. We present a method for measuring activity in an entire, non-transparent CNS with high spatiotemporal resolution. We combine a light-sheet microscope capable of simultaneous multi-view imaging at volumetric speeds 25-fold faster than the state-of-the-art, a whole-CNS imaging assay for the isolated Drosophila larval CNS and a computational framework for analysing multi-view, whole-CNS calcium imaging data. We image both brain and ventral nerve cord, covering the entire CNS at 2 or 5 Hz with two- or one-photon excitation, respectively. By mapping network activity during fictive behaviours and quantitatively comparing high-resolution whole-CNS activity maps across individuals, we predict functional connections between CNS regions and reveal neurons in the brain that identify type and temporal state of motor programs executed in the ventral nerve cord.

}, doi = {10.1038/ncomms8924}, author = {Lemon, William C and Pulver, Stefan R and H{\"o}ckendorf, Burkhard and McDole, Katie and Branson, Kristin M and Freeman, Jeremy and Keller, Philipp J} } @article {45886, title = {3D imaging of Sox2 enhancer clusters in embryonic stem cells.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 Dec 24}, abstract = {

Combinatorial cis-regulatory networks encoded in animal genomes represent the foundational gene expression mechanism for directing cell-fate commitment and maintenance of cell identity by transcription factors (TFs). However, the 3D spatial organization of cis-elements and how such sub-nuclear structures influence TF activity remain poorly understood. Here, we combine lattice light-sheet imaging, single-molecule tracking, numerical simulations, and ChIP-exo mapping to localize and functionally probe Sox2 enhancer-organization in living embryonic stem cells. Sox2 enhancers form 3D-clusters that are segregated from heterochromatin but overlap with a subset of Pol II enriched regions. Sox2 searches for specific binding targets via a 3D-diffusion dominant mode when shuttling long-distances between clusters while chromatin-bound states predominate within individual clusters. Thus, enhancer clustering may reduce global search efficiency but enables rapid local fine-tuning of TF search parameters. Our results suggest an integrated model linking cis-element 3D spatial distribution to local-versus-global target search modalities essential for regulating eukaryotic gene transcription.

}, issn = {2050-084X}, doi = {10.7554/eLife.04236}, author = {Liu, Zhe and Legant, Wesley R and Chen, Bi-Chang and Li, Li and Grimm, Jonathan B and Lavis, Luke D and Betzig, Eric and Tjian, Robert} } @article {6951, title = {3D live fluorescence imaging of cellular dynamics using Bessel beam plane illumination microscopy.}, journal = {Nature Protocols}, volume = {9}, year = {2014}, month = {2014 May}, pages = {1083-101}, abstract = {

3D live imaging is important for a better understanding of biological processes, but it is challenging with current techniques such as spinning-disk confocal microscopy. Bessel beam plane illumination microscopy allows high-speed 3D live fluorescence imaging of living cellular and multicellular specimens with nearly isotropic spatial resolution, low photobleaching and low photodamage. Unlike conventional fluorescence imaging techniques that usually have a unique operation mode, Bessel plane illumination has several modes that offer different performance with different imaging metrics. To achieve optimal results from this technique, the appropriate operation mode needs to be selected and the experimental setting must be optimized for the specific application and associated sample properties. Here we explain the fundamental working principles of this technique, discuss the pros and cons of each operational mode and show through examples how to optimize experimental parameters. We also describe the procedures needed to construct, align and operate a Bessel beam plane illumination microscope by using our previously reported system as an example, and we list the necessary equipment to build such a microscope. Assuming all components are readily available, it would take a person skilled in optical instrumentation \~{}1 month to assemble and operate a microscope according to this protocol.

}, issn = {1750-2799}, doi = {10.1038/nprot.2014.087}, author = {Gao, Liang and Shao, Lin and Chen, Bi-Chang and Betzig, Eric} } @article {45043, title = {Abdominal-B neurons control Drosophila virgin female receptivity.}, journal = {Current Biology}, volume = {24}, year = {2014}, month = {2014 Jul 21}, pages = {1584-95}, abstract = {

BACKGROUND: Female sexual receptivity offers an excellent model for complex behavioral decisions. The female must parse her own reproductive state, the external environment, and male sensory cues to decide whether to copulate. In the\ fly Drosophila melanogaster, virgin female receptivity has received relatively little attention, and its neural circuitry and individual behavioral components remain unmapped. Using a genome-wide neuronal RNAi screen, we identify a subpopulation of neurons responsible for pausing, a novel behavioral aspect of virgin female receptivity characterized in this study.

RESULTS: We show that Abdominal-B (Abd-B), a homeobox transcription factor, is required in developing neurons for high levels of virgin female receptivity. Silencing adult Abd-B neurons significantly decreased receptivity. We characterize two components of receptivity that are elicited in sexually mature females by male courtship: pausing and vaginal plate opening. Silencing Abd-B neurons decreased pausing but did not affect vaginal plate opening, demonstrating that these two components of female sexual behavior are functionally separable. Synthetic activation of Abd-B neurons increased pausing, but male courtship song alone was not sufficient to elicit this behavior.

CONCLUSIONS: Our results provide an entry point to the neural circuit controlling virgin female receptivity. The female integrates multiple sensory cues from the male to execute discrete motor programs prior to copulation. Abd-B neurons control pausing, a key aspect of female sexual receptivity, in response to male courtship.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2014.06.011}, author = {Bussell, Jennifer J and Yapici, Nilay and Zhang, Stephen X and Dickson, Barry J and Vosshall, Leslie B} } @article {45102, title = {Accessing the third dimension in localization-based super-resolution microscopy.}, journal = {Physical Chemistry Chemical Physics}, volume = {16}, year = {2014}, month = {2014 Jul 16}, pages = {16340-8}, abstract = {

Only a few years after its inception, localization-based super-resolution microscopy has become widely employed in biological studies. Yet, it is primarily used in two-dimensional imaging and accessing the organization of cellular structures at the nanoscale in three dimensions (3D) still poses important challenges. Here, we review optical and computational techniques that enable the 3D localization of individual emitters and the reconstruction of 3D super-resolution images. These techniques are grouped into three main categories: PSF engineering, multiple plane imaging and interferometric approaches. We provide an overview of their technical implementation as well as commentary on their applicability. Finally, we discuss future trends in 3D localization-based super-resolution microscopy.

}, issn = {1463-9084}, doi = {10.1039/c4cp01380h}, author = {Hajj, Bassam and El Beheiry, Mohamed and Izeddin, Ignacio and Darzacq, Xavier and Dahan, Maxime} } @article {45180, title = {Accurate design of co-assembling multi-component protein nanomaterials.}, journal = {Nature}, volume = {510}, year = {2014}, month = {2014 Jun 5}, pages = {103-8}, abstract = {

The self-assembly of proteins into highly ordered nanoscale architectures is a hallmark of biological systems. The sophisticated functions of these molecular machines have inspired the development of methods to engineer self-assembling protein nanostructures; however, the design of multi-component protein nanomaterials with high accuracy remains an outstanding challenge. Here we report a computational method for designing protein nanomaterials in which multiple copies of two distinct subunits co-assemble into a specific architecture. We use the method to design five 24-subunit cage-like protein nanomaterials in two distinct symmetric architectures and experimentally demonstrate that their structures are in close agreement with the computational design models. The accuracy of the method and the number and variety of two-component materials that it makes accessible suggest a route to the construction of functional protein nanomaterials tailored to specific applications.

}, keywords = {Computer Simulation, Crystallography, X-Ray, Drug Design, Models, Molecular, Nanostructures, Protein Subunits, Proteins}, issn = {1476-4687}, doi = {10.1038/nature13404}, author = {King, Neil P and Bale, Jacob B and Sheffler, William and McNamara, Dan E and Gonen, Shane and Gonen, Tamir and Yeates, Todd O and Baker, David} } @article {48164, title = {Active graph matching for automatic joint segmentation and annotation of C. elegans.}, journal = {Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention}, volume = {17}, year = {2014}, month = {2014}, pages = {81-8}, abstract = {

In this work we present a novel technique we term active graph matching, which integrates the popular active shape model into a sparse graph matching problem. This way we are able to combine the benefits of a global, statistical deformation model with the benefits of a local deformation model in form of a second-order random field. We present a new iterative energy minimization technique which achieves empirically good results. This enables us to exceed state-of-the art results for the task of annotating nuclei in 3D microscopic images of C. elegans. Furthermore with the help of the generalized Hough transform we are able to jointly segment and annotate a large set of nuclei in a fully automatic fashion for the first time.

}, keywords = {Algorithms, Animals, Caenorhabditis elegans, Cell Nucleus, Image Enhancement, Image Interpretation, Computer-Assisted, Microscopy, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity, Subtraction Technique}, author = {Kainmueller, Dagmar and Jug, Florian and Rother, Carsten and Myers, Gene} } @article {46049, title = {Adaptation to background light enables contrast coding at rod bipolar cell synapses.}, journal = {Neuron}, volume = {81}, year = {2014}, month = {2014 Jan 22}, pages = {388-401}, abstract = {

Rod photoreceptors contribute to vision over an \~{} 6-log-unit range of light intensities. The wide dynamic range of rod vision is thought to depend upon light intensity-dependent switching between two parallel pathways linking rods to ganglion cells: a rod {\textrightarrow} rod bipolar (RB) cell pathway that operates at dim backgrounds and a rod {\textrightarrow} cone {\textrightarrow} cone bipolar cell pathway that operates at brighter backgrounds. We evaluated this conventional model of rod vision by recording rod-mediated light responses from ganglion and AII amacrine cells and by recording RB-mediated synaptic currents from AII amacrine cells in mouse retina. Contrary to the conventional model, we found that the RB pathway functioned at backgrounds sufficient to activate the rod {\textrightarrow} cone pathway. As background light intensity increased, the RB{\textquoteright}s role changed from encoding the absorption of single photons to encoding contrast modulations around mean luminance. This transition is explained by the intrinsic dynamics of transmission from RB synapses.

}, keywords = {2-Amino-5-phosphonovalerate, Adaptation, Ocular, Animals, Biophysics, Computer Simulation, Excitatory Amino Acid Antagonists, Glucosamine 6-Phosphate N-Acetyltransferase, Green Fluorescent Proteins, In Vitro Techniques, Light, Mice, Mice, Inbred C57BL, Mice, Knockout, Mice, Transgenic, Models, Neurological, Patch-Clamp Techniques, Quinoxalines, Retinal Bipolar Cells, Retinal Rod Photoreceptor Cells, Synapses, Visual Pathways}, issn = {1097-4199}, doi = {10.1016/j.neuron.2013.10.054}, author = {Ke, Jiang-Bin and Wang, Yanbin V and Borghuis, Bart G and Cembrowski, Mark S and Riecke, Hermann and Kath, William L and Demb, Jonathan B and Singer, Joshua H} } @article {45717, title = {Agouti-related protein neuron circuits that regulate appetite.}, journal = {Neuroendocrinology}, volume = {507}, year = {2014}, month = {2014 Nov 6}, pages = {238-42}, abstract = {

New tools for mapping and manipulating molecularly defined neural circuits have improved understanding of how the central nervous system regulates appetite. Studies focused on AGRP neurons, a starvation-sensitive hypothalamic population, have identified multiple circuit elements that can elicit or suppress feeding behavior. Distinct axon projections of this neuron population point to different circuits that regulate long-term appetite, short-term feeding, or visceral malaise-mediated anorexia. Here, we review recent studies examining these neural circuits that control food intake. {\textcopyright} 2014 S. Karger AG, Basel.

}, issn = {1423-0194}, doi = {10.1159/000369072}, author = {Sternson, Scott M and Atasoy, Deniz} } @article {6935, title = {Allelic heterogeneity in NCF2 associated with systemic lupus erythematosus (SLE) susceptibility across four ethnic populations.}, journal = {Human Molecular Genetics}, volume = {23}, year = {2014}, month = {2014 Mar 15}, pages = {1656-68}, abstract = {

Recent reports have associated NCF2, encoding a core component of the multi-protein NADPH oxidase (NADPHO), with systemic lupus erythematosus (SLE) susceptibility in individuals of European ancestry. To identify ethnicity-specific and -robust variants within NCF2, we assessed 145 SNPs in and around the NCF2 gene in 5325 cases and 21 866 controls of European-American (EA), African-American (AA), Hispanic (HS) and Korean (KR) ancestry. Subsequent imputation, conditional, haplotype and bioinformatic analyses identified seven potentially functional SLE-predisposing variants. Association with non-synonymous rs17849502, previously reported in EA, was detected in EA, HS and AA (P(EA) = 1.01 {\texttimes} 10(-54), PHS = 3.68 {\texttimes} 10(-10), P(AA) = 0.03); synonymous rs17849501 was similarly significant. These SNPs were monomorphic in KR. Novel associations were detected with coding variants at rs35937854 in AA (PAA = 1.49 {\texttimes} 10(-9)), and rs13306575 in HS and KR (P(HS) = 7.04 {\texttimes} 10(-7), P(KR) = 3.30 {\texttimes} 10(-3)). In KR, a 3-SNP haplotype was significantly associated (P = 4.20 {\texttimes} 10(-7)), implying that SLE predisposing variants were tagged. Significant SNP-SNP interaction (P = 0.02) was detected between rs13306575 and rs17849502 in HS, and a dramatically increased risk (OR = 6.55) with a risk allele at each locus. Molecular modeling predicts that these non-synonymous mutations could disrupt NADPHO complex assembly. The risk allele of rs17849501, located in a conserved transcriptional regulatory region, increased reporter gene activity, suggesting in vivo enhancer function. Our results not only establish allelic heterogeneity within NCF2 associated with SLE, but also emphasize the utility of multi-ethnic cohorts to identify predisposing variants explaining additional phenotypic variance ({\textquoteright}missing heritability{\textquoteright}) of complex diseases like SLE.

}, issn = {1460-2083}, doi = {10.1093/hmg/ddt532}, author = {Kim-Howard, Xana and Sun, Celi and Molineros, Julio E and Maiti, Amit K and Chandru, Hema and Adler, Adam and Wiley, Graham B and Kaufman, Kenneth M and Kottyan, Leah and Guthridge, Joel M and Rasmussen, Astrid and Kelly, Jennifer and S{\'a}nchez, Elena and Raj, Prithvi and Li, Quan-Zhen and Bang, So-Young and Lee, Hye-Soon and Kim, Tae-Hwan and Kang, Young Mo and Suh, Chang-Hee and Chung, Won Tae and Park, Yong-Beom and Choe, Jung-Yoon and Shim, Seung Cheol and Lee, Shin-Seok and Han, Bok-Ghee and Olsen, Nancy J and Karp, David R and Moser, Kathy and Pons-Estel, Bernardo A and Wakeland, Edward K and James, Judith A and Harley, John B and Bae, Sang-Cheol and Gaffney, Patrick M and Alarc{\'o}n-Riquelme, Marta and Looger, Loren L and Nath, Swapan K} } @article {6932, title = {Amphotericin forms an extramembranous and fungicidal sterol sponge.}, journal = {Nature Chemical Biology}, volume = {10}, year = {2014}, month = {2014 Mar 30}, pages = {400-6}, abstract = {

For over 50 years, amphotericin has remained the powerful but highly toxic last line of defense in treating life-threatening fungal infections in humans with minimal development of microbial resistance. Understanding how this small molecule kills yeast is thus critical for guiding development of derivatives with an improved therapeutic index and other resistance-refractory antimicrobial agents. In the widely accepted ion channel model for its mechanism of cytocidal action, amphotericin forms aggregates inside lipid bilayers that permeabilize and kill cells. In contrast, we report that amphotericin exists primarily in the form of large, extramembranous aggregates that kill yeast by extracting ergosterol from lipid bilayers. These findings reveal that extraction of a polyfunctional lipid underlies the resistance-refractory antimicrobial action of amphotericin and suggests a roadmap for separating its cytocidal and membrane-permeabilizing activities. This new mechanistic understanding is also guiding development of what are to our knowledge the first derivatives of amphotericin that kill yeast but not human cells.

}, issn = {1552-4469}, doi = {10.1038/nchembio.1496}, author = {Anderson, Thomas M and Clay, Mary C and Cioffi, Alexander G and Diaz, Katrina A and Hisao, Grant S and Tuttle, Marcus D and Nieuwkoop, Andrew J and Comellas, Gemma and Maryum, Nashrah and Wang, Shu and Uno, Brice E and Wildeman, Erin L and Gonen, Tamir and Rienstra, Chad M and Burke, Martin D} } @article {45787, title = {Anesthetized- and awake-patched whole-cell recordings in freely moving rats using UV-cured collar-based electrode stabilization.}, journal = {Nature Protocols}, volume = {9}, year = {2014}, month = {2014 Nov 06}, pages = {2784-95}, abstract = {

Intracellular recording allows precise measurement and manipulation of individual neurons, but it requires stable mechanical contact between the electrode and the cell membrane, and thus it has remained challenging to perform in behaving animals. Whole-cell recordings in freely moving animals can be obtained by rigidly fixing ({\textquoteright}anchoring{\textquoteright}) the pipette electrode to the head; however, previous anchoring procedures were slow and often caused substantial pipette movement, resulting in loss of the recording or of recording quality. We describe a UV-transparent collar and UV-cured adhesive technique that rapidly (within 15 s) anchors pipettes in place with virtually no movement, thus substantially improving the reliability, yield and quality of freely moving whole-cell recordings. Recordings are first obtained from anesthetized or awake head-fixed rats. UV light cures the thin adhesive layers linking pipette to collar to head. Then, the animals are rapidly and smoothly released for recording during unrestrained behavior. The anesthetized-patched version can be completed in \~{}4-7 h (excluding histology) and the awake-patched version requires \~{}1-4 h per day for \~{}2 weeks. These advances should greatly facilitate studies of neuronal integration and plasticity in identified cells during natural behaviors.

}, issn = {1750-2799}, doi = {10.1038/nprot.2014.190}, author = {Lee, Doyun and Shtengel, Gleb and Osborne, Jason E and Lee, Albert K} } @article {6937, title = {Annotating functional RNAs in genomes using infernal.}, journal = {Methods in Molecular Biology}, volume = {1097}, year = {2014}, month = {2014}, pages = {163-97}, abstract = {

Many different types of functional non-coding RNAs participate in a wide range of important cellular functions but the large majority of these RNAs are not routinely annotated in published genomes. Several programs have been developed for identifying RNAs, including specific tools tailored to a particular RNA family as well as more general ones designed to work for any family. Many of these tools utilize covariance models (CMs), statistical models of the conserved sequence, and structure of an RNA family. In this chapter, as an illustrative example, the Infernal software package and CMs from the Rfam database are used to identify RNAs in the genome of the archaeon Methanobrevibacter ruminantium, uncovering some additional RNAs not present in the genome{\textquoteright}s initial annotation. Analysis of the results and comparison with family-specific methods demonstrate some important strengths and weaknesses of this general approach.

}, issn = {1940-6029}, doi = {10.1007/978-1-62703-709-9_9}, author = {Nawrocki, Eric P} } @article {46226, title = {Annotating synapses in large EM datasets.}, journal = {arXiv}, year = {2014}, month = {2014 Sep 5}, pages = {arXiv:1409.1801 [q-bio.QM]}, abstract = {

Reconstructing neuronal circuits at the level of synapses is a central problem in neuroscience and becoming a focus of the emerging field of connectomics. To date, electron microscopy (EM) is the most proven technique for identifying and quantifying synaptic connections. As advances in EM make acquiring larger datasets possible, subsequent manual synapse identification ({\em i.e.}, proofreading) for deciphering a connectome becomes a major time bottleneck. Here we introduce a large-scale, high-throughput, and semi-automated methodology to efficiently identify synapses. We successfully applied our methodology to the Drosophila medulla optic lobe, annotating many more synapses than previous connectome efforts. Our approaches are extensible and will make the often complicated process of synapse identification accessible to a wider-community of potential proofreaders.

}, url = {http://arxiv.org/abs/1409.1801}, author = {Plaza, Stephen M and Parag, Toufiq and Huang, Gary and Olbris, Donald J. and Saunders, Mathew A. and Rivlin, Patricia K.} } @article {45048, title = {Ascending SAG neurons control sexual receptivity of Drosophila females.}, journal = {Neuron}, volume = {83}, year = {2014}, month = {2014 Jul 2}, pages = {135-48}, abstract = {

Mating induces pronounced changes in female reproductive behavior, typically including a dramatic reduction in sexual receptivity. In Drosophila, postmating behavioral changes are triggered by sex peptide (SP), a male seminal fluid peptide that acts via a\ receptor (SPR) expressed in sensory neurons (SPSNs) of the female reproductive tract. Here, we identify second-order neurons that mediate the behavioral changes induced by SP. These SAG neurons receive synaptic input from SPSNs in the abdominal ganglion and project to the dorsal protocerebrum. Silencing SAG neurons renders virgin females unreceptive, whereas activating them increases the receptivity of females that have already mated. Physiological experiments demonstrate that SP downregulates the excitability of the SPSNs, and hence their input onto SAG neurons. These data thus provide a physiological correlate of mating status in the female central nervous system and a key entry point into the brain circuits that control sexual receptivity.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2014.05.017}, author = {Feng, Kai and Palfreyman, Mark T and H{\"a}semeyer, Martin and Talsma, Aaron and Dickson, Barry J} } @article {45788, title = {Assembling cell ensembles.}, journal = {Cell}, volume = {157}, year = {2014}, month = {2014 Jun 19}, pages = {1502-4}, abstract = {

The way the hippocampus processes information and encodes memories in the form of "cell assemblies" is likely determined in part by how its circuits are wired up during development. In this issue, Xu et\ al. now provide new insight into how neurons arising from a single common precursor migrate to their final destination and form functionally synchronous ensembles.

}, keywords = {Animals, Hippocampus}, issn = {1097-4172}, doi = {10.1016/j.cell.2014.05.032}, author = {Spruston, Nelson} } @article {45418, title = {Atlas-builder software and the eNeuro atlas: resources for developmental biology and neuroscience.}, journal = {Development}, volume = {141}, year = {2014}, month = {2014 Jun}, pages = {2524-32}, abstract = {

A major limitation in understanding embryonic development is the lack of cell type-specific markers. Existing gene expression and marker atlases provide valuable tools, but they typically have one or more limitations: a lack of single-cell resolution; an inability to register multiple expression patterns to determine their precise relationship; an inability to be upgraded by users; an inability to compare novel patterns with the database patterns; and a lack of three-dimensional images. Here, we develop new {\textquoteright}atlas-builder{\textquoteright} software that overcomes each of these limitations. A newly generated atlas is three-dimensional, allows the precise registration of an infinite number of cell type-specific markers, is searchable and is open-ended. Our software can be used to create an atlas of any tissue in any organism that contains stereotyped cell positions. We used the software to generate an {\textquoteright}eNeuro{\textquoteright} atlas of the Drosophila embryonic CNS containing eight transcription factors that mark the major CNS cell types (motor neurons, glia, neurosecretory cells and interneurons). We found neuronal, but not glial, nuclei occupied stereotyped locations. We added 75 new Gal4 markers to the atlas to identify over 50\% of all interneurons in the ventral CNS, and these lines allowed functional access to those interneurons for the first time. We expect the atlas-builder software to benefit a large proportion of the developmental biology community, and the eNeuro atlas to serve as a publicly accessible hub for integrating neuronal attributes - cell lineage, gene expression patterns, axon/dendrite projections, neurotransmitters--and linking them to individual neurons.

}, keywords = {Animals, Axons, Cell Lineage, Central Nervous System, Computational Biology, Databases, Genetic, Dendrites, Drosophila melanogaster, Drosophila Proteins, Gene Expression Profiling, Gene Expression Regulation, Developmental, Genetic Markers, Interneurons, Mice, Neurons, Neurotransmitter Agents, Rats, Software}, issn = {1477-9129}, doi = {10.1242/dev.108720}, author = {Heckscher, Ellie S and Long, Fuhui and Layden, Michael J and Chuang, Chein-Hui and Manning, Laurina and Richart, Jourdain and Pearson, Joseph C and Crews, Stephen T and Peng, Hanchuan and Myers, Eugene and Doe, Chris Q} } @article {6880, title = {Automated detection of synapses in serial section transmission electron microscopy image stacks.}, journal = {PloS one}, volume = {9}, year = {2014}, month = {2014}, pages = {e87351}, abstract = {We describe a method for fully automated detection of chemical synapses in serial electron microscopy images with highly anisotropic axial and lateral resolution, such as images taken on transmission electron microscopes. Our pipeline starts from classification of the pixels based on 3D pixel features, which is followed by segmentation with an Ising model MRF and another classification step, based on object-level features. Classifiers are learned on sparse user labels; a fully annotated data subvolume is not required for training. The algorithm was validated on a set of 238 synapses in 20 serial 7197{\texttimes}7351 pixel images (4.5{\texttimes}4.5{\texttimes}45 nm resolution) of mouse visual cortex, manually labeled by three independent human annotators and additionally re-verified by an expert neuroscientist. The error rate of the algorithm (12\% false negative, 7\% false positive detections) is better than state-of-the-art, even though, unlike the state-of-the-art method, our algorithm does not require a prior segmentation of the image volume into cells. The software is based on the ilastik learning and segmentation toolkit and the vigra image processing library and is freely available on our website, along with the test data and gold standard annotations (http://www.ilastik.org/synapse-detection/sstem).}, issn = {1932-6203}, doi = {10.1371/journal.pone.0087351}, author = {Kreshuk, Anna and Koethe, Ullrich and Pax, Elizabeth and Bock, Davi D and Hamprecht, Fred A} } @article {45098, title = {Automated image-based tracking and its application in ecology.}, journal = {Trends in Ecology and Evolution}, volume = {29}, year = {2014}, month = {2014 Jul}, pages = {417-428}, abstract = {

The behavior of individuals determines the strength and outcome of ecological interactions, which drive population, community, and ecosystem organization. Bio-logging, such as telemetry and animal-borne imaging, provides essential individual viewpoints, tracks, and life histories, but requires capture of individuals and is often impractical to scale. Recent developments in automated image-based tracking offers opportunities to remotely quantify and understand individual behavior at scales and resolutions not previously possible, providing an essential supplement to other tracking methodologies in ecology. Automated image-based tracking should continue to advance the field of ecology by enabling better understanding of the linkages between individual and higher-level ecological processes, via high-throughput quantitative analysis of complex ecological patterns and processes across scales, including analysis of environmental drivers.

}, issn = {1872-8383}, doi = {10.1016/j.tree.2014.05.004}, author = {Dell, Anthony I and Bender, John A and Branson, Kristin and Couzin, Iain D and de Polavieja, Gonzalo G and Noldus, Lucas P J J and P{\'e}rez-Escudero, Alfonso and Perona, Pietro and Straw, Andrew D and Wikelski, Martin and Brose, Ulrich} } @article {46227, title = {Automatic neuron type identification by neurite localization in the Drosophila medulla.}, journal = {arXiv}, year = {2014}, month = {2014 Sep 5}, pages = {arXiv:1409.1892 [q-bio.NC]}, abstract = {

Mapping the connectivity of neurons in the brain (i.e., connectomics) is a challenging problem due to both the number of connections in even the smallest organisms and the nanometer resolution required to resolve them. Because of this, previous connectomes contain only hundreds of neurons, such as in the C.elegans connectome. Recent technological advances will unlock the mysteries of increasingly large connectomes (or partial connectomes). However, the value of these maps is limited by our ability to reason with this data and understand any underlying motifs. To aid connectome analysis, we introduce algorithms to cluster similarly-shaped neurons, where 3D neuronal shapes are represented as skeletons. In particular, we propose a novel location-sensitive clustering algorithm. We show clustering results on neurons reconstructed from the Drosophila medulla that show high-accuracy.

}, author = {Plaza, Stephen M and Zhao, Ting} } @article {46706, title = {Background free imaging of single mRNAs in live cells using split fluorescent proteins.}, journal = {Scientific Reports}, volume = {4}, year = {2014}, month = {2014 Jan 9}, pages = {3615}, abstract = {

We describe a technique for imaging single mRNAs in living cells based on fluorescent protein (FP) complementation. We employ the high affinity interaction between the bacterial phage MS2/PP7 coat proteins and their respective RNA binding motifs as an RNA scaffold to bring two halves of a split-FP together to image single reporter mRNAs without background fluorescence.

}, keywords = {Bacteriophages, Fluorescence, Luminescent Proteins, RNA, Messenger}, issn = {2045-2322}, doi = {10.1038/srep03615}, author = {Wu, Bin and Chen, Jiahao and Singer, Robert H} } @inbook {47132, title = {The basal ganglia }, booktitle = {The Rat Nervous System}, year = {2014}, pages = {391-440}, edition = {Fourth Edition}, abstract = {

The basal ganglia plays a significant role in transforming activity in the cerebral cortex into directed behavior, involving motor learning, habit formation and the selection of actions based on desirable outcomes, and the organization of the basal ganglia is intimately linked to that of the cerebral cortex. In this chapter, we focus primarily on the neocortical part of the basal ganglia. A general canonical organizational plan of the neocortical-related basal ganglia is described. An understanding of the canonical organization of the neostriatal part of the basal ganglia, provides a framework for determining the general organizational principles of the parts of the basal ganglia connected with allocortical areas and the amygdala, and this is discussed. While it has been proposed that the basal ganglia provide interactions between disparate functional circuits, another approach might be that there are parallel functional circuits, in which distinct functions are for the most part maintained, or segregated, one from the other. This chapter, however, is biased toward the view that there is maintenance of functional parallel circuits in the organization of the basal ganglia, but that the circuit contains neuroanatomical features that provide for considerable interaction between adjacent circuits.

}, doi = {10.1016/B978-0-12-374245-2.00017-6}, author = {Dudman, Joshua T and Cerfan, C R} } @article {45458, title = {Behavioral variability through stochastic choice and its gating by anterior cingulate cortex.}, journal = {Cell}, volume = {159}, year = {2014}, month = {2014 Sep 25}, pages = {21-32}, abstract = {

Behavioral choices that ignore prior experience promote exploration and unpredictability but are seemingly at odds with the brain{\textquoteright}s tendency to use experience to optimize behavioral choice. Indeed, when faced with virtual competitors, primates resort to strategic counterprediction rather than to stochastic choice. Here, we show that rats also use history- and model-based strategies when faced with similar competitors but can switch to a "stochastic" mode when challenged with a competitor that they cannot defeat by counterprediction. In this mode, outcomes associated with an animal{\textquoteright}s actions are ignored, and normal engagement of anterior cingulate cortex (ACC) is suppressed. Using circuit perturbations in\ transgenic rats, we demonstrate that switching between strategic and stochastic behavioral modes is controlled by locus coeruleus input into ACC. Our\ findings suggest that, under conditions of uncertainty about environmental rules, changes in noradrenergic input alter ACC output and prevent erroneous beliefs from guiding decisions, thus enabling behavioral variation.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2014.08.037}, author = {Tervo, Dougal G R and Proskurin, Mikhail and Manakov, Maxim and Kabra, Mayank and Vollmer, Alison and Branson, Kristin and Karpova, Alla Y} } @article {45049, title = {Bioimage informatics in the context of Drosophila research.}, journal = {Methods}, volume = {68}, year = {2014}, month = {2014 Jun 15}, pages = {60-73}, abstract = {

Modern biological research relies heavily on microscopic imaging. The advanced genetic toolkit of Drosophila makes it possible to label molecular and cellular components with unprecedented level of specificity necessitating the application of the most sophisticated imaging technologies. Imaging in Drosophila spans all scales from single molecules to the entire populations of adult organisms, from electron microscopy to live imaging of developmental processes. As the imaging approaches become more complex and ambitious, there is an increasing need for quantitative, computer-mediated image processing and analysis to make sense of the imagery. Bioimage Informatics is an emerging research field that covers all aspects of biological image analysis from data handling, through processing, to quantitative measurements, analysis and data presentation. Some of the most advanced, large scale projects, combining cutting edge imaging with complex bioimage informatics pipelines, are realized in the Drosophila research community. In this review, we discuss the current research in biological image analysis specifically relevant to the type of systems level image datasets that are uniquely available for the Drosophila model system. We focus on how state-of-the-art computer vision algorithms are impacting the ability of Drosophila researchers to analyze biological systems in space and time. We pay particular attention to how these algorithmic advances from computer science are made usable to practicing biologists through open source platforms and how biologists can themselves participate in their further development.

}, issn = {1095-9130}, doi = {10.1016/j.ymeth.2014.04.004}, author = {Jug, Florian and Pietzsch, Tobias and Preibisch, Stephan and Tomancak, Pavel} } @article {45700, title = {Bone-free: soft mechanics for adaptive locomotion.}, journal = {Integrative and Comparative Biology}, volume = {54}, year = {2014}, month = {2014 Dec}, pages = {1122-35}, abstract = {

Muscular hydrostats (such as mollusks), and fluid-filled animals (such as annelids), can exploit their constant-volume tissues to transfer forces and displacements in predictable ways, much as articulated animals use hinges and levers. Although larval insects contain pressurized fluids, they also have internal air tubes that are compressible and, as a result, they have more uncontrolled degrees of freedom. Therefore, the mechanisms by which larval insects control their movements are expected to reveal useful strategies for designing soft biomimetic robots. Using caterpillars as a tractable model system, it is now possible to identify the biomechanical and neural strategies for controlling movements in such highly deformable animals. For example, the tobacco hornworm, Manduca sexta, can stiffen its body by increasing muscular tension (and therefore body pressure) but the internal cavity (hemocoel) is not iso-barometric, nor is pressure used to directly control the movements of its limbs. Instead, fluid and tissues flow within the hemocoel and the body is soft and flexible to conform to the substrate. Even the gut contributes to the biomechanics of locomotion; it is decoupled from the movements of the body wall and slides forward within the body cavity at the start of each step. During crawling the body is kept in tension for part of the stride and compressive forces are exerted on the substrate along the axis of the caterpillar, thereby using the environment as a skeleton. The timing of muscular activity suggests that crawling is coordinated by proleg-retractor motoneurons and that the large segmental muscles produce anterograde waves of lifting that do not require precise timing. This strategy produces a robust form of locomotion in which the kinematics changes little with orientation. In different species of caterpillar, the presence of prolegs on particular body segments is related to alternative kinematics such as "inching." This suggests a mechanism for the evolution of different gaits through changes in the usage of prolegs, rather than, through extensive alterations in the motor program controlling the body wall. Some of these findings are being used to design and test novel control-strategies for highly deformable robots. These "softworm" devices are providing new insights into the challenges faced by any soft animal navigating in a terrestrial environment.

}, issn = {1557-7023}, doi = {10.1093/icb/icu076}, author = {Trimmer, B A and Lin, Huai-Ti} } @article {6893, title = {Bright building blocks for chemical biology.}, journal = {ACS Chemical Biology}, volume = {9}, year = {2014}, month = {2014 Mar 20}, pages = {855-66}, abstract = {

Small-molecule fluorophores manifest the ability of chemistry to solve problems in biology. As we noted in a previous review (Lavis, L. D.; Raines, R. T. ACS Chem. Biol. 2008, 3, 142-155), the extant collection of fluorescent probes is built on a modest set of "core" scaffolds that evolved during a century of academic and industrial research. Here, we survey traditional and modern synthetic routes to small-molecule fluorophores and highlight recent biological insights attained with customized fluorescent probes. Our intent is to inspire the design and creation of new high-precision tools that empower chemical biologists.

}, issn = {1554-8937}, doi = {10.1021/cb500078u}, author = {Lavis, Luke D and Raines, Ronald T} } @article {6910, title = {The catalytic subunit of the SWR1 remodeler is a histone chaperone for the H2A.Z-H2B dimer.}, journal = {Molecular Cell}, volume = {53}, year = {2014}, month = {2014 Feb 6}, pages = {498-505}, abstract = {

Histone variant H2A.Z-containing nucleosomes exist at most eukaryotic promoters and play important roles in gene transcription and genome stability. The multisubunit nucleosome-remodeling enzyme complex SWR1, conserved from yeast to mammals, catalyzes the ATP-dependent replacement of histone H2A in canonical nucleosomes with H2A.Z. How SWR1 catalyzes the replacement reaction is largely unknown. Here, we determined the crystal structure of the N-terminal region (599-627) of the catalytic subunit Swr1, termed Swr1-Z domain, in complex with the H2A.Z-H2B dimer at 1.78 {\r A} resolution. The Swr1-Z domain forms a 310 helix and an irregular chain. A conserved LxxLF motif in the Swr1-Z 310 helix specifically recognizes the αC helix of H2A.Z. Our results show that the Swr1-Z domain can deliver the H2A.Z-H2B dimer to the DNA-(H3-H4)2 tetrasome to form the nucleosome by a histone chaperone mechanism.

}, issn = {1097-4164}, doi = {10.1016/j.molcel.2014.01.010}, author = {Hong, Jingjun and Feng, Hanqiao and Wang, Feng and Ranjan, Anand and Chen, Jianhong and Jiang, Jiansheng and Ghirlando, Rodolfo and Xiao, T Sam and Wu, Carl and Bai, Yawen} } @article {47621, title = {Cell Biology. Fixing problems with cell lines.}, journal = {Science (New York, N.Y.)}, volume = {346}, year = {2014}, month = {2014 Dec 19}, pages = {1452-3}, keywords = {Animals, Biological Specimen Banks, Biomedical Research, Cell Line, Drug Evaluation, Preclinical, Humans, National Institutes of Health (U.S.), Policy, Reproducibility of Results, United States}, issn = {1095-9203}, doi = {10.1126/science.1259110}, author = {Lorsch, Jon R and Collins, Francis S and Lippincott-Schwartz, Jennifer} } @article {46347, title = {Cell types and coincident synapses in the ellipsoid body of Drosophila.}, journal = {The European Journal of Neuroscience}, volume = {39}, year = {2014}, month = {2014 May}, pages = {1586-601}, abstract = {

Cellular ultrastructures for signal integration are unknown in any nervous system. The ellipsoid body (EB) of the Drosophila brain is thought to control locomotion upon integration of various modalities of sensory signals with the animal internal status. However, the expected excitatory and inhibitory input convergence that virtually all brain centres exhibit is not yet described in the EB. Based on the EB expression domains of genetic constructs from the choline acetyl transferase (Cha), glutamic acid decarboxylase (GAD) and tyrosine hydroxylase (TH) genes, we identified a new set of neurons with the characteristic ring-shaped morphology (R\ neurons) which are presumably cholinergic, in addition to the existing GABA-expressing neurons. The R1 morphological subtype is represented in the Cha- and TH-expressing classes. In addition, using transmission electron microscopy, we identified a novel type of synapse in the EB, which exhibits the precise array of two independent active zones over the same postsynaptic dendritic domain, that we named {\textquoteright}agora{\textquoteright}. This array is compatible with a coincidence detector role, and represents ~8\% of all EB synapses in Drosophila. Presumably excitatory R\ neurons contribute to coincident synapses. Functional silencing of EB neurons by driving genetically tetanus toxin expression either reduces walking speed or alters movement orientation depending on the targeted R\ neuron subset, thus revealing functional specialisations in the EB for locomotion control.

}, keywords = {Animals, Animals, Genetically Modified, Bees, Brain, Choline O-Acetyltransferase, Drosophila, Drosophila Proteins, Female, gamma-Aminobutyric Acid, Green Fluorescent Proteins, Male, Microscopy, Electron, Transmission, Nerve Tissue Proteins, Neurons, Orientation, Paired Box Transcription Factors, Synapses, Tetanus Toxin, Transcription Factors, Visual Perception, Walking}, issn = {1460-9568}, doi = {10.1111/ejn.12537}, author = {Mart{\'\i}n-Pe{\~n}a, Alfonso and Acebes, Angel and Rodr{\'\i}guez, Jos{\'e}-Rodrigo and Chevalier, Valerie and Casas-Tinto, Sergio and Triphan, Tilman and Strauss, Roland and Ferr{\'u}s, Alberto} } @article {6952, title = {Cell-type-based model explaining coexpression patterns of genes in the brain.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, year = {2014}, month = {2014 Apr 8}, pages = {5397-402}, abstract = {

Spatial patterns of gene expression in the vertebrate brain are not independent, as pairs of genes can exhibit complex patterns of coexpression. Two genes may be similarly expressed in one region, but differentially expressed in other regions. These correlations have been studied quantitatively, particularly for the Allen Atlas of the adult mouse brain, but their biological meaning remains obscure. We propose a simple model of the coexpression patterns in terms of spatial distributions of underlying cell types and establish its plausibility using independently measured cell-type-specific transcriptomes. The model allows us to predict the spatial distribution of cell types in the mouse brain.

}, issn = {1091-6490}, doi = {10.1073/pnas.1312098111}, author = {Grange, Pascal and Bohland, Jason W and Okaty, Benjamin W and Sugino, Ken and Bokil, Hemant and Nelson, Sacha B and Ng, Lydia and Hawrylycz, Michael and Mitra, Partha P} } @article {6890, title = {Cell-type-specific labeling of synapses in vivo through synaptic tagging with recombination.}, journal = {Neuron}, volume = {81}, year = {2014}, month = {2014 Jan 22}, pages = {280-93}, abstract = {

The study of synaptic specificity and plasticity in the CNS is limited by the inability to efficiently visualize synapses in identified neurons using light microscopy. Here, we describe synaptic tagging with recombination (STaR), a method for labeling endogenous presynaptic and postsynaptic proteins in a cell-type-specific fashion. We modified genomic loci encoding synaptic proteins within bacterial artificial chromosomes such that these proteins, expressed at endogenous levels and with normal spatiotemporal patterns, were labeled in an inducible fashion in specific neurons through targeted expression of site-specific recombinases. Within the Drosophila visual system, the number and distribution of synapses correlate with electron microscopy studies. Using two different recombination systems, presynaptic and postsynaptic specializations of synaptic pairs can be colabeled. STaR also allows synapses within the CNS to be studied in live animals noninvasively. In principle, STaR can be adapted to the mammalian nervous system.

}, keywords = {Animals, Drosophila, Drosophila Proteins, Electron, Genetic, Genetically Modified, Luminescent Proteins, Medulla Oblongata, Microscopy, Nerve Tissue Proteins, Neurons, Neurotransmitter, Presynaptic Terminals, Receptors, Recombinases, Recombination, Synapses, Transcription Factors, Transmission, Visual Pathways}, issn = {1097-4199}, doi = {10.1016/j.neuron.2013.12.021}, author = {Chen, Yi and Akin, Orkun and Nern, Aljoscha and Tsui, C Y Kimberly and Pecot, Matthew Y and Zipursky, S Lawrence} } @article {45638, title = {Cell-type-specific repression by methyl-CpG-binding protein 2 is biased toward long genes.}, journal = {Journal of Neuroscience}, volume = {34}, year = {2014}, month = {2014 Sep 17}, pages = {12877-83}, abstract = {

Mutations in methyl-CpG-binding protein 2 (MeCP2) cause Rett syndrome and related autism spectrum disorders (Amir et al., 1999). MeCP2 is believed to be required for proper regulation of brain gene expression, but prior microarray studies in Mecp2 knock-out mice using brain tissue homogenates have revealed only subtle changes in gene expression (Tudor et al., 2002; Nuber et al., 2005; Jordan et al., 2007; Chahrour et al., 2008). Here, by profiling discrete subtypes of neurons we uncovered more dramatic effects of MeCP2 on gene expression, overcoming the "dilution problem" associated with assaying homogenates of complex tissues. The results reveal misregulation of genes involved in neuronal connectivity and communication. Importantly, genes upregulated following loss of MeCP2 are biased toward longer genes but this is not true for downregulated genes, suggesting MeCP2 may selectively repress long genes. Because genes involved in neuronal connectivity and communication, such as cell adhesion and cell-cell signaling genes, are enriched among longer genes, their misregulation following loss of MeCP2 suggests a possible etiology for altered circuit function in Rett syndrome.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2674-14.2014}, author = {Sugino, Ken and Hempel, Chris M and Okaty, Benjamin W and Arnson, Hannah A and Kato, Saori and Dani, Vardhan S and Nelson, Sacha B} } @article {6826, title = {Cellular and behavioral functions of fruitless isoforms in Drosophila courtship.}, journal = {Current Biology }, volume = {24}, year = {2014}, month = {2014 Feb 3}, pages = {242-51}, abstract = {

BACKGROUND: Male-specific products of the fruitless (fru) gene control the development and function of neuronal circuits that underlie male-specific behaviors in Drosophila, including courtship. Alternative splicing generates at least three distinct Fru isoforms, each containing a different zinc-finger domain. Here, we examine the expression and function of each of these isoforms. RESULTS: We show that most fru(+) cells express all three isoforms, yet each isoform has a distinct function in the elaboration of sexually dimorphic circuitry and behavior. The strongest impairment in courtship behavior is observed in fru(C) mutants, which fail to copulate, lack sine song, and do not generate courtship song in the absence of visual stimuli. Cellular dimorphisms in the fru circuit are dependent on Fru(C) rather than other single Fru isoforms. Removal of Fru(C) from the neuronal classes vAB3 or aSP4 leads to cell-autonomous feminization of arborizations and loss of courtship in the dark. CONCLUSIONS: These data map specific aspects of courtship behavior to the level of single fru isoforms and fru(+) cell types-an important step toward elucidating the chain of causality from gene to circuit to behavior.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2013.12.015}, author = {von Philipsborn, Anne C and J{\"o}rchel, Sabrina and Tirian, Laszlo and Demir, Ebru and Morita, Tomoko and Stern, David L and Dickson, Barry J} } @article {45055, title = {Central brain neurons expressing doublesex regulate female receptivity in Drosophila.}, journal = {Neuron}, volume = {83}, year = {2014}, month = {2014 Jul 2}, pages = {149-63}, abstract = {

Drosophila melanogaster females respond to male courtship by either rejecting the male or allowing copulation. The neural mechanisms underlying these female behaviors likely involve the integration of sensory information in the brain. Because doublesex (dsx) controls other aspects of female differentiation, we asked whether dsx-expressing neurons mediate virgin female receptivity to courting males. Using intersectional techniques to manipulate the activities of defined subsets of dsx-expressing neurons, we found that activation of neurons in either the pCd or pC1 clusters promotes receptivity, while silencing these neurons makes females unreceptive. Furthermore, pCd and pC1 neurons physiologically respond to the male-specific pheromone cis-vaccenyl acetate (cVA), while pC1 neurons also respond to male courtship song. The pCd and pC1 neurons expressing dsx in females do not express transcripts from the fruitless (fru) P1 promoter. Thus, virgin female receptivity is controlled at least in part by neurons that are distinct from those governing male courtship.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2014.05.038}, author = {Zhou, Chuan and Pan, Yufeng and Robinett, Carmen C and Meissner, Geoffrey W and Baker, Bruce S} } @article {6894, title = {Charting Brachyury-mediated developmental pathways during early mouse embryogenesis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, year = {2014}, month = {2014 Mar 10}, pages = {4478-83}, abstract = {

To gain insights into coordinated lineage-specification and morphogenetic processes during early embryogenesis, here we report a systematic identification of transcriptional programs mediated by a key developmental regulator-Brachyury. High-resolution chromosomal localization mapping of Brachyury by ChIP sequencing and ChIP-exonuclease revealed distinct sequence signatures enriched in Brachyury-bound enhancers. A combination of genome-wide in vitro and in vivo perturbation analysis and cross-species evolutionary comparison unveiled a detailed Brachyury-dependent gene-regulatory network that directly links the function of Brachyury to diverse developmental pathways and cellular housekeeping programs. We also show that Brachyury functions primarily as a transcriptional activator genome-wide and that an unexpected gene-regulatory feedback loop consisting of Brachyury, Foxa2, and Sox17 directs proper stem-cell lineage commitment during streak formation. Target gene and mRNA-sequencing correlation analysis of the T(c) mouse model supports a crucial role of Brachyury in up-regulating multiple key hematopoietic and muscle-fate regulators. Our results thus chart a comprehensive map of the Brachyury-mediated gene-regulatory network and how it influences in vivo developmental homeostasis and coordination.

}, issn = {1091-6490}, doi = {10.1073/pnas.1402612111}, author = {Lolas, Macarena and Valenzuela, Pablo D T and Tjian, Robert and Liu, Zhe} } @article {45167, title = {Chemogenetic synaptic silencing of neural circuits localizes a hypothalamus{\textrightarrow}midbrain pathway for feeding behavior.}, journal = {Neuron}, volume = {82}, year = {2014}, month = {2014 May 21}, pages = {797-808}, abstract = {

Brain function is mediated by neural circuit connectivity, and elucidating the role of connections is aided by techniques to block their output. We developed cell-type-selective, reversible synaptic inhibition tools for mammalian neural circuits by leveraging G protein signaling pathways to suppress synaptic vesicle release. Here, we find that the pharmacologically selective designer Gi-protein-coupled receptor hM4D is a presynaptic silencer in the presence of its cognate ligand clozapine-N-oxide (CNO). Activation of hM4D signaling sharply reduced synaptic release probability and synaptic current amplitude. To demonstrate the utility of this tool for neural circuit perturbations, we developed an axon-selective hM4D-neurexin variant and used spatially targeted intracranial CNO injections to localize circuit connections from the hypothalamus to the midbrain responsible for feeding behavior. This synaptic silencing approach is broadly applicable for cell-type-specific and axon projection-selective functional analysis of diverse neural circuits.

}, keywords = {Agouti-Related Protein, Animals, Basic Helix-Loop-Helix Transcription Factors, Clozapine, Feeding Behavior, Humans, Hypothalamus, Membrane Potentials, Mesencephalon, Mice, Mice, Inbred C57BL, Mice, Transgenic, Models, Molecular, Molecular Sequence Data, Nerve Net, Neural Inhibition, Neurons, Receptor, Muscarinic M4, Repressor Proteins, Rhodopsin, Time Factors}, issn = {1097-4199}, doi = {10.1016/j.neuron.2014.04.008}, author = {Stachniak, Tevye J and Ghosh, Anirvan and Sternson, Scott M} } @article {45051, title = {Chemogenetic tools to interrogate brain functions.}, journal = {Annual Review of Neuroscience}, volume = {37}, year = {2014}, month = {2014 Jul 8}, pages = {387-407}, abstract = {

Elucidating the roles of neuronal cell types for physiology and behavior is essential for understanding brain functions. Perturbation of neuron electrical activity can be used to probe the causal relationship between neuronal cell types and behavior. New genetically encoded neuron perturbation tools have been developed for remotely controlling neuron function using small molecules that activate engineered receptors that can be targeted to cell types using genetic methods. Here we describe recent progress for approaches using genetically engineered receptors that selectively interact with small molecules. Called "chemogenetics," receptors with diverse cellular functions have been developed that facilitate the selective pharmacological control over a diverse range of cell-signaling processes, including electrical activity, for molecularly defined cell types. These tools have revealed remarkably specific behavioral physiological influences for molecularly defined cell types that are often intermingled with populations having different or even opposite functions.

}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-071013-014048}, author = {Sternson, Scott M and Roth, Bryan L} } @article {45332, title = {ChIP for hox proteins from Drosophila imaginal discs.}, journal = {Methods in Molecular Biology}, volume = {1196}, year = {2014}, month = {2014 August 15}, pages = {241-53}, abstract = {

Chromatin immunoprecipitation (ChIP) is a technique that reveals in vivo location of a protein bound to DNA. ChIP coupled with DNA microarrays (ChIP-chip) or next-generation sequencing (ChIP-seq) allows for identification of binding sites of transcription factors on a global scale. Here we describe a protocol for ChIP to identify binding of the Ultrabithorax (Ubx) Hox transcription factors from imaginal discs of Drosophila larvae. The protocol can be extended to other model organisms and transcription factors.

}, issn = {1940-6029}, doi = {10.1007/978-1-4939-1242-1_15}, author = {Agrawal, Pavan and Shashidhara, L S} } @article {45181, title = {Combined protein- and nucleic acid-level effects of rs1143679 (R77H), a lupus-predisposing variant within ITGAM.}, journal = {Human Molecular Genetics}, volume = {23}, year = {2014}, month = {2014 Aug 1}, pages = {4161-76}, abstract = {

Integrin alpha M (ITGAM; CD11b) is a component of the macrophage-1 antigen complex, which mediates leukocyte adhesion, migration and phagocytosis as part of the immune system. We previously identified a missense polymorphism, rs1143679 (R77H), strongly associated with systemic lupus erythematosus (SLE). However, the molecular mechanisms of this variant are incompletely understood. A meta-analysis of published and novel data on 28 439 individuals with European, African, Hispanic and Asian ancestries reinforces genetic association between rs1143679 and SLE [Pmeta = 3.60 {\texttimes} 10(-90), odds ratio (OR) = 1.76]. Since rs1143679 is in the most active region of chromatin regulation and transcription factor binding in ITGAM, we quantitated ITGAM RNA and surface protein levels in monocytes from patients with each rs1143679 genotype. We observed that transcript levels significantly decreased for the risk allele ({\textquoteright}A{\textquoteright}) relative to the non-risk allele ({\textquoteright}G{\textquoteright}), in a dose-dependent fashion: ({\textquoteright}AA{\textquoteright} \< {\textquoteright}AG{\textquoteright} \< {\textquoteright}GG{\textquoteright}). CD11b protein levels in patients{\textquoteright} monocytes were directly correlated with RNA levels. Strikingly, heterozygous individuals express much lower (average 10- to 15-fold reduction) amounts of the {\textquoteright}A{\textquoteright} transcript than {\textquoteright}G{\textquoteright} transcript. We found that the non-risk sequence surrounding rs1143679 exhibits transcriptional enhancer activity in vivo and binds to Ku70/80, NFKB1 and EBF1 in vitro, functions that are significantly reduced with the risk allele. Mutant CD11b protein shows significantly reduced binding to fibrinogen and vitronectin, relative to non-risk, both in purified protein and in cellular models. This two-pronged contribution (nucleic acid- and protein-level) of the rs1143679 risk allele to decreasing ITGAM activity provides insight into the molecular mechanisms of its potent association with SLE.

}, issn = {1460-2083}, doi = {10.1093/hmg/ddu106}, author = {Maiti, Amit K and Kim-Howard, Xana and Motghare, Prasenjeet and Pradhan, Vandana and Chua, Kek Heng and Sun, Celi and Arango-Guerrero, Mar{\'\i}a Teresa and Ghosh, Kanjaksha and Niewold, Timothy B and Harley, John B and Anaya, Juan-Manual and Looger, Loren L and Nath, Swapan K} } @article {46482, title = {Comparing strategies to reactivate fetal globin expression for the treatment of beta-globinopathies.}, journal = {Blood}, volume = {124}, year = {2014}, month = {2014 Dec 6}, pages = {333}, abstract = {

The hemoglobinopathies, such as β-thalassemia and sickle cell anemia (SCA), are characterized by mutations of the β-globin gene resulting in either decreased or functionally abnormal hemoglobin (Hb) production. As bone marrow transplant is the only curative option for these patients, there is a strong need for new therapeutic approaches. Both β-thalassemia and SCA represent ideal targets for gene therapy since introduction of a normal β-globin gene can ameliorate the phenotype, as we and others have shown previously. Overcoming the developmental silencing of the fetal γ-globin gene represents an additional approach for the treatment of hemoglobinopathies. Here, we directly compare a recently established approach to activate the γ-globin gene using forced chromatin looping with pharmacologic approaches to raise γ-globin expression.

The β-type globin genes are activated through dynamic interactions with a distal upstream enhancer, the locus control region (LCR). The LCR physically contacts the developmental stage appropriate globin gene via chromatin looping, a process partially dependent on the protein Ldb1. Previously, we have shown that tethering Ldb1 to the murine β-globin promoter with a custom designed zinc finger protein (ZF-Ldb1) can induce loop formation and β-globin transcription in an erythroid cell line (Deng et al., 2012). Further work showed that forced chromatin looping can be exploited to potently reactivate fetal globin gene expression in adult human erythroid cells (Deng et al., 2014). Here we compared the efficacy and toxicity of ZF-Ldb1 to pharmacologic compounds that induce HbF in cultured hematopoietic stem progenitor cell-derived erythroid cultures from normal and SCA donors.

ZF-Ldb1 increased HbF synthesis in SCA erythroid cells (N=8) up to 86\% and, concurrently, reduced sickle Hb (HbS) below 15\%, consistent with previous studies of erythroid cells from normal probands. Preliminary results obtained from treating SCA specimens (N=3) show that the induction of HbF in cells treated with ZF-Ldb1 is twice as high (+35.55\% {\textpm} 8.34\%, at a dose of ~ one ZF-Ldb1 transgene copy per cell) as that observed using pomalidomide (+16.50\% {\textpm} 14.57\%, 20μM) and decitabine (+15.60\% {\textpm} 12.36\%, 0.5μM). Tranylcypromine and hydroxyurea showed the lowest HbF increase (+9.67\% {\textpm} 3.26\% and +5.06 {\textpm} 2.82\%, 1.5μM and 150μM respectively).

Importantly, decitabine and pomalidomide treatment lowered cell viability to 39\% and 26\%, respectively, while ZF-Ldb1 expressing cells retained normal viability similar to control populations.

In related experiments, we are comparing the expression of a battery of genes known to regulate HbF levels (BCL11A, SOX6, KLF1 and C-Myb) in normal and SCA derived erythroid cells treated with ZF-Ldb1 or HbF inducers and compared to controls. Preliminary analyses indicate altered expression of KLF1 in SCA versus normal cells, consistent with a superior response of SCA cells to HbF induction.

In conclusion, lentiviral-mediated ZF-Ldb1 gene transfer appears superior to pharmacologic compounds in terms of efficacy and cell viability further supporting suitability for the reactivation of HbF in SCA erythroid cells.

}, url = {http://www.bloodjournal.org/content/124/21/333} } @article {6877, title = {Comparing thoracic and intra-nasal pressure transients to monitor active odor sampling during odor-guided decision making in the mouse.}, journal = {Journal of Neuroscience Methods}, volume = {221}, year = {2014}, month = {2014 Jan 15}, pages = {8-14}, abstract = {

BACKGROUND: Recording of physiological parameters in behaving mice has seen an immense increase over recent years driven by, for example, increased miniaturization of recording devices. One parameter particularly important for odorant-driven behaviors is the breathing frequency, since the latter dictates the rate of odorant delivery to the nasal cavity and the olfactory receptor neurons located therein. NEW METHOD: Typically, breathing patterns are monitored by either measuring the breathing-induced temperature or pressure changes in the nasal cavity. Both require the implantation of a nasal cannula and tethering of the mouse to either a cable or tubing. To avoid these limitations we used an implanted pressure sensor which reads the thoracic pressure and transmits the data telemetrically, thus making it suitable for experiments which require a freely moving animal. RESULTS: Mice performed a Go/NoGo odorant-driven behavioral task with the implanted pressure sensor, which proved to work reliably to allow recording of breathing signals over several weeks from a given animal. COMPARISON TO EXISTING METHOD(S): We simultaneously recorded the thoracic and nasal pressure changes and found that measuring the thoracic pressure change yielded similar results compared to measurements of nasal pressure changes. CONCLUSION: Telemetrically recorded breathing signals are a feasible method to monitor odorant-guided behavioral changes in breathing rates. Its advantages are most significant when recording from a freely moving animal over several weeks. The advantages and disadvantages of different methods to record breathing patterns are discussed.

}, issn = {1872-678X}, doi = {10.1016/j.jneumeth.2013.09.006}, author = {Reisert, Johannes and Golden, Glen J and Matsumura, Koichi and Smear, Matt and Rinberg, Dmitry and Gelperin, Alan} } @article {45856, title = {Computational analysis of conserved RNA secondary structure in transcriptomes and genomes.}, journal = {Annual Review of Biophysics and Biomolecular Structure}, volume = {43}, year = {2014}, month = {2014}, pages = {433-56}, abstract = {

Transcriptomics experiments and computational predictions both enable systematic discovery of new functional RNAs. However, many putative noncoding transcripts arise instead from artifacts and biological noise, and current computational prediction methods have high false positive rates. I discuss prospects for improving computational methods for analyzing and identifying functional RNAs, with a focus on detecting signatures of conserved RNA secondary structure. An interesting new front is the application of chemical and enzymatic experiments that probe RNA structure on a transcriptome-wide scale. I review several proposed approaches for incorporating structure probing data into the computational prediction of RNA secondary structure. Using probabilistic inference formalisms, I show how all these approaches can be unified in a well-principled framework, which in turn allows RNA probing data to be easily integrated into a wide range of analyses that depend on RNA secondary structure inference. Such analyses include homology search and genome-wide detection of new structural RNAs.

}, keywords = {Algorithms, Animals, Bacteria, Computational Biology, Humans, Nucleic Acid Conformation, RNA}, issn = {1936-1238}, doi = {10.1146/annurev-biophys-051013-022950}, author = {Eddy, Sean R} } @article {6960, title = {Conditions and constraints for astrocyte calcium signaling in the hippocampal mossy fiber pathway.}, journal = {Neuron}, volume = {82}, year = {2014}, month = {2014 Apr 16}, pages = {413-29}, abstract = {

The spatiotemporal activities of astrocyte Ca(2+) signaling in mature neuronal circuits remain unclear. We used genetically encoded Ca(2+) and glutamate indicators as well as pharmacogenetic and electrical control of neurotransmitter release to explore astrocyte activity in the hippocampal mossy fiber pathway. Our data revealed numerous localized, spontaneous Ca(2+) signals in astrocyte branches and territories, but these were not driven by neuronal activity or glutamate. Moreover, evoked astrocyte Ca(2+) signaling changed linearly with the number of mossy fiber action potentials. Under these settings, astrocyte responses were global, suppressed by neurotransmitter clearance, and mediated by glutamate and GABA. Thus, astrocyte engagement in the fully developed mossy fiber pathway was slow and territorial, contrary to that frequently proposed for astrocytes within microcircuits. We show that astrocyte Ca(2+) signaling functionally segregates large volumes of neuropil and that these transients are not suited for responding to, or regulating, single synapses in the mossy fiber pathway.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2014.02.041}, author = {Haustein, Martin D and Kracun, Sebastian and Lu, Xiao-Hong and Shih, Tiffany and Jackson-Weaver, Olan and Tong, Xiaoping and Xu, Ji and Yang, X William and O{\textquoteright}Dell, Thomas J and Marvin, Jonathan S and Ellisman, Mark H and Bushong, Eric A and Looger, Loren L and Khakh, Baljit S.} } @article {46224, title = {A context-aware delayed agglomeration framework for EM segmentation.}, journal = {arXiv}, year = {2014}, month = {2014 Jun 5}, pages = {arXiv:1406.1476 [cs.CV]}, abstract = {

This paper proposes a novel agglomerative framework for Electron Microscopy (EM) image (or volume) segmentation. For the overall segmentation methodology, we propose a context-aware algorithm that clusters the over-segmented regions of different sub-classes (representing different biological entities) in different stages. Furthermore, a delayed scheme for agglomerative clustering, which postpones the merge of newly formed bodies, is also proposed to generate a more confident boundary prediction. We report significant improvements in both segmentation accuracy and speed attained by the proposed approaches over existing standard methods on both 2D and 3D datasets.

}, url = {http://arxiv.org/abs/1406.1476}, author = {Parag, Toufiq and Chakraborty, Anirban and Plaza, Stephen M} } @article {46286, title = {Continuous attractor network model for conjunctive position-by-velocity tuning of grid cells.}, journal = {PLoS Computational Biology}, volume = {10}, year = {2014}, month = {2014 Apr 17}, pages = {e1003558}, abstract = {

The spatial responses of many of the cells recorded in layer II of rodent medial entorhinal cortex (MEC) show a triangular grid pattern, which appears to provide an accurate population code for animal spatial position. In layer III, V and VI of the rat MEC, grid cells are also selective to head-direction and are modulated by the speed of the animal. Several putative mechanisms of grid-like maps were proposed, including attractor network dynamics, interactions with theta oscillations or single-unit mechanisms such as firing rate adaptation. In this paper, we present a new attractor network model that accounts for the conjunctive position-by-velocity selectivity of grid cells. Our network model is able to perform robust path integration even when the recurrent connections are subject to random perturbations.

}, keywords = {Animals, Models, Theoretical, Movement, Rodentia}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1003558}, author = {Si, Bailu and Romani, Sandro and Tsodyks, Misha} } @article {45153, title = {A contractile and counterbalancing adhesion system controls the 3D shape of crawling cells.}, journal = {Journal of Cell Biology}, volume = {205}, year = {2014}, month = {2014 Apr 14}, pages = {83-96}, abstract = {

How adherent and contractile systems coordinate to promote cell shape changes is unclear. Here, we define a counterbalanced adhesion/contraction model for cell shape control. Live-cell microscopy data showed a crucial role for a contractile meshwork at the top of the cell, which is composed of actin arcs and myosin IIA filaments. The contractile actin meshwork is organized like muscle sarcomeres, with repeating myosin II filaments separated by the actin bundling protein α-actinin, and is mechanically coupled to noncontractile dorsal actin fibers that run from top to bottom in the cell. When the meshwork contracts, it pulls the dorsal fibers away from the substrate. This pulling force is counterbalanced by the dorsal fibers{\textquoteright} attachment to focal adhesions, causing the fibers to bend downward and flattening the cell. This model is likely to be relevant for understanding how cells configure themselves to complex surfaces, protrude into tight spaces, and generate three-dimensional forces on the growth substrate under both healthy and diseased conditions.

}, keywords = {Actin Cytoskeleton, Actinin, Actins, Animals, Cell Adhesion, Cell Line, Tumor, Cell Movement, Cell Shape, Cercopithecus aethiops, COS Cells, Focal Adhesions, Humans, Mechanotransduction, Cellular, Models, Biological, Nonmuscle Myosin Type IIA, Pressure, Time Factors, Transfection}, issn = {1540-8140}, doi = {10.1083/jcb.201311104}, author = {Burnette, Dylan T and Shao, Lin and Ott, Carolyn and Pasapera, Ana M and Fischer, Robert S and Baird, Michelle A and Der Loughian, Christelle and Delanoe-Ayari, Helene and Paszek, Matthew J and Davidson, Michael W and Betzig, Eric and Lippincott-Schwartz, Jennifer} } @article {47629, title = {A contractile and counterbalancing adhesion system controls the 3D shape of crawling cells.}, journal = {The Journal of cell biology}, volume = {205}, year = {2014}, month = {2014 Apr 14}, pages = {83-96}, abstract = {

How adherent and contractile systems coordinate to promote cell shape changes is unclear. Here, we define a counterbalanced adhesion/contraction model for cell shape control. Live-cell microscopy data showed a crucial role for a contractile meshwork at the top of the cell, which is composed of actin arcs and myosin IIA filaments. The contractile actin meshwork is organized like muscle sarcomeres, with repeating myosin II filaments separated by the actin bundling protein α-actinin, and is mechanically coupled to noncontractile dorsal actin fibers that run from top to bottom in the cell. When the meshwork contracts, it pulls the dorsal fibers away from the substrate. This pulling force is counterbalanced by the dorsal fibers{\textquoteright} attachment to focal adhesions, causing the fibers to bend downward and flattening the cell. This model is likely to be relevant for understanding how cells configure themselves to complex surfaces, protrude into tight spaces, and generate three-dimensional forces on the growth substrate under both healthy and diseased conditions.

}, keywords = {Actin Cytoskeleton, Actinin, Actins, Animals, Cell Adhesion, Cell Line, Tumor, Cell Movement, Cell Shape, Cercopithecus aethiops, COS Cells, Focal Adhesions, Humans, Mechanotransduction, Cellular, Models, Biological, Nonmuscle Myosin Type IIA, Pressure, Time Factors, Transfection}, issn = {1540-8140}, doi = {10.1083/jcb.201311104}, author = {Burnette, Dylan T and Shao, Lin and Ott, Carolyn and Pasapera, Ana M and Fischer, Robert S and Baird, Michelle A and Der Loughian, Christelle and Delanoe-Ayari, Helene and Paszek, Matthew J and Davidson, Michael W and Betzig, Eric and Lippincott-Schwartz, Jennifer} } @article {6711, title = {Correlative super-resolution fluorescence and metal-replica transmission electron microscopy.}, journal = {Nature Methods}, volume = {11}, year = {2014}, month = {2014 Jan 26}, pages = {305-8}, abstract = {

We combine super-resolution localization fluorescence microscopy with transmission electron microscopy of metal replicas to locate proteins on the landscape of the cellular plasma membrane at the nanoscale. We validate robust correlation on the scale of 20 nm by imaging endogenous clathrin (in two and three dimensions) and apply the method to find the previously unknown three-dimensional position of the endocytic protein epsin on clathrin-coated structures at the plasma membrane.

}, issn = {1548-7105}, doi = {10.1038/nmeth.2816}, author = {Sochacki, Kem A and Shtengel, Gleb and Van Engelenburg, Schuyler B and Hess, Harald F and Taraska, Justin W} } @article {68450, title = {Cytoplasmic tyrosine phosphatase Shp2 coordinates hepatic regulation of bile acid and FGF15/19 signaling to repress bile acid synthesis.}, journal = {Cell Metab}, volume = {20}, year = {2014}, month = {08/2014}, pages = {320-32}, abstract = {

Bile acid (BA) biosynthesis is tightly controlled by intrahepatic negative feedback signaling elicited by BA binding to farnesoid X receptor (FXR) and also by enterohepatic communication involving ileal BA reabsorption and FGF15/19 secretion. However, how these pathways are coordinated is poorly understood. We show here that nonreceptor tyrosine phosphatase Shp2 is a critical player that couples and regulates the intrahepatic and enterohepatic signals for repression of BA synthesis. Ablating Shp2 in hepatocytes suppressed signal relay from FGFR4, receptor for FGF15/19, and attenuated BA activation of FXR signaling, resulting in elevation of systemic BA levels and chronic hepatobiliary disorders in mice. Acting immediately downstream of FGFR4, Shp2 associates with FRS2α and promotes the receptor activation and signal relay to several pathways. These results elucidate a molecular mechanism for the control of BA homeostasis by Shp2 through the orchestration of multiple signals in hepatocytes.

}, keywords = {Animals, Bile Acids and Salts, Bile Ducts, Cell Line, Cholesterol 7-alpha-Hydroxylase, Fibroblast Growth Factors, Liver, Membrane Proteins, Mice, Mice, Knockout, Protein Tyrosine Phosphatase, Non-Receptor Type 11, Receptor, Fibroblast Growth Factor, Type 4, Signal Transduction, Up-Regulation}, issn = {1932-7420}, doi = {10.1016/j.cmet.2014.05.020}, author = {Li, Shuangwei and Hsu, Diane D F and Li, Bing and Luo, Xiaolin and Alderson, Nazilla and Qiao, Liping and Ma, Lina and Zhu, Helen H and He, Zhao and Suino-Powell, Kelly and Ji, Kaihong and Li, Jiefu and Shao, Jianhua and Xu, H Eric and Li, Tiangang and Feng, Gen-Sheng} } @article {45419, title = {Development of the annelid axochord: insights into notochord evolution.}, journal = {Science}, volume = {345}, year = {2014}, month = {2014 Sep 12}, pages = {1365-8}, abstract = {

The origin of chordates has been debated for more than a century, with one key issue being the emergence of the notochord. In vertebrates, the notochord develops by convergence and extension of the chordamesoderm, a population of midline cells of unique molecular identity. We identify a population of mesodermal cells in a developing invertebrate, the marine annelid Platynereis dumerilii, that converges and extends toward the midline and expresses a notochord-specific combination of genes. These cells differentiate into a longitudinal muscle, the axochord, that is positioned between central nervous system and axial blood vessel and secretes a strong collagenous extracellular matrix. Ancestral state reconstruction suggests that contractile mesodermal midline cells existed in bilaterian ancestors. We propose that these cells, via vacuolization and stiffening, gave rise to the chordate notochord.

}, issn = {1095-9203}, doi = {10.1126/science.1253396}, author = {Lauri, Antonella and Brunet, Thibaut and Handberg-Thorsager, Mette and Fischer, Antje H L and Simakov, Oleg and Steinmetz, Patrick R H and Tomer, Raju and Keller, Philipp J and Arendt, Detlev} } @article {6883, title = {The developmental control of size in insects.}, journal = {Wiley Interdisciplinary Reviews: Developmental Biology}, volume = {3}, year = {2014}, month = {2014 Jan/Feb}, pages = {113-34}, abstract = {

The mechanisms that control the sizes of a body and its many parts remain among the great puzzles in developmental biology. Why do animals grow to a species-specific body size, and how is the relative growth of their body parts controlled to so they grow to the right size, and in the correct proportion with body size, giving an animal its species-characteristic shape? Control of size must involve mechanisms that somehow assess some aspect of size and are upstream of mechanisms that regulate growth. These mechanisms are now beginning to be understood in the insects, in particular in Manduca sexta and Drosophila melanogaster. The control of size requires control of the rate of growth and control of the cessation of growth. Growth is controlled by genetic and environmental factors. Insulin and ecdysone, their receptors, and intracellular signaling pathways are the principal genetic regulators of growth. The secretion of these growth hormones, in turn, is controlled by complex interactions of other endocrine and molecular mechanisms, by environmental factors such as nutrition, and by the physiological mechanisms that sense body size. Although the general mechanisms of growth regulation appear to be widely shared, the mechanisms that regulate final size can be quite diverse. WIREs Dev Biol 2014, 3:113{\textendash}134. doi: 10.1002/wdev.124

}, issn = {1759-7684}, doi = {10.1002/wdev.124}, author = {Nijhout, H. Frederik and Riddiford, Lynn M and Mirth, Christen and Shingleton, Alexander W and Suzuki, Yuichiro and Callier, Viviane} } @article {45175, title = {Direct observation of ON and OFF pathways in the Drosophila visual system.}, journal = {Current Biology}, volume = {24}, year = {2014}, month = {2014 May 5}, pages = {976-83}, abstract = {

Visual motion perception is critical to many animal behaviors, and flies have emerged as a powerful model system for exploring this fundamental neural computation. Although numerous studies have suggested that fly motion vision is governed by a simple neural circuit [1-3], the implementation of this circuit has remained mysterious for decades. Connectomics and neurogenetics have produced a surge in recent progress, and several studies have shown selectivity for light increments (ON) or decrements (OFF) in key elements associated with this circuit [4-7]. However, related studies have reached disparate conclusions about where this selectivity emerges and whether it plays a major role in motion vision [8-13]. To address these questions, we examined activity in the neuropil thought to be responsible for visual motion detection, the medulla, of Drosophila melanogaster in response to a range of visual stimuli using two-photon calcium imaging. We confirmed that the input neurons of the medulla, the LMCs, are not responsible for light-on and light-off selectivity. We then examined the pan-neural response of medulla neurons and found prominent selectivity for light-on and light-off in layers of the medulla associated with two anatomically derived pathways (L1/L2 associated) [14, 15]. We next examined the activity of prominent interneurons within each pathway (Mi1 and Tm1) and found that these neurons have corresponding selectivity for light-on or light-off. These results provide direct evidence that motion is computed in parallel light-on and light-off pathways, demonstrate that this selectivity emerges in neurons immediately downstream of the LMCs, and specify where crucial elements of motion computation occur.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2014.03.017}, author = {Strother, James A and Nern, Aljoscha and Reiser, Michael B} } @article {6891, title = {Direct phase measurement in zonal wavefront reconstruction using multidither coherent optical adaptive technique.}, journal = {Optics Express}, volume = {22}, year = {2014}, month = {2014 Jan 27}, pages = {1619-28}, abstract = {

In traditional zonal wavefront sensing for adaptive optics, after local wavefront gradients are obtained, the entire wavefront can be calculated by assuming that the wavefront is a continuous surface. Such an approach will lead to sub-optimal performance in reconstructing wavefronts which are either discontinuous or undersampled by the zonal wavefront sensor. Here, we report a new method to reconstruct the wavefront by directly measuring local wavefront phases in parallel using multidither coherent optical adaptive technique. This method determines the relative phases of each pupil segment independently, and thus produces an accurate wavefront for even discontinuous wavefronts. We implemented this method in an adaptive optical two-photon fluorescence microscopy and demonstrated its superior performance in correcting large or discontinuous aberrations.

}, issn = {1094-4087}, doi = {10.1364/OE.22.001619}, author = {Liu, Rui and Milkie, Daniel E and Kerlin, Aaron and Maclennan, Bryan and Ji, Na} } @article {6911, title = {Discovery of brainwide neural-behavioral maps via multiscale unsupervised structure learning}, journal = {Science}, volume = {344}, year = {2014}, month = {2014 Mar 27}, pages = {386-92}, chapter = {386}, abstract = {

A single nervous system can generate many distinct motor patterns. Identifying which neurons and circuits control which behaviors has been a laborious piecemeal process, usually for one observer-defined behavior at a time. We present a fundamentally different approach to neuron-behavior mapping. We optogenetically activated 1,054 identified neuron lines in Drosophila larva and tracked the behavioral responses from 37,780 animals. Applying multiscale unsupervised structure learning methods to the behavioral data identified 29 discrete statistically distinguishable and observer-unbiased behavioral phenotypes. Mapping the neural lines to the behavior(s) they evoke provides a behavioral reference atlas for neuron subsets covering a large fraction of larval neurons. This atlas is a starting point for connectivity- and activity-mapping studies to further investigate the mechanisms by which neurons mediate diverse behaviors.

}, issn = {1095-9203}, doi = {10.1126/science.1250298}, author = {Vogelstein, Joshua T and Park, Youngser and Ohyama, Tomoko and Kerr, Rex and Truman, James W and Priebe, Carey E. and Zlatic, Marta} } @article {45686, title = {Distinct representation and distribution of visual information by specific cell types in mouse superficial superior colliculus.}, journal = {The Journal of Neuroscience}, volume = {34}, year = {2014}, month = {2014 Oct 1}, pages = {13458-71}, abstract = {

The superficial superior colliculus (sSC) occupies a critical node in the mammalian visual system; it is one of two major retinorecipient areas, receives visual cortical input, and innervates visual thalamocortical circuits. Nonetheless, the contribution of sSC neurons to downstream neural activity and visually guided behavior is unknown and frequently neglected. Here we identified the visual stimuli to which specific classes of sSC neurons respond, the downstream regions they target, and transgenic mice enabling class-specific manipulations. One class responds to small, slowly moving stimuli and projects exclusively to lateral posterior thalamus; another, comprising GABAergic neurons, responds to the sudden appearance or rapid movement of large stimuli and projects to multiple areas, including the lateral geniculate nucleus. A third class exhibits direction-selective responses and targets deeper SC layers. Together, our results show how specific sSC neurons represent and distribute diverse information and enable direct tests of their functional role.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2768-14.2014}, author = {Gale, Samuel D and Murphy, Gabe J} } @article {45779, title = {Distinct substrate selectivity of a metabolic hydrolase from Mycobacterium tuberculosis.}, journal = {Biochemistry}, volume = {53}, year = {2014}, month = {2014 Oct 29}, pages = {7386-95}, abstract = {

The transition between dormant and active Mycobacterium tuberculosis infection requires reorganization of its lipid metabolism and activation of a battery of serine hydrolase enzymes. Among these serine hydrolases, Rv0045c is a mycobacterial-specific serine hydrolase with limited sequence homology outside mycobacteria but structural homology to divergent bacterial hydrolase families. Herein, we determined the global substrate specificity of Rv0045c against a library of fluorogenic hydrolase substrates, constructed a combined experimental and computational model for its binding pocket, and performed comprehensive substitutional analysis to develop a structural map of its binding pocket. Rv0045c showed strong substrate selectivity toward short, straight chain alkyl esters with the highest activity toward four atom chains. This strong substrate preference was maintained through the combined action of residues in a flexible loop connecting the cap and α/β hydrolase domains and in residues close to the catalytic triad. Two residues bracketing the substrate-binding pocket (Gly90 and His187) were essential to maintaining the narrow substrate selectivity of Rv0045c toward various acyl ester substituents, as independent conversion of these residues significantly increased its catalytic activity and broadened its substrate specificity. Focused saturation mutagenesis of position 187 implicated this residue, as the differentiation point between the substrate specificity of Rv0045c and the structurally homologous ybfF hydrolase family. Insertion of the analogous tyrosine residue from ybfF hydrolases into Rv0045c increased the catalytic activity of Rv0045 by over 20-fold toward diverse ester substrates. The unique binding pocket structure and selectivity of Rv0045c provide molecular indications of its biological role and evidence for expanded substrate diversity in serine hydrolases from M. tuberculosis.

}, issn = {1520-4995}, doi = {10.1021/bi501108u}, author = {Lukowski, Jessica K and Savas, Christopher P and Gehring, Alexandra M and McKary, Magy G and Adkins, Chinessa T and Lavis, Luke D and Hoops, Geoffrey C and Johnson, R Jeremy} } @article {45052, title = {Distinguishing seemingly indistinguishable animals with computer vision.}, journal = {Nature Methods}, volume = {11}, year = {2014}, month = {2014 Jun 27}, pages = {721-2}, abstract = {

A general method to recognize and track unmarked animals within a population will enable new studies of social behavior and individuality.

}, issn = {1548-7105}, doi = {10.1038/nmeth.3004}, author = {Branson, Kristin} } @article {47631, title = {Distribution of ESCRT machinery at HIV assembly sites reveals virus scaffolding of ESCRT subunits.}, journal = {Science (New York, N.Y.)}, volume = {343}, year = {2014}, month = {2014 Feb 7}, pages = {653-6}, abstract = {

The human immunodeficiency virus (HIV) hijacks the endosomal sorting complexes required for transport (ESCRT) to mediate virus release from infected cells. The nanoscale organization of ESCRT machinery necessary for mediating viral abscission is unclear. Here, we applied three-dimensional superresolution microscopy and correlative electron microscopy to delineate the organization of ESCRT components at HIV assembly sites. We observed ESCRT subunits localized within the head of budding virions and released particles, with head-localized levels of CHMP2A decreasing relative to Tsg101 and CHMP4B upon virus abscission. Thus, the driving force for HIV release may derive from initial scaffolding of ESCRT subunits within the viral bud interior followed by plasma membrane association and selective remodeling of ESCRT subunits.

}, keywords = {Endosomal Sorting Complexes Required for Transport, gag Gene Products, Human Immunodeficiency Virus, HIV Infections, HIV-1, Humans, Imaging, Three-Dimensional, Microscopy, Protein Subunits, Virion, Virus Assembly, Virus Release}, issn = {1095-9203}, doi = {10.1126/science.1247786}, author = {Van Engelenburg, Schuyler B and Shtengel, Gleb and Sengupta, Prabuddha and Waki, Kayoko and Jarnik, Michal and Ablan, Sherimay D and Freed, Eric O and Hess, Harald F and Lippincott-Schwartz, Jennifer} } @article {6710, title = {Distribution of ESCRT machinery at HIV assembly sites reveals virus scaffolding of ESCRT subunits.}, journal = {Science}, volume = {343}, year = {2014}, month = {2014 Jan 16}, pages = {653-6}, abstract = {

The human immunodeficiency virus (HIV) hijacks the endosomal sorting complexes required for transport (ESCRT) to mediate virus release from infected cells. The nanoscale organization of ESCRT machinery necessary for mediating viral abscission is unclear. Here, we applied three-dimensional superresolution microscopy and correlative electron microscopy to delineate the organization of ESCRT components at HIV assembly sites. We observed ESCRT subunits localized within the head of budding virions and released particles, with head-localized levels of CHMP2A decreasing relative to Tsg101 and CHMP4B upon virus abscission. Thus, the driving force for HIV release may derive from initial scaffolding of ESCRT subunits within the viral bud interior followed by plasma membrane association and selective remodeling of ESCRT subunits.

}, issn = {1095-9203}, doi = {10.1126/science.1247786}, author = {Van Engelenburg, Schuyler B and Shtengel, Gleb and Sengupta, Prabuddha and Waki, Kayoko and Jarnik, Michal and Ablan, Sherimay D and Freed, Eric O and Hess, Harald F and Lippincott-Schwartz, Jennifer} } @article {6876, title = {Drosophila intermediate neural progenitors produce lineage-dependent related series of diverse neurons.}, journal = {Development}, volume = {141}, year = {2014}, month = {2014 Jan}, pages = {253-8}, abstract = {

Drosophila type II neuroblasts (NBs), like mammalian neural stem cells, deposit neurons through intermediate neural progenitors (INPs) that can each produce a series of neurons. Both type II NBs and INPs exhibit age-dependent expression of various transcription factors, potentially specifying an array of diverse neurons by combinatorial temporal patterning. Not knowing which mature neurons are made by specific INPs, however, conceals the actual variety of neuron types and limits further molecular studies. Here we mapped neurons derived from specific type II NB lineages and found that sibling INPs produced a morphologically similar but temporally regulated series of distinct neuron types. This suggests a common fate diversification program operating within each INP that is modulated by NB age to generate slightly different sets of diverse neurons based on the INP birth order. Analogous mechanisms might underlie the expansion of neuron diversity via INPs in mammalian brain.

}, keywords = {Animals, Brain, Cell Lineage, Drosophila, Genetically Modified, Models, Neural Stem Cells, Neurogenesis, Neurological}, issn = {1477-9129}, doi = {10.1242/dev.103069}, author = {Wang, Yu-Chun and Yang, Jacob S and Johnston, Rebecca and Ren, Qingzhong and Lee, Ying-Jou and Luan, Haojiang and Brody, Thomas and Odenwald, Ward F and Lee, Tzumin} } @article {45842, title = {The Drosophila surface glia transcriptome: evolutionary conserved blood-brain barrier processes.}, journal = {Frontiers in Neuroscience}, volume = {8}, year = {2014}, month = {2014 Nov 7}, pages = {346}, abstract = {

Central nervous system (CNS) function is dependent on the stringent regulation of metabolites, drugs, cells, and pathogens exposed to the CNS space. Cellular blood-brain barrier (BBB) structures are highly specific checkpoints governing entry and exit of all small molecules to and from the brain interstitial space, but the precise mechanisms that regulate the BBB are not well understood. In addition, the BBB has long been a challenging obstacle to the pharmacologic treatment of CNS diseases; thus model systems that can parse the functions of the BBB are highly desirable. In this study, we sought to define the transcriptome of the adult Drosophila melanogaster BBB by isolating the BBB surface glia with fluorescence activated cell sorting (FACS) and profiling their gene expression with microarrays. By comparing the transcriptome of these surface glia to that of all brain glia, brain neurons, and whole brains, we present a catalog of transcripts that are selectively enriched at the Drosophila BBB. We found that the fly surface glia show high expression of many ATP-binding cassette (ABC) and solute carrier (SLC) transporters, cell adhesion molecules, metabolic enzymes, signaling molecules, and components of xenobiotic metabolism pathways. Using gene sequence-based alignments, we compare the Drosophila and Murine BBB transcriptomes and discover many shared chemoprotective and small molecule control pathways, thus affirming the relevance of invertebrate models for studying evolutionary conserved BBB properties. The Drosophila BBB transcriptome is valuable to vertebrate and insect biologists alike as a resource for studying proteins underlying diffusion barrier development and maintenance, glial biology, and regulation of drug transport at tissue barriers.

}, issn = {1662-4548}, doi = {10.3389/fnins.2014.00346}, author = {DeSalvo, Michael K and Hindle, Samantha J and Rusan, Zeid M and Orng, Souvinh and Eddison, Mark and Halliwill, Kyle and Bainton, Roland J} } @article {46708, title = {Dynamics of survival of motor neuron (SMN) protein interaction with the mRNA-binding protein IMP1 facilitates its trafficking into motor neuron axons.}, journal = {Developmental Neurobiology}, volume = {74}, year = {2014}, month = {2014 Mar}, pages = {319-32}, abstract = {

Spinal muscular atrophy (SMA) is a lethal neurodegenerative disease specifically affecting spinal motor neurons. SMA is caused by the homozygous deletion or mutation of the survival of motor neuron 1 (SMN1) gene. The SMN protein plays an essential role in the assembly of spliceosomal ribonucleoproteins. However, it is still unclear how low levels of the ubiquitously expressed SMN protein lead to the selective degeneration of motor neurons. An additional role for SMN in the regulation of the axonal transport of mRNA-binding proteins (mRBPs) and their target mRNAs has been proposed. Indeed, several mRBPs have been shown to interact with SMN, and the axonal levels of few mRNAs, such as the β-actin mRNA, are reduced in SMA motor neurons. In this study we have identified the β-actin mRNA-binding protein IMP1/ZBP1 as a novel SMN-interacting protein. Using a combination of biochemical assays and quantitative imaging techniques in primary motor neurons, we show that IMP1 associates with SMN in individual granules that are actively transported in motor neuron axons. Furthermore, we demonstrate that IMP1 axonal localization depends on SMN levels, and that SMN deficiency in SMA motor neurons leads to a dramatic reduction of IMP1 protein levels. In contrast, no difference in IMP1 protein levels was detected in whole brain lysates from SMA mice, further suggesting neuron specific roles of SMN in IMP1 expression and localization. Taken together, our data support a role for SMN in the regulation of mRNA localization and axonal transport through its interaction with mRBPs such as IMP1.

}, keywords = {Animals, Axonal Transport, Axons, Biological Transport, Active, Brain, Cells, Cultured, Chromaffin Granules, Humans, Mice, Mice, Transgenic, Motor Neurons, Protein Interaction Domains and Motifs, Rats, RNA-Binding Proteins, Survival of Motor Neuron 1 Protein, Survival of Motor Neuron 2 Protein}, issn = {1932-846X}, doi = {10.1002/dneu.22111}, author = {Fallini, Claudia and Rouanet, Jeremy P and Donlin-Asp, Paul G and Guo, Peng and Zhang, Honglai and Singer, Robert H and Rossoll, Wilfried and Bassell, Gary J} } @article {45835, title = {Editorial overview: Membranes: recent methods in the study of membrane protein structure.}, journal = {Current Opinion in Structural Biology}, volume = {27}, year = {2014}, month = {2014 Aug}, pages = {iv-v}, issn = {1879-033X}, doi = {10.1016/j.sbi.2014.09.002}, author = {Gonen, Tamir and Waksman, Gabriel} } @article {6962, title = {Efficient Bayesian-based multiview deconvolution.}, journal = {Nature Methods}, volume = {11}, year = {2014}, month = {2014 Apr 20}, pages = {645-8}, abstract = {

Light-sheet fluorescence microscopy is able to image large specimens with high resolution by capturing the samples from multiple angles. Multiview deconvolution can substantially improve the resolution and contrast of the images, but its application has been limited owing to the large size of the data sets. Here we present a Bayesian-based derivation of multiview deconvolution that drastically improves the convergence time, and we provide a fast implementation using graphics hardware.

}, issn = {1548-7105}, doi = {10.1038/nmeth.2929}, author = {Preibisch, Stephan and Amat, Fernando and Stamataki, Evangelia and Sarov, Mihail and Singer, Robert H and Myers, Eugene and Tomancak, Pavel} } @article {46595, title = {EGFR and FGFR pathways have distinct roles in Drosophila mushroom body development and ethanol-induced behavior.}, journal = {PLoS One}, volume = {9}, year = {2014}, month = {2014 Jan 31}, pages = {e87714}, abstract = {

Epidermal Growth Factor Receptor (EGFR) signaling has a conserved role in ethanol-induced behavior in flies and mice, affecting ethanol-induced sedation in both species. However it is not known what other effects EGFR signaling may have on ethanol-induced behavior, or what roles other Receptor Tyrosine Kinase (RTK) pathways may play in ethanol induced behaviors. We examined the effects of both the EGFR and Fibroblast Growth Factor Receptor (FGFR) RTK signaling pathways on ethanol-induced enhancement of locomotion, a behavior distinct from sedation that may be associated with the rewarding effects of ethanol. We find that both EGFR and FGFR genes influence ethanol-induced locomotion, though their effects are opposite - EGFR signaling suppresses this behavior, while FGFR signaling promotes it. EGFR signaling affects development of the Drosophila mushroom bodies in conjunction with the JNK MAP kinase basket (bsk), and with the Ste20 kinase tao, and we hypothesize that the EGFR pathway affects ethanol-induced locomotion through its effects on neuronal development. We find, however, that FGFR signaling most likely affects ethanol-induced behavior through a different mechanism, possibly through acute action in adult neurons.

}, keywords = {Animals, Behavior, Animal, Central Nervous System Depressants, Drosophila melanogaster, Drosophila Proteins, Ethanol, Locomotion, Mice, Mushroom Bodies, Receptor, Epidermal Growth Factor, Receptors, Invertebrate Peptide, Signal Transduction}, issn = {1932-6203}, doi = {10.1371/journal.pone.0087714}, author = {King, Ian F G and Eddison, Mark and Kaun, Karla R and Heberlein, Ulrike} } @article {47626, title = {ER stress-induced clearance of misfolded GPI-anchored proteins via the secretory pathway.}, journal = {Cell}, volume = {158}, year = {2014}, month = {2014 Jul 31}, pages = {522-33}, abstract = {

Proteins destined for the cell surface are first assessed in the endoplasmic reticulum (ER) for proper folding before release into the secretory pathway. This ensures that defective proteins are normally prevented from entering the extracellular environment, where they could be disruptive. Here, we report that, when ER folding capacity is saturated during stress, misfolded glycosylphosphatidylinositol-anchored proteins dissociate from resident ER chaperones, engage export receptors, and quantitatively leave the ER via vesicular transport to the Golgi. Clearance from the ER commences within minutes of acute ER stress, before the transcriptional component of the unfolded protein response is activated. These aberrant proteins then access the cell surface transiently before destruction in lysosomes. Inhibiting this stress-induced pathway by depleting the ER-export receptors leads to aggregation of the ER-retained misfolded protein. Thus, this rapid response alleviates the elevated burden of misfolded proteins in the ER at the onset of ER stress, promoting protein homeostasis in the ER.

}, keywords = {Animals, Cell Line, Endoplasmic Reticulum Stress, Humans, Lysosomes, Mice, Prions, Protein Folding, Rats, Secretory Pathway, Unfolded Protein Response}, issn = {1097-4172}, doi = {10.1016/j.cell.2014.06.026}, author = {Satpute-Krishnan, Prasanna and Ajinkya, Monica and Bhat, Savithri and Itakura, Eisuke and Hegde, Ramanujan S and Lippincott-Schwartz, Jennifer} } @article {45781, title = {Evolved differences in larval social behavior mediated by novel pheromones.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 Dec 12}, abstract = {

Pheromones, chemical signals that convey social information, mediate many insect social behaviors, including navigation and aggregation. Several studies have suggested that behavior during the immature larval stages of Drosophila development is influenced by pheromones, but none of these compounds or the pheromone-receptor neurons that sense them have been identified. Here we report a larval pheromone-signaling pathway. We found that larvae produce two novel long-chain fatty acids that are attractive to other larvae. We identified a single larval chemosensory neuron that detects these molecules. Two members of the pickpocket family of DEG/ENaC channel subunits (ppk23 and ppk29) are required to respond to these pheromones. This pheromone system is evolving quickly, since the larval exudates of D. simulans, the sister species of D. melanogaster, are not attractive to other larvae. Our results define a new pheromone signaling system in Drosophila that shares characteristics with pheromone systems in a wide diversity of insects.

}, issn = {2050-084X}, doi = {10.7554/eLife.04205}, author = {Mast, Joshua D and De Moraes, Consuelo M and Alborn, Hans T and Lavis, Luke D and Stern, David L} } @article {6895, title = {Excitatory synaptic inputs to mouse on-off direction-selective retinal ganglion cells lack direction tuning.}, journal = {The Journal of Neuroscience : the Official Journal of the Society for Neuroscience}, volume = {34}, year = {2014}, month = {2014 Mar 12}, pages = {3976-81}, abstract = {

Direction selectivity represents a fundamental visual computation. In mammalian retina, On-Off direction-selective ganglion cells (DSGCs) respond strongly to motion in a preferred direction and weakly to motion in the opposite, null direction. Electrical recordings suggested three direction-selective (DS) synaptic mechanisms: DS GABA release during null-direction motion from starburst amacrine cells (SACs) and DS acetylcholine and glutamate release during preferred direction motion from SACs and bipolar cells. However, evidence for DS acetylcholine and glutamate release has been inconsistent and at least one bipolar cell type that contacts another DSGC (On-type) lacks DS release. Here, whole-cell recordings in mouse retina showed that cholinergic input to On-Off DSGCs lacked DS, whereas the remaining (glutamatergic) input showed apparent DS. Fluorescence measurements with the glutamate biosensor intensity-based glutamate-sensing fluorescent reporter (iGluSnFR) conditionally expressed in On-Off DSGCs showed that glutamate release in both On- and Off-layer dendrites lacked DS, whereas simultaneously recorded excitatory currents showed apparent DS. With GABA-A receptors blocked, both iGluSnFR signals and excitatory currents lacked DS. Our measurements rule out DS release from bipolar cells onto On-Off DSGCs and support a theoretical model suggesting that apparent DS excitation in voltage-clamp recordings results from inadequate voltage control of DSGC dendrites during null-direction inhibition. SAC GABA release is the apparent sole source of DS input onto On-Off DSGCs.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.5017-13.2014}, author = {Park, Silvia J H and Kim, In-Jung and Looger, Loren L and Demb, Jonathan B and Borghuis, Bart G} } @article {45058, title = {Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data.}, journal = {Nature Methods}, volume = {11}, year = {2014}, month = {2014 Jul 20}, pages = {951-8}, abstract = {

The comprehensive reconstruction of cell lineages in complex multicellular organisms is a central goal of developmental biology. We present an open-source computational framework for the segmentation and tracking of cell nuclei with high accuracy and speed. We demonstrate its (i) generality by reconstructing cell lineages in four-dimensional, terabyte-sized image data sets of fruit fly, zebrafish and mouse embryos acquired with three types of fluorescence microscopes, (ii) scalability by analyzing advanced stages of development with up to 20,000 cells per time point at 26,000 cells min(-1) on a single computer workstation and (iii) ease of use by adjusting only two parameters across all data sets and providing visualization and editing tools for efficient data curation. Our approach achieves on average 97.0\% linkage accuracy across all species and imaging modalities. Using our system, we performed the first cell lineage reconstruction of early Drosophila melanogaster nervous system development, revealing neuroblast dynamics throughout an entire embryo.

}, issn = {1548-7105}, doi = {10.1038/nmeth.3036}, author = {Amat, Fernando and Lemon, William and Mossing, Daniel P and McDole, Katie and Wan, Yinan and Branson, Kristin and Myers, Eugene W and Keller, Philipp J} } @article {47624, title = {Flat clathrin lattices: stable features of the plasma membrane.}, journal = {Molecular biology of the cell}, volume = {25}, year = {2014}, month = {2014 Nov 5}, pages = {3581-94}, abstract = {

Clathrin-mediated endocytosis (CME) is a fundamental property of eukaryotic cells. Classical CME proceeds via the formation of clathrin-coated pits (CCPs) at the plasma membrane, which invaginate to form clathrin-coated vesicles, a process that is well understood. However, clathrin also assembles into flat clathrin lattices (FCLs); these structures remain poorly described, and their contribution to cell biology is unclear. We used quantitative imaging to provide the first comprehensive description of FCLs and explore their influence on plasma membrane organization. Ultrastructural analysis by electron and superresolution microscopy revealed two discrete populations of clathrin structures. CCPs were typified by their sphericity, small size, and homogeneity. FCLs were planar, large, and heterogeneous and present on both the dorsal and ventral surfaces of cells. Live microscopy demonstrated that CCPs are short lived and culminate in a peak of dynamin recruitment, consistent with classical CME. In contrast, FCLs were long lived, with sustained association with dynamin. We investigated the biological relevance of FCLs using the chemokine receptor CCR5 as a model system. Agonist activation leads to sustained recruitment of CCR5 to FCLs. Quantitative molecular imaging indicated that FCLs partitioned receptors at the cell surface. Our observations suggest that FCLs provide stable platforms for the recruitment of endocytic cargo.

}, keywords = {Animals, Chemokine CCL5, CHO Cells, Clathrin, Clathrin-Coated Vesicles, Coated Pits, Cell-Membrane, Cricetulus, Dynamins, Endocytosis, Genes, Reporter, Green Fluorescent Proteins, HEK293 Cells, Hela Cells, Humans, Microscopy, Electron, Microscopy, Fluorescence, Molecular Imaging, Protein Transport, Receptors, CCR5}, issn = {1939-4586}, doi = {10.1091/mbc.E14-06-1154}, author = {Grove, Joe and Metcalf, Daniel J and Knight, Alex E and Wavre-Shapton, Sil{\`e}ne T and Sun, Tony and Protonotarios, Emmanouil D and Griffin, Lewis D and Lippincott-Schwartz, Jennifer and Marsh, Mark} } @article {48390, title = {Flies and humans share a motion estimation strategy that exploits natural scene statistics.}, journal = {Nature neuroscience}, volume = {17}, year = {2014}, month = {2014 Feb}, pages = {296-303}, abstract = {

Sighted animals extract motion information from visual scenes by processing spatiotemporal patterns of light falling on the retina. The dominant models for motion estimation exploit intensity correlations only between pairs of points in space and time. Moving natural scenes, however, contain more complex correlations. We found that fly and human visual systems encode the combined direction and contrast polarity of moving edges using triple correlations that enhance motion estimation in natural environments. Both species extracted triple correlations with neural substrates tuned for light or dark edges, and sensitivity to specific triple correlations was retained even as light and dark edge motion signals were combined. Thus, both species separately process light and dark image contrasts to capture motion signatures that can improve estimation accuracy. This convergence argues that statistical structures in natural scenes have greatly affected visual processing, driving a common computational strategy over 500 million years of evolution.

}, keywords = {Adaptation, Physiological, Animals, Contrast Sensitivity, Drosophila, Electroencephalography, Evoked Potentials, Visual, Genotype, Humans, Models, Neurological, Motion Perception, Pattern Recognition, Visual, Photic Stimulation, Psychophysics}, issn = {1546-1726}, doi = {10.1038/nn.3600}, author = {Clark, Damon A and Fitzgerald, James E and Ales, Justin M and Gohl, Daryl M and Silies, Marion A and Norcia, Anthony M and Clandinin, Thomas R} } @article {6879, title = {Flow of cortical activity underlying a tactile decision in mice.}, journal = {Neuron}, volume = {81}, year = {2014}, month = {2014 Jan 8}, pages = {179-94}, abstract = {

Perceptual decisions involve distributed cortical activity. Does information flow sequentially from one cortical area to another, or do networks of interconnected areas contribute at the same time? Here we delineate when and how activity in specific areas drives a whisker-based decision in mice. A short-term memory component temporally separated tactile "sensation" and "action" (licking). Using optogenetic inhibition (spatial resolution, 2 mm; temporal resolution, 100 ms), we surveyed the neocortex for regions driving behavior during specific behavioral epochs. Barrel cortex was critical for sensation. During the short-term memory, unilateral inhibition of anterior lateral motor cortex biased responses to the ipsilateral side. Consistently, barrel cortex showed stimulus-specific activity during sensation, whereas motor cortex showed choice-specific preparatory activity and movement-related activity, consistent with roles in motor planning and movement. These results suggest serial information flow from sensory to motor areas during perceptual decision making.

}, keywords = {Action Potentials, Afferent Pathways, Animals, Cerebral Cortex, Conditioning, Decision Making, Discrimination (Psychology), Female, Green Fluorescent Proteins, Male, Mice, Motion Perception, Nerve Net, Neurons, Operant, Photic Stimulation, Rhodopsin, Touch, Transgenic, Vesicular Inhibitory Amino Acid Transport Proteins, Vibrissae}, issn = {1097-4199}, doi = {10.1016/j.neuron.2013.10.020}, author = {Guo, Zengcai V and Li, Nuo and Huber, Daniel and Ophir, Eran and Gutnisky, Diego and Ting, Jonathan T and Feng, Guoping and Svoboda, Karel} } @article {6953, title = {Flying Drosophila stabilize their vision-based velocity controller by sensing wind with their antennae.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, year = {2014}, month = {2014 Apr 1}, pages = {E1182-91}, abstract = {

Flies and other insects use vision to regulate their groundspeed in flight, enabling them to fly in varying wind conditions. Compared with mechanosensory modalities, however, vision requires a long processing delay (\ 100 ms) that might introduce instability if operated at high gain. Flies also sense air motion with their antennae, but how this is used in flight control is unknown. We manipulated the antennal function of fruit flies by ablating their aristae, forcing them to rely on vision alone to regulate groundspeed. Arista-ablated flies in flight exhibited significantly greater groundspeed variability than intact flies. We then subjected them to a series of controlled impulsive wind gusts delivered by an air piston and experimentally manipulated antennae and visual feedback. The results show that an antenna-mediated response alters wing motion to cause flies to accelerate in the same direction as the gust. This response opposes flying into a headwind, but flies regularly fly upwind. To resolve this discrepancy, we obtained a dynamic model of the fly{\textquoteright}s velocity regulator by fitting parameters of candidate models to our experimental data. The model suggests that the groundspeed variability of arista-ablated flies is the result of unstable feedback oscillations caused by the delay and high gain of visual feedback. The antenna response drives active damping with a shorter delay (\ 20 ms) to stabilize this regulator, in exchange for increasing the effect of rapid wind disturbances. This provides insight into flies{\textquoteright} multimodal sensory feedback architecture and constitutes a previously unknown role for the antennae.

}, issn = {1091-6490}, doi = {10.1073/pnas.1323529111}, author = {Fuller, Sawyer Buckminster and Straw, Andrew D and Peek, Martin Y and Murray, Richard M and Dickinson, Michael H} } @article {45059, title = {FlyMAD: rapid thermogenetic control of neuronal activity in freely walking Drosophila.}, journal = {Nature Methods}, volume = {11}, year = {2014}, month = {2014 Jul 11}, pages = {756-62}, abstract = {

Rapidly and selectively modulating the activity of defined neurons in unrestrained animals is a powerful approach in investigating the circuit mechanisms that shape behavior. In Drosophila melanogaster, temperature-sensitive silencers and activators are widely used to control the activities of genetically defined neuronal cell types. A limitation of these thermogenetic approaches, however, has been their poor temporal resolution. Here we introduce FlyMAD (the fly mind-altering device), which allows thermogenetic silencing or activation within seconds or even fractions of a second. Using computer vision, FlyMAD targets an infrared laser to freely walking flies. As a proof of principle, we demonstrated the rapid silencing and activation of neurons involved in locomotion, vision and courtship. The spatial resolution of the focused beam enabled preferential targeting of neurons in the brain or ventral nerve cord. Moreover, the high temporal resolution of FlyMAD allowed us to discover distinct timing relationships for two neuronal cell types previously linked to courtship song.

}, issn = {1548-7105}, doi = {10.1038/nmeth.2973}, author = {Bath, Daniel E and Stowers, John R and H{\"o}rmann, Dorothea and Poehlmann, Andreas and Dickson, Barry J and Straw, Andrew D} } @article {46229, title = {Focused proofreading: efficiently extracting connectomes from segmented EM images.}, journal = {arXiv}, year = {2014}, month = {2014 Sep 3}, pages = {arXiv:1409.1199 [q-bio.QM]}, abstract = {

Pixel and superpixel classifiers have become essential tools for EM segmentation algorithms. Training these classifiers remains a major bottleneck primarily due to the requirement of completely annotating the dataset which is tedious, error-prone and costly. In this paper, we propose an interactive learning scheme for the superpixel classifier for EM segmentation. Our algorithm is "active semi-supervised" because it requests the labels of a small number of examples from user and applies label propagation technique to generate these queries. Using only a small set (\<20\%) of all datapoints, the proposed algorithm consistently generates a classifier almost as accurate as that estimated from a complete groundtruth. We provide segmentation results on multiple datasets to show the strength of these classifiers.

}, url = {http://arxiv.org/abs/1409.1199}, author = {Plaza, Stephen M} } @article {6959, title = {Frealix: Model-based refinement of helical filament structures from electron micrographs.}, journal = {Journal of Structural Biology}, volume = {186}, year = {2014}, month = {2014 Mar 20}, pages = {234-44}, abstract = {

The structures of many helical protein filaments can be derived from electron micrographs of their suspensions in thin films of vitrified aqueous solutions. The most successful and generally-applicable approach treats short segments of these filaments as independent "single particles", yielding near-atomic resolution for rigid and well-ordered filaments. The single-particle approach can also accommodate filament deformations, yielding sub-nanometer resolution for more flexible filaments. However, in the case of thin and flexible filaments, such as some amyloid-β (Aβ) fibrils, the single-particle approach may fail because helical segments can be curved or otherwise distorted and their alignment can be inaccurate due to low contrast in the micrographs. We developed new software called Frealix that allows the use of arbitrarily short filament segments during alignment to approximate even high curvatures. All segments in a filament are aligned simultaneously with constraints that ensure that they connect to each other in space to form a continuous helical structure. In this paper, we describe the algorithm and benchmark it against datasets of Aβ(1-40) fibrils and tobacco mosaic virus (TMV), both analyzed in earlier work. In the case of TMV, our algorithm achieves similar results to single-particle analysis. In the case of Aβ(1-40) fibrils, we match the previously-obtained resolution but we are also able to obtain reliable alignments and \~{}8-{\r A} reconstructions from curved filaments. Our algorithm also offers a detailed characterization of filament deformations in three dimensions and enables a critical evaluation of the worm-like chain model for biological filaments.

}, issn = {1095-8657}, doi = {10.1016/j.jsb.2014.03.012}, author = {Rohou, Alexis and Grigorieff, Nikolaus} } @article {48037, title = {A fully genetically encoded protein architecture for optical control of peptide ligand concentration.}, year = {2014}, abstract = {

Ion channels are among the most important proteins in biology, regulating the activity of excitable cells and changing in diseases. Ideally it would be possible to actuate endogenous ion channels, in a temporally precise and reversible manner, and without requiring chemical cofactors. Here we present a modular protein architecture for fully genetically encoded, light-modulated control of ligands that modulate ion channels of a targeted cell. Our reagent, which we call a lumitoxin, combines a photoswitch and an ion channel-blocking peptide toxin. Illumination causes the photoswitch to unfold, lowering the toxin{\textquoteright}s local concentration near the cell surface, and enabling the ion channel to function. We explore lumitoxin modularity by showing operation with peptide toxins that target different voltage-dependent K+\ channels. The lumitoxin architecture may represent a new kind of modular protein-engineering strategy for designing light-activated proteins, and thus may enable development of novel tools for modulating cellular physiology.

}, author = {Daniel Schmidt and Paul Tillberg and Fei Chen and Edward Boyden} } @article {45334, title = {A GAL4 driver resource for developmental and behavioral studies on the larval CNS of Drosophila.}, journal = {Cell Reports}, volume = {8}, year = {2014}, month = {2014 Aug 7}, pages = {897-908}, abstract = {

We report the larval CNS expression patterns for 6,650 GAL4 lines based on cis-regulatory regions (CRMs) from the Drosophila genome. Adult CNS expression patterns were previously reported for this collection, thereby providing a unique resource for determining the origins of adult cells. An illustrative example reveals the origin of the astrocyte-like glia of the ventral\ CNS. Besides larval neurons and glia, the larval CNS\ contains scattered lineages of immature, adult-specific\ neurons. Comparison of lineage expression within this large collection of CRMs provides insight into the codes used for designating neuronal types. The CRMs encode both dense and sparse patterns of lineage expression. There is little correlation between brain and thoracic lineages in patterns of sparse expression, but expression in the two regions is highly correlated in the dense mode. The optic lobes, by comparison, appear to use a different set of genetic instructions in their development.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2014.06.065}, author = {Li, Hsing-Hsi and Kroll, Jason R and Lennox, Sara M and Ogundeyi, Omotara and Jeter, Jennifer and Depasquale, Gina and Truman, James W} } @article {46703, title = {Gene regulation: the HSP70 gene jumps when shocked.}, journal = {Current Biology}, volume = {24}, year = {2014}, month = {2014 May 19}, pages = {R396-8}, abstract = {

Limited chromosome mobility has been observed in mammalian interphase nuclei. Live imaging shows unidirectional and actin-dependent movement of HSP70 loci towards speckles upon heat shock, resulting in enhanced transcription. This adds further impetus to understanding compartmentalization of function in the nucleus.

}, keywords = {Animals, Heat-Shock Response, Humans, Transcriptional Activation, Transgenes}, issn = {1879-0445}, doi = {10.1016/j.cub.2014.03.070}, author = {Vera, Maria and Singer, Robert H} } @article {6882, title = {Generating mosaics for lineage analysis in flies.}, journal = {Wiley Interdisciplinary Reviews - Developmental Biology}, volume = {3}, year = {2014}, month = {2014 Jan}, pages = {69-81}, abstract = {

By generating and studying mosaic organisms, we are learning how intricate tissues form as cells proliferate and diversify through organism development. FLP/FRT-mediated site-specific mitotic recombination permits the generation of mosaic flies with efficiency and control. With heat-inducible or tissue-specific FLP transgenes at our disposal, we can engineer mosaics carrying clones of homozygous cells that come from specific pools of heterozygous precursors. This permits detailed cell lineage analysis followed by mosaic analysis of gene functions in the underlying developmental processes. Expression of transgenes (e.g., reporters) only in the homozygous cells enables mosaic analysis in the complex nervous system. Tracing neuronal lineages by using mosaics revolutionized mechanistic studies of neuronal diversification and differentiation, exemplifying the power of genetic mosaics in developmental biology. WIREs Dev Biol 2014, 3:69{\textendash}81. doi: 10.1002/wdev.122

}, issn = {1759-7684}, doi = {10.1002/wdev.122}, author = {Lee, Tzumin} } @article {6709, title = {Genetic identification and separation of innate and experience-dependent courtship behaviors in Drosophila.}, journal = {Cell}, volume = {156}, year = {2014}, month = {2014 Jan 16}, pages = {236-48}, abstract = {

Wild-type D.\ melanogaster males innately possess the ability to perform a multistep courtship ritual to conspecific females. The potential for this behavior is specified by the male-specific products of the fruitless (fru(M)) gene; males without fru(M) do not court females when held in isolation. We show that such fru(M) null males acquire the potential for courtship when grouped with other flies; they apparently learn to court flies with which they were grouped, irrespective of sex or species and retain this behavior for at least a week. The male-specific product of the doublesex gene (dsx(M)) is necessary and sufficient for the acquisition of the potential for such experience-dependent courtship. These results reveal a process that builds, via dsx(M) and social experience, the potential for a more flexible sexual behavior, which could be evolutionarily conserved as dsx-related genes that function in sexual development are found throughout the animal kingdom.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2013.11.041}, author = {Pan, Yufeng and Baker, Bruce S} } @article {45696, title = {A genetically specified connectomics approach applied to long-range feeding regulatory circuits.}, journal = {Nature Neuroscience}, volume = {17}, year = {2014}, month = {2014 Dec}, pages = {1830-9}, abstract = {

Synaptic connectivity and molecular composition provide a blueprint for information processing in neural circuits. Detailed structural analysis of neural circuits requires nanometer resolution, which can be obtained with serial-section electron microscopy. However, this technique remains challenging for reconstructing molecularly defined synapses. We used a genetically encoded synaptic marker for electron microscopy (GESEM) based on intra-vesicular generation of electron-dense labeling in axonal boutons. This approach allowed the identification of synapses from Cre recombinase-expressing or GAL4-expressing neurons in the mouse and fly with excellent preservation of ultrastructure. We applied this tool to visualize long-range connectivity of AGRP and POMC neurons in the mouse, two molecularly defined hypothalamic populations that are important for feeding behavior. Combining selective ultrastructural reconstruction of neuropil with functional and viral circuit mapping, we characterized some basic features of circuit organization for axon projections of these cell types. Our findings demonstrate that GESEM labeling enables long-range connectomics with molecularly defined cell types.

}, issn = {1546-1726}, doi = {10.1038/nn.3854}, author = {Atasoy, Deniz and Betley, J Nicholas and Li, Wei-Ping and Su, Helen H and Sertel, Sinem M and Scheffer, Louis K and Simpson, Julie H and Fetter, Richard D and Sternson, Scott M} } @article {45099, title = {Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis.}, journal = {Science}, volume = {344}, year = {2014}, month = {2014 Apr 25}, pages = {380-6}, abstract = {

Tsetse flies are the sole vectors of human African trypanosomiasis throughout sub-Saharan Africa. Both sexes of adult tsetse feed exclusively on blood and contribute to disease transmission. Notable differences between tsetse and other disease vectors include obligate microbial symbioses, viviparous reproduction, and lactation. Here, we describe the sequence and annotation of the 366-megabase Glossina morsitans morsitans genome. Analysis of the genome and the 12,308 predicted protein-encoding genes led to multiple discoveries, including chromosomal integrations of bacterial (Wolbachia) genome sequences, a family of lactation-specific proteins, reduced complement of host pathogen recognition proteins, and reduced olfaction/chemosensory associated genes. These genome data provide a foundation for research into trypanosomiasis prevention and yield important insights with broad implications for multiple aspects of tsetse biology.

}, keywords = {Animals, Blood, Feeding Behavior, Female, Genes, Insect, Genome, Insect, Insect Proteins, Insect Vectors, Microbiota, Molecular Sequence Annotation, Molecular Sequence Data, Reproduction, Salivary Glands, Sensation, Sequence Analysis, DNA, Symbiosis, Trypanosoma, Trypanosomiasis, African, Tsetse Flies, Wolbachia}, issn = {1095-9203}, doi = {10.1126/science.1249656} } @article {6954, title = {Genome-wide identification of Drosophila Hb9 targets reveals a pivotal role in directing the transcriptome within eight neuronal lineages, including activation of nitric oxide synthase and Fd59a/Fox-D.}, journal = {Developmental Biology}, volume = {388}, year = {2014}, month = {2014 Apr 1}, pages = {117-33}, abstract = {

Hb9 is a homeodomain-containing transcription factor that acts in combination with Nkx6, Lim3, and Tail-up (Islet) to guide the stereotyped differentiation, connectivity, and function of a subset of neurons in Drosophila. The role of Hb9 in directing neuronal differentiation is well documented, but the lineage of Hb9(+) neurons is only partly characterized, its regulation is poorly understood, and most of the downstream genes through which it acts remain at large. Here, we complete the lineage tracing of all embryonic Hb9(+) neurons (to eight neuronal lineages) and provide evidence that hb9, lim3, and tail-up are coordinately regulated by a common set of upstream factors. Through the parallel use of micro-array gene expression profiling and the Dam-ID method, we searched for Hb9-regulated genes, uncovering transcription factors as the most over-represented class of genes regulated by Hb9 (and Nkx6) in the CNS. By a nearly ten-to-one ratio, Hb9 represses rather than activates transcription factors, highlighting transcriptional repression of other transcription factors as a core mechanism by which Hb9 governs neuronal determination. From the small set of genes activated by Hb9, we characterized the expression and function of two - fd59a/foxd, which encodes a transcription factor, and Nitric oxide synthase. Under standard lab conditions, both genes are dispensable for Drosophila development, but Nos appears to inhibit hyper-active behavior and fd59a appears to act in octopaminergic neurons to control egg-laying behavior. Together our data clarify the mechanisms through which Hb9 governs neuronal specification and differentiation and provide an initial characterization of the expression and function of Nos and fd59a in the Drosophila CNS.

}, issn = {1095-564X}, doi = {10.1016/j.ydbio.2014.01.029}, author = {Lacin, Haluk and Rusch, Jannette and Yeh, Raymond T and Fujioka, Miki and Wilson, Beth A and Zhu, Yi and Robie, Alice A and Mistry, Hemlata and Wang, Ting and Jaynes, James B and Skeath, James B} } @article {45592, title = {A giant fibre bypass for the fly.}, journal = {Journal of Experimental Biology}, volume = {217}, year = {2014}, month = {2014 Oct 24}, pages = {2988-89}, doi = {10.1242/​jeb.095000 }, author = {Zwart, Maarten} } @article {6934, title = {Graph-based active learning of agglomeration (GALA): a Python library to segment 2D and 3D neuroimages}, journal = {Frontiers in Neuroinformatics}, volume = {8}, year = {2014}, month = {2014 Apr 4}, pages = {34}, abstract = {

The aim in high-resolution connectomics is to reconstruct complete neuronal connectivity in a tissue. Currently, the only technology capable of resolving the smallest neuronal processes is electron microscopy (EM). Thus, a common approach to network reconstruction is to perform (error-prone) automatic segmentation of EM images, followed by manual proofreading by experts to fix errors. We have developed an algorithm and software library to not only improve the accuracy of the initial automatic segmentation, but also point out the image coordinates where it is likely to have made errors. Our software, called gala (graph-based active learning of agglomeration), improves the state of the art in agglomerative image segmentation. It is implemented in Python and makes extensive use of the scientific Python stack (numpy, scipy, networkx, scikit-learn, scikit-image, and others). We present here the software architecture of the gala library, and discuss several designs that we consider would be generally useful for other segmentation packages. We also discuss the current limitations of the gala library and how we intend to address them.

}, issn = {1662-5196}, doi = {10.3389/fninf.2014.00034}, author = {Nunez-Iglesias, Juan and Kennedy, Ryan and Plaza, Stephen M and Chakraborty, Anirban and William T. Katz} } @conference {65046, title = {A Hebbian/Anti-Hebbian network derived from online non-negative matrix factorization can cluster and discover sparse features.}, booktitle = {2014 48th Asilomar Conference on Signals, Systems and Computers2014 48th Asilomar Conference on Signals, Systems and Computers}, year = {2014}, month = {2015 Mar 02}, publisher = {IEEE}, organization = {IEEE}, address = {Pacific Grove, CA, USA}, abstract = {

Olshausen and Field (OF) proposed that neural computations in the primary visual cortex (V1) can be partially modelled by sparse dictionary learning. By minimizing the regularized representation error they derived an online algorithm, which learns Gabor-filter receptive fields from a natural image ensemble in agreement with physiological experiments. Whereas the OF algorithm can be mapped onto the dynamics and synaptic plasticity in a single-layer neural network, the derived learning rule is nonlocal - the synaptic weight update depends on the activity of neurons other than just pre- and postsynaptic ones {\textendash} and hence biologically implausible. Here, to overcome this problem, we derive sparse dictionary learning from a novel cost-function - a regularized error of the symmetric factorization of the input{\textquoteright}s similarity matrix. Our algorithm maps onto a neural network of the same architecture as OF but using only biologically plausible local learning rules. When trained on natural images our network learns Gabor-filter receptive fields and reproduces the correlation among synaptic weights hard-wired in the OF network. Therefore, online symmetric matrix factorization may serve as an algorithmic theory of neural computation.\ 

}, doi = {10.1109/ACSSC.2014.7094553}, url = {http://ieeexplore.ieee.org/document/7094553/http://xplorestaging.ieee.org/ielx7/7066991/7094373/07094553.pdf?arnumber=7094553}, author = {Pehlevan, Cengiz and Chklovskii, Dmitri B.} } @article {46704, title = {Heterogeneity in periodontitis prevalence in the Hispanic Community Health Study/Study of Latinos.}, journal = {Annals of Epidemiology}, volume = {24}, year = {2014}, month = {2014 Jun}, pages = {455-62}, abstract = {

PURPOSE: The aim of the study was to examine acculturation and established risk factors in explaining variation in periodontitis prevalence among Hispanic/Latino subgroups.

METHODS: Participants were 12,730 dentate adults aged 18-74 years recruited into the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) from four U.S. field centers between 2008 and 2011. A standardized periodontal assessment measured probing pocket depth and gingival recession at six sites per tooth for up to 28 teeth. Periodontitis was defined according to the Centers for Disease Control and Prevention and American Academy of Periodontology case classifications developed for population surveillance. Covariates included acculturation indicators and established periodontitis risk factors. Survey estimation procedures took account of the complex sampling design. Adjusted multivariate binomial regression estimated prevalence ratios and 95\% confidence limits (CLs).

RESULTS: Unadjusted prevalence of moderate and severe periodontitis was 38.5\% and ranged from 24.7\% among Dominicans to 52.1\% among Cubans. Adjusted prevalence ratios for subgroups relative to Dominicans were as follows: (1) 1.34 (95\% CL, 1.13-1.58) among South Americans; (2) 1.37 (95\% CL, 1.17-1.61) among Puerto Ricans; (3) 1.43 (95\% CL, 1.25-1.64) among Mexicans; (4) 1.53 (95\% CL, 1.32-1.76) among Cubans; and (5) 1.55 (95\% CL, 1.35-1.78) among Central Americans.

CONCLUSIONS: Heterogeneity in prevalence of moderate/severe periodontitis among Hispanic/Latino subpopulations was not explained by acculturation or periodontitis risk factors.

}, keywords = {Adult, Aged, Attitude to Health, Dental Health Surveys, Female, Hispanic Americans, Humans, Male, Middle Aged, Oral Hygiene, Periodontitis, Population Surveillance, Prevalence, Risk Assessment, Risk Factors, United States, Young Adult}, issn = {1873-2585}, doi = {10.1016/j.annepidem.2014.02.018}, author = {Sanders, Anne E and Campbell, Steven M and Mauriello, Sally M and Beck, James D and Jimenez, Monik C and Kaste, Linda M and Singer, Richard H and Beaver, Shirley M and Finlayson, Tracy L and Badner, Victor M} } @article {45637, title = {High thermodynamic stability of parametrically designed helical bundles.}, journal = {Science}, volume = {346}, year = {2014}, month = {2014 Oct 24}, pages = {481-5}, abstract = {

We describe a procedure for designing proteins with backbones produced by varying the parameters in the Crick coiled coil-generating equations. Combinatorial design calculations identify low-energy sequences for alternative helix supercoil arrangements, and the helices in the lowest-energy arrangements are connected by loop building. We design an antiparallel monomeric untwisted three-helix bundle with 80-residue helices, an antiparallel monomeric right-handed four-helix bundle, and a pentameric parallel left-handed five-helix bundle. The designed proteins are extremely stable (extrapolated ΔGfold \> 60 kilocalories per mole), and their crystal structures are close to those of the design models with nearly identical core packing between the helices. The approach enables the custom design of hyperstable proteins with fine-tuned geometries for a wide range of applications.

}, issn = {1095-9203}, doi = {10.1126/science.1257481}, author = {Huang, Po-Ssu and Oberdorfer, Gustav and Xu, Chunfu and Pei, Xue Y and Nannenga, Brent L and Rogers, Joseph M and DiMaio, Frank and Gonen, Tamir and Luisi, Ben and Baker, David} } @article {47897, title = {A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain.}, journal = {Neuron}, volume = {83}, year = {2014}, month = {2014 Jul 16}, pages = {309-23}, abstract = {

To provide a temporal framework for the genoarchitecture of brain development, we generated in situ hybridization data for embryonic and postnatal mouse brain at seven developmental stages for \~{}2,100 genes, which were processed with an automated informatics pipeline and manually annotated. This resource comprises 434,946 images, seven reference atlases, an ontogenetic ontology, and tools to explore coexpression of genes across neurodevelopment. Gene sets coinciding with developmental phenomena were identified. A temporal shift in the principles governing the molecular organization of the brain was detected, with transient neuromeric, plate-based organization of the brain present at E11.5 and E13.5. Finally, these data provided a transcription factor code that discriminates brain structures and identifies the developmental age of a tissue, providing a foundation for eventual genetic manipulation or tracking of specific brain structures over development. The resource is available as the Allen Developing Mouse Brain Atlas (http://developingmouse.brain-map.org).

}, keywords = {Animals, Brain, Brain Mapping, Gene Expression, Gene Expression Profiling, Gene Expression Regulation, Developmental, Mice}, issn = {1097-4199}, doi = {10.1016/j.neuron.2014.05.033}, author = {Thompson, Carol L and Ng, Lydia and Menon, Vilas and Martinez, Salvador and Lee, Chang-Kyu and Glattfelder, Katie and Sunkin, Susan M and Henry, Alex and Lau, Christopher and Dang, Chinh and Garcia-Lopez, Raquel and Martinez-Ferre, Almudena and Pombero, Ana and Rubenstein, John L R and Wakeman, Wayne B and Hohmann, John and Dee, Nick and Sodt, Andrew J and Young, Rob and Smith, Kimberly and Nguyen, Thuc-Nghi and Kidney, Jolene and Kuan, Leonard and Jeromin, Andreas and Kaykas, Ajamete and Miller, Jeremy and Page, Damon and Orta, Geri and Bernard, Amy and Riley, Zackery and Smith, Simon and Wohnoutka, Paul and Hawrylycz, Michael J and Puelles, Luis and Jones, Allan R} } @article {45860, title = {High-resolution structure determination by continuous-rotation data collection in MicroED.}, journal = {Nature Methods}, volume = {11}, year = {2014}, month = {2014 Sep}, pages = {927-30}, abstract = {

MicroED uses very small three-dimensional protein crystals and electron diffraction for structure determination. We present an improved data collection protocol for MicroED called {\textquoteright}continuous rotation{\textquoteright}. Microcrystals are continuously rotated during data collection, yielding more accurate data. The method enables data processing with the crystallographic software tool MOSFLM, which resulted in improved resolution for the model protein lysozyme. These improvements are paving the way for the broad implementation and application of MicroED in structural biology.

}, keywords = {Algorithms, Databases, Protein, Electrons, Imaging, Three-Dimensional, Information Storage and Retrieval, Lasers, Microscopy, Video, Protein Conformation, Proteins, Rotation, Scattering, Small Angle, X-Ray Diffraction}, issn = {1548-7105}, doi = {10.1038/nmeth.3043}, author = {Nannenga, Brent L and Shi, Dan and Leslie, Andrew G W and Gonen, Tamir} } @article {45695, title = {Identification of loci that cause phenotypic variation in diverse species with the reciprocal hemizygosity test.}, journal = {Trends in Genetics}, volume = {30}, year = {2014}, month = {2014 Dec}, pages = {547-554}, abstract = {

The reciprocal hemizygosity test is a straightforward genetic test that can positively identify genes that have evolved to contribute to a phenotypic difference between strains or between species. The test involves a comparison between hybrids that are genetically identical throughout the genome except at the test locus, which is rendered hemizygous for alternative alleles from the two parental strains. If the two reciprocal hemizygotes display different phenotypes, then the two parental alleles must have evolved. New methods for targeted mutagenesis will allow application of the reciprocal hemizygosity test in many organisms. This review discusses the principles, advantages, and limitations of the test.

}, issn = {0168-9525}, doi = {10.1016/j.tig.2014.09.006}, author = {Stern, David L} } @article {46231, title = {Identifying synapses using deep and wide multiscale recursive networks.}, journal = {arXiv}, year = {2014}, month = {2014 Sep 5}, pages = {arXiv:1409.1789 [cs.CV]}, abstract = {

In this work, we propose a learning framework for identifying synapses using a deep and wide multi-scale recursive (DAWMR) network, previously considered in image segmentation applications. We apply this approach on electron microscopy data from invertebrate fly brain tissue. By learning features directly from the data, we are able to achieve considerable improvements over existing techniques that rely on a small set of hand-designed features. We show that this system can reduce the amount of manual annotation required, in both acquisition of training data as well as verification of inferred detections.

}, url = {http://arxiv.org/abs/1409.1789}, author = {Huang, Gary and Plaza, Stephen M} } @article {45032, title = {Imaging ATUM ultrathin section libraries with WaferMapper: a multi-scale approach to EM reconstruction of neural circuits.}, journal = {Frontiers in Neural Circuits}, volume = {8}, year = {2014}, month = {2014 Jun 27}, pages = {68}, abstract = {

The automated tape-collecting ultramicrotome (ATUM) makes it possible to collect large numbers of ultrathin sections quickly-the equivalent of a petabyte of high resolution images each day. However, even high throughput image acquisition strategies generate images far more slowly (at present ~1 terabyte per day). We therefore developed WaferMapper, a software package that takes a multi-resolution approach to mapping and imaging select regions within a library of ultrathin sections. This automated method selects and directs imaging of corresponding regions within each section of an ultrathin section library (UTSL) that may contain many thousands of sections. Using WaferMapper, it is possible to map thousands of tissue sections at low resolution and target multiple points of interest for high resolution imaging based on anatomical landmarks. The program can also be used to expand previously imaged regions, acquire data under different imaging conditions, or re-image after additional tissue treatments.

}, issn = {1662-5110}, doi = {10.3389/fncir.2014.00068}, author = {Hayworth, Kenneth J and Morgan, Josh L and Schalek, Richard and Berger, Daniel R and Hildebrand, David G C and Lichtman, Jeff W} } @article {45060, title = {Imaging cellular ultrastructure by PALM, iPALM, and correlative iPALM-EM.}, journal = {Methods in Cell Biology}, volume = {123}, year = {2014}, month = {2014}, pages = {273-94}, abstract = {

Many biomolecules in cells can be visualized with high sensitivity and specificity by fluorescence microscopy. However, the resolution of conventional light microscopy is limited by diffraction to ~200-250nm laterally and \>500nm axially. Here, we describe superresolution methods based on single-molecule localization analysis of photoswitchable fluorophores (PALM: photoactivated localization microscopy) as well as our recent three-dimensional (3D) method (iPALM: interferometric PALM) that allows imaging with a resolution better than 20nm in all three dimensions. Considerations for their implementations, applications to multicolor imaging, and a recent development that extend the imaging depth of iPALM to ~750nm are discussed. As the spatial resolution of superresolution fluorescence microscopy converges with that of electron microscopy (EM), direct imaging of the same specimen using both approaches becomes feasible. This could be particularly useful for cross validation of experiments, and thus, we also describe recent methods that were developed for correlative superresolution fluorescence and EM.

}, issn = {0091-679X}, doi = {10.1016/B978-0-12-420138-5.00015-X}, author = {Shtengel, Gleb and Wang, Yilin and Zhang, Zhen and Goh, Wah Ing and Hess, Harald F and Kanchanawong, Pakorn} } @article {45166, title = {Imaging the fate of histone Cse4 reveals de novo replacement in S phase and subsequent stable residence at centromeres.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 May 20}, pages = {e02203}, abstract = {

The budding yeast centromere contains Cse4, a specialized histone H3 variant. Fluorescence pulse-chase analysis of an internally tagged Cse4 reveals that it is replaced with newly synthesized molecules in S phase, remaining stably associated with centromeres thereafter. In contrast, C-terminally-tagged Cse4 is functionally impaired, showing slow cell growth, cell lethality at elevated temperatures, and extra-centromeric nuclear accumulation. Recent studies using such strains gave conflicting findings regarding the centromeric abundance and cell cycle dynamics of Cse4. Our findings indicate that internally tagged Cse4 is a better reporter of the biology of this histone variant. Furthermore, the size of centromeric Cse4 clusters was precisely mapped with a new 3D-PALM method, revealing substantial compaction during anaphase. Cse4-specific chaperone Scm3 displays steady-state, stoichiometric co-localization with Cse4 at centromeres throughout the cell cycle, while undergoing exchange with a nuclear pool. These findings suggest that a stable Cse4 nucleosome is maintained by dynamic chaperone-in-residence Scm3.DOI: http://dx.doi.org/10.7554/eLife.02203.001.

}, issn = {2050-084X}, doi = {10.7554/eLife.02203}, author = {Wisniewski, Jan and Hajj, Bassam and Chen, Jiji and Mizuguchi, Gaku and Xiao, Hua and Wei, Debbie and Dahan, Maxime and Wu, Carl} } @article {47898, title = {Improving reliability and absolute quantification of human brain microarray data by filtering and scaling probes using RNA-Seq.}, journal = {BMC genomics}, volume = {15}, year = {2014}, month = {2014}, pages = {154}, abstract = {

BACKGROUND: High-throughput sequencing is gradually replacing microarrays as the preferred method for studying mRNA expression levels, providing nucleotide resolution and accurately measuring absolute expression levels of almost any transcript, known or novel. However, existing microarray data from clinical, pharmaceutical, and academic settings represent valuable and often underappreciated resources, and methods for assessing and improving the quality of these data are lacking.

RESULTS: To quantitatively assess the quality of microarray probes, we directly compare RNA-Seq to Agilent microarrays by processing 231 unique samples from the Allen Human Brain Atlas using RNA-Seq. Both techniques provide highly consistent, highly reproducible gene expression measurements in adult human brain, with RNA-Seq slightly outperforming microarray results overall. We show that RNA-Seq can be used as ground truth to assess the reliability of most microarray probes, remove probes with off-target effects, and scale probe intensities to match the expression levels identified by RNA-Seq. These sequencing scaled microarray intensities (SSMIs) provide more reliable, quantitative estimates of absolute expression levels for many genes when compared with unscaled intensities. Finally, we validate this result in two human cell lines, showing that linear scaling factors can be applied across experiments using the same microarray platform.

CONCLUSIONS: Microarrays provide consistent, reproducible gene expression measurements, which are improved using RNA-Seq as ground truth. We expect that our strategy could be used to improve probe quality for many data sets from major existing repositories.

}, keywords = {Brain, Cluster Analysis, Computational Biology, Gene Expression, Gene Expression Profiling, High-Throughput Nucleotide Sequencing, Humans, Neocortex, Oligonucleotide Array Sequence Analysis, Reproducibility of Results, Sequence Analysis, RNA, Transcriptome}, issn = {1471-2164}, doi = {10.1186/1471-2164-15-154}, author = {Miller, Jeremy A and Menon, Vilas and Goldy, Jeff and Kaykas, Ajamete and Lee, Chang-Kyu and Smith, Kimberly A and Shen, Elaine H and Phillips, John W and Lein, Ed S and Hawrylycz, Mike J} } @article {45786, title = {In vivo fluorescence microscopy via iterative multi-photon adaptive compensation technique.}, journal = {Optical Express}, volume = {22}, year = {2014}, month = {2014 Oct 6}, pages = {23786-94}, abstract = {

Iterative multi-photon adaptive compensation technique (IMPACT) has been developed for wavefront measurement and compensation in highly scattering tissues. Our previous report was largely based on the measurements of fixed tissue. Here we demonstrate the advantages of IMPACT for in vivo imaging and report the latest results. In particular, we show that IMPACT can be used for functional imaging of awake mice, and greatly improve the in vivo neuron imaging in mouse cortex at large depth (~660 microns). Moreover, IMPACT enables neuron imaging through the intact skull of adult mice, which promises noninvasive optical measurements in mouse brain.

}, issn = {1094-4087}, doi = {10.1364/OE.22.023786}, author = {Kong, Lingjie and Cui, Meng} } @article {6719, title = {Independent optical excitation of distinct neural populations.}, journal = {Nature Methods}, volume = {11}, year = {2014}, month = {2014 Feb 9}, pages = {338-46}, abstract = {

Optogenetic tools enable examination of how specific cell types contribute to brain circuit functions. A long-standing question is whether it is possible to independently activate two distinct neural populations in mammalian brain tissue. Such a capability would enable the study of how different synapses or pathways interact to encode information in the brain. Here we describe two channelrhodopsins, Chronos and Chrimson, discovered through sequencing and physiological characterization of opsins from over 100 species of alga. Chrimson{\textquoteright}s excitation spectrum is red shifted by 45 nm relative to previous channelrhodopsins and can enable experiments in which red light is preferred. We show minimal visual system-mediated behavioral interference when using Chrimson in neurobehavioral studies in Drosophila melanogaster. Chronos has faster kinetics than previous channelrhodopsins yet is effectively more light sensitive. Together these two reagents enable two-color activation of neural spiking and downstream synaptic transmission in independent neural populations without detectable cross-talk in mouse brain slice.

}, issn = {1548-7105}, doi = {10.1038/nmeth.2836}, author = {Klapoetke, Nathan C and Murata, Yasunobu and Kim, Sung Soo and Pulver, Stefan R and Birdsey-Benson, Amanda and Cho, Yong Ku and Morimoto, Tania K and Chuong, Amy S and Carpenter, Eric J and Tian, Zhijian and Wang, Jun and Xie, Yinlong and Yan, Zhixiang and Zhang, Yong and Chow, Brian Y and Surek, Barbara and Melkonian, Michael and Jayaraman, Vivek and Constantine-Paton, Martha and Wong, Gane Ka-Shu and Boyden, Edward S} } @article {45178, title = {The inhibitory microcircuit of the substantia nigra provides feedback gain control of the basal ganglia output.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 May 21}, pages = {e02397}, abstract = {

Dysfunction of the basal ganglia produces severe deficits in the timing, initiation, and vigor of movement. These diverse impairments suggest a control system gone awry. In engineered systems, feedback is critical for control. By contrast, models of the basal ganglia highlight feedforward circuitry and ignore intrinsic feedback circuits. In this study, we show that feedback via axon collaterals of substantia nigra projection neurons control the gain of the basal ganglia output. Through a combination of physiology, optogenetics, anatomy, and circuit mapping, we elaborate a general circuit mechanism for gain control in a microcircuit lacking interneurons. Our data suggest that diverse tonic firing rates, weak unitary connections and a spatially diffuse collateral circuit with distinct topography and kinetics from feedforward input is sufficient to implement divisive feedback inhibition. The importance of feedback for engineered systems implies that the intranigral microcircuit, despite its absence from canonical models, could be essential to basal ganglia function. DOI: http://dx.doi.org/10.7554/eLife.02397.001.

}, issn = {2050-084X}, doi = {10.7554/eLife.02397}, author = {Brown, Jennifer and Pan, Wei-Xing and Dudman, Joshua Tate} } @article {45371, title = {Integrated action of pheromone signals in promoting courtship behavior in male mice.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 Jul 29}, pages = {e03025}, abstract = {

The mammalian vomeronasal organ encodes pheromone information about gender, reproductive status, genetic background and individual differences. It remains unknown how pheromone information interacts to trigger innate behaviors. In this study, we identify vomeronasal receptors responsible for detecting female pheromones. A sub-group of V1re clade members recognizes gender-identifying cues in female urine. Multiple members of the V1rj clade are cognate receptors for urinary estrus signals, as well as for sulfated estrogen (SE) compounds. In both cases, the same cue activates multiple homologous receptors, suggesting redundancy in encoding female pheromone cues. Neither gender-specific cues nor SEs alone are sufficient to promote courtship behavior in male mice, whereas robust courtship behavior can be induced when the two cues are applied together. Thus, integrated action of different female cues is required in pheromone-triggered mating behavior. These results suggest a gating mechanism in the vomeronasal circuit in promoting specific innate behavior.DOI: http://dx.doi.org/10.7554/eLife.03025.001.

}, issn = {2050-084X}, doi = {10.7554/eLife.03025}, author = {Haga-Yamanaka, Sachiko and Ma, Limei and He, Jie and Qiu, Qiang and Lavis, Luke D and Looger, Loren L and Yu, C Ron} } @article {49004, title = {Interference and shaping in sensorimotor adaptations with rewards.}, journal = {PLoS Computational B2014-01-09iology}, volume = {10}, year = {2014}, month = {2014 Jan}, pages = {e1003377}, abstract = {

When a perturbation is applied in a sensorimotor transformation task, subjects can adapt and maintain performance by either relying on sensory feedback, or, in the absence of such feedback, on information provided by rewards. For example, in a classical rotation task where movement endpoints must be rotated to reach a fixed target, human subjects can successfully adapt their reaching movements solely on the basis of binary rewards, although this proves much more difficult than with visual feedback. Here, we investigate such a reward-driven sensorimotor adaptation process in a minimal computational model of the task. The key assumption of the model is that synaptic plasticity is gated by the reward. We study how the learning dynamics depend on the target size, the movement variability, the rotation angle and the number of targets. We show that when the movement is perturbed for multiple targets, the adaptation process for the different targets can interfere destructively or constructively depending on the similarities between the sensory stimuli (the targets) and the overlap in their neuronal representations. Destructive interferences can result in a drastic slowdown of the adaptation. As a result of interference, the time to adapt varies non-linearly with the number of targets. Our analysis shows that these interferences are weaker if the reward varies smoothly with the subject{\textquoteright}s performance instead of being binary. We demonstrate how shaping the reward or shaping the task can accelerate the adaptation dramatically by reducing the destructive interferences. We argue that experimentally investigating the dynamics of reward-driven sensorimotor adaptation for more than one sensory stimulus can shed light on the underlying learning rules.

}, keywords = {Adaptation, Physiological, Algorithms, Biomechanical Phenomena, Brain, Computational Biology, Computer Simulation, Feedback, Sensory, Humans, Learning, Models, Neurological, Movement, Neuronal Plasticity, Neurons, Psychomotor Performance, Reproducibility of Results, Reward, Rotation, Synapses}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1003377}, author = {Darshan, Ran and Leblois, Arthur and Hansel, David} } @article {45720, title = {Internal models direct dragonfly interception steering.}, journal = {Nature}, year = {2014}, month = {2014 Dec 10}, abstract = {

Sensorimotor control in vertebrates relies on internal models. When extending an arm to reach for an object, the brain uses predictive models of both limb dynamics and target properties. Whether invertebrates use such models remains unclear. Here we examine to what extent prey interception by dragonflies (Plathemis lydia), a behaviour analogous to targeted reaching, requires internal models. By simultaneously tracking the position and orientation of a dragonfly{\textquoteright}s head and body during flight, we provide evidence that interception steering is driven by forward and inverse models of dragonfly body dynamics and by models of prey motion. Predictive rotations of the dragonfly{\textquoteright}s head continuously track the prey{\textquoteright}s angular position. The head-body angles established by prey tracking appear to guide systematic rotations of the dragonfly{\textquoteright}s body to align it with the prey{\textquoteright}s flight path. Model-driven control thus underlies the bulk of interception steering manoeuvres, while vision is used for reactions to unexpected prey movements. These findings illuminate the computational sophistication with which insects construct behaviour.

}, issn = {1476-4687}, doi = {10.1038/nature14045}, author = {Mischiati, Matteo and Lin, Huai-Ti and Herold, Paul and Imler, Elliot and Olberg, Robert and Leonardo, Anthony} } @article {45459, title = {Intrinsic bursting of aII amacrine cells underlies oscillations in the rd1 mouse retina.}, journal = {Journal of Neurophysiology}, volume = {112}, year = {2014}, month = {2014 Sep 15}, pages = {1491-504}, abstract = {

In many forms of retinal degeneration, photoreceptors die but inner retinal circuits remain intact. In the rd1 mouse, an established model for blinding retinal diseases, spontaneous activity in the coupled network of AII amacrine and ON cone bipolar cells leads to rhythmic bursting of ganglion cells. Since such activity could impair retinal and/or cortical responses to restored photoreceptor function, understanding its nature is important for developing treatments of retinal pathologies. Here we analyzed a compartmental model of the wild-type mouse AII amacrine cell to predict that the cell{\textquoteright}s intrinsic membrane properties, specifically, interacting fast Na and slow, M-type K conductances, would allow its membrane potential to oscillate when light-evoked excitatory synaptic inputs were withdrawn following photoreceptor degeneration. We tested and confirmed this hypothesis experimentally by recording from AIIs in a slice preparation of rd1 retina. Additionally, recordings from ganglion cells in a whole mount preparation of rd1 retina demonstrated that activity in AIIs was propagated unchanged to elicit bursts of action potentials in ganglion cells. We conclude that oscillations are not an emergent property of a degenerated retinal network. Rather, they arise largely from the intrinsic properties of a single retinal interneuron, the AII amacrine cell.

}, issn = {1522-1598}, doi = {10.1152/jn.00437.2014}, author = {Choi, Hannah and Zhang, Lei and Cembrowski, Mark S and Sabottke, Carl F and Markowitz, Alexander L and Butts, Daniel A and Kath, William L and Singer, Joshua H and Riecke, Hermann} } @article {6887, title = {iPfam: a database of protein family and domain interactions found in the Protein Data Bank.}, journal = {Nucleic acids research}, volume = {42}, year = {2014}, month = {2014 Jan}, pages = {D364-73}, abstract = {The database iPfam, available at http://ipfam.org, catalogues Pfam domain interactions based on known 3D structures that are found in the Protein Data Bank, providing interaction data at the molecular level. Previously, the iPfam domain-domain interaction data was integrated within the Pfam database and website, but it has now been migrated to a separate database. This allows for independent development, improving data access and giving clearer separation between the protein family and interactions datasets. In addition to domain-domain interactions, iPfam has been expanded to include interaction data for domain bound small molecule ligands. Functional annotations are provided from source databases, supplemented by the incorporation of Wikipedia articles where available. iPfam (version 1.0) contains >9500 domain-domain and 15 500 domain-ligand interactions. The new website provides access to this data in a variety of ways, including interactive visualizations of the interaction data.}, keywords = {Databases, Internet, Ligands, Protein, Protein Interaction Domains and Motifs, Protein Interaction Mapping, Protein Interaction Maps, Proteins, Software}, issn = {1362-4962}, doi = {10.1093/nar/gkt1210}, author = {Finn, Robert D and Miller, Benjamin L and Clements, Jody and Bateman, Alex} } @article {45782, title = {Isolation of mitochondria from animal tissue.}, journal = {Cold Spring Harbor Protocols}, volume = {2014}, year = {2014}, month = {2014 Oct}, pages = {pdb.prot080010}, abstract = {

Rat or mouse liver is the most frequently used tissue for mitochondrial preparations because it is readily available, easy to homogenize, and replete with mitochondria. A motor-driven Teflon and glass Potter-Elvehjem homogenizer is the best choice for homogenizing liver, but if one is not available, this tissue is soft enough that a Dounce homogenizer with a loose (A) pestle can also be used. The yield and purity of the mitochondrial preparation will be influenced by the method and speed of preparation and the age and physiological condition of the animal.

}, issn = {1559-6095}, doi = {10.1101/pdb.prot080010}, author = {Clayton, David A and Shadel, Gerald S} } @article {47884, title = {Isolation of mitochondria from cells and tissues.}, journal = {Cold Spring Harbor Protocols}, volume = {2014}, year = {2014}, month = {2014 Oct}, pages = {pdb.top074542}, abstract = {

Mitochondria are complex organelles at the center of cellular metabolism, apoptosis, and signaling. They continue to be the subject of intense basic investigation to understand their composition and function, but they have also captivated the attention of clinical researchers because of the growing knowledge of the (sometimes unexpected) roles of mitochondria in human diseases and aging. A full understanding of these intriguing organelles often requires their purification from cells or tissues under specific physiological or pathological conditions. Here we provide some introductory considerations for those interested in purifying mitochondria for subsequent downstream biophysical, structural, and functional analysis.

}, keywords = {Animals, Cell Fractionation, Cells, Cultured, Humans, Mitochondria, Tissue Culture Techniques}, issn = {1559-6095}, doi = {10.1101/pdb.top074542}, author = {Clayton, David A and Shadel, Gerald S} } @article {45783, title = {Isolation of mitochondria from tissue culture cells.}, journal = {Cold Spring Harbor Protocols}, volume = {2014}, year = {2014}, month = {2014 Oct}, pages = {pdb.prot080002}, abstract = {

The number of mitochondria per cell varies substantially from cell line to cell line. For example, human HeLa cells contain at least twice as many mitochondria as smaller mouse L cells. This protocol starts with a washed cell pellet of 1-2 mL derived from \~{}10$^{9}$ cells grown in culture. The cells are swollen in a hypotonic buffer and ruptured with a Dounce or Potter-Elvehjem homogenizer using a tight-fitting pestle, and mitochondria are isolated by differential centrifugation.

}, issn = {1559-6095}, doi = {10.1101/pdb.prot080002}, author = {Clayton, David A and Shadel, Gerald S} } @article {45190, title = {Juvenile hormone regulates body size and perturbs insulin signaling in Drosophila.}, journal = {Proceedings of the National Academy of Science of the United States of America}, volume = {111}, year = {2014}, month = {2014 May 13}, pages = {7018-23}, abstract = {

The role of juvenile hormone (JH) in regulating the timing and nature of insect molts is well-established. Increasing evidence suggests that JH is also involved in regulating final insect size. Here we elucidate the developmental mechanism through which JH regulates body size in developing Drosophila larvae by genetically ablating the JH-producing organ, the corpora allata (CA). We found that larvae that lack CA pupariated at smaller sizes than control larvae due to a reduced larval growth rate. Neither the timing of the metamorphic molt nor the duration of larval growth was affected by the loss of JH. Further, we show that the effects of JH on growth rate are dependent on the forkhead box O transcription factor (FOXO), which is negatively regulated by the insulin-signaling pathway. Larvae that lacked the CA had elevated levels of FOXO activity, whereas a loss-of-function mutation of FOXO rescued the effects of CA ablation on final body size. Finally, the effect of JH on growth appears to be mediated, at least in part, via ecdysone synthesis in the prothoracic gland. These results indicate a role of JH in regulating growth rate via the ecdysone- and insulin-signaling pathways.

}, keywords = {Animals, Basic Helix-Loop-Helix Transcription Factors, Body Size, Corpora Allata, Denervation, Drosophila melanogaster, Drosophila Proteins, Ecdysone, Forkhead Transcription Factors, Insulin, Juvenile Hormones, Larva, Signal Transduction}, issn = {1091-6490}, doi = {10.1073/pnas.1313058111}, author = {Mirth, C K and Tang, H Y and Makohon-Moore, S C and Salhadar, S and Gokhale, R H and Warner, R D and Koyama, T and Riddiford, L M and Shingleton, A W} } @article {45182, title = {Kainate receptors mediate signaling in both transient and sustained OFF bipolar cell pathways in mouse retina.}, journal = {Journal of Neuroscience}, volume = {34}, year = {2014}, month = {2014 Apr 30}, pages = {6128-39}, abstract = {

A fundamental question in sensory neuroscience is how parallel processing is implemented at the level of molecular and circuit mechanisms. In the retina, it has been proposed that distinct OFF cone bipolar cell types generate fast/transient and slow/sustained pathways by the differential expression of AMPA- and kainate-type glutamate receptors, respectively. However, the functional significance of these receptors in the intact circuit during light stimulation remains unclear. Here, we measured glutamate release from mouse bipolar cells by two-photon imaging of a glutamate sensor (iGluSnFR) expressed on postsynaptic amacrine and ganglion cell dendrites. In both transient and sustained OFF layers, cone-driven glutamate release from bipolar cells was blocked by antagonists to kainate receptors but not AMPA receptors. Electrophysiological recordings from bipolar and ganglion cells confirmed the essential role of kainate receptors for signaling in both transient and sustained OFF pathways. Kainate receptors mediated responses to contrast modulation up to 20 Hz. Light-evoked responses in all mouse OFF bipolar pathways depend on kainate, not AMPA, receptors.

}, keywords = {Action Potentials, Animals, Drug Interactions, Excitatory Amino Acid Antagonists, Female, Glutamic Acid, Hexamethonium, Light, Male, Mice, Mice, Inbred C57BL, Nicotinic Antagonists, Patch-Clamp Techniques, Photic Stimulation, Propionates, Receptors, Kainic Acid, Retina, Retinal Bipolar Cells, Signal Transduction, Visual Pathways}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4941-13.2014}, author = {Borghuis, Bart G and Looger, Loren L and Tomita, Susumu and Demb, Jonathan B} } @article {45203, title = {Large environments reveal the statistical structure governing hippocampal representations.}, journal = {Science}, volume = {345}, year = {2014}, month = {2014 Aug 15}, pages = {814-7}, abstract = {

The rules governing the formation of spatial maps in the hippocampus have not been determined. We investigated the large-scale structure of place field activity by recording hippocampal neurons in rats exploring a previously unencountered 48-meter-long track. Single-cell and population activities were well described by a two-parameter stochastic model. Individual neurons had their own characteristic propensity for forming fields randomly along the track, with some cells expressing many fields and many exhibiting few or none. Because of the particular distribution of propensities across cells, the number of neurons with fields scaled logarithmically with track length over a wide, ethological range. These features constrain hippocampal memory mechanisms, may allow efficient encoding of environments and experiences of vastly different extents and durations, and could reflect general principles of population coding.

}, issn = {1095-9203}, doi = {10.1126/science.1255635}, author = {Rich, P Dylan and Liaw, Hua-Peng and Lee, Albert K} } @article {45186, title = {Large-scale, high-density (up to 512 channels) recording of local circuits in behaving animals.}, journal = {Journal of Neurophysiology}, volume = {111}, year = {2014}, month = {2014 Mar}, pages = {1132-49}, abstract = {

Monitoring representative fractions of neurons from multiple brain circuits in behaving animals is necessary for understanding neuronal computation. Here, we describe a system that allows high-channel-count recordings from a small volume of neuronal tissue using a lightweight signal multiplexing headstage that permits free behavior of small rodents. The system integrates multishank, high-density recording silicon probes, ultraflexible interconnects, and a miniaturized microdrive. These improvements allowed for simultaneous recordings of local field potentials and unit activity from hundreds of sites without confining free movements of the animal. The advantages of large-scale recordings are illustrated by determining the electroanatomic boundaries of layers and regions in the hippocampus and neocortex and constructing a circuit diagram of functional connections among neurons in real anatomic space. These methods will allow the investigation of circuit operations and behavior-dependent interregional interactions for testing hypotheses of neural networks and brain function.

}, issn = {1522-1598}, doi = {10.1152/jn.00785.2013}, author = {Berenyi, Antal and Somogyv{\'a}ri, Zolt{\'a}n and Nagy, Anett J and Roux, Lisa and Long, John D and Fujisawa, Shigeyoshi and Stark, Eran and Leonardo, Anthony and Harris, Timothy D and Buzs{\'a}ki, Gy{\"o}rgy} } @article {45617, title = {Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution.}, journal = {Science}, volume = {346}, year = {2014}, month = {2014 Oct 24}, pages = {1257998}, abstract = {

Although fluorescence microscopy provides a crucial window into the physiology of living specimens, many biological processes are too fragile, are too small, or occur too rapidly to see clearly with existing tools. We crafted ultrathin light sheets from two-dimensional optical lattices that allowed us to image three-dimensional (3D) dynamics for hundreds of volumes, often at subsecond intervals, at the diffraction limit and beyond. We applied this to systems spanning four orders of magnitude in space and time, including the diffusion of single transcription factor molecules in stem cell spheroids, the dynamic instability of mitotic microtubules, the immunological synapse, neutrophil motility in a 3D matrix, and embryogenesis in Caenorhabditis elegans and Drosophila melanogaster. The results provide a visceral reminder of the beauty and the complexity of living systems.

}, issn = {1095-9203}, doi = {10.1126/science.1257998}, author = {Chen, Bi-Chang and Legant, Wesley R and Wang, Kai and Shao, Lin and Milkie, Daniel E and Davidson, Michael W and Janetopoulos, Chris and Wu, Xufeng S and Hammer, John A and Liu, Zhe and English, Brian P and Mimori-Kiyosue, Yuko and Romero, Daniel P and Ritter, Alex T and Lippincott-Schwartz, Jennifer and Fritz-Laylin, Lillian and Mullins, R Dyche and Mitchell, Diana M and Bembenek, Joshua N and Reymann, Anne-Cecile and B{\"o}hme, Ralph and Grill, Stephan W and Wang, Jennifer T and Seydoux, Geraldine and Tulu, U Serdar and Kiehart, Daniel P and Betzig, Eric} } @article {45841, title = {Leptin mediates the increase in blood pressure associated with obesity.}, journal = {Cell}, volume = {159}, year = {2014}, month = {2014 Dec 4}, pages = {1404-16}, abstract = {

Obesity is associated with increased blood pressure (BP), which in turn increases the risk of cardiovascular diseases. We found that the increase in leptin levels seen in diet-induced obesity (DIO) drives an increase in BP in rodents, an effect that was not seen in animals deficient in leptin or leptin receptors (LepR). Furthermore, humans with loss-of-function mutations in leptin and the LepR have low BP despite severe obesity. Leptin{\textquoteright}s effects on BP are mediated by neuronal circuits in the dorsomedial hypothalamus (DMH), as blocking leptin with a specific antibody, antagonist, or inhibition of the activity of LepR-expressing neurons in the DMH caused a rapid reduction of BP in DIO mice, independent of changes in weight. Re-expression of LepRs in the DMH of DIO LepR-deficient mice caused an increase in BP. These studies demonstrate that leptin couples changes in weight to changes in BP in mammalian species.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2014.10.058}, author = {Simonds, Stephanie E and Pryor, Jack T and Ravussin, Eric and Greenway, Frank L and Dileone, Ralph and Allen, Andrew M and Bassi, Jaspreet and Elmquist, Joel K and Keogh, Julia M and Henning, Elana and Myers, Martin G and Licinio, Julio and Brown, Russell D and Enriori, Pablo J and O{\textquoteright}Rahilly, Stephen and Sternson, Scott M and Grove, Kevin L and Spanswick, David C and Farooqi, I Sadaf and Cowley, Michael A} } @article {46547, title = {Lessons from the neurons themselves.}, journal = {Design Automation Conference (ASP-DAC), 2014 19th Asia and South Pacific}, year = {2014}, month = {2014 Jan 20-23}, pages = {197-200}, abstract = {

Natural neural circuits, optimized by millions of years of evolution, are fast, low power, robust, and adapt in response to experience, all characteristics we would love to have in systems we ourselves design. Recently there have been enormous advances in understanding how neurons implement computations within the brain of living creatures. Can we use this new-found knowledge to create better artificial system? What lessons can we learn from the neurons themselves, that can help us create better neuromorphic circuits?

}, doi = {10.1109/ASPDAC.2014.6742889}, author = {Scheffer, LK} } @article {45177, title = {Light-sheet functional imaging in fictively behaving zebrafish.}, journal = {Nature Methods}, volume = {11}, year = {2014}, month = {2014 Jul 27}, pages = {883-4}, abstract = {

The processing of sensory input and the generation of behavior involves large networks of neurons, which necessitates new technology for recording from many neurons in behaving animals. In the larval zebrafish, light-sheet microscopy can be used to record the activity of almost all neurons in the brain simultaneously at single-cell resolution. Existing implementations, however, cannot be combined with visually driven behavior because the light sheet scans over the eye, interfering with presentation of controlled visual stimuli. Here we describe a system that overcomes the confounding eye stimulation through the use of two light sheets and combines whole-brain light-sheet imaging with virtual reality for fictively behaving larval zebrafish.

}, issn = {1548-7105}, doi = {10.1038/nmeth.3040}, author = {Vladimirov, Nikita and Mu, Yu and Kawashima, Takashi and Bennett, Davis V and Yang, Chao-Tsung and Looger, Loren L and Keller, Philipp J and Freeman, Jeremy and Ahrens, Misha B} } @article {45868, title = {Light-sheet imaging for systems neuroscience.}, journal = {Nature Methods}, volume = {12}, year = {2014}, month = {2014 Dec 30}, pages = {27-9}, abstract = {

Developments in electrical and optical recording technology are scaling up the size of neuronal populations that can be monitored simultaneously. Light-sheet imaging is rapidly gaining traction as a method for optically interrogating activity in large networks and presents both opportunities and challenges for understanding circuit function.

}, issn = {1548-7105}, doi = {10.1038/nmeth.3214}, author = {Keller, Philipp J and Ahrens, Misha B and Freeman, Jeremy} } @article {6896, title = {Live imaging and quantitative analysis of gastrulation in mouse embryos using light-sheet microscopy and 3D tracking tools.}, journal = {Nature Protocols}, volume = {9}, year = {2014}, month = {2014 Mar}, pages = {575-85}, abstract = {

This protocol describes how to observe gastrulation in living mouse embryos by using light-sheet microscopy and computational tools to analyze the resulting image data at the single-cell level. We describe a series of techniques needed to image the embryos under physiological conditions, including how to hold mouse embryos without agarose embedding, how to transfer embryos without air exposure and how to construct environmental chambers for live imaging by digital scanned light-sheet microscopy (DSLM). Computational tools include manual and semiautomatic tracking programs that are developed for analyzing the large 4D data sets acquired with this system. Note that this protocol does not include details of how to build the light-sheet microscope itself. Time-lapse imaging ends within 12 h, with subsequent tracking analysis requiring 3-6 d. Other than some mouse-handling skills, this protocol requires no advanced skills or knowledge. Light-sheet microscopes are becoming more widely available, and thus the techniques outlined in this paper should be helpful for investigating mouse embryogenesis.

}, issn = {1750-2799}, doi = {10.1038/nprot.2014.035}, author = {Ichikawa, Takehiko and Nakazato, Kenichi and Keller, Philipp J and Kajiura-Kobayashi, Hiroko and Stelzer, Ernst H K and Mochizuki, Atsushi and Nonaka, Shigenori} } @article {45852, title = {Live imaging of endogenous PSD-95 using ENABLED: a conditional strategy to fluorescently label endogenous proteins.}, journal = {Journal of Neuroscience}, volume = {34}, year = {2014}, month = {2014 Dec 10}, pages = {16698-712}, abstract = {

Stoichiometric labeling of endogenous synaptic proteins for high-contrast live-cell imaging in brain tissue remains challenging. Here, we describe a conditional mouse genetic strategy termed endogenous labeling via exon duplication (ENABLED), which can be used to fluorescently label endogenous proteins with near ideal properties in all neurons, a sparse subset of neurons, or specific neuronal subtypes. We used this method to label the postsynaptic density protein PSD-95 with mVenus without overexpression side effects. We demonstrated that mVenus-tagged PSD-95 is functionally equivalent to wild-type PSD-95 and that PSD-95 is present in nearly all dendritic spines in CA1 neurons. Within spines, while PSD-95 exhibited low mobility under basal conditions, its levels could be regulated by chronic changes in neuronal activity. Notably, labeled PSD-95 also allowed us to visualize and unambiguously examine otherwise-unidentifiable excitatory shaft synapses in aspiny neurons, such as parvalbumin-positive interneurons and dopaminergic neurons. Our results demonstrate that the ENABLED strategy provides a valuable new approach to study the dynamics of endogenous synaptic proteins in vivo.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3888-14.2014}, author = {Fortin, Dale A and Tillo, Shane E and Yang, Guang and Rah, Jong-Cheol and Melander, Joshua B and Bai, Suxia and Soler-Cede{\~n}o, Omar and Qin, Maozhen and Zemelman, Boris V and Guo, Caiying and Mao, Tianyi and Zhong, Haining} } @article {47630, title = {LKB1/AMPK and PKA control ABCB11 trafficking and polarization in hepatocytes.}, journal = {PloS one}, volume = {9}, year = {2014}, month = {2014}, pages = {e91921}, abstract = {

Polarization of hepatocytes is manifested by bile canalicular network formation and activation of LKB1 and AMPK, which control cellular energy metabolism. The bile acid, taurocholate, also regulates development of the canalicular network through activation of AMPK. In the present study, we used collagen sandwich hepatocyte cultures from control and liver-specific LKB1 knockout mice to examine the role of LKB1 in trafficking of ABCB11, the canalicular bile acid transporter. In polarized hepatocytes, ABCB11 traffics from Golgi to the apical plasma membrane and endogenously cycles through the rab 11a-myosin Vb recycling endosomal system. LKB1 knockout mice were jaundiced, lost weight and manifested impaired bile canalicular formation and intracellular trafficking of ABCB11, and died within three weeks. Using live cell imaging, fluorescence recovery after photobleaching (FRAP), particle tracking, and biochemistry, we found that LKB1 activity is required for microtubule-dependent trafficking of ABCB11 to the canalicular membrane. In control hepatocytes, ABCB11 trafficking was accelerated by taurocholate and cAMP; however, in LKB1 knockout hepatocytes, ABCB11 trafficking to the apical membrane was greatly reduced and restored only by cAMP, but not taurocholate. cAMP acted through a PKA-mediated pathway which did not activate AMPK. Our studies establish a regulatory role for LKB1 in ABCB11 trafficking to the canalicular membrane, hepatocyte polarization, and canalicular network formation.

}, keywords = {AMP-Activated Protein Kinases, Animals, ATP-Binding Cassette Transporters, Bile Acids and Salts, Cell Membrane, Cell Polarity, Cyclic AMP, Cyclic AMP-Dependent Protein Kinases, Endosomes, Gene Expression Regulation, Golgi Apparatus, Hepatocytes, Mice, Mice, Knockout, Myosin Type V, Primary Cell Culture, Protein Transport, Protein-Serine-Threonine Kinases, rab GTP-Binding Proteins, Signal Transduction, Taurocholic Acid}, issn = {1932-6203}, doi = {10.1371/journal.pone.0091921}, author = {Homolya, L{\'a}szl{\'o} and Fu, Dong and Sengupta, Prabuddha and Jarnik, Michal and Gillet, Jean-Pierre and Vitale-Cross, Lynn and Gutkind, J Silvio and Lippincott-Schwartz, Jennifer and Arias, Irwin M} } @article {45061, title = {Looking under the lamp post: neither fruitless nor doublesex has evolved to generate divergent male courtship in Drosophila.}, journal = {Cell Reports}, volume = {8}, year = {2014}, month = {2014 Jul 24}, pages = {363-70}, abstract = {

How do evolved genetic changes alter the nervous system to produce different patterns of behavior? We address this question using Drosophila male courtship behavior, which is innate, stereotyped, and evolves rapidly between species. D. melanogaster male courtship requires the male-specific isoforms of two transcription factors, fruitless\ and doublesex. These genes underlie genetic switches between female and male behaviors, making them excellent candidate genes for courtship behavior evolution. We tested their role in courtship evolution by transferring the entire locus for each gene from divergent species to D.\ melanogaster. We found that despite differences in Fru+ and Dsx+ cell numbers in wild-type species, cross-species transgenes rescued D.\ melanogaster courtship behavior and no species-specific behaviors were conferred. Therefore, fru and dsx are not a significant source of evolutionary variation in courtship behavior.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2014.06.023}, author = {Cande, Jessica and Stern, David L and Morita, Tomoko and Prud{\textquoteright}homme, Benjamin and Gompel, Nicolas} } @article {45718, title = {Making biology transparent.}, journal = {Nature Biotechnology}, volume = {32}, year = {2014}, month = {2014 Nov 7}, pages = {1104-5}, abstract = {

The molecular and cellular architecture of the organs in a whole mouse is revealed through optical clearing.

}, issn = {1546-1696}, doi = {10.1038/nbt.3061}, author = {H{\"o}ckendorf, Burkhard and Lavis, Luke D and Keller, Philipp J} } @article {6898, title = {Making Drosophila lineage-restricted drivers via patterned recombination in neuroblasts.}, journal = {Nature Neuroscience}, volume = {17}, year = {2014}, month = {2014 Apr}, pages = {631-7}, abstract = {

The Drosophila cerebrum originates from about 100 neuroblasts per hemisphere, with each neuroblast producing a characteristic set of neurons. Neurons from a neuroblast are often so diverse that many neuron types remain unexplored. We developed new genetic tools that target neuroblasts and their diverse descendants, increasing our ability to study fly brain structure and development. Common enhancer-based drivers label neurons on the basis of terminal identities rather than origins, which provides limited labeling in the heterogeneous neuronal lineages. We successfully converted conventional drivers that are temporarily expressed in neuroblasts, into drivers expressed in all subsequent neuroblast progeny. One technique involves immortalizing GAL4 expression in neuroblasts and their descendants. Another depends on loss of the GAL4 repressor, GAL80, from neuroblasts during early neurogenesis. Furthermore, we expanded the diversity of MARCM-based reagents and established another site-specific mitotic recombination system. Our transgenic tools can be combined to map individual neurons in specific lineages of various genotypes.

}, issn = {1546-1726}, doi = {10.1038/nn.3654}, author = {Awasaki, Takeshi and Kao, Chih-Fei and Lee, Ying-Jou and Yang, Ching-Po and Huang, Yaling and Pfeiffer, Barret D and Luan, Haojiang and Jing, Xiaotang and Huang, Yu-Fen and He, Yisheng and Schroeder, Mark David and Kuzin, Alexander and Brody, Thomas and Zugates, Christopher T and Odenwald, Ward F and Lee, Tzumin} } @article {45054, title = {Manipulating nuclear architecture.}, journal = {Current Opinion in Genetics \& Development}, volume = {25}, year = {2014}, month = {2014 Apr 25}, pages = {1-7}, abstract = {

The eukaryotic genome is highly organized in the nucleus. Genes can be localized to specific nuclear compartments in a manner reflecting their activity. A plethora of recent reports has described multiple levels of chromosomal folding that can be related to gene-specific expression states. Here we discuss studies designed to probe the causal impact of genome organization on gene expression. The picture that emerges is that of a reciprocal relationship in which nuclear organization is not only shaped by gene expression states but also directly influences them.

}, issn = {1879-0380}, doi = {10.1016/j.gde.2013.10.014}, author = {Deng, Wulan and Blobel, Gerd A} } @article {45065, title = {Mapping brain activity at scale with cluster computing.}, journal = {Nature Methods}, volume = {11}, year = {2014}, month = {2014 Jul 27}, pages = {941-950}, abstract = {

Understanding brain function requires monitoring and interpreting the activity of large networks of neurons during behavior. Advances in recording technology are greatly increasing the size and complexity of neural data. Analyzing such data will pose a fundamental bottleneck for neuroscience. We present a library of analytical tools called Thunder built on the open-source Apache Spark platform for large-scale distributed computing. The library implements a variety of univariate and multivariate analyses with a modular, extendable structure well-suited to interactive exploration and analysis development. We demonstrate how these analyses find structure in large-scale neural data, including whole-brain light-sheet imaging data from fictively behaving larval zebrafish, and two-photon imaging data from behaving mouse. The analyses relate neuronal responses to sensory input and behavior, run in minutes or less and can be used on a private cluster or in the cloud. Our open-source framework thus holds promise for turning brain activity mapping efforts into biological insights.

}, issn = {1548-7091}, doi = {10.1038/nmeth.3041}, author = {Freeman, Jeremy and Vladimirov, Nikita and Kawashima, Takashi and Mu, Yu and Sofroniew, Nicholas J. and Bennett, Davis V. and Rosen, Joshua and Yang, Chao-Tsung and Looger, Loren L. and Ahrens, Misha B.} } @article {6955, title = {Microfabrication of a platform to measure and manipulate the mechanics of engineered microtissues.}, journal = {Methods in Cell Biology}, volume = {121}, year = {2014}, month = {2014}, pages = {191-211}, abstract = {

Engineered tissues can be used to understand fundamental features of biology, develop organotypic in vitro model systems, and as engineered tissue constructs for replacing damaged tissue in vivo. However, a key limitation is an inability to test the wide range of parameters that might impact the engineered tissue in a high-throughput manner and in an environment that mimics the three-dimensional (3D) native architecture. We developed a microfabricated platform to generate arrays of microtissues embedded within 3D micropatterned matrices. Microcantilevers simultaneously constrain microtissue formation and report forces generated by the microtissues in real time, opening the possibility to use high-throughput, low-volume screening for studies on engineered tissues. Thanks to the micrometer scale of the microtissues, this platform is also suitable for high-throughput monitoring of drug-induced effect on architecture and contractility in engineered tissues. Moreover, independent variations of the mechanical stiffness of the cantilevers and collagen matrix allow the measurement and manipulation of the mechanics of the microtissues. Thus, our approach will likely provide valuable opportunities to elucidate how biomechanical, electrical, biochemical, and genetic/epigenetic cues modulate the formation and maturation of 3D engineered tissues. In this chapter, we describe the microfabrication, preparation, and experimental use of such microfabricated tissue gauges.

}, issn = {0091-679X}, doi = {10.1016/B978-0-12-800281-0.00013-0}, author = {Ramade, Alexandre and Legant, Wesley R and Picart, Catherine and Chen, Christopher S and Boudou, Thomas} } @article {47627, title = {MicroRNA binding to the HIV-1 Gag protein inhibits Gag assembly and virus production.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, year = {2014}, month = {2014 Jul 1}, pages = {E2676-83}, abstract = {

MicroRNAs (miRNAs) are small, 18-22 nt long, noncoding RNAs that act as potent negative gene regulators in a variety of physiological and pathological processes. To repress gene expression, miRNAs are packaged into RNA-induced silencing complexes (RISCs) that target mRNAs for degradation and/or translational repression in a sequence-specific manner. Recently, miRNAs have been shown to also interact with proteins outside RISCs, impacting cellular processes through mechanisms not involving gene silencing. Here, we define a previously unappreciated activity of miRNAs in inhibiting RNA-protein interactions that in the context of HIV-1 biology blocks HIV virus budding and reduces virus infectivity. This occurs by miRNA binding to the nucleocapsid domain of the Gag protein, the main structural component of HIV-1 virions. The resulting miRNA-Gag complexes interfere with viral-RNA-mediated Gag assembly and viral budding at the plasma membrane, with imperfectly assembled Gag complexes endocytosed and delivered to lysosomes. The blockade of virus production by miRNA is reversed by adding the miRNA{\textquoteright}s target mRNA and stimulated by depleting Argonaute-2, suggesting that when miRNAs are not mediating gene silencing, they can block HIV-1 production through disruption of Gag assembly on membranes. Overall, our findings have significant implications for understanding how cells modulate HIV-1 infection by miRNA expression and raise the possibility that miRNAs can function to disrupt RNA-mediated protein assembly processes in other cellular contexts.

}, keywords = {Argonaute Proteins, Cluster Analysis, DNA Primers, HEK293 Cells, HIV-1, Humans, MicroRNAs, Microscopy, Fluorescence, Multiprotein Complexes, Protein Precursors, RNA, Small Interfering, Virus Assembly, Virus Release}, issn = {1091-6490}, doi = {10.1073/pnas.1408037111}, author = {Chen, Antony K and Sengupta, Prabuddha and Waki, Kayoko and Van Engelenburg, Schuyler B and Ochiya, Takahiro and Ablan, Sherimay D and Freed, Eric O and Lippincott-Schwartz, Jennifer} } @article {68767, title = {The Microtubule Minus-End-Binding Protein Patronin/PTRN-1 Is Required for Axon Regeneration in C.~elegans}, journal = {Cell Reports}, volume = {9}, year = {2014}, month = {11/2014}, pages = {874-883}, abstract = {

Summary Precise regulation of microtubule (MT) dynamics is increasingly recognized as a critical determinant of\ axon regeneration. In contrast to developing neurons, mature axons exhibit noncentrosomal microtubule nucleation. The factors regulating noncentrosomal MT architecture in axon regeneration remain poorly understood. We report that PTRN-1, the C.\ elegans member of the Patronin/Nezha/calmodulin- and spectrin-associated protein (CAMSAP) family of microtubule minus-end-binding proteins, is critical for efficient axon regeneration in\ vivo. ptrn-1-null mutants display generally normal developmental axon outgrowth but significantly impaired regenerative regrowth after laser axotomy. Unexpectedly, mature axons in ptrn-1 mutants display elevated numbers of dynamic axonal MTs before and after injury, suggesting that PTRN-1 inhibits MT dynamics. The CKK domain of PTRN-1 is necessary and sufficient for its functions in axon regeneration and MT dynamics and appears to stabilize MTs independent of minus-end localization. Whereas in developing neurons, PTRN-1 inhibits activity of the DLK-1 mitogen-activated protein kinase (MAPK) cascade, we find that, in regeneration, PTRN-1 and DLK-1 function together to promote axonal regrowth.

}, issn = {2211-1247}, doi = {https://doi.org/10.1016/j.celrep.2014.09.054}, url = {https://www.sciencedirect.com/science/article/pii/S2211124714008377}, author = {Marian Chuang and Alexandr Goncharov and Shaohe Wang and Karen Oegema and Yishi Jin and Andrew~D. Chisholm} } @article {45184, title = {Molecular basis for age-dependent microtubule acetylation by tubulin acetyltransferase.}, journal = {Cell}, volume = {157}, year = {2014}, month = {2014 Jun 5}, pages = {1405-15}, abstract = {

Acetylation of α-tubulin Lys40 by tubulin acetyltransferase (TAT) is the only known posttranslational modification in the microtubule lumen. It marks stable microtubules and is required for polarity establishment and directional migration. Here, we elucidate the mechanistic underpinnings for TAT activity and its preference for microtubules with slow turnover. 1.35\ {\r A} TAT cocrystal structures with bisubstrate analogs constrain TAT action to the microtubule lumen and reveal Lys40 engaged in a suboptimal active site. Assays with diverse tubulin polymers show that TAT is stimulated by microtubule interprotofilament contacts. Unexpectedly, despite the confined intraluminal location of Lys40, TAT efficiently scans the microtubule bidirectionally and acetylates stochastically without preference for ends. First-principles modeling and single-molecule measurements demonstrate that TAT catalytic activity, not constrained luminal diffusion, is rate limiting for acetylation. Thus, because of its preference for microtubules over free tubulin and its modest catalytic rate, TAT can function as a slow clock for microtubule lifetimes.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2014.03.061}, author = {Szyk, Agnieszka and Deaconescu, Alexandra M and Spector, Jeffrey and Goodman, Benjamin and Valenstein, Max L and Ziolkowska, Natasza E and Kormendi, Vasilisa and Grigorieff, Nikolaus and Roll-Mecak, Antonina} } @article {45861, title = {Motor effort alters changes of mind in sensorimotor decision making.}, journal = {PLoS One}, volume = {9}, year = {2014}, month = {2014 Mar 20}, pages = {e92681}, abstract = {

After committing to an action, a decision-maker can change their mind to revise the action. Such changes of mind can even occur when the stream of information that led to the action is curtailed at movement onset. This is explained by the time delays in sensory processing and motor planning which lead to a component at the end of the sensory stream that can only be processed after initiation. Such post-initiation processing can explain the pattern of changes of mind by asserting an accumulation of additional evidence to a criterion level, termed change-of-mind bound. Here we test the hypothesis that physical effort associated with the movement required to change one{\textquoteright}s mind affects the level of the change-of-mind bound and the time for post-initiation deliberation. We varied the effort required to change from one choice target to another in a reaching movement by varying the geometry of the choice targets or by applying a force field between the targets. We show that there is a reduction in the frequency of change of mind when the separation of the choice targets would require a larger excursion of the hand from the initial to the opposite choice. The reduction is best explained by an increase in the evidence required for changes of mind and a reduced time period of integration after the initial decision. Thus the criteria to revise an initial choice is sensitive to energetic costs.

}, keywords = {Adult, Choice Behavior, Decision Making, Female, Humans, Male, Psychometrics, Psychomotor Performance, Young Adult}, issn = {1932-6203}, doi = {10.1371/journal.pone.0092681}, author = {Burk, Diana and Ingram, James N and Franklin, David W and Shadlen, Michael N and Wolpert, Daniel M} } @article {45373, title = {Multiplexed aberration measurement for deep tissue imaging in vivo.}, journal = {Nature Methods}, year = {2014}, month = {2014 Aug 17}, abstract = {

We describe an adaptive optics method that modulates the intensity or phase of light rays at multiple pupil segments in parallel to determine the sample-induced aberration. Applicable to fluorescent protein-labeled structures of arbitrary complexity, it allowed us to obtain diffraction-limited resolution in various samples in vivo. For the strongly scattering mouse brain, a single aberration correction improved structural and functional imaging of fine neuronal processes over a large imaging volume.

}, issn = {1548-7105}, doi = {10.1038/nmeth.3068}, author = {Wang, Chen and Liu, Rui and Milkie, Daniel E and Sun, Wenzhi and Tan, Zhongchao and Kerlin, Aaron and Chen, Tsai-Wen and Kim, Douglas S and Ji, Na} } @article {45811, title = {Mushroom body output neurons encode valence and guide memory-based action selection in Drosophila.}, journal = {eLife}, volume = {4}, year = {2014}, month = {12/2014}, abstract = {

Animals discriminate stimuli, learn their predictive value and use this knowledge to modify their behavior. In Drosophila, the mushroom body (MB) plays a key role in these processes. Sensory stimuli are sparsely represented by \~{}2000 Kenyon cells, which converge onto 34 output neurons (MBONs) of 21 types. We studied the role of MBONs in several associative learning tasks and in sleep regulation, revealing the extent to which information flow is segregated into distinct channels and suggesting possible roles for the multi-layered MBON network. We also show that optogenetic activation of MBONs can, depending on cell type, induce repulsion or attraction in flies. The behavioral effects of MBON perturbation are combinatorial, suggesting that the MBON ensemble collectively represents valence. We propose that local, stimulus-specific dopaminergic modulation selectively alters the balance within the MBON network for those stimuli. Our results suggest that valence encoded by the MBON ensemble biases memory-based action selection.

}, issn = {2050-084X}, doi = {10.7554/eLife.04580}, author = {Aso, Yoshinori and Sitaraman, Divya and Ichinose, Toshiharu and Kaun, Karla R and Vogt, Katrin and Belliart-Gu{\'e}rin, Ghislain and Placais, Pierre-Yves and Robie, Alice A and Yamagata, Nobuhiro and Schnaitmann, Christopher and Rowell, William J and Johnston, Rebecca M and Ngo, Teri-T B and Chen, Nan and Korff, Wyatt and Nitabach, Michael N and Heberlein, Ulrike and Preat, Thomas and Branson, Kristin M and Tanimoto, Hiromu and Rubin, Gerald M} } @article {46426, title = {Nanometer-resolution fluorescence electron microscopy (nano-EM) in cultured cells.}, journal = {Methods in Molecular Biology}, volume = {1117}, year = {2014}, month = {2014}, pages = {503-26}, abstract = {

Nano-resolution fluorescence electron microscopy (nano-fEM) pinpoints the location of individual proteins in electron micrographs. Plastic sections are first imaged using a super-resolution fluorescence microscope and then imaged on an electron microscope. The two images are superimposed to correlate the position of labeled proteins relative to subcellular structures. Here, we describe the method in detail and present five technical advancements: the use of uranyl acetate during the freeze-substitution to enhance the contrast of tissues and reduce the loss of fluorescence, the use of ground-state depletion instead of photoactivation for temporal control of fluorescence, the use of organic fluorophores instead of fluorescent proteins to obtain brighter fluorescence signals, the use of tissue culture cells to broaden the utility of the method, and the use of a transmission electron microscope to achieve sharper images of ultrastructure.

}, keywords = {Animals, Caenorhabditis elegans, Cells, Cultured, Histocytological Preparation Techniques, Image Processing, Computer-Assisted, Mice, Microscopy, Electron, Microscopy, Fluorescence}, issn = {1940-6029}, doi = {10.1007/978-1-62703-776-1_22}, author = {Watanabe, Shigeki and Lehmann, Martin and Hujber, Edward and Fetter, Richard D and Richards, Jackson and S{\"o}hl-Kielczynski, Berit and Felies, Annegret and Rosenmund, Christian and Schmoranzer, Jan and Jorgensen, Erik M} } @article {45062, title = {Natural whisker-guided behavior by head-fixed mice in tactile virtual reality.}, journal = {Journal of Neuroscience}, volume = {34}, year = {2014}, month = {2014 Jul 16}, pages = {9537-50}, abstract = {

During many natural behaviors the relevant sensory stimuli and motor outputs are difficult to quantify. Furthermore, the high dimensionality of the space of possible stimuli and movements compounds the problem of experimental control. Head fixation facilitates stimulus control and movement tracking, and can be combined with techniques for recording and manipulating neural activity. However, head-fixed mouse behaviors are typically trained through extensive instrumental conditioning. Here we present a whisker-based, tactile virtual reality system for head-fixed mice running on a spherical treadmill. Head-fixed mice displayed natural movements, including running and rhythmic whisking at 16 Hz. Whisking was centered on a set point that changed in concert with running so that more protracted whisking was correlated with faster running. During turning, whiskers moved in an asymmetric manner, with more retracted whisker positions in the turn direction and protracted whisker movements on the other side. Under some conditions, whisker movements were phase-coupled to strides. We simulated a virtual reality tactile corridor, consisting of two moveable walls controlled in a closed-loop by running speed and direction. Mice used their whiskers to track the walls of the winding corridor without training. Whisker curvature changes, which cause forces in the sensory follicles at the base of the whiskers, were tightly coupled to distance from the walls. Our behavioral system allows for precise control of sensorimotor variables during natural tactile navigation.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0712-14.2014}, author = {Sofroniew, Nicholas J and Cohen, Jeremy D and Lee, Albert K and Svoboda, Karel} } @article {6824, title = {Neural circuit components of the drosophila OFF motion vision pathway.}, journal = {Current Biology}, volume = {24}, year = {2014}, month = {2014 Feb 17}, pages = {385-92}, abstract = {

BACKGROUND: Detecting the direction of visual motion is an\ essential task of the early visual system. The Reichardt detector has been proven to be a faithful description of the underlying computation in insects. A series of recent studies addressed the neural implementation of the Reichardt detector in Drosophila revealing the overall layout in parallel ON and OFF channels, its input neurons from the lamina (L1{\textrightarrow}ON, and L2{\textrightarrow}OFF), and the respective output neurons to the lobula plate (ON{\textrightarrow}T4, and OFF{\textrightarrow}T5). While anatomical studies showed that T4 cells receive input from L1 via Mi1 and Tm3 cells, the neurons connecting L2 to T5 cells have not been identified so far. It is, however, known that L2 contacts, among others, two neurons, called Tm2 and L4, which show a pronounced directionality in their wiring. RESULTS: We characterized the visual response properties of both Tm2 and L4 neurons via Ca(2+) imaging. We found that Tm2 and L4 cells respond with an increase in activity to moving OFF edges in a direction-unselective manner. To investigate their participation in motion vision, we blocked their output while recording from downstream tangential cells in the lobula plate. Silencing of Tm2 and L4 completely abolishes the response to moving OFF edges. CONCLUSIONS: Our results demonstrate that both cell types are essential components of the Drosophila OFF motion vision pathway, prior to the computation of directionality in the dendrites of T5 cells.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2014.01.006}, author = {Meier, Matthias and Serbe, Etienne and Maisak, Matthew S and Haag, J{\"u}rgen and Dickson, Barry J and Borst, Alexander} } @article {45721, title = {Neural coding for effective rehabilitation.}, journal = {Biomed Research International}, volume = {2014}, year = {2014}, month = {2014}, pages = {286505}, abstract = {

Successful neurological rehabilitation depends on accurate diagnosis, effective treatment, and quantitative evaluation. Neural coding, a technology for interpretation of functional and structural information of the nervous system, has contributed to the advancements in neuroimaging, brain-machine interface (BMI), and design of training devices for rehabilitation purposes. In this review, we summarized the latest breakthroughs in neuroimaging from microscale to macroscale levels with potential diagnostic applications for rehabilitation. We also reviewed the achievements in electrocorticography (ECoG) coding with both animal models and human beings for BMI design, electromyography (EMG) interpretation for interaction with external robotic systems, and robot-assisted quantitative evaluation on the progress of rehabilitation programs. Future rehabilitation would be more home-based, automatic, and self-served by patients. Further investigations and breakthroughs are mainly needed in aspects of improving the computational efficiency in neuroimaging and multichannel ECoG by selection of localized neuroinformatics, validation of the effectiveness in BMI guided rehabilitation programs, and simplification of the system operation in training devices.

}, issn = {2314-6141}, doi = {10.1155/2014/286505}, author = {Hu, Xiaoling and Wang, Yiwen and Zhao, Ting and Gunduz, Aysegul} } @article {46188, title = {Neural computation for rehabilitation.}, journal = {Biomed Research International}, volume = {2014}, year = {2014}, month = {2014}, pages = {603985}, issn = {2314-6141}, doi = {10.1155/2014/603985}, author = {Hu, Xiaoling and Wang, Yiwen and Zhao, Ting and Gunduz, Aysegul} } @article {45147, title = {Neural pathways for the detection and discrimination of conspecific song in D. melanogaster.}, journal = {Current Biology}, volume = {24}, year = {2014}, month = {2014 May 19}, pages = {1039-49}, abstract = {

BACKGROUND: During courtship, male Drosophila melanogaster sing a multipart courtship song to female flies. This song is of particular interest because (1) it is species specific and varies widely within the genus, (2) it is a gating stimulus for females, who are sensitive detectors of conspecific song, and (3) it is the only sexual signal that is under both neural and genetic control. This song is perceived via mechanosensory neurons in the antennal Johnston{\textquoteright}s organ, which innervate the antennal mechanosensory and motor center (AMMC) of the brain. However, AMMC outputs that are responsible for detection and discrimination of conspecific courtship song remain unknown.

RESULTS: Using a large-scale anatomical screen of AMMC interneurons, we identify seven projection neurons (aPNs) and five local interneurons (aLNs) that outline a complex architecture for the ascending mechanosensory pathway. Neuronal inactivation and hyperactivation during behavior reveal that only two classes of interneurons are necessary for song responses--the projection neuron aPN1 and GABAergic interneuron aLN(al). These neurons are necessary in both male and female flies. Physiological recordings in aPN1 reveal the integration of courtship song as a function of pulse rate and outline an intracellular transfer function that likely facilitates the response to conspecific song.

CONCLUSIONS: These results reveal a critical pathway for courtship hearing in male and female flies, in which both aLN(al) and aPN1 mediate the detection of conspecific song. The pathways arising from these neurons likely serve as a critical neural substrate for behavioral reproductive isolation in D. melanogaster.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2014.03.048}, author = {Vaughan, Alexander G and Zhou, Chuan and Manoli, Devanand S and Baker, Bruce S} } @article {45810, title = {The neuronal architecture of the mushroom body provides a logic for associative learning.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 Dec 23}, abstract = {

We identified the neurons comprising the Drosophila mushroom body (MB), an associative center in invertebrate brains, and provide a comprehensive map describing their potential connections. Each of the 21 MB output neuron (MBON) types elaborates segregated dendritic arbors along the parallel axons of \~{}2000 Kenyon cells, forming 15 compartments that collectively tile the MB lobes. MBON axons project to five discrete neuropils outside of the MB and three MBON types form a feedforward network in the lobes. Each of the 20 dopaminergic neuron (DAN) types projects axons to one, or at most two, of the MBON compartments. Convergence of DAN axons on compartmentalized Kenyon cell-MBON synapses creates a highly ordered unit that can support learning to impose valence on sensory representations. The elucidation of the complement of neurons of the MB provides a comprehensive anatomical substrate from which one can infer a functional logic of associative olfactory learning and memory.

}, issn = {2050-084X}, doi = {10.7554/eLife.04577}, author = {Aso, Yoshinori and Hattori, Daisuke and Yu, Yang and Johnston, Rebecca M and Iyer, Nirmala A and Ngo, Teri-Tb and Dionne, Heather and Abbott, Lf and Axel, Richard and Tanimoto, Hiromu and Rubin, Gerald M} } @article {46899, title = {The neuronal basis of how sexual experience modulates male aggression.}, journal = {National Science Review}, volume = {1}, year = {2014}, month = {2014 Dec }, pages = {473-4}, doi = {10.1093/nsr/nwu059}, author = {Liang, X H and Rao, Y and Zhou, Chuan} } @article {45974, title = {Neuronal control of Drosophila walking direction.}, journal = {Science}, volume = {344}, year = {2014}, month = {2014 Apr 4}, pages = {97-101}, abstract = {

Most land animals normally walk forward but switch to backward walking upon sensing an obstacle or danger in the path ahead. A change in walking direction is likely to be triggered by descending "command" neurons from the brain that act upon local motor circuits to alter the timing of leg muscle activation. Here we identify descending neurons for backward walking in Drosophila--the MDN neurons. MDN activity is required for flies to walk backward when they encounter an impassable barrier and is sufficient to trigger backward walking under conditions in which flies would otherwise walk forward. We also identify ascending neurons, MAN, that promote persistent backward walking, possibly by inhibiting forward walking. These findings provide an initial glimpse into the circuits and logic that control walking direction in Drosophila.

}, keywords = {Animals, Brain, Drosophila, Extremities, Female, Gait, Ganglia, Invertebrate, Male, Neurons, Walking}, issn = {1095-9203}, doi = {10.1126/science.1249964}, author = {Bidaye, Salil S and Machacek, Christian and Wu, Yang and Dickson, Barry J} } @article {45152, title = {Nonmuscle myosin II isoforms coassemble in living cells.}, journal = {Current Biology}, volume = {24}, year = {2014}, month = {2014 May 19}, pages = {1160-6}, abstract = {

Nonmuscle myosin II (NM II) powers myriad developmental and cellular processes, including embryogenesis, cell migration, and cytokinesis [1]. To exert its functions, monomers of NM II assemble into bipolar filaments that produce a contractile force on the actin cytoskeleton. Mammalian cells express up to three isoforms of NM II (NM IIA, IIB, and IIC), each of which possesses distinct biophysical properties and supports unique as well as redundant cellular functions [2-8]. Despite previous efforts [9-13], it remains unclear whether NM II isoforms assemble in living cells to produce mixed (heterotypic) bipolar filaments or whether filaments consist entirely of a single isoform (homotypic). We addressed this question using fluorescently tagged versions of NM IIA, IIB, and IIC, isoform-specific immunostaining of the endogenous proteins, and two-color total internal reflection fluorescence structured-illumination microscopy, or TIRF-SIM, to visualize individual myosin II bipolar filaments inside cells. We show that NM II isoforms coassemble into heterotypic filaments in a variety of settings, including various types of stress fibers, individual filaments throughout the cell, and the contractile ring. We also show that the differential distribution of NM IIA and NM IIB typically seen in confocal micrographs of well-polarized cells is reflected in the composition of individual bipolar filaments. Interestingly, this differential distribution is less pronounced in freshly spread cells, arguing for the existence of a sorting mechanism acting over time. Together, our work argues that individual NM II isoforms are potentially performing both isoform-specific and isoform-redundant functions while coassembled with other NM II isoforms.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2014.03.071}, author = {Beach, Jordan R and Shao, Lin and Remmert, Kirsten and Li, Dong and Betzig, Eric and Hammer, John A} } @article {46297, title = {Novel cell-based odorant sensor elements based on insect odorant receptors.}, journal = {Biosensors \& Bioelectronics}, volume = {65C}, year = {2014}, month = {2014 Oct 17}, pages = {287-294}, abstract = {

Development of cell-based odorant sensor elements combined not only high degree of sensitivity and selectivity but also long-term stability is crucial for their practical applications. Here we report the development of a novel cell-based odorant sensor element that sensitively and selectively detects odorants and displays increased fluorescent intensities over a long period of time. Our odorant sensor elements, based on Sf21 cell lines expressing insect odorant receptors, are sensitive to the level of several tens of parts per billion in solution, can selectively distinguish between different types of odorants based on the odorant selectivity intrinsic to the expressed receptors, and have response times of approximately 13s. Specifically, with the use of Sf21 cells and insect odorant receptors, we demonstrated that the established cell lines stably expressing insect odorant receptors are able to detect odorants with consistent responsiveness for at least 2 months, thus exceeding the short life-span normally associated with cell-based sensors. We also demonstrated the development of a compact odorant sensor chip by integrating the established insect cell lines into a microfluidic chip. The methodology we established in this study, in conjunction with the large repertoire of insect odorant receptors, will aid in the development of practical cell-based odorant sensors for various applications, including food administration and health management.

}, issn = {1873-4235}, doi = {10.1016/j.bios.2014.10.026}, author = {Mitsuno, Hidefumi and Sakurai, Takeshi and Namiki, Shigehiro and Mitsuhashi, Hiroyuki and Kanzaki, Ryohei} } @article {47218, title = {OpenStage: a low-cost motorized microscope stage with sub-micron positioning accuracy.}, journal = {PloS One}, volume = {9}, year = {2014}, month = {2014 Feb 26}, pages = {e88977}, abstract = {

Recent progress in intracellular calcium sensors and other fluorophores has promoted the widespread adoption of functional optical imaging in the life sciences. Home-built multiphoton microscopes are easy to build, highly customizable, and cost effective. For many imaging applications a 3-axis motorized stage is critical, but commercially available motorization hardware (motorized translators, controller boxes, etc) are often very expensive. Furthermore, the firmware on commercial motor controllers cannot easily be altered and is not usually designed with a microscope stage in mind. Here we describe an open-source motorization solution that is simple to construct, yet far cheaper and more customizable than commercial offerings. The cost of the controller and motorization hardware are under $1000. Hardware costs are kept low by replacing linear actuators with high quality stepper motors. Electronics are assembled from commonly available hobby components, which are easy to work with. Here we describe assembly of the system and quantify the positioning accuracy of all three axes. We obtain positioning repeatability of the order of 1 μm in X/Y and 0.1 μm in Z. A hand-held control-pad allows the user to direct stage motion precisely over a wide range of speeds (10(-1) to 10(2) μm{\textperiodcentered}s(-1)), rapidly store and return to different locations, and execute "jumps" of a fixed size. In addition, the system can be controlled from a PC serial port. Our "OpenStage" controller is sufficiently flexible that it could be used to drive other devices, such as micro-manipulators, with minimal modifications.

}, keywords = {Costs and Cost Analysis, Equipment Design, Microscopy, Reproducibility of Results}, issn = {1932-6203}, doi = {10.1371/journal.pone.0088977}, author = {Campbell, Robert A A and Eifert, Robert W and Turner, Glenn C} } @article {45063, title = {Optimized CRISPR/Cas tools for efficient germline and somatic genome engineering in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, year = {2014}, month = {2014 Jul 22}, pages = {E2967-76}, abstract = {

The type II clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system has emerged recently as a powerful method to manipulate the genomes of various organisms. Here, we report a toolbox for high-efficiency genome engineering of Drosophila melanogaster consisting of transgenic Cas9 lines and versatile guide RNA (gRNA) expression plasmids. Systematic evaluation reveals Cas9 lines with ubiquitous or germ-line-restricted patterns of activity. We also demonstrate differential activity of the same gRNA expressed from different U6 snRNA promoters, with the previously untested U6:3 promoter giving the most potent effect. An appropriate combination of Cas9 and gRNA allows targeting of essential and nonessential genes with transmission rates ranging from 25-100\%. We also demonstrate that our optimized CRISPR/Cas tools can be used for offset nicking-based mutagenesis. Furthermore, in combination with oligonucleotide or long double-stranded donor templates, our reagents allow precise genome editing by homology-directed repair with rates that make selection markers unnecessary. Last, we demonstrate a novel application of CRISPR/Cas-mediated technology in revealing loss-of-function phenotypes in somatic cells following efficient biallelic targeting by Cas9 expressed in a ubiquitous or tissue-restricted manner. Our CRISPR/Cas tools will facilitate the rapid evaluation of mutant phenotypes of specific genes and the precise modification of the genome with single-nucleotide precision. Our results also pave the way for high-throughput genetic screening with CRISPR/Cas.

}, issn = {1091-6490}, doi = {10.1073/pnas.1405500111}, author = {Port, Fillip and Chen, Hui-Min and Lee, Tzumin and Bullock, Simon L} } @article {6892, title = {Optimized ratiometric calcium sensors for functional in vivo imaging of neurons and T lymphocytes.}, journal = {Nature Methods}, volume = {11}, year = {2014}, month = {2014 Feb}, pages = {175-82}, abstract = {

The quality of genetically encoded calcium indicators (GECIs) has improved dramatically in recent years, but high-performing ratiometric indicators are still rare. Here we describe a series of fluorescence resonance energy transfer (FRET)-based calcium biosensors with a reduced number of calcium binding sites per sensor. These {\textquoteright}Twitch{\textquoteright} sensors are based on the C-terminal domain of Opsanus troponin C. Their FRET responses were optimized by a large-scale functional screen in bacterial colonies, refined by a secondary screen in rat hippocampal neuron cultures. We tested the in vivo performance of the most sensitive variants in the brain and lymph nodes of mice. The sensitivity of the Twitch sensors matched that of synthetic calcium dyes and allowed visualization of tonic action potential firing in neurons and high resolution functional tracking of T lymphocytes. Given their ratiometric readout, their brightness, large dynamic range and linear response properties, Twitch sensors represent versatile tools for neuroscience and immunology.

}, issn = {1548-7105}, doi = {10.1038/nmeth.2773}, author = {Thestrup, Thomas and Litzlbauer, Julia and Bartholom{\"a}us, Ingo and Mues, Marsilius and Russo, Luigi and Dana, Hod and Kovalchuk, Yuri and Liang, Yajie and Kalamakis, Georgios and Laukat, Yvonne and Becker, Stefan and Witte, Gregor and Geiger, Anselm and Allen, Taylor and Rome, Lawrence C and Chen, Tsai-Wen and Kim, Douglas S. and Garaschuk, Olga and Griesinger, Christian and Griesbeck, Oliver} } @article {45698, title = {Oscillatory activity in the medial prefrontal cortex and nucleus accumbens correlates with impulsivity and reward outcome.}, journal = {PLoS One}, volume = {9}, year = {2014}, month = {2014 Oct 21}, pages = {e111300}, abstract = {

Actions expressed prematurely without regard for their consequences are considered impulsive. Such behaviour is governed by a network of brain regions including the prefrontal cortex (PFC) and nucleus accumbens (NAcb) and is prevalent in disorders including attention deficit hyperactivity disorder (ADHD) and drug addiction. However, little is known of the relationship between neural activity in these regions and specific forms of impulsive behaviour. In the present study we investigated local field potential (LFP) oscillations in distinct sub-regions of the PFC and NAcb on a 5-choice serial reaction time task (5-CSRTT), which measures sustained, spatially-divided visual attention and action restraint. The main findings show that power in gamma frequency (50-60 Hz) LFP oscillations transiently increases in the PFC and NAcb during both the anticipation of a cue signalling the spatial location of a nose-poke response and again following correct responses. Gamma oscillations were coupled to low-frequency delta oscillations in both regions; this coupling strengthened specifically when an error response was made. Theta (7-9 Hz) LFP power in the PFC and NAcb increased during the waiting period and was also related to response outcome. Additionally, both gamma and theta power were significantly affected by upcoming premature responses as rats waited for the visual cue to respond. In a subgroup of rats showing persistently high levels of impulsivity we found that impulsivity was associated with increased error signals following a nose-poke response, as well as reduced signals of previous trial outcome during the waiting period. Collectively, these in-vivo neurophysiological findings further implicate the PFC and NAcb in anticipatory impulsive responses and provide evidence that abnormalities in the encoding of rewarding outcomes may underlie trait-like impulsive behaviour.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0111300}, author = {Donnelly, Nicholas A and Holtzman, Tahl and Rich, P Dylan and Nevado-Holgado, Alejo J and Fernando, Anushka B P and Van Dijck, Gert and Holzhammer, Tobias and Paul, Oliver and Ruther, Patrick and Paulsen, Ole and Robbins, Trevor W and Dalley, Jeffrey W} } @article {45719, title = {The PAR complex controls the spatiotemporal dynamics of F-actin and the MTOC in directionally migrating leukocytes.}, journal = {Journal of Cell Science}, volume = {127}, year = {2014}, month = {2014 Oct 15}, pages = {4381-95}, abstract = {

Inflammatory cells acquire a polarized phenotype to migrate towards sites of infection or injury. A conserved polarity complex comprising PAR-3, PAR-6 and atypical protein kinase C (aPKC) relays extracellular polarizing cues to control cytoskeletal and signaling networks affecting morphological and functional polarization. However, there is no evidence that myeloid cells use PAR signaling to migrate vectorially in three-dimensional (3D) environments in vivo. Using genetically encoded bioprobes and high-resolution live imaging, we reveal the existence of F-actin oscillations in the trailing edge and constant repositioning of the microtubule organizing center (MTOC) to direct leukocyte migration in wounded medaka fish larvae (Oryzias latipes). Genetic manipulation in live myeloid cells demonstrates that the catalytic activity of aPKC and the regulated interaction with PAR-3 and PAR-6 are required for consistent F-actin oscillations, MTOC perinuclear mobility, aPKC repositioning and wound-directed migration upstream of Rho kinase (also known as ROCK or ROK) activation. We propose that the PAR complex coordinately controls cytoskeletal changes affecting both the generation of traction force and the directionality of leukocyte migration to sites of injury.

}, issn = {1477-9137}, doi = {10.1242/jcs.146217}, author = {Crespo, Carolina and Vernieri, Claudio and Keller, Philipp J and Garr{\`e}, Massimiliano and Bender, Jeffrey R and Wittbrodt, Joachim and Pardi, Ruggero} } @article {68336, title = {Parasympathetic ganglia derive from Schwann cell precursors}, journal = {Science}, volume = {345}, year = {2014}, month = {06/2014}, pages = {87-90}, abstract = {

The parasympathetic nervous system helps regulate the functions of many tissues and organs, including the salivary glands and the esophagus. To do so, it needs to reach throughout the body, connecting central systems to peripheral ones. Dyachuk et al. and Espinosa-Medina et al. explored how these connections are established in mice (see the Perspective by Kalcheim and Rohrer). Progenitor cells that travel along with the developing nerves can give rise to both myelinforming Schwann cells and to parasympathetic neurons. That means the interacting nerves do not have to find each other. Instead, the beginnings of the connections are laid down as the nervous system develops. Science, this issue p. 82, p. 87; see also p. 32 Parasympathetic neurons are born from Schwann cell precursors located in the nerves that carry preganglionic fibers. [Also see Perspective by Kalcheim and Rohrer] Neural crest cells migrate extensively and give rise to most of the peripheral nervous system, including sympathetic, parasympathetic, enteric, and dorsal root ganglia. We studied how parasympathetic ganglia form close to visceral organs and what their precursors are. We find that many cranial nerve-associated crest cells coexpress the pan-autonomic determinant Paired-like homeodomain 2b (Phox2b) together with markers of Schwann cell precursors. Some give rise to Schwann cells after down-regulation of PHOX2b. Others form parasympathetic ganglia after being guided to the site of ganglion formation by the nerves that carry preganglionic fibers, a parsimonious way of wiring the pathway. Thus, cranial Schwann cell precursors are the source of parasympathetic neurons during normal development.

}, doi = {10.1126/science.1253286}, url = {https://www.science.org/doi/abs/10.1126/science.1253286}, author = {I. Espinosa-Medina and E. Outin and C. A. Picard and Z. Chettouh and S. Dymecki and G. G. Consalez and E. Coppola and J.-F. Brunet} } @article {6886, title = {Pfam: the protein families database.}, journal = {Nucleic acids research}, volume = {42}, year = {2014}, month = {2014 Jan}, pages = {D222-30}, abstract = {Pfam, available via servers in the UK (http://pfam.sanger.ac.uk/) and the USA (http://pfam.janelia.org/), is a widely used database of protein families, containing 14 831 manually curated entries in the current release, version 27.0. Since the last update article 2 years ago, we have generated 1182 new families and maintained sequence coverage of the UniProt Knowledgebase (UniProtKB) at nearly 80\%, despite a 50\% increase in the size of the underlying sequence database. Since our 2012 article describing Pfam, we have also undertaken a comprehensive review of the features that are provided by Pfam over and above the basic family data. For each feature, we determined the relevance, computational burden, usage statistics and the functionality of the feature in a website context. As a consequence of this review, we have removed some features, enhanced others and developed new ones to meet the changing demands of computational biology. Here, we describe the changes to Pfam content. Notably, we now provide family alignments based on four different representative proteome sequence data sets and a new interactive DNA search interface. We also discuss the mapping between Pfam and known 3D structures.}, keywords = {Databases, DNA, Internet, Intrinsically Disordered Proteins, Protein, Protein Conformation, Proteins, Proteome, Sequence Alignment, Sequence Analysis}, issn = {1362-4962}, doi = {10.1093/nar/gkt1223}, author = {Finn, Robert D and Bateman, Alex and Clements, Jody and Coggill, Penelope and Eberhardt, Ruth Y and Sean R. Eddy and Heger, Andreas and Hetherington, Kirstie and Holm, Liisa and Mistry, Jaina and Sonnhammer, Erik L L and Tate, John and Punta, Marco} } @article {45053, title = {Phase shifts in binaural stimuli provide directional cues for sound localisation in the field cricket Gryllus bimaculatus.}, journal = {Journal of Experimental Biology}, volume = {217}, year = {2014}, month = {2014 Jul 1}, pages = {2390-8}, abstract = {

The cricket{\textquoteright}s auditory system is a highly directional pressure difference receiver whose function is hypothesised to depend on phase relationships between the sound waves propagating through the auditory trachea that connects the left and right hearing organs. We tested this hypothesis by measuring the effect of experimentally constructed phase shifts in acoustic stimuli on phonotactic behavior of Gryllus bimaculatus, the oscillatory response patterns of the tympanic membrane, and the activity of the auditory afferents. The same artificial calling song was played simultaneously at the left and right sides of the cricket, but one sound pattern was shifted in phase by 90 deg (carrier frequencies between 3.6 and 5.4 kHz). All three levels of auditory processing are sensitive to experimentally induced acoustic phase shifts, and the response characteristics are dependent on the carrier frequency of the sound stimulus. At lower frequencies, crickets steered away from the sound leading in phase, while tympanic membrane vibrations and auditory afferent responses were smaller when the ipsilateral sound was leading. In contrast, opposite responses were observed at higher frequencies in all three levels of auditory processing. Minimal responses occurred near the carrier frequency of the cricket{\textquoteright}s calling song, suggesting a stability at this frequency. Our results indicate that crickets may use directional cues arising from phase shifts in acoustic signals for sound localisation, and that the response properties of pressure difference receivers may be analysed with phase-shifted sound stimuli to further our understanding of how insect auditory systems are adapted for directional processing.

}, issn = {1477-9145}, doi = {10.1242/jeb.101402}, author = {Seagraves, Kelly M and Hedwig, Berthold} } @article {47628, title = {Photocontrollable fluorescent proteins for superresolution imaging.}, journal = {Annual review of biophysics}, volume = {43}, year = {2014}, month = {2014}, pages = {303-29}, abstract = {

Superresolution fluorescence microscopy permits the study of biological processes at scales small enough to visualize fine subcellular structures that are unresolvable by traditional diffraction-limited light microscopy. Many superresolution techniques, including those applicable to live cell imaging, utilize genetically encoded photocontrollable fluorescent proteins. The fluorescence of these proteins can be controlled by light of specific wavelengths. In this review, we discuss the biochemical and photophysical properties of photocontrollable fluorescent proteins that are relevant to their use in superresolution microscopy. We then describe the recently developed photoactivatable, photoswitchable, and reversibly photoswitchable fluorescent proteins, and we detail their particular usefulness in single-molecule localization-based and nonlinear ensemble-based superresolution techniques. Finally, we discuss recent applications of photocontrollable proteins in superresolution imaging, as well as how these applications help to clarify properties of intracellular structures and processes that are relevant to cell and developmental biology, neuroscience, cancer biology and biomedicine.

}, keywords = {Animals, Cells, Luminescent Proteins, Mammals, Microscopy, Fluorescence}, issn = {1936-1238}, doi = {10.1146/annurev-biophys-051013-022836}, author = {Shcherbakova, Daria M and Sengupta, Prabuddha and Lippincott-Schwartz, Jennifer and Verkhusha, Vladislav V} } @article {45699, title = {Photoswitchable red fluorescent protein with a large stokes shift.}, journal = {Chemistry \& Biology}, volume = {21}, year = {2014}, month = {2014 Oct 23}, pages = {1402-14}, abstract = {

A subclass of fluorescent proteins (FPs), large Stokes shift (LSS) FP, are characterized by increased spread between excitation and emission maxima. We report a photoswitchable variant of a red FP with an LSS, PSLSSmKate, which initially exhibits excitation and emission at 445 and 622\ nm, but violet irradiation photoswitches PSLSSmKate into a common red form with excitation and emission at 573 and 621\ nm. We characterize spectral, photophysical, and biochemical properties of PSLSSmKate in\ vitro and in mammalian cells and determine its crystal structure in the LSS form. Mass spectrometry, mutagenesis, and spectroscopy of PSLSSmKate allow us\ to propose molecular mechanisms for the LSS, pH dependence, and light-induced chromophore transformation. We demonstrate the applicability of PSLSSmKate to superresolution photoactivated localization microscopy and protein dynamics in live cells. Given its promising properties, we expect that PSLSSmKate-like phenotype will be further used for photoactivatable imaging and tracking multiple populations of intracellular objects.

}, issn = {1879-1301}, doi = {10.1016/j.chembiol.2014.08.010}, author = {Piatkevich, Kiryl D and English, Brian P and Malashkevich, Vladimir N and Xiao, Hui and Almo, Steven C and Singer, Robert H and Verkhusha, Vladislav V} } @article {6717, title = {Population genomics of the honey bee reveals strong signatures of positive selection on worker traits.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, year = {2014}, month = {2014 Jan 31}, pages = {2614-19}, abstract = {

Most theories used to explain the evolution of eusociality rest upon two key assumptions: mutations affecting the phenotype of sterile workers evolve by positive selection if the resulting traits benefit fertile kin, and that worker traits provide the primary mechanism allowing social insects to adapt to their environment. Despite the common view that positive selection drives phenotypic evolution of workers, we know very little about the prevalence of positive selection acting on the genomes of eusocial insects. We mapped the footprints of positive selection in Apis mellifera through analysis of 40 individual genomes, allowing us to identify thousands of genes and regulatory sequences with signatures of adaptive evolution over multiple timescales. We found Apoidea- and Apis-specific genes to be enriched for signatures of positive selection, indicating that novel genes play a disproportionately large role in adaptive evolution of eusocial insects. Worker-biased proteins have higher signatures of adaptive evolution relative to queen-biased proteins, supporting the view that worker traits are key to adaptation. We also found genes regulating worker division of labor to be enriched for signs of positive selection. Finally, genes associated with worker behavior based on analysis of brain gene expression were highly enriched for adaptive protein and cis-regulatory evolution. Our study highlights the significant contribution of worker phenotypes to adaptive evolution in social insects, and provides a wealth of knowledge on the loci that influence fitness in honey bees.

}, issn = {1091-6490}, doi = {10.1073/pnas.1315506111}, author = {Harpur, Brock A and Kent, Clement F and Molodtsova, Daria and Lebon, Jonathan M D and Alqarni, Abdulaziz S and Owayss, Ayman A and Zayed, Amro} } @article {45336, title = {Population of sensory neurons essential for asthmatic hyperreactivity of inflamed airways.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, year = {2014}, month = {2014 Aug 5}, pages = {11515-20}, abstract = {

Asthma is a common debilitating inflammatory lung disease affecting over 200 million people worldwide. Here, we investigated neurogenic components involved in asthmatic-like attacks using the ovalbumin-sensitized murine model of the disease, and identified a specific population of neurons that are required for airway hyperreactivity. We show that ablating or genetically silencing these neurons abolished the hyperreactive broncho-constrictions, even in the presence of a fully developed lung inflammatory immune response. These neurons are found in the vagal ganglia and are characterized by the expression of the transient receptor potential vanilloid 1 (TRPV1) ion channel. However, the TRPV1 channel itself is not required for the asthmatic-like hyperreactive airway response. We also demonstrate that optogenetic stimulation of this population of TRP-expressing cells with channelrhodopsin dramatically exacerbates airway hyperreactivity of inflamed airways. Notably, these cells express the sphingosine-1-phosphate receptor 3 (S1PR3), and stimulation with a S1PR3 agonist efficiently induced broncho-constrictions, even in the absence of ovalbumin sensitization and inflammation. Our results show that the airway hyperreactivity phenotype can be physiologically dissociated from the immune component, and provide a platform for devising therapeutic approaches to asthma that target these pathways separately.

}, issn = {1091-6490}, doi = {10.1073/pnas.1411032111}, author = {Tr{\"a}nkner, Dimitri and Hahne, Nadeau and Sugino, Ken and Hoon, Mark A and Zuker, Charles} } @inbook {65784, title = {Porphyrins and Metalloporphyrins at Components in Artificial Photosynthesis Research}, booktitle = {Handbook of Porphyrin Science}, volume = {34}, year = {2014}, pages = {196 {\textendash} 233}, publisher = {World Scientific Pulishing}, organization = {World Scientific Pulishing}, isbn = {978-981-4425-10-0}, doi = {10.1142/9789814417297_0016}, author = {Tebo, Alison G. and Herrero, C and Aukauloo, A}, editor = {Kadish, Karl M and Smith, Kevin M and undefined, and Guilard, Roger} } @article {45374, title = {The practical and fundamental limits of optical imaging in mammalian brains.}, journal = {Neuron}, volume = {83}, year = {2014}, month = {2014 Sep 17}, pages = {1242-1245}, abstract = {

Advances in chemistry and physics have profound effects on neuroimaging. Current and future progress in\ these disciplines will continue to aid in efforts to visualize neural circuitry, particularly in deeper layers of the brain.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2014.08.009}, author = {Ji, Na} } @article {45067, title = {Precise spatial coding is preserved along the longitudinal hippocampal axis.}, journal = {Hippocampus}, volume = {24}, year = {2014}, month = {2014 Jul 18}, pages = {1-16}, abstract = {

Compared to the dorsal hippocampus, relatively few studies have characterized neuronal responses in the ventral hippocampus. In particular, it is unclear whether and how cells in the ventral region represent space and/or respond to contextual changes. We recorded from dorsal and ventral CA1 neurons in freely moving mice exposed to manipulations of visuospatial and olfactory contexts. We found that ventral cells respond to alterations of the visuospatial environment such as exposure to novel local cues, cue rotations, and contextual expansion in similar ways to dorsal cells, with the exception of cue rotations. Furthermore, we found that ventral cells responded to odors much more strongly than dorsal cells, particularly to odors of high valence. Similar to earlier studies recording from the ventral hippocampus in CA3, we also found increased scaling of place cell field size along the longitudinal hippocampal axis. Although the increase in place field size observed toward the ventral pole has previously been taken to suggest a decrease in spatial information coded by ventral place cells, we hypothesized that a change in spatial scaling could instead signal a shift in representational coding that preserves the resolution of spatial information. To explore this possibility, we examined population activity using principal component analysis (PCA) and neural location reconstruction techniques. Our results suggest that ventral populations encode a distributed representation of space, and that the resolution of spatial information at the population level is comparable to that of dorsal populations of similar size. Finally, through the use of neural network modeling, we suggest that the redundancy in spatial representation along the longitudinal hippocampal axis may allow the hippocampus to overcome the conflict between memory interference and generalization inherent in neural network memory. Our results suggest that ventral population activity is well suited for generalization across locations and contexts. {\textcopyright} 2014 Wiley Periodicals, Inc.

}, issn = {1098-1063}, doi = {10.1002/hipo.22333}, author = {Keinath, Alexander T and Wang, Melissa E and Wann, Ellen G and Yuan, Robin K and Dudman, Joshua T and Muzzio, Isabel A} } @article {47625, title = {Probing the stochastic, motor-driven properties of the cytoplasm using force spectrum microscopy.}, journal = {Cell}, volume = {158}, year = {2014}, month = {2014 Aug 14}, pages = {822-32}, abstract = {

Molecular motors in cells typically produce highly directed motion; however, the aggregate, incoherent effect of all active processes also creates randomly fluctuating forces, which drive diffusive-like, nonthermal motion. Here, we introduce force-spectrum-microscopy (FSM) to directly quantify random forces within the cytoplasm of cells and thereby probe stochastic motor activity. This technique combines measurements of the random motion of probe particles with independent micromechanical measurements of the cytoplasm to quantify the spectrum of force fluctuations. Using FSM, we show that force\ fluctuations substantially enhance intracellular movement of small and large components. The fluctuations are three times larger in malignant cells than in their benign counterparts. We further demonstrate that vimentin acts globally to anchor organelles against randomly fluctuating forces in the cytoplasm, with no effect on their magnitude. Thus, FSM has broad applications for understanding the cytoplasm and its intracellular processes in relation to cell physiology in healthy and diseased states.

}, keywords = {Animals, Biomechanical Phenomena, Cytoplasm, Embryo, Mammalian, Fibroblasts, Mice, Microscopy, Atomic Force, Proteins, Vimentin}, issn = {1097-4172}, doi = {10.1016/j.cell.2014.06.051}, author = {Guo, Ming and Ehrlicher, Allen J and Jensen, Mikkel H and Renz, Malte and Moore, Jeffrey R and Goldman, Robert D and Lippincott-Schwartz, Jennifer and Mackintosh, Frederick C and Weitz, David A} } @article {6897, title = {Procedures for behavioral experiments in head-fixed mice.}, journal = {PLoS One}, volume = {9}, year = {2014}, month = {2014}, pages = {e88678}, abstract = {

The mouse is an increasingly prominent model for the analysis of mammalian neuronal circuits. Neural circuits ultimately have to be probed during behaviors that engage the circuits. Linking circuit dynamics to behavior requires precise control of sensory stimuli and measurement of body movements. Head-fixation has been used for behavioral research, particularly in non-human primates, to facilitate precise stimulus control, behavioral monitoring and neural recording. However, choice-based, perceptual decision tasks by head-fixed mice have only recently been introduced. Training mice relies on motivating mice using water restriction. Here we describe procedures for head-fixation, water restriction and behavioral training for head-fixed mice, with a focus on active, whisker-based tactile behaviors. In these experiments mice had restricted access to water (typically 1 ml/day). After ten days of water restriction, body weight stabilized at approximately 80\% of initial weight. At that point mice were trained to discriminate sensory stimuli using operant conditioning. Head-fixed mice reported stimuli by licking in go/no-go tasks and also using a forced choice paradigm using a dual lickport. In some cases mice learned to discriminate sensory stimuli in a few trials within the first behavioral session. Delay epochs lasting a second or more were used to separate sensation (e.g. tactile exploration) and action (i.e. licking). Mice performed a variety of perceptual decision tasks with high performance for hundreds of trials per behavioral session. Up to four months of continuous water restriction showed no adverse health effects. Behavioral performance correlated with the degree of water restriction, supporting the importance of controlling access to water. These behavioral paradigms can be combined with cellular resolution imaging, random access photostimulation, and whole cell recordings.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0088678}, author = {Guo, Zengcai V and Hires, S Andrew and Li, Nuo and O{\textquoteright}Connor, Daniel H and Komiyama, Takaki and Ophir, Eran and Huber, Daniel and Bonardi, Claudia and Morandell, Karin and Gutnisky, Diego and Peron, Simon and Xu, Ning-long and Cox, James and Svoboda, Karel} } @article {46941, title = {Protecting integrated circuits from piracy with test-aware logic locking.}, journal = {ICCAD {\textquoteright}14 Proceedings of the 2014 IEEE/ACM International Conference on Computer-Aided Design}, year = {2014}, month = {2014 Nov 03}, pages = {262-269}, abstract = {The increasing IC manufacturing cost encourages a business model where design houses outsource IC fabrication to remote foundries. Despite cost savings, this model exposes design houses to IC piracy as remote foundries can manufacture in excess to sell on the black market. Recent efforts in digital hardware security aim to thwart piracy by using XOR-based chip locking, cryptography, and active metering. To counter direct attacks and lower the exposure of unlocked circuits to the foundry, we introduce a multiplexor-based locking strategy that preserves test response allowing IC testing by an untrusted party before activation. We demonstrate a simple yet effective attack against a locked circuit that does not preserve test response, and validate the effectiveness of our locking strategy on IWLS 2005 benchmarks.}, doi = {10.1109/ICCAD.2014.7001361}, author = {Plaza, Stephen M and Markov, Igor L} } @article {65783, title = {Protein design: toward functional metalloenzymes.}, journal = {Chemical reviews}, volume = {114}, year = {2014}, month = {03/2014}, pages = {3495 {\textendash} 3578}, doi = {10.1021/cr400458x}, author = {Yu, Fangting and Cangelosi, Virginia M and Zastrow, Melissa L and Tegoni, Matteo and Plegaria, Jefferson S and Tebo, Alison G and Mocny, Catherine S and Ruckthong, Leela and Qayyum, Hira and Pecoraro, Vincent L} } @article {6933, title = {Protein structure determination by MicroED.}, journal = {Current Opinion in Structural Biology}, volume = {27C}, year = {2014}, month = {2014 Apr 4}, pages = {24-31}, abstract = {

In this review we discuss the current advances relating to structure determination from protein microcrystals with special emphasis on the newly developed method called MicroED. This method uses a transmission electron cryo-microscope to collect electron diffraction data from extremely small 3-dimensional (3D) crystals. MicroED has been used to solve the 3D structure of the model protein lysozyme to 2.9A resolution. As the method further matures, MicroED promises to offer a unique and widely applicable approach to protein crystallography using nanocrystals.

}, issn = {1879-033X}, doi = {10.1016/j.sbi.2014.03.004}, author = {Nannenga, Brent L and Gonen, Tamir} } @article {6936, title = {Proteome analysis and conditional deletion of the EAAT2 glutamate transporter provide evidence against a role of EAAT2 in pancreatic insulin secretion in mice.}, journal = {The Journal of Biological Chemistry}, volume = {289}, year = {2014}, month = {2014 Jan 17}, pages = {1329-44}, abstract = {

Islet function is incompletely understood in part because key steps in glutamate handling remain undetermined. The glutamate (excitatory amino acid) transporter 2 (EAAT2; Slc1a2) has been hypothesized to (a) provide islet cells with glutamate, (b) protect islet cells against high extracellular glutamate concentrations, (c) mediate glutamate release, or (d) control the pH inside insulin secretory granules. Here we floxed the EAAT2 gene to produce the first conditional EAAT2 knock-out mice. Crossing with Nestin-cyclization recombinase (Cre) eliminated EAAT2 from the brain, resulting in epilepsy and premature death, confirming the importance of EAAT2 for brain function and validating the genetic construction. Crossing with insulin-Cre lines (RIP-Cre and IPF1-Cre) to obtain pancreas-selective deletion did not appear to affect survival, growth, glucose tolerance, or β-cell number. We found (using TaqMan RT-PCR, immunoblotting, immunocytochemistry, and proteome analysis) that the EAAT2 levels were too low to support any of the four hypothesized functions. The proteome analysis detected more than 7,000 islet proteins of which more than 100 were transporters. Although mitochondrial glutamate transporters and transporters for neutral amino acids were present at high levels, all other transporters with known ability to transport glutamate were strikingly absent. Glutamate-metabolizing enzymes were abundant. The level of glutamine synthetase was 2 orders of magnitude higher than that of glutaminase. Taken together this suggests that the uptake of glutamate by islets from the extracellular fluid is insignificant and that glutamate is intracellularly produced. Glutamine synthetase may be more important for islets than assumed previously.

}, keywords = {Animals, Crosses, Excitatory Amino Acid Transporter 2, Gene Deletion, Genetic, Glutamic Acid, Insulin, Insulin-Secreting Cells, Knockout, Mice, Proteome}, issn = {1083-351X}, doi = {10.1074/jbc.M113.529065}, author = {Zhou, Yun and Waanders, Leonie F and Holmseth, Silvia and Guo, Caiying and Berger, Urs V and Li, Yuchuan and Lehre, Anne-Catherine and Lehre, Knut P and Danbolt, Niels C} } @article {45904, title = {Proton-coupled sugar transport in the prototypical major facilitator superfamily protein XylE.}, journal = {Nature Communication}, volume = {5}, year = {2014}, month = {2014 - Aug}, pages = {4521}, abstract = {

The major facilitator superfamily (MFS) is the largest collection of structurally related membrane proteins that transport a wide array of substrates. The proton-coupled sugar transporter XylE is the first member of the MFS that has been structurally characterized in multiple transporting conformations, including both the outward and inward-facing states. Here we report the crystal structure of XylE in a new inward-facing open conformation, allowing us to visualize the rocker-switch movement of the N-domain against the C-domain during the transport cycle. Using molecular dynamics simulation, and functional transport assays, we describe the movement of XylE that facilitates sugar translocation across a lipid membrane and identify the likely candidate proton-coupling residues as the conserved Asp27 and Arg133. This study addresses the structural basis for proton-coupled substrate transport and release mechanism for the sugar porter family of proteins.

}, issn = {2041-1723}, doi = {10.1038/ncomms5521}, author = {Wisedchaisri, Goragot and Park, Min-Sun and Iadanza, Matthew G and Zheng, Hongjin and Gonen, Tamir} } @article {45784, title = {Purification of mitochondria by sucrose step density gradient centrifugation.}, journal = {Cold Spring Harbor Protocols}, volume = {2014}, year = {2014}, month = {2014 Oct}, pages = {pdb.prot080028}, abstract = {

Mitochondrial fractions isolated from tissue culture cells or tissue such as liver after differential centrifugation can be purified further by density gradient centrifugation. Here we describe the use of sucrose for this purpose because it is commonly used and inexpensive and the resulting mitochondria preparations are useful for many purposes.

}, issn = {1559-6095}, doi = {10.1101/pdb.prot080028}, author = {Clayton, David A and Shadel, Gerald S} } @article {46062, title = {Quantifying histone and RNA polymerase II post-translational modification dynamics in mother and daughter cells.}, journal = {Methods}, volume = {70}, year = {2014}, month = {2014 Dec}, pages = {77-88}, abstract = {

Post-translational histone modifications are highly correlated with transcriptional activity, but the relative timing of these marks and their dynamic interplay during gene regulation remains controversial. To shed light on this problem and clarify the connections between histone modifications and transcription, we demonstrate how FabLEM (Fab-based Live Endogenous Modification labeling) can be used to simultaneously track histone H3 Lysine 9 acetylation (H3K9ac) together with RNA polymerase II Serine 2 and Serine 5 phosphorylation (RNAP2 Ser2ph/Ser5ph) in single living cells and their progeny. We provide a detailed description of the FabLEM methodology, including helpful tips for preparing and loading fluorescently conjugated antigen binding fragments (Fab) into cells for optimal results. We also introduce simple procedures for analyzing and visualizing FabLEM data, including color-coded scatterplots to track correlations between modifications through the cell cycle and temporal cross-correlation analysis to dissect modification dynamics. Using these methods, we find significant correlations that span cell generations, with a relatively strong correlation between H3K9ac and Ser5ph that appears to peak a few hours before mitosis and may reflect the bookmarking of genes for efficient re-initiation following mitosis. The techniques we have developed are broadly applicable and should help clarify how histone modifications dynamically contribute to gene regulation.

}, issn = {1095-9130}, doi = {10.1016/j.ymeth.2014.08.002}, author = {Stasevich, Timothy J and Sato, Yuko and Nozaki, Naohito and Kimura, Hiroshi} } @article {68483, title = {Quantitative biology: where modern biology meets physical sciences.}, journal = {Mol Biol Cell}, volume = {25}, year = {2014}, month = {11/2014}, pages = {3482-5}, abstract = {

Quantitative methods and approaches have been playing an increasingly important role in cell biology in recent years. They involve making accurate measurements to test a predefined hypothesis in order to compare experimental data with predictions generated by theoretical models, an approach that has benefited physicists for decades. Building quantitative models in experimental biology not only has led to discoveries of counterintuitive phenomena but has also opened up novel research directions. To make the biological sciences more quantitative, we believe a two-pronged approach needs to be taken. First, graduate training needs to be revamped to ensure biology students are adequately trained in physical and mathematical sciences and vice versa. Second, students of both the biological and the physical sciences need to be provided adequate opportunities for hands-on engagement with the methods and approaches necessary to be able to work at the intersection of the biological and physical sciences. We present the annual Physiology Course organized at the Marine Biological Laboratory (Woods Hole, MA) as a case study for a hands-on training program that gives young scientists the opportunity not only to acquire the tools of quantitative biology but also to develop the necessary thought processes that will enable them to bridge the gap between these disciplines.

}, keywords = {Cell Biology, Computer Simulation, Education, Graduate, Humans, Models, Biological, Natural Science Disciplines, Students}, issn = {1939-4586}, doi = {10.1091/mbc.E14-08-1286}, author = {Shekhar, Shashank and Zhu, Lian and Mazutis, Linas and Sgro, Allyson E and Fai, Thomas G and Podolski, Marija} } @article {47622, title = {Quantitative cell biology: transforming the conceptual, theoretical, instrumental, and methodological approaches to cell biology.}, journal = {Molecular biology of the cell}, volume = {25}, year = {2014}, month = {2014 Nov 5}, pages = {3437}, keywords = {Animals, Cell Biology, Computer Simulation, Humans, Models, Biological, Molecular Imaging}, issn = {1939-4586}, doi = {10.1091/mbc.E14-08-1297}, author = {Lippincott-Schwartz, Jennifer} } @article {45812, title = {Quantum dot-based multiphoton fluorescent pipettes for targeted neuronal electrophysiology.}, journal = {Nature Methods}, volume = {11}, year = {2014}, month = {2014 Dec}, pages = {1237-41}, abstract = {

Targeting visually identified neurons for electrophysiological recording is a fundamental neuroscience technique; however, its potential is hampered by poor visualization of pipette tips in deep brain tissue. We describe quantum dot-coated glass pipettes that provide strong two-photon contrast at deeper penetration depths than those achievable with current methods. We demonstrated the pipettes{\textquoteright} utility in targeted patch-clamp recording experiments and single-cell electroporation of identified rat and mouse neurons in vitro and in vivo.

}, issn = {1548-7105}, doi = {10.1038/nmeth.3146}, author = {Andrasfalvy, Bertalan K and Gali{\~n}anes, Gregorio L and Huber, Daniel and Barbic, Mladen and Macklin, John J and Susumu, Kimihiro and Delehanty, James B and Huston, Alan L and Makara, Judit K and Medintz, Igor L} } @article {6938, title = {Rapid adaptive optical recovery of optimal resolution over large volumes.}, journal = {Nature Methods}, volume = {11}, year = {2014}, month = {2014 Apr}, pages = {625-8}, abstract = {

Using a descanned, laser-induced guide star and direct wavefront sensing, we demonstrate adaptive correction of complex optical aberrations at high numerical aperture (NA) and a 14-ms update rate. This correction permits us to compensate for the rapid spatial variation in aberration often encountered in biological specimens and to recover diffraction-limited imaging over large volumes (\>240 mm per side). We applied this to image fine neuronal processes and subcellular dynamics within the zebrafish brain.

}, doi = {10.1038/nmeth.2925}, author = {Wang, Kai and Milkie, Daniel E and Saxena, Ankur and Engerer, Peter and Misgeld, Thomas and Bronner, Marianne E. and Mumm, Jeff and Betzig, Eric} } @article {45412, title = {Reactivation of developmentally silenced globin genes by forced chromatin looping.}, journal = {Cell}, volume = {158}, year = {2014}, month = {2014 Aug 14}, pages = {849-60}, abstract = {

Distal enhancers commonly contact target promoters via chromatin looping. In erythroid cells, the locus control region (LCR) contacts β-type globin genes in a developmental stage-specific manner to\ stimulate transcription. Previously, we induced LCR-promoter looping by tethering the self-association domain (SA) of Ldb1 to the β-globin promoter via artificial zinc fingers. Here, we show that targeting the SA to a developmentally silenced embryonic globin gene in adult murine erythroblasts triggers its transcriptional reactivation. This activity depends on the LCR, consistent with an LCR-promoter looping mechanism. Strikingly, targeting the SA to the fetal γ-globin promoter in primary adult human erythroblasts increases γ-globin promoter-LCR contacts, stimulating transcription to approximately 85\% of total β-globin synthesis, with a reciprocal reduction in adult β-globin expression. Our findings demonstrate that forced chromatin looping can override a stringent developmental gene expression program and suggest a novel approach to control the balance\ of globin gene transcription for therapeutic applications.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2014.05.050}, author = {Deng, Wulan and Rupon, Jeremy W and Krivega, Ivan and Breda, Laura and Motta, Irene and Jahn, Kristen S and Reik, Andreas and Gregory, Philip D and Rivella, Stefano and Dean, Ann and Blobel, Gerd A} } @article {45045, title = {Receptive field properties of bipolar cell axon terminals in the direction-selective sublaminas of the mouse retina.}, journal = {Journal of Neurophysiology}, volume = {112}, year = {2014}, month = {2014 Jul 16}, pages = {1950-62}, abstract = {

Retinal bipolar cells (BCs) transmit visual signals in parallel channels from the outer to the inner retina, where they provide glutamatergic inputs to specific networks of amacrine and ganglion cells. Intricate network computation at BC axon terminals has been proposed as a mechanism for complex network computation, such as direction selectivity, but direct knowledge of the receptive field property and the synaptic connectivity of the axon terminals of various BC types is required in order to understand the role of axonal computation by BCs. The present study tested the essential assumptions of the presynaptic model of direction selectivity at axon terminals of three functionally distinct BC types that ramify in the direction-selective strata of the mouse retina. Results from two-photon Ca2+ imaging, optogenetic stimulation, and dual patch-clamp recording demonstrated that (1) CB5 cells do not receive fast GABAergic synaptic feedback from starburst amacrine cells (SACs), (2) light-evoked and spontaneous Ca2+ responses are well coordinated among various local regions of CB5 axon terminals, (3) CB5 axon terminals are not directionally selective, (4) CB5 cells consist of two novel functional subtypes with distinct receptive field structures, (5) CB7 cells provide direct excitatory synaptic inputs to, but receive no direct GABAergic synaptic feedback from SACs, and (6) CB7 axon terminals are not directionally selective either. These findings help to simplify models of direction selectivity by ruling out complex computation at BC terminals. They also show that CB5 comprises two functional subclasses of BCs.

}, issn = {1522-1598}, doi = {10.1152/jn.00283.2014}, author = {Chen, Minggang and Lee, Seunghoon and Park, Silvia J H and Looger, Loren L and Zhou, Z Jimmy} } @article {45038, title = {Reconciling the deep homology of neuromodulation with the evolution of behavior.}, journal = {Current Opinion in Neurobiology}, volume = {29C}, year = {2014}, month = {2014 May 27}, pages = {39-47}, abstract = {

The evolution of behavior seems inconsistent with the deep homology of neuromodulatory signaling. G protein coupled receptors (GPCRs) evolved slowly from a common ancestor through a process involving gene duplication, neofunctionalization, and loss. Neuropeptides co-evolved with their receptors and exhibit many conserved functions. Furthermore, brain areas are highly conserved with suggestions of deep anatomical homology between arthropods and vertebrates. Yet, behavior evolved more rapidly; even members of the same genus or species can differ in heritable behavior. The solution to the paradox involves changes in the compartmentalization, or subfunctionalization, of neuromodulation; neurons shift their expression of GPCRs and the content of monoamines and neuropeptides. Furthermore, parallel evolution of neuromodulatory signaling systems suggests a route for repeated evolution of similar behaviors.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2014.05.002}, author = {Katz, Paul S and Lillvis, Joshua L} } @article {45866, title = {Regulation of branching dynamics by axon-intrinsic asymmetries in Tyrosine Kinase Receptor signaling.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 Apr 22}, pages = {e01699}, abstract = {

Axonal branching allows a neuron to connect to several targets, increasing neuronal circuit complexity. While axonal branching is well described, the mechanisms that control it remain largely unknown. We find that in the Drosophila CNS branches develop through a process of excessive growth followed by pruning. In vivo high-resolution live imaging of developing brains as well as loss and gain of function experiments show that activation of Epidermal Growth Factor Receptor (EGFR) is necessary for branch dynamics and the final branching pattern. Live imaging also reveals that intrinsic asymmetry in EGFR localization regulates the balance between dynamic and static filopodia. Elimination of signaling asymmetry by either loss or gain of EGFR function results in reduced dynamics leading to excessive branch formation. In summary, we propose that the dynamic process of axon branch development is mediated by differential local distribution of signaling receptors. DOI: http://dx.doi.org/10.7554/eLife.01699.001.

}, issn = {2050-084X}, doi = {10.7554/eLife.01699}, author = {Zsch{\"a}tzsch, Marlen and Oliva, Carlos and Langen, Marion and De Geest, Natalie and Ozel, Mehmet Neset and Williamson, W Ryan and Lemon, William C and Soldano, Alessia and Munck, Sebastian and Hiesinger, P Robin and Sanchez-Soriano, Natalia and Hassan, Bassem A} } @article {45880, title = {Regulation of RNA granule dynamics by phosphorylation of serine-rich, intrinsically disordered proteins in C. elegans.}, journal = {eLife}, volume = {4}, year = {2014}, month = {2014 Dec 23}, abstract = {

RNA granules have been likened to liquid droplets whose dynamics depend on the controlled dissolution and condensation of internal components. The molecules and reactions that drive these dynamics in vivo are not well understood. In this study, we present evidence that a group of intrinsically disordered, serine-rich proteins regulate the dynamics of P granules in C. elegans embryos. The MEG (maternal-effect germline defective) proteins are germ plasm components that are required redundantly for fertility. We demonstrate that MEG-1 and MEG-3 are substrates of the kinase MBK-2/DYRK and the phosphatase PP2A(PPTR-{\textonehalf}). Phosphorylation of the MEGs promotes granule disassembly and dephosphorylation promotes granule assembly. Using lattice light sheet microscopy on live embryos, we show that GFP-tagged MEG-3 localizes to a dynamic domain that surrounds and penetrates each granule. We conclude that, despite their liquid-like behavior, P granules are non-homogeneous structures whose assembly in embryos is regulated by phosphorylation.

}, issn = {2050-084X}, doi = {10.7554/eLife.04591}, author = {Wang, Jennifer T and Smith, Jarrett and Chen, Bi-Chang and Schmidt, Helen and Rasoloson, Dominique and Paix, Alexandre and Lambrus, Bramwell G and Calidas, Deepika and Betzig, Eric and Seydoux, Geraldine} } @article {45843, title = {Regulation of RNA polymerase II activation by histone acetylation in single living cells.}, journal = {Nature}, volume = {516}, year = {2014}, month = {2014 Dec 11}, pages = {272-5}, abstract = {

In eukaryotic cells, post-translational histone modifications have an important role in gene regulation. Starting with early work on histone acetylation, a variety of residue-specific modifications have now been linked to RNA polymerase II (RNAP2) activity, but it remains unclear if these markers are active regulators of transcription or just passive byproducts. This is because studies have traditionally relied on fixed cell populations, meaning temporal resolution is limited to minutes at best, and correlated factors may not actually be present in the same cell at the same time. Complementary approaches are therefore needed to probe the dynamic interplay of histone modifications and RNAP2 with higher temporal resolution in single living cells. Here we address this problem by developing a system to track residue-specific histone modifications and RNAP2 phosphorylation in living cells by fluorescence microscopy. This increases temporal resolution to the tens-of-seconds range. Our single-cell analysis reveals histone H3 lysine-27 acetylation at a gene locus can alter downstream transcription kinetics by as much as 50\%, affecting two temporally separate events. First acetylation enhances the search kinetics of transcriptional activators, and later the acetylation accelerates the transition of RNAP2 from initiation to elongation. Signatures of the latter can be found genome-wide using chromatin immunoprecipitation followed by sequencing. We argue that this regulation leads to a robust and potentially tunable transcriptional response.

}, issn = {1476-4687}, doi = {10.1038/nature13714}, author = {Stasevich, Timothy J and Hayashi-Takanaka, Yoko and Sato, Yuko and Maehara, Kazumitsu and Ohkawa, Yasuyuki and Sakata-Sogawa, Kumiko and Tokunaga, Makio and Nagase, Takahiro and Nozaki, Naohito and McNally, James G and Kimura, Hiroshi} } @article {45029, title = {Reported Drosophila courtship song rhythms are artifacts of data analysis.}, journal = {BMC Biology}, volume = {12}, year = {2014}, month = {2014 Jun 26}, pages = {38}, abstract = {

BACKGROUND: In a series of landmark papers, Kyriacou, Hall, and colleagues reported that the average inter-pulse interval of Drosophila melanogaster male courtship song varies rhythmically (KH cycles), that the period gene controls this rhythm, and that evolution of the period gene determines species differences in the rhythm{\textquoteright}s frequency. Several groups failed to recover KH cycles, but this may have resulted from differences in recording chamber size.

RESULTS: Here, using recording chambers of the same dimensions as used by Kyriacou and Hall, I found no compelling evidence for KH cycles at any frequency. By replicating the data analysis procedures employed by Kyriacou and Hall, I found that two factors--data binned into 10-second intervals and short recordings--imposed non-significant periodicity in the frequency range reported for KH cycles. Randomized data showed similar patterns.

CONCLUSIONS: All of the results related to KH cycles are likely to be artifacts of binning data from short songs. Reported genotypic differences in KH cycles cannot be explained by this artifact and may have resulted from the use of small sample sizes and/or from the exclusion of samples that did not exhibit song rhythms.

}, issn = {1741-7007}, doi = {10.1186/1741-7007-12-38}, author = {Stern, David L} } @article {6961, title = {Reproductive status, endocrine physiology and chemical signaling in the Neotropical, swarm-founding eusocial wasp, Polybia micans Ducke (Vespidae: Epiponini).}, journal = {The Journal of Experimental Biology}, volume = {217}, year = {2014}, month = {2014 Apr 17}, pages = {2399-410}, abstract = {

In the evolution of caste-based societies in Hymenoptera, the classical insect hormones, juvenile hormone (JH) and ecdysteroids, were co-opted into new functions. Social wasps, which show all levels of sociality and lifestyles, are an ideal group to study such functional changes. Virtually all studies on the physiological mechanisms underlying reproductive division of labor and caste functions in wasps have been done on independent-founding paper wasps, and the majority of these studies have focused on species specially adapted for overwintering. The relatively little studied tropical swarming-founding wasps of the Epiponini (Vespidae) are a diverse group of permanently social wasps, with some species maintaining caste flexibility well into the adult phase. We investigated the behavior, reproductive status, JH and ecdysteroid titers in hemolymph, ecdysteroid content of the ovary and cuticular hydrocarbon (CHC) profiles in the caste-monomorphic, epiponine wasp Polybia micans Ducke. We found that the JH titer was not elevated in competing queens from established multiple-queen nests, but increased in lone queens that lack direct competition. In queenless colonies, JH titers rose transiently in young potential reproductives upon challenge by nestmates, suggesting that JH may prime the ovaries for further development. Ovarian ecdysteroids were very low in workers but higher and correlated with the number of vitellogenic oocytes in the queens. Hemolymph ecdysteroid levels were low and variable in both. Profiles of P. micans CHCs reflected caste, age and reproductive status, but were not tightly linked to either hormone. These findings show a significant divergence in hormone function in swarm-founding wasps compared to independent-founding ones.

}, issn = {1477-9145}, doi = {10.1242/jeb.096750}, author = {Kelstrup, Hans C and Hartfelder, Klaus and Nascimento, Fabio S and Riddiford, Lynn M} } @article {65887, title = {Retrograde Plasticity and Differential Competition of Bipolar Cell Dendrites and Axons in the Developing Retina}, journal = {Current Biology}, volume = {24}, year = {2014}, month = {Jan/2014}, pages = {2301 - 2306}, abstract = {

Most neurons function in the context of pathways that process and propagate information through a series of stages, e.g., from the sensory periphery to cerebral cortex. Because activity at each stage of a neural pathway depends on connectivity at the preceding one, we hypothesized that during development, axonal output of a neuron may regulate synaptic development of its dendrites (i.e., retrograde plasticity). Within pathways, neurons often receive input from multiple partners and provide output to targets shared with other neurons (i.e., convergence). Converging axons can intermingle or occupy separate territories on target dendrites. Activity-dependent competition has been shown to bias target innervation by overlapping axons in several systems. By contrast, whether territorial axons or dendrites compete for targets and inputs, respectively, has not been tested. Here, we generate transgenic mice in which glutamate release from specific sets of retinal bipolar cells (BCs) is suppressed. We find that dendrites of silenced BCs recruit fewer inputs when their neighbors are active and that dendrites of active BCs recruit more inputs when their neighbors are silenced than either active or silenced BCs with equal neighbors. By contrast, axons of silenced BCs form fewer synapses with their targets, irrespective of the activity of their neighbors. These findings reveal that retrograde plasticity guides BC dendritic development in vivo and demonstrate that dendrites, but not territorial axons, in a convergent neural pathway engage in activity-dependent competition. We propose that at a population level, retrograde plasticity serves to maximize functional representation of inputs.

}, issn = {09609822}, doi = {10.1016/j.cub.2014.08.018}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982214010318https://api.elsevier.com/content/article/PII:S0960982214010318?httpAccept=text/xmlhttps://api.elsevier.com/content/article/PII:S0960982214010318?httpAccept=text/plain}, author = {Johnson, Robert~E. and Kerschensteiner, Daniel} } @article {6885, title = {RIVETS: A mechanical system for in vivo and in vitro electrophysiology and imaging.}, journal = {PLoS One}, volume = {9}, year = {2014}, month = {2014 Feb 14}, pages = {e89007}, abstract = {

A number of recent studies have provided compelling demonstrations that both mice and rats can be trained to perform a variety of behavioral tasks while restrained by mechanical elements mounted to the skull. The independent development of this technique by a number of laboratories has led to diverse solutions. We found that these solutions often used expensive materials and impeded future development and modification in the absence of engineering support. In order to address these issues, here we report on the development of a flexible single hardware design for electrophysiology and imaging both in brain tissue in vitro. Our hardware facilitates the rapid conversion of a single preparation between physiology and imaging system and the conversion of a given system between preparations. In addition, our use of rapid prototyping machines ("3D printers") allows for the deployment of new designs within a day. Here, we present specifications for design and manufacturing as well as some data from our lab demonstrating the suitability of the design for physiology in behaving animals and imaging in vitro and in vivo.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0089007}, author = {Osborne, Jason E and Dudman, Joshua T} } @article {45697, title = {Role of adaptor TrfA and ClpPC in controlling levels of SsrA-tagged proteins and antitoxins in staphylococcus aureus.}, journal = {Journal of Bacteriology}, volume = {196}, year = {2014}, month = {2014 Dec 1}, pages = {4140-51}, abstract = {

Staphylococcus aureus responds to changing extracellular environments in part by adjusting its proteome through alterations of transcriptional priorities and selective degradation of the preexisting pool of proteins. In Bacillus subtilis, the proteolytic adaptor protein MecA has been shown to play a role in assisting with the proteolytic degradation of proteins involved in competence and the oxidative stress response. However, the targets of TrfA, the MecA homolog in S. aureus, have not been well characterized. In this work, we investigated how TrfA assists chaperones and proteases to regulate the proteolysis of several classes of proteins in S. aureus. By fusing the last 3 amino acids of the SsrA degradation tag to Venus, a rapidly folding yellow fluorescent protein, we obtained both fluorescence-based and Western blot assay-based evidence that TrfA and ClpCP are the adaptor and protease, respectively, responsible for the degradation of the SsrA-tagged protein in S. aureus. Notably, the impact of TrfA on degradation was most prominent during late log phase and early stationary phase, due in part to a combination of transcriptional regulation and proteolytic degradation of TrfA by ClpCP. We also characterized the temporal transcriptional regulation governing TrfA activity, wherein Spx, a redox-sensitive transcriptional regulator degraded by ClpXP, activates trfA transcription while repressing its own promoter. Finally, the scope of TrfA-mediated proteolysis was expanded by identifying TrfA as the adaptor that works with ClpCP to degrade antitoxins in S. aureus. Together, these results indicate that the adaptor TrfA adds temporal nuance to protein degradation by ClpCP in S. aureus.

}, issn = {1098-5530}, doi = {10.1128/JB.02222-14}, author = {Donegan, Niles P and Marvin, Jonathan S and Cheung, Ambrose L} } @article {45785, title = {The role of juvenile hormone in dominance behavior, reproduction and cuticular pheromone signaling in the caste-flexible epiponine wasp, Synoeca surinama.}, journal = {Frontiers in Zoology}, volume = {11}, year = {2014}, month = {2014}, pages = {78}, abstract = {

BACKGROUND: The popular view on insect sociality is that of a harmonious division of labor among two morphologically distinct and functionally non-overlapping castes. But this is a highly derived state and not a prerequisite for a functional society. Rather, caste-flexibility is a central feature in many eusocial wasps, where adult females have the potential to become queens or workers, depending on the social environment. In non-swarming paper wasps (e.g., Polistes), prospective queens fight one another to assert their dominance, with losers becoming workers if they remain on the nest. This aggression is fueled by juvenile hormone (JH) and ecdysteroids, major factors involved in caste differentiation in most eusocial insects. We tested whether these hormones have conserved aggression-promoting functions in Synoeca surinama, a caste-flexible swarm-founding wasp (Epiponini) where reproductive competition is high and aggressive displays are common.

RESULTS: We observed the behavioral interactions of S. surinama females in field nests before and after we had removed the egg-laying queen(s). We measured the ovarian reproductive status, hemolymph JH and ecdysteroid titers, ovarian ecdysteroid content, and analyzed the cuticular hydrocarbon (CHC) composition of females engaged in competitive interactions in both queenright and queenless contexts. These data, in combination with hormone manipulation experiments, revealed that neither JH nor ecdysteroids are necessary for the expression of dominance behaviors in S. surinama. Instead, we show that JH likely functions as a gonadotropin and directly modifies the cuticular hydrocarbon blend of young workers to match that of a reproductive. Hemolymph ecdysteroids, in contrast, are not different between queens and workers despite great differences in ovarian ecdysteroid content.

CONCLUSIONS: The endocrine profile of S. surinama shows surprising differences from those of other caste-flexible wasps, although a rise in JH titers in replacement queens is a common theme. Extensive remodeling of hormone functions is also evident in the highly eusocial bees, which has been attributed to the evolution of morphologically defined castes. Our results show that hormones which regulate caste-plasticity can lose these roles even while caste-plasticity is preserved.

}, issn = {1742-9994}, doi = {10.1186/s12983-014-0078-5}, author = {Kelstrup, Hans C and Hartfelder, Klaus and Nascimento, Fabio S and Riddiford, Lynn M} } @article {6958, title = {Sample drift correction following 4D confocal time-lapse imaging.}, journal = {Journal of Visualized Experiments: JoVE}, year = {2014}, month = {2014 Apr 12}, abstract = {

The generation of four-dimensional (4D) confocal datasets; consisting of 3D image sequences over time; provides an excellent methodology to capture cellular behaviors involved in developmental processes.\  The ability to track and follow cell movements is limited by sample movements that occur due to drift of the sample or, in some cases, growth during image acquisition. Tracking cells in datasets affected by drift and/or growth will incorporate these movements into any analysis of cell position. This may result in the apparent movement of static structures within the sample. Therefore prior to cell tracking, any sample drift should be corrected. Using the open source Fiji distribution (1) \ of ImageJ (2,3) and the incorporated LOCI tools (4), we developed the Correct 3D drift plug-in to remove erroneous sample movement in confocal datasets. This protocol effectively compensates for sample translation or alterations in focal position by utilizing phase correlation to register each time-point of a four-dimensional confocal datasets while maintaining the ability to visualize and measure cell movements over extended time-lapse experiments.

}, issn = {1940-087X}, doi = {10.3791/51086}, author = {Parslow, Adam and Cardona, Albert and Bryson-Richardson, Robert J} } @article {45337, title = {A self-adaptive method for creating high efficiency communication channels through random scattering media.}, journal = {Science Reports}, volume = {4}, year = {2014}, month = {2014 Jul 29}, pages = {5874}, abstract = {

Controlling the propagation of electromagnetic waves is important to a broad range of applications. Recent advances in controlling wave propagation in random scattering media have enabled optical focusing and imaging inside random scattering media. In this work, we propose and demonstrate a new method to deliver optical power more efficiently through scattering media. Drastically different from the random matrix characterization approach, our method can rapidly establish high efficiency communication channels using just a few measurements, regardless of the number of optical modes, and provides a practical and robust solution to boost the signal levels in optical or short wave communications. We experimentally demonstrated analog and digital signal transmission through highly scattering media with greatly improved performance. Besides scattering, our method can also reduce the loss of signal due to absorption. Experimentally, we observed that our method forced light to go around absorbers, leading to even higher signal improvement than in the case of purely scattering media. Interestingly, the resulting signal improvement is highly directional, which provides a new means against eavesdropping.

}, issn = {2045-2322}, doi = {10.1038/srep05874}, author = {Hao, Xiang and Martin-Rouault, Laure and Cui, Meng} } @article {45416, title = {Shared mushroom body circuits underlie visual and olfactory memories in Drosophila.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014}, pages = {e02395}, abstract = {

In nature, animals form memories associating reward or punishment with stimuli from different sensory modalities, such as smells and colors. It is unclear, however, how distinct sensory memories are processed in the brain. We established appetitive and aversive visual learning assays for Drosophila that are comparable to the widely used olfactory learning assays. These assays share critical features, such as reinforcing stimuli (sugar reward and electric shock punishment), and allow direct comparison of the cellular requirements for visual and olfactory memories. We found that the same subsets of dopamine neurons drive formation of both sensory memories. Furthermore, distinct yet partially overlapping subsets of mushroom body intrinsic neurons are required for visual and olfactory memories. Thus, our results suggest that distinct sensory memories are processed in a common brain center. Such centralization of related brain functions is an economical design that avoids the repetition of similar circuit motifs.

}, issn = {2050-084X}, doi = {10.7554/eLife.02395}, author = {Vogt, Katrin and Schnaitmann, Christopher and Dylla, Kristina V and Knapek, Stephan and Aso, Yoshinori and Rubin, Gerald M and Tanimoto, Hiromu} } @article {65749, title = {Simultaneous computation of dynamical and equilibrium information using a weighted ensemble of trajectories}, journal = {Journal of chemical theory and computation}, volume = {10}, year = {2014}, pages = {2658{\textendash}2667}, author = {Suarez, Ernesto and Lettieri, Steven and Stringer, Carsen A and Zwier, Matthew C and Subramanian, Sundar Raman and Chong, Lillian T and Zuckerman, Daniel M} } @article {65750, title = {Simultaneous computation of dynamical and equilibrium information using a weighted ensemble of trajectories}, journal = {Journal of Chemical Theory and Computation}, volume = {10}, year = {2014}, month = {03/2014}, pages = {2658{\textendash}2667}, abstract = {

Equilibrium formally can be represented as an ensemble of uncoupled systems undergoing unbiased dynamics in which detailed balance is maintained. Many nonequilibrium processes can be described by suitable subsets of the equilibrium ensemble. Here, we employ the {\textquotedblleft}weighted ensemble{\textquotedblright} (WE) simulation protocol [Huber and Kim,\ Biophys. J.1996,\ 70, 97{\textendash}110] to generate equilibrium trajectory ensembles and extract nonequilibrium subsets for computing kinetic quantities. States do not need to be chosen in advance. The procedure formally allows estimation of kinetic rates between arbitrary states chosen after the simulation, along with their equilibrium populations. We also describe a related history-dependent matrix procedure for estimating equilibrium and nonequilibrium observables when phase space has been divided into arbitrary non-Markovian regions, whether in WE or ordinary simulation. In this proof-of-principle study, these methods are successfully applied and validated on two molecular systems: explicitly solvated methane association and the implicitly solvated Ala4 peptide. We comment on challenges remaining in WE calculations.

}, doi = {https://doi.org/10.1021/ct401065r}, author = {Suarez, Ernesto and Lettieri, Steven and Stringer, Carsen A and Zwier, Matthew C and Subramanian, Sundar Raman and Chong, Lillian T and Zuckerman, Daniel M} } @article {65747, title = {Simultaneous computation of dynamical and equilibrium information using a weighted ensemble of trajectories}, journal = {Journal of chemical theory and computation}, volume = {10}, year = {2014}, pages = {2658{\textendash}2667}, author = {Suarez, Ernesto and Lettieri, Steven and Stringer, Carsen A and Zwier, Matthew C and Subramanian, Sundar Raman and Chong, Lillian T and Zuckerman, Daniel M} } @article {65748, title = {Simultaneous computation of dynamical and equilibrium information using a weighted ensemble of trajectories}, journal = {Journal of chemical theory and computation}, volume = {10}, year = {2014}, pages = {2658{\textendash}2667}, author = {Suarez, Ernesto and Lettieri, Steven and Stringer, Carsen A and Zwier, Matthew C and Subramanian, Sundar Raman and Chong, Lillian T and Zuckerman, Daniel M} } @article {46705, title = {Single β-actin mRNA detection in neurons reveals a mechanism for regulating its translatability.}, journal = {Science}, volume = {343}, year = {2014}, month = {2014 Jan 24}, pages = {419-22}, abstract = {

The physical manifestation of learning and memory formation in the brain can be expressed by strengthening or weakening of synaptic connections through morphological changes. Local actin remodeling underlies some forms of plasticity and may be facilitated by local β-actin synthesis, but dynamic information is lacking. In this work, we use single-molecule in situ hybridization to demonstrate that dendritic β-actin messenger RNA (mRNA) and ribosomes are in a masked, neuron-specific form. Chemically induced long-term potentiation prompts transient mRNA unmasking, which depends on factors active during synaptic activity. Ribosomes and single β-actin mRNA motility increase after stimulation, indicative of release from complexes. Hence, the single-molecule assays we developed allow for the quantification of activity-induced unmasking and availability for active translation. Further, our work demonstrates that β-actin mRNA and ribosomes are in a masked state that is alleviated by stimulation.

}, keywords = {Actins, Animals, Cells, Cultured, Dendrites, In Situ Hybridization, Fluorescence, Long-Term Potentiation, Memory, Mice, Mice, Transgenic, Neuronal Plasticity, Neurons, Protein Biosynthesis, Ribosomes, RNA, Messenger, RNA, Ribosomal, Synapses}, issn = {1095-9203}, doi = {10.1126/science.1242939}, author = {Buxbaum, Adina R and Wu, Bin and Singer, Robert H} } @article {6919, title = {Single-molecule dynamics of enhanceosome assembly in embryonic stem cells.}, journal = {Cell}, volume = {156}, year = {2014}, month = {2014 Mar 13}, pages = {1274-85}, abstract = {

Enhancer-binding pluripotency regulators (Sox2 and Oct4) play a seminal role in embryonic stem (ES) cell-specific gene regulation. Here, we combine in\ vivo and in\ vitro single-molecule imaging, transcription factor (TF) mutagenesis, and ChIP-exo mapping to\ determine how TFs dynamically search for and assemble on their cognate DNA target sites. We find that enhanceosome assembly is hierarchically ordered with kinetically favored Sox2 engaging the target DNA first, followed by assisted binding of Oct4. Sox2/Oct4 follow a trial-and-error sampling mechanism involving 84-97 events of 3D diffusion (3.3-3.7 s) interspersed with brief nonspecific collisions (0.75-0.9 s) before acquiring and dwelling at specific target DNA (12.0-14.6 s). Sox2 employs a 3D diffusion-dominated search mode facilitated by 1D sliding along open DNA to efficiently locate targets. Our findings also reveal fundamental aspects of gene and developmental regulation by fine-tuning TF dynamics and influence of the epigenome on target search parameters.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2014.01.062}, author = {Chen, Jiji and Zhang, Zhengjian and Li Li and Chen, Bi-Chang and Revyakin, Andrey and Hajj, Bassam and Legant, Wesley and Dahan, Maxime and Lionnet, Timoth{\'e}e and Betzig, Eric and Tjian, Robert and Liu, Zhe} } @article {45338, title = {Single-molecule tracking in live cells reveals distinct target-search strategies of transcription factors in the nucleus.}, journal = {eLife}, year = {2014}, month = {2014 Jun 12}, pages = {e02230}, abstract = {

Gene regulation relies on transcription factors (TFs) exploring the nucleus searching their targets. So far, most studies have focused on how fast TFs diffuse, underestimating the role of nuclear architecture. We implemented a single-molecule tracking assay to determine TFs dynamics. We found that c-Myc is a global explorer of the nucleus. In contrast, the positive transcription elongation factor P-TEFb is a local explorer that oversamples its environment. Consequently, each c-Myc molecule is equally available for all nuclear sites while P-TEFb reaches its targets in a position-dependent manner. Our observations are consistent with a model in which the exploration geometry of TFs is restrained by their interactions with nuclear structures and not by exclusion. The geometry-controlled kinetics of TFs target-search illustrates the influence of nuclear architecture on gene regulation, and has strong implications on how proteins react in the nucleus and how their function can be regulated in space and time.

}, issn = {2050-084X}, doi = {10.7554/eLife.02230}, author = {Izeddin, Ignacio and R{\'e}camier, Vincent and Bosanac, Lana and Cisse, Ibrahim I and Boudarene, Lydia and Dugast-Darzacq, Claire and Proux, Florence and B{\'e}nichou, Olivier and Voituriez, Rapha{\"e}l and Bensaude, Olivier and Dahan, Maxime and Darzacq, Xavier} } @article {6845, title = {Single-molecule tracking of the transcription cycle by sub-second RNA detection.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 Jan 28}, pages = {e01775}, abstract = {

Transcription is an inherently stochastic, noisy, and multi-step process, in which fluctuations at every step can cause variations in RNA synthesis, and affect physiology and differentiation decisions in otherwise identical cells. However, it has been an experimental challenge to directly link the stochastic events at the promoter to transcript production. Here we established a fast fluorescence in situ hybridization (fastFISH) method that takes advantage of intrinsically unstructured nucleic acid sequences to achieve exceptionally fast rates of specific hybridization (\~{}10e7 M(-1)s(-1)), and allows deterministic detection of single nascent transcripts. Using a prototypical RNA polymerase, we demonstrated the use of fastFISH to measure the kinetic rates of promoter escape, elongation, and termination in one assay at the single-molecule level, at sub-second temporal resolution. The principles of fastFISH design can be used to study stochasticity in gene regulation, to select targets for gene silencing, and to design nucleic acid nanostructures. DOI: http://dx.doi.org/10.7554/eLife.01775.001.

}, issn = {2050-084X}, doi = {10.7554/eLife.01775}, author = {Zhang, Zhengjian and Revyakin, Andrey and Grimm, Jonathan B and Lavis, Luke D and Tjian, Robert} } @article {6878, title = {Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models.}, journal = {BMC Bioinformatics}, volume = {15}, year = {2014}, month = {2014 Jan 13}, pages = {7}, abstract = {

BACKGROUND: Logos are commonly used in molecular biology to provide a compact graphical representation of the conservation pattern of a set of sequences. They render the information contained in sequence alignments or profile hidden Markov models by drawing a stack of letters for each position, where the height of the stack corresponds to the conservation at that position, and the height of each letter within a stack depends on the frequency of that letter at that position. RESULTS: We present a new tool and web server, called Skylign, which provides a unified framework for creating logos for both sequence alignments and profile hidden Markov models. In addition to static image files, Skylign creates a novel interactive logo plot for inclusion in web pages. These interactive logos enable scrolling, zooming, and inspection of underlying values. Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequences and by combining observed counts with informed priors. It also simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position. CONCLUSION: Skylign is available as a website, a scriptable web service with a RESTful interface, and as a software package for download. Skylign{\textquoteright}s interactive logos are easily incorporated into a web page with just a few lines of HTML markup. Skylign may be found at http://skylign.org.

}, issn = {1471-2105}, doi = {10.1186/1471-2105-15-7}, author = {Wheeler, Travis J and Clements, Jody and Finn, Robert D} } @article {46228, title = {Small sample learning of superpixel classifiers for EM segmentation- extended version.}, journal = {arXiv}, year = {2014}, month = {2014 Jun 6}, pages = {arXiv:1406.1774 [cs.CV]}, abstract = {

Pixel and superpixel classifiers have become essential tools for EM segmentation algorithms. Training these classifiers remains a major bottleneck primarily due to the requirement of completely annotating the dataset which is tedious, error-prone and costly. In this paper, we propose an interactive learning scheme for the superpixel classifier for EM segmentation. Our algorithm is "active semi-supervised" because it requests the labels of a small number of examples from user and applies label propagation technique to generate these queries. Using only a small set (\<20\%) of all datapoints, the proposed algorithm consistently generates a classifier almost as accurate as that estimated from a complete groundtruth. We provide segmentation results on multiple datasets to show the strength of these classifiers.

}, url = {http://arxiv.org/abs/1406.1774}, author = {Parag, Toufiq and Plaza, Stephen M and Scheffer, Louis K} } @proceedings {46298, title = {Small sample learning of superpixel classifiers for EM segmentation.}, volume = {17}, year = {2014}, month = {2014}, pages = {389-97}, abstract = {

Pixel and superpixel classifiers have become essential tools for EM segmentation algorithms. Training these classifiers remains a major bottleneck primarily due to the requirement of completely annotating the dataset which is tedious, error-prone and costly. In this paper, we propose an interactive learning scheme for the superpixel classifier for EM segmentation. Our algorithm is {\textquoteright}active semi-supervised{\textquoteright} because it requests the labels of a small number of examples from user and applies label propagation technique to generate these queries. Using only a small set (\< 20\%) of all datapoints, the proposed algorithm consistently generates a classifier almost as accurate as that estimated from a complete groundtruth. We provide segmentation results on multiple datasets to show the strength of these classifiers.

}, keywords = {Algorithms, Artificial Intelligence, Cells, Cultured, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Microscopy, Electron, Transmission, Neurites, Pattern Recognition, Automated, Reproducibility of Results, Sample Size, Sensitivity and Specificity}, author = {Parag, Toufiq and Plaza, Stephen and Scheffer, Louis} } @article {6957, title = {A small subset of fruitless subesophageal neurons modulate early courtship in Drosophila.}, journal = {PLoS One}, volume = {9}, year = {2014}, month = {2014 Apr 16}, pages = {e95472}, abstract = {

We show that a small subset of two to six subesophageal neurons, expressing the male products of the male courtship master regulator gene products fruitlessMale (fruM), are required in the early stages of the Drosophila melanogaster male courtship behavioral program. Loss of fruM expression or inhibition of synaptic transmission in these fruM(+) neurons results in delayed courtship initiation and a failure to progress to copulation primarily under visually-deficient conditions. We identify a fruM-dependent sexually dimorphic arborization in the tritocerebrum made by two of these neurons. Furthermore, these SOG neurons extend descending projections to the thorax and abdominal ganglia. These anatomical and functional characteristics place these neurons in the position to integrate gustatory and higher-order signals in order to properly initiate and progress through early courtship.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0095472}, author = {Tran, David H and Meissner, Geoffrey W and French, Rachael L and Baker, Bruce S} } @article {46327, title = {Space-time wiring specificity supports direction selectivity in the retina.}, journal = {Nature}, volume = {509}, year = {2014}, month = {2014 May 15}, pages = {331-6}, abstract = {

How does the mammalian retina detect motion? This classic problem in visual neuroscience has remained unsolved for 50 years. In search of clues, here we reconstruct Off-type starburst amacrine cells (SACs) and bipolar cells (BCs) in serial electron microscopic images with help from EyeWire, an online community of {\textquoteright}citizen neuroscientists{\textquoteright}. On the basis of quantitative analyses of contact area and branch depth in the retina, we find evidence that one BC type prefers to wire with a SAC dendrite near the SAC soma, whereas another BC type prefers to wire far from the soma. The near type is known to lag the far type in time of visual response. A mathematical model shows how such {\textquoteright}space-time wiring specificity{\textquoteright} could endow SAC dendrites with receptive fields that are oriented in space-time and therefore respond selectively to stimuli that move in the outward direction from the soma.

}, keywords = {Amacrine Cells, Animals, Artificial Intelligence, Brain Mapping, Crowdsourcing, Dendrites, Mice, Models, Neurological, Motion, Neural Pathways, Presynaptic Terminals, Retina, Retinal Bipolar Cells, Spatio-Temporal Analysis}, issn = {1476-4687}, doi = {10.1038/nature13240}, author = {Kim, Jinseop S and Greene, Matthew J and Zlateski, Aleksandar and Lee, Kisuk and Richardson, Mark and Turaga, Srinivas C and Purcaro, Michael and Balkam, Matthew and Robinson, Amy and Behabadi, Bardia F and Campos, Michael and Denk, Winfried and Seung, H Sebastian} } @article {6899, title = {Sparse, decorrelated odor coding in the mushroom body enhances learned odor discrimination.}, journal = {Nature Neuroscience}, volume = {17}, year = {2014}, month = {2014 Feb 23}, pages = {559-68}, abstract = {

Sparse coding may be a general strategy of neural systems for augmenting memory capacity. In Drosophila melanogaster, sparse odor coding by the Kenyon cells of the mushroom body is thought to generate a large number of precisely addressable locations for the storage of odor-specific memories. However, it remains untested how sparse coding relates to behavioral performance. Here we demonstrate that sparseness is controlled by a negative feedback circuit between Kenyon cells and the GABAergic anterior paired lateral (APL) neuron. Systematic activation and blockade of each leg of this feedback circuit showed that Kenyon cells activated APL and APL inhibited Kenyon cells. Disrupting the Kenyon cell-APL feedback loop decreased the sparseness of Kenyon cell odor responses, increased inter-odor correlations and prevented flies from learning to discriminate similar, but not dissimilar, odors. These results suggest that feedback inhibition suppresses Kenyon cell activity to maintain sparse, decorrelated odor coding and thus the odor specificity of memories.

}, issn = {1546-1726}, doi = {10.1038/nn.3660}, author = {Lin, Andrew C and Bygrave, Alexei M and de Calignon, Alix and Lee, Tzumin and Miesenb{\"o}ck, Gero} } @conference {65048, title = {Sparse LMS via online linearized Bregman iteration.}, booktitle = {ICASSP 2014 - 2014 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)2014 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)}, year = {2014}, month = {2014 Jul 14}, publisher = {IEEE}, organization = {IEEE}, address = {Florence, Italy}, abstract = {

We propose a version of least-mean-square (LMS) algorithm for sparse system identification. Our algorithm called online linearized Bregman iteration (OLBI) is derived from minimizing the cumulative prediction error squared along with an l\ 1\ -l\ 2\ norm regularizer. By systematically treating the non-differentiable regularizer we arrive at a simple two-step iteration. We demonstrate that OLBI is bias free and compare its operation with existing sparse LMS algorithms by rederiving them in the online convex optimization framework. We perform convergence analysis of OLBI for white input signals and derive theoretical expressions for the steady state mean square deviations (MSD). We demonstrate numerically that OLBI improves the performance of LMS type algorithms for signals generated from sparse tap weights.

}, doi = {10.1109/ICASSP.2014.6855000}, url = {http://ieeexplore.ieee.org/document/6855000/http://xplorestaging.ieee.org/ielx7/6844297/6853544/06855000.pdf?arnumber=6855000}, author = {Hu, Tao and Chklovskii, Dmitri B.} } @article {45165, title = {A spike-timing mechanism for action selection.}, journal = {Nature Neuroscience}, volume = {17}, year = {2014}, month = {2014 Jul 17}, pages = {962-70}, abstract = {

We discovered a bimodal behavior in the genetically tractable organism Drosophila melanogaster that allowed us to directly probe the neural mechanisms of an action selection process. When confronted by a predator-mimicking looming stimulus, a fly responds with either a long-duration escape behavior sequence that initiates stable flight or a distinct, short-duration sequence that sacrifices flight stability for speed. Intracellular recording of the descending giant fiber (GF) interneuron during head-fixed escape revealed that GF spike timing relative to parallel circuits for escape actions determined which of the two behavioral responses was elicited. The process was well described by a simple model in which the GF circuit has a higher activation threshold than the parallel circuits, but can override ongoing behavior to force a short takeoff. Our findings suggest a neural mechanism for action selection in which relative activation timing of parallel circuits creates the appropriate motor output.

}, issn = {1546-1726}, doi = {10.1038/nn.3741}, author = {von Reyn, Catherine R and Breads, Patrick and Peek, Martin Y and Zheng, Grace Zhiyu and Williamson, W Ryan and Yee, Alyson L and Leonardo, Anthony and Card, Gwyneth M} } @article {6956, title = {Structural basis for the prion-like MAVS filaments in antiviral innate immunity.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 Jan 1}, pages = {e01489}, abstract = {

Mitochondrial antiviral signaling (MAVS) protein is required for innate immune responses against RNA viruses. In virus-infected cells MAVS forms prion-like aggregates to activate antiviral signaling cascades, but the underlying structural mechanism is unknown. Here we report cryo-electron microscopic structures of the helical filaments formed by both the N-terminal caspase activation and recruitment domain (CARD) of MAVS and a truncated MAVS lacking part of the proline-rich region and the C-terminal transmembrane domain. Both structures are left-handed three-stranded helical filaments, revealing specific interfaces between individual CARD subunits that are dictated by electrostatic interactions between neighboring strands and hydrophobic interactions within each strand. Point mutations at multiple locations of these two interfaces impaired filament formation and antiviral signaling. Super-resolution imaging of virus-infected cells revealed rod-shaped MAVS clusters on mitochondria. These results elucidate the structural mechanism of MAVS polymerization, and explain how an α-helical domain uses distinct chemical interactions to form self-perpetuating filaments. DOI: http://dx.doi.org/10.7554/eLife.01489.001.

}, issn = {2050-084X}, doi = {10.7554/eLife.01489}, author = {Xu, Hui and He, Xiaojing and Zheng, Hui and Huang, Lily J and Hou, Fajian and Yu, Zhiheng and de la Cruz, Michael Jason and Borkowski, Brian and Zhang, Xuewu and Chen, Zhijian J and Jiang, Qiu-Xing} } @article {6963, title = {Structural plasticity within the barrel cortex during initial phases of whisker-dependent learning.}, journal = {The Journal of Neuroscience}, volume = {34}, year = {2014}, month = {2014 Apr 23}, pages = {6078-83}, abstract = {

We report learning-related structural plasticity in layer 1 branches of pyramidal neurons in the barrel cortex, a known site of sensorimotor integration. In mice learning an active, whisker-dependent object localization task, layer 2/3 neurons showed enhanced spine growth during initial skill acquisition that both preceded and predicted expert performance. Preexisting spines were stabilized and new persistent spines were formed. These findings suggest rapid changes in connectivity between motor centers and sensory cortex guide subsequent sensorimotor learning.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4919-12.2014}, author = {Kuhlman, Sandra J and O{\textquoteright}Connor, Daniel H and Fox, Kevin and Svoboda, Karel} } @article {47704, title = {Structurally-constrained relationships between cognitive states in the human brain.}, journal = {PLoS computational biology}, volume = {10}, year = {2014}, month = {2014 May}, pages = {e1003591}, abstract = {

The anatomical connectivity of the human brain supports diverse patterns of correlated neural activity that are thought to underlie cognitive function. In a manner sensitive to underlying structural brain architecture, we examine the extent to which such patterns of correlated activity systematically vary across cognitive states. Anatomical white matter connectivity is compared with functional correlations in neural activity measured via blood oxygen level dependent (BOLD) signals. Functional connectivity is separately measured at rest, during an attention task, and during a memory task. We assess these structural and functional measures within previously-identified resting-state functional networks, denoted task-positive and task-negative networks, that have been independently shown to be strongly anticorrelated at rest but also involve regions of the brain that routinely increase and decrease in activity during task-driven processes. We find that the density of anatomical connections within and between task-positive and task-negative networks is differentially related to strong, task-dependent correlations in neural activity. The space mapped out by the observed structure-function relationships is used to define a quantitative measure of separation between resting, attention, and memory states. We find that the degree of separation between states is related to both general measures of behavioral performance and relative differences in task-specific measures of attention versus memory performance. These findings suggest that the observed separation between cognitive states reflects underlying organizational principles of human brain structure and function.

}, keywords = {Attention, Brain, Cognition, Computer Simulation, Connectome, Humans, Memory, Models, Anatomic, Models, Neurological, Nerve Net, White Matter}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1003591}, author = {Hermundstad, Ann M and Brown, Kevin S and Bassett, Danielle S and Aminoff, Elissa M and Frithsen, Amy and Johnson, Arianne and Tipper, Christine M and Miller, Michael B and Grafton, Scott T and Carlson, Jean M} } @article {45865, title = {Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis.}, journal = {BMC Bioinformatics}, volume = {15}, year = {2014}, month = {2014 Mar 19}, pages = {75}, abstract = {

BACKGROUND: CA_C2195 from Clostridium acetobutylicum is a protein of unknown function. Sequence analysis predicted that part of the protein contained a metallopeptidase-related domain. There are over 200 homologs of similar size in large sequence databases such as UniProt, with pairwise sequence identities in the range of ~40-60\%. CA_C2195 was chosen for crystal structure determination for structure-based function annotation of novel protein sequence space.

RESULTS: The structure confirmed that CA_C2195 contained an N-terminal metallopeptidase-like domain. The structure revealed two extra domains: an α+β domain inserted in the metallopeptidase-like domain and a C-terminal circularly permuted winged-helix-turn-helix domain.

CONCLUSIONS: Based on our sequence and structural analyses using the crystal structure of CA_C2195 we provide a view into the possible functions of the protein. From contextual information from gene-neighborhood analysis, we propose that rather than being a peptidase, CA_C2195 and its homologs might play a role in biosynthesis of a modified cell-surface carbohydrate in conjunction with several sugar-modification enzymes. These results provide the groundwork for the experimental verification of the function.

}, keywords = {Bacterial Proteins, Clostridium acetobutylicum, Crystallography, X-Ray, Metalloproteases, Models, Molecular, Protein Structure, Tertiary}, issn = {1471-2105}, doi = {10.1186/1471-2105-15-75}, author = {Das, Debanu and Murzin, Alexey G and Rawlings, Neil D and Finn, Robert D and Coggill, Penelope and Bateman, Alex and Godzik, Adam and Aravind, L} } @article {45552, title = {Structure of catalase determined by MicroED.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 Oct 17}, pages = {e03600}, abstract = {

MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 {\r A} resolution with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 {\r A} resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination.

}, issn = {2050-084X}, doi = {10.7554/eLife.03600}, author = {Nannenga, Brent L and Shi, Dan and Hattne, Johan and Reyes, Francis E and Gonen, Tamir} } @article {6825, title = {Structure-based neuron retrieval across Drosophila brains.}, journal = {Neuroinformatics}, volume = {12}, year = {2014}, month = {2014 Jan 21}, pages = {423-34}, abstract = {

Comparing local neural structures across large sets of examples is crucial when studying gene functions, and their effect in the Drosophila brain. The current practice of aligning brain volume data to a joint reference frame is based on the neuropil. However, even after alignment neurons exhibit residual location and shape variability that, together with image noise, hamper direct quantitative comparison and retrieval of similar structures on an intensity basis. In this paper, we propose and evaluate an image-based retrieval method for neurons, relying on local appearance, which can cope with spatial variability across the population. For an object of interest marked in a query case, the method ranks cases drawn from a large data set based on local neuron appearance in confocal microscopy data. The approach is based on capturing the orientation of neurons based on structure tensors and expanding this field via Gradient Vector Flow. During retrieval, the algorithm compares fields across cases, and calculates a corresponding ranking of most similar cases with regard to the local structure of interest. Experimental results demonstrate that the similarity measure and ranking mechanisms yield high precision and recall in realistic search scenarios.

}, issn = {1559-0089}, doi = {10.1007/s12021-014-9219-4}, author = {Ganglberger, Florian and Schulze, Florian and Tirian, Laszlo and Novikov, Alexey and Dickson, Barry and B{\"u}hler, Katja and Langs, Georg} } @inbook {47131, title = {Structured illumination microscopy (Chapter 15.)}, booktitle = {Fluorescence Microscopy: Super-resolution and other novel techniques}, year = {2014}, pages = {213{\textendash}225}, doi = {10.1016/B978-0-12-409513-7.00015-4}, author = {Shao, Lin and Rego, E Hesper} } @article {6713, title = {Structured synaptic connectivity between hippocampal regions.}, journal = {Neuron}, volume = {81}, year = {2014}, month = {2014 Feb 5}, pages = {629-40}, abstract = {

The organization of synaptic connectivity within a neuronal circuit is a prime determinant of circuit function. We performed a comprehensive fine-scale circuit mapping of hippocampal regions (CA3-CA1) using the newly developed synapse labeling method, mGRASP. This mapping revealed spatially nonuniform and clustered synaptic connectivity patterns. Furthermore, synaptic clustering was enhanced between groups of neurons that shared a similar developmental/migration time window, suggesting a mechanism for establishing the spatial structure of synaptic connectivity. Such connectivity patterns are thought to effectively engage active dendritic processing and storage mechanisms, thereby potentially enhancing neuronal feature selectivity.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2013.11.026}, author = {Shaul Druckmann and Feng, Linqing and Lee, Bokyoung and Yook, Chaehyun and Zhao, Ting and Magee, Jeffrey C and Kim, Jinhyun} } @article {45179, title = {A suite of software for processing MicroED data of extremely small protein crystals.}, journal = {Journal of Applied Crystallography}, volume = {47}, year = {2014}, month = {2014 Jun 1}, pages = {1140-45}, abstract = {

Electron diffraction of extremely small three-dimensional crystals (MicroED) allows for structure determination from crystals orders of magnitude smaller than those used for X-ray crystallography. MicroED patterns, which are collected in a transmission electron microscope, were initially not amenable to indexing and intensity extraction by standard software, which necessitated the development of a suite of programs for data processing. The MicroED suite was developed to accomplish the tasks of unit-cell determination, indexing, background subtraction, intensity measurement and merging, resulting in data that can be carried forward to molecular replacement and structure determination. This ad hoc solution has been modified for more general use to provide a means for processing MicroED data until the technique can be fully implemented into existing crystallographic software packages. The suite is written in Python and the source code is available under a GNU General Public License.

}, issn = {0021-8898}, doi = {10.1107/S1600576714008073}, author = {Iadanza, Matthew G and Gonen, Tamir} } @article {47632, title = {Superresolution imaging of biological systems using photoactivated localization microscopy.}, journal = {Chemical reviews}, volume = {114}, year = {2014}, month = {2014 Mar 26}, pages = {3189-202}, keywords = {Image Processing, Computer-Assisted, Luminescent Proteins, Microscopy, Mitochondria, Nanotechnology, Time-Lapse Imaging}, issn = {1520-6890}, doi = {10.1021/cr400614m}, author = {Sengupta, Prabuddha and Van Engelenburg, Schuyler B and Lippincott-Schwartz, Jennifer} } @article {47623, title = {Superresolution imaging reveals structural features of EB1 in microtubule plus-end tracking.}, journal = {Molecular biology of the cell}, volume = {25}, year = {2014}, month = {2014 Dec 15}, pages = {4166-73}, abstract = {

Visualization of specific molecules and their interactions in real time and space is essential to delineate how cellular dynamics and the signaling circuit are orchestrated. Spatial regulation of conformational dynamics and structural plasticity of protein interactions is required to rewire signaling circuitry in response to extracellular cues. We introduce a method for optically imaging intracellular protein interactions at nanometer spatial resolution in live cells, using photoactivatable complementary fluorescent (PACF) proteins. Subsets of complementary fluorescent protein molecules were activated, localized, and then bleached; this was followed by the assembly of superresolution images from aggregate position of sum interactive molecules. Using PACF, we obtained precise localization of dynamic microtubule plus-end hub protein EB1 dimers and their distinct distributions at the leading edges and in the cell bodies of migrating cells. We further delineated the structure-function relationship of EB1 by generating EB1-PACF dimers (EB1(wt):EB1(wt), EB1(wt):EB1(mt), and EB1(mt):EB1(mt)) and imaging their precise localizations in culture cells. Surprisingly, our analyses revealed critical role of a previously uncharacterized EB1 linker region in tracking microtubule plus ends in live cells. Thus PACF provides a unique approach to delineating spatial dynamics of homo- or heterodimerized proteins at the nanometer scale and establishes a platform to report the precise regulation of protein interactions in space and time in live cells.

}, keywords = {Amino Acid Sequence, Cell Movement, Hela Cells, Humans, MCF-7 Cells, Microscopy, Fluorescence, Microtubule-Associated Proteins, Microtubules, Molecular Sequence Data, Protein Transport}, issn = {1939-4586}, doi = {10.1091/mbc.E14-06-1133}, author = {Xia, Peng and Liu, Xing and Wu, Bing and Zhang, Shuyuan and Song, Xiaoyu and Yao, Phil Y and Lippincott-Schwartz, Jennifer and Yao, Xuebiao} } @article {45417, title = {A suppression hierarchy among competing motor programs drives sequential grooming in Drosophila.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 Aug 19}, pages = {e02951}, abstract = {

Motor sequences are formed through the serial execution of different movements, but how nervous systems implement this process remains largely unknown. We determined the organizational principles governing how dirty fruit flies groom their bodies with sequential movements. Using genetically targeted activation of neural subsets, we drove distinct motor programs that clean individual body parts. This enabled competition experiments revealing that the motor programs are organized into a suppression hierarchy; motor programs that occur first suppress those that occur later. Cleaning one body part reduces the sensory drive to its motor program, which relieves suppression of the next movement, allowing the grooming sequence to progress down the hierarchy. A model featuring independently evoked cleaning movements activated in parallel, but selected serially through hierarchical suppression, was successful in reproducing the grooming sequence. This provides the first example of an innate motor sequence implemented by the prevailing model for generating human action sequences.

}, issn = {2050-084X}, doi = {10.7554/eLife.02951}, author = {Seeds, Andrew M and Ravbar, Primoz and Chung, Phuong and Hampel, Stefanie and Midgley, Frank M and Mensh, Brett D and Simpson, Julie H} } @article {6884, title = {A systematic nomenclature for the insect brain.}, journal = {Neuron}, volume = {81}, year = {2014}, month = {2014 Feb 19}, pages = {755-65}, abstract = {

Despite the importance of the insect nervous system for functional and developmental neuroscience, descriptions of insect brains have suffered from a lack of uniform nomenclature. Ambiguous definitions of brain regions and fiber bundles have contributed to the variation of names used to describe the same structure. The lack of clearly determined neuropil boundaries has made it difficult to document precise locations of neuronal projections for connectomics study. To address such issues, a consortium of\ neurobiologists studying arthropod brains, the Insect Brain Name Working Group, has established the present hierarchical nomenclature system, using the brain of Drosophila melanogaster as the reference framework, while taking the brains of other taxa into careful consideration for maximum consistency and expandability. The following summarizes the consortium{\textquoteright}s nomenclature system and highlights examples of existing ambiguities and remedies for them. This nomenclature is intended to serve as a\ standard of reference for the study of the brain of Drosophila and other insects.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2013.12.017}, author = {Ito, Kei and Shinomiya, Kazunori and Ito, Masayoshi and Armstrong, J Douglas and Boyan, George and Hartenstein, Volker and Harzsch, Steffen and Heisenberg, Martin and Homberg, Uwe and Jenett, Arnim and Keshishian, Haig and Restifo, Linda L and R{\"o}ssler, Wolfgang and Simpson, Julie H and Strausfeld, Nicholas J and Strauss, Roland and Vosshall, Leslie B} } @article {65021, title = {Taura syndrome virus IRES initiates translation by binding its tRNA-mRNA-like structural element in the ribosomal decoding center.}, journal = {Proc Natl Acad Sci U S A}, volume = {111}, year = {2014}, month = {2014 Jun 24}, pages = {9139-44}, abstract = {

In cap-dependent translation initiation, the open reading frame (ORF) of mRNA is established by the placement of the AUG start codon and initiator tRNA in the ribosomal peptidyl (P) site. Internal ribosome entry sites (IRESs) promote translation of mRNAs in a cap-independent manner. We report two structures of the ribosome-bound Taura syndrome virus (TSV) IRES belonging to the family of Dicistroviridae intergenic IRESs. Intersubunit rotational states differ in these structures, suggesting that ribosome dynamics play a role in IRES translocation. Pseudoknot I of the IRES occupies the ribosomal decoding center at the aminoacyl (A) site in a manner resembling that of the tRNA anticodon-mRNA codon. The structures reveal that the TSV IRES initiates translation by a previously unseen mechanism, which is conceptually distinct from initiator tRNA-dependent mechanisms. Specifically, the ORF of the IRES-driven mRNA is established by the placement of the preceding tRNA-mRNA-like structure in the A site, whereas the 40S P site remains unoccupied during this initial step.

}, keywords = {Nucleic Acid Conformation, Open Reading Frames, Peptide Chain Initiation, Translational, Picornaviridae, Ribosomes, RNA, Messenger, RNA, Transfer, RNA, Viral}, issn = {1091-6490}, doi = {10.1073/pnas.1406335111}, author = {Koh, Cha San and Brilot, Axel F and Grigorieff, Nikolaus and Korostelev, Andrei A} } @article {45591, title = {Thorough GABAergic innervation of the entire axon initial segment revealed by an optogenetic {\textquoteright}laserspritzer{\textquoteright}.}, journal = {Journal of Physiology - London}, volume = {592}, year = {2014}, month = {2014 Oct 1}, pages = {4257-76}, abstract = {

GABAergic terminals of chandelier cells exclusively innervate the axon initial segment (AIS) of excitatory neurons. Although the anatomy of these synapses has been well-studied in several brain areas, relatively little is known about their physiological properties. Using vesicular γ-aminobutyric acid transporter-channelrhodopsin\ 2-enhanced yellow fluorescence protein (VGAT-ChR2-YFP)-expressing mice and a novel fibreoptic {\textquoteright}laserspritzer{\textquoteright} approach that we developed, we investigated the physiological properties of axo-axonic synapses (AASs) in brain slices from the piriform cortex (PC) of mice. AASs were in close proximity to voltage-gated Na(+) (NaV) channels located at the AIS. AASs were selectively activated by a 5\ μm laserspritzer placed in close proximity to the AIS. Under a minimal laser stimulation condition and using whole-cell somatic voltage-clamp recordings, the amplitudes and kinetics of IPSCs mediated by AASs were similar to those mediated by perisomatic inhibitions. Results were further validated with channelrhodopsin\ 2-assisted circuit mapping (CRACM) of the entire inhibitory inputs map. For the first time, we revealed that the laserspritzer-induced AAS-IPSCs persisted in the presence of TTX and TEA but not 4-AP. Next, using gramicidin-based perforated patch recordings, we found that the GABA reversal potential (EGABA) was -73.6\ {\textpm}\ 1.2\ mV when induced at the AIS and -72.8\ {\textpm}\ 1.1\ mV when induced at the perisomatic site. Our anatomical and physiological results lead to the novel conclusions that: (1) AASs innervate the entire length of the AIS, as opposed to forming a highly concentrated cartridge, (2) AAS inhibition suppresses action potentials and epileptiform activity more robustly than perisomatic inhibitions, and (3) AAS activation alone can be sufficient to inhibit action potential generation and epileptiform activities in vitro.

}, issn = {1469-7793}, doi = {10.1113/jphysiol.2014.275719}, author = {Wang, Xinjun and Hooks, Bryan M and Sun, Qian-Quan} } @article {45353, title = {Thy1 - GCaMP6 transgenic mice for neuronal population imaging in vivo.}, journal = {PLoS One}, volume = {9}, year = {2014}, month = {2014}, pages = {e108697}, chapter = {e108697}, abstract = {

Genetically-encoded calcium indicators (GECIs) facilitate imaging activity of genetically defined neuronal populations in vivo. The high intracellular GECI concentrations required for in vivo imaging are usually achieved by viral gene transfer using adeno-associated viruses. Transgenic expression of GECIs promises important advantages, including homogeneous, repeatable, and stable expression without the need for invasive virus injections. Here we present the generation and characterization of transgenic mice expressing the GECIs GCaMP6s or GCaMP6f under the Thy1 promoter. We quantified GCaMP6 expression across brain regions and neurons and compared to other transgenic mice and AAV-mediated expression. We tested three mouse lines for imaging in the visual cortex in vivo and compared their performance to mice injected with AAV expressing GCaMP6. Furthermore, we show that GCaMP6 Thy1 transgenic mice are useful for long-term, high-sensitivity imaging in behaving mice.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0108697}, author = {Dana, Hod and Chen, Tsai-Wen and Hu, Amy and Shields, Brenda C and Cui, Guohong and Looger, Loren and Kim, Douglas S. and Svoboda, Karel} } @article {6905, title = {Toward large-scale connectome reconstructions.}, journal = {Current Opinion in Neurobiology}, volume = {25C}, year = {2014}, month = {2014 Mar 2}, pages = {201-10}, abstract = {

Recent results have shown the possibility of both reconstructing connectomes of small but biologically interesting circuits and extracting from these connectomes insights into their function. However, these reconstructions were heroic proof-of-concept experiments, requiring person-months of effort per neuron reconstructed, and will not scale to larger circuits, much less the brains of entire animals. In this paper we examine what will be required to generate and use substantially larger connectomes, finding five areas that need increased attention: firstly, imaging better suited to automatic reconstruction, with excellent z-resolution; secondly, automatic detection, validation, and measurement of synapses; thirdly, reconstruction methods that keep and use uncertainty metrics for every object, from initial images, through segmentation, reconstruction, and connectome queries; fourthly, processes that are fully incremental, so that the connectome may be used before it is fully complete; and finally, better tools for analysis of connectomes, once they are obtained.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2014.01.019}, author = {Plaza, Stephen M and Scheffer, Louis K and Chklovskii, Dmitri B} } @conference {48180, title = {Tracking by assignment facilitates data curation.}, booktitle = {Medical Image Computing and Computer-Assisted Intervention {\textendash} MICCAI Workshop 2014}, year = {2014}, month = {2014 Sep 14}, address = {Boston, MA}, abstract = {

Object tracking is essential for a multitude of biomedical re- search projects. Automated methods are desired in order to avoid im- possible amounts of manual tracking efforts. However, automatically found solutions are not free of errors, and these errors again have to be identified and resolved manually. We propose six innovative ways for semi-automatic curation of automatically found tracking solutions. Respective user interactions are six simple operations: Inclusion and ex- clusion of objects and tracking decisions, specification of the number of objects, and one-click altering of object segmentations. We show how all proposed interactions can be elegantly incorporated into {\textquotedblleft}assignment models{\textquotedblright} [1,2,3,4,5,6], an innovative and increasingly popular tracking paradigm. Given some user interaction, the tracking engine is capable of computing the respective globally optimal tracking solution efficiently, even benefitting from {\textquotedblleft}warm start{\textquotedblright}-capabilities. We show that after in- teractively pointing at a single mistake, multiple segmentation and track- ing errors can be fixed automatically in one single re-evaluation, provably leading to the new, feedback-conscious global optimum.\ 

}, url = {http://interactivemedical.org/imic2014/CameraReadyPapers/Paper\%203/Jug_Interactive_IMIC2014.pdf}, author = {Jug, Florian and Tobias Pietzsch and Kainmueller, Dagmar and Myers, Eugene W} } @article {45031, title = {Transcription factors modulate c-Fos transcriptional bursts.}, journal = {Cell Reports}, volume = {8}, year = {2014}, month = {2014 Jul 10}, pages = {75-83}, abstract = {

Transcription is a stochastic process occurring mostly in episodic bursts. Although the local chromatin environment is known to influence the bursting behavior on long timescales, the impact of transcription factors (TFs)-especially in rapidly inducible systems-is largely unknown. Using fluorescence in\ situ hybridization and computational models, we quantified the transcriptional activity of the proto-oncogene c-Fos with single mRNA accuracy at individual endogenous alleles. We showed that, during MAPK induction, the TF concentration modulates the burst frequency of c-Fos, whereas other bursting parameters remain mostly unchanged. By using synthetic TFs with TALE DNA-binding domains, we systematically altered different aspects of these bursts. Specifically, we linked the polymerase initiation frequency to the strength of the transactivation domain and the burst duration to the TF lifetime on the promoter. Our results show how TFs and promoter binding domains collectively act to regulate different bursting parameters, offering a vast, evolutionarily tunable regulatory range for individual genes.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2014.05.053}, author = {Senecal, Adrien and Munsky, Brian and Proux, Florence and Ly, Nathalie and Braye, Floriane E and Zimmer, Christophe and Mueller, Florian and Darzacq, Xavier} } @article {46377, title = {Transgenesis in non-model organisms: the case of Parhyale.}, journal = {Methods Mol Biol}, volume = {1196}, year = {2014}, month = {2014}, pages = {145-81}, abstract = {

One of the most striking manifestations of Hox gene activity is the morphological and functional diversity of arthropod body plans, segments, and associated appendages. Among arthropod models, the amphipod crustacean Parhyale hawaiensis satisfies a number of appealing biological and technical requirements to study the Hox control of tissue and organ morphogenesis. Parhyale embryos undergo direct development from fertilized eggs into miniature adults within 10 days and are amenable to all sorts of embryological and functional genetic manipulations. Furthermore, each embryo develops a series of specialized appendages along the anterior-posterior body axis, offering exceptional material to probe the genetic basis of appendage patterning, growth, and differentiation. Here, we describe the methodologies and techniques required for transgenesis-based gain-of-function studies of Hox genes in Parhyale embryos. First, we introduce a protocol for efficient microinjection of early-stage Parhyale embryos. Second, we describe the application of fast and reliable assays to test the activity of the Minos DNA transposon in embryos. Third, we present the use of Minos-based transgenesis vectors to generate stable and transient transgenic Parhyale. Finally, we describe the development and application of a conditional heat-inducible misexpression system to study the role of the Hox gene Ultrabithorax in Parhyale appendage specialization. Beyond providing a useful resource for Parhyalists, this chapter also aims to provide a road map for researchers working on other emerging model organisms. Acknowledging the time and effort that need to be invested in developing transgenic approaches in new species, it is all worth it considering the wide scope of experimentation that opens up once transgenesis is established.

}, issn = {1940-6029}, doi = {10.1007/978-1-4939-1242-1_10}, author = {Kontarakis, Zacharias and Pavlopoulos, Anastasios} } @article {46702, title = {The translation elongation factor eEF1A1 couples transcription to translation during heat shock response.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 Sep 16}, pages = {e03164}, abstract = {

Translation elongation factor eEF1A has a well-defined role in protein synthesis. In this study, we demonstrate a new role for eEF1A: it participates in the entire process of the heat shock response (HSR) in mammalian cells from transcription through translation. Upon stress, isoform 1 of eEF1A rapidly activates transcription of HSP70 by recruiting the master regulator HSF1 to its promoter. eEF1A1 then associates with elongating RNA polymerase II and the 3{\textquoteright}UTR of HSP70 mRNA, stabilizing it and facilitating its transport from the nucleus to active ribosomes. eEF1A1-depleted cells exhibit severely impaired HSR and compromised thermotolerance. In contrast, tissue-specific isoform 2 of eEF1A does not support HSR. By adjusting transcriptional yield to translational needs, eEF1A1 renders HSR rapid, robust, and highly selective; thus, representing an attractive therapeutic target for numerous conditions associated with disrupted protein homeostasis, ranging from neurodegeneration to cancer.

}, issn = {2050-084X}, doi = {10.7554/eLife.03164}, author = {Vera, Maria and Pani, Bibhusita and Griffiths, Lowri A and Muchardt, Christian and Abbott, Catherine M and Singer, Robert H and Nudler, Evgeny} } @article {46378, title = {Tribolium embryo morphogenesis: may the force be with you.}, journal = {Bioarchitecture}, volume = {4}, year = {2014}, month = {2014 Jan-Feb}, pages = {16-21}, abstract = {

Development of multicellular organisms depends on patterning and growth mechanisms encoded in the genome, but also on the physical properties and mechanical interactions of the constituent cells that interpret these genetic cues. This fundamental biological problem requires integrated studies at multiple levels of biological organization: from genes, to cell behaviors, to tissue morphogenesis. We have recently combined functional genetics with live imaging approaches in embryos of the insect Tribolium castaneum, in order to understand their remarkable transformation from a uniform single-layered blastoderm into a condensed multi-layered embryo covered by extensive extra-embryonic tissues. We first developed a quick and reliable methodology to fluorescently label various cell components in entire Tribolium embryos. Live imaging of labeled embryos at single cell resolution provided detailed descriptions of cell behaviors and tissue movements during normal embryogenesis. We then compared cell and tissue dynamics between wild-type and genetically perturbed embryos that exhibited altered relative proportions of constituent tissues. This systematic comparison led to a qualitative model of the molecular, cellular and tissue interactions that orchestrate the observed epithelial rearrangements. We expect this work to establish the Tribolium embryo as a powerful and attractive model system for biologists and biophysicists interested in the molecular, cellular and mechanical control of tissue morphogenesis.

}, keywords = {Animals, Tribolium}, issn = {1949-100X}, doi = {10.4161/bioa.27815}, author = {Benton, Matthew A and Pavlopoulos, Anastasios} } @article {45372, title = {A type VI secretion-related pathway in bacteroidetes mediates interbacterial antagonism.}, journal = {Cell Host Microbe}, volume = {16}, year = {2014}, month = {2014 Aug 13}, pages = {227-36}, abstract = {

Bacteroidetes are a phylum of Gram-negative bacteria abundant in mammalian-associated polymicrobial communities, where they impact digestion, immunity, and resistance to infection. Despite the extensive competition at high cell density that occurs in these settings, cell contact-dependent mechanisms of interbacterial antagonism, such as the type VI secretion system (T6SS), have not been defined in this group of organisms. Herein we report the bioinformatic and functional characterization of a T6SS-like pathway in diverse Bacteroidetes. Using prominent human gut commensal and soil-associated species, we demonstrate that these systems localize dynamically within the cell, export antibacterial proteins, and target competitor bacteria. The Bacteroidetes system is a distinct pathway with marked differences in gene content and high evolutionary divergence from the canonical T6S pathway. Our findings offer a potential molecular explanation for the abundance of Bacteroidetes in polymicrobial environments, the observed stability of Bacteroidetes in healthy humans, and the barrier presented by the microbiota against pathogens.

}, issn = {1934-6069}, doi = {10.1016/j.chom.2014.07.007}, author = {Russell, Alistair B and Wexler, Aaron G and Harding, Brittany N and Whitney, John C and Bohn, Alan J and Goo, Young Ah and Tran, Bao Q and Barry, Natasha A and Zheng, Hongjin and Peterson, S Brook and Chou, Seemay and Gonen, Tamir and Goodlett, David R and Goodman, Andrew L and Mougous, Joseph D} } @article {48277, title = {Unilateral whisker trimming in newborn rats alters neuronal coincident discharge among mature barrel cortex neurons.}, journal = {Journal of neurophysiology}, volume = {112}, year = {2014}, month = {2014 Oct 15}, pages = {1925-35}, abstract = {

It is known that sensory deprivation, including postnatal whisker trimming, can lead to severe deficits in the firing rate properties of cortical neurons. Recent results indicate that development of synchronous discharge among cortical neurons is also activity influenced, and that correlated discharge is significantly impaired following loss of bilateral sensory input in rats. Here we investigate whether unilateral whisker trimming (unilateral deprivation or UD) after birth interferes in the same way with the development of synchronous discharge in cortex. We measured the coincidence of spikes among pairs of neurons recorded under urethane anesthesia in one whisker barrel field deprived by trimming all contralateral whiskers for 60 days after birth (UD), and in untrimmed controls (CON). In the septal columns around barrels, UD significantly increased the coincident discharge among cortical neurons compared with CON, most notably in layers II/III. In contrast, synchronous discharge was normal between layer IV UD barrel neurons: i.e., not different from CON. Thus, while bilateral whisker deprivation (BD) produced a global deficit in the development of synchrony in layer IV, UD did not block the development of synchrony between neurons in layer IV barrels and increased synchrony within septal circuits. We conclude that changes in synchronous discharge after UD are unexpectedly different from those recorded after BD, and we speculate that this effect may be due to the driven activity from active commissural inputs arising from the contralateral hemisphere that received normal activity levels during postnatal development.

}, keywords = {Animals, Animals, Newborn, Female, Male, Neurons, Physical Stimulation, Rats, Rats, Long-Evans, Sensory Deprivation, Somatosensory Cortex, Touch, Touch Perception, Vibrissae}, issn = {1522-1598}, doi = {10.1152/jn.00562.2013}, author = {Ghoshal, Ayan and Lustig, Brian and Popescu, Maria and Ebner, Ford and Pouget, Pierre} } @article {47703, title = {Variance predicts salience in central sensory processing.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014}, abstract = {

Information processing in the sensory periphery is shaped by natural stimulus statistics. In the periphery, a transmission bottleneck constrains performance; thus efficient coding implies that natural signal components with a predictably wider range should be compressed. In a different regime--when sampling limitations constrain performance--efficient coding implies that more resources should be allocated to informative features that are more variable. We propose that this regime is relevant for sensory cortex when it extracts complex features from limited numbers of sensory samples. To test this prediction, we use central visual processing as a model: we show that visual sensitivity for local multi-point spatial correlations, described by dozens of independently-measured parameters, can be quantitatively predicted from the structure of natural images. This suggests that efficient coding applies centrally, where it extends to higher-order sensory features and operates in a regime in which sensitivity increases with feature variability.

}, keywords = {Humans, Sensory Receptor Cells, Visual Cortex, Visual Perception}, issn = {2050-084X}, doi = {10.7554/eLife.03722}, author = {Hermundstad, Ann M and Briguglio, John J and Conte, Mary M and Victor, Jonathan D and Balasubramanian, Vijay and Tka{\v c}ik, Ga{\v s}per} } @article {45064, title = {Virtual finger boosts three-dimensional imaging and microsurgery as well as terabyte volume image visualization and analysis.}, journal = {Nature Communications}, volume = {5}, year = {2014}, month = {2014 Jul 11}, pages = {4342}, abstract = {

Three-dimensional (3D) bioimaging, visualization and data analysis are in strong need of powerful 3D exploration techniques. We develop virtual finger (VF) to generate 3D curves, points and regions-of-interest in the 3D space of a volumetric image with a single finger operation, such as a computer mouse stroke, or click or zoom from the 2D-projection plane of an image as visualized with a computer. VF provides efficient methods for acquisition, visualization and analysis of 3D images for roundworm, fruitfly, dragonfly, mouse, rat and human. Specifically, VF enables instant 3D optical zoom-in imaging, 3D free-form optical microsurgery, and 3D visualization and annotation of terabytes of whole-brain image volumes. VF also leads to orders of magnitude better efficiency of automated 3D reconstruction of neurons and similar biostructures over our previous systems. We use VF to generate from images of 1,107 Drosophila GAL4 lines a projectome of a Drosophila brain.

}, issn = {2041-1723}, doi = {10.1038/ncomms5342}, author = {Peng, Hanchuan and Tang, Jianyong and Xiao, Hang and Bria, Alessandro and Zhou, Jianlong and Butler, Victoria and Zhou, Zhi and Gonzalez-Bellido, Paloma T and Oh, Seung W and Chen, Jichao and Mitra, Ananya and Tsien, Richard W and Zeng, Hongkui and Ascoli, Giorgio A and Iannello, Giulio and Hawrylycz, Michael and Myers, Eugene and Long, Fuhui} } @article {46676, title = {Visualization of dynamics of single endogenous mRNA labeled in live mouse.}, journal = {Science}, volume = {343}, year = {2014}, month = {2014 Jan 24}, pages = {422-4}, abstract = {

The transcription and transport of messenger RNA (mRNA) are critical steps in regulating the spatial and temporal components of gene expression, but it has not been possible to observe the dynamics of endogenous mRNA in primary mammalian tissues. We have developed a transgenic mouse in which all β-actin mRNA is fluorescently labeled. We found that β-actin mRNA in primary fibroblasts localizes predominantly by diffusion and trapping as single mRNAs. In cultured neurons and acute brain slices, we found that multiple β-actin mRNAs can assemble together, travel by active transport, and disassemble upon depolarization by potassium chloride. Imaging of brain slices revealed immediate early induction of β-actin transcription after depolarization. Studying endogenous mRNA in live mouse tissues provides insight into its dynamic regulation within the context of the cellular and tissue microenvironment.

}, keywords = {Actins, Animals, Brain, Cells, Cultured, Fibroblasts, Fluorescent Dyes, Mice, Mice, Transgenic, Neuroimaging, Neurons, Protein Biosynthesis, RNA, Messenger, Staining and Labeling}, issn = {1095-9203}, doi = {10.1126/science.1239200}, author = {Park, Hye Yoon and Lim, Hyungsik and Yoon, Young J and Follenzi, Antonia and Nwokafor, Chiso and Lopez-Jones, Melissa and Meng, Xiuhua and Singer, Robert H} } @article {45778, title = {Whole-cell, multicolor superresolution imaging using volumetric multifocus microscopy.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, year = {2014}, month = {2014 Dec 9}, pages = {17480-5}, abstract = {

Single molecule-based superresolution imaging has become an essential tool in modern cell biology. Because of the limited depth of field of optical imaging systems, one of the major challenges in superresolution imaging resides in capturing the 3D nanoscale morphology of the whole cell. Despite many previous attempts to extend the application of photo-activated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM) techniques into three dimensions, effective localization depths do not typically exceed 1.2 {\textmu}m. Thus, 3D imaging of whole cells (or even large organelles) still demands sequential acquisition at different axial positions and, therefore, suffers from the combined effects of out-of-focus molecule activation (increased background) and bleaching (loss of detections). Here, we present the use of multifocus microscopy for volumetric multicolor superresolution imaging. By simultaneously imaging nine different focal planes, the multifocus microscope instantaneously captures the distribution of single molecules (either fluorescent proteins or synthetic dyes) throughout an \~{}4-{\textmu}m-deep volume, with lateral and axial localization precisions of \~{}20 and 50 nm, respectively. The capabilities of multifocus microscopy to rapidly image the 3D organization of intracellular structures are illustrated by superresolution imaging of the mammalian mitochondrial network and yeast microtubules during cell division.

}, issn = {1091-6490}, doi = {10.1073/pnas.1412396111}, author = {Hajj, Bassam and Wisniewski, Jan and El Beheiry, Mohamed and Chen, Jiji and Revyakin, Andrey and Wu, Carl and Dahan, Maxime} } @article {45041, title = {Whole-cell patch-clamp recordings in freely moving animals.}, journal = {Methods in Molecular Biology}, volume = {1183}, year = {2014}, month = {2014 Jun 20}, pages = {263-76}, abstract = {

The patch-clamp technique and the whole-cell measurements derived from it have greatly advanced our understanding of the coding properties of individual neurons by allowing for a detailed analysis of their excitatory/inhibitory synaptic inputs, intrinsic electrical properties, and morphology. Because such measurements require a high level of mechanical stability they have for a long time been limited to in vitro and anesthetized preparations. Recently, however, a considerable amount of effort has been devoted to extending these techniques to awake restrained/head-fixed preparations allowing for the study of the input-output functions of neurons during behavior. In this chapter we describe a technique extending patch-clamp recordings to awake animals free to explore their environments.

}, issn = {1940-6029}, doi = {10.1007/978-1-4939-1096-0_17}, author = {Lee, Albert K and Epsztein, J{\'e}r{\^o}me and Brecht, Michael} } @article {45176, title = {Wide-field feedback neurons dynamically tune early visual processing.}, journal = {Neuron}, volume = {82}, year = {2014}, month = {2014 May 21}, pages = {887-95}, abstract = {

An important strategy for efficient neural coding is to match the range of cellular responses to the distribution of relevant input signals. However, the structure and relevance of sensory signals depend on behavioral state. Here, we show that behavior modifies neural activity at the earliest stages of fly vision. We describe a class of wide-field neurons that provide feedback to the most peripheral layer of the Drosophila visual system, the lamina. Using in vivo patch-clamp electrophysiology, we found that lamina wide-field neurons respond to low-frequency luminance fluctuations. Recordings in flying flies revealed that the gain and frequency tuning of wide-field neurons change during flight, and that these effects are mimicked by the neuromodulator octopamine. Genetically silencing wide-field neurons increased behavioral responses to slow-motion stimuli. Together, these findings identify a cell type that is gated by behavior to enhance neural coding by subtracting low-frequency signals from the inputs to motion detection circuits.

}, keywords = {Adrenergic alpha-Agonists, Anesthetics, Local, Animals, Animals, Genetically Modified, Brain, Choline O-Acetyltransferase, Drosophila, Drosophila Proteins, Feedback, Sensory, Flight, Animal, Green Fluorescent Proteins, Membrane Potentials, Motion Perception, Neurons, Octopamine, Photic Stimulation, Tetrodotoxin, Transcription Factors, Visual Pathways}, issn = {1097-4199}, doi = {10.1016/j.neuron.2014.04.023}, author = {Tuthill, John C and Nern, Aljoscha and Rubin, Gerald M and Reiser, Michael B} } @article {6881, title = {Wiring economy can account for cell body placement across species and brain areas.}, journal = {Current biology : CB}, volume = {24}, year = {2014}, month = {2014 Feb 3}, pages = {R109-10}, abstract = {The placement of neuronal cell bodies relative to the neuropile differs among species and brain areas. Cell bodies can be either embedded as in mammalian cortex or segregated as in invertebrates and some other vertebrate brain areas. Why are there such different arrangements? Here we suggest that the observed arrangements may simply be a reflection of wiring economy, a general principle that tends to reduce the total volume of the neuropile and hence the volume of the inclusions in it. Specifically, we suggest that the choice of embedded versus segregated arrangement is determined by which neuronal component - the cell body or the neurite connecting the cell body to the arbor - has a smaller volume. Our quantitative predictions are in agreement with existing and new measurements.}, issn = {1879-0445}, doi = {10.1016/j.cub.2013.12.012}, author = {Rivera-Alba, Marta and Peng, Hanchuan and de Polavieja, Gonzalo G and Chklovskii, Dmitri B} } @article {46284, title = {Word length effect in free recall of randomly assembled word lists.}, journal = {Frontiers in Computational Neuroscience}, volume = {8}, year = {2014}, month = {2014 Oct 14}, pages = {129}, abstract = {

In serial recall experiments, human subjects are requested to retrieve a list of words in the same order as they were presented. In a classical study, participants were reported to recall more words from study lists composed of short words compared to lists of long words, the word length effect. The world length effect was also observed in free recall experiments, where subjects can retrieve the words in any order. Here we analyzed a large dataset from free recall experiments of unrelated words, where short and long words were randomly mixed, and found a seemingly opposite effect: long words are recalled better than the short ones. We show that our recently proposed mechanism of associative retrieval can explain both these observations. Moreover, the direction of the effect depends solely on the way study lists are composed.

}, issn = {1662-5188}, doi = {10.3389/fncom.2014.00129}, author = {Katkov, Mikhail and Romani, Sandro and Tsodyks, Misha} } @conference {5905, title = {3D Haar-like elliptical features for object classification in microscopy.}, booktitle = {International Symposium on Biomedical Imaging}, year = {2013}, month = {2013 Apr}, abstract = {

Object detection and classification are key tasks in computer vision that can facilitate high-throughput image analysis of microscopy data. We present a set of local image descriptors for three-dimensional (3D) microscopy datasets inspired by the well-known Haar wavelet framework. We add orientation, illumination and scale information by assuming that the neighborhood surrounding points of interests in the image can be described with ellipsoids, and we increase discriminative power by incorporating edge and shape information into the features. The calculation of the local image descriptors is implemented in a Graphics Processing Unit (GPU) in order to reduce computation time to 1 millisecond per object of interest. We present results for cell division detection in 3D time-lapse fluorescence microscopy with 97.6\% accuracy.

}, author = {Amat, Fernando and Keller, Philipp J} } @article {47642, title = {Accelerating 3B single-molecule super-resolution microscopy with cloud computing.}, journal = {Nature methods}, volume = {10}, year = {2013}, month = {2013 Feb}, pages = {96-7}, keywords = {Computational Biology, Computers, Fluorescent Dyes, Microscopy, Fluorescence, Nanotechnology}, issn = {1548-7105}, doi = {10.1038/nmeth.2335}, author = {Hu, Ying S and Nan, Xiaolin and Sengupta, Prabuddha and Lippincott-Schwartz, Jennifer and Cang, Hu} } @article {6534, title = {Addiction.}, journal = {Current Opinion in Neurobiology}, volume = {23}, year = {2013}, month = {2013 Aug}, pages = {463-6}, abstract = {

Drug addiction and obesity share the core feature that those afflicted by the disorders express a desire to limit drug or food consumption yet persist despite negative consequences. Emerging evidence suggests that the compulsivity that defines these disorders may arise, to some degree at least, from common underlying neurobiological mechanisms. In particular, both disorders are associated with diminished striatal dopamine D2 receptor (D2R) availability, likely reflecting their decreased maturation and surface expression. In striatum, D2Rs are expressed by approximately half of the principal medium spiny projection neurons (MSNs), the striatopallidal neurons of the so-called {\textquoteright}indirect{\textquoteright} pathway. D2Rs are also expressed presynaptically on dopamine terminals and on cholinergic interneurons. This heterogeneity of D2R expression has hindered attempts, largely using traditional pharmacological approaches, to understand their contribution to compulsive drug or food intake. The emergence of genetic technologies to target discrete populations of neurons, coupled to optogenetic and chemicogenetic tools to manipulate their activity, have provided a means to dissect striatopallidal and cholinergic contributions to compulsivity. Here, we review recent evidence supporting an important role for striatal D2R signaling in compulsive drug use and food intake. We pay particular attention to striatopallidal projection neurons and their role in compulsive responding for food and drugs. Finally, we identify opportunities for future obesity research using known mechanisms of addiction as a heuristic, and leveraging new tools to manipulate activity of specific populations of striatal neurons to understand their contributions to addiction and obesity.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2013.07.003}, author = {Everitt, Barry J and Heberlein, Ulrike} } @article {6127, title = {Admixture mapping in lupus identifies multiple functional variants within IFIH1 associated with apoptosis, inflammation, and autoantibody production.}, journal = {PLoS Genetics}, volume = {9}, year = {2013}, month = {2013 Feb 18}, pages = {e1003222}, abstract = {

Systemic lupus erythematosus (SLE) is an inflammatory autoimmune disease with a strong genetic component. African-Americans (AA) are at increased risk of SLE, but the genetic basis of this risk is largely unknown. To identify causal variants in SLE loci in AA, we performed admixture mapping followed by fine mapping in AA and European-Americans (EA). Through genome-wide admixture mapping in AA, we identified a strong SLE susceptibility locus at 2q22-24 (LOD=6.28), and the admixture signal is associated with the European ancestry (ancestry risk ratio \ 1.5). Large-scale genotypic analysis on 19,726 individuals of African and European ancestry revealed three independently associated variants in the IFIH1 gene: an intronic variant, rs13023380 [P(meta) = 5.20{\texttimes}10(-14); odds ratio, 95\% confidence interval = 0.82 (0.78-0.87)], and two missense variants, rs1990760 (Ala946Thr) [P(meta) = 3.08{\texttimes}10(-7); 0.88 (0.84-0.93)] and rs10930046 (Arg460His) [P(dom) = 1.16{\texttimes}10(-8); 0.70 (0.62-0.79)]. Both missense variants produced dramatic phenotypic changes in apoptosis and inflammation-related gene expression. We experimentally validated function of the intronic SNP by DNA electrophoresis, protein identification, and in vitro protein binding assays. DNA carrying the intronic risk allele rs13023380 showed reduced binding efficiency to a cellular protein complex including nucleolin and lupus autoantigen Ku70/80, and showed reduced transcriptional activity in vivo. Thus, in SLE patients, genetic susceptibility could create a biochemical imbalance that dysregulates nucleolin, Ku70/80, or other nucleic acid regulatory proteins. This could promote antibody hypermutation and auto-antibody generation, further destabilizing the cellular network. Together with molecular modeling, our results establish a distinct role for IFIH1 in apoptosis, inflammation, and autoantibody production, and explain the molecular basis of these three risk alleles for SLE pathogenesis.

}, keywords = {African Americans, Alleles, Antigens, Apoptosis, Autoantibodies, Chromosome Mapping, DEAD-box RNA Helicases, DNA-Binding Proteins, European Continental Ancestry Group, Genetic Predisposition to Disease, Genome, Haplotypes, Human, Humans, Inflammation, Lupus Erythematosus, Nuclear, Polymorphism, Protein Binding, Single Nucleotide, Systemic}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1003222}, author = {Molineros, Julio E and Maiti, Amit K and Sun, Celi and Looger, Loren L and Han, Shizhong and Kim-Howard, Xana and Glenn, Stuart and Adler, Adam and Kelly, Jennifer A and Niewold, Timothy B and Gilkeson, Gary S and Brown, Elizabeth E and Alarc{\'o}n, Graciela S and Edberg, Jeffrey C and Petri, Michelle and Ramsey-Goldman, Rosalind and Reveille, John D and Vil{\'a}, Luis M and Freedman, Barry I and Tsao, Betty P and Criswell, Lindsey A and Jacob, Chaim O and Moore, Jason H and Vyse, Timothy J and Langefeld, Carl L and Guthridge, Joel M and Gaffney, Patrick M and Moser, Kathy L and Scofield, R Hal and Alarc{\'o}n-Riquelme, Marta E and Williams, Scott M and Merrill, Joan T and James, Judith A and Kaufman, Kenneth M and Kimberly, Robert P and Harley, John B and Nath, Swapan K} } @article {6252, title = {Allosteric mechanism of water-channel gating by Ca(2+)-calmodulin.}, journal = {Nature Structural \& Molecular Biology}, volume = {20}, year = {2013}, month = {2013 Jul 28}, pages = {1085-92}, abstract = {

Calmodulin (CaM) is a universal regulatory protein that communicates the presence of calcium to its molecular targets and correspondingly modulates their function. This key signaling protein is important for controlling the activity of hundreds of membrane channels and transporters. However, understanding of the structural mechanisms driving CaM regulation of full-length membrane proteins has remained elusive. In this study, we determined the pseudoatomic structure of full-length mammalian aquaporin-0 (AQP0, Bos taurus) in complex with CaM, using EM to elucidate how this signaling protein modulates water-channel function. Molecular dynamics and functional mutation studies reveal how CaM binding inhibits AQP0 water permeability by allosterically closing the cytoplasmic gate of AQP0. Our mechanistic model provides new insight, only possible in the context of the fully assembled channel, into how CaM regulates multimeric channels by facilitating cooperativity between adjacent subunits.

}, issn = {1545-9985}, doi = {10.1038/nsmb.2630}, author = {Reichow, Steve L and Clemens, Daniel M and Freites, J Alfredo and N{\'e}meth-Cahalan, Karin L and Heyden, Matthias and Tobias, Douglas J and Hall, James E and Gonen, Tamir} } @article {45724, title = {Aphids evolved novel secreted proteins for symbiosis with bacterial endosymbiont.}, journal = {Proc Biol Sci}, volume = {280}, year = {2013}, month = {2013 Jan 7}, pages = {20121952}, abstract = {

Aphids evolved novel cells, called bacteriocytes, that differentiate specifically to harbour the obligatory mutualistic endosymbiotic bacteria Buchnera aphidicola. The genome of the host aphid Acyrthosiphon pisum contains many orphan genes that display no similarity with genes found in other sequenced organisms, prompting us to hypothesize that some of these orphan genes are related to lineage-specific traits, such as symbiosis. We conducted deep sequencing of bacteriocytes mRNA followed by whole mount in situ hybridizations of over-represented transcripts encoding aphid-specific orphan proteins. We identified a novel class of genes that encode small proteins with signal peptides, which are often cysteine-rich, that are over-represented in bacteriocytes. These genes are first expressed at a developmental time point coincident with the incorporation of symbionts strictly in the cells that contribute to the bacteriocyte and this bacteriocyte-specific expression is maintained throughout the aphid{\textquoteright}s life. The expression pattern suggests that recently evolved secretion proteins act within bacteriocytes, perhaps to mediate the symbiosis with beneficial bacterial partners, which is reminiscent of the evolution of novel cysteine-rich secreted proteins of leguminous plants that regulate nitrogen-fixing endosymbionts.

}, keywords = {Amino Acid Sequence, Animals, Aphids, Buchnera, DNA, Complementary, Evolution, Molecular, High-Throughput Nucleotide Sequencing, In Situ Hybridization, Insect Proteins, Protein Sorting Signals, RNA, Messenger, Sequence Alignment, Sequence Analysis, RNA, Symbiosis}, issn = {1471-2954}, doi = {10.1098/rspb.2012.1952}, author = {Shigenobu, Shuji and Stern, David L} } @article {6101, title = {APP2: automatic tracing of 3D neuron morphology based on hierarchical pruning of a gray-weighted image distance-tree.}, journal = {Bioinformatics (Oxford, England)}, volume = {29}, year = {2013}, month = {2013 Jun 1}, pages = {1448-54}, abstract = {Tracing of neuron morphology is an essential technique in computational neuroscience. However, despite a number of existing methods, few open-source techniques are completely or sufficiently automated and at the same time are able to generate robust results for real 3D microscopy images.}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btt170}, author = {Xiao, Hang and Peng, Hanchuan} } @article {6452, title = {ASI regulates satiety quiescence in C. elegans.}, journal = {The Journal of Neuroscience : The Official Journal of the Society for Neuroscience}, volume = {33}, year = {2013}, month = {2013 Jun 5}, pages = {9716-24}, abstract = {

In Caenorhabditis elegans, satiety quiescence mimics behavioral aspects of satiety and postprandial sleep in mammals. On the basis of calcium-imaging, genetics, and behavioral studies, here we report that a pair of amphid neurons, ASI, is activated by nutrition and regulates worms{\textquoteright} behavioral states specifically promoting satiety quiescence; ASI inhibits the switch from quiescence to dwelling (a browsing state) and accelerates the switch from dwelling to quiescence. The canonical TGFβ pathway, whose ligand is released from ASI, regulates satiety quiescence. The mutants of a ligand, a receptor and SMADs in the TGFβ pathway all eat more and show less quiescence than wild-type. The TGFβ receptor in downstream neurons RIM and RIC is sufficient for worms to exhibit satiety quiescence, suggesting neuronal connection from ASI to RIM and RIC is essential for feeding regulation through the TGFβ pathway. ASI also regulates satiety quiescence partly through cGMP signaling; restoring cGMP signaling in ASI rescues the satiety quiescence defect of cGMP signaling mutants. From these results, we propose that TGFβ and cGMP pathways in ASI connect nutritional status to promotion of satiety quiescence, a sleep-like behavioral state.

}, keywords = {Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Cyclic GMP, Eating, Genetically Modified, Motor Activity, Protein Kinases, Satiation, Sensory Receptor Cells, Transforming Growth Factor beta}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4493-12.2013}, author = {Gallagher, Thomas and Kim, Jeongho and Oldenbroek, Marieke and Kerr, Rex and You, Young-Jai} } @article {6174, title = {Automated alignment of imperfect EM images for neural reconstruction.}, journal = {arXiv}, year = {2013}, month = {2013 Apr-22}, pages = {arXiv:1304.6034 [q-bio.QM]}, abstract = {

The most established method of reconstructing neural circuits from animals involves slicing tissue very thin, then taking mosaics of electron microscope (EM) images. To trace neurons across different images and through different sections, these images must be accurately aligned, both with the others in the same section and to the sections above and below. Unfortunately, sectioning and imaging are not ideal processes - some of the problems that make alignment difficult include lens distortion, tissue shrinkage during imaging, tears and folds in the sectioned tissue, and dust and other artifacts. In addition the data sets are large (hundreds of thousands of images) and each image must be aligned with many neighbors, so the process must be automated and reliable. This paper discusses methods of dealing with these problems, with numeric results describing the accuracy of the resulting alignments.

}, url = {http://arxiv.org/abs/1304.6034}, author = {Scheffer, L. K. and Karsh, Bill and Vitaladevun, S.} } @article {45850, title = {Automated long-term tracking and social behavioural phenotyping of animal colonies within a semi-natural environment.}, journal = {Nature Communications}, volume = {4}, year = {2013}, month = {2013}, pages = {2018}, abstract = {

Social behaviour has a key role in animal survival across species, ranging from insects to primates and humans. However, the biological mechanisms driving natural interactions between multiple animals, over long-term periods, are poorly studied and remain elusive. Rigorous and objective quantification of behavioural parameters within a group poses a major challenge as it requires simultaneous monitoring of the positions of several individuals and comprehensive consideration of many complex factors. Automatic tracking and phenotyping of interacting animals could thus overcome the limitations of manual tracking methods. Here we report a broadly applicable system that automatically tracks the locations of multiple, uniquely identified animals, such as mice, within a semi-natural setting. The system combines video and radio frequency identified tracking data to obtain detailed behavioural profiles of both individuals and groups. We demonstrate the usefulness of these data in characterizing individual phenotypes, interactions between pairs and the collective social organization of groups.

}, keywords = {Animals, Automation, Behavior, Animal, Crosses, Genetic, Data Collection, Environment, Female, Hierarchy, Social, Locomotion, Male, Mice, Mice, Inbred C57BL, Phenotype, Radio Frequency Identification Device, Social Behavior, Time Factors, Video Recording}, issn = {2041-1723}, doi = {10.1038/ncomms3018}, author = {Weissbrod, Aharon and Shapiro, Alexander and Vasserman, Genadiy and Edry, Liat and Dayan, Molly and Yitzhaky, Assif and Hertzberg, Libi and Feinerman, Ofer and Kimchi, Tali} } @article {6148, title = {Automated multi-day tracking of marked mice for the analysis of social behaviour.}, journal = {Journal of Neuroscience Methods}, volume = {219}, year = {2013}, month = {2013 Sep 30}, pages = {10-19}, abstract = {

A quantitative description of animal social behaviour is informative for behavioural biologists and clinicians developing drugs to treat social disorders. Social interaction in a group of animals has been difficult to measure because behaviour develops over long periods of time and requires tedious manual scoring, which is subjective and often non-reproducible. Computer-vision systems with the ability to measure complex social behaviour automatically would have a transformative impact on biology. Here, we present a method for tracking group-housed mice individually as they freely interact over multiple days. Each mouse is bleach-marked with a unique fur pattern. The patterns are automatically learned by the tracking software and used to infer identities. Trajectories are analysed to measure behaviour as it develops over days, beyond the range of acute experiments. We demonstrate how our system may be used to study the development of place preferences, associations and social relationships by tracking four mice continuously for five days. Our system enables accurate and reproducible characterisation of wild-type mouse social behaviour and paves the way for high-throughput long-term observation of the effects of genetic, pharmacological and environmental manipulations.

}, issn = {1872-678X}, doi = {10.1016/j.jneumeth.2013.05.013}, author = {Ohayon, Shay and Avni, Ofer and Taylor, Adam L and Perona, Pietro and Roian Egnor, S E} } @article {6268, title = {Aβ induces astrocytic glutamate release, extrasynaptic NMDA receptor activation, and synaptic loss.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, year = {2013}, month = {2013 Jul 2}, pages = {E2518-27}, abstract = {

Synaptic loss is the cardinal feature linking neuropathology to cognitive decline in Alzheimer{\textquoteright}s disease (AD). However, the mechanism of synaptic damage remains incompletely understood. Here, using FRET-based glutamate sensor imaging, we show that amyloid-β peptide (Aβ) engages α7 nicotinic acetylcholine receptors to induce release of astrocytic glutamate, which in turn activates extrasynaptic NMDA receptors (eNMDARs) on neurons. In hippocampal autapses, this eNMDAR activity is followed by reduction in evoked and miniature excitatory postsynaptic currents (mEPSCs). Decreased mEPSC frequency may reflect early synaptic injury because of concurrent eNMDAR-mediated NO production, tau phosphorylation, and caspase-3 activation, each of which is implicated in spine loss. In hippocampal slices, oligomeric Aβ induces eNMDAR-mediated synaptic depression. In AD-transgenic mice compared with wild type, whole-cell recordings revealed excessive tonic eNMDAR activity accompanied by eNMDAR-sensitive loss of mEPSCs. Importantly, the improved NMDAR antagonist NitroMemantine, which selectively inhibits extrasynaptic over physiological synaptic NMDAR activity, protects synapses from Aβ-induced damage both in vitro and in vivo.

}, issn = {1091-6490}, doi = {10.1073/pnas.1306832110}, author = {Talantova, Maria and Sanz-Blasco, Sara and Zhang, Xiaofei and Xia, Peng and Akhtar, Mohd Waseem and Okamoto, Shu-ichi and Dziewczapolski, Gustavo and Nakamura, Tomohiro and Cao, Gang and Pratt, Alexander E and Kang, Yeon-Joo and Tu, Shichun and Molokanova, Elena and McKercher, Scott R and Hires, Samuel Andrew and Sason, Hagit and Stouffer, David G and Buczynski, Matthew W and Solomon, James P and Michael, Sarah and Powers, Evan T and Kelly, Jeffery W and Roberts, Amanda and Tong, Gary and Fang-Newmeyer, Traci and Parker, James and Holland, Emily A and Zhang, Dongxian and Nakanishi, Nobuki and Chen, H-S Vincent and Wolosker, Herman and Wang, Yuqiang and Parsons, Loren H and Ambasudhan, Rajesh and Masliah, Eliezer and Heinemann, Stephen F and Pi{\~n}a-Crespo, Juan C and Lipton, Stuart A} } @article {6715, title = {Balanced synaptic impact via distance-dependent synapse distribution and complementary expression of AMPARs and NMDARs in hippocampal dendrites.}, journal = {Neuron}, volume = {80}, year = {2013}, month = {2013 Dec 18}, pages = {1451-63}, abstract = {

Neuronal computation involves the integration of synaptic inputs that are often distributed over expansive dendritic trees, suggesting the need for compensatory mechanisms that enable spatially disparate synapses to influence neuronal output. In hippocampal CA1 pyramidal neurons, such mechanisms have indeed been reported, which normalize either the ability of distributed synapses to drive action potential initiation in the axon or their ability to drive dendritic spiking locally. Here we report that these mechanisms can coexist, through an elegant combination of distance-dependent regulation of synapse number and synaptic expression of AMPA and NMDA receptors. Together, these complementary gradients allow individual dendrites in both the apical and basal dendritic trees of hippocampal neurons to operate as facile computational subunits capable of supporting both global integration in the soma/axon and local integration in the dendrite.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2013.09.027}, author = {Menon, Vilas and Musial, Timothy F and Liu, Annie and Katz, Yael and Kath, William L and Spruston, Nelson and Nicholson, Daniel A} } @article {46052, title = {Bidirectional NMDA receptor plasticity controls CA3 output and heterosynaptic metaplasticity.}, journal = {Nature Neuroscience}, volume = {16}, year = {2013}, month = {2013 Aug}, pages = {1049-59}, abstract = {

NMDA receptors (NMDARs) are classically known as coincidence detectors for the induction of long-term synaptic plasticity and have been implicated in hippocampal CA3 cell-dependent spatial memory functions that likely rely on dynamic cellular ensemble encoding of space. The unique functional properties of both NMDARs and mossy fiber projections to CA3 pyramidal cells place mossy fiber NMDARs in a prime position to influence CA3 ensemble dynamics. By mimicking presynaptic and postsynaptic activity patterns observed in vivo, we found a burst timing-dependent pattern of activity that triggered bidirectional long-term NMDAR plasticity at mossy fiber-CA3 synapses in rat hippocampal slices. This form of plasticity imparts bimodal control of mossy fiber-driven CA3 burst firing and spike temporal fidelity. Moreover, we found that mossy fiber NMDARs mediate heterosynaptic metaplasticity between mossy fiber and associational-commissural synapses. Thus, bidirectional NMDAR plasticity at mossy fiber-CA3 synapses could substantially contribute to the formation, storage and recall of CA3 cell assembly patterns.

}, keywords = {2-Amino-5-phosphonovalerate, Action Potentials, Animals, CA3 Region, Hippocampal, Dentate Gyrus, Dynamins, Egtazic Acid, Endocytosis, Female, Indoles, Long-Term Potentiation, Long-Term Synaptic Depression, Male, Mossy Fibers, Hippocampal, Nerve Tissue Proteins, Nifedipine, Okadaic Acid, Patch-Clamp Techniques, Phosphoric Monoester Hydrolases, Pyramidal Cells, Rats, Rats, Long-Evans, Rats, Wistar, Receptor, Metabotropic Glutamate 5, Receptors, Metabotropic Glutamate, Receptors, N-Methyl-D-Aspartate, Synaptic Transmission}, issn = {1546-1726}, doi = {10.1038/nn.3461}, author = {Hunt, David L and Puente, Nagore and Grandes, Pedro and Castillo, Pablo E} } @article {65015, title = {Biophysical mechanisms of computation in a looming sensitive neuron.}, journal = {The Computing Dendrite}, volume = {11}, year = {2013}, month = {2013 Oct 19}, pages = {277-293}, abstract = {

The lobula giant movement detector (LGMD) is a large-field visual interneuron believed to be involved in collision avoidance and escape behaviors in orthopteran insects, such as locusts. Responses to approaching{\textemdash}or looming{\textemdash}stimuli are highly stereotypical, producing a peak that signals an angular size threshold. Over the past several decades, investigators have elucidated many of the mechanisms underpinning this response, demonstrating that the LGMD implements a multiplication in log-transformed coordinates. Furthermore, the LGMD possesses several mechanisms that preclude it responding to non-looming stimuli. This chapter explores these biophysical mechanisms, as well as highlighting insights the LGMD provides into general principles of dendritic integration.

}, doi = {10.1007/978-1-4614-8094-5_17}, author = {Simon P. Peron} } @article {6514, title = {Caged naloxone reveals opioid signaling deactivation kinetics.}, journal = {Molecular Pharmacology}, volume = {84}, year = {2013}, month = {2013 Nov}, pages = {687-95}, abstract = {

The spatiotemporal dynamics of opioid signaling in the brain remain poorly defined. Photoactivatable opioid ligands provide a means to quantitatively measure these dynamics and their underlying mechanisms in brain tissue. Although activation kinetics can be assessed using caged agonists, deactivation kinetics are obscured by slow clearance of agonist in tissue. To reveal deactivation kinetics of opioid signaling we developed a caged competitive antagonist that can be quickly photoreleased in sufficient concentrations to render agonist dissociation effectively irreversible. Carboxynitroveratryl-naloxone (CNV-NLX), a caged analog of the competitive opioid antagonist NLX, was readily synthesized from commercially available NLX in good yield and found to be devoid of antagonist activity at heterologously expressed opioid receptors. Photolysis in slices of rat locus coeruleus produced a rapid inhibition of the ionic currents evoked by multiple agonists of the μ-opioid receptor (MOR), but not of α-adrenergic receptors, which activate the same pool of ion channels. Using the high-affinity peptide agonist dermorphin, we established conditions under which light-driven deactivation rates are independent of agonist concentration and thus intrinsic to the agonist-receptor complex. Under these conditions, some MOR agonists yielded deactivation rates that are limited by G protein signaling, whereas others appeared limited by agonist dissociation. Therefore, the choice of agonist determines which feature of receptor signaling is unmasked by CNV-NLX photolysis.

}, issn = {1521-0111}, doi = {10.1124/mol.113.088096}, author = {Banghart, Matthew R and Williams, John T and Shah, Ruchir C and Lavis, Luke D and Sabatini, Bernardo L} } @article {6273, title = {Carbofluoresceins and carborhodamines as scaffolds for high-contrast fluorogenic probes.}, journal = {ACS Chemical Biology}, volume = {8}, year = {2013}, month = {2013 Apr 24}, pages = {1303-10}, abstract = {

Fluorogenic molecules are important tools for advanced biochemical and biological experiments. The extant collection of fluorogenic probes is incomplete, however, leaving regions of the electromagnetic spectrum unutilized. Here, we synthesize green-excited fluorescent and fluorogenic analogues of the classic fluorescein and rhodamine 110 fluorophores by replacement of the xanthene oxygen with a quaternary carbon. These anthracenyl "carbofluorescein" and "carborhodamine 110" fluorophores exhibit excellent fluorescent properties and can be masked with enzyme- and photolabile groups to prepare high-contrast fluorogenic molecules useful for live cell imaging experiments and super-resolution microscopy. Our divergent approach to these red-shifted dye scaffolds will enable the preparation of numerous novel fluorogenic probes with high biological utility.

}, issn = {1554-8937}, doi = {10.1021/cb4000822}, author = {Grimm, Jonathan B and Sung, Andrew J and Legant, Wesley R and Hulamm, Phuson and Matlosz, Sylwia M and Betzig, Eric and Lavis, Luke D} } @article {6282, title = {Cbl-associated protein regulates assembly and function of two tension-sensing structures in Drosophila.}, journal = {Development}, volume = {140}, year = {2013}, month = {2013 Feb 1}, pages = {627-38}, abstract = {

Cbl-associated protein (CAP) localizes to focal adhesions and associates with numerous cytoskeletal proteins; however, its physiological roles remain unknown. Here, we demonstrate that Drosophila CAP regulates the organization of two actin-rich structures in Drosophila: muscle attachment sites (MASs), which connect somatic muscles to the body wall; and scolopale cells, which form an integral component of the fly chordotonal organs and mediate mechanosensation. Drosophila CAP mutants exhibit aberrant junctional invaginations and perturbation of the cytoskeletal organization at the MAS. CAP depletion also results in collapse of scolopale cells within chordotonal organs, leading to deficits in larval vibration sensation and adult hearing. We investigate the roles of different CAP protein domains in its recruitment to, and function at, various muscle subcellular compartments. Depletion of the CAP-interacting protein Vinculin results in a marked reduction in CAP levels at MASs, and vinculin mutants partially phenocopy Drosophila CAP mutants. These results show that CAP regulates junctional membrane and cytoskeletal organization at the membrane-cytoskeletal interface of stretch-sensitive structures, and they implicate integrin signaling through a CAP/Vinculin protein complex in stretch-sensitive organ assembly and function.

}, keywords = {Actin Cytoskeleton, Amino Acid, Amino Acid Sequence, Animal Structures, Animals, Binding Sites, Cell Membrane, Cell-Matrix Junctions, Cellular, Cytoskeletal Proteins, Developmental, Drosophila, Electron, Electrophysiological Phenomena, Gene Expression Regulation, Genome, Hearing Disorders, Insect, Integrins, Larva, Mechanotransduction, Microscopy, Multiprotein Complexes, Muscles, Protein Interaction Mapping, Sequence Homology, Signal Transduction, src Homology Domains, Talin, Transmission, Vibration, Vinculin}, issn = {1477-9129}, doi = {10.1242/dev.085100}, author = {Bharadwaj, Rajnish and Roy, Madhuparna and Ohyama, Tomoko and Sivan-Loukianova, Elena and Delannoy, Michael and Lloyd, Thomas E and Zlatic, Marta and Eberl, Daniel F and Kolodkin, Alex L} } @article {6356, title = {Cell and tissue dynamics during Tribolium embryogenesis revealed by versatile fluorescence labeling approaches.}, journal = {Development}, volume = {140}, year = {2013}, month = {2013 Aug}, pages = {3210-20}, abstract = {

Studies on new arthropod models such as the beetle Tribolium castaneum are shifting our knowledge of embryonic patterning and morphogenesis beyond the Drosophila paradigm. In contrast to Drosophila, Tribolium embryos exhibit the short-germ type of development and become enveloped by extensive extra-embryonic membranes, the amnion and serosa. The genetic basis of these processes has been the focus of active research. Here, we complement genetic approaches with live fluorescence imaging of Tribolium embryos to make the link between gene function and morphogenetic cell behaviors during blastoderm formation and differentiation, germband condensation and elongation, and extra-embryonic development. We first show that transient labeling methods result in strong, homogeneous and persistent expression of fluorescent markers in Tribolium embryos, labeling the chromatin, membrane, cytoskeleton or combinations thereof. We then use co-injection of fluorescent markers with dsRNA for live imaging of embryos with disrupted caudal gene function caused by RNA interference. Using these approaches, we describe and compare cell and tissue dynamics in Tribolium embryos with wild-type and altered fate maps. We find that Tribolium germband condensation is effected by cell contraction and intercalation, with the latter being dependent on the anterior-posterior patterning system. We propose that germband condensation drives initiation of amnion folding, whereas expansion of the amniotic fold and closure of the amniotic cavity are likely driven by contraction of an actomyosin cable at the boundary between the amnion and serosa. Our methodology provides a comprehensive framework for testing quantitative models of patterning, growth and morphogenetic mechanisms in Tribolium and other arthropod species.

}, issn = {1477-9129}, doi = {10.1242/dev.096271}, author = {Benton, Matthew A and Akam, Michael and Pavlopoulos, Anastasios} } @article {6272, title = {Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions.}, journal = {Nucleic Acids Research}, volume = {41}, year = {2013}, month = {2013 Jul}, pages = {e121}, abstract = {

Detection of protein homology via sequence similarity has important applications in biology, from protein structure and function prediction to reconstruction of phylogenies. Although current methods for aligning protein sequences are powerful, challenges remain, including problems with homologous overextension of alignments and with regions under convergent evolution. Here, we test the ability of the profile hidden Markov model method HMMER3 to correctly assign homologous sequences to \>13,000 manually curated families from the Pfam database. We identify problem families using protein regions that match two or more Pfam families not currently annotated as related in Pfam. We find that HMMER3 E-value estimates seem to be less accurate for families that feature periodic patterns of compositional bias, such as the ones typically observed in coiled-coils. These results support the continued use of manually curated inclusion thresholds in the Pfam database, especially on the subset of families that have been identified as problematic in experiments such as these. They also highlight the need for developing new methods that can correct for this particular type of compositional bias.

}, issn = {1362-4962}, doi = {10.1093/nar/gkt263}, author = {Mistry, Jaina and Finn, Robert D and Eddy, Sean R. and Bateman, Alex and Punta, Marco} } @article {6675, title = {Characterization and improvement of three-dimensional imaging performance of GRIN-lens-based two-photon fluorescence endomicroscopes with adaptive optics.}, journal = {Optics Express}, volume = {21}, year = {2013}, month = {2013 Nov 4}, pages = {27142-54}, abstract = {

Inherent aberrations of gradient index (GRIN) lenses used in fluorescence endomicroscopes deteriorate imaging performance. Using adaptive optics, we characterized and corrected the on-axis and off-axis aberrations of a GRIN lens with NA 0.8 at multiple focal planes. We demonstrated a rotational-transformation-based correction procedure, which enlarged the imaging area with diffraction-limited resolution with only two aberration measurements. 204.8 {\texttimes} 204.8 {\textmu}m2 images of fluorescent beads and brain slices before and after AO corrections were obtained, with evident improvements in both image sharpness and brightness after AO correction. These results show great promises of applying adaptive optical two-photon fluorescence endomicroscope to three-dimensional (3D) imaging.

}, issn = {1094-4087}, doi = {10.1364/OE.21.027142}, author = {Wang, Chen and Ji, Na} } @inbook {6304, title = {The chemistry of small-molecule fluorogenic probes.}, booktitle = {Progress in Molecular Biology and Translational Science}, volume = {113}, year = {2013}, pages = {1-34}, abstract = {

Chemical fluorophores find wide use in biology to detect and visualize different phenomena. A key advantage of small-molecule dyes is the ability to construct compounds where fluorescence is activated by chemical or biochemical processes. Fluorogenic molecules, in which fluorescence is activated by enzymatic activity, light, or environmental changes, enable advanced bioassays and sophisticated imaging experiments. Here, we detail the collection of fluorophores and highlight both general strategies and unique approaches that are employed to control fluorescence using chemistry.

}, issn = {1878-0814}, doi = {10.1016/B978-0-12-386932-6.00001-6}, author = {Grimm, Jonathan B and Heckman, Laurel M and Lavis, Luke D} } @article {6284, title = {Clonal development and organization of the adult Drosophila central brain.}, journal = {Current biology : CB}, volume = {23}, year = {2013}, month = {2013 Apr 22}, pages = {633-43}, abstract = {BACKGROUND: The insect brain can be divided into neuropils that are formed by neurites of both local and remote origin. The complexity of the interconnections obscures how these neuropils are established and interconnected through development. The Drosophila central brain develops from a fixed number of neuroblasts (NBs) that deposit neurons in regional clusters. RESULTS: By determining individual NB clones and pursuing their projections into specific neuropils, we unravel the regional development of the brain neural network. Exhaustive clonal analysis revealed 95 stereotyped neuronal lineages with characteristic cell-body locations and neurite trajectories. Most clones show complex projection patterns, but despite the complexity, neighboring clones often coinnervate the same local neuropil or neuropils and further target a restricted set of distant neuropils. CONCLUSIONS: These observations argue for regional clonal development of both neuropils and neuropil connectivity throughout the Drosophila central brain.}, issn = {1879-0445}, doi = {10.1016/j.cub.2013.02.057}, author = {Yu, Hung-Hsiang and Awasaki, Takeshi and Schroeder, Mark David and Long, Fuhui and Yang, Jacob S and He, Yisheng and Ding, Peng and Kao, Jui-Chun and Wu, Gloria Yueh-Yi and Peng, Hanchuan and Myers, Gene and Lee, Tzumin} } @article {4057, title = {The collection of high-resolution electron diffraction data.}, journal = {Methods in Molecular Biology}, volume = {955}, year = {2013}, month = {2013}, pages = {153-169}, abstract = {

A number of atomic-resolution structures of membrane proteins (better than 3{\r A} resolution) have been determined recently by electron crystallography. While this technique was established more than 40 years ago, it is still in its infancy with regard to the two-dimensional (2D) crystallization, data collection, data analysis, and protein structure determination. In terms of data collection, electron crystallography encompasses both image acquisition and electron diffraction data collection. Other chapters in this volume outline protocols for image collection and analysis. This chapter, however, outlines detailed protocols for data collection by electron diffraction. These include microscope setup, electron diffraction data collection, and troubleshooting.

}, issn = {1940-6029}, doi = {10.1007/978-1-62703-176-9_9}, author = {Gonen, T} } @article {46712, title = {Colocalization of different influenza viral RNA segments in the cytoplasm before viral budding as shown by single-molecule sensitivity FISH analysis.}, journal = {PLoS Pathogens}, volume = {9}, year = {2013}, month = {2013}, pages = {e1003358}, abstract = {

The Influenza A virus genome consists of eight negative sense, single-stranded RNA segments. Although it has been established that most virus particles contain a single copy of each of the eight viral RNAs, the packaging selection mechanism remains poorly understood. Influenza viral RNAs are synthesized in the nucleus, exported into the cytoplasm and travel to the plasma membrane where viral budding and genome packaging occurs. Due to the difficulties in analyzing associated vRNPs while preserving information about their positions within the cell, it has remained unclear how and where during cellular trafficking the viral RNAs of different segments encounter each other. Using a multicolor single-molecule sensitivity fluorescence in situ hybridization (smFISH) approach, we have quantitatively monitored the colocalization of pairs of influenza viral RNAs in infected cells. We found that upon infection, the viral RNAs from the incoming particles travel together until they reach the nucleus. The viral RNAs were then detected in distinct locations in the nucleus; they are then exported individually and initially remain separated in the cytoplasm. At later time points, the different viral RNA segments gather together in the cytoplasm in a microtubule independent manner. Viral RNAs of different identities colocalize at a high frequency when they are associated with Rab11 positive vesicles, suggesting that Rab11 positive organelles may facilitate the association of different viral RNAs. Using engineered influenza viruses lacking the expression of HA or M2 protein, we showed that these viral proteins are not essential for the colocalization of two different viral RNAs in the cytoplasm. In sum, our smFISH results reveal that the viral RNAs travel together in the cytoplasm before their arrival at the plasma membrane budding sites. This newly characterized step of the genome packaging process demonstrates the precise spatiotemporal regulation of the infection cycle.

}, keywords = {Active Transport, Cell Nucleus, Animals, Cell Nucleus, Dogs, Hemagglutinin Glycoproteins, Influenza Virus, Humans, In Situ Hybridization, Fluorescence, Influenza A virus, Madin Darby Canine Kidney Cells, rab GTP-Binding Proteins, RNA, Viral, Viral Matrix Proteins, Virus Assembly}, issn = {1553-7374}, doi = {10.1371/journal.ppat.1003358}, author = {Chou, Yi-ying and Heaton, Nicholas S and Gao, Qinshan and Palese, Peter and Singer, Robert H and Singer, Robert and Lionnet, Timoth{\'e}e} } @article {46414, title = {Common genetic variation at the IL1RL1 locus regulates IL-33/ST2 signaling.}, journal = {The Journal of Clinical Investigation}, volume = {123}, year = {2013}, month = {2013 Oct}, pages = {4208-18}, abstract = {

The suppression of tumorigenicity 2/IL-33 (ST2/IL-33) pathway has been implicated in several immune and inflammatory diseases. ST2 is produced as 2 isoforms. The membrane-bound isoform (ST2L) induces an immune response when bound to its ligand, IL-33. The other isoform is a soluble protein (sST2) that is thought to be a decoy receptor for IL-33 signaling. Elevated sST2 levels in serum are associated with an increased risk for cardiovascular disease. We investigated the determinants of sST2 plasma concentrations in 2,991 Framingham Offspring Cohort participants. While clinical and environmental factors explained some variation in sST2 levels, much of the variation in sST2 production was driven by genetic factors. In a genome-wide association study (GWAS), multiple SNPs within IL1RL1 (the gene encoding ST2) demonstrated associations with sST2 concentrations. Five missense variants of IL1RL1 correlated with higher sST2 levels in the GWAS and mapped to the intracellular domain of ST2, which is absent in sST2. In a cell culture model, IL1RL1 missense variants increased sST2 expression by inducing IL-33 expression and enhancing IL-33 responsiveness (via ST2L). Our data suggest that genetic variation in IL1RL1 can result in increased levels of sST2 and alter immune and inflammatory signaling through the ST2/IL-33 pathway.

}, keywords = {Amino Acid Substitution, Female, Gene Expression, Gene Expression Regulation, Genetic Association Studies, HEK293 Cells, Humans, Interleukins, Male, Middle Aged, Models, Molecular, Myelin and Lymphocyte-Associated Proteolipid Proteins, Myeloid Differentiation Factor 88, NF-kappa B, Polymorphism, Single Nucleotide, Promoter Regions, Genetic, Prospective Studies, Protein Structure, Tertiary, Receptors, Cell Surface, Signal Transduction, Transcription Factor AP-1}, issn = {1558-8238}, doi = {10.1172/JCI67119}, author = {Ho, Jennifer E and Chen, Wei-Yu and Chen, Ming-Huei and Larson, Martin G and McCabe, Elizabeth L and Cheng, Susan and Ghorbani, Anahita and Coglianese, Erin and Emilsson, Valur and Johnson, Andrew D and Walter, Stefan and Franceschini, Nora and O{\textquoteright}Donnell, Christopher J and Dehghan, Abbas and Lu, Chen and Levy, Daniel and Newton-Cheh, Christopher and Lin, Honghuang and Felix, Janine F and Schreiter, Eric R and Vasan, Ramachandran S and Januzzi, James L and Lee, Richard T and Wang, Thomas J} } @article {46596, title = {Competing dopamine neurons drive oviposition choice for ethanol in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, year = {2013}, month = {2013 Dec 24}, pages = {21153-8}, abstract = {

The neural circuits that mediate behavioral choice evaluate and integrate information from the environment with internal demands and then initiate a behavioral response. Even circuits that support simple decisions remain poorly understood. In Drosophila melanogaster, oviposition on a substrate containing ethanol enhances fitness; however, little is known about the neural mechanisms mediating this important choice behavior. Here, we characterize the neural modulation of this simple choice and show that distinct subsets of dopaminergic neurons compete to either enhance or inhibit egg-laying preference for ethanol-containing food. Moreover, activity in α{\textquoteright}β{\textquoteright} neurons of the mushroom body and a subset of ellipsoid body ring neurons (R2) is required for this choice. We propose a model where competing dopaminergic systems modulate oviposition preference to adjust to changes in natural oviposition substrates.

}, keywords = {Analysis of Variance, Animals, Choice Behavior, Dopaminergic Neurons, Drosophila melanogaster, Ethanol, Female, Fermentation, Fruit, Mushroom Bodies, Oviposition}, issn = {1091-6490}, doi = {10.1073/pnas.1320208110}, author = {Azanchi, Reza and Kaun, Karla R and Heberlein, Ulrike} } @article {6828, title = {A comprehensive wiring diagram of the protocerebral bridge for visual information processing in the Drosophila brain.}, journal = {Cell Reports}, volume = {3}, year = {2013}, month = {2013 May 30}, pages = {1739-53}, abstract = {

How the brain perceives sensory information and generates meaningful behavior depends critically on its underlying circuitry. The protocerebral bridge (PB) is a major part of the insect central complex (CX), a premotor center that may be analogous to the human basal ganglia. Here, by deconstructing hundreds of PB single neurons and reconstructing them into a common three-dimensional framework, we have constructed a comprehensive map of PB circuits with labeled polarity and predicted directions of information flow. Our analysis reveals a highly ordered information processing system that involves directed information flow among CX subunits through 194 distinct PB neuron types. Circuitry properties such as mirroring, convergence, divergence, tiling, reverberation, and parallel signal propagation were observed; their functional and evolutional significance is discussed. This layout of PB neuronal circuitry may provide guidelines for further investigations on transformation of sensory (e.g., visual) input into locomotor commands in fly brains.

}, keywords = {Animals, Biological, Brain, Drosophila, Models, Neurons}, issn = {2211-1247}, doi = {10.1016/j.celrep.2013.04.022}, author = {Lin, Chih-Yung and Chuang, Chao-Chun and Hua, Tzu-En and Chen, Chun-Chao and Dickson, Barry J and Greenspan, Ralph J and Chiang, Ann-Shyn} } @article {6266, title = {Computational identification of functional RNA homologs in metagenomic data.}, journal = {RNA Biology}, volume = {10}, year = {2013}, month = {2013 Jul 1}, pages = {1170-9}, abstract = {

A key step toward understanding a metagenomics data set is the identification of functional sequence elements within it, such as protein coding genes and structural RNAs. Relative to protein coding genes, structural RNAs are more difficult to identify because of their reduced alphabet size, lack of open reading frames, and short length. Infernal is a software package that implements "covariance models" (CMs) for RNA homology search, which harness both sequence and structural conservation when searching for RNA homologs. Thanks to the added statistical signal inherent in the secondary structure conservation of many RNA families, Infernal is more powerful than sequence-only based methods such as BLAST and profile HMMs. Together with the Rfam database of CMs, Infernal is a useful tool for identifying RNAs in metagenomics data sets.

}, issn = {1555-8584}, doi = {10.4161/rna.25038}, author = {Nawrocki, Eric P and Eddy, Sean R.} } @article {6668, title = {A computational model of flow between the microscale respiratory structures of fish gills.}, journal = {Journal of Theoretical Biology}, volume = {338}, year = {2013}, month = {2013 Dec 7}, pages = {23-40}, abstract = {

The gills of most teleost fishes are covered by plate-like structures, the secondary lamellae, that provide the bulk of the respiratory surface area. Water passing over the secondary lamellae exchanges gases with blood passing through the secondary lamellae, forming a system that has served as a classic model of counter-current exchange. In this study, a computational model of flow around the secondary lamellae is used to examine the hydrodynamic consequences of changes to the lamellar morphology. Consistent with previous studies, the interlamellar distance is found to strongly affect the hydrodynamic resistance of the gills. However, the presence of a small gap between the tips of the secondary lamellae is found to have a similarly strong effect on the hydrodynamic resistance and flow patterns within the gills. The results from this model have been generally formulated, allowing the calculation of the hydrodynamic resistance for measured morphometric parameters. These results provide a new basis for comparing theoretical predictions of the gill resistance with measured values, and provide a general model for examining the diversity gill morphologies observed in teleost fishes.

}, issn = {1095-8541}, doi = {10.1016/j.jtbi.2013.08.015}, author = {Strother, James A} } @article {6261, title = {Connectomic reconstruction of the inner plexiform layer in the mouse retina.}, journal = {Nature}, volume = {500}, year = {2013}, month = {2013 Aug 8}, pages = {168-74}, abstract = {

Comprehensive high-resolution structural maps are central to functional exploration and understanding in biology. For the nervous system, in which high resolution and large spatial extent are both needed, such maps are scarce as they challenge data acquisition and analysis capabilities. Here we present for the mouse inner plexiform layer{\textendash}the main computational neuropil region in the mammalian retina{\textendash}the dense reconstruction of 950 neurons and their mutual contacts. This was achieved by applying a combination of crowd-sourced manual annotation and machine-learning-based volume segmentation to serial block-face electron microscopy data. We characterize a new type of retinal bipolar interneuron and show that we can subdivide a known type based on connectivity. Circuit motifs that emerge from our data indicate a functional mechanism for a known cellular response in a ganglion cell that detects localized motion, and predict that another ganglion cell is motion sensitive.

}, keywords = {Amacrine Cells, Animals, Biological, Cell Communication, Computer-Assisted, Connectome, Electron, Image Processing, Inbred C57BL, Mice, Microscopy, Models, Neuropil, Retina, Retinal Ganglion Cells}, issn = {1476-4687}, doi = {10.1038/nature12346}, author = {Helmstaedter, Moritz and Briggman, Kevin L and Turaga, Srinivas C and Jain, Viren and Seung, H Sebastian and Denk, Winfried} } @article {6091, title = {Contributions of the 12 neuron classes in the fly lamina to motion vision.}, journal = {Neuron}, volume = {79}, year = {2013}, month = {07/2013}, pages = {128-140}, abstract = {

Motion detection is a fundamental neural computation performed by many sensory systems. In the fly, local motion computation is thought to occur within the first two layers of the visual system, the lamina and medulla. We constructed specific genetic driver lines for each of the 12 neuron classes in the lamina. We then depolarized and hyperpolarized each neuron type and quantified fly behavioral responses to a diverse set of motion stimuli. We found that only a small number of lamina output neurons are essential for motion detection, while most neurons serve to sculpt and enhance these feedforward pathways. Two classes of feedback neurons (C2 and C3), and lamina output neurons (L2 and L4), are required for normal detection of directional motion stimuli. Our results reveal a prominent role for feedback and lateral interactions in motion processing and demonstrate that motion-dependent behaviors rely on contributions from nearly all lamina neuron classes.

}, doi = {http://dx.doi.org/10.1016/j.neuron.2013.05.024}, author = {Tuthill, John C and Nern, Aljoscha and Stephen L. Holtz and Rubin, Gerald M and Reiser, Michael B} } @article {5893, title = {Convergence of pontine and proprioceptive streams onto multimodal cerebellar granule cells.}, journal = {eLife}, volume = {2}, year = {2013}, month = {2013 Feb 26}, pages = {e00400}, abstract = {

Cerebellar granule cells constitute the majority of neurons in the brain and are the primary conveyors of sensory and motor-related mossy fiber information to Purkinje cells. The functional capability of the cerebellum hinges on whether individual granule cells receive mossy fiber inputs from multiple precerebellar nuclei or are instead unimodal; this distinction is unresolved. Using cell-type-specific projection mapping with synaptic resolution, we observed the convergence of separate sensory (upper body proprioceptive) and basilar pontine pathways onto individual granule cells and mapped this convergence across cerebellar cortex. These findings inform the long-standing debate about the multimodality of mammalian granule cells and substantiate their associative capacity predicted in the Marr-Albus theory of cerebellar function. We also provide evidence that the convergent basilar pontine pathways carry corollary discharges from upper body motor cortical areas. Such merging of related corollary and sensory streams is a critical component of circuit models of predictive motor control. DOI:http://dx.doi.org/10.7554/eLife.00400.001.

}, issn = {2050-084X}, doi = {10.7554/eLife.00400}, author = {Huang, Cheng-Chiu and Sugino, Ken and Shima, Yasuyuki and Guo, Caiying and Bai, Suxia and Mensh, Brett D and Nelson, Sacha B and Hantman, Adam W} } @article {47640, title = {Coordinated elevation of mitochondrial oxidative phosphorylation and autophagy help drive hepatocyte polarization.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, year = {2013}, month = {2013 Apr 30}, pages = {7288-93}, abstract = {

Cell polarization requires increased cellular energy and metabolic output, but how these energetic demands are met by polarizing cells is unclear. To address these issues, we investigated the roles of mitochondrial bioenergetics and autophagy during cell polarization of hepatocytes cultured in a collagen sandwich system. We found that as the hepatocytes begin to polarize, they use oxidative phosphorylation to raise their ATP levels, and this energy production is required for polarization. After the cells are polarized, the hepatocytes shift to become more dependent on glycolysis to produce ATP. Along with this central reliance on oxidative phosphorylation as the main source of ATP production in polarizing cultures, several other metabolic processes are reprogrammed during the time course of polarization. As the cells polarize, mitochondria elongate and mitochondrial membrane potential increases. In addition, lipid droplet abundance decreases over time. These findings suggest that polarizing cells are reliant on fatty acid oxidation, which is supported by pharmacologic inhibition of β-oxidation by etomoxir. Finally, autophagy is up-regulated during cell polarization, with inhibition of autophagy retarding cell polarization. Taken together, our results describe a metabolic shift involving a number of coordinated metabolic pathways that ultimately serve to increase energy production during cell polarization.

}, keywords = {Adenosine Triphosphate, Adenylate Kinase, Animals, Autophagy, Cell Polarity, Energy Metabolism, Fatty Acids, Glycolysis, Hepatocytes, Lipids, Membrane Potential, Mitochondrial, Mitochondria, Mitochondrial Dynamics, Mitochondrial Proteins, Oxidation-Reduction, Oxidative Phosphorylation, Rats, Up-Regulation}, issn = {1091-6490}, doi = {10.1073/pnas.1304285110}, author = {Fu, Dong and Mitra, Kasturi and Sengupta, Prabuddha and Jarnik, Michal and Lippincott-Schwartz, Jennifer and Arias, Irwin M} } @article {6712, title = {Correlative photoactivated localization and scanning electron microscopy.}, journal = {PLoS One}, volume = {8}, year = {2013}, month = {2013 Oct 25}, pages = {e77209}, abstract = {

The ability to localize proteins precisely within subcellular space is crucial to understanding the functioning of biological systems. Recently, we described a protocol that correlates a precise map of fluorescent fusion proteins localized using three-dimensional super-resolution optical microscopy with the fine ultrastructural context of three-dimensional electron micrographs. While it achieved the difficult simultaneous objectives of high photoactivated fluorophore preservation and ultrastructure preservation, it required a super-resolution optical and specialized electron microscope that is not available to many researchers. We present here a faster and more practical protocol with the advantage of a simpler two-dimensional optical (Photoactivated Localization Microscopy (PALM)) and scanning electron microscope (SEM) system that retains the often mutually exclusive attributes of fluorophore preservation and ultrastructure preservation. As before, cryosections were prepared using the Tokuyasu protocol, but the staining protocol was modified to be amenable for use in a standard SEM without the need for focused ion beam ablation. We show the versatility of this technique by labeling different cellular compartments and structures including mitochondrial nucleoids, peroxisomes, and the nuclear lamina. We also demonstrate simultaneous two-color PALM imaging with correlated electron micrographs. Lastly, this technique can be used with small-molecule dyes as demonstrated with actin labeling using phalloidin conjugated to a caged dye. By retaining the dense protein labeling expected for super-resolution microscopy combined with ultrastructural preservation, simplifying the tools required for correlative microscopy, and expanding the number of useful labels we expect this method to be accessible and valuable to a wide variety of researchers.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0077209}, author = {Kopek, Benjamin G and Shtengel, Gleb and Grimm, Jonathan B and Clayton, David A and Hess, Harald F} } @article {5958, title = {Crystal structure of a nitrate/nitrite exchanger.}, journal = {Nature}, volume = {497}, year = {2013}, month = {2013 May 12}, pages = {647-51}, abstract = {

Mineral nitrogen in nature is often found in the form of nitrate (NO3(-)). Numerous microorganisms evolved to assimilate nitrate and use it as a major source of mineral nitrogen uptake. Nitrate, which is central in nitrogen metabolism, is first reduced to nitrite (NO2(-)) through a two-electron reduction reaction. The accumulation of cellular nitrite can be harmful because nitrite can be reduced to the cytotoxic nitric oxide. Instead, nitrite is rapidly removed from the cell by channels and transporters, or reduced to ammonium or dinitrogen through the action of assimilatory enzymes. Despite decades of effort no structure is currently available for any nitrate transport protein and the mechanism by which nitrate is transported remains largely unknown. Here we report the structure of a bacterial nitrate/nitrite transport protein, NarK, from Escherichia coli, with and without substrate. The structures reveal a positively charged substrate-translocation pathway lacking protonatable residues, suggesting that NarK functions as a nitrate/nitrite exchanger and that protons are unlikely to be co-transported. Conserved arginine residues comprise the substrate-binding pocket, which is formed by association of helices from the two halves of NarK. Key residues that are important for substrate recognition and transport are identified and related to extensive mutagenesis and functional studies. We propose that NarK exchanges nitrate for nitrite by a rocker switch mechanism facilitated by inter-domain hydrogen bond networks.

}, issn = {1476-4687}, doi = {10.1038/nature12139}, author = {Zheng, Hongjin and Wisedchaisri, Goragot and Gonen, Tamir} } @article {6586, title = {Decoupled roles for the atypical, bifurcated binding pocket of the ybfF hydrolase.}, journal = {Chembiochem : A European Journal of Chemical Biology}, volume = {14}, year = {2013}, month = {2013 Jun 17}, pages = {1134-44}, abstract = {

Serine hydrolases have diverse intracellular substrates, biological functions, and structural plasticity, and are thus important for biocatalyst design. Amongst serine hydrolases, the recently described ybfF enzyme family are promising novel biocatalysts with an unusual bifurcated substrate-binding cleft and the ability to recognize commercially relevant substrates. We characterized in detail the substrate selectivity of a novel ybfF enzyme from Vibrio cholerae (Vc-ybfF) by using a 21-member library of fluorogenic ester substrates. We assigned the roles of the two substrate-binding clefts in controlling the substrate selectivity and folded stability of Vc-ybfF by comprehensive substitution analysis. The overall substrate preference of Vc-ybfF was for short polar chains, but it retained significant activity with a range of cyclic and extended esters. This broad substrate specificity combined with the substitutional analysis demonstrates that the larger binding cleft controls the substrate specificity of Vc-ybfF. Key selectivity residues (Tyr116, Arg120, Tyr209) are also located at the larger binding pocket and control the substrate specificity profile. In the structure of ybfF the narrower binding cleft contains water molecules prepositioned for hydrolysis, but based on substitution this cleft showed only minimal contribution to catalysis. Instead, the residues surrounding the narrow binding cleft and at the entrance to the binding pocket contributed significantly to the folded stability of Vc-ybfF. The relative contributions of each cleft of the binding pocket to the catalytic activity and folded stability of Vc-ybfF provide a valuable map for designing future biocatalysts based on the ybfF scaffold.

}, issn = {1439-7633}, doi = {10.1002/cbic.201300085}, author = {Ellis, Elizabeth E and Adkins, Chinessa T and Galovska, Natalie M and Lavis, Luke D and Johnson, R Jeremy} } @article {46040, title = {Depletion of polysialic acid from neural cell adhesion molecule (PSA-NCAM) increases CA3 dendritic arborization and increases vulnerability to excitotoxicity.}, journal = {Experimental Neurology}, volume = {241}, year = {2013}, month = {2013 Mar}, pages = {5-12}, abstract = {

Chronic immobilization stress (CIS) shortens apical dendritic trees of CA3 pyramidal neurons in the hippocampus of the male rat, and dendritic length may be a determinant of vulnerability to stress. Expression of the polysialylated form of neural cell adhesion molecule (PSA-NCAM) in the hippocampal formation is increased by stress, while PSA removal by Endo-neuraminidase-N (endo-N) is known to cause the mossy fibers to defasciculate and synapse ectopically in their CA3 target area. We show here that enzymatic removal of PSA produced a remarkable expansion of dendritic arbors of CA3 pyramidal neurons, with a lesser effect in CA1. This expansion eclipsed the CIS-induced shortening of CA3 dendrites, with the expanded dendrites of both no-stress-endo-N and CIS-endo-N rats being longer than those in no-stress-control rats and much longer than those in CIS-control rats. As predicted by the hypothesis that endo-N-induced dendritic expansion might increase vulnerability to excitotoxic challenge, systemic injection with kainic acid, showed markedly increased neuronal degeneration, as assessed by fluorojade B histochemistry, in rats that had been treated with endo-N compared to vehicle-treated rats throughout the entire hippocampal formation. PSA removal also exacerbated the CIS-induced reduction in body weight and abolished effects of CIS on NPY and NR2B mRNA levels. These findings support the hypothesis that CA3 arbor plasticity plays a protective role during prolonged stress and clarify the role of PSA-NCAM in stress-induced dendritic plasticity.

}, keywords = {Analysis of Variance, Animals, Body Mass Index, CA3 Region, Hippocampal, Dendrites, Disease Models, Animal, Excitatory Amino Acid Agonists, Fluoresceins, Gene Expression Regulation, Kainic Acid, Male, Metalloendopeptidases, Nerve Degeneration, Neural Cell Adhesion Molecules, Organic Chemicals, Pyramidal Cells, Rats, Rats, Sprague-Dawley, Receptors, N-Methyl-D-Aspartate, Sialic Acids, Silver Staining, Stress, Psychological}, issn = {1090-2430}, doi = {10.1016/j.expneurol.2012.11.028}, author = {McCall, Trudy and Weil, Zachary M and Nacher, Juan and Bloss, Erik B and El Maarouf, Abderrahman and Rutishauser, Urs and McEwen, Bruce S} } @article {6285, title = {Dfam: a database of repetitive DNA based on profile hidden Markov models.}, journal = {Nucleic Acids Research}, volume = {41}, year = {2013}, month = {2013 Jan}, pages = {D70-82}, abstract = {

We present a database of repetitive DNA elements, called Dfam (http://dfam.janelia.org). Many genomes contain a large fraction of repetitive DNA, much of which is made up of remnants of transposable elements (TEs). Accurate annotation of TEs enables research into their biology and can shed light on the evolutionary processes that shape genomes. Identification and masking of TEs can also greatly simplify many downstream genome annotation and sequence analysis tasks. The commonly used TE annotation tools RepeatMasker and Censor depend on sequence homology search tools such as cross_match and BLAST variants, as well as Repbase, a collection of known TE families each represented by a single consensus sequence. Dfam contains entries corresponding to all Repbase TE entries for which instances have been found in the human genome. Each Dfam entry is represented by a profile hidden Markov model, built from alignments generated using RepeatMasker and Repbase. When used in conjunction with the hidden Markov model search tool nhmmer, Dfam produces a 2.9\% increase in coverage over consensus sequence search methods on a large human benchmark, while maintaining low false discovery rates, and coverage of the full human genome is 54.5\%. The website provides a collection of tools and data views to support improved TE curation and annotation efforts. Dfam is also available for download in flat file format or in the form of MySQL table dumps.

}, keywords = {Databases, DNA Transposable Elements, Genome, Human, Humans, Internet, Markov Chains, Models, Molecular Sequence Annotation, Nucleic Acid, Statistical}, issn = {1362-4962}, doi = {10.1093/nar/gks1265}, author = {Wheeler, Travis J and Clements, Jody and Eddy, Sean R. and Hubley, Robert and Jones, Thomas A and Jurka, Jerzy and Smit, Arian F A and Finn, Robert D} } @article {6325, title = {Direct detection pays off for electron cryo-microscopy.}, journal = {eLife}, volume = {2}, year = {2013}, month = {2013 Feb 19}, pages = {e00573}, abstract = {

Improved electron detectors and image-processing techniques will allow the structures of macromolecules to be determined from tens of thousands of single-particle cryo-EM images, rather than the hundreds of thousands needed previously.

}, issn = {2050-084X}, doi = {10.7554/eLife.00573}, author = {Grigorieff, Nikolaus} } @article {46707, title = {Direct observation of frequency modulated transcription in single cells using light activation.}, journal = {eLife}, volume = {2}, year = {2013}, month = {2013 Sep 24}, pages = {e00750}, abstract = {

Single-cell analysis has revealed that transcription is dynamic and stochastic, but tools are lacking that can determine the mechanism operating at a single gene. Here we utilize single-molecule observations of RNA in fixed and living cells to develop a single-cell model of steroid-receptor mediated gene activation. We determine that steroids drive mRNA synthesis by frequency modulation of transcription. This digital behavior in single cells gives rise to the well-known analog dose response across the population. To test this model, we developed a light-activation technology to turn on a single steroid-responsive gene and follow dynamic synthesis of RNA from the activated locus. DOI:http://dx.doi.org/10.7554/eLife.00750.001.

}, issn = {2050-084X}, doi = {10.7554/eLife.00750}, author = {Larson, Daniel R and Fritzsch, Christoph and Sun, Liang and Meng, Xiuhau and Lawrence, David S and Singer, Robert H} } @article {6275, title = {A directional tuning map of Drosophila elementary motion detectors.}, journal = {Nature}, volume = {500}, year = {2013}, month = {2013 Aug 8}, pages = {212-6}, abstract = {

The extraction of directional motion information from changing retinal images is one of the earliest and most important processing steps in any visual system. In the fly optic lobe, two parallel processing streams have been anatomically described, leading from two first-order interneurons, L1 and L2, via T4 and T5 cells onto large, wide-field motion-sensitive interneurons of the lobula plate. Therefore, T4 and T5 cells are thought to have a pivotal role in motion processing; however, owing to their small size, it is difficult to obtain electrical recordings of T4 and T5 cells, leaving their visual response properties largely unknown. We circumvent this problem by means of optical recording from these cells in Drosophila, using the genetically encoded calcium indicator GCaMP5 (ref. 2). Here we find that specific subpopulations of T4 and T5 cells are directionally tuned to one of the four cardinal directions; that is, front-to-back, back-to-front, upwards and downwards. Depending on their preferred direction, T4 and T5 cells terminate in specific sublayers of the lobula plate. T4 and T5 functionally segregate with respect to contrast polarity: whereas T4 cells selectively respond to moving brightness increments (ON edges), T5 cells only respond to moving brightness decrements (OFF edges). When the output from T4 or T5 cells is blocked, the responses of postsynaptic lobula plate neurons to moving ON (T4 block) or OFF edges (T5 block) are selectively compromised. The same effects are seen in turning responses of tethered walking flies. Thus, starting with L1 and L2, the visual input is split into separate ON and OFF pathways, and motion along all four cardinal directions is computed separately within each pathway. The output of these eight different motion detectors is then sorted such that ON (T4) and OFF (T5) motion detectors with the same directional tuning converge in the same layer of the lobula plate, jointly providing the input to downstream circuits and motion-driven behaviours.

}, keywords = {Animal, Animals, Behavior, Drosophila, Interneurons, Locomotion, Motion Perception, Neurons, Signal Transduction, Visual Pathways}, issn = {1476-4687}, doi = {10.1038/nature12320}, author = {Maisak, Matthew S and Haag, Juergen and Ammer, Georg and Serbe, Etienne and Meier, Matthias and Leonhardt, Aljoscha and Schilling, Tabea and Bahl, Armin and Rubin, Gerald M and Nern, Aljoscha and Dickson, Barry J and Reiff, Dierk F and Hopp, Elisabeth and Borst, Alexander} } @article {6447, title = {Distance preserving embeddings for general n-dimensional manifolds.}, journal = {Journal of Machine Learning Research}, volume = {14}, year = {2013}, month = {2013 Aug}, pages = {2415-48}, author = {Verma, N} } @article {6100, title = {A distance-field based automatic neuron tracing method.}, journal = {BMC Bioinformatics}, volume = {14}, year = {2013}, month = {2013 Mar 12}, pages = {93}, abstract = {

Automatic 3D digital reconstruction (tracing) of neurons embedded in noisy microscopic images is challenging, especially when the cell morphology is complex.

}, issn = {1471-2105}, doi = {10.1186/1471-2105-14-93}, author = {Yang, Jinzhu and Gonzalez-Bellido, Paloma T and Peng, Hanchuan} } @article {6588, title = {Distinct balance of excitation and inhibition in an interareal feedforward and feedback circuit of mouse visual cortex.}, journal = {The Journal of Neuroscience}, volume = {33}, year = {2013}, month = {2013 Oct 30}, pages = {17373-84}, abstract = {

Mouse visual cortex is subdivided into multiple distinct, hierarchically organized areas that are interconnected through feedforward (FF) and feedback (FB) pathways. The principal synaptic targets of FF and FB axons that reciprocally interconnect primary visual cortex (V1) with the higher lateromedial extrastriate area (LM) are pyramidal cells (Pyr) and parvalbumin (PV)-expressing GABAergic interneurons. Recordings in slices of mouse visual cortex have shown that layer 2/3 Pyr cells receive excitatory monosynaptic FF and FB inputs, which are opposed by disynaptic inhibition. Most notably, inhibition is stronger in the FF than FB pathway, suggesting pathway-specific organization of feedforward inhibition (FFI). To explore the hypothesis that this difference is due to diverse pathway-specific strengths of the inputs to PV neurons we have performed subcellular Channelrhodopsin-2-assisted circuit mapping in slices of mouse visual cortex. Whole-cell patch-clamp recordings were obtained from retrobead-labeled FFV1{\textrightarrow}LM- and FBLM{\textrightarrow}V1-projecting Pyr cells, as well as from tdTomato-expressing PV neurons. The results show that the FFV1{\textrightarrow}LM pathway provides on average 3.7-fold stronger depolarizing input to layer 2/3 inhibitory PV neurons than to neighboring excitatory Pyr cells. In the FBLM{\textrightarrow}V1 pathway, depolarizing inputs to layer 2/3 PV neurons and Pyr cells were balanced. Balanced inputs were also found in the FFV1{\textrightarrow}LM pathway to layer 5 PV neurons and Pyr cells, whereas FBLM{\textrightarrow}V1 inputs to layer 5 were biased toward Pyr cells. The findings indicate that FFI in FFV1{\textrightarrow}LM and FBLM{\textrightarrow}V1 circuits are organized in a pathway- and lamina-specific fashion.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2515-13.2013}, author = {Yang, Weiguo and Carrasquillo, Yarimar and Hooks, Bryan M and Nerbonne, Jeanne M and Burkhalter, Andreas} } @article {6277, title = {Diverse neuronal lineages make stereotyped contributions to the Drosophila locomotor control center, the central complex.}, journal = {The Journal of Comparative Neurology}, volume = {521}, year = {2013}, month = {2013 Aug 15}, pages = {2645-62, Spc1}, abstract = {

The Drosophila central brain develops from a fixed number of neuroblasts. Each neuroblast makes a clone of neurons that exhibit common trajectories. Here we identified 15 distinct clones that carry larval-born neurons innervating the Drosophila central complex (CX), which consists of four midline structures including the protocerebral bridge (PB), fan-shaped body (FB), ellipsoid body (EB), and noduli (NO). Clonal analysis revealed that the small-field CX neurons, which establish intricate projections across different CX substructures, exist in four isomorphic groups that respectively derive from four complex posterior asense-negative lineages. In terms of the region-characteristic large-field CX neurons, we found that two lineages make PB neurons, 10 lineages produce FB neurons, three lineages generate EB neurons, and two lineages yield NO neurons. The diverse FB developmental origins reflect the discrete input pathways for different FB subcompartments. Clonal analysis enlightens both development and anatomy of the insect locomotor control center.

}, issn = {1096-9861}, doi = {10.1002/cne.23339}, author = {Yang, Jacob S and Awasaki, Takeshi and Yu, Hung-Hsiang and He, Yisheng and Ding, Peng and Kao, Jui-Chun and Lee, Tzumin} } @article {6846, title = {Dual functions of TAF7L in adipocyte differentiation.}, journal = {eLife}, volume = {2}, year = {2013}, month = {2013 Jan 8}, pages = {e00170}, abstract = {

The diverse transcriptional mechanisms governing cellular differentiation and development of mammalian tissue remains poorly understood. Here we report that TAF7L, a paralogue of TFIID subunit TAF7, is enriched in adipocytes and white fat tissue (WAT) in mouse. Depletion of TAF7L reduced adipocyte-specific gene expression, compromised adipocyte differentiation, and WAT development as well. Ectopic expression of TAF7L in myoblasts reprograms these muscle precursors into adipocytes upon induction. Genome-wide mRNA-seq expression profiling and ChIP-seq binding studies confirmed that TAF7L is required for activating adipocyte-specific genes via a dual mechanism wherein it interacts with PPARγ at enhancers and TBP/Pol II at core promoters. In vitro binding studies confirmed that TAF7L forms complexes with both TBP and PPARγ. These findings suggest that TAF7L plays an integral role in adipocyte gene expression by targeting enhancers as a cofactor for PPARγ and promoters as a component of the core transcriptional machinery.DOI:http://dx.doi.org/10.7554/eLife.00170.001.

}, issn = {2050-084X}, doi = {10.7554/eLife.00170}, author = {Zhou, Haiying and Kaplan, Tommy and Li, Yan and Grubisic, Ivan and Zhang, Zhengjian and Wang, P Jeremy and Eisen, Michael B and Tjian, Robert} } @article {47900, title = {Dynamic Bayesian clustering.}, journal = {Journal of bioinformatics and computational biology}, volume = {11}, year = {2013}, month = {2013 Oct}, pages = {1342001}, abstract = {

Clusters of time series data may change location and memberships over time; in gene expression data, this occurs as groups of genes or samples respond differently to stimuli or experimental conditions at different times. In order to uncover this underlying temporal structure, we consider dynamic clusters with time-dependent parameters which split and merge over time, enabling cluster memberships to change. These interesting time-dependent structures are useful in understanding the development of organisms or complex organs, and could not be identified using traditional clustering methods. In cell cycle data, these time-dependent structure may provide links between genes and stages of the cell cycle, whilst in developmental data sets they may highlight key developmental transitions.

}, keywords = {Algorithms, Animals, Bayes Theorem, Brain, Cell Cycle, Cluster Analysis, Computational Biology, Databases, Genetic, Gene Expression Regulation, Developmental, Markov Chains, Mice, Models, Statistical, Monte Carlo Method}, issn = {1757-6334}, doi = {10.1142/S0219720013420018}, author = {Fowler, Anna and Menon, Vilas and Heard, Nicholas A} } @article {5523, title = {Eight pairs of descending visual neurons in the dragonfly give wing motor centers accurate population vector of prey direction.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, year = {2013}, month = {2013 Jan 8}, pages = {696-701}, chapter = {696}, abstract = {

Intercepting a moving object requires prediction of its future location. This complex task has been solved by dragonflies, who intercept their prey in midair with a 95\% success rate. In this study, we show that a group of 16 neurons, called target-selective descending neurons (TSDNs), code a population vector that reflects the direction of the target with high accuracy and reliability across 360{\textdegree}. The TSDN spatial (receptive field) and temporal (latency) properties matched the area of the retina where the prey is focused and the reaction time, respectively, during predatory flights. The directional tuning curves and morphological traits (3D tracings) for each TSDN type were consistent among animals, but spike rates were not. Our results emphasize that a successful neural circuit for target tracking and interception can be achieved with few neurons and that in dragonflies this information is relayed from the brain to the wing motor centers in population vector form.

}, issn = {1091-6490}, doi = {10.1073/pnas.1210489109}, author = {Gonzalez-Bellido, Paloma T and Peng, Hanchuan and Yang, Jinzhu and Georgopoulos, Apostolos P and Olberg, Robert M} } @article {6274, title = {Electron cryotomography of ESCRT assemblies and dividing Sulfolobus cells suggests that spiraling filaments are involved in membrane scission.}, journal = {Molecular Biology of the Cell}, volume = {24}, year = {2013}, month = {2013 Aug}, pages = {2319-27}, abstract = {

The endosomal-sorting complex required for transport (ESCRT) is evolutionarily conserved from Archaea to eukaryotes. The complex drives membrane scission events in a range of processes, including cytokinesis in Metazoa and some Archaea. CdvA is the protein in Archaea that recruits ESCRT-III to the membrane. Using electron cryotomography (ECT), we find that CdvA polymerizes into helical filaments wrapped around liposomes. ESCRT-III proteins are responsible for the cinching of membranes and have been shown to assemble into helical tubes in vitro, but here we show that they also can form nested tubes and nested cones, which reveal surprisingly numerous and versatile contacts. To observe the ESCRT-CdvA complex in a physiological context, we used ECT to image the archaeon Sulfolobus acidocaldarius and observed a distinct protein belt at the leading edge of constriction furrows in dividing cells. The known dimensions of ESCRT-III proteins constrain their possible orientations within each of these structures and point to the involvement of spiraling filaments in membrane scission.

}, issn = {1939-4586}, doi = {10.1091/mbc.E12-11-0785}, author = {Dobro, Megan J and Samson, Rachel Y and Yu, Zhiheng and McCullough, John and Ding, H Jane and Chong, Parkson Lee-Gau and Bell, Stephen D and Jensen, Grant J} } @article {6676, title = {Electron microscopy reconstruction of brain structure using sparse representations over learned dictionaries.}, journal = {IEEE Transactions on Medical Imaging}, volume = {32}, year = {2013}, month = {2013 Aug 2}, pages = {2179-88}, abstract = {

A central problem in neuroscience is reconstructing neuronal circuits on the synapse level. Due to a wide range of scales in brain architecture such reconstruction requires imaging that is both high-resolution and high-throughput. Existing electron microscopy (EM) techniques possess required resolution in the lateral plane and either high-throughput or high depth resolution but not both. Here, we exploit recent advances in unsupervised learning and signal processing to obtain high depth-resolution EM images computationally without sacrificing throughput. First, we show that the brain tissue can be represented as a sparse linear combination of localized basis functions that are learned using high-resolution datasets. We then develop compressive sensing-inspired techniques that can reconstruct the brain tissue from very few (typically 5) tomographic views of each section. This enables tracing of neuronal processes and, hence, high throughput reconstruction of neural circuits on the level of individual synapses.

}, issn = {1558-254X}, doi = {10.1109/TMI.2013.2276018}, author = {Hu, Tao and Nunez-Iglesias, Juan and Vitaladevuni, Shiv and Scheffer, Lou and Xu, Shan and Bolorizadeh, Mehdi and Hess, Harald and Fetter, Richard and Chklovskii, Dmitri} } @article {6287, title = {The ENCODE project: missteps overshadowing a success.}, journal = {Current Biology}, volume = {23}, year = {2013}, month = {2013 Apr 8}, pages = {R259-61}, abstract = {

Two clich{\'e}s of science journalism have now played out around the ENCODE project. ENCODE{\textquoteright}s publicity first presented a misleading "all the textbooks are wrong" narrative about noncoding human DNA. Now several critiques of ENCODE{\textquoteright}s narrative have been published, and one was so vitriolic that it fueled "undignified academic squabble" stories that focused on tone more than substance. Neither story line does justice to our actual understanding of genomes, to ENCODE{\textquoteright}s results, or to the role of big science in biology.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2013.03.023}, author = {Eddy, Sean R.} } @article {6270, title = {Essential role of the mushroom body in context-dependent CO2 avoidance in Drosophila.}, journal = {Current Biology}, volume = {23}, year = {2013}, month = {2013 Jul 8}, pages = {1228-34}, abstract = {

Internal state as well as environmental conditions influence choice behavior. The neural circuits underpinning state-dependent behavior remain largely unknown. Carbon dioxide (CO2) is an important olfactory cue for many insects, including mosquitoes, flies, moths, and honeybees [1]. Concentrations of CO2 higher than 0.02\% above atmospheric level trigger a strong innate avoidance in the fly Drosophila melanogaster [2, 3]. Here, we show that the mushroom body (MB), a brain center essential for olfactory associative memories [4-6] but thought to be dispensable for innate odor processing [7], is essential for CO2 avoidance behavior only in the context of starvation or in the context of a food-related odor. Consistent with this, CO2 stimulation elicits Ca(2+) influx into the MB intrinsic cells (Kenyon cells: KCs) in\ vivo. We identify an atypical projection neuron (bilateral ventral projection neuron, biVPN) that connects CO2 sensory input bilaterally to the MB calyx. Blocking synaptic output of the biVPN completely abolishes CO2 avoidance in food-deprived flies, but not in fed flies. These findings show that two alternative neural pathways control innate choice behavior, and they are dependent on the animal{\textquoteright}s internal state. In addition, they suggest that, during innate choice behavior, the MB serves as an integration site for internal state and olfactory input.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2013.05.029}, author = {Br{\"a}cker, Lasse B and Siju, K P and Varela, N{\'e}lia and Aso, Yoshinori and Zhang, Mo and Hein, Irina and Vasconcelos, Maria Lu{\'\i}sa and Grunwald Kadow, Ilona C} } @article {46709, title = {Eukaryotic transcriptional dynamics: from single molecules to cell populations.}, journal = {Nature Reviews Genetics}, volume = {14}, year = {2013}, month = {2013 Aug}, pages = {572-84}, abstract = {

Transcriptional regulation is achieved through combinatorial interactions between regulatory elements in the human genome and a vast range of factors that modulate the recruitment and activity of RNA polymerase. Experimental approaches for studying transcription in vivo now extend from single-molecule techniques to genome-wide measurements. Parallel to these developments is the need for testable quantitative and predictive models for understanding gene regulation. These conceptual models must also provide insight into the dynamics of transcription and the variability that is observed at the single-cell level. In this Review, we discuss recent results on transcriptional regulation and also the models those results engender. We show how a non-equilibrium description informs our view of transcription by explicitly considering time- and energy-dependence at the molecular level.

}, keywords = {DNA-Directed RNA Polymerases, Gene Expression Regulation, Genome, Human, Humans, Transcription Factors, Transcription, Genetic}, issn = {1471-0064}, doi = {10.1038/nrg3484}, author = {Coulon, Antoine and Chow, Carson C and Singer, Robert H and Larson, Daniel R} } @article {46599, title = {The evolution of Drosophila melanogaster as a model for alcohol research.}, journal = {Annual Reviews of Neuroscience}, volume = {36}, year = {2013}, month = {2013 Jul 8}, pages = {121-38}, abstract = {

Animal models have been widely used to gain insight into the mechanisms underlying the acute and long-term effects of alcohol exposure. The fruit fly Drosophila melanogaster encounters ethanol in its natural habitat and possesses many adaptations that allow it to survive and thrive in ethanol-rich environments. Several assays to study ethanol-related behaviors in flies, ranging from acute intoxication to self-administration and reward, have been developed in the past 20 years. These assays have provided the basis for studying the physiological and behavioral effects of ethanol and for identifying genes mediating these effects. In this review we describe the ecological relationship between flies and ethanol, the effects of ethanol on fly development and behavior, the use of flies as a model for alcohol addiction, and the interaction between ethanol and social behavior. We discuss these advances in the context of their utility to help decipher the mechanisms underlying the diverse effects of ethanol, including those that mediate ethanol dependence and addiction in humans.

}, keywords = {Alcoholism, Animals, Biological Evolution, Disease Models, Animal, Drosophila melanogaster, Ethanol, Humans, Reward, Self Administration}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-062012-170256}, author = {Devineni, Anita V and Heberlein, Ulrike} } @conference {48833, title = {Extracting regions of interest from biological images with convolutional sparse block coding.}, booktitle = {Neural Information Processing Systems (NIPS 2013)}, year = {2013}, month = {2013 Dec 05}, address = {Lake Tahoe}, abstract = {

Biological tissue is often composed of cells with similar morphologies replicated throughout large volumes and many biological applications rely on the accurate identification of these cells and their locations from image data. Here we develop a generative model that captures the regularities present in images composed of repeating elements of a few different types. Formally, the model can be described as convolutional sparse block coding. For inference we use a variant of convolutional matching pursuit adapted to block-based representations. We extend the K-SVD learning algorithm to subspaces by retaining several principal vectors from the SVD decomposition instead of just one. Good models with little cross-talk between subspaces can be obtained by learning the blocks incrementally. We perform extensive experiments on simulated images and the inference algorithm consistently recovers a large proportion of the cells with a small number of false positives. We fit the convolutional model to noisy GCaMP6 two-photon images of spiking neurons and to Nissl-stained slices of cortical tissue and show that it recovers cell body locations without supervision. The flexibility of the block-based representation is reflected in the variability of the recovered cell shapes.

}, url = {http://papers.nips.cc/paper/5167-extracting-regions-of-interest-from-biological-images-with-convolutional-sparse-block-coding}, author = {Pachitariu, Marius and Packer, Adam M and Pettit, Noah and Dalgleish, Henry and H{\"a}usser, Michael and Sahani, Maneesh} } @article {6454, title = {Extremes of lineage plasticity in the Drosophila brain.}, journal = {Current Biology}, volume = {23}, year = {2013}, month = {2013 Sep 19}, pages = {1908-13}, abstract = {

An often-overlooked aspect of neural plasticity is the plasticity of neuronal composition, in which the numbers of neurons of particular classes are altered in response to environment and experience. The Drosophila brain features several well-characterized lineages in which a single neuroblast gives rise to multiple neuronal classes in a stereotyped sequence during development [1]. We find that in the\ intrinsic mushroom body neuron lineage, the numbers for each class are highly plastic, depending on the timing of temporal fate transitions and the rate of neuroblast proliferation. For example, mushroom body neuroblast cycling can continue under starvation conditions, uncoupled from\ temporal fate transitions that depend on extrinsic cues reflecting organismal growth and development. In contrast, the proliferation rates of antennal lobe lineages are closely associated with organismal development, and\ their temporal fate changes appear to be cell cycle-dependent, such that the same numbers and types of uniglomerular projection neurons innervate the antennal lobe following various perturbations. We propose that this surprising difference in plasticity for these brain lineages is adaptive, given their respective roles as parallel\ processors versus discrete carriers of olfactory information.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2013.07.074}, author = {Lin, Suewei and Marin, Elizabeth C and Yang, Ching-Po and Kao, Chih-Fei and Apenteng, Bettye A and Huang, Yaling and O{\textquoteright}Connor, Michael B and Truman, James W and Lee, Tzumin} } @article {5536, title = {Fast and robust optical flow for time-lapse microscopy using super-voxels.}, journal = {Bioinformatics}, volume = {29}, year = {2013}, month = {2013 Feb}, pages = {373-80}, abstract = {

Optical flow is a key method used for quantitative motion estimation of biological structures in light microscopy. It has also been used as a key module in segmentation and tracking systems and is considered a mature technology in the field of computer vision. However, most of the research focused on 2D natural images, which are small in size and rich in edges and texture information. In contrast, 3D time-lapse recordings of biological specimens comprise up to several terabytes of image data and often exhibit complex object dynamics as well as blurring due to the point-spread-function of the microscope. Thus, new approaches to optical flow are required to improve performance for such data. We solve optical flow in large 3D time-lapse microscopy datasets by defining a Markov random field (MRF) over super-voxels in the foreground and applying motion smoothness constraints between super-voxels instead of voxel-wise. This model is tailored to the specific characteristics of light microscopy datasets: super-voxels help registration in textureless areas, the MRF over super-voxels efficiently propagates motion information between neighboring cells and the background subtraction and super-voxels reduce the dimensionality of the problem by an order of magnitude. We validate our approach on large 3D time-lapse datasets of Drosophila and zebrafish development by analyzing cell motion patterns. We show that our approach is, on average, 10x faster than commonly used optical flow implementations in the Insight Tool-Kit (ITK) and reduces the average flow end point error by 50\% in regions with complex dynamic processes, such as cell divisions.

}, issn = {1367-4811}, doi = {10.1093/bioinformatics/bts706}, author = {Amat, Fernando and Myers, Eugene W and Keller, Philipp J} } @article {5522, title = {Fast multicolor 3D imaging using aberration-corrected multifocus microscopy.}, journal = {Nature Methods}, volume = {10}, year = {2013}, month = {2013}, pages = {60-3}, abstract = {

Conventional acquisition of three-dimensional (3D) microscopy data requires sequential z scanning and is often too slow to capture biological events. We report an aberration-corrected multifocus microscopy method capable of producing an instant focal stack of nine 2D images. Appended to an epifluorescence microscope, the multifocus system enables high-resolution 3D imaging in multiple colors with single-molecule sensitivity, at speeds limited by the camera readout time of a single image.

}, issn = {1548-7105}, doi = {10.1038/nmeth.2277}, author = {Abrahamsson, Sara and Chen, Jiji and Hajj, Bassam and Stallinga, Sjoerd and Katsov, Alexander Y and Wisniewski, Jan and Mizuguchi, Gaku and Soule, Pierre and Mueller, Florian and Darzacq, Claire Dugast and Darzacq, Xavier and Wu, Carl and Bargmann, Cornelia I and Agard, David A and Dahan, Maxime and Gustafsson, Mats G L} } @article {6669, title = {Fast structural responses of gap junction membrane domains to AB5 toxins.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, year = {2013}, month = {2013 Oct 29}, pages = {E4125-33}, abstract = {

Gap junctions (GJs) represent connexin-rich membrane domains that connect interiors of adjoining cells in mammalian tissues. How fast GJs can respond to bacterial pathogens has not been known previously. Using Bessel beam plane illumination and confocal spinning disk microscopy, we found fast (\ 500 ms) formation of connexin-depleted regions (CDRs) inside GJ plaques between cells exposed to AB5 toxins. CDR formation appears as a fast redistribution of connexin channels within GJ plaques with minor changes in outline or geometry. CDR formation does not depend on membrane trafficking or submembrane cytoskeleton and has no effect on GJ conductance. However, CDR responses depend on membrane lipids, can be modified by cholesterol-clustering agents and extracellular K(+) ion concentration, and influence cAMP signaling. The CDR response of GJ plaques to bacterial toxins is a phenomenon observed for all tested connexin isoforms. Through signaling, the CDR response may enable cells to sense exposure to AB5 toxins. CDR formation may reflect lipid-phase separation events in the biological membrane of the GJ plaque, leading to increased connexin packing and lipid reorganization. Our data demonstrate very fast dynamics (in the millisecond-to-second range) within GJ plaques, which previously were considered to be relatively stable, long-lived structures.

}, issn = {1091-6490}, doi = {10.1073/pnas.1315850110}, author = {Majoul, Irina V and Gao, Liang and Betzig, Eric and Onichtchouk, Daria and Butkevich, Eugenia and Kozlov, Yuri and Bukauskas, Feliksas and Bennett, Michael V L and Lippincott-Schwartz, Jennifer and Duden, Rainer} } @article {47637, title = {Fast structural responses of gap junction membrane domains to AB5 toxins.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, year = {2013}, month = {2013 Oct 29}, pages = {E4125-33}, abstract = {

Gap junctions (GJs) represent connexin-rich membrane domains that connect interiors of adjoining cells in mammalian tissues. How fast GJs can respond to bacterial pathogens has not been known previously. Using Bessel beam plane illumination and confocal spinning disk microscopy, we found fast (~500 ms) formation of connexin-depleted regions (CDRs) inside GJ plaques between cells exposed to AB5 toxins. CDR formation appears as a fast redistribution of connexin channels within GJ plaques with minor changes in outline or geometry. CDR formation does not depend on membrane trafficking or submembrane cytoskeleton and has no effect on GJ conductance. However, CDR responses depend on membrane lipids, can be modified by cholesterol-clustering agents and extracellular K(+) ion concentration, and influence cAMP signaling. The CDR response of GJ plaques to bacterial toxins is a phenomenon observed for all tested connexin isoforms. Through signaling, the CDR response may enable cells to sense exposure to AB5 toxins. CDR formation may reflect lipid-phase separation events in the biological membrane of the GJ plaque, leading to increased connexin packing and lipid reorganization. Our data demonstrate very fast dynamics (in the millisecond-to-second range) within GJ plaques, which previously were considered to be relatively stable, long-lived structures.

}, keywords = {Analysis of Variance, Animals, Bacterial Toxins, Bicyclo Compounds, Heterocyclic, Cercopithecus aethiops, Connexins, Cyclic AMP, DNA Primers, Filipin, Fluorescence, Gap Junctions, Image Processing, Computer-Assisted, Membrane Lipids, Microscopy, Confocal, Patch-Clamp Techniques, Potassium, Thiazolidines, Vero Cells}, issn = {1091-6490}, doi = {10.1073/pnas.1315850110}, author = {Majoul, Irina V and Gao, Liang and Betzig, Eric and Onichtchouk, Daria and Butkevich, Eugenia and Kozlov, Yuri and Bukauskas, Feliksas and Bennett, Michael V L and Lippincott-Schwartz, Jennifer and Duden, Rainer} } @article {46714, title = {The fate of the messenger is pre-determined: a new model for regulation of gene expression.}, journal = {Biochimica et Biophysica Acta (BBA)}, volume = {1829}, year = {2013}, month = {2013 Jun-Jul}, pages = {643-53}, abstract = {

Recent years have seen a rise in publications demonstrating coupling between transcription and mRNA decay. This coupling most often accompanies cellular processes that involve transitions in gene expression patterns, for example during mitotic division and cellular differentiation and in response to cellular stress. Transcription can affect the mRNA fate by multiple mechanisms. The most novel finding is the process of co-transcriptional imprinting of mRNAs with proteins, which in turn regulate cytoplasmic mRNA stability. Transcription therefore is not only a catalyst of mRNA synthesis but also provides a platform that enables imprinting, which coordinates between transcription and mRNA decay. Here we present an overview of the literature, which provides the evidence of coupling between transcription and decay, review the mechanisms and regulators by which the two processes are coupled, discuss why such coupling is beneficial and present a new model for regulation of gene expression. This article is part of a Special Issue entitled: RNA Decay mechanisms.

}, keywords = {Cytoplasm, Gene Expression Regulation, Fungal, Genomic Imprinting, Humans, Poly(A)-Binding Proteins, Ribonucleases, RNA Polymerase II, RNA Stability, RNA, Messenger, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription, Genetic}, issn = {0006-3002}, doi = {10.1016/j.bbagrm.2013.01.004}, author = {Haimovich, Gal and Choder, Mordechai and Singer, Robert H and Trcek, Tatjana} } @article {6481, title = {Feature detection and orientation tuning in the Drosophila central complex.}, journal = {Nature}, volume = {503}, year = {2013}, month = {2013 Oct 9}, pages = {262-66}, abstract = {

Many animals, including insects, are known to use visual landmarks to orient in their environment. In Drosophila melanogaster, behavioural genetics studies have identified a higher brain structure called the central complex as being required for the fly{\textquoteright}s innate responses to vertical visual features and its short- and long-term memory for visual patterns. But whether and how neurons of the fly central complex represent visual features are unknown. Here we use two-photon calcium imaging in head-fixed walking and flying flies to probe visuomotor responses of ring neurons{\textemdash}a class of central complex neurons that have been implicated in landmark-driven spatial memory in walking flies and memory for visual patterns in tethered flying flies. We show that dendrites of ring neurons are visually responsive and arranged retinotopically. Ring neuron receptive fields comprise both excitatory and inhibitory subfields, resembling those of simple cells in the mammalian primary visual cortex. Ring neurons show strong and, in some cases, direction-selective orientation tuning, with a notable preference for vertically oriented features similar to those that evoke innate responses in flies. Visual responses were diminished during flight, but, in contrast with the hypothesized role of the central complex in the control of locomotion, not modulated during walking. Taken together, these results indicate that ring neurons represent behaviourally relevant visual features in the fly{\textquoteright}s environment, enabling downstream central complex circuits to produce appropriate motor commands. More broadly, this study opens the door to mechanistic investigations of circuit computations underlying visually guided action selection in the Drosophila central complex.

}, issn = {1476-4687}, doi = {10.1038/nature12601}, author = {Seelig, Johannes D and Jayaraman, Vivek} } @article {6122, title = {Fine time-course expression analysis identifies cascades of activation and repression and maps a regulator of mammalian sex determination.}, journal = {PLoS Genetics}, volume = {9}, year = {2013}, month = {2013 Jul}, pages = {e1003630}, abstract = {

In vertebrates, primary sex determination refers to the decision within a bipotential organ precursor to differentiate as a testis or ovary. Bifurcation of organ fate begins between embryonic day (E) 11.0{\textendash}E12.0 in mice and likely involves a dynamic transcription network that is poorly understood. To elucidate the first steps of sexual fate specification, we profiled the XX and XY gonad transcriptomes at fine granularity during this period and resolved cascades of gene activation and repression. C57BL/6J (B6) XY gonads showed a consistent \ 5-hour delay in the activation of most male pathway genes and repression of female pathway genes relative to 129S1/SvImJ, which likely explains the sensitivity of the B6 strain to male-to-female sex reversal. Using this fine time course data, we predicted novel regulatory genes underlying expression QTLs (eQTLs) mapped in a previous study. To test predictions, we developed an in vitro gonad primary cell assay and optimized a lentivirus-based shRNA delivery method to silence candidate genes and quantify effects on putative targets. We provide strong evidence that Lmo4 (Lim-domain only 4) is a novel regulator of sex determination upstream of SF1 (Nr5a1), Sox9, Fgf9, and Col9a3. This approach can be readily applied to identify regulatory interactions in other systems.

}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1003630}, author = {Munger, Steven C. and Natarajan, Anirudh and Looger, Loren L and Ohler, Uwe and Capel, Blanche} } @article {6519, title = {The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective.}, journal = {RNA Biology}, volume = {10}, year = {2013}, month = {2013 Jul 1}, pages = {1185-96}, abstract = {

Any method for RNA secondary structure prediction is determined by four ingredients. The architecture is the choice of features implemented by the model (such as stacked basepairs, loop length distributions, etc.). The architecture determines the number of parameters in the model. The scoring scheme is the nature of those parameters (whether thermodynamic, probabilistic, or weights). The parameterization stands for the specific values assigned to the parameters. These three ingredients are referred to as "the model." The fourth ingredient is the folding algorithms used to predict plausible secondary structures given the model and the sequence of a structural RNA. Here, I make several unifying observations drawn from looking at more than 40 years of methods for RNA secondary structure prediction in the light of this classification. As a final observation, there seems to be a performance ceiling that affects all methods with complex architectures, a ceiling that impacts all scoring schemes with remarkable similarity. This suggests that modeling RNA secondary structure by using intrinsic sequence-based plausible "foldability" will require the incorporation of other forms of information in order to constrain the folding space and to improve prediction accuracy. This could give an advantage to probabilistic scoring systems since a probabilistic framework is a natural platform to incorporate different sources of information into one single inference problem.

}, issn = {1555-8584}, doi = {10.4161/rna.24971}, author = {Rivas, Elena} } @article {6133, title = {Functional labeling of neurons and their projections using the synthetic activity-dependent promoter E-SARE.}, journal = {Nature Methods}, volume = {10}, year = {2013}, month = {2013 Jul 14}, pages = {889-95}, abstract = {

Identifying the neuronal ensembles that respond to specific stimuli and mapping their projection patterns in living animals are fundamental challenges in neuroscience. To this end, we engineered a synthetic promoter, the enhanced synaptic activity-responsive element (E-SARE), that drives neuronal activity-dependent gene expression more potently than other existing immediate-early gene promoters. Expression of a drug-inducible Cre recombinase downstream of E-SARE enabled imaging of neuronal populations that respond to monocular visual stimulation and tracking of their long-distance thalamocortical projections in living mice. Targeted cell-attached recordings and calcium imaging of neurons in sensory cortices revealed that E-SARE reporter expression correlates with sensory-evoked neuronal activity at the single-cell level and is highly specific to the type of stimuli presented to the animals. This activity-dependent promoter can expand the repertoire of genetic approaches for high-resolution anatomical and functional analysis of neural circuits.

}, issn = {1548-7105}, doi = {10.1038/nmeth.2559}, author = {Kawashima, Takashi and Kitamura, Kazuo and Suzuki, Kanzo and Nonaka, Mio and Kamijo, Satoshi and Takemoto-Kimura, Sayaka and Kano, Masanobu and Okuno, Hiroyuki and Ohki, Kenichi and Bito, Haruhiko} } @article {6923, title = {Genetic and neural mechanisms that inhibit Drosophila from mating with other species.}, journal = {Cell}, volume = {154}, year = {2013}, month = {2013 Jul 3}, pages = {89-102}, abstract = {

Genetically hard-wired neural mechanisms must enforce behavioral reproductive isolation because interspecies courtship is rare even in sexually na{\"{\i}ve animals of most species. We find that the chemoreceptor Gr32a inhibits male D. melanogaster from courting diverse fruit fly species. Gr32a recognizes nonvolatile aversive cues present on these reproductively dead-end targets, and activity of Gr32a neurons is necessary and sufficient to inhibit interspecies courtship. Male-specific Fruitless (Fru(M)), a master regulator of courtship, also inhibits interspecies courtship. Gr32a and Fru(M) are not coexpressed, but Fru(M) neurons contact Gr32a neurons, suggesting that these genes influence a shared neural circuit that inhibits interspecies courtship. Gr32a and Fru(M) also suppress within-species intermale courtship, but we show that distinct mechanisms preclude sexual displays toward conspecific males and other species. Although this chemosensory pathway does not inhibit interspecies mating in D. melanogaster females, similar mechanisms appear to inhibit this behavior in many other male drosophilids.

}, keywords = {Animal, Animals, Cell Surface, Courtship, Drosophila, Drosophila melanogaster, Drosophila Proteins, Female, Genetic Speciation, Male, Mating Preference, Nerve Tissue Proteins, Neurons, Receptors, Transcription Factors}, issn = {1097-4172}, doi = {10.1016/j.cell.2013.06.008}, author = {Fan, Pu and Manoli, Devanand S and Ahmed, Osama M and Chen, Yi and Agarwal, Neha and Kwong, Sara and Cai, Allen G and Neitz, Jeffrey and Renslo, Adam and Baker, Bruce S and Shah, Nirao M} } @article {6477, title = {The genetic causes of convergent evolution.}, journal = {Nature Reviews Genetics}, volume = {14}, year = {2013}, month = {2013 Oct 9}, pages = {751-4}, type = {Review}, abstract = {

The evolution of phenotypic similarities between species, known as convergence, illustrates that populations can respond predictably to ecological challenges. Convergence often results from similar genetic changes, which can emerge in two ways: the evolution of similar or identical mutations in independent lineages, which is termed parallel evolution; and the evolution in independent lineages of alleles that are shared among populations, which I call collateral genetic evolution. Evidence for parallel and collateral evolution has been found in many taxa, and an emerging hypothesis is that they result from the fact that mutations in some genetic targets minimize pleiotropic effects while simultaneously maximizing adaptation. If this proves correct, then the molecular changes underlying adaptation might be more predictable than has been appreciated previously.

}, issn = {1471-0064}, doi = {10.1038/nrg3483advance online publication}, author = {Stern, David L} } @article {6126, title = {Genetically encoded calcium indicators and astrocyte calcium microdomains.}, journal = {The Neuroscientist : A Review Journal Bringing Neurobiology, Neurology and Psychiatry}, volume = {19}, year = {2013}, month = {2013 Jun}, pages = {274-91}, abstract = {

The discovery of intracellular Ca(2+) signals within astrocytes has changed our view of how these ubiquitous cells contribute to brain function. Classically thought merely to serve supportive functions, astrocytes are increasingly thought to respond to, and regulate, neurons. The use of organic Ca(2+) indicator dyes such as Fluo-4 and Fura-2 has proved instrumental in the study of astrocyte physiology. However, progress has recently been accelerated by the use of cytosolic and membrane targeted genetically encoded calcium indicators (GECIs). Herein, we review these recent findings, discuss why studying astrocyte Ca(2+) signals is important to understand brain function, and summarize work that led to the discovery of TRPA1 channel-mediated near-membrane Ca(2+) signals in astrocytes and their indirect neuromodulatory roles at inhibitory synapses in the CA1 stratum radiatum region of the hippocampus. We suggest that the use of membrane-targeted and cytosolic GECIs holds great promise to explore the diversity of Ca(2+) signals within single astrocytes and also to study diversity of function for astrocytes in different parts of the brain.

}, issn = {1089-4098}, doi = {10.1177/1073858412468794}, author = {Tong, Xiaoping and Shigetomi, Eiji and Looger, Loren L and Khakh, Baljit S.} } @article {6541, title = {Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics.}, journal = {Frontiers in Molecular Neuroscience}, volume = {6}, year = {2013}, month = {2013 Mar 4}, pages = {2}, abstract = {

Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Here we describe red, single-wavelength GECIs, "RCaMPs," engineered from circular permutation of the thermostable red fluorescent protein mRuby. High-resolution crystal structures of mRuby, the red sensor RCaMP, and the recently published red GECI R-GECO1 give insight into the chromophore environments of the Ca(2+)-bound state of the sensors and the engineered protein domain interfaces of the different indicators. We characterized the biophysical properties and performance of RCaMP sensors in vitro and in vivo in Caenorhabditis elegans, Drosophila larvae, and larval zebrafish. Further, we demonstrate 2-color calcium imaging both within the same cell (registering mitochondrial and somatic [Ca(2+)]) and between two populations of cells: neurons and astrocytes. Finally, we perform integrated optogenetics experiments, wherein neural activation via channelrhodopsin-2 (ChR2) or a red-shifted variant, and activity imaging via RCaMP or GCaMP, are conducted simultaneously, with the ChR2/RCaMP pair providing independently addressable spectral channels. Using this paradigm, we measure calcium responses of naturalistic and ChR2-evoked muscle contractions in vivo in crawling C. elegans. We systematically compare the RCaMP sensors to R-GECO1, in terms of action potential-evoked fluorescence increases in neurons, photobleaching, and photoswitching. R-GECO1 displays higher Ca(2+) affinity and larger dynamic range than RCaMP, but exhibits significant photoactivation with blue and green light, suggesting that integrated channelrhodopsin-based optogenetics using R-GECO1 may be subject to artifact. Finally, we create and test blue, cyan, and yellow variants engineered from GCaMP by rational design. This engineered set of chromatic variants facilitates new experiments in functional imaging and optogenetics.

}, issn = {1662-5099}, doi = {10.3389/fnmol.2013.00002}, author = {Akerboom, Jasper and Carreras Calder{\'o}n, Nicole and Tian, Lin and Wabnig, Sebastian and Prigge, Matthias and Tol{\"o}, Johan and Gordus, Andrew and Orger, Michael B. and Severi, Kristen E and Macklin, John J and Patel, Ronak and Pulver, Stefan R and Wardill, Trevor J. and Fischer, Elisabeth and Sch{\"u}ler, Christina and Chen, Tsai-Wen and Sarkisyan, Karen S and Marvin, Jonathan S and Bargmann, Cornelia I and Kim, Douglas S. and K{\"u}gler, Sebastian and Lagnado, Leon and Hegemann, Peter and Gottschalk, Alexander and Schreiter, Eric R and Looger, Loren L} } @article {6414, title = {Haemolysin coregulated protein is an exported receptor and chaperone of type VI secretion substrates.}, journal = {Molecular Cell}, volume = {51}, year = {2013}, month = {2013 Sep 12}, pages = {584-93}, abstract = {

Secretion systems require high-fidelity mechanisms to discriminate substrates among the vast cytoplasmic pool of proteins. Factors mediating substrate recognition by the type VI secretion system (T6SS) of Gram-negative bacteria, a widespread pathway that translocates effector proteins into target bacterial cells, have not been defined. We report that haemolysin coregulated protein (Hcp), a ring-shaped hexamer secreted by all characterized T6SSs, binds specifically to cognate effector molecules. Electron microscopy analysis of an Hcp-effector complex from Pseudomonas aeruginosa revealed the effector bound to the inner surface of Hcp. Further studies demonstrated that interaction with the Hcp pore is a general requirement for secretion of diverse effectors encompassing several enzymatic classes. Though previous models depict Hcp as a static conduit, our data indicate it is a chaperone and receptor of substrates. These unique functions of a secreted protein highlight fundamental differences between the export mechanism of T6 and other characterized secretory pathways.

}, issn = {1097-4164}, doi = {10.1016/j.molcel.2013.07.025}, author = {Silverman, Julie M and Agnello, Danielle M and Zheng, Hongjin and Andrews, Benjamin T and Li, Mo and Catalano, Carlos E and Gonen, Tamir and Mougous, Joseph D} } @article {5803, title = {HCV IRES manipulates the ribosome to promote the switch from translation initiation to elongation.}, journal = {Nature Structural \& Molecular Biology}, volume = {20}, year = {2013}, month = {2013 Feb}, pages = {150-8}, abstract = {

The internal ribosome entry site (IRES) of the hepatitis C virus (HCV) drives noncanonical initiation of protein synthesis necessary for viral replication. Functional studies of the HCV IRES have focused on 80S ribosome formation but have not explored its role after the 80S ribosome is poised at the start codon. Here, we report that mutations of an IRES domain that docks in the 40S subunit{\textquoteright}s decoding groove cause only a local perturbation in IRES structure and result in conformational changes in the IRES-rabbit 40S subunit complex. Functionally, the mutations decrease IRES activity by inhibiting the first ribosomal translocation event, and modeling results suggest that this effect occurs through an interaction with a single ribosomal protein. The ability of the HCV IRES to manipulate the ribosome provides insight into how the ribosome{\textquoteright}s structure and function can be altered by bound RNAs, including those derived from cellular invaders.

}, issn = {1545-9985}, doi = {10.1038/nsmb.2465}, author = {Filbin, Megan E and Vollmar, Breanna S and Shi, Dan and Gonen, Tamir and Kieft, Jeffrey S} } @article {6279, title = {High speed phase distortion measurement and compensation for focusing in space and time.}, journal = {Proceedings of SPIE}, volume = {8589}, year = {2013}, month = {2013}, pages = {85890V}, abstract = {

Random scattering and aberrations severely limit the imaging depth in optical microscopy. We introduce a rapid, parallel wavefront compensation technique that efficiently compensates even highly complex phase distortions. Using coherence gated backscattered light as a feedback signal, we focus light deep inside highly scattering brain tissue. We demonstrate that the same wavefront optimization technique can also be used to compensate spectral phase distortions in ultrashort laser pulses using nonlinear iterative feedback. We can restore transform limited pulse durations at any selected target location and compensate for dispersion that has occurred in the optical train and within the sample.

}, doi = {10.1117/12.2001121}, author = {Fiolka, Reto and Cui, Meng} } @article {4056, title = {High throughput methods for electron crystallography.}, journal = {Methods in Molecular Biology}, volume = {955}, year = {2013}, month = {2013}, pages = {273-96}, abstract = {

Membrane proteins play a tremendously important role in cell physiology and serve as a target for an increasing number of drugs. Structural information is key to understanding their function and for developing new strategies for combating disease. However, the complex physical chemistry associated with membrane proteins has made them more difficult to study than their soluble cousins. Electron crystallography has historically been a successful method for solving membrane protein structures and has the advantage of providing a native lipid environment for these proteins. Specifically, when membrane proteins form two-dimensional arrays within a lipid bilayer, electron microscopy can be used to collect images and diffraction and the corresponding data can be combined to produce a three-dimensional reconstruction, which under favorable conditions can extend to atomic resolution. Like X-ray crystallography, the quality of the structures are very much dependent on the order and size of the crystals. However, unlike X-ray crystallography, high-throughput methods for screening crystallization trials for electron crystallography are not in general use. In this chapter, we describe two alternative methods for high-throughput screening of membrane protein crystallization within the lipid bilayer. The first method relies on the conventional use of dialysis for removing detergent and thus reconstituting the bilayer; an array of dialysis wells in the standard 96-well format allows the use of a liquid-handling robot and greatly increases throughput. The second method relies on titration of cyclodextrin as a chelating agent for detergent; a specialized pipetting robot has been designed not only to add cyclodextrin in a systematic way, but to use light scattering to monitor the reconstitution process. In addition, the use of liquid-handling robots for making negatively stained grids and methods for automatically imaging samples in the electron microscope are described.

}, doi = {10.1007/978-1-62703-176-9_15}, author = {Stoke, DL and Ubarretxena-Belandia, I and Gonen, T and Engel, A} } @article {6262, title = {High-throughput analysis of stimulus-evoked behaviors in Drosophila larva reveals multiple modality-specific escape strategies.}, journal = {PLoS One}, volume = {8}, year = {2013}, month = {2013 Aug 20}, pages = {e71706}, abstract = {

All organisms react to noxious and mechanical stimuli but we still lack a complete understanding of cellular and molecular mechanisms by which somatosensory information is transformed into appropriate motor outputs. The small number of neurons and excellent genetic tools make Drosophila larva an especially tractable model system in which to address this problem. We developed high throughput assays with which we can simultaneously expose more than 1,000 larvae per man-hour to precisely timed noxious heat, vibration, air current, or optogenetic stimuli. Using this hardware in combination with custom software we characterized larval reactions to somatosensory stimuli in far greater detail than possible previously. Each stimulus evoked a distinctive escape strategy that consisted of multiple actions. The escape strategy was context-dependent. Using our system we confirmed that the nociceptive class IV multidendritic neurons were involved in the reactions to noxious heat. Chordotonal (ch) neurons were necessary for normal modulation of head casting, crawling and hunching, in response to mechanical stimuli. Consistent with this we observed increases in calcium transients in response to vibration in ch neurons. Optogenetic activation of ch neurons was sufficient to evoke head casting and crawling. These studies significantly increase our understanding of the functional roles of larval ch neurons. More generally, our system and the detailed description of wild type reactions to somatosensory stimuli provide a basis for systematic identification of neurons and genes underlying these behaviors.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0071706}, author = {Ohyama, Tomoko and Jovanic, Tihana and Denisov, Gennady and Dang, Tam C and Hoffmann, Dominik and Kerr, Rex A and Zlatic, Marta} } @article {68819, title = {Hindbrain V2a Neurons in the Excitation of Spinal Locomotor Circuits during Zebrafish Swimming}, journal = {Current Biology}, volume = {23}, year = {2013}, month = {05/2013}, pages = {843-849}, abstract = {

During locomotion in vertebrates, reticulospinal neurons in the hindbrain play critical roles in providing descending excitation to the spinal cord locomotor systems. However, despite the fact that many genes that are used to classify the neuronal identities of neurons in the hindbrain have been identified, the molecular identity of the reticulospinal neurons that are critically involved in locomotor drive is not well understood. Chx10-expressing neurons (V2a neurons) are ipsilaterally projecting glutamatergic neurons in the spinal cord and the hindbrain. Many of the V2a neurons in the hindbrain are known to project to the spinal cord in zebrafish, making hindbrain V2a neurons a prime candidate in descending locomotor drive. Results We investigated the roles of hindbrain V2a neurons using optogenetic and electrophysiological approaches. The forced activation of hindbrain V2a neurons using channelrhodopsin efficiently evoked swimming, whereas the forced inactivation of them using Archearhodopsin3 or Halorhodpsin reliably stopped ongoing swimming. Electrophysiological recordings of two populations of hindbrain reticulospinal V2a neurons showed that they were active during swimming. One population of neurons, small V2a neurons in the caudal hindbrain, fired with low rhythmicity, whereas the other population of neurons, large reticulospinal V2a neurons, called MiV1 neurons, fired more rhythmically. Conclusions These results indicated that hindbrain reticulospinal V2a neurons play critical roles in providing excitation to the spinal locomotor circuits during swimming by providing both tonic and phasic inputs to the circuits.

}, issn = {0960-9822}, doi = {https://doi.org/10.1016/j.cub.2013.03.066}, url = {https://www.sciencedirect.com/science/article/pii/S0960982213003680}, author = {Yukiko Kimura and Chie Satou and Shunji Fujioka and Wataru Shoji and Keiko Umeda and Toru Ishizuka and Hiromu Yawo and Shin-ichi Higashijima} } @article {5889, title = {Hypothalamic survival circuits: blueprints for purposive behaviors.}, journal = {Neuron}, volume = {77}, year = {2013}, month = {2013 Mar 6}, pages = {810-24}, abstract = {

Neural processes that direct an animal{\textquoteright}s actions toward environmental goals are critical elements for understanding behavior. The hypothalamus is closely associated with motivated behaviors required for survival and reproduction. Intense feeding, drinking, aggressive, and sexual behaviors can be produced by a simple neuronal stimulus applied to discrete hypothalamic regions. What can these "evoked behaviors" teach us about the neural processes that determine behavioral intent and intensity? Small populations of neurons sufficient to evoke a complex motivated behavior may be used as entry points to identify circuits that energize and direct behavior to specific goals. Here, I review recent applications of molecular genetic, optogenetic, and pharmacogenetic approaches that overcome previous limitations for analyzing anatomically complex hypothalamic circuits and their interactions with the rest of the brain. These new tools have the potential to bridge the gaps between neurobiological and psychological thinking about the mechanisms of complex motivated behavior.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2013.02.018}, author = {Sternson, Scott M} } @article {5840, title = {Identification of nonvisual photomotor response cells in the vertebrate hindbrain.}, journal = {The Journal of Neuroscience}, volume = {33}, year = {2013}, month = {2013 Feb 27}, pages = {3834-43}, abstract = {

Nonvisual photosensation enables animals to sense light without sight. However, the cellular and molecular mechanisms of nonvisual photobehaviors are poorly understood, especially in vertebrate animals. Here, we describe the photomotor response (PMR), a robust and reproducible series of motor behaviors in zebrafish that is elicited by visual wavelengths of light but does not require the eyes, pineal gland, or other canonical deep-brain photoreceptive organs. Unlike the relatively slow effects of canonical nonvisual pathways, motor circuits are strongly and quickly (seconds) recruited during the PMR behavior. We find that the hindbrain is both necessary and sufficient to drive these behaviors. Using in vivo calcium imaging, we identify a discrete set of neurons within the hindbrain whose responses to light mirror the PMR behavior. Pharmacological inhibition of the visual cycle blocks PMR behaviors, suggesting that opsin-based photoreceptors control this behavior. These data represent the first known light-sensing circuit in the vertebrate hindbrain.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3689-12.2013}, author = {Kokel, David and Dunn, Timothy W. and Ahrens, Misha B and Alshut, R{\"u}diger and Cheung, Chung Yan J. and Saint-Amant, Louis and Bruni, Giancarlo and Mateus, Rita and van Ham, Tjakko J. and Shiraki, Tomoya and Fukada, Yoshitaka and Kojima, Daisuke and Yeh, Jing-Ruey J. and Mikut, Ralf and von Lintig, Johannes and Engert, Florian and Peters, Randall T.} } @article {47220, title = {Imaging a population code for odor identity in the Drosophila mushroom body.}, journal = {The Journal of Neuroscience : the official journal of the Society for Neuroscience}, volume = {33}, year = {2013}, month = {2013 Jun 19}, pages = {10568-81}, abstract = {

The brain represents sensory information in the coordinated activity of neuronal ensembles. Although the microcircuits underlying olfactory processing are well characterized in Drosophila, no studies to date have examined the encoding of odor identity by populations of neurons and related it to the odor specificity of olfactory behavior. Here we used two-photon Ca(2+) imaging to record odor-evoked responses from \>100 neurons simultaneously in the Drosophila mushroom body (MB). For the first time, we demonstrate quantitatively that MB population responses contain substantial information on odor identity. Using a series of increasingly similar odor blends, we identified conditions in which odor discrimination is difficult behaviorally. We found that MB ensemble responses accounted well for olfactory acuity in this task. Kenyon cell ensembles with as few as 25 cells were sufficient to match behavioral discrimination accuracy. Using a generalization task, we demonstrated that the MB population code could predict the flies{\textquoteright} responses to novel odors. The degree to which flies generalized a learned aversive association to unfamiliar test odors depended upon the relative similarity between the odors{\textquoteright} evoked MB activity patterns. Discrimination and generalization place different demands on the animal, yet the flies{\textquoteright} choices in these tasks were reliably predicted based on the amount of overlap between MB activity patterns. Therefore, these different behaviors can be understood in the context of a single physiological framework.

}, keywords = {Animals, Calcium, Discrimination (Psychology), Drosophila, Generalization (Psychology), Image Processing, Computer-Assisted, Learning, Linear Models, Mushroom Bodies, Neuroimaging, Odors, Olfactory Pathways, Olfactory Perception, Psychomotor Performance, Synaptic Transmission}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0682-12.2013}, author = {Campbell, Robert A A and Honegger, Kyle S and Qin, Hongtao and Li, Wanhe and Demir, Ebru and Turner, Glenn C} } @article {5982, title = {Imaging morphogenesis: technological advances and biological insights.}, journal = {Science}, volume = {340}, year = {2013}, month = {2013 Jun 7}, pages = {1234168}, abstract = {

Morphogenesis, the development of the shape of an organism, is a dynamic process on a multitude of scales, from fast subcellular rearrangements and cell movements to slow structural changes at the whole-organism level. Live-imaging approaches based on light microscopy reveal the intricate dynamics of this process and are thus indispensable for investigating the underlying mechanisms. This Review discusses emerging imaging techniques that can record morphogenesis at temporal scales from seconds to days and at spatial scales from hundreds of nanometers to several millimeters. To unlock their full potential, these methods need to be matched with new computational approaches and physical models that help convert highly complex image data sets into biological insights.

Science Profile: A Research Career in Focus

}, issn = {1095-9203}, doi = {10.1126/science.1234168}, author = {Keller, Philipp J} } @article {6670, title = {Imaging neuronal populations in behaving rodents: paradigms for studying neural circuits underlying behavior in the mammalian cortex.}, journal = {The Journal of Neuroscience : the Official Journal of the Society for Neuroscience}, volume = {33}, year = {2013}, month = {2013 Nov 6}, pages = {17631-40}, abstract = {

Understanding the neural correlates of behavior in the mammalian cortex requires measurements of activity in awake, behaving animals. Rodents have emerged as a powerful model for dissecting the cortical circuits underlying behavior attributable to the convergence of several methods. Genetically encoded calcium indicators combined with viral-mediated or transgenic tools enable chronic monitoring of calcium signals in neuronal populations and subcellular structures of identified cell types. Stable one- and two-photon imaging of neuronal activity in awake, behaving animals is now possible using new behavioral paradigms in head-fixed animals, or using novel miniature head-mounted microscopes in freely moving animals. This mini-symposium will highlight recent applications of these methods for studying sensorimotor integration, decision making, learning, and memory in cortical and subcortical brain areas. We will outline future prospects and challenges for identifying the neural underpinnings of task-dependent behavior using cellular imaging in rodents.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3255-13.2013}, author = {Chen, Jerry L and Andermann, Mark L and Keck, Tara and Xu, Ning-long and Ziv, Yaniv} } @article {6655, title = {Imaging the transcriptome.}, journal = {Molecular Systems Biology}, volume = {9}, year = {2013}, month = {2013 Nov 26}, pages = {710}, issn = {1744-4292}, doi = {10.1038/msb.2013.67}, author = {Lionnet, Timoth{\'e}e} } @article {5884, title = {In vivo imaging of zebrafish embryogenesis.}, journal = {Methods}, volume = {62}, year = {2013}, month = {2013 Aug 15}, pages = {268-78}, abstract = {

The zebrafish Danio rerio has emerged as a powerful vertebrate model system that lends itself particularly well to quantitative investigations with live imaging approaches, owing to its exceptionally high optical clarity in embryonic and larval stages. Recent advances in light microscopy technology enable comprehensive analyses of cellular dynamics during zebrafish embryonic development, systematic mapping of gene expression dynamics, quantitative reconstruction of mutant phenotypes and the system-level biophysical study of morphogenesis. Despite these technical breakthroughs, it remains challenging to design and implement experiments for in vivo long-term imaging at high spatio-temporal resolution. This article discusses the fundamental challenges in zebrafish long-term live imaging, provides experimental protocols and highlights key properties and capabilities of advanced fluorescence microscopes. The article focuses in particular on experimental assays based on light sheet-based fluorescence microscopy, an emerging imaging technology that achieves exceptionally high imaging speeds and excellent signal-to-noise ratios, while minimizing light-induced damage to the specimen. This unique combination of capabilities makes light sheet microscopy an indispensable tool for the in vivo long-term imaging of large developing organisms.

}, issn = {1095-9130}, doi = {10.1016/j.ymeth.2013.03.015}, author = {Keller, Philipp J} } @article {47634, title = {Incisive imaging and computation for cellular mysteries: lessons from abscission.}, journal = {Cell}, volume = {155}, year = {2013}, month = {2013 Dec 5}, pages = {1220-31}, abstract = {

The final cleavage event that terminates cell division, abscission of the small, dense intercellular bridge, has been particularly challenging to resolve. Here, we describe imaging innovations that helped answer long-standing questions about the mechanism of abscission. We further explain how computational modeling of high-resolution data was employed to test hypotheses and generate additional insights. We present the model that emerges from application of these complimentary approaches. Similar experimental strategies will undoubtedly reveal exciting details about other underresolved cellular structures.

}, keywords = {Animals, Cell Physiological Processes, Cytokinesis, Humans, Models, Biological, Plant Cells}, issn = {1097-4172}, doi = {10.1016/j.cell.2013.11.011}, author = {Elia, Natalie and Ott, Carolyn and Lippincott-Schwartz, Jennifer} } @article {47636, title = {Increased mitochondrial fusion and autophagy help isolated hepatocytes repolarize in collagen sandwich cultures.}, journal = {Autophagy}, volume = {9}, year = {2013}, month = {2013 Dec}, pages = {2154-5}, abstract = {

Freshly isolated, depolarized rat hepatocytes can repolarize into bile canalicular networks when plated in collagen sandwich cultures. We studied the events underlying this repolarization process, focusing on how hepatocytes restore ATP synthesis and resupply biosynthetic precursors after the stress of being isolated from liver. We found that soon after being plated in collagen sandwich cultures, hepatocytes converted their mitochondria into highly fused networks. This occurred through a combination of upregulation of mitochondrial fusion proteins and downregulation of a mitochondrial fission protein. Mitochondria also became more active for oxidative phosphorylation, leading to overall increased ATP levels within cells. We further observed that autophagy was upregulated in the repolarizing hepatocytes. Boosted autophagy levels likely served to recycle cellular precursors, supplying building blocks for repolarization. Repolarizing hepatocytes also extensively degraded lipid droplets, whose fatty acids provide precursors for ?-oxidation to fuel oxidative phosphorylation in mitochondria. Thus, through coordination of mitochondrial fusion, autophagy, and lipid droplet consumption, depolarized hepatocytes are able to boost ATP synthesis and biosynthetic precursors to efficiently repolarize in collagen sandwich cultures.

}, keywords = {Animals, Autophagy, Cell Culture Techniques, Cell Polarity, Cell Separation, Cells, Cultured, Collagen, Hepatocytes, Mitochondrial Dynamics, Primary Cell Culture, Rats, Tissue Scaffolds}, issn = {1554-8635}, doi = {10.4161/auto.26167}, author = {Fu, Dong and Lippincott-Schwartz, Jennifer and Arias, Irwin M} } @article {6453, title = {Infernal 1.1: 100-fold faster RNA homology searches.}, journal = {Bioinformatics}, volume = {29}, year = {2013}, month = {2013 Sep 19}, pages = {2933-5}, abstract = {

SUMMARY: Infernal builds probabilistic profiles of the sequence and secondary structure of an RNA family called covariance models (CMs) from structurally annotated multiple sequence alignments given as input. Infernal uses CMs to search for new family members in sequence databases and to create potentially large multiple sequence alignments. Version 1.1 of Infernal introduces a new filter pipeline for RNA homology search based on accelerated profile hidden Markov model (HMM) methods and HMM-banded CM alignment methods. This enables \~{}100-fold acceleration over the previous version and \~{}10 000-fold acceleration over exhaustive non-filtered CM searches. AVAILABILITY: Source code, documentation and the benchmark are downloadable from http://infernal.janelia.org. Infernal is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and Mac OS/X. Documentation includes a user{\textquoteright}s guide with a tutorial, a discussion of file formats and user options and additional details on methods implemented in the software. CONTACT: nawrockie@janelia.hhmi.org.

}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btt509}, author = {Nawrocki, Eric P and Eddy, Sean R.} } @article {46575, title = {Inferring neural population dynamics from multiple partial recordings of the same neural circuit.}, journal = {Advances in Neural Information Processing Systems (NIPS) }, volume = {26}, year = {2013}, month = {2013}, abstract = {

Simultaneous recordings of the activity of large neural populations are extremely valuable as they can be used to infer the dynamics and interactions of neurons in a local circuit, shedding light on the computations performed. It is now possible to measure the activity of hundreds of neurons using 2-photon calcium imaging. However, many computations are thought to involve circuits consisting of thousands of neurons, such as cortical barrels in rodent somatosensory cortex. Here we contribute a statistical method for stitching" together sequentially imaged sets of neurons into one model by phrasing the problem as fitting a latent dynamical system with missing observations. This method allows us to substantially expand the population-sizes for which population dynamics can be characterized---beyond the number of simultaneously imaged neurons. In particular, we demonstrate using recordings in mouse somatosensory cortex that this method makes it possible to predict noise correlations between non-simultaneously recorded neuron pairs.

}, url = {http://papers.nips.cc/paper/4874-inferring-neural-population-dynamics-from-multiple-partial-recordings-of-the-same-neural-circuit}, author = {Turaga, Srinivas C and Buesing, Lars and Packer, Adam M. and Dalgleish, Henry and Pettit, Noah and H{\"a}usser, Michael and Macke, Jakob H.} } @article {47899, title = {The influence of synaptic weight distribution on neuronal population dynamics.}, journal = {PLoS computational biology}, volume = {9}, year = {2013}, month = {2013 Oct}, pages = {e1003248}, abstract = {

The manner in which different distributions of synaptic weights onto cortical neurons shape their spiking activity remains open. To characterize a homogeneous neuronal population, we use the master equation for generalized leaky integrate-and-fire neurons with shot-noise synapses. We develop fast semi-analytic numerical methods to solve this equation for either current or conductance synapses, with and without synaptic depression. We show that its solutions match simulations of equivalent neuronal networks better than those of the Fokker-Planck equation and we compute bounds on the network response to non-instantaneous synapses. We apply these methods to study different synaptic weight distributions in feed-forward networks. We characterize the synaptic amplitude distributions using a set of measures, called tail weight numbers, designed to quantify the preponderance of very strong synapses. Even if synaptic amplitude distributions are equated for both the total current and average synaptic weight, distributions with sparse but strong synapses produce higher responses for small inputs, leading to a larger operating range. Furthermore, despite their small number, such synapses enable the network to respond faster and with more stability in the face of external fluctuations.

}, keywords = {Action Potentials, Computer Simulation, Models, Neurological, Neurons, Synapses}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1003248}, author = {Iyer, Ramakrishnan and Menon, Vilas and Buice, Michael and Koch, Christof and Mihalas, Stefan} } @article {47638, title = {Insulin triggers surface-directed trafficking of sequestered GLUT4 storage vesicles marked by Rab10.}, journal = {Small GTPases}, volume = {4}, year = {2013}, month = {2013 Jul-Sep}, pages = {193-7}, abstract = {

Understanding how glucose transporter isoform 4 (GLUT4) redistributes to the plasma membrane during insulin stimulation is a major goal of glucose transporter research. GLUT4 molecules normally reside in numerous intracellular compartments, including specialized storage vesicles and early/recycling endosomes. It is unclear how these diverse compartments respond to insulin stimulation to deliver GLUT4 molecules to the plasma membrane. For example, do they fuse with each other first or remain as separate compartments with different trafficking characteristics? Our recent live cell imaging studies are helping to clarify these issues. Using Rab proteins as specific markers to distinguish between storage vesicles and endosomes containing GLUT4, we demonstrate that it is primarily internal GLUT4 storage vesicles (GSVs) marked by Rab10 that approach and fuse at the plasma membrane and GSVs don{\textquoteright}t interact with endosomes on their way to the plasma membrane. These new findings add strong support to the model that GSV release from intracellular retention plays a major role in supplying GLUT4 molecules onto the PM under insulin stimulation.

}, keywords = {Adipocytes, Animals, Cell Line, Cell Membrane, Endosomes, Glucose Transporter Type 4, Insulin, Mice, rab GTP-Binding Proteins, RNA Interference, RNA, Small Interfering}, issn = {2154-1256}, doi = {10.4161/sgtp.26471}, author = {Chen, Yu and Lippincott-Schwartz, Jennifer} } @article {47746, title = {Integration of the olfactory code across dendritic claws of single mushroom body neurons.}, journal = {Nature Neuroscience}, volume = {16}, year = {2013}, month = {2013 Oct 20}, pages = {1821-9}, abstract = {

In the olfactory system, sensory inputs are arranged in different glomerular channels, which respond in combinatorial ensembles to the various chemical features of an odor. Here we investigate where and how this combinatorial code is read out deeper in the brain. We exploit the unique morphology of neurons in the mushroom body (MB), which receive input on large dendritic claws. Imaging odor responses of these dendritic claws shows that input channels with distinct odor tuning converge on individual MB neurons. We determined how these inputs interact to drive the cell to spike threshold using intracellular recordings to examine MB responses to optogenetically controlled input. Our results provide an elegant explanation for the characteristic selectivity of MB neurons: these cells receive different types of input, and require those inputs to be coactive in order to spike. These results establish the MB as an important site of integration in the fly olfactory system.

}, doi = {10.1038/nn.3547}, author = {Gruntman, Eyal and Turner, Glenn C} } @article {47219, title = {Integration of the olfactory code across dendritic claws of single mushroom body neurons.}, journal = {Nature Neuroscience}, volume = {16}, year = {2013}, month = {2013 Dec}, pages = {1821-9}, abstract = {

In the olfactory system, sensory inputs are arranged in different glomerular channels, which respond in combinatorial ensembles to the various chemical features of an odor. We investigated where and how this combinatorial code is read out deeper in the brain. We exploited the unique morphology of neurons in the Drosophila mushroom body, which receive input on large dendritic claws. Imaging odor responses of these dendritic claws revealed that input channels with distinct odor tuning converge on individual mushroom body neurons. We determined how these inputs interact to drive the cell to spike threshold using intracellular recordings to examine mushroom body responses to optogenetically controlled input. Our results provide an elegant explanation for the characteristic selectivity of mushroom body neurons: these cells receive different types of input and require those inputs to be coactive to spike. These results establish the mushroom body as an important site of integration in the fly olfactory system.

}, keywords = {Animals, Animals, Genetically Modified, Calcium, Dendrites, Drosophila, Drosophila Proteins, Electric Stimulation, Female, Luminescent Proteins, Membrane Potentials, Models, Neurological, Mushroom Bodies, Neurons, Odors, Olfactory Pathways, Patch-Clamp Techniques, Photic Stimulation, Rhodopsin, Synapses}, issn = {1546-1726}, doi = {10.1038/nn.3547}, author = {Gruntman, Eyal and Turner, Glenn C} } @article {6528, title = {Intensity discrimination deficits cause habituation changes in middle-aged Caenorhabditis elegans.}, journal = {Neurobiology of Aging}, volume = {34}, year = {2013}, month = {2013 Feb}, pages = {621-31}, abstract = {

The ability to learn and remember is critical for all animals to survive in the ever-changing environment. As we age, many of our biological faculties decay and of these, decline in learning and memory can be the most distressing. To carefully define age-dependent changes in learning during reproductive age in the nematode Caenorhabditis elegans, we performed a parametric behavioral study of habituation to nonlocalized mechanical stimuli (petri plate taps) over a range of intensities in middle-aged worms. We found that as worms age (from the onset of reproduction to the end of egg laying), response probability habituation increases (at both 10- and 60-second interstimulus intervals) and that these age-related changes were associated with a decrease in the discrimination between stimuli of different intensities. We also used optogenetics to investigate where these age-dependent changes occur. Our data suggest that the changes occur upstream of mechanosensory neuron depolarization. These data support the idea that declines in stimulus intensity discrimination abilities during aging may be one variable underlying age-related cognitive deficits.

}, keywords = {Age Factors, Aging, Animal, Animals, Behavior, Caenorhabditis elegans, Discrimination (Psychology), Habituation, Memory, Physical Stimulation, Psychophysiologic, Short-Term}, issn = {1558-1497}, doi = {10.1016/j.neurobiolaging.2012.03.016}, author = {Timbers, Tiffany A and Giles, Andrew C and Ardiel, Evan L and Kerr, Rex A and Rankin, Catharine H} } @article {6578, title = {Intrinsic disorder within an AKAP-protein kinase A complex guides local substrate phosphorylation.}, journal = {eLife}, volume = {2}, year = {2013}, month = {2013 Nov 5}, pages = {e01319}, abstract = {

Anchoring proteins sequester kinases with their substrates to locally disseminate intracellular signals and avert indiscriminate transmission of these responses throughout the cell. Mechanistic understanding of this process is hampered by limited structural information on these macromolecular complexes. A-kinase anchoring proteins (AKAPs) spatially constrain phosphorylation by cAMP-dependent protein kinases (PKA). Electron microscopy and three-dimensional reconstructions of type-II PKA-AKAP18γ complexes reveal hetero-pentameric assemblies that adopt a range of flexible tripartite configurations. Intrinsically disordered regions within each PKA regulatory subunit impart the molecular plasticity that affords an \~{}16 nanometer radius of motion to the associated catalytic subunits. Manipulating flexibility within the PKA holoenzyme augmented basal and cAMP responsive phosphorylation of AKAP-associated substrates. Cell-based analyses suggest that the catalytic subunit remains within type-II PKA-AKAP18γ complexes upon cAMP elevation. We propose that the dynamic movement of kinase sub-structures, in concert with the static AKAP-regulatory subunit interface, generates a solid-state signaling microenvironment for substrate phosphorylation. DOI: http://dx.doi.org/10.7554/eLife.01319.001.

}, issn = {2050-084X}, doi = {10.7554/eLife.01319}, author = {Smith, F Donelson and Reichow, Steve L and Esseltine, Jessica L and Shi, Dan and Langeberg, Lorene K and Scott, John D and Gonen, Tamir} } @article {5763, title = {JAABA: interactive machine learning for automatic annotation of animal behavior.}, journal = {Nature Methods}, volume = {10}, year = {2013}, month = {2012 Dec}, pages = {64-7}, abstract = {

We present a machine learning{\textendash}based system for automatically computing interpretable, quantitative measures of animal behavior. Through our interactive system, users encode their intuition about behavior by annotating a small set of video frames. These manual labels are converted into classifiers that can automatically annotate behaviors in screen-scale data sets. Our general-purpose system can create a variety of accurate individual and social behavior classifiers for different organisms, including mice and adult and larval Drosophila.

}, issn = {1548-7091}, author = {Kabra, Mayank and Robie, Alice A and Rivera-Alba, Marta and Branson, Steven and Branson, Kristin} } @article {6390, title = {Juvenile hormone and insulin suppress lipolysis between periods of lactation during tsetse fly pregnancy.}, journal = {Molecular and Cellular Endocrinology}, volume = {372}, year = {2013}, month = {2013 Jun 15}, pages = {30-41}, abstract = {

Tsetse flies are viviparous insects that nurture a single intrauterine progeny per gonotrophic cycle. The developing larva is nourished by the lipid-rich, milk-like secretions from a modified female accessory gland (milk gland). An essential feature of the lactation process involves lipid mobilization for incorporation into the milk. In this study, we examined roles for juvenile hormone (JH) and insulin/IGF-like (IIS) signaling pathways during tsetse pregnancy. In particular, we examined the roles for these pathways in regulating lipid homeostasis during transitions between non-lactating (dry) and lactating periods. The dry period occurs over the course of oogenesis and embryogenesis, while the lactation period spans intrauterine larvigenesis. Genes involved in the JH and IIS pathways were upregulated during dry periods, correlating with lipid accumulation between bouts of lactation. RNAi suppression of Forkhead Box Sub Group O (FOXO) expression impaired lipolysis during tsetse lactation and reduced fecundity. Similar reduction of the JH receptor Methoprene tolerant (Met), but not its paralog germ cell expressed (gce), reduced lipid accumulation during dry periods, indicating functional divergence between Met and gce during tsetse reproduction. Reduced lipid levels following Met knockdown led to impaired fecundity due to inadequate fat reserves at the initiation of milk production. Both the application of the JH analog (JHA) methoprene and injection of insulin into lactating females increased stored lipids by suppressing lipolysis and reduced transcripts of lactation-specific genes, leading to elevated rates of larval abortion. To our knowledge, this study is the first to address the molecular physiology of JH and IIS in a viviparous insect, and specifically to provide a role for JH signaling through Met in the regulation of lipid metabolism during insect lactation.

}, issn = {1872-8057}, doi = {10.1016/j.mce.2013.02.019}, author = {Baumann, Aaron A and Benoit, Joshua B and Michalkova, Veronika and Mireji, Paul O and Attardo, Geoffrey M and Moulton, John K and Wilson, Thomas G and Aksoy, Serap} } @article {5635, title = {The juvenile hormone signaling pathway in insect development.}, journal = {Annual Review of Entomology}, volume = {58}, year = {2013}, month = {2013 Jan 7}, pages = {181-204}, abstract = {

The molecular action of juvenile hormone (JH), a regulator of vital importance to insects, was until recently regarded as a mystery. The past few years have seen an explosion of studies of JH signaling, sparked by a finding that a JH-resistance gene, Methoprene-tolerant (Met), plays a critical role in insect metamorphosis. Here, we summarize the recently acquired knowledge on the capacity of Met to bind JH, which has been mapped to a particular ligand-binding domain, thus establishing this bHLH-PAS protein as a novel type of an intracellular hormone receptor. Next, we consider the significance of JH-dependent interactions of Met with other transcription factors and signaling pathways. We examine the regulation and biological roles of genes acting downstream of JH and Met in insect metamorphosis. Finally, we discuss the current gaps in our understanding of JH action and outline directions for future research.

}, issn = {1545-4487}, doi = {10.1146/annurev-ento-120811-153700}, author = {Jindra, Marek and Palli, Subba R and Riddiford, Lynn M} } @article {65022, title = {Large scale structural rearrangement of a serine hydrolase from Francisella tularensis facilitates catalysis.}, journal = {J Biol Chem}, volume = {288}, year = {2013}, month = {2013 Apr 12}, pages = {10522-35}, abstract = {

Tularemia is a deadly, febrile disease caused by infection by the gram-negative bacterium, Francisella tularensis. Members of the ubiquitous serine hydrolase protein family are among current targets to treat diverse bacterial infections. Herein we present a structural and functional study of a novel bacterial carboxylesterase (FTT258) from F. tularensis, a homologue of human acyl protein thioesterase (hAPT1). The structure of FTT258 has been determined in multiple forms, and unexpectedly large conformational changes of a peripheral flexible loop occur in the presence of a mechanistic cyclobutanone ligand. The concomitant changes in this hydrophobic loop and the newly exposed hydrophobic substrate binding pocket suggest that the observed structural changes are essential to the biological function and catalytic activity of FTT258. Using diverse substrate libraries, site-directed mutagenesis, and liposome binding assays, we determined the importance of these structural changes to the catalytic activity and membrane binding activity of FTT258. Residues within the newly exposed hydrophobic binding pocket and within the peripheral flexible loop proved essential to the hydrolytic activity of FTT258, indicating that structural rearrangement is required for catalytic activity. Both FTT258 and hAPT1 also showed significant association with liposomes designed to mimic bacterial or human membranes, respectively, even though similar structural rearrangements for hAPT1 have not been reported. The necessity for acyl protein thioesterases to have maximal catalytic activity near the membrane surface suggests that these conformational changes in the protein may dually regulate catalytic activity and membrane association in bacterial and human homologues.

}, keywords = {Bacterial Proteins, Cell Membrane, Francisella tularensis, Humans, Mutagenesis, Site-Directed, Serine Endopeptidases, Structural Homology, Protein, Structure-Activity Relationship, Thiolester Hydrolases}, issn = {1083-351X}, doi = {10.1074/jbc.M112.446625}, author = {Filippova, Ekaterina V and Weston, Leigh A and Kuhn, Misty L and Geissler, Brett and Gehring, Alexandra M and Armoush, Nicola and Adkins, Chinessa T and Minasov, George and Dubrovska, Ievgeniia and Shuvalova, Ludmilla and Winsor, James R and Lavis, Luke D and Satchell, Karla J F and Becker, Daniel P and Anderson, Wayne F and Johnson, R Jeremy} } @article {5346, title = {Light sheet microscopy in cell biology.}, journal = {Methods in Molecular Biology}, volume = {931}, year = {2013}, month = {2013}, pages = {123-37}, abstract = {

Light sheet-based fluorescence microscopy (LSFM) is emerging as a powerful imaging technique for the life sciences. LSFM provides an exceptionally high imaging speed, high signal-to-noise ratio, low level of photo-bleaching, and good optical penetration depth. This unique combination of capabilities makes light sheet-based microscopes highly suitable for live imaging applications. Here, we provide an overview of light sheet-based microscopy assays for in vitro and in vivo imaging of biological samples, including cell extracts, soft gels, and large multicellular organisms. We furthermore describe computational tools for basic image processing and data inspection.

}, issn = {1940-6029}, doi = {10.1007/978-1-62703-056-4_7}, author = {Tomer, Raju and Khairy, Khaled and Keller, Philipp J} } @article {6318, title = {Likelihood-based classification of cryo-EM images using FREALIGN.}, journal = {Journal of Structural Biology}, volume = {183}, year = {2013}, month = {2013 Sep}, pages = {377-88}, abstract = {

We describe an implementation of maximum likelihood classification for single particle electron cryo-microscopy that is based on the FREALIGN software. Particle alignment parameters are determined by maximizing a joint likelihood that can include hierarchical priors, while classification is performed by expectation maximization of a marginal likelihood. We test the FREALIGN implementation using a simulated dataset containing computer-generated projection images of three different 70S ribosome structures, as well as a publicly available dataset of 70S ribosomes. The results show that the mixed strategy of the new FREALIGN algorithm yields performance on par with other maximum likelihood implementations, while remaining computationally efficient.

}, issn = {1095-8657}, doi = {10.1016/j.jsb.2013.07.005}, author = {Lyumkis, Dmitry and Brilot, Axel F and Theobald, Douglas L and Grigorieff, Nikolaus} } @article {6918, title = {Live imaging of nervous system development and function using light-sheet microscopy.}, journal = {Molecular Reproduction and Development}, volume = {82}, year = {2013}, month = {2015 Jul}, pages = {605-18}, abstract = {

In vivo imaging applications typically require carefully balancing conflicting parameters. Often it is necessary to achieve high imaging speed, low photo-bleaching, and photo-toxicity, good three-dimensional resolution, high signal-to-noise ratio, and excellent physical coverage at the same time. Light-sheet microscopy provides good performance in all of these categories, and is thus emerging as a particularly powerful live imaging method for the life sciences. We see an outstanding potential for applying light-sheet microscopy to the study of development and function of the early nervous system in vertebrates and higher invertebrates. Here, we review state-of-the-art approaches to live imaging of early development, and show how the unique capabilities of light-sheet microscopy can further advance our understanding of the development and function of the nervous system. We discuss key considerations in the design of light-sheet microscopy experiments, including sample preparation and fluorescent marker strategies, and provide an outlook for future directions in the field.

}, issn = {1098-2795}, doi = {10.1002/mrd.22258}, author = {Lemon, William C and Keller, Philipp J} } @article {6073, title = {Live imaging of whole mouse embryos during gastrulation: migration analyses of epiblast and mesodermal cells.}, journal = {PLoS One}, volume = {8}, year = {2013}, month = {2013 Jul 8}, pages = {e64506}, abstract = {

During gastrulation in the mouse embryo, dynamic cell movements including epiblast invagination and mesodermal layer expansion lead to the establishment of the three-layered body plan. The precise details of these movements, however, are sometimes elusive, because of the limitations in live imaging. To overcome this problem, we developed techniques to enable observation of living mouse embryos with digital scanned light sheet microscope (DSLM). The achieved deep and high time-resolution images of GFP-expressing nuclei and following 3D tracking analysis revealed the following findings: (i) Interkinetic nuclear migration (INM) occurs in the epiblast at embryonic day (E)6 and 6.5. (ii) INM-like migration occurs in the E5.5 embryo, when the epiblast is a monolayer and not yet pseudostratified. (iii) Primary driving force for INM at E6.5 is not pressure from neighboring nuclei. (iv) Mesodermal cells migrate not as a sheet but as individual cells without coordination.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0064506}, author = {Ichikawa, Takehiko and Nakazato, Kenichi and Keller, Philipp J and Kajiura-Kobayashi, Hiroko and Stelzer, Ernst H K and Mochizuki, Atsushi and Nonaka, Shigenori} } @article {6523, title = {Local cAMP signaling in disease at a glance.}, journal = {Journal of Cell Science}, volume = {126}, year = {2013}, month = {2013 Oct 15}, pages = {4537-43}, abstract = {

The second messenger cyclic AMP (cAMP) operates in discrete subcellular regions within which proteins that synthesize, break down or respond to the second messenger are precisely organized. A burgeoning knowledge of compartmentalized cAMP signaling is revealing how the local control of signaling enzyme activity impacts upon disease. The aim of this Cell Science at a Glance article and the accompanying poster is to highlight how misregulation of local cyclic AMP signaling can have pathophysiological consequences. We first introduce the core molecular machinery for cAMP signaling, which includes the cAMP-dependent protein kinase (PKA), and then consider the role of A-kinase anchoring proteins (AKAPs) in coordinating different cAMP-responsive proteins. The latter sections illustrate the emerging role of local cAMP signaling in four disease areas: cataracts, cancer, diabetes and cardiovascular diseases.

}, issn = {1477-9137}, doi = {10.1242/jcs.133751}, author = {Gold, Matthew G and Gonen, Tamir and Scott, John D} } @article {6291, title = {A localized Wnt signal orients asymmetric stem cell division in vitro.}, journal = {Science}, volume = {339}, year = {2013}, month = {2013 Mar 22}, pages = {1445-8}, abstract = {

Developmental signals such as Wnts are often presented to cells in an oriented manner. To examine the consequences of local Wnt signaling, we immobilized Wnt proteins on beads and introduced them to embryonic stem cells in culture. At the single-cell level, the Wnt-bead induced asymmetric distribution of Wnt-β-catenin signaling components, oriented the plane of mitotic division, and directed asymmetric inheritance of centrosomes. Before cytokinesis was completed, the Wnt-proximal daughter cell expressed high levels of nuclear β-catenin and pluripotency genes, whereas the distal daughter cell acquired hallmarks of differentiation. We suggest that a spatially restricted Wnt signal induces an oriented cell division that generates distinct cell fates at predictable positions relative to the Wnt source.

}, keywords = {Animals, Asymmetric Cell Division, beta Catenin, Cell Differentiation, Cells, Centrosome, Cultured, Cytokinesis, Embryonic Stem Cells, Gene Expression, Homeodomain Proteins, Mice, Mitosis, Octamer Transcription Factor-3, Pluripotent Stem Cells, Recombinant Proteins, Single-Cell Analysis, Transcription Factors, Wnt Proteins, Wnt Signaling Pathway, Wnt3A Protein}, issn = {1095-9203}, doi = {10.1126/science.1231077}, author = {Habib, Shukry J and Chen, Bi-Chang and Tsai, Feng-Chiao and Anastassiadis, Konstantinos and Meyer, Tobias and Betzig, Eric and Nusse, Roel} } @article {6324, title = {Location of the dsRNA-dependent polymerase, VP1, in rotavirus particles.}, journal = {Journal of Molecular Biology}, volume = {425}, year = {2013}, month = {2013 Jan 9}, pages = {124-32}, abstract = {

Double-stranded RNA (dsRNA) viruses transcribe and replicate RNA within an assembled, inner capsid particle; only plus-sense mRNA emerges into the intracellular milieu. During infectious entry of a rotavirus particle, the outer layer of its three-layer structure dissociates, delivering the inner double-layered particle (DLP) into the cytosol. DLP structures determined by X-ray crystallography and electron cryomicroscopy (cryoEM) show that the RNA coils uniformly into the particle interior, avoiding a "fivefold hub" of more structured density projecting inward from the VP2 shell of the DLP along each of the twelve 5-fold axes. Analysis of the X-ray crystallographic electron density map suggested that principal contributors to the hub are the N-terminal arms of VP2, but reexamination of the cryoEM map has shown that many features come from a molecule of VP1, randomly occupying five equivalent and partly overlapping positions. We confirm here that the electron density in the X-ray map leads to the same conclusion, and we describe the functional implications of the orientation and position of the polymerase. The exit channel for the nascent transcript directs the nascent transcript toward an opening along the 5-fold axis. The template strand enters from within the particle, and the dsRNA product of the initial replication step exits in a direction tangential to the inner surface of the VP2 shell, allowing it to coil optimally within the DLP. The polymerases of reoviruses appear to have similar positions and functional orientations.

}, keywords = {Capsid, Computer-Assisted, Cryoelectron Microscopy, Crystallography, Double-Stranded, Image Processing, Messenger, Models, Molecular, RNA, Rotavirus, Viral, Viral Core Proteins, Virus Assembly, X-Ray}, issn = {1089-8638}, doi = {10.1016/j.jmb.2012.10.011}, author = {Estrozi, Leandro F and Settembre, Ethan C and Goret, Ga{\"e}l and McClain, Brian and Zhang, Xing and Chen, James Z and Grigorieff, Nikolaus and Harrison, Stephen C} } @article {6144, title = {A low-bandwidth camera sensor platform with applications in smart camera networks.}, journal = {ACM Transactions on Sensor Networks}, volume = {9}, year = {2013}, month = {2013 Mar}, abstract = {

Smart camera networks have recently emerged as a new class of sensor network infrastructure that is capable of supporting high-power in-network signal processing and enabling a wide range of applications. In this article, we provide an exposition of our efforts to build a low-bandwidth wireless camera network platform, called CITRIC, and its applications in smart camera networks. The platform integrates a camera, a microphone, a frequency-scalable (up to 624 MHz) CPU, 16 MB FLASH, and 64 MB RAM onto a single device. The device then connects with a standard sensor network mote to form a wireless camera mote. With reasonably low power consumption and extensive algorithmic libraries running on a decent operating system that is easy to program, CITRIC is ideal for research and applications in distributed image and video processing. Its capabilities of in-network image processing also reduce communication requirements, which has been high in other existing camera networks with centralized processing. Furthermore, the mote easily integrates with other low-bandwidth sensor networks via the IEEE 802.15.4 protocol. To justify the utility of CITRIC, we present several representative applications. In particular, concrete research results will be demonstrated in two areas, namely, distributed coverage hole identification and distributed object recognition.

}, issn = {1550-4859}, url = {http://dl.acm.org/citation.cfm?doid=2422966.2422978}, author = {Phoebus Chen and Kirak Hong and Nikhil Naikal and S. Shankar Sastry and Doug Tygar and Yan, Posu and Yang, Allen and Chang, Lung-Chung and Lin, Leon and Wang, Simon and Lobaton, Edgar and Oh, Songhwai and Ahammad, Parvez} } @article {6263, title = {Machine learning of hierarchical clustering to segment 2D and 3D images.}, journal = {PLoS One}, volume = {8}, year = {2013}, month = {2013}, pages = {e71715}, abstract = {

We aim to improve segmentation through the use of machine learning tools during region agglomeration. We propose an active learning approach for performing hierarchical agglomerative segmentation from superpixels. Our method combines multiple features at all scales of the agglomerative process, works for data with an arbitrary number of dimensions, and scales to very large datasets. We advocate the use of variation of information to measure segmentation accuracy, particularly in 3D electron microscopy (EM) images of neural tissue, and using this metric demonstrate an improvement over competing algorithms in EM and natural images.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0071715}, author = {Nunez-Iglesias, Juan and Kennedy, Ryan and Toufiq Parag and Shi, Jianbo and Chklovskii, Dmitri B} } @article {6925, title = {Male-specific fruitless isoforms have different regulatory roles conferred by distinct zinc finger DNA binding domains.}, journal = {BMC Genomics}, volume = {14}, year = {2013}, month = {2013 Sep 27}, pages = {659}, abstract = {

BACKGROUND: Drosophila melanogaster adult males perform an elaborate courtship ritual to entice females to mate. fruitless (fru), a gene that is one of the key regulators of male courtship behavior, encodes multiple male-specific isoforms (Fru(M)). These isoforms vary in their carboxy-terminal zinc finger domains, which are predicted to facilitate DNA binding. RESULTS: By over-expressing individual Fru(M) isoforms in fru-expressing neurons in either males or females and assaying the global transcriptional response by RNA-sequencing, we show that three Fru(M) isoforms have different regulatory activities that depend on the sex of the fly. We identified several sets of genes regulated downstream of Fru(M) isoforms, including many annotated with neuronal functions. By determining the binding sites of individual Fru(M) isoforms using SELEX we demonstrate that the distinct zinc finger domain of each Fru(M) isoforms confers different DNA binding specificities. A genome-wide search for these binding site sequences finds that the gene sets identified as induced by over-expression of Fru(M) isoforms in males are enriched for genes that contain the binding sites. An analysis of the chromosomal distribution of genes downstream of Fru(M) shows that those that are induced and repressed in males are highly enriched and depleted on the X chromosome, respectively. CONCLUSIONS: This study elucidates the different regulatory and DNA binding activities of three Fru(M) isoforms on a genome-wide scale and identifies genes regulated by these isoforms. These results add to our understanding of sex chromosome biology and further support the hypothesis that in some cell-types genes with male-biased expression are enriched on the X chromosome.

}, issn = {1471-2164}, doi = {10.1186/1471-2164-14-659}, author = {Dalton, Justin E and Fear, Justin M and Knott, Simon and Baker, Bruce S and McIntyre, Lauren M and Arbeitman, Michelle N} } @article {6714, title = {Mapping mammalian synaptic connectivity.}, journal = {Cellular and Molecular Life Sciences: CMLS}, volume = {70}, year = {2013}, month = {2013 Dec}, pages = {4747-57}, abstract = {

Mapping mammalian synaptic connectivity has long been an important goal of neuroscientists since it is considered crucial for explaining human perception and behavior. Yet, despite enormous efforts, the overwhelming complexity of the neural circuitry and the lack of appropriate techniques to unravel it have limited the success of efforts to map connectivity. However, recent technological advances designed to overcome the limitations of conventional methods for connectivity mapping may bring about a turning point. Here, we address the promises and pitfalls of these new mapping technologies.

}, keywords = {Animals, Brain, Computational Biology, Connectome, Humans, Mammals, Nervous System Diseases, Synapses}, issn = {1420-9071}, doi = {10.1007/s00018-013-1417-y}, author = {Yook, Chaehyun and Druckmann, S and Kim, Jinhyun} } @article {6158, title = {The mechanical variables underlying object localization along the axis of the whisker.}, journal = {The Journal of Neuroscience}, volume = {33}, year = {2013}, month = {2013 Apr 17}, pages = {6726-41}, abstract = {

Rodents move their whiskers to locate objects in space. Here we used psychophysical methods to show that head-fixed mice can localize objects along the axis of a single whisker, the radial dimension, with one-millimeter precision. High-speed videography allowed us to estimate the forces and bending moments at the base of the whisker, which underlie radial distance measurement. Mice judged radial object location based on multiple touches. Both the number of touches (1-17) and the forces exerted by the pole on the whisker (up to 573 μN; typical peak amplitude, 100 μN) varied greatly across trials. We manipulated the bending moment and lateral force pressing the whisker against the sides of the follicle and the axial force pushing the whisker into the follicle by varying the compliance of the object during behavior. The behavioral responses suggest that mice use multiple variables (bending moment, axial force, lateral force) to extract radial object localization. Characterization of whisker mechanics revealed that whisker bending stiffness decreases gradually with distance from the face over five orders of magnitude. As a result, the relative amplitudes of different stress variables change dramatically with radial object distance. Our data suggest that mice use distance-dependent whisker mechanics to estimate radial object location using an algorithm that does not rely on precise control of whisking, is robust to variability in whisker forces, and is independent of object compliance and object movement. More generally, our data imply that mice can measure the amplitudes of forces in the sensory follicles for tactile sensation.

}, keywords = {Algorithms, Animals, Biological, Computer Simulation, Corneal Topography, Cues, Decision Making, Electron, Exploratory Behavior, Functional Laterality, Inbred C57BL, Male, Mice, Microscopy, Models, Physical Stimulation, Psychophysics, Scanning, Time Factors, Touch, Vibrissae}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4316-12.2013}, author = {Pammer, Lorenz and O{\textquoteright}Connor, Daniel H and Hires, S Andrew and Clack, Nathan G and Huber, Daniel and Myers, Eugene W and Svoboda, Karel} } @article {6486, title = {Mechanisms of retroaxonal barrage firing in hippocampal interneurons.}, journal = {The Journal of Physiology}, volume = {591}, year = {2013}, month = {2013 Oct 1}, pages = {4793-805}, abstract = {

Abstract We recently described a new form of neural integration and firing in a subset of interneurons, in which evoking hundreds of action potentials over tens of seconds to minutes produces a sudden barrage of action potentials lasting about a minute beyond the inciting stimulation. During this persistent firing, action potentials are generated in the distal axon and propagate retrogradely to the soma. To distinguish this from other forms of persistent firing, we refer to it here as {\textquoteright}retroaxonal barrage firing{\textquoteright}, or {\textquoteright}barrage firing{\textquoteright} for short. Its induction is blocked by chemical inhibitors of gap junctions and curiously, stimulation of one interneuron in some cases triggers barrage firing in a nearby, unstimulated interneuron. Beyond these clues, the mechanisms of barrage firing are unknown. Here we report new results related to these mechanisms. Induction of barrage firing was blocked by lowering extracellular calcium, as long as normal action potential threshold was maintained, and it was inhibited by blocking L-type voltage-gated calcium channels. Despite its calcium dependence, barrage firing was not prevented by inhibiting chemical synaptic transmission. Furthermore, loading the stimulated/recorded interneuron with BAPTA did not block barrage firing, suggesting that the required calcium entry occurs in other cells. Finally, barrage firing was normal in mice with deletion of the primary gene for neuronal gap junctions (connexin36), suggesting that non-neuronal gap junctions may be involved. Together, these findings suggest that barrage firing is probably triggered by a multicellular mechanism involving calcium signalling and gap junctions, but operating independently of chemical synaptic transmission.

}, issn = {1469-7793}, doi = {10.1113/jphysiol.2013.258418}, author = {Sheffield, Mark E J and Edgerton, Gabrielle B and Heuermann, Robert J and Deemyad, Tara and Mensh, Brett D and Spruston, Nelson} } @article {6485, title = {Mice infer probabilistic models for timing.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, year = {2013}, month = {2013 Sep 30}, pages = {17154-9}, abstract = {

Animals learn both whether and when a reward will occur. Neural models of timing posit that animals learn the mean time until reward perturbed by a fixed relative uncertainty. Nonetheless, animals can learn to perform actions for reward even in highly variable natural environments. Optimal inference in the presence of variable information requires probabilistic models, yet it is unclear whether animals can infer such models for reward timing. Here, we develop a behavioral paradigm in which optimal performance required knowledge of the distribution from which reward delays were chosen. We found that mice were able to accurately adjust their behavior to the SD of the reward delay distribution. Importantly, mice were able to flexibly adjust the amount of prior information used for inference according to the moment-by-moment demands of the task. The ability to infer probabilistic models for timing may allow mice to adapt to complex and dynamic natural environments.

}, issn = {1091-6490}, doi = {10.1073/pnas.1310666110}, author = {Li, Yi and Dudman, Joshua Tate} } @article {6271, title = {Microarrays reveal discrete phases in juvenile hormone regulation of mosquito reproduction.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, year = {2013}, month = {2013 Jun 11}, pages = {9623-4}, keywords = {Aedes, Animals, Female, Gene Expression Profiling, Juvenile Hormones, Methoprene}, issn = {1091-6490}, doi = {10.1073/pnas.1307487110}, author = {Riddiford, Lynn M} } @article {47902, title = {Modeling proteins using a super-secondary structure library and NMR chemical shift information.}, journal = {Structure (London, England : 1993)}, volume = {21}, year = {2013}, month = {2013 Jun 4}, pages = {891-9}, abstract = {

A remaining challenge in protein modeling is to predict structures for sequences with no sequence similarity to any experimentally solved structure. Based on earlier observations, the library of protein backbone supersecondary structure motifs (Smotifs) saturated about a decade ago. Therefore, it should be possible to build any structure from a combination of existing Smotifs with the help of limited experimental data that are sufficient to relate the backbone conformations of Smotifs between target proteins and known structures. Here, we present a hybrid modeling algorithm that relies on an exhaustive Smotif library and on nuclear magnetic resonance chemical shift patterns without any input of primary sequence information. In a test of 102 proteins, the algorithm delivered 90 homology-model-quality models, among them 24 high-quality ones, and a topologically correct solution for almost all cases. The current approach opens a venue to address the modeling of larger protein structures for which chemical shifts are available.

}, keywords = {Algorithms, Models, Molecular, Nuclear Magnetic Resonance, Biomolecular, Protein Structure, Secondary, Proteins}, issn = {1878-4186}, doi = {10.1016/j.str.2013.04.012}, author = {Menon, Vilas and Vallat, Brinda K and Dybas, Joseph M and Fiser, Andras} } @article {6413, title = {Molecular architecture of the ATP-dependent chromatin-remodeling complex SWR1.}, journal = {Cell}, volume = {154}, year = {2013}, month = {2013 Sep 12}, pages = {1220-31}, abstract = {

The ATP-dependent chromatin-remodeling complex SWR1 exchanges a variant histone H2A.Z/H2B dimer\ for a canonical H2A/H2B dimer at nucleosomes flanking histone-depleted regions, such as promoters. This localization of H2A.Z is conserved throughout eukaryotes. SWR1 is a 1 megadalton complex containing 14 different polypeptides, including the AAA+ ATPases Rvb1 and Rvb2. Using electron microscopy, we obtained the three-dimensional structure of SWR1 and mapped its major functional components. Our data show that SWR1 contains a single heterohexameric Rvb1/Rvb2 ring that, together with the catalytic subunit Swr1, brackets two independently assembled multisubunit modules. We also show that SWR1 undergoes a large conformational change upon engaging a limited region of the nucleosome core particle. Our work suggests an important structural role for the Rvbs and a distinct substrate-handling mode by SWR1, thereby providing a structural framework for understanding the complex dimer-exchange reaction.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2013.08.018}, author = {Nguyen, Vu Q and Ranjan, Anand and Stengel, Florian and Wei, Debbie and Aebersold, Ruedi and Wu, Carl and Leschziner, Andres E} } @article {6383, title = {A molt timer is involved in the metamorphic molt in Manduca sexta larvae.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, year = {2013}, month = {2013 Jul 30}, pages = {12518-25}, abstract = {

Manduca sexta larvae are a model for growth control in insects, particularly for the demonstration of critical weight, a threshold weight that the larva must surpass before it can enter metamorphosis on a normal schedule, and the inhibitory action of juvenile hormone on this checkpoint. We examined the effects of nutrition on allatectomized (CAX) larvae that lack juvenile hormone to impose the critical weight checkpoint. Normal larvae respond to prolonged starvation at the start of the last larval stage, by extending their subsequent feeding period to ensure that they begin metamorphosis above critical weight. CAX larvae, by contrast, show no homeostatic adjustment to starvation but start metamorphosis 4 d after feeding onset, regardless of larval size or the state of development of their imaginal discs. By feeding starved CAX larvae for various durations, we found that feeding for only 12-24 h was sufficient to result in metamorphosis on day 4, regardless of further feeding or body size. Manipulation of diet composition showed that protein was the critical macronutrient to initiate this timing. This constant period between the start of feeding and the onset of metamorphosis suggests that larvae possess a molt timer that establishes a minimal time to metamorphosis. Ligation experiments indicate that a portion of the timing may occur in the prothoracic glands. This positive system that promotes molting and the negative control via the critical weight checkpoint provide antagonistic pathways that evolution can modify to adapt growth to the ecological needs of different insects.

}, issn = {1091-6490}, doi = {10.1073/pnas.1311405110}, author = {Suzuki, Yuichiro and Koyama, Takashi and Hiruma, Kiyoshi and Riddiford, Lynn M and Truman, James W} } @article {46044, title = {Morphological and molecular changes in aging rat prelimbic prefrontal cortical synapses.}, journal = {Neurobiology of Aging}, volume = {34}, year = {2013}, month = {2013 Jan}, pages = {200-10}, abstract = {

Age-related impairments of executive functions appear to be related to reductions of the number and plasticity of dendritic spine synapses in the prefrontal cortex (PFC). Experimental evidence suggests that synaptic plasticity is mediated by the spine actin cytoskeleton, and a major pathway regulating actin-based plasticity is controlled by phosphorylated LIM kinase (pLIMK). We asked whether aging resulted in altered synaptic density, morphology, and pLIMK expression in the rat prelimbic region of the PFC. Using unbiased electron microscopy, we found an approximate 50\% decrease in the density of small synapses with aging, while the density of large synapses remained unchanged. Postembedding immunogold revealed that pLIMK localized predominantly to the postsynaptic density where it was increased in aging synapses by approximately 50\%. Furthermore, the age-related increase in pLIMK occurred selectively within the largest subset of prelimbic PFC synapses. Because pLIMK is known to inhibit actin filament plasticity, these data support the hypothesis that age-related increases in pLIMK may explain the stability of large synapses at the expense of their plasticity.

}, keywords = {Age Factors, Aging, Analysis of Variance, Animals, Gene Expression Regulation, Lim Kinases, Male, Microscopy, Electron, Transmission, Microscopy, Immunoelectron, Neurons, Post-Synaptic Density, Prefrontal Cortex, Rats, Rats, Sprague-Dawley, Synapses}, issn = {1558-1497}, doi = {10.1016/j.neurobiolaging.2012.05.014}, author = {Bloss, Erik B and Puri, Rishi and Yuk, Frank and Punsoni, Michael and Hara, Yuko and Janssen, William G and McEwen, Bruce S and Morrison, John H} } @article {6671, title = {Motor control of Drosophila courtship song.}, journal = {Cell Reports}, volume = {5}, year = {2013}, month = {2013 Nov 14}, pages = {678-86}, abstract = {

Many animals utilize acoustic signals-or songs-to attract mates. During courtship, Drosophila melanogaster males vibrate a wing to produce trains of pulses and extended tone, called pulse and sine song, respectively. Courtship songs in the genus Drosophila are exceedingly diverse, and different song features appear to have evolved independently of each other. How the nervous system allows such diversity to evolve is not understood. Here, we identify a wing muscle in D.\ melanogaster (hg1) that is uniquely male-enlarged. The hg1 motoneuron and the sexually dimorphic development of the hg1 muscle are required specifically for the sine component of the male song. In contrast, the motoneuron innervating a sexually monomorphic wing muscle, ps1, is required specifically for a feature of pulse song. Thus, individual wing motor pathways can control separate aspects of courtship song and may provide a "modular" anatomical substrate for the evolution of diverse songs.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2013.09.039}, author = {Shirangi, Troy R and Stern, David L and Truman, James W} } @article {46710, title = {mRNA on the move: the road to its biological destiny.}, journal = {The Journal of Biological Chemistry}, volume = {288}, year = {2013}, month = {2013 Jul 12}, pages = {20361-8}, abstract = {

Cells have evolved to regulate the asymmetric distribution of specific mRNA targets to institute spatial and temporal control over gene expression. Over the last few decades, evidence has mounted as to the importance of localization elements in the mRNA sequence and their respective RNA-binding proteins. Live imaging methodologies have shown mechanistic details of this phenomenon. In this minireview, we focus on the advanced biochemical and cell imaging techniques used to tweeze out the finer aspects of mechanisms of mRNA movement.

}, keywords = {Animals, Cytoplasm, Humans, In Situ Hybridization, Microscopy, Fluorescence, Models, Genetic, RNA Precursors, RNA Transport, RNA, Messenger, RNA-Binding Proteins}, issn = {1083-351X}, doi = {10.1074/jbc.R113.452094}, author = {Eliscovich, Carolina and Buxbaum, Adina R and Katz, Zachary B and Singer, Robert H} } @article {6090, title = {Multi-channel acoustic recording and automated analysis of Drosophila courtship songs.}, journal = {BMC Biology}, volume = {11}, year = {2013}, month = {2013 Jan 31}, pages = {11}, abstract = {

Drosophila melanogaster has served as a powerful model system for genetic studies of courtship songs. To accelerate research on the genetic and neural mechanisms underlying courtship song, we have developed a sensitive recording system to simultaneously capture the acoustic signals from 32 separate pairs of courting flies as well as software for automated segmentation of songs.

}, keywords = {Animal, Animal Communication, Animals, Drosophila melanogaster, Genetic Variation, Sexual Behavior, Videotape Recording}, issn = {1741-7007}, doi = {10.1186/1741-7007-11-11}, author = {Arthur, Benjamin J and Sunayama-Morita, Tomoko and Coen, Philip and Murthy, Mala and Stern, David L} } @article {6292, title = {Multidimensional traction force microscopy reveals out-of-plane rotational moments about focal adhesions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, year = {2013}, month = {2013 Jan 15}, pages = {881-6}, abstract = {

Recent methods have revealed that cells on planar substrates exert both shear (in-plane) and normal (out-of-plane) tractions against the extracellular matrix (ECM). However, the location and origin of the normal tractions with respect to the adhesive and cytoskeletal elements of cells have not been elucidated. We developed a high-spatiotemporal-resolution, multidimensional (2.5D) traction force microscopy to measure and model the full 3D nature of cellular forces on planar 2D surfaces. We show that shear tractions are centered under elongated focal adhesions whereas upward and downward normal tractions are detected on distal (toward the cell edge) and proximal (toward the cell body) ends of adhesions, respectively. Together, these forces produce significant rotational moments about focal adhesions in both protruding and retracting peripheral regions. Temporal 2.5D traction force microscopy analysis of migrating and spreading cells shows that these rotational moments are highly dynamic, propagating outward with the leading edge of the cell. Finally, we developed a finite element model to examine how rotational moments could be generated about focal adhesions in a thin lamella. Our model suggests that rotational moments can be generated largely via shear lag transfer to the underlying ECM from actomyosin contractility applied at the intracellular surface of a rigid adhesion of finite thickness. Together, these data demonstrate and probe the origin of a previously unappreciated multidimensional stress profile associated with adhesions and highlight the importance of new approaches to characterize cellular forces.

}, keywords = {Animals, Biological, Biophysical Phenomena, Cellular, Fibroblasts, Finite Element Analysis, Fluorescence, Focal Adhesions, Green Fluorescent Proteins, Mechanotransduction, Mice, Microscopy, Models, Recombinant Proteins, Rotation}, issn = {1091-6490}, doi = {10.1073/pnas.1207997110}, author = {Legant, Wesley R and Choi, Colin K and Miller, Jordan S and Shao, Lin and Gao, Liang and Betzig, Eric and Chen, Christopher S} } @article {6926, title = {Multiple interactions control synaptic layer specificity in the Drosophila visual system.}, journal = {Neuron}, volume = {77}, year = {2013}, month = {2013 Jan 23}, pages = {299-310}, abstract = {

How neurons form synapses within specific layers remains poorly understood. In the Drosophila medulla, neurons target to discrete layers in a precise fashion. Here we demonstrate that the targeting of L3 neurons to a specific layer occurs in two steps. Initially, L3 growth cones project to a common domain in the outer medulla, overlapping with the growth cones of other neurons destined for a different layer through the redundant functions of N-Cadherin (CadN) and Semaphorin-1a (Sema-1a). CadN mediates adhesion within the domain and Sema-1a mediates repulsion through Plexin A (PlexA) expressed in an adjacent region. Subsequently, L3 growth cones segregate from the domain into their target layer in part through Sema-1a/PlexA-dependent remodeling. Together, our results and recent studies argue that the early medulla is organized into common domains, comprising processes bound for different layers, and that discrete layers later emerge through successive interactions between processes within domains and developing layers.

}, keywords = {Animals, Cell Communication, Drosophila, Drosophila Proteins, Genetically Modified, Growth Cones, Medulla Oblongata, Protein Interaction Mapping, Synapses, Visual Pathways}, issn = {1097-4199}, doi = {10.1016/j.neuron.2012.11.007}, author = {Pecot, Matthew Y and Tadros, Wael and Nern, Aljoscha and Bader, Maya and Chen, Yi and Zipursky, S Lawrence} } @article {6455, title = {Multiple perceptible signals from a single olfactory glomerulus.}, journal = {Nature Neuroscience}, volume = {16}, year = {2013}, month = {2013 Sep 22}, pages = {1687-91}, abstract = {

Glomeruli are functional units in the olfactory system. The mouse olfactory bulb contains roughly 2,000 glomeruli, each receiving inputs from olfactory sensory neurons (OSNs) that express a specific odorant receptor gene. Odors typically activate many glomeruli in complex combinatorial patterns and it is unknown which features of neuronal activity in individual glomeruli contribute to odor perception. To address this, we used optogenetics to selectively activate single, genetically identified glomeruli in behaving mice. We found that mice could perceive the stimulation of a single glomerulus. Single-glomerulus stimulation was also detected on an intense odor background. In addition, different input intensities and the timing of input relative to sniffing were discriminated through one glomerulus. Our data suggest that each glomerulus can transmit odor information using identity, intensity and temporal coding cues. These multiple modes of information transmission may enable the olfactory system to efficiently identify and localize odor sources.

}, issn = {1546-1726}, doi = {10.1038/nn.3519}, author = {Smear, Matthew and Resulaj, Admir and Zhang, Jingji and Bozza, Thomas and Rinberg, Dmitry} } @article {6384, title = {Nancy E. Beckage 1950-2012: Pioneer in insect host-parasite interactions.}, journal = {Annual Review of Entomology}, volume = {59}, year = {2013}, month = {2013 Oct 9}, pages = {1-12}, abstract = {

Nancy E. Beckage is widely recognized for her pioneering work in the field of insect host-parasitoid interactions beginning with endocrine influences of the tobacco hornworm, Manduca sexta, host and its parasitoid wasp Apanteles congregatus (now Cotesia congregata) on each other{\textquoteright}s development. Moreover, her studies show that the polydnavirus carried by the parasitoid wasp not only protects the parasitoid from the host{\textquoteright}s immune defenses, but also is responsible for some of the developmental effects of parasitism. Nancy was a highly regarded mentor of both undergraduate and graduate students and more widely of women students and colleagues in entomology. Her service both to her particular area and to entomology in general through participation on federal grant review panels and in the governance of the Entomological Society of America, organization of symposia at both national and international meetings, and editorship of several different journal issues and of several books, is legendary. She has left behind a lasting legacy of increased understanding of multilevel endocrine and physiological interactions among insects and other organisms and a strong network of interacting scientists and colleagues in her area of entomology.

}, issn = {1545-4487}, doi = {10.1146/annurev-ento-052913-021246}, author = {Riddiford, L M and Webb, B A} } @article {6130, title = {Nanotools for neuroscience and brain activity mapping.}, journal = {ACS Nano}, volume = {7}, year = {2013}, month = {2013 Mar 26}, pages = {1850-66}, abstract = {

Neuroscience is at a crossroads. Great effort is being invested into deciphering specific neural interactions and circuits. At the same time, there exist few general theories or principles that explain brain function. We attribute this disparity, in part, to limitations in current methodologies. Traditional neurophysiological approaches record the activities of one neuron or a few neurons at a time. Neurochemical approaches focus on single neurotransmitters. Yet, there is an increasing realization that neural circuits operate at emergent levels, where the interactions between hundreds or thousands of neurons, utilizing multiple chemical transmitters, generate functional states. Brains function at the nanoscale, so tools to study brains must ultimately operate at this scale, as well. Nanoscience and nanotechnology are poised to provide a rich toolkit of novel methods to explore brain function by enabling simultaneous measurement and manipulation of activity of thousands or even millions of neurons. We and others refer to this goal as the Brain Activity Mapping Project. In this Nano Focus, we discuss how recent developments in nanoscale analysis tools and in the design and synthesis of nanomaterials have generated optical, electrical, and chemical methods that can readily be adapted for use in neuroscience. These approaches represent exciting areas of technical development and research. Moreover, unique opportunities exist for nanoscientists, nanotechnologists, and other physical scientists and engineers to contribute to tackling the challenging problems involved in understanding the fundamentals of brain function.

}, issn = {1936-086X}, doi = {10.1021/nn4012847}, author = {Alivisatos, A Paul and Andrews, Anne M and Boyden, Edward S and Chun, Miyoung and Church, George M and Deisseroth, Karl and Donoghue, John P and Fraser, Scott E and Lippincott-Schwartz, Jennifer and Looger, Loren L and Masmanidis, Sotiris and McEuen, Paul L and Nurmikko, Arto V and Park, Hongkun and Peterka, Darcy S and Reid, Clay and Roukes, Michael L and Scherer, Axel and Schnitzer, Mark and Sejnowski, Terrence J and Shepard, Kenneth L and Tsao, Doris and Turrigiano, Gina and Weiss, Paul S and Xu, Chris and Yuste, Rafael and Zhuang, Xiaowei} } @article {47641, title = {Nanotools for neuroscience and brain activity mapping.}, journal = {ACS nano}, volume = {7}, year = {2013}, month = {2013 Mar 26}, pages = {1850-66}, abstract = {

Neuroscience is at a crossroads. Great effort is being invested into deciphering specific neural interactions and circuits. At the same time, there exist few general theories or principles that explain brain function. We attribute this disparity, in part, to limitations in current methodologies. Traditional neurophysiological approaches record the activities of one neuron or a few neurons at a time. Neurochemical approaches focus on single neurotransmitters. Yet, there is an increasing realization that neural circuits operate at emergent levels, where the interactions between hundreds or thousands of neurons, utilizing multiple chemical transmitters, generate functional states. Brains function at the nanoscale, so tools to study brains must ultimately operate at this scale, as well. Nanoscience and nanotechnology are poised to provide a rich toolkit of novel methods to explore brain function by enabling simultaneous measurement and manipulation of activity of thousands or even millions of neurons. We and others refer to this goal as the Brain Activity Mapping Project. In this Nano Focus, we discuss how recent developments in nanoscale analysis tools and in the design and synthesis of nanomaterials have generated optical, electrical, and chemical methods that can readily be adapted for use in neuroscience. These approaches represent exciting areas of technical development and research. Moreover, unique opportunities exist for nanoscientists, nanotechnologists, and other physical scientists and engineers to contribute to tackling the challenging problems involved in understanding the fundamentals of brain function.

}, keywords = {Animals, Brain Mapping, Humans, Models, Neurological, Nanomedicine, Nanoparticles, Nanotechnology, Nervous System Physiological Phenomena}, issn = {1936-086X}, doi = {10.1021/nn4012847}, author = {Alivisatos, A Paul and Andrews, Anne M and Boyden, Edward S and Chun, Miyoung and Church, George M and Deisseroth, Karl and Donoghue, John P and Fraser, Scott E and Lippincott-Schwartz, Jennifer and Looger, Loren L and Masmanidis, Sotiris and McEuen, Paul L and Nurmikko, Arto V and Park, Hongkun and Peterka, Darcy S and Reid, Clay and Roukes, Michael L and Scherer, Axel and Schnitzer, Mark and Sejnowski, Terrence J and Shepard, Kenneth L and Tsao, Doris and Turrigiano, Gina and Weiss, Paul S and Xu, Chris and Yuste, Rafael and Zhuang, Xiaowei} } @article {47644, title = {NBR1 acts as an autophagy receptor for peroxisomes.}, journal = {Journal of cell science}, volume = {126}, year = {2013}, month = {2013 Feb 15}, pages = {939-52}, abstract = {

Selective macro-autophagy is an intracellular process by which large cytoplasmic materials are selectively sequestered and degraded in the lysosomes. Substrate selection is mediated by ubiquitylation and recruitment of ubiquitin-binding autophagic receptors such as p62, NBR1, NDP52 and Optineurin. Although it has been shown that these receptors act cooperatively to target some types of substrates to nascent autophagosomes, their precise roles are not well understood. We examined selective autophagic degradation of peroxisomes (pexophagy), and found that NBR1 is necessary and sufficient for pexophagy. Mutagenesis studies of NBR1 showed that the amphipathic α-helical J domain, the ubiquitin-associated (UBA) domain, the LC3-interacting region and the coiled-coil domain are necessary to mediate pexophagy. Strikingly, substrate selectivity is partly achieved by NBR1 itself by coincident binding of the J and UBA domains to peroxisomes. Although p62 is not required when NBR1 is in excess, its binding to NBR1 increases the efficiency of NBR1-mediated pexophagy. Together, these results suggest that NBR1 is the specific autophagy receptor for pexophagy.

}, keywords = {Autophagy, Blotting, Western, Cell Line, Hela Cells, Humans, Microscopy, Confocal, Microscopy, Electron, Peroxisomes, Proteins}, issn = {1477-9137}, doi = {10.1242/jcs.114819}, author = {Deosaran, Elizabeth and Larsen, Kenneth B and Hua, Rong and Sargent, Graeme and Wang, Yuqing and Kim, Sarah and Lamark, Trond and Jauregui, Miluska and Law, Kelsey and Lippincott-Schwartz, Jennifer and Brech, Andreas and Johansen, Terje and Kim, Peter K} } @article {6417, title = {Neural circuits and motivational processes for hunger.}, journal = {Current Opinion in Neurobiology}, volume = {23}, year = {2013}, month = {2013 Jun}, pages = {353-60}, abstract = {

How does an organism{\textquoteright}s internal state direct its actions? At one moment an animal forages for food with acrobatic feats such as tree climbing and jumping between branches. At another time, it travels along the ground to find water or a mate, exposing itself to predators along the way. These behaviors are costly in terms of energy or physical risk, and the likelihood of performing one set of actions relative to another is strongly modulated by internal state. For example, an animal in energy deficit searches for food and a dehydrated animal looks for water. The crosstalk between physiological state and motivational processes influences behavioral intensity and intent, but the underlying neural circuits are poorly understood. Molecular genetics along with optogenetic and pharmacogenetic tools for perturbing neuron function have enabled cell type-selective dissection of circuits that mediate behavioral responses to physiological state changes. Here, we review recent progress into neural circuit analysis of hunger in the mouse by focusing on a starvation-sensitive neuron population in the hypothalamus that is sufficient to promote voracious eating. We also consider research into the motivational processes that are thought to underlie hunger in order to outline considerations for bridging the gap between homeostatic and motivational neural circuits.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2013.04.006}, author = {Sternson, Scott M and Betley, J Nicholas and Cao, Zhen Fang Huang} } @article {6146, title = {Neural coding during active somatosensation revealed using illusory touch.}, journal = {Nature Neuroscience}, volume = {16}, year = {2013}, month = {2013 Jun 2}, pages = {958-65}, abstract = {

Active sensation requires the convergence of external stimuli with representations of body movements. We used mouse behavior, electrophysiology and optogenetics to dissect the temporal interactions among whisker movement, neural activity and sensation of touch. We photostimulated layer 4 activity in single barrels in a closed loop with whisking. Mimicking touch-related neural activity caused illusory perception of an object at a particular location, but scrambling the timing of the spikes over one whisking cycle (tens of milliseconds) did not abolish the illusion, indicating that knowledge of instantaneous whisker position is unnecessary for discriminating object locations. The illusions were induced only during bouts of directed whisking, when mice expected touch, and in the relevant barrel. Reducing activity biased behavior, consistent with a spike count code for object detection at a particular location. Our results show that mice integrate coding of touch with movement over timescales of a whisking bout to produce perception of active touch.

}, issn = {1546-1726}, doi = {10.1038/nn.3419}, author = {O{\textquoteright}Connor, Daniel H and Hires, S Andrew and Guo, Zengcai V and Li, Nuo and Yu, Jianing and Sun, Qian-Quan and Huber, Daniel and Svoboda, Karel} } @article {5539, title = {Neural signals of extinction in the inhibitory microcircuit of the ventral midbrain.}, journal = {Nature Neuroscience}, volume = {16}, year = {2013}, month = {2013 Jan}, pages = {71-8}, abstract = {

Midbrain dopaminergic (DA) neurons are thought to guide learning via phasic elevations of firing in response to reward predicting stimuli. The mechanism for these signals remains unclear. Using extracellular recording during associative learning, we found that inhibitory neurons in the ventral midbrain of mice responded to salient auditory stimuli with a burst of activity that occurred before the onset of the phasic response of DA neurons. This population of inhibitory neurons exhibited enhanced responses during extinction and was anticorrelated with the phasic response of simultaneously recorded DA neurons. Optogenetic stimulation revealed that this population was, in part, derived from inhibitory projection neurons of the substantia nigra that provide a robust monosynaptic inhibition of DA neurons. Thus, our results elaborate on the dynamic upstream circuits that shape the phasic activity of DA neurons and suggest that the inhibitory microcircuit of the midbrain is critical for new learning in extinction.

}, issn = {1546-1726}, doi = {10.1038/nn.3283}, author = {Pan, Wei-Xing and Brown, Jennifer and Dudman, Joshua Tate} } @conference {45640, title = {A neuron as a signal processing device}, booktitle = {2013 Asilomar Conference on Signals, Systems and Computers}, year = {2013}, month = {05/2014}, publisher = {IEEE}, organization = {IEEE}, address = {Pacific Grove, CA}, abstract = {

A neuron is a basic physiological and computational unit of the brain. While much is known about the physiological properties of a neuron, its computational role is poorly understood. Here we propose to view a neuron as a signal processing device that represents the incoming streaming data matrix as a sparse vector of synaptic weights scaled by an outgoing sparse activity vector. Formally, a neuron minimizes a cost function comprising a cumulative squared representation error and regularization terms. We derive an online algorithm that minimizes such cost function by alternating between the minimization with respect to activity and with respect to synaptic weights. The steps of this algorithm reproduce well-known physiological properties of a neuron, such as weighted summation and leaky integration of synaptic inputs, as well as an Oja-like, but parameter-free, synaptic learning rule. Our theoretical framework makes several predictions, some of which can be verified by the existing data, others require further experiments. Such framework should allow modeling the function of neuronal circuits without necessarily measuring all the microscopic biophysical parameters, as well as facilitate the design of neuromorphic electronics.

}, isbn = {9781479923885}, doi = {10.1109/ACSSC.2013.6810296}, author = {Tao Hu and Towfic, Z.J. and Pehlevan, C. and Genkin, A. and Chklovskii, D.B.} } @article {6579, title = {A neuron-based screening platform for optimizing genetically-encoded calcium indicators.}, journal = {PLoS One}, volume = {8}, year = {2013}, month = {2013}, pages = {e77728}, abstract = {

Fluorescent protein-based sensors for detecting neuronal activity have been developed largely based on non-neuronal screening systems. However, the dynamics of neuronal state variables (e.g., voltage, calcium, etc.) are typically very rapid compared to those of non-excitable cells. We developed an electrical stimulation and fluorescence imaging platform based on dissociated rat primary neuronal cultures. We describe its use in testing genetically-encoded calcium indicators (GECIs). Efficient neuronal GECI expression was achieved using lentiviruses containing a neuronal-selective gene promoter. Action potentials (APs) and thus neuronal calcium levels were quantitatively controlled by electrical field stimulation, and fluorescence images were recorded. Images were segmented to extract fluorescence signals corresponding to individual GECI-expressing neurons, which improved sensitivity over full-field measurements. We demonstrate the superiority of screening GECIs in neurons compared with solution measurements. Neuronal screening was useful for efficient identification of variants with both improved response kinetics and high signal amplitudes. This platform can be used to screen many types of sensors with cellular resolution under realistic conditions where neuronal state variables are in relevant ranges with respect to timing and amplitude.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0077728}, author = {Wardill, Trevor J. and Chen, Tsai-Wen and Schreiter, Eric R and Hasseman, Jeremy P and Tsegaye, Getahun and Fosque, Benjamin F and Behnam, Reza and Shields, Brenda C and Ramirez, Melissa and Kimmel, Bruce E and Kerr, Rex A and Jayaraman, Vivek and Looger, Loren L and Svoboda, Karel and Kim, Douglas S.} } @article {5883, title = {New technologies in imaging.}, journal = {Molecular Biology of the Cell}, volume = {24}, year = {2013}, month = {2013 Mar}, pages = {669}, abstract = {

Visualization of cellular and molecular processes is an indispensable tool for cell biologists, and innovations in microscopy methods unfailingly lead to new biological discoveries. Today, light microscopy (LM) provides ever-higher spatial and temporal resolution and visualization of biological process over enormous ranges. Electron microscopy (EM) is moving into the atomic resolution regime and allowing cellular analyses that are more physiological and sophisticated in scope. Importantly, much is being gained by combining multiple approaches, (e.g., LM and EM) to take advantage of their complementary strengths. The advent of high-throughput microscopies has led to a common need for sophisticated computational methods to quantitatively analyze huge amounts of data and translate images into new biological insights.

}, issn = {1939-4586}, doi = {10.1091/mbc.E12-12-0867}, author = {Galbraith, Catherine G and Keller, Philipp J and Nogales, Eva} } @article {65888, title = {NGL-2 Regulates Pathway-Specific Neurite Growth and Lamination, Synapse Formation, and Signal Transmission in the Retina}, journal = {Journal of Neuroscience}, volume = {33}, year = {2013}, month = {May-07-2014}, pages = {11949 - 11959}, abstract = {

Parallel processing is an organizing principle of many neural circuits. In the retina, parallel neuronal pathways process signals from rod and cone photoreceptors and support vision over a wide range of light levels. Toward this end, rods and cones form triad synapses with dendrites of distinct bipolar cell types, and the axons or dendrites, respectively, of horizontal cells (HCs). The molecular cues that promote the formation of specific neuronal pathways remain largely unknown. Here, we discover that developing and mature HCs express the leucine-rich repeat (LRR)-containing protein netrin-G ligand 2 (NGL-2). NGL-2 localizes selectively to the tips of HC axons, which form reciprocal connections with rods. In mice with null mutations in Ngl-2 (Ngl-2$^{-}$/$^{-}$), many branches of HC axons fail to stratify in the outer plexiform layer (OPL) and invade the outer nuclear layer. In addition, HC axons expand lateral territories and increase coverage of the OPL, but establish fewer synapses with rods. NGL-2 can form transsynaptic adhesion complexes with netrin-G2, which we show to be expressed by photoreceptors. In Ngl-2$^{-}$/$^{-}$ mice, we find specific defects in the assembly of presynaptic ribbons in rods, indicating that reverse signaling of complexes involving NGL-2 regulates presynaptic maturation. The development of HC dendrites and triad synapses of cone photoreceptors proceeds normally in the absence of NGL-2 and in vivo electrophysiology reveals selective defects in rod-mediated signal transmission in Ngl-2$^{-}$/$^{-}$ mice. Thus, our results identify NGL-2 as a central component of pathway-specific development in the outer retina.

}, issn = {0270-6474}, doi = {10.1523/JNEUROSCI.1521-13.2013}, url = {http://www.jneurosci.org/cgi/doi/10.1523/JNEUROSCI.1521-13.2013}, author = {Soto, F. and Watkins, K. L. and Johnson, R. E. and Schottler, F. and Kerschensteiner, D.} } @article {6435, title = {nhmmer: DNA homology search with profile HMMs.}, journal = {Bioinformatics}, volume = {29}, year = {2013}, month = {2013 Oct 1}, pages = {2487-9}, abstract = {

SUMMARY: Sequence database searches are an essential part of molecular biology, providing information about the function and evolutionary history of proteins, RNA molecules and DNA sequence elements. We present a tool for DNA/DNA sequence comparison that is built on the HMMER framework, which applies probabilistic inference methods based on hidden Markov models to the problem of homology search. This tool, called nhmmer, enables improved detection of remote DNA homologs, and has been used in combination with Dfam and RepeatMasker to improve annotation of transposable elements in the human genome. AVAILABILITY: nhmmer is a part of the new HMMER3.1 release. Source code and documentation can be downloaded from http://hmmer.org. HMMER3.1 is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and Mac OS/X. CONTACT: wheelert@janelia.hhmi.org.

}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btt403}, author = {Wheeler, Travis J and Eddy, Sean R.} } @article {6580, title = {Nonlinear dynamics support a linear population code in a retinal target-tracking circuit.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {33}, year = {2013}, month = {2013 Oct 23}, pages = {16971-82}, abstract = {

A basic task faced by the visual system of many organisms is to accurately track the position of moving prey. The retina is the first stage in the processing of such stimuli; the nature of the transformation here, from photons to spike trains, constrains not only the ultimate fidelity of the tracking signal but also the ease with which it can be extracted by other brain regions. Here we demonstrate that a population of fast-OFF ganglion cells in the salamander retina, whose dynamics are governed by a nonlinear circuit, serve to compute the future position of the target over hundreds of milliseconds. The extrapolated position of the target is not found by stimulus reconstruction but is instead computed by a weighted sum of ganglion cell outputs, the population vector average (PVA). The magnitude of PVA extrapolation varies systematically with target size, speed, and acceleration, such that large targets are tracked most accurately at high speeds, and small targets at low speeds, just as is seen in the motion of real prey. Tracking precision reaches the resolution of single photoreceptors, and the PVA algorithm performs more robustly than several alternative algorithms. If the salamander brain uses the fast-OFF cell circuit for target extrapolation as we suggest, the circuit dynamics should leave a microstructure on the behavior that may be measured in future experiments. Our analysis highlights the utility of simple computations that, while not globally optimal, are efficiently implemented and have close to optimal performance over a limited but ethologically relevant range of stimuli.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2257-13.2013}, author = {Leonardo, Anthony and Meister, Markus} } @article {6927, title = {Non-redundant coding of aversive odours in the main olfactory pathway.}, journal = {Nature}, volume = {497}, year = {2013}, month = {2013 May 23}, pages = {486-9}, abstract = {

Many species are critically dependent on olfaction for survival. In the main olfactory system of mammals, odours are detected by sensory neurons that express a large repertoire of canonical odorant receptors and a much smaller repertoire of trace amine-associated receptors (TAARs). Odours are encoded in a combinatorial fashion across glomeruli in the main olfactory bulb, with each glomerulus corresponding to a specific receptor. The degree to which individual receptor genes contribute to odour perception is unclear. Here we show that genetic deletion of the olfactory Taar gene family, or even a single Taar gene (Taar4), eliminates the aversion that mice display to low concentrations of volatile amines and to the odour of predator urine. Our findings identify a role for the TAARs in olfaction, namely, in the high-sensitivity detection of innately aversive odours. In addition, our data reveal that aversive amines are represented in a non-redundant fashion, and that individual main olfactory receptor genes can contribute substantially to odour perception.

}, keywords = {Amines, Animals, Avoidance Learning, Female, G-Protein-Coupled, Male, Mice, Models, Neurological, Odorant, Odors, Olfactory Bulb, Olfactory Pathways, Olfactory Receptor Neurons, Predatory Behavior, Receptors, Smell, Urine}, issn = {1476-4687}, doi = {10.1038/nature12114}, author = {Dewan, Adam and Pacifico, Rodrigo and Zhan, Ross and Rinberg, Dmitry and Bozza, Thomas} } @article {46597, title = {The novel gene tank, a tumor suppressor homolog, regulates ethanol sensitivity in Drosophila.}, journal = {The Journal of Neuroscience}, volume = {33}, year = {2013}, month = {2013 May 8}, pages = {8134-43}, abstract = {

In both mammalian and insect models of ethanol intoxication, high doses of ethanol induce motor impairment and eventually sedation. Sensitivity to the sedative effects of ethanol is inversely correlated with risk for alcoholism. However, the genes regulating ethanol sensitivity are largely unknown. Based on a previous genetic screen in Drosophila for ethanol sedation mutants, we identified a novel gene, tank (CG15626), the homolog of the mammalian tumor suppressor EI24/PIG8, which has a strong role in regulating ethanol sedation sensitivity. Genetic and behavioral analyses revealed that tank acts in the adult nervous system to promote ethanol sensitivity. We localized the function of tank in regulating ethanol sensitivity to neurons within the pars intercerebralis that have not been implicated previously in ethanol responses. We show that acutely manipulating the activity of all tank-expressing neurons, or of pars intercerebralis neurons in particular, alters ethanol sensitivity in a sexually dimorphic manner, since neuronal activation enhanced ethanol sedation in males, but not females. Finally, we provide anatomical evidence that tank-expressing neurons form likely synaptic connections with neurons expressing the neural sex determination factor fruitless (fru), which have been implicated recently in the regulation of ethanol sensitivity. We suggest that a functional interaction with fru neurons, many of which are sexually dimorphic, may account for the sex-specific effect induced by activating tank neurons. Overall, we have characterized a novel gene and corresponding set of neurons that regulate ethanol sensitivity in Drosophila.

}, keywords = {Adaptor Proteins, Signal Transducing, Analysis of Variance, Animals, Animals, Genetically Modified, Apoptosis Regulatory Proteins, Behavior, Animal, Central Nervous System Depressants, Dose-Response Relationship, Drug, Drosophila, Drosophila Proteins, Ethanol, Gene Expression Regulation, Green Fluorescent Proteins, Humans, Molecular Biology, Mutation, Nuclear Proteins, RNA Interference, TRPC Cation Channels, Tumor Suppressor Proteins}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3695-12.2013}, author = {Devineni, Anita V and Eddison, Mark and Heberlein, Ulrike} } @article {6412, title = {Nucleosome-free region dominates histone acetylation in targeting SWR1 to promoters for H2A.Z replacement.}, journal = {Cell}, volume = {154}, year = {2013}, month = {2013 Sep 12}, pages = {1232-45}, abstract = {

The histone variant H2A.Z is a genome-wide signature of nucleosomes proximal to eukaryotic regulatory DNA. Whereas the multisubunit chromatin remodeler SWR1 is known to catalyze ATP-dependent deposition of H2A.Z, the mechanism of SWR1 recruitment to S.\ cerevisiae promoters has been unclear. A sensitive assay for competitive binding of dinucleosome substrates revealed that SWR1 preferentially binds long nucleosome-free DNA and the adjoining nucleosome core particle, allowing discrimination of gene promoters over gene bodies. Analysis of mutants indicates that the conserved Swc2/YL1 subunit and the adenosine triphosphatase domain of Swr1 are mainly responsible for binding to substrate. SWR1 binding is enhanced on nucleosomes acetylated by the NuA4 histone acetyltransferase, but recognition of nucleosome-free and nucleosomal DNA is dominant over interaction with acetylated histones. Such hierarchical cooperation between DNA and histone signals expands the dynamic range of genetic switches, unifying classical gene regulation by DNA-binding factors with ATP-dependent nucleosome remodeling and posttranslational histone modifications.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2013.08.005}, author = {Ranjan, Anand and Mizuguchi, Gaku and Fitzgerald, Peter C and Wei, Debbie and Wang, Feng and Huang, Yingzi and Luk, Ed and Woodcock, Christopher L and Wu, Carl} } @article {48165, title = {Omnidirectional displacements for deformable surfaces.}, journal = {Medical image analysis}, volume = {17}, year = {2013}, month = {2013 May}, pages = {429-41}, abstract = {

Deformable surface models are often represented as triangular meshes in image segmentation applications. For a fast and easily regularized deformation onto the target object boundary, the vertices of the mesh are commonly moved along line segments (typically surface normals). However, in case of high mesh curvature, these lines may not intersect with the target boundary at all. Consequently, certain deformations cannot be achieved. We propose omnidirectional displacements for deformable surfaces (ODDS) to overcome this limitation. ODDS allow each vertex to move not only along a line segment but within the volumetric inside of a surrounding sphere, and achieve globally optimal deformations subject to local regularization constraints. However, allowing a ball-shaped instead of a linear range of motion per vertex significantly increases runtime and memory. To alleviate this drawback, we propose a hybrid approach, fastODDS, with improved runtime and reduced memory requirements. Furthermore, fastODDS can also cope with simultaneous segmentation of multiple objects. We show the theoretical benefits of ODDS with experiments on synthetic data, and evaluate ODDS and fastODDS quantitatively on clinical image data of the mandible and the hip bones. There, we assess both the global segmentation accuracy as well as local accuracy in high curvature regions, such as the tip-shaped mandibular coronoid processes and the ridge-shaped acetabular rims of the hip bones.

}, keywords = {Algorithms, Computer Simulation, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Models, Biological, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity}, issn = {1361-8423}, doi = {10.1016/j.media.2012.11.006}, author = {Kainmueller, Dagmar and Lamecker, Hans and Heller, Markus O and Weber, Britta and Hege, Hans-Christian and Zachow, Stefan} } @article {6904, title = {The Open Connectome Project Data Cluster: Scalable analysis and vision for high-throughput neuroscience.}, journal = {Scientific and Statistical Database Management: International Conference, SSDBM ... : Proceedings. International Conference on Scientific and Statistical Database Management}, year = {2013}, month = {2013 Jun 18}, abstract = {

We describe a scalable database cluster for the spatial analysis and annotation of high-throughput brain imaging data, initially for 3-d electron microscopy image stacks, but for time-series and multi-channel data as well. The system was designed primarily for workloads that build connectomes- neural connectivity maps of the brain-using the parallel execution of computer vision algorithms on high-performance compute clusters. These services and open-science data sets are publicly available at openconnecto.me. The system design inherits much from NoSQL scale-out and data-intensive computing architectures. We distribute data to cluster nodes by partitioning a spatial index. We direct I/O to different systems-reads to parallel disk arrays and writes to solid-state storage-to avoid I/O interference and maximize throughput. All programming interfaces are RESTful Web services, which are simple and stateless, improving scalability and usability. We include a performance evaluation of the production system, highlighting the effec-tiveness of spatial data organization.

}, doi = {10.1145/2484838.2484870}, author = {Burns, Randal and Roncal, William Gray and Kleissas, Dean and Lillaney, Kunal and Manavalan, Priya and Perlman, Eric and Berger, Daniel R. and Bock, Davi D and Chung, Kwanghun and Grosenick, Logan and Kasthuri, Narayanan and Weiler, Nicholas C and Deisseroth, Karl and Kazhdan, Michael and Lichtman, Jeff and Reid, R Clay and Smith, Stephen J and Szalay, Alexander S and Vogelstein, Joshua T and Vogelstein, R Jacob} } @article {6128, title = {An optimized fluorescent probe for visualizing glutamate neurotransmission.}, journal = {Nature Methods}, volume = {10}, year = {2013}, month = {2013 Feb}, pages = {162-70}, abstract = {

We describe an intensity-based glutamate-sensing fluorescent reporter (iGluSnFR) with signal-to-noise ratio and kinetics appropriate for in vivo imaging. We engineered iGluSnFR in vitro to maximize its fluorescence change, and we validated its utility for visualizing glutamate release by neurons and astrocytes in increasingly intact neurological systems. In hippocampal culture, iGluSnFR detected single field stimulus-evoked glutamate release events. In pyramidal neurons in acute brain slices, glutamate uncaging at single spines showed that iGluSnFR responds robustly and specifically to glutamate in situ, and responses correlate with voltage changes. In mouse retina, iGluSnFR-expressing neurons showed intact light-evoked excitatory currents, and the sensor revealed tonic glutamate signaling in response to light stimuli. In worms, glutamate signals preceded and predicted postsynaptic calcium transients. In zebrafish, iGluSnFR revealed spatial organization of direction-selective synaptic activity in the optic tectum. Finally, in mouse forelimb motor cortex, iGluSnFR expression in layer V pyramidal neurons revealed task-dependent single-spine activity during running.

}, keywords = {Animals, Astrocytes, Biosensing Techniques, Caenorhabditis elegans, Calcium Signaling, Escherichia coli Proteins, Excitatory Postsynaptic Potentials, Fluorescent Dyes, Glutamic Acid, Green Fluorescent Proteins, Hippocampus, Mice, Motor Cortex, Neurons, Photic Stimulation, Pyramidal Cells, Recombinant Fusion Proteins, Retina, Signal-To-Noise Ratio, Synaptic Transmission, Zebrafish}, issn = {1548-7105}, doi = {10.1038/nmeth.2333}, author = {Marvin, Jonathan S and Borghuis, Bart G and Tian, Lin and Cichon, Joseph and Harnett, Mark T and Akerboom, Jasper and Gordus, Andrew and Renninger, Sabine L. and Chen, Tsai-Wen and Bargmann, Cornelia I and Orger, Michael B. and Schreiter, Eric R and Demb, Jonathan B and Gan, Wen-Biao and Hires, S Andrew and Looger, Loren L} } @article {6581, title = {Optimizing the quantity/quality trade-off in connectome inference.}, journal = {Communications in Statistics-Theory and Methods}, volume = {42}, year = {2013}, month = {2013 Oct}, pages = {3455-62}, chapter = {3455}, abstract = {

We demonstrate a meaningful prospective power analysis for an (admittedly idealized) illustrative connectome inference task. Modeling neurons as vertices and synapses as edges in a simple random graph model, we optimize the trade-off between the number of (putative) edges identified and the accuracy of the edge identification procedure. We conclude that explicit analysis of the quantity/quality trade-off is imperative for optimal neuroscientific experimental design. In particular, identifying edges faster/more cheaply, but with more error, can yield superior inferential performance.

}, issn = {0361-0926}, doi = {10.1080/03610926.2011.630768}, author = {Priebe, C. E. and Vogelstein, J. and Bock, D.} } @article {5677, title = {Optogenetics in a transparent animal: circuit function in the larval zebrafish.}, journal = {Current Opinion in Neurobiology}, volume = {23}, year = {2013}, month = {2013 Feb}, pages = {119-26}, abstract = {

Optogenetic tools can be used to manipulate neuronal activity in a reversible and specific manner. In recent years, such methods have been applied to uncover causal relationships between activity in specified neuronal circuits and behavior in the larval zebrafish. In this small, transparent, genetic model organism, noninvasive manipulation and monitoring of neuronal activity with light is possible throughout the nervous system. Here we review recent work in which these new tools have been applied to zebrafish, and discuss some of the existing challenges of these approaches.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2012.11.001}, author = {Portugues, Ruben and Severi, Kristen E and Wyart, Claire and Ahrens, Misha B} } @article {48275, title = {Optogenetics through windows on the brain in the nonhuman primate.}, journal = {Journal of neurophysiology}, volume = {110}, year = {2013}, month = {2013 Sep}, pages = {1455-67}, abstract = {

Optogenetics combines optics and genetics to control neuronal activity with cell-type specificity and millisecond temporal precision. Its use in model organisms such as rodents, Drosophila, and Caenorhabditis elegans is now well-established. However, application of this technology in nonhuman primates (NHPs) has been slow to develop. One key challenge has been the delivery of viruses and light to the brain through the thick dura mater of NHPs, which can only be penetrated with large-diameter devices that damage the brain. The opacity of the NHP dura prevents visualization of the underlying cortex, limiting the spatial precision of virus injections, electrophysiological recordings, and photostimulation. Here, we describe a new optogenetics approach in which the native dura is replaced with an optically transparent artificial dura. This artificial dura can be penetrated with fine glass micropipettes, enabling precisely targeted injections of virus into brain tissue with minimal damage to cortex. The expression of optogenetic agents can be monitored visually over time. Most critically, this optical window permits targeted, noninvasive photostimulation and concomitant measurements of neuronal activity via intrinsic signal imaging and electrophysiological recordings. We present results from both anesthetized-paralyzed (optical imaging) and awake-behaving NHPs (electrophysiology). The improvements over current methods made possible by the artificial dura should enable the widespread use of optogenetic tools in NHP research, a key step toward the development of therapies for neuropsychiatric and neurological diseases in humans.

}, keywords = {Animals, Brain, Dura Mater, Gene Transfer Techniques, Haplorhini, Neurosurgical Procedures, Optogenetics}, issn = {1522-1598}, doi = {10.1152/jn.00153.2013}, author = {Ruiz, Octavio and Lustig, Brian R and Nassi, Jonathan J and Cetin, Ali and Reynolds, John H and Albright, Thomas D and Callaway, Edward M and Stoner, Gene R and Roe, Anna W} } @article {6295, title = {Organization of cortical and thalamic input to pyramidal neurons in mouse motor cortex.}, journal = {The Journal of Neuroscience}, volume = {33}, year = {2013}, month = {2013 Jan 9}, pages = {748-60}, abstract = {

Determining how long-range synaptic inputs engage pyramidal neurons in primary motor cortex (M1) is important for understanding circuit mechanisms involved in regulating movement. We used channelrhodopsin-2-assisted circuit mapping to characterize the long-range excitatory synaptic connections made by multiple cortical and thalamic areas onto pyramidal neurons in mouse vibrissal motor cortex (vM1). Each projection innervated vM1 pyramidal neurons with a unique laminar profile. Collectively, the profiles for different sources of input partially overlapped and spanned all cortical layers. Specifically, orbital cortex (OC) inputs primarily targeted neurons in L6. Secondary motor cortex (M2) inputs excited neurons mainly in L5B, including pyramidal tract neurons. In contrast, thalamocortical inputs from anterior motor-related thalamic regions, including VA/VL (ventral anterior thalamic nucleus/ventrolateral thalamic nucleus), targeted neurons in L2/3 through L5B, but avoided L6. Inputs from posterior sensory-related thalamic areas, including POm (posterior thalamic nuclear group), targeted neurons only in the upper layers (L2/3 and L5A), similar to inputs from somatosensory (barrel) cortex. Our results show that long-range excitatory inputs target vM1 pyramidal neurons in a layer-specific manner. Inputs from sensory-related cortical and thalamic areas preferentially target the upper-layer pyramidal neurons in vM1. In contrast, inputs from OC and M2, areas associated with volitional and cognitive aspects of movements, bypass local circuitry and have direct monosynaptic access to neurons projecting to brainstem and thalamus.

}, keywords = {Animals, Cerebral Cortex, Data Interpretation, Efferent Pathways, Electric Stimulation, Electrophysiological Phenomena, Female, Inbred C57BL, Male, Mice, Motor Cortex, Neurons, Patch-Clamp Techniques, Pons, Pyramidal Tracts, Statistical, Thalamus}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4338-12.2013}, author = {Hooks, Bryan M and Mao, Tianyi and Gutnisky, Diego A and Yamawaki, Naoki and Svoboda, Karel and Shepherd, Gordon M G} } @article {5959, title = {Overview of electron crystallography of membrane proteins: crystallization and screening strategies using negative stain electron microscopy.}, journal = {Current Protocols in Protein Science }, volume = {Chapter 17}, year = {2013}, month = {2013 Apr 2}, pages = {Unit 17.15}, abstract = {

Electron cryomicroscopy, or cryoEM, is an emerging technique for studying the three-dimensional structures of proteins and large macromolecular machines. Electron crystallography is a branch of cryoEM in which structures of proteins can be studied at resolutions that rival those achieved by X-ray crystallography. Electron crystallography employs two-dimensional crystals of a membrane protein embedded within a lipid bilayer. The key to a successful electron crystallographic experiment is the crystallization, or reconstitution, of the protein of interest. This unit describes ways in which protein can be expressed, purified, and reconstituted into well-ordered two-dimensional crystals. A protocol is also provided for negative stain electron microscopy as a tool for screening crystallization trials. When large and well-ordered crystals are obtained, the structures of both protein and its surrounding membrane can be determined to atomic resolution.

}, issn = {1934-3663}, doi = {10.1002/0471140864.ps1715s72}, author = {Nannenga, Brent L and Iadanza, Matthew G and Vollmar, Breanna S and Gonen, Tamir} } @article {6526, title = {The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes.}, journal = {PLoS Biology}, volume = {11}, year = {2013}, month = {2013 Jan}, pages = {e1001473}, abstract = {

The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic genome architecture with extensive genomic variation. During sexual genome development, the expressed, somatic macronuclear genome is whittled down to the genic portion of a small fraction (\~{}5\%) of its precursor "silent" germline micronuclear genome by a process of "unscrambling" and fragmentation. The tiny macronuclear "nanochromosomes" typically encode single, protein-coding genes (a small portion, 10\%, encode 2-8 genes), have minimal noncoding regions, and are differentially amplified to an average of \~{}2,000 copies. We report the high-quality genome assembly of \~{}16,000 complete nanochromosomes (\~{}50 Mb haploid genome size) that vary from 469 bp to 66 kb long (mean \~{}3.2 kb) and encode \~{}18,500 genes. Alternative DNA fragmentation processes \~{}10\% of the nanochromosomes into multiple isoforms that usually encode complete genes. Nucleotide diversity in the macronucleus is very high (SNP heterozygosity is \~{}4.0\%), suggesting that Oxytricha trifallax may have one of the largest known effective population sizes of eukaryotes. Comparison to other ciliates with nonscrambled genomes and long macronuclear chromosomes (on the order of 100 kb) suggests several candidate proteins that could be involved in genome rearrangement, including domesticated MULE and IS1595-like DDE transposases. The assembly of the highly fragmented Oxytricha macronuclear genome is the first completed genome with such an unusual architecture. This genome sequence provides tantalizing glimpses into novel molecular biology and evolution. For example, Oxytricha maintains tens of millions of telomeres per cell and has also evolved an intriguing expansion of telomere end-binding proteins. In conjunction with the micronuclear genome in progress, the O. trifallax macronuclear genome will provide an invaluable resource for investigating programmed genome rearrangements, complementing studies of rearrangements arising during evolution and disease.

}, keywords = {Base Sequence, DNA, DNA Copy Number Variations, DNA Fragmentation, Gene Amplification, Gene Rearrangement, Genes, Genetic Variation, Genome, Macronucleus, Messenger, Molecular Sequence Data, Oxytricha, Protein Binding, Protozoan, RNA, Sequence Analysis, Telomere}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1001473}, author = {Swart, Estienne C and Bracht, John R and Magrini, Vincent and Minx, Patrick and Chen, Xiao and Zhou, Yi and Khurana, Jaspreet S and Goldman, Aaron D and Nowacki, Mariusz and Schotanus, Klaas and Jung, Seolkyoung and Fulton, Robert S and Ly, Amy and McGrath, Sean and Haub, Kevin and Wiggins, Jessica L and Storton, Donna and Matese, John C and Parsons, Lance and Chang, Wei-Jen and Bowen, Michael S and Stover, Nicholas A and Jones, Thomas A and Eddy, Sean R. and Herrick, Glenn A and Doak, Thomas G and Wilson, Richard K and Mardis, Elaine R and Landweber, Laura F} } @article {6827, title = {Parallel neural pathways mediate CO2 avoidance responses in Drosophila.}, journal = {Science}, volume = {340}, year = {2013}, month = {2013 Jun 14}, pages = {1338-41}, abstract = {

Different stimulus intensities elicit distinct perceptions, implying that input signals are either conveyed through an overlapping but distinct subpopulation of sensory neurons or channeled into divergent brain circuits according to intensity. In Drosophila, carbon dioxide (CO2) is detected by a single type of olfactory sensory neuron, but information is conveyed to higher brain centers through second-order projection neurons (PNs). Two distinct pathways, PN(v)-1 and PN(v)-2, are necessary and sufficient for avoidance responses to low and high CO2 concentrations, respectively. Whereas low concentrations activate PN(v)-1, high concentrations activate both PN(v)s and GABAergic PN(v)-3, which may inhibit PN(v)-1 pathway-mediated avoidance behavior. Channeling a sensory input into distinct neural pathways allows the perception of an odor to be further modulated by both stimulus intensity and context.

}, keywords = {Animals, Carbon Dioxide, Drosophila melanogaster, Escape Reaction, Olfactory Pathways, Olfactory Receptor Neurons}, issn = {1095-9203}, doi = {10.1126/science.1236693}, author = {Lin, Hui-Hao and Chu, Li-An and Fu, Tsai-Feng and Dickson, Barry J and Chiang, Ann-Shyn} } @article {6672, title = {Parallel, redundant circuit organization for homeostatic control of feeding behavior.}, journal = {Cell}, volume = {155}, year = {2013}, month = {2013 Dec 5}, pages = {1337-50}, abstract = {

Neural circuits for essential natural behaviors are shaped by selective pressure to coordinate reliable execution of flexible goal-directed actions. However, the structural and functional organization of survival-oriented circuits is poorly understood due to exceptionally complex neuroanatomy. This is exemplified by AGRP neurons, which are a molecularly defined population that is sufficient to rapidly coordinate voracious food seeking and consumption behaviors. Here, we use cell-type-specific techniques for neural circuit manipulation and projection-specific anatomical analysis to examine the organization of this critical homeostatic circuit that regulates feeding. We show that AGRP neuronal circuits use a segregated, parallel, and redundant output configuration. AGRP neuron axon projections that target different brain regions originate from distinct subpopulations, several of which are sufficient to independently evoke feeding. The concerted anatomical and functional analysis of AGRP neuron projection populations reveals a constellation of core forebrain nodes, which are part of an extended circuit that mediates feeding behavior.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2013.11.002}, author = {Betley, J Nicholas and Cao, Zhen Fang Huang and Ritola, Kimberly D and Sternson, Scott M} } @article {45715, title = {The pea aphid uses a version of the terminal system during oviparous, but not viviparous, development.}, journal = {Evodevo}, volume = {4}, year = {2013}, month = {2013}, pages = {10}, abstract = {

BACKGROUND: In most species of aphid, female nymphs develop into either sexual or asexual adults depending on the length of the photoperiod to which their mothers were exposed. The progeny of these sexual and asexual females, in turn, develop in dramatically different ways. The fertilized oocytes of sexual females begin embryogenesis after being deposited on leaves (oviparous development) while the oocytes of asexual females complete embryogenesis within the mother (viviparous development). Compared with oviparous development, viviparous development involves a smaller transient oocyte surrounded by fewer somatic epithelial cells and a smaller early embryo that comprises fewer cells. To investigate whether patterning mechanisms differ between the earliest stages of the oviparous and viviparous modes of pea aphid development, we examined the expression of pea aphid orthologs of genes known to specify embryonic termini in other insects.

RESULTS: Here we show that pea aphid oviparous ovaries express torso-like in somatic posterior follicle cells and activate ERK MAP kinase at the posterior of the oocyte. In addition to suggesting that some posterior features of the terminal system are evolutionarily conserved, our detection of activated ERK in the oocyte, rather than in the embryo, suggests that pea aphids may transduce the terminal signal using a mechanism distinct from the one used in Drosophila. In contrast with oviparous development, the pea aphid version of the terminal system does not appear to be used during viviparous development, since we did not detect expression of torso-like in the somatic epithelial cells that surround either the oocyte or the blastoderm embryo and we did not observe restricted activated ERK in the oocyte.

CONCLUSIONS: We suggest that while oviparous oocytes and embryos may specify posterior fate through an aphid terminal system, viviparous oocytes and embryos employ a different mechanism, perhaps one that does not rely on an interaction between the oocyte and surrounding somatic cells. Together, these observations provide a striking example of a difference in the fundamental events of early development that is both environmentally induced and encoded by the same genome.

}, issn = {2041-9139}, doi = {10.1186/2041-9139-4-10}, author = {Bickel, Ryan D and Cleveland, Hillary C and Barkas, Joanna and Jeschke, Caitlin C and Raz, Amelie A and Stern, David L and Davis, Gregory K} } @article {4058, title = {Phasing electron diffraction data by molecular replacement: strategy for structure determination and refinement.}, journal = {Methods in Molecular Biology}, volume = {955}, year = {2013}, month = {2013}, pages = {243-72}, abstract = {

Electron crystallography is arguably the only electron cryomicroscopy (cryo EM) technique able to deliver atomic resolution data (better then 3 {\r A}) for membrane proteins embedded in a membrane. The progress in hardware improvements and sample preparation for diffraction analysis resulted in a number of recent examples where increasingly higher resolutions were achieved. Other chapters in this book detail the improvements in hardware and delve into the intricate art of sample preparation for microscopy and electron diffraction data collection and processing. In this chapter, we describe in detail the protocols for molecular replacement for electron diffraction studies. The use of a search model for phasing electron diffraction data essentially eliminates the need of acquiring image data rendering it immune to aberrations from drift and charging effects that effectively lower the attainable resolution.

}, issn = {1940-6029}, doi = {10.1007/978-1-62703-176-9_14}, author = {Wisedchaisri, G and Gonen, T} } @article {47635, title = {Photohighlighting approaches to access membrane dynamics of the Golgi apparatus.}, journal = {Methods in cell biology}, volume = {118}, year = {2013}, month = {2013}, pages = {217-34}, abstract = {

By providing quantitative, visual data of live cells, fluorescent protein-based microscopy techniques are furnishing novel insights into the complexities of membrane trafficking pathways and organelle dynamics. In this chapter, we describe experimental protocols employing fluorescent protein-based photohighlighting techniques to quantify protein movement into and out of the Golgi apparatus, an organelle that serves as the central sorting and processing station of the secretory pathway. The methods allow kinetic characteristics of Golgi-associated protein trafficking to be deciphered, which can help clarify how the Golgi maintains itself as a steady-state structure despite a continuous flux of secretory cargo passing into and out of this organelle. The guidelines presented in this chapter can also be applied to examine the dynamics of other intracellular organelle systems, elucidating mechanisms for how proteins are maintained in specific organelles and/or circulated to other destinations within the cell.

}, keywords = {Animals, Cercopithecus aethiops, CHO Cells, COS Cells, Cricetinae, Cricetulus, Fluorescence Recovery After Photobleaching, Golgi Apparatus, Green Fluorescent Proteins, Hela Cells, Humans, Membrane Glycoproteins, Protein Transport, Recombinant Fusion Proteins, Secretory Pathway, Viral Envelope Proteins}, issn = {0091-679X}, doi = {10.1016/B978-0-12-417164-0.00013-6}, author = {Sengupta, Prabuddha and Lippincott-Schwartz, Jennifer} } @article {48391, title = {Photon shot noise limits on optical detection of neuronal spikes and estimation of spike timing.}, journal = {Biophysical journal}, volume = {104}, year = {2013}, month = {2013 Jan 08}, pages = {51-62}, abstract = {

Optical approaches for tracking neural dynamics are of widespread interest, but a theoretical framework quantifying the physical limits of these techniques has been lacking. We formulate such a framework by using signal detection and estimation theory to obtain physical bounds on the detection of neural spikes and the estimation of their occurrence times as set by photon counting statistics (shot noise). These bounds are succinctly expressed via a discriminability index that depends on the kinetics of the optical indicator and the relative fluxes of signal and background photons. This approach facilitates quantitative evaluations of different indicators, detector technologies, and data analyses. Our treatment also provides optimal filtering techniques for optical detection of spikes. We compare various types of Ca(2+) indicators and show that background photons are a chief impediment to voltage sensing. Thus, voltage indicators that change color in response to membrane depolarization may offer a key advantage over those that change intensity. We also examine fluorescence resonance energy transfer indicators and identify the regimes in which the widely used ratiometric analysis of signals is substantially suboptimal. Overall, by showing how different optical factors interact to affect signal quality, our treatment offers a valuable guide to experimental design and provides measures of confidence to assess optically extracted traces of neural activity.

}, keywords = {Action Potentials, Animals, Computer Simulation, Fluorescence Resonance Energy Transfer, Neurons, Optical Imaging, Photons, Signal Processing, Computer-Assisted, Time Factors}, issn = {1542-0086}, doi = {10.1016/j.bpj.2012.07.058}, author = {Wilt, Brian A and Fitzgerald, James E and Schnitzer, Mark J} } @article {6267, title = {Potassium channels control the interaction between active dendritic integration compartments in layer 5 cortical pyramidal neurons.}, journal = {Neuron}, volume = {79}, year = {2013}, month = {2013 Aug 7}, pages = {516-29}, abstract = {

Active dendritic synaptic integration enhances the computational power of neurons. Such nonlinear processing generates an object-localization signal in the apical dendritic tuft of layer 5B cortical pyramidal neurons during sensory-motor behavior. Here, we employ electrophysiological and optical approaches in brain slices and behaving animals to investigate how excitatory synaptic input to this distal dendritic compartment influences neuronal output. We find that active dendritic integration throughout the apical dendritic tuft is highly compartmentalized by voltage-gated potassium (KV) channels. A high density of both transient and sustained KV channels was observed in all apical dendritic compartments. These channels potently regulated the interaction between apical dendritic tuft, trunk, and axosomatic integration zones to control neuronal output in\ vitro as well as the engagement of dendritic nonlinear processing in\ vivo during sensory-motor behavior. Thus, KV channels dynamically tune the interaction between active dendritic integration compartments in layer 5B pyramidal neurons to shape behaviorally relevant neuronal computations.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2013.06.005}, author = {Harnett, Mark T and Xu, Ning-long and Magee, Jeffrey C and Williams, Stephen R} } @proceedings {45794, title = {Potential Patterning Differences Underlying Oviparous and Viviparous Development in the Pea Aphid}, volume = {53}, year = {2013}, month = {01/2013}, pages = {E247-E247}, publisher = {OXFORD UNIV PRESS INC}, abstract = {

The pea aphid, Acyrthosiphon pisum, exhibits several environmentally cued, discrete, alternate phenotypes (polyphenisms) during its life cycle. In the case of the reproductive polyphenism, differences in day length determine whether mothers will produce daughters that reproduce either sexually by laying fertilized eggs (oviparous sexual reproduction), or asexually by allowing oocytes to complete embryogenesis within the mother without fertilization (viviparous parthenogenesis). Oocytes and embryos that are produced asexually develop more rapidly, are yolk-free, and much smaller than oocytes and embryos that are produced sexually. Perhaps most striking, the process of oocyte differentiation is truncated in the case of asexual/viviparous development, potentially precluding interactions between the oocyte and surrounding follicle cells that might take place during sexual/oviparous development. Given the important patterning roles that oocyte-follicle cell interactions play in Drosophila, these overt differences suggest that there may be underlying differences in the molecular mechanisms of pattern formation. We have found differences in the expression of homologs of torso-like and tailless, as well as activated MAP kinase, suggesting that there are important differences in the hemipteran version of the terminal patterning system between viviparous and oviparous development. Establishing such differences in the expression of patterning genes between these developmental modes is a first step toward understanding how a single genome manages to direct patterning events in such different embryological contexts.

}, url = {http://www.sicb.org/meetings/2013/schedule/abstractdetails.php?id=1253}, author = {R Bickel and H Cleveland and J Barkas and N Belletier and DL Stern and GK Davis} } @article {45716, title = {Pupariation site preference within and between Drosophila sibling species.}, journal = {Evolution}, volume = {67}, year = {2013}, month = {2013 Sep}, pages = {2714-27}, abstract = {

Holometabolous insects pass through a sedentary pupal stage and often choose a location for pupation that is different from the site of larval feeding. We have characterized a difference in pupariation site choice within and between sibling species of Drosophila. We found that, in nature, Drosophila sechellia pupariate within their host fruit, Morinda citrifolia, and that they perform this behavior in laboratory assays. In contrast, in the laboratory, geographically diverse strains of Drosophila simulans vary in their pupariation site preference; D. simulans lines from the ancestral range in southeast Africa pupariate on fruit, or a fruit substitute, whereas populations from Europe or the New World select sites off of fruit. We explored the genetic basis for the evolved preference in puariation site preference by performing quantitative trait locus mapping within and between species. We found that the interspecific difference is controlled largely by loci on chromosomes X and II. In contrast, variation between two strains of D. simulans appears to be highly polygenic, with the majority of phenotypic effects due to loci on chromosome III. These data address the genetic basis of how new traits arise as species diverge and populations disperse.

}, keywords = {Africa, Animal Distribution, Animals, Chromosomes, Insect, Drosophila, Europe, Evolution, Molecular, Genetic Speciation, Genetic Variation, Morinda, Phylogeography, Pupa, Quantitative Trait Loci, X Chromosome}, issn = {1558-5646}, doi = {10.1111/evo.12146}, author = {Erezyilmaz, Deniz F and Stern, David L} } @article {47643, title = {Quantifying spatial organization in point-localization superresolution images using pair correlation analysis.}, journal = {Nature protocols}, volume = {8}, year = {2013}, month = {2013 Feb}, pages = {345-54}, abstract = {

The distinctive distributions of proteins within subcellular compartments both at steady state and during signaling events have essential roles in cell function. Here we describe a method for delineating the complex arrangement of proteins within subcellular structures visualized using point-localization superresolution (PL-SR) imaging. The approach, called pair correlation photoactivated localization microscopy (PC-PALM), uses a pair-correlation algorithm to precisely identify single molecules in PL-SR imaging data sets, and it is used to decipher quantitative features of protein organization within subcellular compartments, including the existence of protein clusters and the size, density and number of proteins in these clusters. We provide a step-by-step protocol for PC-PALM, illustrating its analysis capability for four plasma membrane proteins tagged with photoactivatable GFP (PAGFP). The experimental steps for PC-PALM can be carried out in 3 d and the analysis can be done in \~{}6-8 h. Researchers need to have substantial experience in single-molecule imaging and statistical analysis to conduct the experiments and carry out this analysis.

}, keywords = {Algorithms, Green Fluorescent Proteins, Image Processing, Computer-Assisted, Intracellular Space, Membrane Proteins, Microscopy}, issn = {1750-2799}, doi = {10.1038/nprot.2013.005}, author = {Sengupta, Prabuddha and Jovanovic-Talisman, Tijana and Lippincott-Schwartz, Jennifer} } @article {6875, title = {Quantitative characterization of electron detectors for transmission electron microscopy.}, journal = {Journal of Structural Biology}, volume = {184}, year = {2013}, month = {2013 Dec}, pages = {385-93}, abstract = {

A new generation of direct electron detectors for transmission electron microscopy (TEM) promises significant improvement over previous detectors in terms of their modulation transfer function (MTF) and detective quantum efficiency (DQE). However, the performance of these new detectors needs to be carefully monitored in order to optimize imaging conditions and check for degradation over time. We have developed an easy-to-use software tool, FindDQE, to measure MTF and DQE of electron detectors using images of a microscope{\textquoteright}s built-in beam stop. Using this software, we have determined the DQE curves of four direct electron detectors currently available: the Gatan K2 Summit, the FEI Falcon I and II, and the Direct Electron DE-12, under a variety of total dose and dose rate conditions. We have additionally measured the curves for the Gatan US4000 and TVIPS TemCam-F416 scintillator-based cameras. We compare the results from our new method with published curves.

}, issn = {1095-8657}, doi = {10.1016/j.jsb.2013.10.016}, author = {Ruskin, Rachel S and Yu, Zhiheng and Grigorieff, Nikolaus} } @article {47639, title = {Rab10 delivers GLUT4 storage vesicles to the plasma membrane.}, journal = {Communicative \& integrative biology}, volume = {6}, year = {2013}, month = {2013 May 1}, pages = {e23779}, abstract = {

The glucose transporter, GLUT4, redistributes to the plasma membrane (PM) upon insulin stimulation, but also recycles through endosomal compartments. Different Rab proteins control these transport itineraries of GLUT4. However, the specific roles played by different Rab proteins in GLUT4 trafficking has been difficult to assess, primarily due to the complexity of endomembrane organization and trafficking. To address this problem, we recently performed advanced live cell imaging using total internal reflection fluorescence (TIRF) microscopy, which images objects ~150 nm from the PM, directly visualizing GLUT4 trafficking in response to insulin stimulation. Using IRAP-pHluorin to selectively label GSVs undergoing PM fusion in response to insulin, we identified Rab10 as the only Rab protein that binds this compartment. Rab14 was found to label transferrin-positive, endosomal compartments containing GLUT4. These also could fuse with the PM in response to insulin, albeit more slowly. Several other Rab proteins, including Rab4A, 4B and 8A, were found to mediate GLUT4 intra-endosomal recycling, serving to internalize surface-bound GLUT4 into endosomal compartments for ultimate delivery to GSVs. Thus, multiple Rab proteins regulate the circulation of GLUT4 molecules within the endomembrane system, maintaining optimal insulin responsiveness within cells.

}, issn = {1942-0889}, doi = {10.4161/cib.23779}, author = {Chen, Yu and Lippincott-Schwartz, Jennifer} } @article {6594, title = {Real-time dynamics of RNA polymerase II clustering in live human cells.}, journal = {Science}, volume = {341}, year = {2013}, month = {2013 Aug 9}, pages = {664-7}, abstract = {

Transcription is reported to be spatially compartmentalized in nuclear transcription factories with clusters of RNA polymerase II (Pol II). However, little is known about when these foci assemble or their relative stability. We developed a quantitative single-cell approach to characterize protein spatiotemporal organization, with single-molecule sensitivity in live eukaryotic cells. We observed that Pol II clusters form transiently, with an average lifetime of 5.1 ({\textpm} 0.4) seconds, which refutes the notion that they are statically assembled substructures. Stimuli affecting transcription yielded orders-of-magnitude changes in the dynamics of Pol II clusters, which implies that clustering is regulated and plays a role in the cell{\textquoteright}s ability to effect rapid response to external signals. Our results suggest that transient crowding of enzymes may aid in rate-limiting steps of gene regulation.

}, keywords = {Cell Line, Flavonoids, Gene Expression Regulation, Genetic, Humans, Piperidines, RNA Polymerase II, Single-Cell Analysis, Time Factors, Transcription, Transcription Elongation, Tumor}, issn = {1095-9203}, doi = {10.1126/science.1239053}, author = {Cisse, Ibrahim I and Izeddin, Ignacio and Causse, Sebastien Z and Boudarene, Lydia and Senecal, Adrien and Muresan, Leila and Dugast-Darzacq, Claire and Hajj, Bassam and Dahan, Maxime and Darzacq, Xavier} } @conference {48834, title = {Recurrent linear models of simultaneously-recorded neural populations.}, booktitle = {Neural Information Processing Systems (NIPS 2013)}, year = {2013}, month = {2013 Dec 05}, address = {Lake Tahoe}, abstract = {

Population neural recordings with long-range temporal structure are often best understood in terms of a shared underlying low-dimensional dynamical process. Advances in recording technology provide access to an ever larger fraction of the population, but the standard computational approaches available to identify the collective dynamics scale poorly with the size of the dataset. Here we describe a new, scalable approach to discovering the low-dimensional dynamics that underlie simultaneously recorded spike trains from a neural population. Our method is based on recurrent linear models (RLMs), and relates closely to timeseries models based on recurrent neural networks. We formulate RLMs for neural data by generalising the Kalman-filter-based likelihood calculation for latent linear dynamical systems (LDS) models to incorporate a generalised-linear observation process. We show that RLMs describe motor-cortical population data better than either directly-coupled generalised-linear models or latent linear dynamical system models with generalised-linear observations. We also introduce the cascaded linear model (CLM) to capture low-dimensional instantaneous correlations in neural populations. The CLM describes the cortical recordings better than either Ising or Gaussian models and, like the RLM, can be fit exactly and quickly. The CLM can also be seen as a generalization of a low-rank Gaussian model, in this case factor analysis. The computational tractability of the RLM and CLM allow both to scale to very high-dimensional neural data.

}, url = {http://papers.nips.cc/paper/4877-recurrent-linear-models-of-simultaneously-recorded-neural-populations}, author = {Pachitariu, Marius and Petreska, Biljana and Sahani, Maneesh} } @article {48841, title = {Regularization and nonlinearities for neural language models: when are they needed?}, journal = {arXiv}, year = {2013}, month = {2013 Jan 23}, pages = {arXiv:1301.5650}, abstract = {

Neural language models (LMs) based on recurrent neural networks (RNN) are some of the most successful word and character-level LMs. Why do they work so well, in particular better than linear neural LMs? Possible explanations are that RNNs have an implicitly better regularization or that RNNs have a higher capacity for storing patterns due to their nonlinearities or both. Here we argue for the first explanation in the limit of little training data and the second explanation for large amounts of text data. We show state-of-the-art performance on the popular and small Penn dataset when RNN LMs are regularized with random dropout. Nonetheless, we show even better performance from a simplified, much less expressive linear RNN model without off-diagonal entries in the recurrent matrix. We call this model an impulse-response LM (IRLM). Using random dropout, column normalization and annealed learning rates, IRLMs develop neurons that keep a memory of up to 50 words in the past and achieve a perplexity of 102.5 on the Penn dataset. On two large datasets however, the same regularization methods are unsuccessful for both models and the RNN{\textquoteright}s expressivity allows it to overtake the IRLM by 10 and 20 percent perplexity, respectively. Despite the perplexity gap, IRLMs still outperform RNNs on the Microsoft Research Sentence Completion (MRSC) task. We develop a slightly modified IRLM that separates long-context units (LCUs) from short-context units and show that the LCUs alone achieve a state-of-the-art performance on the MRSC task of 60.8\%. Our analysis indicates that a fruitful direction of research for neural LMs lies in developing more accessible internal representations, and suggests an optimization regime of very high momentum terms for effectively training such models.

}, url = {https://arxiv.org/abs/1301.5650}, author = {Pachitariu, Marius and Sahani, Maneesh} } @article {6654, title = {Regulation of onset of female mating and sex pheromone production by juvenile hormone in Drosophila melanogaster.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, year = {2013}, month = {2013 Nov 5}, pages = {18321-6}, abstract = {Juvenile hormone (JH) coordinates timing of female reproductive maturation in most insects. In Drosophila melanogaster, JH plays roles in both mating and egg maturation. However, very little is known about the molecular pathways associated with mating. Our behavioral analysis of females genetically lacking the corpora allata, the glands that produce JH, showed that they were courted less by males and mated later than control females. Application of the JH mimic, methoprene, to the allatectomized females just after eclosion rescued both the male courtship and the mating delay. Our studies of the null mutants of the JH receptors, Methoprene tolerant (Met) and germ cell-expressed (gce), showed that lack of Met in Met(27) females delayed the onset of mating, whereas lack of Gce had little effect. The Met(27) females were shown to be more attractive but less behaviorally receptive to copulation attempts. The behavioral but not the attractiveness phenotype was rescued by the Met genomic transgene. Analysis of the female cuticular hydrocarbon profiles showed that corpora allata ablation caused a delay in production of the major female-specific sex pheromones (the 7,11-C27 and -C29 dienes) and a change in the cuticular hydrocarbon blend. In the Met(27) null mutant, by 48 h, the major C27 diene was greatly increased relative to wild type. In contrast, the gce(2.5k) null mutant females were courted similarly to control females despite changes in certain cuticular hydrocarbons. Our findings indicate that JH acts primarily via Met to modulate the timing of onset of female sex pheromone production and mating.}, issn = {1091-6490}, doi = {10.1073/pnas.1318119110}, author = {Bilen, Julide and Atallah, Jade and Azanchi, Reza and Levine, Joel D and Riddiford, Lynn M} } @article {6298, title = {Rfam 11.0: 10 years of RNA families.}, journal = {Nucleic Acids Research}, volume = {41}, year = {2013}, month = {2013 Jan}, pages = {D226-32}, abstract = {

The Rfam database (available via the website at http://rfam.sanger.ac.uk and through our mirror at http://rfam.janelia.org) is a collection of non-coding RNA families, primarily RNAs with a conserved RNA secondary structure, including both RNA genes and mRNA cis-regulatory elements. Each family is represented by a multiple sequence alignment, predicted secondary structure and covariance model. Here we discuss updates to the database in the latest release, Rfam 11.0, including the introduction of genome-based alignments for large families, the introduction of the Rfam Biomart as well as other user interface improvements. Rfam is available under the Creative Commons Zero license.

}, keywords = {Base Sequence, Databases, Genomics, Internet, Molecular Sequence Annotation, Nucleic Acid, Nucleic Acid Conformation, RNA, Sequence Alignment, Untranslated, User-Computer Interface}, issn = {1362-4962}, doi = {10.1093/nar/gks1005}, author = {Burge, Sarah W and Daub, Jennifer and Eberhardt, Ruth and Tate, John and Barquist, Lars and Nawrocki, Eric P and Eddy, Sean R. and Gardner, Paul P and Bateman, Alex} } @article {46299, title = {Scaling laws of associative memory retrieval.}, journal = {Neural Computation}, volume = {25}, year = {2013}, month = {2013 Oct}, pages = {2523-44}, abstract = {

Most people have great difficulty in recalling unrelated items. For example, in free recall experiments, lists of more than a few randomly selected words cannot be accurately repeated. Here we introduce a phenomenological model of memory retrieval inspired by theories of neuronal population coding of information. The model predicts nontrivial scaling behaviors for the mean and standard deviation of the number of recalled words for lists of increasing length. Our results suggest that associative information retrieval is a dominating factor that limits the number of recalled items.

}, keywords = {Algorithms, Association Learning, Computer Simulation, Humans, Memory, Mental Recall, Models, Neurological, Neural Networks (Computer)}, issn = {1530-888X}, doi = {10.1162/NECO_a_00499}, author = {Romani, Sandro and Pinkoviezky, Itai and Rubin, Alon and Tsodyks, Misha} } @article {65031, title = {A Schnurri/Mad/Medea complex attenuates the dorsal-twist gradient readout at vnd.}, journal = {Dev Biol}, volume = {378}, year = {2013}, month = {2013 Jun 01}, pages = {64-72}, abstract = {

Morphogen gradients are used in developing embryos, where they subdivide a field of cells into territories characterized by distinct cell fate potentials. Such systems require both a spatially-graded distribution of the morphogen, and an ability to encode different responses at different target genes. However, the potential for different temporal responses is also present because morphogen gradients typically provide temporal cues, which may be a potential source of conflict. Thus, a low threshold response adapted for an early temporal onset may be inappropriate when the desired spatial response is a spatially-limited, high-threshold expression pattern. Here, we identify such a case with the Drosophila vnd locus, which is a target of the dorsal (dl) nuclear concentration gradient that patterns the dorsal/ventral (D/V) axis of the embryo. The vnd gene plays a critical role in the "ventral dominance" hierarchy of vnd, ind, and msh, which individually specify distinct D/V neural columnar fates in increasingly dorsal ectodermal compartments. The role of vnd in this regulatory hierarchy requires early temporal expression, which is characteristic of low-threshold responses, but its specification of ventral neurogenic ectoderm demands a relatively high-threshold response to dl. We show that the Neurogenic Ectoderm Enhancer (NEE) at vnd takes additional input from the complementary Dpp gradient via a conserved Schnurri/Mad/Medea silencer element (SSE) unlike NEEs at brk, sog, rho, and vn. These results show how requirements for conflicting temporal and spatial responses to the same gradient can be solved by additional inputs from complementary gradients.

}, keywords = {Animals, Base Sequence, Computational Biology, DNA-Binding Proteins, Drosophila melanogaster, Drosophila Proteins, Ectoderm, Enhancer Elements, Genetic, Gene Expression Profiling, Gene Expression Regulation, Developmental, Gene Silencing, Homeodomain Proteins, Molecular Sequence Data, Smad4 Protein, Time Factors, Tissue Distribution, Transcription Factors}, issn = {1095-564X}, doi = {10.1016/j.ydbio.2013.03.002}, author = {Crocker, Justin and Erives, Albert} } @article {6436, title = {Sensorimotor structure of Drosophila larva phototaxis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, year = {2013}, month = {2013 Sep 16}, pages = {E3868-77}, abstract = {

The avoidance of light by fly larvae is a classic paradigm for sensorimotor behavior. Here, we use behavioral assays and video microscopy to quantify the sensorimotor structure of phototaxis using the Drosophila larva. Larval locomotion is composed of sequences of runs (periods of forward movement) that are interrupted by abrupt turns, during which the larva pauses and sweeps its head back and forth, probing local light information to determine the direction of the successive run. All phototactic responses are mediated by the same set of sensorimotor transformations that require temporal processing of sensory inputs. Through functional imaging and genetic inactivation of specific neurons downstream of the sensory periphery, we have begun to map these sensorimotor circuits into the larval central brain. We find that specific sensorimotor pathways that govern distinct light-evoked responses begin to segregate at the first relay after the photosensory neurons.

}, issn = {1091-6490}, doi = {10.1073/pnas.1215295110}, author = {Kane, Elizabeth A and Gershow, Marc and Afonso, Bruno and Larderet, Ivan and Klein, Mason and Carter, Ashley R and de Bivort, Benjamin L and Sprecher, Simon G and Samuel, Aravinthan D. T.} } @article {6278, title = {Shortening of the elastic tandem immunoglobulin segment of titin leads to diastolic dysfunction.}, journal = {Circulation}, volume = {128}, year = {2013}, month = {2013 Jul 2}, pages = {19-28}, abstract = {

BACKGROUND: Diastolic dysfunction is a poorly understood but clinically pervasive syndrome that is characterized by increased diastolic stiffness. Titin is the main determinant of cellular passive stiffness. However, the physiological role that the tandem immunoglobulin (Ig) segment of titin plays in stiffness generation and whether shortening this segment is sufficient to cause diastolic dysfunction need to be established. METHODS AND RESULTS: We generated a mouse model in which 9 Ig-like domains (Ig3-Ig11) were deleted from the proximal tandem Ig segment of the spring region of titin (IG KO). Exon microarray analysis revealed no adaptations in titin splicing, whereas novel phospho-specific antibodies did not detect changes in titin phosphorylation. Passive myocyte stiffness was increased in the IG KO, and immunoelectron microscopy revealed increased extension of the remaining titin spring segments as the sole likely underlying mechanism. Diastolic stiffness was increased at the tissue and organ levels, with no consistent changes in extracellular matrix composition or extracellular matrix-based passive stiffness, supporting a titin-based mechanism for in vivo diastolic dysfunction. Additionally, IG KO mice have a reduced exercise tolerance, a phenotype often associated with diastolic dysfunction. CONCLUSIONS: Increased titin-based passive stiffness is sufficient to cause diastolic dysfunction with exercise intolerance.

}, issn = {1524-4539}, doi = {10.1161/CIRCULATIONAHA.112.001268}, author = {Chung, Charles S and Hutchinson, Kirk R and Methawasin, Mei and Saripalli, Chandra and Smith, John E and Hidalgo, Carlos G and Luo, Xiuju and Labeit, Siegfried and Guo, Caiying and Granzier, Henk L} } @article {46711, title = {Single cell analysis of RNA-mediated histone H3.3 recruitment to a cytomegalovirus promoter-regulated transcription site.}, journal = {The Journal of Biological Chemistry}, volume = {288}, year = {2013}, month = {2013 Jul 5}, pages = {19882-99}, abstract = {

Unlike the core histones, which are incorporated into nucleosomes concomitant with DNA replication, histone H3.3 is synthesized throughout the cell cycle and utilized for replication-independent (RI) chromatin assembly. The RI incorporation of H3.3 into nucleosomes is highly conserved and occurs at both euchromatin and heterochromatin. However, neither the mechanism of H3.3 recruitment nor its essential function is well understood. Several different chaperones regulate H3.3 assembly at distinct sites. The H3.3 chaperone, Daxx, and the chromatin-remodeling factor, ATRX, are required for H3.3 incorporation and heterochromatic silencing at telomeres, pericentromeres, and the cytomegalovirus (CMV) promoter. By evaluating H3.3 dynamics at a CMV promoter-regulated transcription site in a genetic background in which RI chromatin assembly is blocked, we have been able to decipher the regulatory events upstream of RI nucleosomal deposition. We find that at the activated transcription site, H3.3 accumulates with sense and antisense RNA, suggesting that it is recruited through an RNA-mediated mechanism. Sense and antisense transcription also increases after H3.3 knockdown, suggesting that the RNA signal is amplified when chromatin assembly is blocked and attenuated by nucleosomal deposition. Additionally, we find that H3.3 is still recruited after Daxx knockdown, supporting a chaperone-independent recruitment mechanism. Sequences in the H3.3 N-terminal tail and αN helix mediate both its recruitment to RNA at the activated transcription site and its interaction with double-stranded RNA in vitro. Interestingly, the H3.3 gain-of-function pediatric glioblastoma mutations, G34R and K27M, differentially affect H3.3 affinity in these assays, suggesting that disruption of an RNA-mediated regulatory event could drive malignant transformation.

}, keywords = {Cell Line, Chromatin Assembly and Disassembly, Cytomegalovirus, Histones, Humans, Nucleosomes, Promoter Regions, Genetic, Protein Structure, Secondary, RNA, Viral, Transcription, Genetic}, issn = {1083-351X}, doi = {10.1074/jbc.M113.473181}, author = {Newhart, Alyshia and Rafalska-Metcalf, Ilona U and Yang, Tian and Joo, Lucy M and Powers, Sara Lawrence and Kossenkov, Andrew V and Lopez-Jones, Melissa and Singer, Robert H and Showe, Louise C and Skordalakes, Emmanuel and Janicki, Susan M} } @article {68484, title = {Single-axonal organelle analysis method reveals new protein-motor associations.}, journal = {ACS Chem Neurosci}, volume = {4}, year = {2013}, month = {02/2013}, pages = {277-84}, abstract = {

Axonal transport of synaptic vesicle proteins is required to maintain neurons{\textquoteright} ability to communicate via synaptic transmission. Neurotransmitter-containing synaptic vesicles are assembled at synaptic terminals via highly regulated endocytosis of membrane proteins. These synaptic vesicle membrane proteins are synthesized in the cell body and transported to synapses in carrier vesicles that make their way down axons via microtubule-based transport utilizing kinesin molecular motors. Identifying the cargos that each kinesin motor protein carries from the cell bodies to the synapse is key to understanding both diseases caused by motor protein dysfunction and how synaptic vesicles are assembled. However, obtaining a bulk sample of axonal transport complexes from central nervous system (CNS) neurons to use for identification of their contents has posed a challenge to researchers. To obtain axonal carrier vesicles from primary cultured neurons, we fabricated a microfluidic chip designed to physically isolate axons from dendrites and cell bodies and developed a method to remove bulk axonal samples and label their contents. Synaptic vesicle protein carrier vesicles in these samples were labeled with antibodies to the synaptic vesicle proteins p38, SV2A, and VAMP2, and the anterograde axonal transport motor KIF1A, after which antibody overlap was evaluated using single-organelle TIRF microscopy. This work confirms a previously discovered association between KIF1A and p38 and shows that KIF1A also transports SV2A- and VAMP2-containing carrier vesicles.

}, keywords = {Animals, Axonal Transport, Cells, Cultured, Fluorescent Antibody Technique, Hippocampus, Kinesins, Membrane Glycoproteins, Mice, Microfluidic Analytical Techniques, Microscopy, Confocal, Nerve Tissue Proteins, Neurons, Organelles, Synaptic Vesicles, Synaptophysin, Transport Vesicles, Vesicle-Associated Membrane Protein 2, Vesicular Transport Proteins}, issn = {1948-7193}, doi = {10.1021/cn300136y}, author = {Sgro, Allyson E and Bajjalieh, Sandra M and Chiu, Daniel T} } @article {46716, title = {Single-molecule analysis of gene expression using two-color RNA labeling in live yeast.}, journal = {Nature Methods}, volume = {10}, year = {2013}, month = {2013 Feb}, pages = {119-21}, abstract = {

Live-cell imaging of mRNA yields important insights into gene expression, but it has generally been limited to the labeling of one RNA species and has never been used to count single mRNAs over time in yeast. We demonstrate a two-color imaging system with single-molecule resolution using MS2 and PP7 RNA labeling. We use this methodology to measure intrinsic noise in mRNA levels and RNA polymerase II kinetics at a single gene.

}, keywords = {Adenosine Triphosphatases, Gene Expression, In Situ Hybridization, Fluorescence, Levivirus, RNA Polymerase II, RNA, Fungal, RNA, Messenger, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins}, issn = {1548-7105}, doi = {10.1038/nmeth.2305}, author = {Hocine, Sami and Raymond, Pascal and Zenklusen, Daniel and Chao, Jeffrey A and Singer, Robert H} } @article {46601, title = {A small group of neurosecretory cells expressing the transcriptional regulator apontic and the neuropeptide corazonin mediate ethanol sedation in Drosophila.}, journal = {The Journal of Neuroscience}, volume = {33}, year = {2013}, month = {2013 Feb 27}, pages = {4044-54}, abstract = {

In the fruit fly Drosophila melanogaster, as in mammals, acute exposure to a high dose of ethanol leads to stereotypical behavioral changes beginning with increased activity, followed by incoordination, loss of postural control, and eventually, sedation. The mechanism(s) by which ethanol impacts the CNS leading to ethanol-induced sedation and the genes required for normal sedation sensitivity remain largely unknown. Here we identify the gene apontic (apt), an Myb/SANT-containing transcription factor that is required in the nervous system for normal sensitivity to ethanol sedation. Using genetic and behavioral analyses, we show that apt mediates sensitivity to ethanol sedation by acting in a small set of neurons that express Corazonin (Crz), a neuropeptide likely involved in the physiological response to stress. The activity of Crz neurons regulates the behavioral response to ethanol, as silencing and activating these neurons affects sedation sensitivity in opposite ways. Furthermore, this effect is mediated by Crz, as flies with reduced crz expression show reduced sensitivity to ethanol sedation. Finally, we find that both apt and crz are rapidly upregulated by acute ethanol exposure. Thus, we have identified two genes and a small set of peptidergic neurons that regulate sensitivity to ethanol-induced sedation. We propose that Apt regulates the activity of Crz neurons and/or release of the neuropeptide during ethanol exposure.

}, keywords = {Animals, Animals, Genetically Modified, Behavior, Animal, Brain, DNA-Binding Proteins, Dose-Response Relationship, Drug, Drosophila, Drosophila Proteins, Ethanol, Gene Expression Regulation, Green Fluorescent Proteins, Hypnotics and Sedatives, Metamorphosis, Biological, Mutation, Neurons, Neuropeptides, Neurosecretory Systems, RNA, Messenger, Transcription Factors}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3413-12.2013}, author = {McClure, Kimberly D and Heberlein, Ulrike} } @article {6222, title = {Spinal projection neurons control turning behaviors in zebrafish.}, journal = {Current Biology}, volume = {23}, year = {2013}, month = {2013 Aug 19}, pages = {1566-73}, abstract = {

Discrete populations of brainstem spinal projection neurons (SPNs) have been shown to exhibit behavior-specific responses during locomotion [1-9], suggesting that separate descending pathways, each dedicated to a specific behavior, control locomotion. In an alternative model, a large variety of motor outputs could be generated from different combinations of a small number of basic motor pathways. We examined this possibility by studying the precise role of ventromedially located hindbrain SPNs (vSPNs) in generating turning behaviors. We found that unilateral laser ablation of vSPNs reduces the tail deflection and cycle period specifically during the first undulation cycle of a swim bout, whereas later tail movements are unaffected. This holds true during phototaxic [10], optomotor [11], dark-flash-induced [12], and spontaneous turns [13], suggesting a universal role of these neurons in controlling turning behaviors. Importantly, we found that the ablation not only abolishes turns but also results in a dramatic increase in the number of forward swims, suggesting that these neurons transform forward swims into turns by introducing turning kinematics into a basic motor pattern of symmetric tail undulations. Finally, we show that vSPN activity is direction specific and graded by turning angle. Together, these results provide a clear example of how a specific motor pattern can be transformed into different behavioral events by the graded activation of a small set of SPNs.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2013.06.044}, author = {Huang, Kuo-Hua and Ahrens, Misha B and Dunn, Timothy W. and Engert, Florian} } @article {6125, title = {{\ss}-synuclein aggregates and induces neurodegeneration in dopaminergic neurons.}, journal = {Annals of Neurology}, volume = {74}, year = {2013}, month = {2013 Mar 28}, pages = {109-18}, abstract = {

Objective: While the contribution of α-Synuclein to neurodegeneration in Parkinson{\textquoteright}s disease is well accepted, the putative impact of its close homologue, β-Synuclein, is enigmatic. β-Synuclein is widely expressed throughout the central nervous system as is α-Synuclein, but the physiological functions of both proteins remain unknown. Recent findings supported the view that β-Synuclein can act as an ameliorating regulator of α-Synuclein-induced neurotoxicity, having neuroprotective rather than neurodegenerative capabilities, and being non-aggregating due to absence of most part of the aggregation-promoting NAC domain. However, a mutation of β-Synuclein linked to dementia with Lewy bodies rendered the protein neurotoxic in transgenic mice and fibrillation of β-Synuclein has been demonstrated in vitro. Methods / Results: Supporting the hypothesis that β-Synuclein can act as a neurodegeneration-inducing factor we now demonstrate that wild-type β-Synuclein is neurotoxic for cultured primary neurons. Furthermore, β-Synuclein formed proteinase K resistant aggregates in dopaminergic neurons in vivo, leading to pronounced and progressive neurodegeneration in rats. Expression of β-Synuclein caused mitochondrial fragmentation, but this fragmentation did not render mitochondria non-functional in terms of ion handling and respiration even in late stages of neurodegeneration. A comparison of the neurodegenerative effects induced by α-, β-, and γ-Synuclein revealed that β-Synuclein was eventually as neurotoxic as α-Synuclein for nigral dopaminergic neurons, while γ-Synuclein proved to be non-toxic and had very low aggregation propensity. Interpretation: Our results suggest that the role of β-Synuclein as a putative modulator of neuropathology in aggregopathies like Parkinson{\textquoteright}s disease and dementia with Lewy bodies needs to be revisited. ANN NEUROL 2013. {\textcopyright} 2013 American Neurological Association.

}, issn = {1531-8249}, doi = {10.1002/ana.23905}, author = {Taschenberger, G and Toloe, J and Tereshchenko, J and Akerboom, J and Wales, P and Benz, R and Becker, S and Outeiro, Tf and Looger, L and B{\"a}hr, M and Zweckstetter, M and K{\"u}gler, S} } @article {47705, title = {Structural foundations of resting-state and task-based functional connectivity in the human brain.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, year = {2013}, month = {2013 Apr 9}, pages = {6169-74}, abstract = {

Magnetic resonance imaging enables the noninvasive mapping of both anatomical white matter connectivity and dynamic patterns of neural activity in the human brain. We examine the relationship between the structural properties of white matter streamlines (structural connectivity) and the functional properties of correlations in neural activity (functional connectivity) within 84 healthy human subjects both at rest and during the performance of attention- and memory-demanding tasks. We show that structural properties, including the length, number, and spatial location of white matter streamlines, are indicative of and can be inferred from the strength of resting-state and task-based functional correlations between brain regions. These results, which are both representative of the entire set of subjects and consistently observed within individual subjects, uncover robust links between structural and functional connectivity in the human brain.

}, keywords = {Aging, Attention, Brain, Brain Mapping, Cognition, Computational Biology, Diffusion Magnetic Resonance Imaging, Humans, Magnetic Resonance Imaging, Memory, Models, Statistical, Neural Pathways, Software}, issn = {1091-6490}, doi = {10.1073/pnas.1219562110}, author = {Hermundstad, Ann M and Bassett, Danielle S and Brown, Kevin S and Aminoff, Elissa M and Clewett, David and Freeman, Scott and Frithsen, Amy and Johnson, Arianne and Tipper, Christine M and Miller, Michael B and Grafton, Scott T and Carlson, Jean M} } @article {46413, title = {Structure, activity, and substrate selectivity of the Orf6 thioesterase from Photobacterium profundum.}, journal = {Journal of Biological Chemistry}, volume = {288}, year = {2013}, month = {2013 Apr 12}, pages = {10841-8}, abstract = {

Thioesterase activity is typically required for the release of products from polyketide synthase enzymes, but no such enzyme has been characterized in deep-sea bacteria associated with the production of polyunsaturated fatty acids. In this work, we have expressed and purified the Orf6 thioesterase from Photobacterium profundum. Enzyme assays revealed that Orf6 has a higher specific activity toward long-chain fatty acyl-CoA substrates (palmitoyl-CoA and eicosapentaenoyl-CoA) than toward short-chain or aromatic acyl-CoA substrates. We determined a high resolution (1.05 A) structure of Orf6 that reveals a hotdog hydrolase fold arranged as a dimer of dimers. The putative active site of this structure is occupied by additional electron density not accounted for by the protein sequence, consistent with the presence of an elongated compound. A second crystal structure (1.40 A) was obtained from a crystal that was grown in the presence of Mg(2+), which reveals the presence of a binding site for divalent cations at a crystal contact. The Mg(2+)-bound structure shows localized conformational changes (root mean square deviation of 1.63 A), and its active site is unoccupied, suggesting a mechanism to open the active site for substrate entry or product release. These findings reveal a new thioesterase enzyme with a preference for long-chain CoA substrates in a deep-sea bacterium whose potential range of applications includes bioremediation and the production of biofuels.

}, keywords = {Bacterial Proteins, Crystallography, X-Ray, Open Reading Frames, Palmitoyl Coenzyme A, Photobacterium, Protein Multimerization, Protein Structure, Quaternary, Substrate Specificity, Thiolester Hydrolases}, issn = {1083-351X}, doi = {10.1074/jbc.M112.446765}, author = {Rodr{\'\i}guez-Guilbe, Mar{\'\i}a and Oyola-Robles, Delise and Schreiter, Eric R and Baerga-Ortiz, Abel} } @article {6673, title = {The structure and evolution of cis-regulatory regions: the shavenbaby story.}, journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences}, volume = {368}, year = {2013}, month = {2013 Dec 19}, pages = {20130028}, abstract = {

In this paper, we provide a historical account of the contribution of a single line of research to our current understanding of the structure of cis-regulatory regions and the genetic basis for morphological evolution. We revisit the experiments that shed light on the evolution of larval cuticular patterns within the genus Drosophila and the evolution and structure of the shavenbaby gene. We describe the experiments that led to the discovery that multiple genetic changes in the cis-regulatory region of shavenbaby caused the loss of dorsal cuticular hairs (quaternary trichomes) in first instar larvae of Drosophila sechellia. We also discuss the experiments that showed that the convergent loss of quaternary trichomes in D. sechellia and Drosophila ezoana was generated by parallel genetic changes in orthologous enhancers of shavenbaby. We discuss the observation that multiple shavenbaby enhancers drive overlapping patterns of expression in the embryo and that these apparently redundant enhancers ensure robust shavenbaby expression and trichome morphogenesis under stressful conditions. All together, these data, collected over 13 years, provide a fundamental case study in the fields of gene regulation and morphological evolution, and highlight the importance of prolonged, detailed studies of single genes.

}, issn = {1471-2970}, doi = {10.1098/rstb.2013.0028}, author = {Stern, David L and Frankel, Nicol{\'a}s} } @article {6582, title = {Structure of fully liganded Hb zeta(2)beta(s)(2) trapped in a tense conformation.}, journal = {Acta Crystallographica Section D:Biological Crystallography}, volume = {69}, year = {2013}, month = {2013 Oct}, pages = {2061-71}, abstract = {

A variant Hb zeta(2)beta(s)(2) that is formed from sickle hemoglobin (Hb S; alpha(2)beta(s)(2)) by exchanging adult alpha-globin with embryonic zeta-globin subunits shows promise as a therapeutic agent for sickle-cell disease (SCD). Hb zeta(2)beta(s)(2) inhibits the polymerization of deoxygenated Hb S in vitro and reverses characteristic features of SCD in vivo in mouse models of the disorder. When compared with either Hb S or with normal human adult Hb A (alpha(2)beta(2)), Hb zeta(2)beta(s)(2) exhibits atypical properties that include a high oxygen affinity, reduced cooperativity, a weak Bohr effect and blunted 2,3-diphosphoglycerate allostery. Here, the 1.95 angstrom resolution crystal structure of human Hb zeta(2)beta(s)(2) that was expressed in complex transgenic knockout mice and purified from their erythrocytes is presented. When fully liganded with carbon monoxide, Hb zeta(2)beta(s)(2) displays a central water cavity, a zeta 1-beta(s)2 (or zeta 2-beta(s)1) interface, intersubunit salt-bridge/hydrogen-bond interactions, C-terminal beta His146 salt-bridge interactions, and a beta-cleft, that are highly unusual for a relaxed hemoglobin structure and are more typical of a tense conformation. These quaternary tense-like features contrast with the tertiary relaxed-like conformations of the zeta 1-beta(s1) dimer and the CD and FG corners, as well as the overall structures of the heme cavities. This crystallographic study provides insights into the altered oxygen-transport properties of Hb zeta(2)beta(s)(2) and, moreover, decouples tertiary- and quaternary-structural events that are critical to Hb ligand binding and allosteric function.

}, issn = {0907-444910.1107/s0907444913019197}, doi = {10.1107/S0907444913019197}, author = {Safo, M. K. and Ko, T. P. and Abdulmalik, O. and He, Z. N. and Wang, A. H. J. and Schreiter, E. R. and Russell, J. E.} } @article {47633, title = {Superresolution imaging with standard fluorescent probes.}, journal = {Current protocols in cell biology / editorial board, Juan S. Bonifacino ... [et al.]}, volume = {60}, year = {2013}, month = {2013}, pages = {Unit 21.8.}, abstract = {

For more than 100 years, the ultimate resolution of a light microscope (\~{} 200 nm) has been constrained by the fundamental physical phenomenon of diffraction, as described by Ernst Abbe in 1873. While this limitation is just as applicable to today{\textquoteright}s light microscopes, it is the combination of high-end optics, clever methods of sample illumination, and computational techniques that has enabled researchers to access information at an order of magnitude greater resolution than once thought possible. This combination, broadly termed superresolution microscopy, has been increasingly practical for many labs to implement from both a hardware and software standpoint, but, as with many cutting-edge techniques, it also comes with limitations. One of the current drawbacks to superresolution microscopy is the limited number of probes and conditions that have been suitable for imaging. Here, a technique termed bleaching/blinking-assisted localization microscopy (BaLM) makes use of the inherent blinking and bleaching properties of almost all fluorophores as a means to generate superresolution images.

}, keywords = {Animals, Cercopithecus aethiops, COS Cells, Microscopy, Fluorescence, Signal-To-Noise Ratio}, issn = {1934-2616}, doi = {10.1002/0471143030.cb2108s60}, author = {Millis, Bryan A and Burnette, Dylan T and Lippincott-Schwartz, Jennifer and Kachar, Bechara} } @article {6089, title = {TALE-mediated modulation of transcriptional enhancers in vivo.}, journal = {Nature Methods}, volume = {10}, year = {2013}, month = {2013 Jun 30}, pages = {762-7}, abstract = {

We tested whether transcription activator-like effectors (TALEs) could mediate repression and activation of endogenous enhancers in the Drosophila genome. TALE repressors (TALERs) targeting each of the five even-skipped (eve) stripe enhancers generated repression specifically of the focal stripes. TALE activators (TALEAs) targeting the eve promoter or enhancers caused increased expression primarily in cells normally activated by the promoter or targeted enhancer, respectively. This effect supports the view that repression acts in a dominant fashion on transcriptional activators and that the activity state of an enhancer influences TALE binding or the ability of the VP16 domain to enhance transcription. In these assays, the Hairy repression domain did not exhibit previously described long-range transcriptional repression activity. The phenotypic effects of TALER and TALEA expression in larvae and adults are consistent with the observed modulations of eve expression. TALEs thus provide a novel tool for detection and functional modulation of transcriptional enhancers in their native genomic context.

}, issn = {1548-7105}, doi = {10.1038/nmeth.2543}, author = {Crocker, Justin and Stern, David L} } @article {46606, title = {Taok2 controls behavioral response to ethanol in mice.}, journal = {Genes, Brain, and Behavior}, volume = {12}, year = {2013}, month = {2013 Feb}, pages = {87-97}, abstract = {

Despite recent advances in the understanding of ethanol{\textquoteright}s biological action, many of the molecular targets of ethanol and mechanisms behind ethanol{\textquoteright}s effect on behavior remain poorly understood. In an effort to identify novel genes, the products of which regulate behavioral responses to ethanol, we recently identified a mutation in the dtao gene that confers resistance to the locomotor stimulating effect of ethanol in Drosophila. dtao encodes a member of the Ste20 family of serine/threonine kinases implicated in MAP kinase signaling pathways. In this study, we report that conditional ablation of the mouse dtao homolog, Taok2, constitutively and specifically in the nervous system, results in strain-specific and overlapping alterations in ethanol-dependent behaviors. These data suggest a functional conservation of dtao and Taok2 in mediating ethanol{\textquoteright}s biological action and identify Taok2 as a putative candidate gene for ethanol use disorders in humans.

}, keywords = {Alcohol Drinking, Alcoholism, Animals, Behavior, Animal, Conditioning, Classical, Ethanol, Gait Ataxia, Locomotion, MAP Kinase Kinase Kinases, Mice, Mice, Inbred C57BL, Mice, Transgenic, Protein-Serine-Threonine Kinases}, issn = {1601-183X}, doi = {10.1111/j.1601-183X.2012.00834.x}, author = {Kapfhamer, D and Taylor, S and Zou, M E and Lim, J P and Kharazia, V and Heberlein, U} } @article {6889, title = {Tapered whiskers are required for active tactile sensation.}, journal = {eLife}, volume = {2}, year = {2013}, month = {2013 Nov 19}, pages = {e01350}, abstract = {

Many mammals forage and burrow in dark constrained spaces. Touch through facial whiskers is important during these activities, but the close quarters makes whisker deployment challenging. The diverse shapes of facial whiskers reflect distinct ecological niches. Rodent whiskers are conical, often with a remarkably linear taper. Here we use theoretical and experimental methods to analyze interactions of mouse whiskers with objects. When pushed into objects, conical whiskers suddenly slip at a critical angle. In contrast, cylindrical whiskers do not slip for biologically plausible movements. Conical whiskers sweep across objects and textures in characteristic sequences of brief sticks and slips, which provide information about the tactile world. In contrast, cylindrical whiskers stick and remain stuck, even when sweeping across fine textures. Thus the conical whisker structure is adaptive for sensor mobility in constrained environments and in feature extraction during active haptic exploration of objects and surfaces. DOI: http://dx.doi.org/10.7554/eLife.01350.001.

}, issn = {2050-084X}, doi = {10.7554/eLife.01350}, author = {Hires, Samuel Andrew and Pammer, Lorenz and Svoboda, Karel and Golomb, David} } @article {46713, title = {Temporal and spatial characterization of nonsense-mediated mRNA decay.}, journal = {Genes \& Development}, volume = {27}, year = {2013}, month = {2013 Mar 1}, pages = {541-51}, abstract = {

Nonsense-mediated mRNA decay (NMD) is a quality control mechanism responsible for "surveying" mRNAs during translation and degrading those that harbor a premature termination codon (PTC). Currently the intracellular spatial location of NMD and the kinetics of its decay step in mammalian cells are under debate. To address these issues, we used single-RNA fluorescent in situ hybridization (FISH) and measured the NMD of PTC-containing β-globin mRNA in intact single cells after the induction of β-globin gene transcription. This approach preserves temporal and spatial information of the NMD process, both of which would be lost in an ensemble study. We determined that decay of the majority of PTC-containing β-globin mRNA occurs soon after its export into the cytoplasm, with a half-life of \<1 min; the remainder is degraded with a half-life of \>12 h, similar to the half-life of normal PTC-free β-globin mRNA, indicating that it had evaded NMD. Importantly, NMD does not occur within the nucleoplasm, thus countering the long-debated idea of nuclear degradation of PTC-containing transcripts. We provide a spatial and temporal model for the biphasic decay of NMD targets.

}, keywords = {Animals, beta-Globins, Cell Line, Cell Nucleus, Cytoplasm, Humans, In Situ Hybridization, Fluorescence, Nonsense Mediated mRNA Decay, RNA, Messenger, Time Factors}, issn = {1549-5477}, doi = {10.1101/gad.209635.112}, author = {Trcek, Tatjana and Sato, Hanae and Singer, Robert H and Maquat, Lynne E} } @article {6674, title = {Thalamocortical input onto layer 5 pyramidal neurons measured using quantitative large-scale array tomography.}, journal = {Frontiers in Neural Circuits}, volume = {7}, year = {2013}, month = {2013}, pages = {177}, abstract = {

The subcellular locations of synapses on pyramidal neurons strongly influences dendritic integration and synaptic plasticity. Despite this, there is little quantitative data on spatial distributions of specific types of synaptic input. Here we use array tomography (AT), a high-resolution optical microscopy method, to examine thalamocortical (TC) input onto layer 5 pyramidal neurons. We first verified the ability of AT to identify synapses using parallel electron microscopic analysis of TC synapses in layer 4. We then use large-scale array tomography (LSAT) to measure TC synapse distribution on L5 pyramidal neurons in a 1.00 {\texttimes} 0.83 {\texttimes} 0.21 mm(3) volume of mouse somatosensory cortex. We found that TC synapses primarily target basal dendrites in layer 5, but also make a considerable input to proximal apical dendrites in L4, consistent with previous work. Our analysis further suggests that TC inputs are biased toward certain branches and, within branches, synapses show significant clustering with an excess of TC synapse nearest neighbors within 5-15 μm compared to a random distribution. Thus, we show that AT is a sensitive and quantitative method to map specific types of synaptic input on the dendrites of entire neurons. We anticipate that this technique will be of wide utility for mapping functionally-relevant anatomical connectivity in neural circuits.

}, issn = {1662-5110}, doi = {10.3389/fncir.2013.00177}, author = {Rah, Jong-Cheol and Bas, Erhan and Colonell, Jennifer and Mishchenko, Yuriy and Karsh, Bill and Fetter, Richard D and Myers, Eugene W and Chklovskii, Dmitri B and Svoboda, Karel and Harris, Timothy D and Isaac, John T R} } @article {6633, title = {Three-dimensional electron crystallography of protein microcrystals.}, journal = {eLife}, volume = {2}, year = {2013}, month = {2013 Nov 19}, pages = {01345}, abstract = {

We demonstrate that it is feasible to determine high-resolution protein structures by electron crystallography of three-dimensional crystals in an electron cryo-microscope (CryoEM). Lysozyme microcrystals were frozen on an electron microscopy grid, and electron diffraction data collected to 1.7 {\r A} resolution. We developed a data collection protocol to collect a full-tilt series in electron diffraction to atomic resolution. A single tilt series contains up to 90 individual diffraction patterns collected from a single crystal with tilt angle increment of 0.1{\textendash}1{\textdegree} and a total accumulated electron dose less than 10 electrons per angstrom squared. We indexed the data from three crystals and used them for structure determination of lysozyme by molecular replacement followed by crystallographic refinement to 2.9 {\r A} resolution. This proof of principle paves the way for the implementation of a new technique, which we name {\textquoteleft}MicroED{\textquoteright}, that may have wide applicability in structural biology.

}, doi = {10.7554/eLife.01345}, author = {Shi, Dan and Nannenga, Brent L and Iadanza, Matthew G and Gonen, Tamir} } @article {6480, title = {Three-dimensional live microscopy beyond the diffraction limit.}, journal = {Journal of Optics}, volume = {15}, year = {2013}, month = {2013 Sep}, pages = {094002}, abstract = {

In fluorescence microscopy it has become possible to fundamentally overcome the diffraction limited resolution in all three spatial dimensions. However, to have the most impact in biological sciences, new optical microscopy techniques need to be compatible with live cell imaging: image acquisition has to be fast enough to capture cellular dynamics at the new resolution limit while light exposure needs to be minimized to prevent photo-toxic effects. With increasing spatial resolution, these requirements become more difficult to meet, even more so when volumetric imaging is performed. In this review, techniques that have been successfully applied to three-dimensional, super-resolution live microscopy are presented and their relative strengths and weaknesses are discussed.

}, issn = {2040-8978}, doi = {10.1088/2040-8978/15/9/094002}, author = {Fiolka, Reto} } @article {46715, title = {Time-integrated fluorescence cumulant analysis and its application in living cells.}, journal = {Methods in Enzymology}, volume = {518}, year = {2013}, month = {2013}, pages = {99-119}, abstract = {

Time-integrated fluorescence cumulant analysis (TIFCA) is a data analysis technique for fluorescence fluctuation spectroscopy (FFS) that extracts information from the cumulants of the integrated fluorescence intensity. It is the first exact theory that describes the effect of sampling time on FFS experiment. Rebinning of data to longer sampling times helps to increase the signal/noise ratio of the experimental cumulants of the photon counts. The sampling time dependence of the cumulants encodes both brightness and diffusion information of the sample. TIFCA analysis extracts this information by fitting the cumulants to model functions. Generalization of TIFCA to multicolor FFS experiment is straightforward. Here, we present an overview of the theory, its implementation, as well as the benefits and requirements of TIFCA. The questions of why, when, and how to use TIFCA will be discussed. We give several examples of practical applications of TIFCA, particularly focused on measuring molecular interaction in living cells.

}, keywords = {Cell Line, Cells, Humans, Protein Binding, Proteins, RNA, Messenger, Spectrometry, Fluorescence}, issn = {1557-7988}, doi = {10.1016/B978-0-12-388422-0.00005-4}, author = {Wu, Bin and Singer, Robert H and Mueller, Joachim D} } @article {5935, title = {Towards comprehensive cell lineage reconstructions in complex organisms using light-sheet microscopy.}, journal = {Development, Growth and Differentiation}, volume = {55}, year = {2013}, month = {2013 Apr 29}, pages = {563-78}, abstract = {

Understanding the development of complex multicellular organisms as a function of the underlying cell behavior is one of the most fundamental goals of developmental biology. The ability to quantitatively follow cell dynamics in entire developing embryos is an indispensable step towards such a system-level understanding. In recent years, light-sheet fluorescence microscopy has emerged as a particularly promising strategy for recording the in vivo data required to realize this goal. Using light-sheet fluorescence microscopy, entire complex organisms can be rapidly imaged in three dimensions at sub-cellular resolution, achieving high temporal sampling and excellent signal-to-noise ratio without damaging the living specimen or bleaching fluorescent markers. The resulting datasets allow following individual cells in vertebrate and higher invertebrate embryos over up to several days of development. However, the complexity and size of these multi-terabyte recordings typically preclude comprehensive manual analyses. Thus, new computational approaches are required to automatically segment cell morphologies, accurately track cell identities and systematically analyze cell behavior throughout embryonic development. We review current efforts in light-sheet microscopy and bioimage informatics towards this goal, and argue that comprehensive cell lineage reconstructions are finally within reach for many key model organisms, including fruit fly, zebrafish and mouse.

}, issn = {1440-169X}, doi = {10.1111/dgd.12063}, author = {Amat, Fernando and Keller, Philipp J} } @article {5680, title = {Towards semi-automatic reconstruction of neural circuits.}, journal = {Neuroinformatics}, volume = {11}, year = {2013}, month = {2013 Jan}, pages = {31-3}, issn = {1559-0089}, doi = {10.1007/s12021-012-9166-x}, author = {Cardona, Albert.} } @proceedings {6535, title = {Tracking multiple neurons on worm images.}, volume = {8669}, year = {2013}, month = {2013 Mar}, pages = {86692P}, publisher = {SPIE}, address = {Lake Buena Vista (Orlando Area), Florida, USA}, abstract = {

We are interested in establishing the correspondence between neuron activity and body curvature during various movements of C. Elegans worms. Given long sequences of images, specifically recorded to glow when the neuron is active, it is required to track all identifiable neurons in each frame. The characteristics of the neuron data, e.g., the uninformative nature of neuron appearance and the sequential ordering of neurons, renders standard single and multi-object tracking methods either ineffective or unnecessary for our task. In this paper, we propose a multi-target tracking algorithm that correctly assigns each neuron to one of several candidate locations in the next frame preserving shape constraint. The results demonstrate how the proposed method can robustly track more neurons than several existing methods in long sequences of images.

}, doi = {10.1117/12.2000087}, author = {Paraq, Toufiq and Butler, Victoria and Chklovskii, Dmitri} } @article {6265, title = {Transcription factors that convert adult cell identity are differentially polycomb repressed.}, journal = {PLoS One}, volume = {8}, year = {2013}, month = {2013 May}, pages = {e63407}, abstract = {

Transcription factors that can convert adult cells of one type to another are usually discovered empirically by testing factors with a known developmental role in the target cell. Here we show that standard genomic methods (RNA-seq and ChIP-seq) can help identify these factors, as most are more strongly Polycomb repressed in the source cell and more highly expressed in the target cell. This criterion is an effective genome-wide screen that significantly enriches for factors that can transdifferentiate several mammalian cell types including neural stem cells, neurons, pancreatic islets, and hepatocytes. These results suggest that barriers between adult cell types, as depicted in Waddington{\textquoteright}s "epigenetic landscape", consist in part of differentially Polycomb-repressed transcription factors. This genomic model of cell identity helps rationalize a growing number of transdifferentiation protocols and may help facilitate the engineering of cell identity for regenerative medicine.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0063407}, author = {Davis, Fred P and Eddy, Sean R.} } @article {68814, title = {Transgenic tools to characterize neuronal properties of discrete populations of zebrafish neurons}, journal = {Development}, volume = {140}, year = {2013}, month = {09/2013}, pages = {3927-3931}, abstract = {

The developing nervous system consists of a variety of cell types. Transgenic animals expressing reporter genes in specific classes of neuronal cells are powerful tools for the study of neuronal network formation. We generated a wide variety of transgenic zebrafish that expressed reporter genes in specific classes of neurons or neuronal progenitors. These include lines in which neurons of specific neurotransmitter phenotypes expressed fluorescent proteins or Gal4, and lines in which specific subsets of the dorsal progenitor domain in the spinal cord expressed fluorescent proteins. Using these, we examined domain organization in the developing dorsal spinal cord, and found that there are six progenitor domains in zebrafish, which is similar to the domain organization in mice. We also systematically characterized neurotransmitter properties of the neurons that are produced from each domain. Given that reporter gene expressions occurs in a wide area of the nervous system in the lines generated, these transgenic fish should serve as powerful tools for the investigation of not only the neurons in the dorsal spinal cord but also neuronal structures and functions in many other regions of the nervous system.

}, issn = {0950-1991}, doi = {10.1242/dev.099531}, url = {https://doi.org/10.1242/dev.099531}, author = {Satou, Chie and Kimura, Yukiko and Hirata, Hiromi and Suster, Maximiliano L. and Kawakami, Koichi and Higashijima, Shin-Ichi} } @article {6537, title = {Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila.}, journal = {BMC Bioinformatics}, volume = {14}, year = {2013}, month = {2013 Sep 3}, pages = {265}, abstract = {

BACKGROUND: Every genome contains a large number of uncharacterized proteins that may encode entirely novel biological systems. Many of these uncharacterized proteins fall into related sequence families. By applying sequence and structural analysis we hope to provide insight into novel biology. RESULTS: We analyze a previously uncharacterized Pfam protein family called DUF4424 [Pfam:PF14415]. The recently solved three-dimensional structure of the protein lpg2210 from Legionella pneumophila provides the first structural information pertaining to this family. This protein additionally includes the first representative structure of another Pfam family called the YARHG domain [Pfam:PF13308]. The Pfam family DUF4424 adopts a 19-stranded beta-sandwich fold that shows similarity to the N-terminal domain of leukotriene A-4 hydrolase. The YARHG domain forms an all-helical domain at the C-terminus. Structure analysis allows us to recognize distant similarities between the DUF4424 domain and individual domains of M1 aminopeptidases and tricorn proteases, which form massive proteasome-like capsids in both archaea and bacteria. CONCLUSIONS: Based on our analyses we hypothesize that the DUF4424 domain may have a role in forming large, multi-component enzyme complexes. We suggest that the YARGH domain may play a role in binding a moiety in proximity with peptidoglycan, such as a hydrophobic outer membrane lipid or lipopolysaccharide.

}, issn = {1471-2105}, doi = {10.1186/1471-2105-14-265}, author = {Coggill, Penelope and Eberhardt, Ruth Y and Finn, Robert D and Chang, Yuanyuan and Jaroszewski, Lukasz and Godzik, Adam and Das, Debanu and Xu, Qingping and Axelrod, Herbert L and Aravind, L and Murzin, Alexey G and Bateman, Alex} } @article {6031, title = {Two-photon calcium imaging during fictive navigation in virtual environments.}, journal = {Frontiers in Neural Circuits}, volume = {7}, year = {2013}, month = {2013 Jun 6}, pages = {104}, abstract = {

A full understanding of nervous system function requires recording from large populations of neurons during naturalistic behaviors. Here we enable paralyzed larval zebrafish to fictively navigate two-dimensional virtual environments while we record optically from many neurons with two-photon imaging. Electrical recordings from motor nerves in the tail are decoded into intended forward swims and turns, which are used to update a virtual environment displayed underneath the fish. Several behavioral features-such as turning responses to whole-field motion and dark avoidance-are well-replicated in this virtual setting. We readily observed neuronal populations in the hindbrain with laterally selective responses that correlated with right or left optomotor behavior. We also observed neurons in the habenula, pallium, and midbrain with response properties specific to environmental features. Beyond single-cell correlations, the classification of network activity in such virtual settings promises to reveal principles of brainwide neural dynamics during behavior.

}, issn = {1662-5110}, doi = {10.3389/fncir.2013.00104 *equal contribution}, author = {Ahrens, Misha B* and Huang, Kuo Hua* and Narayan, Sujatha and Mensh, Brett D and Engert, Florian} } @article {6129, title = {Two-photon imaging of nonlinear glutamate release dynamics at bipolar cell synapses in the mouse retina.}, journal = {The Journal of Neuroscience : The Official Journal of the Society for Neuroscience}, volume = {33}, year = {2013}, month = {2013 Jul 3}, pages = {10972-85}, abstract = {

Alpha/Y-type retinal ganglion cells encode visual information with a receptive field composed of nonlinear subunits. This nonlinear subunit structure enhances sensitivity to patterns composed of high spatial frequencies. The Y-cell{\textquoteright}s subunits are the presynaptic bipolar cells, but the mechanism for the nonlinearity remains incompletely understood. We investigated the synaptic basis of the subunit nonlinearity by combining whole-cell recording of mouse Y-type ganglion cells with two-photon fluorescence imaging of a glutamate sensor (iGluSnFR) expressed on their dendrites and throughout the inner plexiform layer. A control experiment designed to assess iGluSnFR{\textquoteright}s dynamic range showed that fluorescence responses from Y-cell dendrites increased proportionally with simultaneously recorded excitatory current. Spatial resolution was sufficient to readily resolve independent release at intermingled ON and OFF bipolar terminals. iGluSnFR responses at Y-cell dendrites showed strong surround inhibition, reflecting receptive field properties of presynaptic release sites. Responses to spatial patterns located the origin of the Y-cell nonlinearity to the bipolar cell output, after the stage of spatial integration. The underlying mechanism differed between OFF and ON pathways: OFF synapses showed transient release and strong rectification, whereas ON synapses showed relatively sustained release and weak rectification. At ON synapses, the combination of fast release onset with slower release offset explained the nonlinear response of the postsynaptic ganglion cell. Imaging throughout the inner plexiform layer, we found transient, rectified release at the central-most levels, with increasingly sustained release near the borders. By visualizing glutamate release in real time, iGluSnFR provides a powerful tool for characterizing glutamate synapses in intact neural circuits.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.1241-13.2013}, author = {Borghuis, Bart G and Marvin, Jonathan S and Looger, Loren L and Demb, Jonathan B} } @article {6124, title = {Ultrasensitive fluorescent proteins for imaging neuronal activity.}, journal = {Nature}, volume = {499}, year = {2013}, month = {2013 Jul 18}, pages = {295-300}, abstract = {

Fluorescent calcium sensors are widely used to image neural activity. Using structure-based mutagenesis and neuron-based screening, we developed a family of ultrasensitive protein calcium sensors (GCaMP6) that outperformed other sensors in cultured neurons and in zebrafish, flies and mice in vivo. In layer 2/3 pyramidal neurons of the mouse visual cortex, GCaMP6 reliably detected single action potentials in neuronal somata and orientation-tuned synaptic calcium transients in individual dendritic spines. The orientation tuning of structurally persistent spines was largely stable over timescales of weeks. Orientation tuning averaged across spine populations predicted the tuning of their parent cell. Although the somata of GABAergic neurons showed little orientation tuning, their dendrites included highly tuned dendritic segments (5{\textendash}40-{\textmu}m long). GCaMP6 sensors thus provide new windows into the organization and dynamics of neural circuits over multiple spatial and temporal scales.

}, doi = {10.1038/nature12354}, author = {Chen, Tsai-Wen and Wardill, Trevor J. and Sun, Yi and Pulvar, Stefan R. and Renninger, Sabine L. and Baohan, Amy and Schreiter, Eric R and Kerr, Rex A and Orger, Michael B. and Jayaraman, Vivek and Looger, Loren L and Svoboda, Karel and Kim, Douglas S.} } @article {6533, title = {Unclosed HIV-1 capsids suggest a curled sheet model of assembly.}, journal = {Journal of Molecular Biology}, volume = {425}, year = {2013}, month = {2013 Jan 9}, pages = {112-23}, abstract = {

The RNA genome of retroviruses is encased within a protein capsid. To gather insight into the assembly and function of this capsid, we used electron cryotomography to image human immunodeficiency virus (HIV) and equine infectious anemia virus (EIAV) particles. While the majority of viral cores appeared closed, a variety of unclosed structures including rolled sheets, extra flaps, and cores with holes in the tip were also seen. Simulations of nonequilibrium growth of elastic sheets recapitulated each of these aberrations and further predicted the occasional presence of seams, for which tentative evidence was also found within the cryotomograms. To test the integrity of viral capsids in vivo, we observed that \ 25\% of cytoplasmic HIV complexes captured by TRIM5α had holes large enough to allow internal green fluorescent protein (GFP) molecules to escape. Together, these findings suggest that HIV assembly at least sometimes involves the union in space of two edges of a curling sheet and results in a substantial number of unclosed forms.

}, keywords = {Animals, Capsid, Carrier Proteins, Computer Simulation, Cryoelectron Microscopy, Equine, Fluorescence, Green Fluorescent Proteins, HEK293 Cells, HIV-1, Humans, Infectious Anemia Virus, Microscopy, Models, Molecular, Viral Core Proteins, Virus Assembly}, issn = {1089-8638}, doi = {10.1016/j.jmb.2012.10.006}, author = {Yu, Zhiheng and Dobro, Megan J and Woodward, Cora L and Levandovsky, Artem and Danielson, Cindy M and Sandrin, Virginie and Shi, Jiong and Aiken, Christopher and Zandi, Roya and Hope, Thomas J and Jensen, Grant J} } @article {6145, title = {Unsupervised segmentation of noisy electron microscopy images using salient watersheds and region merging.}, journal = {BMC Bioinformatics}, volume = {14}, year = {2013}, month = {2013 Oct 4}, pages = {294}, abstract = {

Background: Segmenting electron microscopy (EM) images of cellular and subcellular processes in the nervous system is a key step in many bioimaging pipelines involving classification and labeling of ultrastructures. However, fully automated techniques to segment images are often susceptible to noise and heterogeneity in EM images (e.g. different histological preparations, different organisms, different brain regions, etc.). Supervised techniques to address this problem are often helpful but require large sets of training data, which are often difficult to obtain in practice, especially across many conditions. Results: We propose a new, principled unsupervised algorithm to segment EM images using a two-step approach: edge detection via salient watersheds following by robust region merging. We performed experiments to gather EM neuroimages of two organisms (mouse and fruit fly) using different histological preparations and generated manually curated ground-truth segmentations. We compared our algorithm against several state-of- the-art unsupervised segmentation algorithms and found superior performance using two standard measures of under-and over-segmentation error. Conclusions: Our algorithm is general and may be applicable to other large-scale segmentation problems for bioimages.

}, issn = {1471-2105}, doi = {10.1186/1471-2105-14-294}, author = {Navlakha, Saket and Ahammad, Parvez and Myers, Eugene W}, editor = {Myers, Eugene W} } @article {6888, title = {Variable dendritic integration in hippocampal CA3 pyramidal neurons.}, journal = {Neuron}, volume = {80}, year = {2013}, month = {2013 Dec 18}, pages = {1438-50}, abstract = {

The hippocampal CA3 region is essential for pattern completion and generation of sharp-wave ripples. During these operations, coordinated activation of ensembles of CA3 pyramidal neurons produces spatiotemporally structured input patterns arriving onto dendrites of recurrently connected CA3 neurons. To understand how such input patterns are translated into specific output patterns, we characterized dendritic integration in CA3 pyramidal cells using two-photon imaging and glutamate uncaging. We found that thin dendrites of CA3 pyramidal neurons integrate synchronous synaptic input in a highly supralinear fashion. The amplification was primarily mediated by NMDA receptor activation and was present over a relatively broad range of spatiotemporal input patterns. The decay of voltage responses, temporal summation, and action potential output was regulated in a compartmentalized fashion mainly by a G-protein-activated inwardly rectifying K(+) current. Our results suggest that plastic dendritic integrative\ mechanisms may support ensemble behavior in pyramidal neurons of the hippocampal circuitry.

}, keywords = {Action Potentials, Animals, CA3 Region, Dendrites, G Protein-Coupled Inwardly-Rectifying Potassium Channels, Glutamic Acid, Hippocampal, Male, N-Methylaspartate, Potassium Channels, Pyramidal Cells, Rats, Sodium}, issn = {1097-4199}, doi = {10.1016/j.neuron.2013.10.033}, author = {Makara, Judit K and Magee, Jeffrey C} } @article {6508, title = {Vertebrate versus invertebrate neural circuits.}, journal = {Current Biology}, volume = {23}, year = {2013}, month = {2013 Jun 17}, pages = {R504-6}, issn = {1879-0445}, author = {Katz, Paul and Grillner, Sten and Wilson, Rachel and Borst, Alexander and Greenspan, Ralph and Buzs{\'a}ki, Gy{\"o}rgy and Martin, Kevan and Marder, Eve and Kristan, William and Friedrich, Rainer and Chklovskii, Dmitri Mitya} } @article {6264, title = {ViSP: representing single-particle localizations in three dimensions.}, journal = {Nature Methods}, volume = {10}, year = {2013}, month = {2013 Jul 30}, pages = {689-90}, issn = {1548-7105}, doi = {10.1038/nmeth.2566}, author = {Beheiry, Mohamed El and Dahan, Maxime} } @article {6178, title = {A visual motion detection circuit suggested by Drosophila connectomics.}, journal = {Nature}, volume = {500}, year = {2013}, month = {2013 Aug 7}, pages = {175{\textendash}81}, abstract = {

Animal behaviour arises from computations in neuronal circuits, but our understanding of these computations has been frustrated by the lack of detailed synaptic connection maps, or connectomes. For example, despite intensive investigations over half a century, the neuronal implementation of local motion detection in the insect visual system remains elusive. Here we develop a semi-automated pipeline using electron microscopy to reconstruct a connectome, containing 379 neurons and 8,637 chemical synaptic contacts, within the Drosophila optic medulla. By matching reconstructed neurons to examples from light microscopy, we assigned neurons to cell types and assembled a connectome of the repeating module of the medulla. Within this module, we identified cell types constituting a motion detection circuit, and showed that the connections onto individual motion-sensitive neurons in this circuit were consistent with their direction selectivity. Our results identify cellular targets for future functional investigations, and demonstrate that connectomes can provide key insights into neuronal computations.

}, issn = {1476-4687}, doi = {doi:10.1038/nature12450}, url = {http://www.nature.com/nature/journal/v500/n7461/full/nature12450.html}, author = {Takemura, Shin-ya and Bharioke, Arjun and Lu, Zhiyuan and Nern, Aljoscha and Vitaladevuni, Shiv and Rivlin, Patricia K. and Katz, William T. and Olbris, Donald J. and Plaza, Stephen M and Winston, Philip and Zhao, Ting and Horne, Jane Anne and Fetter, Richard D and Takemura, Satoko and Blazek, Katerina and Chang, Lei-Ann and Ogundeyi, Omotara and Saunders, Mathew A. and Shapiro, Victor and Sigmund, Christopher and Rubin, Gerald M and Scheffer, Louis K and Meinertzhagen, Ian A. and Chklovskii, Dmitri B} } @article {6102, title = {Visual motion speed determines a behavioral switch from forward flight to expansion avoidance in Drosophila.}, journal = {The Journal of Experimental Biology}, volume = {216}, year = {2013}, month = {2013 Feb 15}, pages = {719-32}, abstract = {

As an animal translates through the world, its eyes will experience a radiating pattern of optic flow in which there is a focus of expansion directly in front and a focus of contraction behind. For flying fruit flies, recent experiments indicate that flies actively steer away from patterns of expansion. Whereas such a reflex makes sense for avoiding obstacles, it presents a paradox of sorts because an insect could not navigate stably through a visual scene unless it tolerated flight towards a focus of expansion during episodes of forward translation. One possible solution to this paradox is that a fly{\textquoteright}s behavior might change such that it steers away from strong expansion, but actively steers towards weak expansion. In this study, we use a tethered flight arena to investigate the influence of stimulus strength on the magnitude and direction of turning responses to visual expansion in flies. These experiments indicate that the expansion-avoidance behavior is speed dependent. At slower speeds of expansion, flies exhibit an attraction to the focus of expansion, whereas the behavior transforms to expansion avoidance at higher speeds. Open-loop experiments indicate that this inversion of the expansion-avoidance response depends on whether or not the head is fixed to the thorax. The inversion of the expansion-avoidance response with stimulus strength has a clear manifestation under closed-loop conditions. Flies will actively orient towards a focus of expansion at low temporal frequency but steer away from it at high temporal frequency. The change in the response with temporal frequency does not require motion stimuli directly in front or behind the fly. Animals in which the stimulus was presented within 120 deg sectors on each side consistently steered towards expansion at low temporal frequency and steered towards contraction at high temporal frequency. A simple model based on an array of Hassenstein-Reichardt type elementary movement detectors suggests that the inversion of the expansion-avoidance reflex can explain the spatial distribution of straight flight segments and collision-avoidance saccades when flies fly freely within an open circular arena.

}, keywords = {Animal, Animals, Avoidance Learning, Behavior, Drosophila melanogaster, Female, Flight, Motion Perception, Orientation, Photic Stimulation, Time Factors, Visual Perception}, issn = {1477-9145}, doi = {10.1242/jeb.074732}, author = {Reiser, Michael B and Dickinson, Michael H} } @article {65045, title = {Voltage sensor ring in a native structure of a membrane-embedded potassium channel.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, year = {2013}, month = {2013 Feb 26}, pages = {3369-74}, abstract = {

Voltage-gated ion channels support electrochemical activity in cells and are largely responsible for information flow throughout the nervous systems. The voltage sensor domains in these channels sense changes in transmembrane potential and control ion flux across membranes. The X-ray structures of a few voltage-gated ion channels in detergents have been determined and have revealed clear structural variations among their respective voltage sensor domains. More recent studies demonstrated that lipids around a voltage-gated channel could directly alter its conformational state in membrane. Because of these disparities, the structural basis for voltage sensing in native membranes remains elusive. Here, through electron-crystallographic analysis of membrane-embedded proteins, we present the detailed view of a voltage-gated potassium channel in its inactivated state. Contrary to all known structures of voltage-gated ion channels in detergents, our data revealed a unique conformation in which the four voltage sensor domains of a voltage-gated potassium channel from Aeropyrum pernix (KvAP) form a ring structure that completely surrounds the pore domain of the channel. Such a structure is named the voltage sensor ring. Our biochemical and electrophysiological studies support that the voltage sensor ring represents a physiological conformation. These data together suggest that lipids exert strong effects on the channel structure and that these effects may be changed upon membrane disruption. Our results have wide implications for lipid-protein interactions in general and for the mechanism of voltage sensing in particular.

}, keywords = {Aeropyrum, Cell Membrane, Cross-Linking Reagents, Crystallography, X-Ray, Electrons, Lipids, Models, Molecular, Potassium Channels, Voltage-Gated, Protein Structure, Secondary, Protein Structure, Tertiary}, issn = {1091-6490}, doi = {10.1073/pnas.1218203110}, author = {Shi, Liang and Zheng, Hongjin and Zheng, Hui and Borkowski, Brian A and Shi, Dan and Gonen, Tamir and Jiang, Qiu-Xing} } @article {48276, title = {Voltage-sensitive dye imaging reveals shifting spatiotemporal spread of whisker-induced activity in rat barrel cortex.}, journal = {Journal of neurophysiology}, volume = {109}, year = {2013}, month = {2013 May}, pages = {2382-92}, abstract = {

In rats, navigating through an environment requires continuous information about objects near the head. Sensory information such as object location and surface texture are encoded by spike firing patterns of single neurons within rat barrel cortex. Although there are many studies using single-unit electrophysiology, much less is known regarding the spatiotemporal pattern of activity of populations of neurons in barrel cortex in response to whisker stimulation. To examine cortical response at the population level, we used voltage-sensitive dye (VSD) imaging to examine ensemble spatiotemporal dynamics of barrel cortex in response to stimulation of single or two adjacent whiskers in urethane-anesthetized rats. Single whisker stimulation produced a poststimulus fluorescence response peak within 12-16 ms in the barrel corresponding to the stimulated whisker (principal whisker). This fluorescence subsequently propagated throughout the barrel field, spreading anisotropically preferentially along a barrel row. After paired whisker stimulation, the VSD signal showed sublinear summation (less than the sum of 2 single whisker stimulations), consistent with previous electrophysiological and imaging studies. Surprisingly, we observed a spatial shift in the center of activation occurring over a 10- to 20-ms period with shift magnitudes of 1-2 barrels. This shift occurred predominantly in the posteromedial direction within the barrel field. Our data thus reveal previously unreported spatiotemporal patterns of barrel cortex activation. We suggest that this nontopographical shift is consistent with known functional and anatomic asymmetries in barrel cortex and that it may provide an important insight for understanding barrel field activation during whisking behavior.

}, keywords = {Action Potentials, Animals, Rats, Rats, Long-Evans, Sensory Receptor Cells, Somatosensory Cortex, Time Factors, Vibrissae, Voltage-Sensitive Dye Imaging}, issn = {1522-1598}, doi = {10.1152/jn.00430.2012}, author = {Lustig, Brian R and Friedman, Robert M and Winberry, Jeremy E and Ebner, Ford F and Roe, Anna W} } @article {5937, title = {Whole-brain functional imaging at cellular resolution using light-sheet microscopy.}, journal = {Nature Methods}, volume = {10}, year = {2013}, month = {2013 May}, pages = {413-20}, abstract = {

Brain function relies on communication between large populations of neurons across multiple brain areas, a full understanding of which would require knowledge of the time-varying activity of all neurons in the central nervous system. Here we use light-sheet microscopy to record activity, reported through the genetically encoded calcium indicator GCaMP5G, from the entire volume of the brain of the larval zebrafish in vivo at 0.8 Hz, capturing more than 80\% of all neurons at single-cell resolution. Demonstrating how this technique can be used to reveal functionally defined circuits across the brain, we identify two populations of neurons with correlated activity patterns. One circuit consists of hindbrain neurons functionally coupled to spinal cord neuropil. The other consists of an anatomically symmetric population in the anterior hindbrain, with activity in the left and right halves oscillating in antiphase, on a timescale of 20 s, and coupled to equally slow oscillations in the inferior olive.

}, issn = {1548-7105}, doi = {10.1038/nmeth.2434}, author = {Ahrens, Misha B and Orger, Michael B. and Robson, Drew N and Li, Jennifer M and Keller, Philipp J} } @article {6490, title = {Activity dynamics and behavioral correlates of CA3 and CA1 hippocampal pyramidal neurons.}, journal = {Hippocampus}, volume = {22}, year = {2012}, month = {2012 Aug}, pages = {1659-80}, abstract = {

The CA3 and CA1 pyramidal neurons are the major principal cell types of the hippocampus proper. The strongly recurrent collateral system of CA3 cells and the largely parallel-organized CA1 neurons suggest that these regions perform distinct computations. However, a comprehensive comparison between CA1 and CA3 pyramidal cells in terms of firing properties, network dynamics, and behavioral correlations is sparse in the intact animal. We performed large-scale recordings in the dorsal hippocampus of rats to quantify the similarities and differences between CA1 (n \> 3,600) and CA3 (n \> 2,200) pyramidal cells during sleep and exploration in multiple environments. CA1 and CA3 neurons differed significantly in firing rates, spike burst propensity, spike entrainment by the theta rhythm, and other aspects of spiking dynamics in a brain state-dependent manner. A smaller proportion of CA3 than CA1 cells displayed prominent place fields, but place fields of CA3 neurons were more compact, more stable, and carried more spatial information per spike than those of CA1 pyramidal cells. Several other features of the two cell types were specific to the testing environment. CA3 neurons showed less pronounced phase precession and a weaker position versus spike-phase relationship than CA1 cells. Our findings suggest that these distinct activity dynamics of CA1 and CA3 pyramidal cells support their distinct computational roles.

}, keywords = {Action Potentials, Animal, Animals, Behavior, CA1 Region, CA3 Region, Electroencephalography, Hippocampal, Long-Evans, Male, Maze Learning, Nonparametric, Pyramidal Cells, Rats, Statistics, Theta Rhythm}, issn = {1098-1063}, doi = {10.1002/hipo.22002}, author = {Mizuseki, Kenji and Royer, S{\'e}bastien and Diba, Kamran and Buzs{\'a}ki, Gy{\"o}rgy} } @article {5162, title = {Activity in motor-sensory projections reveals distributed coding in somatosensation.}, journal = {Nature}, volume = {489}, year = {2012}, month = {2012 Sep 13}, pages = {299-303}, abstract = {

Cortical-feedback projections to primary sensory areas terminate most heavily in layer 1 (L1) of the neocortex, where they make synapses with tuft dendrites of pyramidal neurons. L1 input is thought to provide {\textquoteleft}contextual{\textquoteright} information, but the signals transmitted by L1 feedback remain uncharacterized. In the rodent somatosensory system, the spatially diffuse feedback projection from vibrissal motor cortex (vM1) to vibrissal somatosensory cortex (vS1, also known as the barrel cortex) may allow whisker touch to be interpreted in the context of whisker position to compute object location. When mice palpate objects with their whiskers to localize object features, whisker touch excites vS1 and later vM1 in a somatotopic manner. Here we use axonal calcium imaging to track activity in vM1{\textendash}\>vS1 afferents in L1 of the barrel cortex while mice performed whisker-dependent object localization. Spatially intermingled individual axons represent whisker movements, touch and other behavioural features. In a subpopulation of axons, activity depends on object location and persists for seconds after touch. Neurons in the barrel cortex thus have information to integrate movements and touches of multiple whiskers over time, key components of object identification and navigation by active touch.

}, issn = {1476-4687}, doi = {10.1038/nature11321}, author = {Petreanu, Leopoldo and Gutnisky, Diego A and Huber, Daniel and Xu, Ning-long and O{\textquoteright}Connor, Dan H and Tian, Lin and Looger, Loren and Svoboda, Karel} } @article {46604, title = {Acute ethanol responses in Drosophila are sexually dimorphic.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 Dec 18}, pages = {21087-92}, abstract = {

In mammalian and insect models of ethanol intoxication, low doses of ethanol stimulate locomotor activity whereas high doses induce sedation. Sex differences in acute ethanol responses, which occur in humans, have not been characterized in Drosophila. In this study, we find that male flies show increased ethanol hyperactivity and greater resistance to ethanol sedation compared with females. We show that the sex determination gene transformer (tra) acts in the developing nervous system, likely through regulation of fruitless (fru), to at least partially mediate the sexual dimorphism in ethanol sedation. Although pharmacokinetic differences may contribute to the increased sedation sensitivity of females, neuronal tra expression regulates ethanol sedation independently of ethanol pharmacokinetics. We also show that acute activation of fru-expressing neurons affects ethanol sedation, further supporting a role for fru in regulating this behavior. Thus, we have characterized previously undescribed sex differences in behavioral responses to ethanol, and implicated fru in mediating a subset of these differences.

}, keywords = {Alcoholic Intoxication, Animals, Central Nervous System Stimulants, Crosses, Genetic, Disease Models, Animal, Drosophila melanogaster, Ethanol, Female, Gene Expression Regulation, Male, Models, Statistical, Neurons, Sex Characteristics, Sex Factors}, issn = {1091-6490}, doi = {10.1073/pnas.1218850110}, author = {Devineni, Anita V and Heberlein, Ulrike} } @proceedings {46790, title = {Advanced Programming with ImgLib2}, year = {2012}, month = {2012 Oct 24}, address = {Mondorf-les-Bains, Luxembourg}, author = {Pietzsch, Tobias and Preibisch, Stephan and Tomancak, Pavel and Saalfeld, Stephan} } @article {4922, title = {AKAP2 anchors PKA with aquaporin-0 to support ocular lens transparency.}, journal = {EMBO Molecular Medicine}, volume = {4}, year = {2012}, month = {2012 Jan}, pages = {15-26}, abstract = {

A decline in ocular lens transparency known as cataract afflicts 90\% of individuals by the age 70. Chronic deterioration of lens tissue occurs as a pathophysiological consequence of defective water and nutrient circulation through channel and transporter proteins. A key component is the aquaporin-0 (AQP0) water channel whose permeability is tightly regulated in healthy lenses. Using a variety of cellular and biochemical approaches we have discovered that products of the A-kinase anchoring protein 2 gene (AKAP2/AKAP-KL) form a stable complex with AQP0 to sequester protein kinase A (PKA) with the channel. This permits PKA phosphorylation of serine 235 within a calmodulin (CaM)-binding domain of AQP0. The additional negative charge introduced by phosphoserine 235 perturbs electrostatic interactions between AQP0 and CaM to favour water influx through the channel. In isolated mouse lenses, displacement of PKA from the AKAP2-AQP0 channel complex promotes cortical cataracts as characterized by severe opacities and cellular damage. Thus, anchored PKA modulation of AQP0 is a homeostatic mechanism that must be physically intact to preserve lens transparency.

}, keywords = {A Kinase Anchor Proteins, Animals, Aquaporins, Calmodulin, Cataract, Crystalline, Cyclic AMP-Dependent Protein Kinases, Eye Proteins, Inbred C57BL, Lens, Membrane Proteins, Mice, Phosphopeptides, Phosphorylation, Protein Binding, Sheep, Static Electricity, Water}, issn = {1757-4684}, doi = {10.1002/emmm.201100184}, author = {Gold, Matthew G and Reichow, Steve L and O{\textquoteright}Neill, Susan E and Weisbrod, Chad R and Langeberg, Lorene K and Bruce, James E and Gonen, Tamir and Scott, John D} } @article {5200, title = {Automated tracking of whiskers in videos of head fixed rodents.}, journal = {PLoS Computational Biology}, volume = {8}, year = {2012}, month = {2012 Jul}, pages = {e1002591}, abstract = {

We have developed software for fully automated tracking of vibrissae (whiskers) in high-speed videos (\>500 Hz) of head-fixed, behaving rodents trimmed to a single row of whiskers. Performance was assessed against a manually curated dataset consisting of 1.32 million video frames comprising 4.5 million whisker traces. The current implementation detects whiskers with a recall of 99.998\% and identifies individual whiskers with 99.997\% accuracy. The average processing rate for these images was 8 Mpx/s/cpu (2.6 GHz Intel Core2, 2 GB RAM). This translates to 35 processed frames per second for a 640 px{\texttimes}352 px video of 4 whiskers. The speed and accuracy achieved enables quantitative behavioral studies where the analysis of millions of video frames is required. We used the software to analyze the evolving whisking strategies as mice learned a whisker-based detection task over the course of 6 days (8148 trials, 25 million frames) and measure the forces at the sensory follicle that most underlie haptic perception.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1002591}, author = {Clack, Nathan G and O{\textquoteright}Connor, Daniel H and Huber, Daniel and Petreanu, Leopoldo and Hires, Andrew and Peron, Simon and Svoboda, Karel and Myers, Eugene W} } @article {48166, title = {Automatic detection and classification of teeth in CT data.}, journal = {Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention}, volume = {15}, year = {2012}, month = {2012}, pages = {609-16}, abstract = {

We propose a fully automatic method for tooth detection and classification in CT or cone-beam CT image data. First we compute an accurate segmentation of the maxilla bone. Based on this segmentation, our method computes a complete and optimal separation of the row of teeth into 16 subregions and classifies the resulting regions as existing or missing teeth. This serves as a prerequisite for further individual tooth segmentation. We show the robustness of our approach by providing extensive validation on 43 clinical head CT scans.

}, keywords = {Algorithms, Artifacts, Bone and Bones, Humans, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Maxilla, Models, Statistical, Pattern Recognition, Automated, Radiographic Image Interpretation, Computer-Assisted, Reproducibility of Results, Tomography, X-Ray Computed, Tooth}, author = {Duy, Nguyen The and Lamecker, Hans and Kainmueller, Dagmar and Zachow, Stefan} } @article {6527, title = {A battery-free multichannel digital neural/EMG telemetry system for flying insects.}, journal = {IEEE Transactions on Biomedical Circuits and Systems}, volume = {6}, year = {2012}, month = {2012 Oct}, pages = {424-36}, abstract = {

This paper presents a digital neural/EMG telemetry system small enough and lightweight enough to permit recording from insects in flight. It has a measured flight package mass of only 38 mg. This system includes a single-chip telemetry integrated circuit (IC) employing RF power harvesting for battery-free operation, with communication via modulated backscatter in the UHF (902-928 MHz) band. An on-chip 11-bit ADC digitizes 10 neural channels with a sampling rate of 26.1 kSps and 4 EMG channels at 1.63 kSps, and telemeters this data wirelessly to a base station. The companion base station transceiver includes an RF transmitter of +36 dBm (4 W) output power to wirelessly power the telemetry IC, and a digital receiver with a sensitivity of -70 dBm for 10$^{-}$$^{5}$ BER at 5.0 Mbps to receive the data stream from the telemetry IC. The telemetry chip was fabricated in a commercial 0.35 μ m 4M1P (4 metal, 1 poly) CMOS process. The die measures 2.36 {\texttimes} 1.88 mm, is 250 μm thick, and is wire bonded into a flex circuit assembly measuring 4.6 {\texttimes} 6.8 mm.

}, issn = {1940-9990}, doi = {10.1109/TBCAS.2012.2222881}, author = {Thomas, Stewart J and Harrison, Reid R. and Leonardo, Anthony and Reynolds, Matthew S} } @article {47661, title = {Bayesian localization microscopy reveals nanoscale podosome dynamics.}, journal = {Nature methods}, volume = {9}, year = {2012}, month = {2012 Feb}, pages = {195-200}, abstract = {

We describe a localization microscopy analysis method that is able to extract results in live cells using standard fluorescent proteins and xenon arc lamp illumination. Our Bayesian analysis of the blinking and bleaching (3B analysis) method models the entire dataset simultaneously as being generated by a number of fluorophores that may or may not be emitting light at any given time. The resulting technique allows many overlapping fluorophores in each frame and unifies the analysis of the localization from blinking and bleaching events. By modeling the entire dataset, we were able to use each reappearance of a fluorophore to improve the localization accuracy. The high performance of this technique allowed us to reveal the nanoscale dynamics of podosome formation and dissociation throughout an entire cell with a resolution of 50 nm on a 4-s timescale.

}, keywords = {Bayes Theorem, Cell Line, Tumor, Humans, Nanotechnology}, issn = {1548-7105}, doi = {10.1038/nmeth.1812}, author = {Cox, Susan and Rosten, Edward and Monypenny, James and Jovanovic-Talisman, Tijana and Burnette, Dylan T and Lippincott-Schwartz, Jennifer and Jones, Gareth E and Heintzmann, Rainer} } @article {6320, title = {Beam-induced motion of vitrified specimen on holey carbon film.}, journal = {Journal of Structural Biology}, volume = {177}, year = {2012}, month = {2012 Mar}, pages = {630-7}, abstract = {

The contrast observed in images of frozen-hydrated biological specimens prepared for electron cryo-microscopy falls significantly short of theoretical predictions. In addition to limits imposed by the current instrumentation, it is widely acknowledged that motion of the specimen during its exposure to the electron beam leads to significant blurring in the recorded images. We have studied the amount and direction of motion of virus particles suspended in thin vitrified ice layers across holes in perforated carbon films using exposure series. Our data show that the particle motion is correlated within patches of 0.3-0.5 μm, indicating that the whole ice layer is moving in a drum-like motion, with accompanying particle rotations of up to a few degrees. Support films with smaller holes, as well as lower electron dose rates tend to reduce beam-induced specimen motion, consistent with a mechanical effect. Finally, analysis of movies showing changes in the specimen during beam exposure show that the specimen moves significantly more at the start of an exposure than towards its end. We show how alignment and averaging of movie frames can be used to restore high-resolution detail in images affected by beam-induced motion.

}, keywords = {Computer-Assisted, Cryoelectron Microscopy, Image Processing}, issn = {1095-8657}, doi = {10.1016/j.jsb.2012.02.003}, author = {Brilot, Axel F and Chen, James Z and Cheng, Anchi and Pan, Junhua and Harrison, Stephen C and Potter, Clinton S and Carragher, Bridget and Henderson, Richard and Grigorieff, Nikolaus} } @article {6505, title = {Betamax: towards optimal sampling strategies for high-throughput screens.}, journal = {Journal of Computational Biology: A Journal of Computational Molecular Cell Biology}, volume = {19}, year = {2012}, month = {2012 Jun}, pages = {776-84}, abstract = {

Sample size is a critical component in the design of any high-throughput genetic screening approach. Sample size determination from assumptions or limited data at the planning stages, though standard practice, may at times be unreliable because of the difficulty of a priori modeling of effect sizes and variance. Methods to update the sample size estimate during the course of the study could improve statistical power. In this article, we introduce an approach to estimate the power and update it continuously during the screen. We use this estimate to decide where to sample next to achieve maximum overall statistical power. Finally, in simulations, we demonstrate significant gains in study recall over the naive strategy of equal sample sizes while maintaining the same total number of samples.

}, keywords = {Algorithms, Computer Simulation, Genetic Testing, High-Throughput Screening Assays, Humans, Models, Research Design, Sample Size, Statistical}, issn = {1557-8666}, doi = {10.1089/cmb.2012.0036}, author = {Grover, Dhruv and Nunez-Iglesias, Juan} } @article {6303, title = {The bHLH repressor Deadpan regulates the self-renewal and specification of Drosophila larval neural stem cells independently of Notch.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012 Oct 8}, pages = {e46724}, abstract = {

Neural stem cells (NSCs) are able to self-renew while giving rise to neurons and glia that comprise a functional nervous system. However, how NSC self-renewal is maintained is not well understood. Using the Drosophila larval NSCs called neuroblasts (NBs) as a model, we demonstrate that the Hairy and Enhancer-of-Split (Hes) family protein Deadpan (Dpn) plays important roles in NB self-renewal and specification. The loss of Dpn leads to the premature loss of NBs and truncated NB lineages, a process likely mediated by the homeobox protein Prospero (Pros). Conversely, ectopic/over-expression of Dpn promotes ectopic self-renewing divisions and maintains NB self-renewal into adulthood. In type II NBs, which generate transit amplifying intermediate neural progenitors (INPs) like mammalian NSCs, the loss of Dpn results in ectopic expression of type I NB markers Asense (Ase) and Pros before these type II NBs are lost at early larval stages. Our results also show that knockdown of Notch leads to ectopic Ase expression in type II NBs and the premature loss of type II NBs. Significantly, dpn expression is unchanged in these transformed NBs. Furthermore, the loss of Dpn does not inhibit the over-proliferation of type II NBs and immature INPs caused by over-expression of activated Notch. Our data suggest that Dpn plays important roles in maintaining NB self-renewal and specification of type II NBs in larval brains and that Dpn and Notch function independently in regulating type II NB proliferation and specification.

}, keywords = {Animals, Basic Helix-Loop-Helix Transcription Factors, Drosophila, Drosophila Proteins, Larva, Neural Stem Cells, Notch, Nuclear Proteins, Receptors}, issn = {1932-6203}, doi = {10.1371/journal.pone.0046724}, author = {Zhu, Sijun and Wildonger, Jill and Barshow, Suzanne and Younger, Susan and Huang, Yaling and Lee, Tzumin} } @article {4974, title = {Bioimage informatics: a new category in Bioinformatics.}, journal = {Bioinformatics}, volume = {28}, year = {2012}, month = {2012 Apr 15}, pages = {1057}, issn = {1367-4811}, doi = {10.1093/bioinformatics/bts111}, author = {Peng, Hanchuan and Bateman, Alex and Valencia, Alfonso and Wren, Jonathan D} } @article {4984, title = {Biological imaging software tools.}, journal = {Nature Methods}, volume = {9}, year = {2012}, month = {2012 Jun 28}, pages = {697-710}, abstract = {

Few technologies are more widespread in modern biological laboratories than imaging. Recent advances in optical technologies and instrumentation are providing hitherto unimagined capabilities. Almost all these advances have required the development of software to enable the acquisition, management, analysis and visualization of the imaging data. We review each computational step that biologists encounter when dealing with digital images, the inherent challenges and the overall status of available software for bioimage informatics, focusing on open-source options.

}, issn = {1548-7105}, doi = {10.1038/nmeth.2084}, author = {Eliceiri, Kevin W and Berthold, Michael R and Goldberg, Ilya G and Ib{\'a}{\~n}ez, Luis and Manjunath, B S and Martone, Maryann E and Murphy, Robert F and Peng, Hanchuan and Plant, Anne L and Roysam, Badrinath and Stuurmann, Nico and Swedlow, Jason R and Tomancak, Pavel and Carpenter, Anne E.} } @article {47652, title = {Bone marrow homing and engraftment of human hematopoietic stem and progenitor cells is mediated by a polarized membrane domain.}, journal = {Blood}, volume = {119}, year = {2012}, month = {2012 Feb 23}, pages = {1848-55}, abstract = {

Manipulation of hematopoietic stem/progenitor cells (HSPCs) ex vivo is of clinical importance for stem cell expansion and gene therapy applications. However, most cultured HSPCs are actively cycling, and show a homing and engraftment defect compared with the predominantly quiescent noncultured HSPCs. We previously showed that HSPCs make contact with osteoblasts in vitro via a polarized membrane domain enriched in adhesion molecules such as tetraspanins. Here we show that increased cell cycling during ex vivo culture of HSPCs resulted in disruption of this membrane domain, as evidenced by disruption of polarity of the tetraspanin CD82. Chemical disruption or antibody-mediated blocking of CD82 on noncultured HSPCs resulted in decreased stromal cell adhesion, homing, and engraftment in nonobese diabetic/severe combined immunodeficiency IL-2γ(null) (NSG) mice compared with HSPCs with an intact domain. Most leukemic blasts were actively cycling and correspondingly displayed a loss of domain polarity and decreased homing in NSG mice compared with normal HSPCs. We conclude that quiescent cells, unlike actively cycling cells, display a polarized membrane domain enriched in tetraspanins that mediates homing and engraftment, providing a mechanistic explanation for the homing/engraftment defect of cycling cells and a potential new therapeutic target to enhance engraftment.

}, keywords = {Animals, Antigens, CD34, Antigens, CD82, Bone Marrow, Cell Cycle, Cell Line, Tumor, Cells, Cultured, Cytokines, Flow Cytometry, Fluorescent Antibody Technique, Hematopoietic Stem Cell Transplantation, Hematopoietic Stem Cells, Humans, Interleukin Receptor Common gamma Subunit, Leukemia, Membrane Microdomains, Mice, Mice, Inbred NOD, Mice, Knockout, Mice, SCID, Microscopy, Confocal, Receptors, CXCR4, Tetraspanins, Transplantation, Heterologous}, issn = {1528-0020}, doi = {10.1182/blood-2011-08-371583}, author = {Larochelle, Andre and Gillette, Jennifer M and Desmond, Ronan and Ichwan, Brian and Cantilena, Amy and Cerf, Alexandra and Barrett, A John and Wayne, Alan S and Lippincott-Schwartz, Jennifer and Dunbar, Cynthia E} } @article {47659, title = {Bone marrow homing and engraftment of human hematopoietic stem and progenitor cells is mediated by a polarized membrane domain.}, journal = {Blood}, volume = {119}, year = {2012}, month = {2012 Feb 23}, pages = {1848-55}, abstract = {

Manipulation of hematopoietic stem/progenitor cells (HSPCs) ex vivo is of clinical importance for stem cell expansion and gene therapy applications. However, most cultured HSPCs are actively cycling, and show a homing and engraftment defect compared with the predominantly quiescent noncultured HSPCs. We previously showed that HSPCs make contact with osteoblasts in vitro via a polarized membrane domain enriched in adhesion molecules such as tetraspanins. Here we show that increased cell cycling during ex vivo culture of HSPCs resulted in disruption of this membrane domain, as evidenced by disruption of polarity of the tetraspanin CD82. Chemical disruption or antibody-mediated blocking of CD82 on noncultured HSPCs resulted in decreased stromal cell adhesion, homing, and engraftment in nonobese diabetic/severe combined immunodeficiency IL-2γ(null) (NSG) mice compared with HSPCs with an intact domain. Most leukemic blasts were actively cycling and correspondingly displayed a loss of domain polarity and decreased homing in NSG mice compared with normal HSPCs. We conclude that quiescent cells, unlike actively cycling cells, display a polarized membrane domain enriched in tetraspanins that mediates homing and engraftment, providing a mechanistic explanation for the homing/engraftment defect of cycling cells and a potential new therapeutic target to enhance engraftment.

}, keywords = {Animals, Antigens, CD34, Antigens, CD82, Bone Marrow, Cell Cycle, Cell Line, Tumor, Cells, Cultured, Cytokines, Flow Cytometry, Fluorescent Antibody Technique, Hematopoietic Stem Cell Transplantation, Hematopoietic Stem Cells, Humans, Interleukin Receptor Common gamma Subunit, Leukemia, Membrane Microdomains, Mice, Mice, Inbred NOD, Mice, Knockout, Mice, SCID, Microscopy, Confocal, Receptors, CXCR4, Tetraspanins, Transplantation, Heterologous}, issn = {1528-0020}, doi = {10.1182/blood-2011-08-371583}, author = {Larochelle, Andre and Gillette, Jennifer M and Desmond, Ronan and Ichwan, Brian and Cantilena, Amy and Cerf, Alexandra and Barrett, A John and Wayne, Alan S and Lippincott-Schwartz, Jennifer and Dunbar, Cynthia E} } @article {5671, title = {Brain-wide neuronal dynamics during motor adaptation in zebrafish.}, journal = {Nature}, volume = {485}, year = {2012}, month = {2012 May 24}, pages = {471-7}, abstract = {

A fundamental question in neuroscience is how entire neural circuits generate behaviour and adapt it to changes in sensory feedback. Here we use two-photon calcium imaging to record the activity of large populations of neurons at the cellular level, throughout the brain of larval zebrafish expressing a genetically encoded calcium sensor, while the paralysed animals interact fictively with a virtual environment and rapidly adapt their motor output to changes in visual feedback. We decompose the network dynamics involved in adaptive locomotion into four types of neuronal response properties, and provide anatomical maps of the corresponding sites. A subset of these signals occurred during behavioural adjustments and are candidates for the functional elements that drive motor learning. Lesions to the inferior olive indicate a specific functional role for olivocerebellar circuitry in adaptive locomotion. This study enables the analysis of brain-wide dynamics at single-cell resolution during behaviour.

}, keywords = {Adaptation, Animals, Brain, Genetically Modified, Larva, Learning, Locomotion, Models, Nerve Net, Neurological, Neurons, Neuropil, Photic Stimulation, Physiological, Psychomotor Performance, Single-Cell Analysis, Zebrafish}, issn = {1476-4687}, doi = {10.1038/nature11057}, author = {Ahrens, Misha B and Li, Jennifer M and Orger, Michael B. and Robson, Drew N and Schier, Alexander F and Engert, Florian and Portugues, Ruben} } @article {5278, title = {Breaking the spatial resolution barrier via iterative sound-light interaction in deep tissue microscopy.}, journal = {Scientific Reports}, volume = {2}, year = {2012}, month = {2012 Oct}, pages = {748}, abstract = {

Optical microscopy has so far been restricted to superficial layers, leaving many important biological questions unanswered. Random scattering causes the ballistic focus, which is conventionally used for image formation, to decay exponentially with depth. Optical imaging beyond the ballistic regime has been demonstrated by hybrid techniques that combine light with the deeper penetration capability of sound waves. Deep inside highly scattering media, the sound focus dimensions restrict the imaging resolutions. Here we show that by iteratively focusing light into an ultrasound focus via phase conjugation, we can fundamentally overcome this resolution barrier in deep tissues and at the same time increase the focus to background ratio. We demonstrate fluorescence microscopy beyond the ballistic regime of light with a threefold improved resolution and a fivefold increase in contrast. This development opens up practical high resolution fluorescence imaging in deep tissues.

}, doi = {doi:10.1038/srep00748}, author = {Si, Ke and Fiolka, Reto and Cui, Meng} } @article {65014, title = {Calcium signaling in dendritic spines.}, journal = {Cold Spring Harb Perspect Biol}, volume = {4}, year = {2012}, month = {2012 Apr 01}, pages = {a005686}, abstract = {

Calcium (Ca(2+)) is a ubiquitous signaling molecule that accumulates in the cytoplasm in response to diverse classes of stimuli and, in turn, regulates many aspects of cell function. In neurons, Ca(2+) influx in response to action potentials or synaptic stimulation triggers neurotransmitter release, modulates ion channels, induces synaptic plasticity, and activates transcription. In this article, we discuss the factors that regulate Ca(2+) signaling in mammalian neurons with a particular focus on Ca(2+) signaling within dendritic spines. This includes consideration of the routes of entry and exit of Ca(2+), the cellular mechanisms that establish the temporal and spatial profile of Ca(2+) signaling, and the biophysical criteria that determine which downstream signals are activated when Ca(2+) accumulates in a spine. Furthermore, we also briefly discuss the technical advances that made possible the quantitative study of Ca(2+) signaling in dendritic spines.

}, keywords = {Action Potentials, Animals, Calcium Signaling, Dendritic Spines, Mammals, Neuronal Plasticity}, issn = {1943-0264}, doi = {10.1101/cshperspect.a005686}, author = {Higley, Michael J and Sabatini, Bernardo L} } @article {6283, title = {Cell type-specific genomics of Drosophila neurons.}, journal = {Nucleic Acids Research}, volume = {40}, year = {2012}, month = {2012 Oct}, pages = {9691-704}, abstract = {

Many tools are available to analyse genomes but are often challenging to use in a cell type-specific context. We have developed a method similar to the isolation of nuclei tagged in a specific cell type (INTACT) technique [Deal,R.B. and Henikoff,S. (2010) A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev. Cell, 18, 1030-1040; Steiner,F.A., Talbert,P.B., Kasinathan,S., Deal,R.B. and Henikoff,S. (2012) Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling. Genome Res., doi:10.1101/gr.131748.111], first developed in plants, for use in Drosophila neurons. We profile gene expression and histone modifications in Kenyon cells and octopaminergic neurons in the adult brain. In addition to recovering known gene expression differences, we also observe significant cell type-specific chromatin modifications. In particular, a small subset of differentially expressed genes exhibits a striking anti-correlation between repressive and activating histone modifications. These genes are enriched for transcription factors, recovering those known to regulate mushroom body identity and predicting analogous regulators of octopaminergic neurons. Our results suggest that applying INTACT to specific neuronal populations can illuminate the transcriptional regulatory networks that underlie neuronal cell identity.

}, keywords = {Animals, Cell Fractionation, Cell Nucleus, Chromatin, Drosophila, Gene Expression Profiling, Gene Silencing, Genomics, Histones, Luminescent Proteins, Neurons, Transcription Factors}, issn = {1362-4962}, doi = {10.1093/nar/gks671}, author = {Henry, Gilbert L and Davis, Fred P and Picard, Serge and Eddy, Sean R.} } @article {4446, title = {Characterization and adaptive optical correction of aberrations during in vivo imaging in the mouse cortex.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 Jan 3}, pages = {22-7}, abstract = {

The signal and resolution during in vivo imaging of the mouse brain is limited by sample-induced optical aberrations. We find that, although the optical aberrations can vary across the sample and increase in magnitude with depth, they remain stable for hours. As a result, two-photon adaptive optics can recover diffraction-limited performance to depths of 450\ μm and improve imaging quality over fields of view of hundreds of microns. Adaptive optical correction yielded fivefold signal enhancement for small neuronal structures and a threefold increase in axial resolution. The corrections allowed us to detect smaller neuronal structures at greater contrast and also improve the signal-to-noise ratio during functional Ca(2+) imaging in single neurons.

}, issn = {1091-6490}, doi = {10.1073/pnas.1109202108}, author = {Ji, Na and Sato, Takashi R and Betzig, Eric} } @article {46045, title = {Clinically relevant hormone treatments fail to induce spinogenesis in prefrontal cortex of aged female rhesus monkeys.}, journal = {Journal of Neuroscience}, volume = {32}, year = {2012}, month = {2012 Aug 22}, pages = {11700-5}, abstract = {

Preclinical animal models have provided strong evidence that estrogen (E) therapy (ET) enhances cognition and induces spinogenesis in neuronal circuits. However, clinical studies have been inconsistent, with some studies revealing adverse effects of ET, including an increased risk of dementia. In an effort to bridge this disconnect between the preclinical and clinical data, we have developed a nonhuman primate (NHP) model of ET combined with high-resolution dendritic spine analysis of dorsolateral prefrontal cortical (dlPFC) neurons. Previously, we reported cyclic ET in aged, ovariectomized NHPs increased spine density on dlPFC neurons. Here, we report that monkeys treated with cyclic E treatment paired with cyclic progesterone (P), continuous E combined with P (either cyclic or continuous), or unopposed continuous E failed to increase spines on dlPFC neurons. Given that the most prevalent form of ET prescribed to women is a combined and continuous E and P, these data bring into convergence the human neuropsychological findings and preclinical neurobiological evidence that standard hormone therapy in women is unlikely to yield the synaptic benefit presumed to underlie the cognitive enhancement reported in animal models.

}, keywords = {Aging, Analysis of Variance, Animals, Dendritic Spines, Estrogens, Female, Macaca mulatta, Microscopy, Confocal, Neurons, Ovariectomy, Prefrontal Cortex, Progesterone}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.1881-12.2012}, author = {Ohm, Daniel T and Bloss, Erik B and Janssen, William G and Dietz, Karen C and Wadsworth, Shannon and Lou, Wendy and Gee, Nancy A and Lasley, Bill L and Rapp, Peter R and Morrison, John H} } @article {65028, title = {Columnar cells necessary for motion responses of wide-field visual interneurons in Drosophila.}, journal = {J Comp Physiol A Neuroethol Sens Neural Behav Physiol}, volume = {198}, year = {2012}, month = {2012 May 01}, pages = {389-95}, abstract = {

Wide-field motion-sensitive neurons in the lobula plate (lobula plate tangential cells, LPTCs) of the fly have been studied for decades. However, it has never been conclusively shown which cells constitute their major presynaptic elements. LPTCs are supposed to be rendered directionally selective by integrating excitatory as well as inhibitory input from many local motion detectors. Based on their stratification in the different layers of the lobula plate, the columnar cells T4 and T5 are likely candidates to provide some of this input. To study their role in motion detection, we performed whole-cell recordings from LPTCs in Drosophila with T4 and T5 cells blocked using two different genetically encoded tools. In these flies, motion responses were abolished, while flicker responses largely remained. We thus demonstrate that T4 and T5 cells indeed represent those columnar cells that provide directionally selective motion information to LPTCs. Contrary to previous assumptions, flicker responses seem to be largely mediated by a third, independent pathway. This work thus represents a further step towards elucidating the complete motion detection circuitry of the fly.

}, keywords = {Animals, Drosophila, Ganglia, Invertebrate, Interneurons, Motion Perception, Nerve Net, Sensory Receptor Cells, Visual Fields, Visual Pathways}, issn = {1432-1351}, doi = {10.1007/s00359-012-0716-3}, author = {Schnell, Bettina and Raghu, Shamprasad Varija and Nern, Aljoscha and Borst, Alexander} } @article {5102, title = {Complex wavefront corrections for deep tissue focusing using low coherence backscattered light.}, journal = {Optics Express}, volume = {20}, year = {2012}, month = {2012}, pages = {16532-43}, abstract = {

Aberrations and random scattering severely limit optical imaging in deep tissue. Adaptive optics can in principle drastically extend the penetration depth and improve the image quality. However, for random scattering media a large number of spatial modes need to be measured and controlled to restore a diffraction limited focus. Here, we present a parallel wavefront optimization method using backscattered light as a feedback. Spatial confinement of the feedback signal is realized with a confocal pinhole and coherence gating. We show in simulations and experiments that this approach enables focusing deep into tissue over up to six mean scattering path lengths. Experimentally the technique was tested on tissue phantoms and fixed brain slices.

}, doi = {10.1364/OE.20.016532}, author = {Fiolka, Reto and Si, Ke and Cui, Meng} } @article {4920, title = {Computational design of self-assembling protein nanomaterials with atomic level accuracy.}, journal = {Science}, volume = {336}, year = {2012}, month = {2012 Jun 1}, pages = {1171-4}, abstract = {

We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed between the building blocks in order to drive self-assembly. We used trimeric protein building blocks to design a 24-subunit, 13-nm diameter complex with octahedral symmetry and a 12-subunit, 11-nm diameter complex with tetrahedral symmetry. The designed proteins assembled to the desired oligomeric states in solution, and the crystal structures of the complexes revealed that the resulting materials closely match the design models. The method can be used to design a wide variety of self-assembling protein nanomaterials.

}, issn = {1095-9203}, doi = {10.1126/science.1219364}, author = {King, Neil P and Sheffler, William and Sawaya, Michael R and Vollmar, Breanna S and Sumida, John P and Andr{\'e}, Ingemar and Gonen, Tamir and Yeates, Todd O and Baker, David} } @article {47649, title = {Computational model of cytokinetic abscission driven by ESCRT-III polymerization and remodeling.}, journal = {Biophysical journal}, volume = {102}, year = {2012}, month = {2012 May 16}, pages = {2309-20}, abstract = {

The endosomal sorting complex required for transport (ESCRT)-III complex, capable of polymerization and remodeling, participates in abscission of the intercellular membrane bridge connecting two daughter cells at the end of cytokinesis. Here, we integrate quantitative imaging of ESCRT-III during cytokinetic abscission with biophysical properties of ESCRT-III complexes to formulate and test a computational model for ESCRT-mediated cytokinetic abscission. We propose that cytokinetic abscission is driven by an ESCRT-III fission complex, which arises from ESCRT-III polymerization at the edge of the cytokinetic midbody structure, located at the center of the intercellular bridge. Formation of the fission complex is completed by remodeling and breakage of the ESCRT-III polymer assisted by VPS4. Subsequent spontaneous constriction of the fission complex generates bending deformation of the intercellular bridge membrane. The related membrane elastic force propels\ the fission complex along the intercellular bridge away from the midbody until it reaches an equilibrium position, determining the scission site. Membrane attachment to the dome-like end-cap of the fission complex drives membrane fission, completing the abscission process. We substantiate the model by theoretical analysis of the membrane elastic energy and by experimental verification of the major model assumptions.

}, keywords = {Adenosine Triphosphate, Animals, Cell Line, Cell Membrane, Computer Simulation, Cytokinesis, Dogs, Endosomal Sorting Complexes Required for Transport, Extracellular Space, Humans, Models, Biological, Polymerization, Reproducibility of Results, Vacuolar Proton-Translocating ATPases}, issn = {1542-0086}, doi = {10.1016/j.bpj.2012.04.007}, author = {Elia, Natalie and Fabrikant, Gur and Kozlov, Michael M and Lippincott-Schwartz, Jennifer} } @article {45725, title = {Conserved regulatory architecture underlies parallel genetic changes and convergent phenotypic evolution.}, journal = {Proc Natl Acad Sci U S A}, volume = {109}, year = {2012}, month = {2012 Dec 18}, pages = {20975-9}, abstract = {

Similar morphological, physiological, and behavioral features have evolved independently in different species, a pattern known as convergence. It is known that morphological convergence can occur through changes in orthologous genes. In some cases of convergence, cis-regulatory changes generate parallel modifications in the expression patterns of orthologous genes. Our understanding of how changes in cis-regulatory regions contribute to convergence is hampered, usually, by a limited understanding of the global cis-regulatory structure of the evolving genes. Here we examine the genetic causes of a case of precise phenotypic convergence between Drosophila sechellia and Drosophila ezoana, species that diverged ~40 Mya. Previous studies revealed that changes in multiple transcriptional enhancers of shavenbaby (svb, a transcript of the ovo locus) caused phenotypic evolution in the D. sechellia lineage. It has also been shown that the convergent phenotype of D. ezoana was likely caused by cis-regulatory evolution of svb. Here we show that the large-scale cis-regulatory architecture of svb is conserved between these Drosophila species. Furthermore, we show that the D. ezoana orthologs of the evolved D. sechellia enhancers have also evolved expression patterns that correlate precisely with the changes in the phenotype. Our results suggest that phenotypic convergence resulted from multiple noncoding changes that occurred in parallel in the D. sechellia and D. ezoana lineages.

}, keywords = {Animals, Developmental Biology, Drosophila, Drosophila melanogaster, Enhancer Elements, Genetic, Evolution, Molecular, Gene Expression Regulation, Genes, Reporter, Genetic Vectors, Models, Genetic, Molecular Sequence Data, Phenotype, Species Specificity, Transcription, Genetic}, issn = {1091-6490}, doi = {10.1073/pnas.1207715109}, author = {Frankel, Nicol{\'a}s and Wang, Shu and Stern, David L} } @article {5924, title = {Control of timing, rate and bursts of hippocampal place cells by dendritic and somatic inhibition.}, journal = {Nature neuroscience}, volume = {15}, year = {2012}, month = {2012 May}, pages = {769-75}, abstract = {A consortium of inhibitory neurons control the firing patterns of pyramidal cells, but their specific roles in the behaving animal are largely unknown. We performed simultaneous physiological recordings and optogenetic silencing of either perisomatic (parvalbumin (PV) expressing) or dendrite-targeting (somatostatin (SOM) expressing) interneurons in hippocampal area CA1 of head-fixed mice actively moving a treadmill belt rich with visual-tactile stimuli. Silencing of either PV or SOM interneurons increased the firing rates of pyramidal cells selectively in their place fields, with PV and SOM interneurons having their largest effect during the rising and decaying parts of the place field, respectively. SOM interneuron silencing powerfully increased burst firing without altering the theta phase of spikes. In contrast, PV interneuron silencing had no effect on burst firing, but instead shifted the spikes{\textquoteright} theta phase toward the trough of theta. These findings indicate that perisomatic and dendritic inhibition have distinct roles in controlling the rate, burst and timing of hippocampal pyramidal cells.}, keywords = {Action Potentials, Animal, Animals, Behavior, Biophysics, Dendrites, Electric Stimulation, Exercise Test, Green Fluorescent Proteins, Halorhodopsins, Hippocampus, Humans, Inbred C57BL, Light, Mice, Movement, Neural Inhibition, Neurons, Optics and Photonics, Parvalbumins, Patch-Clamp Techniques, Photic Stimulation, Probability, Somatostatin, Spectrum Analysis, Time Factors, Time Perception, Touch, Transgenic}, issn = {1546-1726}, doi = {10.1038/nn.3077}, author = {Royer, S{\'e}bastien and Zemelman, Boris V and Losonczy, Attila and Kim, Jinhyun and Chance, Frances and Magee, Jeffrey C and Buzs{\'a}ki, Gy{\"o}rgy} } @article {45187, title = {Correlative 3D superresolution fluorescence and electron microscopy reveal the relationship of mitochondrial nucleoids to membranes.}, journal = {Proceedings of the National Academy of Science of the United States of America}, volume = {109}, year = {2012}, month = {2012 Apr 17}, pages = {6136-41}, abstract = {

Microscopic images of specific proteins in their cellular context yield important insights into biological processes and cellular architecture. The advent of superresolution optical microscopy techniques provides the possibility to augment EM with nanometer-resolution fluorescence microscopy to access the precise location of proteins in the context of cellular ultrastructure. Unfortunately, efforts to combine superresolution fluorescence and EM have been stymied by the divergent and incompatible sample preparation protocols of the two methods. Here, we describe a protocol that preserves both the delicate photoactivatable fluorescent protein labels essential for superresolution microscopy and the fine ultrastructural context of EM. This preparation enables direct 3D imaging in 500- to 750-nm sections with interferometric photoactivatable localization microscopy followed by scanning EM images generated by focused ion beam ablation. We use this process to "colorize" detailed EM images of the mitochondrion with the position of labeled proteins. The approach presented here has provided a new level of definition of the in vivo nature of organization of mitochondrial nucleoids, and we expect this straightforward method to be applicable to many other biological questions that can be answered by direct imaging.

}, keywords = {3T3 Cells, Animals, DNA, Mitochondrial, DNA-Binding Proteins, Fibroblasts, High Mobility Group Proteins, Imaging, Three-Dimensional, Luminescent Proteins, Mice, Microscopy, Electron, Microscopy, Fluorescence, Microscopy, Interference, Mitochondria, Mitochondrial Membranes, Mitochondrial Proteins, Reproducibility of Results}, issn = {1091-6490}, doi = {10.1073/pnas.1121558109}, author = {Kopek, Benjamin G and Shtengel, Gleb and Xu, C Shan and Clayton, David A and Hess, Harald F} } @article {4601, title = {A Cre-dependent GCaMP3 reporter mouse for neuronal imaging in vivo.}, journal = {The Journal of Neuroscience}, volume = {32}, year = {2012}, month = {2012 Feb 29}, pages = {3131-41}, abstract = {

Fluorescent calcium indicator proteins, such as GCaMP3, allow imaging of activity in genetically defined neuronal populations. GCaMP3 can be expressed using various gene delivery methods, such as viral infection or electroporation. However, these methods are invasive and provide inhomogeneous and nonstationary expression. Here, we developed a genetic reporter mouse, Ai38, which expresses GCaMP3 in a Cre-dependent manner from the ROSA26 locus, driven by a strong CAG promoter. Crossing Ai38 with appropriate Cre mice produced robust GCaMP3 expression in defined cell populations in the retina, cortex, and cerebellum. In the primary visual cortex, visually evoked GCaMP3 signals showed normal orientation and direction selectivity. GCaMP3 signals were rapid, compared with virally expressed GCaMP3 and synthetic calcium indicators. In the retina, Ai38 allowed imaging spontaneous calcium waves in starburst amacrine cells during development, and light-evoked responses in ganglion cells in adult tissue. Our results show that the Ai38 reporter mouse provides a flexible method for targeted expression of GCaMP3.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4469-11.2012}, author = {Zariwala, Hatim A and Borghuis, Bart G and Hoogland, Tycho M and Madisen, Linda and Tian, Lin and De Zeeuw, Chris I and Zeng, Hongkui and Looger, Loren L and Svoboda, Karel and Chen, Tsai-Wen} } @article {5653, title = {Current challenges in open-source bioimage informatics.}, journal = {Nature Methods}, volume = {9}, year = {2012}, month = {2012 Jul}, pages = {661-5}, abstract = {

We discuss the advantages and challenges of the open-source strategy in biological image analysis and argue that its full impact will not be realized without better support and recognition of software engineers{\textquoteright} contributions to the biological sciences and more support of this development model from funders and institutions.

}, keywords = {Algorithms, Computational Biology, Computer-Assisted, Image Processing, Information Dissemination, Internet, Software, Software Design}, issn = {1548-7105}, doi = {10.1038/nmeth.2082}, author = {Cardona, Albert and Tomancak, Pavel} } @article {4608, title = {Cutting edge: the role of IFN-α receptor and MyD88 signaling in induction of IL-15 expression in vivo.}, journal = {Journal of Immunology}, volume = {188}, year = {2012}, month = {2012 Mar 15}, pages = {2483-7}, abstract = {

IL-15 plays a multifaceted role in immune homeostasis, but the unreliability of IL-15 detection has stymied exploration of IL-15 regulation in vivo. To visualize IL-15 expression, we created a transgenic mouse expressing emerald-GFP (EmGFP) under IL-15 promoter control. EmGFP/IL-15 was prevalent in innate cells including dendritic cells (DCs), macrophages, and monocytes. However, DC subsets expressed varying levels of EmGFP/IL-15 with CD8(+) DCs constitutively expressing EmGFP/IL-15 and CD8(-) DCs expressing low EmGFP/IL-15 levels. Virus infection resulted in IL-15 upregulation in both subsets. By crossing the transgenic mice to mice deficient in specific elements of innate signaling, we found a cell-intrinsic dependency of DCs and Ly6C(+) monocytes on IFN-α receptor expression for EmGFP/IL-15 upregulation after vesicular stomatitis virus infection. In contrast, myeloid cells did not require the expression of MyD88 to upregulate EmGFP/IL-15 expression. These findings provide evidence of previously unappreciated regulation of IL-15 expression in myeloid lineages during homeostasis and following infection.

}, issn = {1550-6606}, doi = {10.4049/jimmunol.1103609}, author = {Colpitts, Sara L and Stoklasek, Thomas A and Plumlee, Courtney R and Obar, Joshua J and Guo, Caiying and Lefran\c cois, Leo} } @article {6280, title = {The C-value paradox, junk DNA and ENCODE.}, journal = {Current Biology}, volume = {22}, year = {2012}, month = {2012 Nov 6}, pages = {R898-9}, abstract = {

paradox? You might expect more complex organisms to have progressively larger genomes, but eukaryotic genome size fails to correlate well with apparent complexity, and instead varies wildly over more than a 100,000-fold range. Single-celled amoebae have some of the largest genomes, up to 100-fold larger than the human genome. This variation suggested that genomes can contain a substantial fraction of DNA other than for genes and their regulatory sequences. C.A. Thomas Jr dubbed it the {\textquoteleft}C-value paradox{\textquoteright} in 1971.

}, keywords = {Animals, DNA, DNA Transposable Elements, Genetic, Genome, Genome Size, Human, Humans, Intergenic, Models}, issn = {1879-0445}, doi = {10.1016/j.cub.2012.10.002}, author = {Eddy, Sean R.} } @article {5136, title = {Deconstruction of a neural circuit for hunger.}, journal = {Nature}, volume = {488}, year = {2012}, month = {2012 Aug 9}, pages = {172-7}, abstract = {

Hunger is a complex behavioural state that elicits intense food seeking and consumption. These behaviours are rapidly recapitulated by activation of starvation-sensitive AGRP neurons, which present an entry point for reverse-engineering neural circuits for hunger. Here we mapped synaptic interactions of AGRP neurons with multiple cell populations in mice and probed the contribution of these distinct circuits to feeding behaviour using optogenetic and pharmacogenetic techniques. An inhibitory circuit with paraventricular hypothalamus (PVH) neurons substantially accounted for acute AGRP neuron-evoked eating, whereas two other prominent circuits were insufficient. Within the PVH, we found that AGRP neurons target and inhibit oxytocin neurons, a small population that is selectively lost in Prader-Willi syndrome, a condition involving insatiable hunger. By developing strategies for evaluating molecularly defined circuits, we show that AGRP neuron suppression of oxytocin neurons is critical for evoked feeding. These experiments reveal a new neural circuit that regulates hunger state and pathways associated with overeating disorders.

}, issn = {1476-4687}, doi = {10.1038/nature11270}, author = {Atasoy, Deniz and Betley, J Nicholas and Su, Helen H and Sternson, Scott M} } @article {6922, title = {Deletion of the γ-aminobutyric acid transporter 2 (GAT2 and SLC6A13) gene in mice leads to changes in liver and brain taurine contents.}, journal = {The Journal of Biological Chemistry}, volume = {287}, year = {2012}, month = {2012 Oct 12}, pages = {35733-46}, abstract = {

The GABA transporters (GAT1, GAT2, GAT3, and BGT1) have mostly been discussed in relation to their potential roles in controlling the action of transmitter GABA in the nervous system. We have generated the first mice lacking the GAT2 (slc6a13) gene. Deletion of GAT2 (both mRNA and protein) neither affected growth, fertility, nor life span under nonchallenging rearing conditions. Immunocytochemistry showed that the GAT2 protein was predominantly expressed in the plasma membranes of periportal hepatocytes and in the basolateral membranes of proximal tubules in the renal cortex. This was validated by processing tissue from wild-type and knockout mice in parallel. Deletion of GAT2 reduced liver taurine levels by 50\%, without affecting the expression of the taurine transporter TAUT. These results suggest an important role for GAT2 in taurine uptake from portal blood into liver. In support of this notion, GAT2-transfected HEK293 cells transported [(3)H]taurine. Furthermore, most of the uptake of [(3)H]GABA by cultured rat hepatocytes was due to GAT2, and this uptake was inhibited by taurine. GAT2 was not detected in brain parenchyma proper, excluding a role in GABA inactivation. It was, however, expressed in the leptomeninges and in a subpopulation of brain blood vessels. Deletion of GAT2 increased brain taurine levels by 20\%, suggesting a taurine-exporting role for GAT2 in the brain.

}, keywords = {Animals, Brain, Brain Chemistry, GABA Plasma Membrane Transport Proteins, HEK293 Cells, Hepatocytes, Humans, Kidney Cortex, Kidney Tubules, Knockout, Liver, Male, Mice, Proximal, Rabbits, Rats, Taurine, Wistar}, issn = {1083-351X}, doi = {10.1074/jbc.M112.368175}, author = {Zhou, Yun and Holmseth, Silvia and Guo, Caiying and Hassel, Bj{\o}rnar and H{\"o}fner, Georg and Huitfeldt, Henrik S and Wanner, Klaus T and Danbolt, Niels C} } @conference {6520, title = {Design tools for artificial nervous systems.}, booktitle = {Design Automation Conference (DAC), 2012 49th ACM/EDAC/IEEE}, year = {2012}, month = {2012}, publisher = {IEEE}, organization = {IEEE}, address = {San Francisco, CA}, abstract = {

Electronic and biological systems both perform complex information processing, but they use very different techniques. Though electronics has the advantage in raw speed, biological systems have the edge in many other areas. They can be produced, and indeed self-reproduce, without expensive and finicky factories. They are tolerant of manufacturing defects, and learn and adapt for better performance. In many cases they can self-repair damage. These advantages suggest that biological systems might be useful in a wide variety of tasks involving information processing. So far, all attempts to use the nervous system of a living organism for information processing have involved selective breeding of existing organisms. This approach, largely independent of the details of internal operation, is used since we do not yet understand how neural systems work, nor exactly how they are constructed. However, as our knowledge increases, the day will come when we can envision useful nervous systems and design them based upon what we want them to do, as opposed to variations on what has been already built. We will then need tools, corresponding to our Electronic Design Automation tools, to help with the design. This paper is concerned with what such tools might look like.

}, isbn = {978-1-4503-1199-1}, author = {Scheffer, LK} } @article {69345, title = {Differential uptake of MRI contrast agents indicates charge-selective blood-brain interface in the crayfish}, journal = {Cell and Tissue Research}, volume = {349}, year = {2012}, month = {2012 Apr 19}, pages = {493 - 503}, abstract = {

This study provides a new perspective on the long-standing problem of the nature of the decapod crustacean blood-brain interface. Previous studies of crustacean blood-brain interface permeability have relied on invasive histological, immunohistochemical and electrophysiological techniques, indicating a leaky non-selective blood-brain barrier. The present investigation involves the use of magnetic resonance imaging (MRI), a method for non-invasive longitudinal tracking of tracers in real-time. Differential uptake rates of two molecularly distinct MRI contrast agents, namely manganese (Mn(II)) and Magnevist{\textregistered} (Gd-DTPA), were observed and quantified in the crayfish,\ Cherax destructor. Contrast agents were injected into the pericardium and uptake was observed with longitudinal MRI for approximately 14.5\ h. Mn(II) was taken up quickly into neural tissue (within 6.5\ min), whereas Gd-DTPA was not taken up into neural tissue and was instead restricted to the intracerebral vasculature or excreted into nearby sinuses. Our results provide evidence for a charge-selective intracerebral blood-brain interface in the crustacean nervous system, a structural characteristic once considered too complex for a lower-order arthropod.

}, issn = {0302-766X}, doi = {10.1007/s00441-012-1413-9}, url = {http://link.springer.com/10.1007/s00441-012-1413-9http://link.springer.com/content/pdf/10.1007/s00441-012-1413-9http://link.springer.com/content/pdf/10.1007/s00441-012-1413-9.pdfhttp://link.springer.com/article/10.1007/s00441-012-1413-9/fulltext.html}, author = {Otopalik, Adriane G. and Shin, Jane and Beltz, Barbara S. and Sandeman, David C. and Kolodny, Nancy H.} } @article {46605, title = {DlgS97/SAP97, a neuronal isoform of discs large, regulates ethanol tolerance.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012 Nov 7}, pages = {e48967}, abstract = {

From a genetic screen for Drosophila melanogaster mutants with altered ethanol tolerance, we identified intolerant (intol), a novel allele of discs large 1 (dlg1). Dlg1 encodes Discs Large 1, a MAGUK (Membrane Associated Guanylate Kinase) family member that is the highly conserved homolog of mammalian PSD-95 and SAP97. The intol mutation disrupted specifically the expression of DlgS97, a SAP97 homolog, and one of two major protein isoforms encoded by dlg1 via alternative splicing. Expression of the major isoform, DlgA, a PSD-95 homolog, appeared unaffected. Ethanol tolerance in the intol mutant could be partially restored by transgenic expression of DlgS97, but not DlgA, in specific neurons of the fly{\textquoteright}s brain. Based on co-immunoprecipitation, DlgS97 forms a complex with N-methyl-D-aspartate (NMDA) receptors, a known target of ethanol. Consistent with these observations, flies expressing reduced levels of the essential NMDA receptor subunit dNR1 also showed reduced ethanol tolerance, as did mutants in the gene calcium/calmodulin-dependent protein kinase (caki), encoding the fly homolog of mammalian CASK, a known binding partner of DlgS97. Lastly, mice in which SAP97, the mammalian homolog of DlgS97, was conditionally deleted in adults failed to develop rapid tolerance to ethanol{\textquoteright}s sedative/hypnotic effects. We propose that DlgS97/SAP97 plays an important and conserved role in the development of tolerance to ethanol via NMDA receptor-mediated synaptic plasticity.

}, keywords = {Alleles, Alternative Splicing, Animals, Drosophila melanogaster, Drosophila Proteins, Ethanol, Female, Guanylate Kinase, Male, Membrane Proteins, Mice, Mice, Inbred C57BL, Mutation, Neurons, Protein Isoforms, Receptors, N-Methyl-D-Aspartate, Repressor Proteins, Tumor Suppressor Proteins}, issn = {1932-6203}, doi = {10.1371/journal.pone.0048967}, author = {Maiya, Rajani and Lee, Seonok and Berger, Karen H and Kong, Eric C and Slawson, Justin B and Griffith, Leslie C and Takamiya, Kogo and Huganir, Richard L and Margolis, Ben and Heberlein, Ulrike} } @article {6854, title = {Dopamine neurons modulate pheromone responses in Drosophila courtship learning.}, journal = {Nature}, volume = {489}, year = {2012}, month = {2012 Sep 6}, pages = {145-9}, abstract = {

Learning through trial-and-error interactions allows animals to adapt innate behavioural {\textquoteleft}rules of thumb{\textquoteright} to the local environment, improving their prospects for survival and reproduction. Naive Drosophila melanogaster males, for example, court both virgin and mated females, but learn through experience to selectively suppress futile courtship towards females that have already mated. Here we show that courtship learning reflects an enhanced response to the male pheromone cis-vaccenyl acetate (cVA), which is deposited on females during mating and thus distinguishes mated females from virgins. Dissociation experiments suggest a simple learning rule in which unsuccessful courtship enhances sensitivity to cVA. The learning experience can be mimicked by artificial activation of dopaminergic neurons, and we identify a specific class of dopaminergic neuron that is critical for courtship learning. These neurons provide input to the mushroom body (MB) γ lobe, and the DopR1 dopamine receptor is required in MBγ neurons for both natural and artificial courtship learning. Our work thus reveals critical behavioural, cellular and molecular components of the learning rule by which Drosophila adjusts its innate mating strategy according to experience.

}, keywords = {Acetates, Animal, Animals, Brain, Courtship, Dopamine, Dopaminergic Neurons, Drosophila melanogaster, Female, Learning, Male, Mushroom Bodies, Oleic Acids, Pheromones, Presynaptic Terminals, Receptors, Sex Attractants, Sexual Behavior, Synaptic Transmission}, issn = {1476-4687}, doi = {10.1038/nature11345}, author = {Keleman, Krystyna and Vrontou, Eleftheria and Kr{\"u}ttner, Sebastian and Yu, Jai Y and Kurtovic-Kozaric, Amina and Dickson, Barry J} } @article {5319, title = {Dorsorostral snout muscles in the rat subserve coordinated movement for whisking and sniffing.}, journal = {Anatomical Record}, volume = {295}, year = {2012}, month = {2012 Jul}, pages = {1181-91}, abstract = {

Histochemical examination of the dorsorostral quadrant of the rat snout revealed superficial and deep muscles that are involved in whisking, sniffing, and airflow control. The part of M. nasolabialis profundus that acts as an intrinsic (follicular) muscle to facilitate protraction and translation of the vibrissae is described. An intraturbinate and selected rostral-most nasal muscles that can influence major routs of inspiratory airflow and rhinarial touch through their control of nostril configuration, atrioturbinate and rhinarium position, were revealed.

}, issn = {1932-8494}, doi = {10.1002/ar.22501}, author = {Haidarliu, Sebastian and Golomb, David and Kleinfeld, David and Ahissar, Ehud} } @article {6269, title = {Doublesex functions early and late in gustatory sense organ development.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012}, pages = {e51489}, abstract = {

Somatic sexual dimorphisms outside of the nervous system in Drosophila melanogaster are largely controlled by the male- and female-specific Doublesex transcription factors (DSX(M) and DSX(F), respectively). The DSX proteins must act at the right times and places in development to regulate the diverse array of genes that sculpt male and female characteristics across a variety of tissues. To explore how cellular and developmental contexts integrate with doublesex (dsx) gene function, we focused on the sexually dimorphic number of gustatory sense organs (GSOs) in the foreleg. We show that DSX(M) and DSX(F) promote and repress GSO formation, respectively, and that their relative contribution to this dimorphism varies along the proximodistal axis of the foreleg. Our results suggest that the DSX proteins impact specification of the gustatory sensory organ precursors (SOPs). DSX(F) then acts later in the foreleg to regulate gustatory receptor neuron axon guidance. These results suggest that the foreleg provides a unique opportunity for examining the context-dependent functions of DSX.

}, keywords = {Animals, Axons, Developmental, DNA-Binding Proteins, Drosophila melanogaster, Drosophila Proteins, Gene Expression Regulation, Neurons, Sense Organs, Sex Characteristics, Taste}, issn = {1932-6203}, doi = {10.1371/journal.pone.0051489}, author = {Mellert, David J and Robinett, Carmen C and Baker, Bruce S} } @article {6856, title = {Drosophila CPEB Orb2A mediates memory independent of Its RNA-binding domain.}, journal = {Neuron}, volume = {76}, year = {2012}, month = {2012 Oct 18}, pages = {383-95}, abstract = {

Long-term memory and synaptic plasticity are thought to require the synthesis of new proteins at activated synapses. The CPEB family of RNA binding proteins, including Drosophila Orb2, has been implicated in this process. The precise mechanism by which these molecules regulate memory formation is however poorly understood. We used gene targeting and site-specific transgenesis to specifically modify the endogenous orb2 gene in order to investigate its role in long-term memory formation. We show that the Orb2A and Orb2B isoforms, while both essential, have distinct functions in memory formation. These two isoforms have common glutamine-rich and RNA-binding domains, yet Orb2A uniquely requires the former and Orb2B the latter. We further show that Orb2A induces Orb2 complexes in a manner dependent upon both its glutamine-rich region and neuronal activity. We propose that Orb2B acts as a conventional CPEB to regulate transport and/or translation of specific mRNAs, whereas Orb2A acts in an unconventional manner to form stable Orb2 complexes that are essential for memory to persist.

}, keywords = {Animals, Biogenic Amines, Brain, Cell Line, Chromatography, Courtship, Developmental, Drosophila, Drosophila Proteins, Embryo, Gene Expression Regulation, Genetically Modified, Genotype, Green Fluorescent Proteins, High Pressure Liquid, Immunoelectron, Immunoprecipitation, Larva, Learning, Male, Mass Spectrometry, Memory, Messenger, Microscopy, Mitogen-Activated Protein Kinases, mRNA Cleavage and Polyadenylation Factors, Mushroom Bodies, Mutation, Nonmammalian, Protein Isoforms, Protein Structure, RNA, RNA-Binding Proteins, Tertiary, Transcription Factors}, issn = {1097-4199}, doi = {10.1016/j.neuron.2012.08.028}, author = {Kr{\"u}ttner, Sebastian and Stepien, Barbara and Noordermeer, Jasprina N and Mommaas, Mieke A and Mechtler, Karl and Dickson, Barry J and Keleman, Krystyna} } @article {6859, title = {The Drosophila female aphrodisiac pheromone activates ppk23(+) sensory neurons to elicit male courtship behavior.}, journal = {Cell Reports}, volume = {1}, year = {2012}, month = {2012 Jun 28}, pages = {599-607}, abstract = {

Females of many animal species emit chemical signals that attract and arouse males for mating. For example, the major aphrodisiac pheromone of Drosophila melanogaster females, 7,11-heptacosadiene (7,11-HD), is a potent inducer of male-specific courtship and copulatory behaviors. Here, we demonstrate that a set of gustatory sensory neurons on the male foreleg, defined by expression of the ppk23 marker, respond to 7,11-HD. Activity of these neurons is required for males to robustly court females or to court males perfumed with 7,11-HD. Artificial activation of these ppk23(+) neurons stimulates male-male courtship even without 7,11-HD perfuming. These data identify the ppk23(+) sensory neurons as the primary targets for female sex pheromones in Drosophila.

}, keywords = {Alkadienes, Animal, Animals, Aphrodisiacs, Courtship, Drosophila melanogaster, Drosophila Proteins, Female, Ion Channels, Male, Pheromones, Sensilla, Sensory Receptor Cells, Sexual Behavior, Taste}, issn = {2211-1247}, doi = {10.1016/j.celrep.2012.05.007}, author = {Toda, Hirofumi and Zhao, Xiaoliang and Dickson, Barry J} } @article {4522, title = {Drosophila melanogaster as a model to study drug addiction.}, journal = {Human Genetics}, volume = {131}, year = {2012}, month = {2012 Feb 17}, pages = {959-75}, abstract = {

Animal studies have been instrumental in providing knowledge about the molecular and neural mechanisms underlying drug addiction. Recently, the fruit fly Drosophila melanogaster has become a valuable system to model not only the acute stimulating and sedating effects of drugs but also their more complex rewarding properties. In this review, we describe the advantages of using the fly to study drug-related behavior, provide a brief overview of the behavioral assays used, and review the molecular mechanisms and neural circuits underlying drug-induced behavior in flies. Many of these mechanisms have been validated in mammals, suggesting that the fly is a useful model to understand the mechanisms underlying addiction.

}, issn = {1432-1203}, doi = {10.1007/s00439-012-1146-6}, author = {Kaun, Karla R and Devineni, Anita V and Heberlein, Ulrike} } @article {47650, title = {DRP1-dependent mitochondrial fission initiates follicle cell differentiation during Drosophila oogenesis.}, journal = {The Journal of cell biology}, volume = {197}, year = {2012}, month = {2012 May 14}, pages = {487-97}, abstract = {

Exit from the cell cycle is essential for cells to initiate a terminal differentiation program during development, but what controls this transition is incompletely understood. In this paper, we demonstrate a regulatory link between mitochondrial fission activity and cell cycle exit in follicle cell layer development during Drosophila melanogaster oogenesis. Posterior-localized clonal cells in the follicle cell layer of developing ovarioles with down-regulated expression of the major mitochondrial fission protein DRP1 had mitochondrial elements extensively fused instead of being dispersed. These cells did not exit the cell cycle. Instead, they excessively proliferated, failed to activate Notch for differentiation, and exhibited downstream developmental defects. Reintroduction of mitochondrial fission activity or inhibition of the mitochondrial fusion protein Marf-1 in posterior-localized DRP1-null clones reversed the block in Notch-dependent differentiation. When DRP1-driven mitochondrial fission activity was unopposed by fusion activity in Marf-1-depleted clones, premature cell differentiation of follicle cells occurred in mitotic stages. Thus, DRP1-dependent mitochondrial fission activity is a novel regulator of the onset of follicle cell differentiation during Drosophila oogenesis.

}, keywords = {Animals, Cell Cycle Proteins, Cell Differentiation, Cytoskeletal Proteins, Drosophila melanogaster, Drosophila Proteins, GTP-Binding Proteins, Mitochondria, Mitosis, Oogenesis, Receptors, Notch}, issn = {1540-8140}, doi = {10.1083/jcb.201110058}, author = {Mitra, Kasturi and Rikhy, Richa and Lilly, Mary and Lippincott-Schwartz, Jennifer} } @conference {5685, title = {Efficient automatic 3D-reconstruction of branching neurons from EM data.}, booktitle = {Computer Vision and Pattern Recognition (CVPR), 2012 IEEE Conference on}, year = {2012}, month = {2012}, abstract = {

We present an approach for the automatic reconstruction of neurons from 3D stacks of electron microscopy sections. The core of our system is a set of possible assignments, each of which proposes with some cost a link between neuron regions in consecutive sections. These can model the continuation, branching, and end of neurons. The costs are trainable on positive assignment samples. An optimal and consistent set of assignments is found for the whole volume at once by solving an integer linear program. This set of assignments determines both the segmentation into neuron regions and the correspondence between such regions in neighboring slices. For each picked assignment, a confidence value helps to prioritize decisions to be reviewed by a human expert. We evaluate the performance of our method on an annotated volume of neural tissue and compare to the current state of the art [26]. Our method is superior in accuracy and can be trained using a small number of samples. The observed inference times are linear with about 2 milliseconds per neuron and section.

}, author = {Funke, Jan and Andres, Bjoern and Hamprecht, Fred and Cardona, Albert and Cook, Matthew} } @article {6286, title = {The effort to make mosaic analysis a household tool.}, journal = {Development}, volume = {139}, year = {2012}, month = {2012 Dec}, pages = {4501-3}, abstract = {

The analysis of genetic mosaics, in which an animal carries populations of cells with differing genotypes, is a powerful tool for understanding developmental and cell biology. In 1990, we set out to improve the methods used to make genetic mosaics in Drosophila by taking advantage of recently developed approaches for genome engineering. These efforts led to the work described in our 1993 Development paper.

}, keywords = {Animals, Biological, DNA Nucleotidyltransferases, Drosophila, Genetic, Genetic Testing, Genetically Modified, Genome, Mice, Models, Mosaicism, Recombination}, issn = {1477-9129}, doi = {10.1242/dev.085183}, author = {Xu, Tian and Rubin, Gerald M} } @article {5681, title = {Elastic volume reconstruction from series of ultra-thin microscopy sections.}, journal = {Nature Methods}, volume = {9}, year = {2012}, month = {2012 Jul}, pages = {717-20}, abstract = {

Anatomy of large biological specimens is often reconstructed from serially sectioned volumes imaged by high-resolution microscopy. We developed a method to reassemble a continuous volume from such large section series that explicitly minimizes artificial deformation by applying a global elastic constraint. We demonstrate our method on a series of transmission electron microscopy sections covering the entire 558-cell Caenorhabditis elegans embryo and a segment of the Drosophila melanogaster larval ventral nerve cord.

}, keywords = {Animals, Automated, Caenorhabditis elegans, Computer-Assisted, Drosophila melanogaster, Elasticity, Electron, Embryo, Image Processing, Larva, Microscopy, Microtomy, Nonmammalian, Pattern Recognition, Transmission}, issn = {1548-7105}, doi = {10.1038/nmeth.2072}, author = {Saalfeld, Stephan and Fetter, Richard D and Cardona, Albert and Tomancak, Pavel.} } @article {5321, title = {Escape behaviors in insects.}, journal = {Current Opinion in Neurobiology}, volume = {22}, year = {2012}, month = {2012 Apr}, pages = {180-6}, abstract = {

Escape behaviors are, by necessity, fast and robust, making them excellent systems with which to study the neural basis of behavior. This is especially true in insects, which have comparatively tractable nervous systems and members who are amenable to manipulation with genetic tools. Recent technical developments in high-speed video reveal that, despite their short duration, insect escape behaviors are more complex than previously appreciated. For example, before initiating an escape jump, a fly performs sophisticated posture and stimulus-dependent preparatory leg movements that enable it to jump away from a looming threat. This newfound flexibility raises the question of how the nervous system generates a behavior that is both rapid and flexible. Recordings from the cricket nervous system suggest that synchrony between the activity of specific interneuron pairs may provide a rapid cue for the cricket to detect the direction of an approaching predator and thus which direction it should run. Technical advances make possible wireless recording from neurons while locusts escape from a looming threat, enabling, for the first time, a direct correlation between the activity of multiple neurons and the time-course of an insect escape behavior.

}, keywords = {Animals, Escape Reaction, Ethology, Insects, Neural Pathways, Neurology, Neurons}, issn = {1873-6882}, doi = {10.1016/j.conb.2011.12.009}, author = {Card, Gwyneth M} } @article {48392, title = {Estimation theoretic measure of resolution for stochastic localization microscopy.}, journal = {Physical review letters}, volume = {109}, year = {2012}, month = {2012 Jul 27}, pages = {048102}, abstract = {

One approach to super-resolution fluorescence microscopy, termed stochastic localization microscopy, relies on the nanometer scale spatial localization of individual fluorescent emitters that stochastically label specific features of the specimen. The precision of emitter localization is an important determinant of the resulting image resolution but is insufficient to specify how well the derived images capture the structure of the specimen. We address this deficiency by considering the inference of specimen structure based on the estimated emitter locations. By using estimation theory, we develop a measure of spatial resolution that jointly depends on the density of the emitter labels, the precision of emitter localization, and prior information regarding the spatial frequency content of the labeled object. The Nyquist criterion does not set the scaling of this measure with emitter number. Given prior information and a fixed emitter labeling density, our resolution measure asymptotes to a finite value as the precision of emitter localization improves. By considering the present experimental capabilities, this asymptotic behavior implies that further resolution improvements require increases in labeling density above typical current values. Our treatment also yields algorithms to enhance reliable image features. Overall, our formalism facilitates the rigorous statistical interpretation of the data produced by stochastic localization imaging techniques.

}, keywords = {Microscopy, Fluorescence, Models, Theoretical, Stochastic Processes}, issn = {1079-7114}, doi = {10.1103/PhysRevLett.109.048102}, author = {Fitzgerald, James E and Lu, Ju and Schnitzer, Mark J} } @article {45726, title = {Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012}, pages = {e43888}, abstract = {

In Drosophila, male flies perform innate, stereotyped courtship behavior. This innate behavior evolves rapidly between fly species, and is likely to have contributed to reproductive isolation and species divergence. We currently understand little about the neurobiological and genetic mechanisms that contributed to the evolution of courtship behavior. Here we describe a novel behavioral difference between the two closely related species D. yakuba and D. santomea: the frequency of wing rowing during courtship. During courtship, D. santomea males repeatedly rotate their wing blades to face forward and then back (rowing), while D. yakuba males rarely row their wings. We found little intraspecific variation in the frequency of wing rowing for both species. We exploited multiplexed shotgun genotyping (MSG) to genotype two backcross populations with a single lane of Illumina sequencing. We performed quantitative trait locus (QTL) mapping using the ancestry information estimated by MSG and found that the species difference in wing rowing mapped to four or five genetically separable regions. We found no evidence that these loci display epistasis. The identified loci all act in the same direction and can account for most of the species difference.

}, keywords = {Animals, Chromosome Mapping, Courtship, Drosophila, Evolution, Molecular, Female, Genetic Markers, Genotyping Techniques, Hybridization, Genetic, Male, Movement, Quantitative Trait Loci, Sexual Behavior, Animal, Species Specificity, Wing}, issn = {1932-6203}, doi = {10.1371/journal.pone.0043888}, author = {Cande, Jessica and Andolfatto, Peter and Prud{\textquoteright}homme, Benjamin and Stern, David L and Gompel, Nicolas} } @article {4596, title = {Excitation spectra and brightness optimization of two-photon excited probes.}, journal = {Biophysical Journal}, volume = {102}, year = {2012}, month = {2012 Feb 22}, pages = {934-44}, abstract = {

Two-photon probe excitation data are commonly presented as absorption cross section or molecular brightness (the detected fluorescence rate per molecule). We report two-photon molecular brightness spectra for a diverse set of organic and genetically encoded probes with an automated spectroscopic system based on fluorescence correlation spectroscopy. The two-photon action cross section can be extracted from molecular brightness measurements at low excitation intensities, while peak molecular brightness (the maximum molecular brightness with increasing excitation intensity) is measured at higher intensities at which probe photophysical effects become significant. The spectral shape of these two parameters was similar across all dye families tested. Peak molecular brightness spectra, which can be obtained rapidly and with reduced experimental complexity, can thus serve as a first-order approximation to cross-section spectra in determining optimal wavelengths for two-photon excitation, while providing additional information pertaining to probe photostability. The data shown should assist in probe choice and experimental design for multiphoton microscopy studies. Further, we show that, by the addition of a passive pulse splitter, nonlinear bleaching can be reduced-resulting in an enhancement of the fluorescence signal in fluorescence correlation spectroscopy by a factor of two. This increase in fluorescence signal, together with the observed resemblance of action cross section and peak brightness spectra, suggests higher-order photobleaching pathways for two-photon excitation.

}, issn = {1542-0086}, doi = {10.1016/j.bpj.2011.12.056}, author = {M{\"u}tze, J{\"o}rg and Iyer, Vijay and Macklin, John J and Colonell, Jennifer and Karsh, Bill and Petr{\'a}\v sek, Zden\v ek and Schwille, Petra and Looger, Loren L and Lavis, Luke D and Harris, Timothy D} } @article {5634, title = {Fiji: an open-source platform for biological-image analysis.}, journal = {Nature Methods}, volume = {9}, year = {2012}, month = {2012 Jul}, pages = {676-82}, abstract = {

Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

}, keywords = {Algorithms, Animals, Brain, Computational Biology, Computer-Assisted, Drosophila melanogaster, Image Enhancement, Image Processing, Imaging, Information Dissemination, Software, Software Design, Three-Dimensional}, issn = {1548-7105}, doi = {10.1038/nmeth.2019}, author = {Schindelin, Johannes and Arganda-Carreras, Ignacio and Frise, Erwin and Kaynig, Verena and Longair, Mark and Pietzsch, Tobias and Preibisch, Stephan and Rueden, Curtis and Saalfeld, Stephan and Schmid, Benjamin and Tinevez, Jean-Yves and White, Daniel James and Hartenstein, Volker and Eliceiri, Kevin and Tomancak, Pavel and Cardona, Albert} } @article {46723, title = {Fluorescence fluctuation spectroscopy enables quantitative imaging of single mRNAs in living cells.}, journal = {Biophysical Journal}, volume = {102}, year = {2012}, month = {2012 Jun 20}, pages = {2936-44}, abstract = {

Imaging mRNA with single-molecule sensitivity in live cells has become an indispensable tool for quantitatively studying RNA biology. The MS2 system has been extensively used due to its unique simplicity and sensitivity. However, the levels of the coat protein needed for consistent labeling of mRNAs limits the sensitivity and quantitation of this technology. Here, we applied fluorescence fluctuation spectroscopy to quantitatively characterize and enhance the MS2 system. Surprisingly, we found that a high fluorescence background resulted from inefficient dimerization of fluorescent protein (FP)-labeled MS2 coat protein (MCP). To mitigate this problem, we used a single-chain tandem dimer of MCP (tdMCP) that significantly increased the uniformity and sensitivity of mRNA labeling. Furthermore, we characterized the PP7 coat protein and the binding to its respective RNA stem loop. We conclude that the PP7 system performs better for RNA labeling. Finally, we used these improvements to study endogenous β-actin mRNA, which has 24xMS2 binding sites inserted into the 3{\textquoteright} untranslated region. The tdMCP-FP allowed uniform RNA labeling and provided quantitative measurements of endogenous mRNA concentration and diffusion. This work provides a foundation for quantitative spectroscopy and imaging of single mRNAs directly in live cells.

}, keywords = {Actins, Animals, Capsid Proteins, Cell Line, Cell Nucleus, Cell Survival, Diffusion, Mice, Molecular Imaging, Protein Multimerization, Protein Structure, Quaternary, RNA, Messenger, Spectrometry, Fluorescence}, issn = {1542-0086}, doi = {10.1016/j.bpj.2012.05.017}, author = {Wu, Bin and Chao, Jeffrey A and Singer, Robert H} } @article {5101, title = {Fluorescence imaging beyond the ballistic regime by ultrasound-pulse-guided digital phase conjugation.}, journal = {Nature Photonics}, volume = {6}, year = {2012}, month = {2012 Aug}, pages = {657}, abstract = {

Fluorescence imaging has revolutionized biomedical research over the past three decades. Its high molecular specificity and unrivalled single-molecule-level sensitivity have enabled breakthroughs in a number of research fields. For in vivo applications its major limitation is its superficial imaging depth, a result of random scattering in biological tissues causing exponential attenuation of the ballistic component of a light wave. Here, we present fluorescence imaging beyond the ballistic regime by combining single-cycle pulsed ultrasound modulation and digital optical phase conjugation. We demonstrate a near-isotropic three-dimensional localized sound{\textendash}light interaction zone. With the exceptionally high optical gain provided by the digital optical phase conjugation system, we can deliver sufficient optical power to a focus inside highly scattering media for not only fluorescence imaging but also a variety of linear and nonlinear spectroscopy measurements. This technology paves the way for many important applications in both fundamental biology research and clinical studies.

}, doi = {doi:10.1038/nphoton.2012.205}, author = {Si, Ke and Fiolka, Reto and Cui, Meng} } @article {5078, title = {From distributed resources to limited slots in multiple-item working memory: a spiking network model with normalization.}, journal = {Journal of Neuroscience}, volume = {32}, year = {2012}, month = {2012 Aug 15}, pages = {11228-40}, abstract = {

Recent behavioral studies have given rise to two contrasting models for limited working memory capacity: a "discrete-slot" model in which memory items are stored in a limited number of slots, and a "shared-resource" model in which the neural representation of items is distributed across a limited pool of resources. To elucidate the underlying neural processes, we investigated a continuous network model for working memory of an analog feature. Our model network fundamentally operates with a shared resource mechanism, and stimuli in cue arrays are encoded by a distributed neural population. On the other hand, the network dynamics and performance are also consistent with the discrete-slot model, because multiple objects are maintained by distinct localized population persistent activity patterns (bump attractors). We identified two phenomena of recurrent circuit dynamics that give rise to limited working memory capacity. As the working memory load increases, a localized persistent activity bump may either fade out (so the memory of the corresponding item is lost) or merge with another nearby bump (hence the resolution of mnemonic representation for the merged items becomes blurred). We identified specific dependences of these two phenomena on the strength and tuning of recurrent synaptic excitation, as well as network normalization: the overall population activity is invariant to set size and delay duration; therefore, a constant neural resource is shared by and dynamically allocated to the memorized items. We demonstrate that the model reproduces salient observations predicted by both discrete-slot and shared-resource models, and propose testable predictions of the merging phenomenon.

}, issn = {1529-2401}, doi = {10.1523/​JNEUROSCI.0735-12.2012}, author = {Wei, Ziqiang and Wang, Xiao-Jing and Wang, Da-Hui} } @article {5423, title = {A GAL4-driver line resource for Drosophila neurobiology.}, journal = {Cell Reports}, volume = {2}, year = {2012}, month = {2012 Oct 25}, pages = {991-1001}, abstract = {

We established a collection of 7,000 transgenic lines of Drosophila melanogaster. Expression of GAL4 in each line is controlled by a different, defined fragment of genomic DNA that serves as a transcriptional enhancer. We used confocal microscopy of dissected nervous systems to determine the expression patterns driven by each fragment in the adult brain and ventral nerve cord. We present image data on 6,650 lines. Using both manual and machine-assisted annotation, we describe the expression patterns in the most useful lines. We illustrate the utility of these data for identifying novel neuronal cell types, revealing brain asymmetry, and describing the nature and extent of neuronal shape stereotypy. The GAL4 lines allow expression of exogenous genes in distinct, small subsets of the adult nervous system. The set of DNA fragments, each driving a documented expression pattern, will facilitate the generation of additional constructs for manipulating neuronal function. synapse was substantially elevated, at the endocytic zone there was no enhanced polymerization activity. We conclude that actin subserves spatially diverse, independently regulated processes throughout spines. Perisynaptic actin forms a uniquely dynamic structure well suited for direct, active regulation of the synapse.

For the overall strategy and methods used to produce the GAL4 lines:
Pfeiffer, B.D., Jenett, A., Hammonds, A.S., Ngo, T.T., Misra, S., Murphy, C., Scully, A., Carlson, J.W., Wan, K.H., Laverty, T.R., Mungall, C., Svirskas, R., Kadonaga, J.T., Doe, C.Q., Eisen, M.B., Celniker, S.E., Rubin, G.M. (2008). Tools for neuroanatomy and neurogenetics in Drosophila. Proc. Natl. Acad. Sci. USA 105, 9715-9720. http://www.pnas.org/content/105/28/9715.full.pdf+html synapse was substantially elevated, at the endocytic zone there was no enhanced polymerization activity. We conclude that actin subserves spatially diverse, independently regulated processes throughout spines. Perisynaptic actin forms a uniquely dynamic structure well suited for direct, active regulation of the synapse.

For data on expression in the embryo:
Manning, L., Purice, M.D., Roberts, J., Pollard, J.L., Bennett, A.L., Kroll, J.R., Dyukareva, A.V., Doan, P.N., Lupton, J.R., Strader, M.E., Tanner, S., Bauer, D., Wilbur, A., Tran, K.D., Laverty, T.R., Pearson, J.C., Crews, S.T., Rubin, G.M., and Doe, C.Q. (2012) Annotated embryonic CNS expression patterns of 5000 GMR GAL4 lines: a resource for manipulating gene expression and analyzing cis-regulatory motifs. Cell Reports (2012) Doi: 10.1016/j.celrep.2012.09.009 http://www.cell.com/cell-reports/fulltext/S2211-1247(12)00290-2 synapse was substantially elevated, at the endocytic zone there was no enhanced polymerization activity. We conclude that actin subserves spatially diverse, independently regulated processes throughout spines. Perisynaptic actin forms a uniquely dynamic structure well suited for direct, active regulation of the synapse.

For data on expression in imaginal discs:
Jory, A., Estella, C., Giorgianni, M.W., Slattery, M., Laverty, T.R., Rubin, G.M., and Mann, R.S. (2012) A survey of 6300 genomic fragments for cis-regulatory activity in the imaginal discs of Drosophila melanogaster. Cell Reports (2012) Doi: 10.1016/j.celrep.2012.09.010 http://www.cell.com/cell-reports/fulltext/S2211-1247(12)00291-4 synapse was substantially elevated, at the endocytic zone there was no enhanced polymerization activity. We conclude that actin subserves spatially diverse, independently regulated processes throughout spines. Perisynaptic actin forms a uniquely dynamic structure well suited for direct, active regulation of the synapse.

For data on expression in the larval nervous system:
Li, H.-H., Kroll, J.R., Lennox, S., Ogundeyi, O., Jeter, J., Depasquale, G., and Truman, J.W. (2013) A GAL4 driver resource for developmental and behavioral studies on the larval CNS of Drosophila. Cell Reports (submitted).

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2012.09.011}, author = {Jenett, Arnim and Rubin, Gerald M and Ngo, Teri-T B and Shepherd, David and Murphy, Christine and Dionne, Heather and Pfeiffer, Barret D and Cavallaro, Amanda and Hall, Donald and Jeter, Jennifer and Iyer, Nirmala and Fetter, Dona and Hausenfluck, Joanna H and Peng, Hanchuan and Trautman, Eric T and Svirskas, Robert R and Myers, Eugene W and Iwinski, Zbigniew R and Aso, Yoshinori and Depasquale, Gina M and Enos, Adrianne and Hulamm, Phuson and Lam, Shing Chun Benny and Li, Hsing-Hsi and Laverty, Todd R and Long, Fuhui and Qu, Lei and Murphy, Sean D and Rokicki, Konrad and Safford, Todd and Shaw, Kshiti and Simpson, Julie H and Sowell, Allison and Tae, Susana and Yu, Yang and Zugates, Christopher T} } @article {4488, title = {Generating neuronal diversity in the Drosophila central nervous system.}, journal = {Developmental Dynamics: An Official Publication of the American Association of Anatomists}, volume = {241}, year = {2012}, month = {2012 Jan}, pages = {57-68}, abstract = {

Generating diverse neurons in the central nervous system involves three major steps. First, heterogeneous neural progenitors are specified by positional cues at early embryonic stages. Second, neural progenitors sequentially produce neurons or intermediate precursors that acquire different temporal identities based on their birth-order. Third, sister neurons produced during asymmetrical terminal mitoses are given distinct fates. Determining the molecular mechanisms underlying each of these three steps of cellular diversification will unravel brain development and evolution. Drosophila has a relatively simple and tractable CNS, and previous studies on Drosophila CNS development have greatly advanced our understanding of neuron fate specification. Here we review those studies and discuss how the lessons we have learned from fly teach us the process of neuronal diversification in general.

}, issn = {1097-0177}, doi = {10.1002/dvdy.22739}, author = {Lin, Suewei and Lee, Tzumin} } @article {68815, title = {Generation of Multiple Classes of V0 Neurons in Zebrafish Spinal Cord: Progenitor Heterogeneity and Temporal Control of Neuronal Diversity}, journal = {Journal of Neuroscience}, volume = {32}, year = {2012}, month = {02/2012}, pages = {1771{\textendash}1783}, abstract = {

The developing spinal cord is subdivided into distinct progenitor domains, each of which gives rise to different types of neurons. However, the developmental mechanisms responsible for generating neuronal diversity within a domain are not well understood. Here, we have studied zebrafish V0 neurons, those that derive from the p0 progenitor domain, to address this question. We find that all V0 neurons have commissural axons, but they can be divided into excitatory and inhibitory classes. V0 excitatory neurons (V0-e) can be further categorized into three groups based on their axonal trajectories; V0-eA (ascending), V0-eB (bifurcating), and V0-eD (descending) neurons. By using time-lapse imaging of p0 progenitors and their progeny, we show that inhibitory and excitatory neurons are produced from different progenitors. We also demonstrate that V0-eA neurons are produced from distinct progenitors, while V0-eB and V0-eD neurons are produced from common progenitors. We then use birth-date analysis to reveal that V0-eA, V0-eB, and V0-eD neurons arise in this order. By perturbing Notch signaling and accelerating neuronal differentiation, we predictably alter the generation of early born V0-e neurons at the expense of later born ones. These results suggest that multiple types of V0 neurons are produced by two distinct mechanisms; from heterogeneous p0 progenitors and from the same p0 progenitor, but in a time-dependent manner.

}, issn = {0270-6474}, doi = {10.1523/JNEUROSCI.5500-11.2012}, url = {https://www.jneurosci.org/content/32/5/1771}, author = {Chie Satou and Yukiko Kimura and Shin-ichi Higashijima} } @article {6288, title = {Genetic architecture and adaptive significance of the selfing syndrome in Capsella.}, journal = {Evolution: International Journal of Organic Evolution}, volume = {66}, year = {2012}, month = {2012 May}, pages = {1360-74}, abstract = {

The transition from outcrossing to predominant self-fertilization is one of the most common evolutionary transitions in flowering plants. This shift is often accompanied by a suite of changes in floral and reproductive characters termed the selfing syndrome. Here, we characterize the genetic architecture and evolutionary forces underlying evolution of the selfing syndrome in Capsella rubella following its recent divergence from the outcrossing ancestor C. grandiflora. We conduct genotyping by multiplexed shotgun sequencing and map floral and reproductive traits in a large (N= 550) F2 population. Our results suggest that in contrast to previous studies of the selfing syndrome, changes at a few loci, some with major effects, have shaped the evolution of the selfing syndrome in Capsella. The directionality of QTL effects, as well as population genetic patterns of polymorphism and divergence at 318 loci, is consistent with a history of directional selection on the selfing syndrome. Our study is an important step toward characterizing the genetic basis and evolutionary forces underlying the evolution of the selfing syndrome in a genetically accessible model system.

}, keywords = {Biological Evolution, Capsella, Chromosome Mapping, DNA, Flowers, Genetic, Genetic Markers, Genotype, Hybridization, Multilocus Sequence Typing, Phenotype, Plant, Pollination, Polymerase Chain Reaction, Quantitative Trait Loci, Reproduction, Selection, Self-Fertilization, Self-Incompatibility in Flowering Plants, Sequence Analysis}, issn = {1558-5646}, doi = {10.1111/j.1558-5646.2011.01540.x}, author = {Slotte, Tanja and Hazzouri, Khaled M and Stern, David and Andolfatto, Peter and Wright, Stephen I} } @article {46602, title = {A genetic screen for olfactory habituation mutations in Drosophila: analysis of novel foraging alleles and an underlying neural circuit.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012 Dec 17}, pages = {e51684}, abstract = {

Habituation is a form of non-associative learning that enables animals to reduce their reaction to repeated harmless stimuli. When exposed to ethanol vapor, Drosophila show an olfactory-mediated startle response characterized by a transient increase in locomotor activity. Upon repeated exposures, this olfactory startle attenuates with the characteristics of habituation. Here we describe the results of a genetic screen to identify olfactory startle habituation (OSH) mutants. One mutation is a transcript specific allele of foraging (for) encoding a cGMP-dependent kinase. We show this allele of for reduces expression of a for-T1 isoform expressed in the head and functions normally to inhibit OSH. We localize for-T1 function to a limited set of neurons that include olfactory receptor neurons (ORNs) and the mushroom body (MB). Overexpression of for-T1 in ORNs inhibits OSH, an effect also seen upon synaptic silencing of the ORNs; for-T1 may therefore function in ORNs to decrease synaptic release upon repeated exposure to ethanol vapor. Overall, this work contributes to our understanding of the genes and neurons underlying olfactory habituation in Drosophila.

}, keywords = {Alleles, Animals, Anti-Infective Agents, Local, Cyclic GMP-Dependent Protein Kinases, Drosophila melanogaster, Drosophila Proteins, Ethanol, Genetic Testing, Habituation, Psychophysiologic, Mushroom Bodies, Mutation, Neurons, Olfactory Receptor Neurons, Reaction Time, Reflex, Startle, Smell}, issn = {1932-6203}, doi = {10.1371/journal.pone.0051684}, author = {Eddison, Mark and Belay, Amsale T and Sokolowski, Marla B and Heberlein, Ulrike} } @article {5387, title = {A genetically encoded fluorescent protein in echinoderms marks the history of neuronal activity.}, journal = {Luminescence}, volume = {27}, year = {2012}, month = {2012 Apr}, pages = {170}, abstract = {

Since the original identification of GFP from jellyfish and corals, the genetically encoded fluorescent proteins have become mainstream indicators for imaging. Functionally homologous candidates exist in more highly evolved bioluminescent invertebrates, including echinoderms. For example, in brittlestars, stimulus-evoked bioluminescence is transient, lasting seconds, and emanates from specialized cells (photocytes). Prior to light emission, we observe little or no green fluorescence. However, concurrent with light emission, an intense green, calcium-dependent fluorescence develops that persists indefinitely.

}, author = {Verdecia, Mark A. and Looger, Loren L and Lavis, Luke and Graumann, Johannes and Mandel, Gail and Brehm, Paul} } @article {4376, title = {Genetically encoded neural activity indicators.}, journal = {Current Opinion in Neurobiology}, volume = {22}, year = {2012}, month = {2012 Feb}, pages = {18-23}, abstract = {

Recording activity from identified populations of neurons is a central goal of neuroscience. Changes in membrane depolarization, particularly action potentials, are the most important features of neural physiology to extract, although ions, neurotransmitters, neuromodulators, second messengers, and the activation state of specific proteins are also crucial. Modern fluorescence microscopy provides the basis for such activity mapping, through multi-photon imaging and other optical schemes. Probes remain the rate-limiting step for progress in this field: they should be bright and photostable, and ideally come in multiple colors. Only protein-based reagents permit chronic imaging from genetically specified cells. Here we review recent progress in the design, optimization and deployment of genetically encoded indicators for calcium ions (a proxy for action potentials), membrane potential, and neurotransmitters. We highlight seminal experiments, and present an outlook for future progress.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2011.10.024}, author = {Looger, Loren L and Griesbeck, Oliver} } @article {4590, title = {Hierarchical deployment of factors regulating temporal fate in a diverse neuronal lineage of the Drosophila central brain.}, journal = {Neuron}, volume = {73}, year = {2012}, month = {2012 Feb 23}, pages = {677-84}, abstract = {

The anterodorsal projection neuron lineage of Drosophila melanogaster produces 40 neuronal types in a stereotypic order. Here we take advantage of this complete lineage sequence to examine the role of known temporal fating factors, including Chinmo and the Hb/Kr/Pdm/Cas transcriptional cascade, within this diverse central brain lineage. Kr mutation affects the temporal fate of the neuroblast (NB) itself, causing a single fate to be skipped, whereas Chinmo null only elicits fate transformation of NB progeny without altering cell counts. Notably, Chinmo operates in two separate windows to prevent fate transformation (into the subsequent Chinmo-indenpendent fate) within each window. By contrast, Hb/Pdm/Cas play no detectable role, indicating that Kr either acts outside of the cascade identified in the ventral nerve cord or that redundancy exists at the level of fating factors. Therefore, hierarchical fating mechanisms operate within the lineage to generate neuronal diversity in an unprecedented fashion.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.12.018}, author = {Kao, Chih-Fei and Yu, Hung-Hsiang and He, Yisheng and Kao, Jui-Chun and Lee, Tzumin} } @article {5659, title = {A hierarchical structure of cortical interneuron electrical diversity revealed by automated statistical analysis.}, journal = {Cerebral Cortex}, volume = {23}, year = {2012}, month = {2012 Sep 17}, pages = {2994-3006}, abstract = {

Although the diversity of cortical interneuron electrical properties is well recognized, the number of distinct electrical types (e-types) is still a matter of debate. Recently, descriptions of interneuron variability were standardized by multiple laboratories on the basis of a subjective classification scheme as set out by the Petilla convention (Petilla Interneuron Nomenclature Group, PING). Here, we present a quantitative, statistical analysis of a database of nearly five hundred neurons manually annotated according to the PING nomenclature. For each cell, 38 features were extracted from responses to suprathreshold current stimuli and statistically analyzed to examine whether cortical interneurons subdivide into e-types. We showed that the partitioning into different e-types is indeed the major component of data variability. The analysis suggests refining the PING e-type classification to be hierarchical, whereby most variability is first captured within a coarse subpartition, and then subsequently divided into finer subpartitions. The coarse partition matches the well-known partitioning of interneurons into fast spiking and adapting cells. Finer subpartitions match the burst, continuous, and delayed subtypes. Additionally, our analysis enabled the ranking of features according to their ability to differentiate among e-types. We showed that our quantitative e-type assignment is more than 90\% accurate and manages to catch several human errors.

}, issn = {1460-2199}, doi = {10.1093/cercor/bhs290}, author = {Druckmann, S and Hill, Sean and Sch{\"u}rmann, Felix and Markram, Henry and Segev, Idan} } @article {6493, title = {Hippocampal phase precession from dual input components.}, journal = {The Journal of neuroscience : the official journal of the Society for Neuroscience}, volume = {32}, year = {2012}, month = {2012 Nov 21}, pages = {16693-703a}, abstract = {

Phase precession is a well known phenomenon in which a hippocampal place cell will fire action potentials at successively earlier phases (relative to the theta-band oscillations recorded in the local field potential) as an animal moves through the cell{\textquoteright}s receptive field (also known as a place field). We present a model in which CA1 pyramidal cell spiking is driven by dual input components arising from CA3 and EC3. The receptive fields of these two input components overlap but are offset in space from each other such that as the animal moves through the model place field, action potentials are driven first by the CA3 input component and then the EC3 input component. As CA3 synaptic input is known to arrive in CA1 at a later theta phase than EC3 input (Mizuseki et al., 2009; Montgomery et al., 2009), CA1 spiking advances in phase as the model transitions from CA3-driven spiking to EC3-driven spiking. Here spike phase is a function of animal location, placing our results in agreement with many experimental observations characterizing CA1 phase precession (O{\textquoteright}Keefe and Recce, 1993; Huxter et al., 2003; Geisler et al., 2007). We predict that experimental manipulations that dramatically enhance or disrupt activity in either of these areas should have a significant effect on phase precession observed in CA1.

}, keywords = {Action Potentials, Algorithms, Animals, CA1 Region, CA3 Region, Computer Simulation, Electric Stimulation, Electroencephalography, Electrophysiological Phenomena, Entorhinal Cortex, Environment, Hippocampal, Hippocampus, Membrane Potentials, Mice, Models, Neurological, Pyramidal Cells, Rats, Synapses, Theta Rhythm}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2786-12.2012}, author = {Chance, Frances S} } @article {5103, title = {Hippocampal place fields emerge upon single-cell manipulation of excitability during behavior.}, journal = {Science}, volume = {337}, year = {2012}, month = {2012 Aug 17}, pages = {849-53}, abstract = {

The origin of the spatial receptive fields of hippocampal place cells has not been established. A hippocampal CA1 pyramidal cell receives thousands of synaptic inputs, mostly from other spatially tuned neurons; however, how the postsynaptic neuron{\textquoteright}s cellular properties determine the response to these inputs during behavior is unknown. We discovered that, contrary to expectations from basic models of place cells and neuronal integration, a small, spatially uniform depolarization of the spatially untuned somatic membrane potential of a silent cell leads to the sudden and reversible emergence of a spatially tuned subthreshold response and place-field spiking. Such gating of inputs by postsynaptic neuronal excitability reveals a cellular mechanism for receptive field origin and may be critical for the formation of hippocampal memory representations.

}, issn = {1095-9203}, doi = {10.1126/science.1221489}, author = {Lee, Doyun and Lin, Bei-Jung and Lee, Albert K} } @article {6720, title = {Hippocampal pyramidal neurons comprise two distinct cell types that are countermodulated by metabotropic receptors.}, journal = {Neuron}, volume = {76}, year = {2012}, month = {2012 Nov 21}, pages = {776-89}, abstract = {

Relating the function of neuronal cell types to information processing and behavior is a central goal of neuroscience. In the hippocampus, pyramidal cells in CA1 and the subiculum process sensory and motor cues to form a cognitive map encoding spatial, contextual, and emotional information, which they transmit throughout the brain. Do these cells constitute a single class or are there multiple cell types with specialized functions? Using unbiased cluster analysis, we show that there are two morphologically and electrophysiologically distinct principal cell types that carry hippocampal output. We show further that these two cell types are inversely modulated by the synergistic action of glutamate and acetylcholine acting on metabotropic receptors that are central to hippocampal function. Combined with prior connectivity studies, our results support a model of hippocampal processing in which the two pyramidal cell types are predominantly segregated into two parallel pathways that process distinct modalities of information.

}, keywords = {3-dione, 6-Cyano-7-nitroquinoxaline-2, Analysis of Variance, Animals, Benzylamines, Biophysics, CA1 Region, Electric Stimulation, Excitatory Amino Acid Antagonists, Excitatory Amino Acid Transporter 3, GABA Antagonists, Glutamate Decarboxylase, Hippocampal, Lysine, Male, Membrane Potentials, Metabotropic Glutamate, Neurons, Newborn, Patch-Clamp Techniques, Phosphinic Acids, Pyridazines, Rats, Receptors, Time Factors}, issn = {1097-4199}, doi = {10.1016/j.neuron.2012.09.036}, author = {Graves, Austin R and Moore, Shannon J and Bloss, Erik B and Mensh, Brett D and Kath, William L and Spruston, Nelson} } @article {5626, title = {How does juvenile hormone control insect metamorphosis and reproduction?}, journal = {General and Comparative Endocrinology}, volume = {179}, year = {2012}, month = {2012 Dec 1}, pages = {477-84}, abstract = {

In insects juvenile hormone (JH) regulates both metamorphosis and reproduction. This lecture focuses on our current understanding of JH action at the molecular level in both of these processes based primarily on studies in the tobacco hornworm Manduca sexta, the flour beetle Tribolium castaneum, the mosquito Aedes aegypti, and the fruit fly Drosophila melanogaster. The roles of the JH receptor complex and the transcription factors that it regulates during larval molting and metamorphosis are summarized. Also highlighted are the intriguing interactions of the JH and insulin signaling pathways in both imaginal disc development and vitellogenesis. Critical actions of JH and its receptor in the timing of maturation of the adult optic lobe and of female receptivity in Drosophila are also discussed.

}, issn = {1095-6840}, doi = {10.1016/j.ygcen.2012.06.001}, author = {Riddiford, Lynn M} } @article {46726, title = {IGF2BP1 promotes cell migration by regulating MK5 and PTEN signaling.}, journal = {Genes \& Development}, volume = {26}, year = {2012}, month = {2012 Jan 15}, pages = {176-89}, abstract = {

In primary neurons, the oncofetal RNA-binding protein IGF2BP1 (IGF2 mRNA-binding protein 1) controls spatially restricted β-actin (ACTB) mRNA translation and modulates growth cone guidance. In cultured tumor-derived cells, IGF2BP1 was shown to regulate the formation of lamellipodia and invadopodia. However, how and via which target mRNAs IGF2BP1 controls the motility of tumor-derived cells has remained elusive. In this study, we reveal that IGF2BP1 promotes the velocity and directionality of tumor-derived cell migration by determining the cytoplasmic fate of two novel target mRNAs: MAPK4 and PTEN. Inhibition of MAPK4 mRNA translation by IGF2BP1 antagonizes MK5 activation and prevents phosphorylation of HSP27, which sequesters actin monomers available for F-actin polymerization. Consequently, HSP27-ACTB association is reduced, mobilizing cellular G-actin for polymerization in order to promote the velocity of cell migration. At the same time, stabilization of the PTEN mRNA by IGF2BP1 enhances PTEN expression and antagonizes PIP(3)-directed signaling. This enforces the directionality of cell migration in a RAC1-dependent manner by preventing additional lamellipodia from forming and sustaining cell polarization intrinsically. IGF2BP1 thus promotes the velocity and persistence of tumor cell migration by controlling the expression of signaling proteins. This fine-tunes and connects intracellular signaling networks in order to enhance actin dynamics and cell polarization.

}, keywords = {Actins, Cell Line, Tumor, Cell Movement, Cell Polarity, Enzyme Activation, Extracellular Signal-Regulated MAP Kinases, HSP27 Heat-Shock Proteins, Humans, Intracellular Signaling Peptides and Proteins, Phosphorylation, Protein-Serine-Threonine Kinases, PTEN Phosphohydrolase, RNA, Messenger, Signal Transduction}, issn = {1549-5477}, doi = {10.1101/gad.177642.111}, author = {St{\"o}hr, Nadine and K{\"o}hn, Marcel and Lederer, Marcell and Glass, Markus and Reinke, Claudia and Singer, Robert H and H{\"u}ttelmaier, Stefan} } @article {6511, title = {Illuminating vertebrate olfactory processing.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {32}, year = {2012}, month = {2012 Oct 10}, pages = {14102-8}, abstract = {

The olfactory system encodes information about molecules by spatiotemporal patterns of activity across distributed populations of neurons and extracts information from these patterns to control specific behaviors. Recent studies used in vivo recordings, optogenetics, and other methods to analyze the mechanisms by which odor information is encoded and processed in the olfactory system, the functional connectivity within and between olfactory brain areas, and the impact of spatiotemporal patterning of neuronal activity on higher-order neurons and behavioral outputs. The results give rise to a faceted picture of olfactory processing and provide insights into fundamental mechanisms underlying neuronal computations. This review focuses on some of this work presented in a Mini-Symposium at the Annual Meeting of the Society for Neuroscience in 2012.

}, keywords = {Animals, Humans, Odors, Olfactory Bulb, Olfactory Pathways, Olfactory Receptor Neurons, Optogenetics}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3328-12.2012}, author = {Spors, Hartwig and Albeanu, Dinu Florin and Murthy, Venkatesh N and Rinberg, Dmitry and Uchida, Naoshige and Wachowiak, Matt and Friedrich, Rainer W} } @article {5163, title = {Imaging neural activity using Thy1-GCaMP transgenic mice.}, journal = {Neuron}, volume = {76}, year = {2012}, month = {2012 Oct 18}, pages = {297-308}, abstract = {

The ability to chronically monitor neuronal activity in the living brain is essential for understanding the organization and function of the nervous system. The genetically encoded green fluorescent protein based calcium sensor GCaMP provides a powerful tool for detecting calcium transients in neuronal somata, processes, and synapses that are triggered by neuronal activities. Here we report the generation and characterization of transgenic mice that express improved GCaMPs in various neuronal subpopulations under the control of the Thy1 promoter. In vitro and in vivo studies show that calcium transients induced by spontaneous and stimulus-evoked neuronal activities can be readily detected at the level of individual cells and synapses in acute brain slices, as well as in awake behaving animals. These GCaMP transgenic mice allow investigation of activity patterns in defined neuronal populations in the living brain, and will greatly facilitate dissecting complex structural and functional relationships of neural networks.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2012.07.011}, author = {Chen, Qian and Cichon, Joseph and Wang, Wenting and Qiu, LI and Lee, Seok-Jin R. and Campbell, Nolan R. and DeStefino, Nicholas and Fu, Zhanyan and Yasuda, Ryohei and Looger, Loren L and Arenkiel, Benjamin R. and Gan, Wenbiao and Feng, Guoping} } @article {3933, title = {Imaging neural activity with genetically encoded calcium indicator.}, journal = {Cold Spring Harbor Protocols}, volume = {2012}, year = {2012}, month = {2012 Jun 1}, pages = {647-56}, abstract = {

Genetically encoded calcium indicators (GECIs), which are based on chimeric fluorescent proteins, can be used to monitor calcium transients in living cells and organisms. Because they are encoded by DNA, GECIs can be delivered to the intact brain noninvasively and targeted to defined populations of neurons and specific subcellular compartments for long-term, repeated measurements in vivo. GECIs have improved iteratively and are becoming useful for imaging neural activity in vivo. Here we summarize extrinsic and intrinsic factors that influence a GECI{\textquoteright}s performance and provides guidelines for selecting the appropriate GECI for a given application. We also review recent progress in GECI design, optimization, and standardized testing protocols.

}, author = {Tian, Lin and Hires, A and Looger, Loren L} } @article {5851, title = {Imaging the post-fusion release and capture of a vesicle membrane protein.}, journal = {Nature Communications}, volume = {3}, year = {2012}, month = {2012}, pages = {1154}, abstract = {

The molecular mechanism responsible for capturing, sorting and retrieving vesicle membrane proteins following triggered exocytosis is not understood. Here we image the post-fusion release and then capture of a vesicle membrane protein, the vesicular acetylcholine transporter, from single vesicles in living neuroendocrine cells. We combine these measurements with super-resolution interferometric photo-activation localization microscopy and electron microscopy, and modelling to map the nanometer-scale topography and architecture of the structures responsible for the transporter{\textquoteright}s capture following exocytosis. We show that after exocytosis, the transporter rapidly diffuses into the plasma membrane, but most travels only a short distance before it is locally captured over a dense network of membrane-resident clathrin-coated structures. We propose that the extreme density of these structures acts as a short-range diffusion trap. They quickly sequester diffusing vesicle material and limit its spread across the membrane. This system could provide a means for clathrin-mediated endocytosis to quickly recycle vesicle proteins in highly excitable cells.

}, issn = {2041-1723}, doi = {10.1038/ncomms2158}, author = {Sochacki, Kem A and Larson, Ben T and Sengupta, Deepali C and Daniels, Mathew P and Shtengel, Gleb and Hess, Harald F and Taraska, Justin W} } @article {46720, title = {Imaging translation in single cells using fluorescent microscopy.}, journal = {Cold Spring Harbor Perspectives in Biology}, volume = {4}, year = {2012}, month = {2012 Nov}, abstract = {

The regulation of translation provides a mechanism to control not only the abundance of proteins, but also the precise time and subcellular location that they are synthesized. Much of what is known concerning the molecular basis for translational control has been gleaned from experiments (e.g., luciferase assays and polysome analysis) that measure average changes in the protein synthesis of a population of cells, however, mechanistic insights can be obscured in ensemble measurements. The development of fluorescent microscopy techniques and reagents has allowed translation to be studied within its cellular context. Here we highlight recent methodologies that can be used to study global changes in protein synthesis or regulation of specific mRNAs in single cells. Imaging of translation has provided direct evidence for local translation of mRNAs at synapses in neurons and will become an important tool for studying translational control.

}, keywords = {Animals, Gene Expression Regulation, Humans, Microscopy, Fluorescence, Neurons, Protein Biosynthesis, Puromycin, Synapses}, issn = {1943-0264}, doi = {10.1101/cshperspect.a012310}, author = {Chao, Jeffrey A and Yoon, Young J and Singer, Robert H} } @article {46160, title = {ImgLib2--generic image processing in Java.}, journal = {Bioinformatics}, volume = {28}, year = {2012}, month = {2012 Nov 15}, pages = {3009-11}, abstract = {

SUMMARY: ImgLib2 is an open-source Java library for n-dimensional data representation and manipulation with focus on image processing. It aims at minimizing code duplication by cleanly separating pixel-algebra, data access and data representation in memory. Algorithms can be implemented for classes of pixel types and generic access patterns by which they become independent of the specific dimensionality, pixel type and data representation. ImgLib2 illustrates that an elegant high-level programming interface can be achieved without sacrificing performance. It provides efficient implementations of common data types, storage layouts and algorithms. It is the data model underlying ImageJ2, the KNIME Image Processing toolbox and an increasing number of Fiji-Plugins.

AVAILABILITY: ImgLib2 is licensed under BSD. Documentation and source code are available at http://imglib2.net and in a public repository at https://github.com/imagej/imglib.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Online.

CONTACT: saalfeld@mpi-cbg.de

}, keywords = {Algorithms, Image Processing, Computer-Assisted, Programming Languages, Software}, issn = {1367-4811}, doi = {10.1093/bioinformatics/bts543}, author = {Pietzsch, Tobias and Preibisch, Stephan and Tomancak, Pavel and Saalfeld, Stephan} } @proceedings {46789, title = {ImgLib2{\textemdash}Generic Image Processing in Java}, year = {2012}, month = {2012 Oct 24}, address = {Mondorf-les-Bains, Luxembourg}, author = {Saalfeld, Stephan and Pietzsch, Tobias and Tomancak, Pavel and Preibisch, Stephan} } @conference {6924, title = {Implantable blood pressure monitoring cuff for small laboratory animal.}, booktitle = {Microsystems for Measurement and Instrumentation (MAMNA), 2012}, year = {2012}, month = {2012 Mar}, publisher = {IEEE}, organization = {IEEE}, address = {Annapolis, MD}, abstract = {

Continuous monitoring of blood pressure in laboratory animals is necessary to understand the effect of treatments for cardiovascular related conditions, such as hypertension. Current methods to measure laboratory rat blood pressure require the animal to be constrained. Our proposed method is a small implantable device which fits around the carotid artery of the rat. Initial data from a mock rat artery setup, with equivalent artery pressure as found in the rat, show that the cuff design effectively detects the pressure change inside the mock artery.

}, isbn = {978-1-4673-1781-8}, doi = {10.1109/MAMNA.2012.6195099}, author = {Pais, R. and Duttaroy, A. and Wolever, J. and Dobbs, M. and Pastalkova, E} } @article {4595, title = {An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.}, journal = {The ISME Journal}, volume = {6}, year = {2012}, month = {2012 Mar}, pages = {610-8}, abstract = {

Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a {\textquoteright}taxonomy to tree{\textquoteright} approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408 315 sequences. We also incorporated explicit rank information provided by the NCBI taxonomy to group names (by prefixing rank designations) for better user orientation and classification consistency. The resulting merged taxonomy improved the classification of 75\% of the sequences by one or more ranks relative to the original NCBI taxonomy with the most pronounced improvements occurring in under-classified environmental sequences. We also assessed candidate phyla (divisions) currently defined by NCBI and present recommendations for consolidation of 34 redundantly named groups. All intermediate results from the pipeline, which includes tree inference, jackknifing and transfer of a donor taxonomy to a recipient tree (tax2tree) are available for download. The improved Greengenes taxonomy should provide important infrastructure for a wide range of megasequencing projects studying ecosystems on scales ranging from our own bodies (the Human Microbiome Project) to the entire planet (the Earth Microbiome Project). The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/.

}, issn = {1751-7370}, doi = {10.1038/ismej.2011.139}, author = {McDonald, Daniel and Price, Morgan N and Goodrich, Julia and Nawrocki, Eric P and Desantis, Todd Z and Probst, Alexander and Andersen, Gary L and Knight, Rob and Hugenholtz, Philip} } @article {4921, title = {The influence of lipids on voltage-gated ion channels.}, journal = {Current Opinion in Structural Biology}, volume = {22}, year = {2012}, month = {2012 Apr 5}, pages = {529-36}, abstract = {

Voltage-gated ion channels are responsible for transmitting electrochemical signals in both excitable and non-excitable cells. Structural studies of voltage-gated potassium and sodium channels by X-ray crystallography have revealed atomic details on their voltage-sensor domains (VSDs) and pore domains, and were put in context of disparate mechanistic views on the voltage-driven conformational changes in these proteins. Functional investigation of voltage-gated channels in membranes, however, showcased a mechanism of lipid-dependent gating for voltage-gated channels, suggesting that the lipids play an indispensible and critical role in the proper gating of many of these channels. Structure determination of membrane-embedded voltage-gated ion channels appears to be the next frontier in fully addressing the mechanism by which the VSDs control channel opening. Currently electron crystallography is the only structural biology method in which a membrane protein of interest is crystallized within a complete lipid-bilayer mimicking the native environment of a biological membrane. At a sufficiently high resolution, an electron crystallographic structure could reveal lipids, the channel and their mutual interactions at the atomic level. Electron crystallography is therefore a promising avenue toward understanding how lipids modulate channel activation through close association with the VSDs.

}, issn = {1879-033X}, doi = {10.1016/j.sbi.2012.03.009}, author = {Jiang, Qiu-Xing and Gonen, Tamir} } @article {5323, title = {Interferometer-based structured-illumination microscopy utilizing complementary phase relationship through constructive and destructive image detection by two cameras.}, journal = {Journal of Microscopy}, volume = {246}, year = {2012}, month = {2012 Jun}, pages = {229-36}, abstract = {

In an interferometer-based fluorescence microscope, a beam splitter is often used to combine two emission wavefronts interferometrically. There are two perpendicular paths along which the interference fringes can propagate and normally only one is used for imaging. However, the other path also contains useful information. Here we introduced a second camera to our interferometer-based three-dimensional structured-illumination microscope (I(5)S) to capture the fringes along the normally unused path, which are out of phase by π relative to the fringes along the other path. Based on this complementary phase relationship and the well-defined phase interrelationships among the I(5)S data components, we can deduce and then computationally eliminate the path length errors within the interferometer loop using the simultaneously recorded fringes along the two imaging paths. This self-correction capability can greatly relax the requirement for eliminating the path length differences before and maintaining that status during each imaging session, which are practically challenging tasks. Experimental data is shown to support the theory.

}, issn = {1365-2818}, doi = {10.1111/j.1365-2818.2012.03604.x}, author = {Shao, L and Winoto, L and Agard, D A and Gustafsson, M G L and Sedat, J W} } @article {6327, title = {Interplay of DNA repair with transcription: from structures to mechanisms.}, journal = {Trends in Biochemical Sciences}, volume = {37}, year = {2012}, month = {2012 Dec}, pages = {543-52}, abstract = {

Many DNA transactions are crucial for maintaining genomic integrity and faithful transfer of genetic information but remain poorly understood. An example is the interplay between nucleotide excision repair (NER) and transcription, also known as transcription-coupled DNA repair (TCR). Discovered decades ago, the mechanisms for TCR have remained elusive, not in small part due to the scarcity of structural studies of key players. Here we summarize recent structural information on NER/TCR factors, focusing on bacterial systems, and integrate it with existing genetic, biochemical, and biophysical data to delineate the mechanisms at play. We also review emerging, alternative modalities for recruitment of NER proteins to DNA lesions.

}, issn = {0968-0004}, doi = {10.1016/j.tibs.2012.09.002}, author = {Deaconescu, Alexandra M and Artsimovitch, Irina and Grigorieff, Nikolaus} } @article {46324, title = {Intracellular recording in behaving animals.}, journal = {Current Opinion in Neurobiology}, volume = {22}, year = {2012}, month = {2012 Feb}, pages = {34-44}, abstract = {

Electrophysiological recordings from behaving animals provide an unparalleled view into the functional role of individual neurons. Intracellular approaches can be especially revealing as they provide information about a neuron{\textquoteright}s inputs and intrinsic cellular properties, which together determine its spiking output. Recent technical developments have made intracellular recording possible during an ever-increasing range of behaviors in both head-fixed and freely moving animals. These recordings have yielded fundamental insights into the cellular and circuit mechanisms underlying neural activity during natural behaviors in such areas as sensory perception, motor sequence generation, and spatial navigation, forging a direct link between cellular and systems neuroscience.

}, keywords = {Animals, Behavior, Animal, Brain, Electrophysiology, Intracellular Space, Neurophysiology}, issn = {1873-6882}, doi = {10.1016/j.conb.2011.10.013}, author = {Long, Michael A and Lee, Albert K} } @article {47653, title = {Intracellular spatial localization regulated by the microtubule network.}, journal = {PloS one}, volume = {7}, year = {2012}, month = {2012}, pages = {e34919}, abstract = {

The commonly recognized mechanisms for spatial regulation inside the cell are membrane-bounded compartmentalization and biochemical association with subcellular organelles. We use computational modeling to investigate another spatial regulation mechanism mediated by the microtubule network in the cell. Our results demonstrate that the mitotic spindle can impose strong sequestration and concentration effects on molecules with binding affinity for microtubules, especially dynein-directed cargoes. The model can recapitulate the essence of three experimental observations on distinct microtubule network morphologies: the sequestration of germ plasm components by the mitotic spindles in the Drosophila syncytial embryo, the asymmetric cell division initiated by the time delay in centrosome maturation in the Drosophila neuroblast, and the diffusional block between neighboring energids in the Drosophila syncytial embryo. Our model thus suggests that the cell cycle-dependent changes in the microtubule network are critical for achieving different spatial regulation effects. The microtubule network provides a spatially extensive docking platform for molecules and gives rise to a "structured cytoplasm", in contrast to a free and fluid environment.

}, keywords = {Animals, Cell Cycle, Centrosome, Cytoplasm, Drosophila, Microtubules, Models, Biological, Spindle Apparatus}, issn = {1932-6203}, doi = {10.1371/journal.pone.0034919}, author = {Chen, Jing and Lippincott-Schwartz, Jennifer and Liu, Jian} } @article {65029, title = {An intra-cerebral drug delivery system for freely moving animals.}, journal = {Biomed Microdevices}, volume = {14}, year = {2012}, month = {2012 Oct 01}, pages = {799-809}, abstract = {

Microinfusions of drugs directly into the central nervous system of awake animals represent a widely used means of unravelling brain functions related to behaviour. However, current approaches generally use tethered liquid infusion systems and a syringe pump to deliver drugs into the brain, which often interfere with behaviour. We address this shortfall with a miniaturised electronically-controlled drug delivery system (20 {\texttimes} 17.5 {\texttimes} 5 mm{\textthreesuperior}) designed to be skull-mounted in rats. The device features a micropump connected to two 8-mm-long silicon microprobes with a cross section of 250 {\texttimes} 250 μm{\texttwosuperior} and integrated fluid microchannels. Using an external electronic control unit, the device allows infusion of 16 metered doses (0.25 μL each, 8 per silicon shaft). Each dosage requires 3.375 Ws of electrical power making the device additionally compatible with state-of-the-art wireless headstages. A dosage precision of 0.25 {\textpm} 0.01 μL was determined in vitro before in vivo tests were carried out in awake rats. No passive leakage from the loaded devices into the brain could be detected using methylene blue dye. Finally, the device was used to investigate the effects of the NMDA-receptor antagonist 3-((R)-2-Carboxypiperazin-4-yl)-propyl-1-phosphonic acid, (R)-CPP, administered directly into the prefrontal cortex of rats during performance on a task to assess visual attention and impulsivity. In agreement with previous findings using conventional tethered infusion systems, acute (R)-CPP administration produced a marked increase in impulsivity.

}, keywords = {Animals, Attention, Brain, Drug Delivery Systems, Equipment Design, Impulsive Behavior, Microinjections, Piperazines, Rats, Receptors, N-Methyl-D-Aspartate}, issn = {1572-8781}, doi = {10.1007/s10544-012-9659-2}, author = {Spieth, Sven and Schumacher, Axel and Holtzman, Tahl and Rich, P Dylan and Theobald, David E and Dalley, Jeffrey W and Nouna, Rachid and Messner, Stephan and Zengerle, Roland} } @article {5325, title = {Intra-nuclear mobility and target search mechanisms of transcription factors: a single-molecule perspective on gene expression.}, journal = {Biochimica et Biophysica Acta}, volume = {1819}, year = {2012}, month = {2012 Jun}, pages = {482-93}, abstract = {

Precise expression of specific genes in time and space is at the basis of cellular viability as well as correct development of organisms. Understanding the mechanisms of gene regulation is fundamental and still one of the great challenges for biology. Gene expression is regulated also by specific transcription factors that recognize and bind to specific DNA sequences. Transcription factors dynamics, and especially the way they sample the nucleoplasmic space during the search for their specific target in the genome, are a key aspect for regulation and it has been puzzling researchers for forty years. The scope of this review is to give a state-of-the-art perspective over the intra-nuclear mobility and the target search mechanisms of specific transcription factors at the molecular level. Going through the seminal biochemical experiments that have raised the first questions about target localization and the theoretical grounds concerning target search processes, we describe the most recent experimental achievements and current challenges in understanding transcription factors dynamics and interactions with DNA using in vitro assays as well as in live prokaryotic and eukaryotic cells. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.

}, issn = {0006-3002}, doi = {10.1016/j.bbagrm.2012.02.001}, author = {Normanno, Davide and Dahan, Maxime and Darzacq, Xavier} } @article {4923, title = {Intrinsic tethering activity of endosomal Rab proteins.}, journal = {Nature Structural \& Molecular Biology}, volume = {19}, year = {2012}, month = {2012 Jan}, pages = {40-7}, abstract = {

Rab small G proteins control membrane trafficking events required for many processes including secretion, lipid metabolism, antigen presentation and growth factor signaling. Rabs recruit effectors that mediate diverse functions including vesicle tethering and fusion. However, many mechanistic questions about Rab-regulated vesicle tethering are unresolved. Using chemically defined reaction systems, we discovered that Vps21, a Saccharomyces cerevisiae ortholog of mammalian endosomal Rab5, functions in trans with itself and with at least two other endosomal Rabs to directly mediate GTP-dependent tethering. Vps21-mediated tethering was stringently and reversibly regulated by an upstream activator, Vps9, and an inhibitor, Gyp1, which were sufficient to drive dynamic cycles of tethering and detethering. These experiments reveal a previously undescribed mode of tethering by endocytic Rabs. In our working model, the intrinsic tethering capacity Vps21 operates in concert with conventional effectors and SNAREs to drive efficient docking and fusion.

}, keywords = {Electron, Endocytosis, Endosomes, GTP-Binding Proteins, GTPase-Activating Proteins, Guanine Nucleotide Exchange Factors, Guanosine Diphosphate, Guanosine Triphosphate, Liposomes, Microscopy, Mutation, Protein Binding, rab GTP-Binding Proteins, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, SNARE Proteins, Transmission, Two-Hybrid System Techniques, Vesicular Transport Proteins}, issn = {1545-9985}, doi = {10.1038/nsmb.2162}, author = {Lo, Sheng-Ying and Brett, Christopher L and Plemel, Rachael L and Vignali, Marissa and Fields, Stanley and Gonen, Tamir and Merz, Alexey J} } @proceedings {46791, title = {Introduction to ImgLib2}, year = {2012}, month = {2012 Oct 24}, address = {Mondorf-les-Bains, Luxembourg}, author = {Preibisch, Stephan and Pietzsch, Tobias and Myers, Eugene and Tomancak, Pavel and Saalfeld, Stephan} } @proceedings {45795, title = {Investigation of the role of Aubergine RNA-binding proteins in the reproductive plasticity of the pea aphid, Acyrthosiphon pisum}, volume = {52}, year = {2012}, month = {01/2012}, pages = {E202-E202}, publisher = {OXFORD UNIV PRESS INC}, abstract = {

Environmental changes can elicit alterations in the form, behavior and/or physiology of all species, and this developmental response to environment is known as phenotypic plasticity. Despite its ubiquity, the molecular basis for phenotypic plasticity is not fully understood. The pea aphid, Acyrthosiphon pisum, serves as a model for an extreme form of phenotypic plasticity, known as polyphenism. Changes in photoperiod stimulate a switch in female aphid reproductive mode from asexual to sexual reproduction over the course of one generation without changes in genotype. This reproductive polyphenism results in female aphids with ovaries of one of two types: sexual ovaries (producing haploid oocytes via meiosis), or asexual ovaries (producing identical diploid aphid clones via parthenogenesis). To better understand how aphid ovaries could produce different outputs, we surveyed the transcriptomes of sexual and asexual ovaries using RNA-seq. Among genes that exhibited greater than two-fold differences in gene expression between sexual and asexual ovaries, we identified several aubergine paralogs, which encode for germline-specific members of the Argonaute small RNA-binding protein family. The A. pisum genome contains eight aubergine paralogs and at least two piwi paralogs. We are currently comparing the expression patterns of these aphid aubergine paralogs between asexual and sexual aphid ovaries. Aubergine proteins in other species are thought to help suppress the activity of transposable elements, which are found in high quantities throughout the A. pisum genome. Together, these experiments will help elucidate a potential relationship between aubergine paralogs and aphid reproductive plasticity.

}, url = {http://sicb.org/meetings/2012/schedule/abstractdetails.php?id=959}, author = {A Abdelhady and R Cortes and S Musumeci and D Srinivasan and S Shigenobu and D Stern and S Kobayashi} } @article {5923, title = {Ion channel gradients in the apical tuft region of CA1 pyramidal neurons.}, journal = {PLoS one}, volume = {7}, year = {2012}, month = {2012}, pages = {e46652}, abstract = {

Dendritic ion channels play a critical role in shaping synaptic input and are fundamentally important for synaptic integration and plasticity. In the hippocampal region CA1, somato-dendritic gradients of AMPA receptors and the hyperpolarization-activated cation conductance (I(h)) counteract the effects of dendritic filtering on the amplitude, time-course, and temporal integration of distal Schaffer collateral (SC) synaptic inputs within stratum radiatum (SR). While ion channel gradients in CA1 distal apical trunk dendrites within SR have been well characterized, little is known about the patterns of ion channel expression in the distal apical tuft dendrites within stratum lacunosum moleculare (SLM) that receive distinct input from the entorhinal cortex via perforant path (PP) axons. Here, we measured local ion channels densities within these distal apical tuft dendrites to determine if the somato-dendritic gradients of I(h) and AMPA receptors extend into distal tuft dendrites. We also determined the densities of voltage-gated sodium channels and NMDA receptors. We found that the densities of AMPA receptors, I(h,) and voltage-gated sodium channels are similar in tuft dendrites in SLM when compared with distal apical dendrites in SR, while the ratio of NMDA receptors to AMPA receptors increases in tuft dendrites relative to distal apical dendrites within SR. These data indicate that the somato-dendritic gradients of I(h) and AMPA receptors in apical dendrites do not extend into the distal tuft, and the relative densities of voltage-gated sodium channels and NMDA receptors are poised to support nonlinear integration of correlated SC and PP input.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0046652}, author = {Bittner, Katie C and Andrasfalvy, Bertalan K and Magee, Jeffrey C} } @article {46603, title = {JNK pathway activation is controlled by Tao/TAOK3 to modulate ethanol sensitivity.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012 Dec 5}, pages = {e50594}, abstract = {

Neuronal signal transduction by the JNK MAP kinase pathway is altered by a broad array of stimuli including exposure to the widely abused drug ethanol, but the behavioral relevance and the regulation of JNK signaling is unclear. Here we demonstrate that JNK signaling functions downstream of the Sterile20 kinase family gene tao/Taok3 to regulate the behavioral effects of acute ethanol exposure in both the fruit fly Drosophila and mice. In flies tao is required in neurons to promote sensitivity to the locomotor stimulant effects of acute ethanol exposure and to establish specific brain structures. Reduced expression of key JNK pathway genes substantially rescued the structural and behavioral phenotypes of tao mutants. Decreasing and increasing JNK pathway activity resulted in increased and decreased sensitivity to the locomotor stimulant properties of acute ethanol exposure, respectively. Further, JNK expression in a limited pattern of neurons that included brain regions implicated in ethanol responses was sufficient to restore normal behavior. Mice heterozygous for a disrupted allele of the homologous Taok3 gene (Taok3Gt) were resistant to the acute sedative effects of ethanol. JNK activity was constitutively increased in brains of Taok3Gt/+ mice, and acute induction of phospho-JNK in brain tissue by ethanol was occluded in Taok3Gt/+ mice. Finally, acute administration of a JNK inhibitor conferred resistance to the sedative effects of ethanol in wild-type but not Taok3Gt/+ mice. Taken together, these data support a role of a TAO/TAOK3-JNK neuronal signaling pathway in regulating sensitivity to acute ethanol exposure in flies and in mice.

}, keywords = {Animals, Base Sequence, Behavior, Animal, DNA Primers, Drosophila, Drosophila Proteins, Ethanol, Immunohistochemistry, MAP Kinase Kinase 4, Mice, Mice, Inbred C57BL, Mutation, Protein-Serine-Threonine Kinases, Reverse Transcriptase Polymerase Chain Reaction}, issn = {1932-6203}, doi = {10.1371/journal.pone.0050594}, author = {Kapfhamer, David and King, Ian and Zou, Mimi E and Lim, Jana P and Heberlein, Ulrike and Wolf, Fred W} } @article {4886, title = {Joint control of Drosophila male courtship behavior by motion cues and activation of male-specific P1 neurons.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 May 29}, pages = {10065-70}, abstract = {

Sexual behaviors in animals are governed by inputs from multiple external sensory modalities. However, how these inputs are integrated to jointly control animal behavior is still poorly understood. Whereas visual information alone is not sufficient to induce courtship behavior in Drosophila melanogaster males, when a subset of male-specific fruitless (fru)- and doublesex (dsx)-expressing neurons that respond to chemosensory cues (P1 neurons) were artificially activated via a temperature-sensitive cation channel (dTRPA1), males followed and extended their wing toward moving objects (even a moving piece of rubber band) intensively. When stationary, these objects were not courted. Our results indicate that motion input and activation of P1 neurons are individually necessary, and under our assay conditions, jointly sufficient to elicit early courtship behaviors, and provide insights into how courtship decisions are made via sensory integration.

}, issn = {1091-6490}, doi = {10.1073/pnas.1207107109}, author = {Pan, Yufeng and Meissner, Geoffrey W and Baker, Bruce S} } @article {5438, title = {A lattice filter model of the visual pathway.}, journal = {Advances in Neural Information Processing Systems}, volume = {24}, year = {2012}, month = {2012}, pages = {1709-17}, abstract = {

Early stages of visual processing are thought to decorrelate, or whiten, the incoming temporally varying signals. Because the typical correlation time of natural stimuli, as well as the extent of temporal receptive fields of lateral geniculate nucleus (LGN) neurons, is much greater than neuronal time constants, such decorrelation must be done in stages combining contributions of multiple neurons. We propose to model temporal decorrelation in the visual pathway with the lattice filter, a signal processing device for stage-wise decorrelation of temporal signals. The stage-wise architecture of the lattice filter maps naturally onto the visual pathway (photoreceptors -\> bipolar cells -\> retinal ganglion cells -\> LGN) and its filter weights can be learned using Hebbian rules in a stage-wise sequential manner. Moreover, predictions of neural activity from the lattice filter model are consistent with physiological measurements in LGN neurons and fruit fly second-order visual neurons. Therefore, the lattice filter model is a useful abstraction that may help unravel visual system function.

}, author = {Gregor, Karol and Chklovskii, Dmitri B} } @proceedings {5767, title = {Learning animal social behavior from trajectory features.}, year = {2012}, month = {2012 Nov}, address = {Tsukuba, Japan}, author = {Eyjolfsdottir, Eyrun and Burgos-Artizzu, Xavier P. and Branson, Steven and Branson, Kristin and Anderson, David and Perona, Pietro} } @conference {6448, title = {Learning hierarchical similarity metrics.}, booktitle = {IEEE Conference on Computer Vision and Pattern Recognition}, year = {2012}, month = {2012}, author = {Verma, N and Mahajan, D and Sellamanickam, S and Nair, V} } @conference {48835, title = {Learning visual motion in recurrent neural networks.}, booktitle = {Neural Information Processing Systems (NIPS 2012)}, year = {2012}, month = {12/2003}, address = {Lake Tahoe}, abstract = {

We present a dynamic nonlinear generative model for visual motion based on a latent representation of binary-gated Gaussian variables. Trained on sequences of images, the model learns to represent different movement directions in different variables. We use an online approximate-inference scheme that can be mapped to the dynamics of networks of neurons. Probed with drifting grating stimuli and moving bars of light, neurons in the model show patterns of responses analogous to those of direction-selective simple cells in primary visual cortex. Most model neurons also show speed tuning and respond equally well to a range of motion directions and speeds aligned to the constraint line of their respective preferred speed. We show how these computations are enabled by a specific pattern of recurrent connections learned by the model.

}, url = {http://papers.nips.cc/paper/4814-learning-visual-motion-in-recurrent-neural-networks}, author = {Pachitariu, Marius and Sahani, Maneesh} } @article {3836, title = {Light sheet microscopy of living or cleared specimens.}, journal = {Current Opinion in Neurobiology}, volume = {22}, year = {2012}, month = {2012 Feb}, pages = {138-43}, abstract = {

Light sheet microscopy is a versatile imaging technique with a unique combination of capabilities. It provides high imaging speed, high signal-to-noise ratio and low levels of photobleaching and phototoxic effects. These properties are crucial in a wide range of applications in the life sciences, from live imaging of fast dynamic processes in single cells to long-term observation of developmental dynamics in entire large organisms. When combined with tissue clearing methods, light sheet microscopy furthermore allows rapid imaging of large specimens with excellent coverage and high spatial resolution. Even samples up to the size of entire mammalian brains can be efficiently recorded and quantitatively analyzed. Here, we provide an overview of the history of light sheet microscopy, review the development of tissue clearing methods, and discuss recent technical breakthroughs that have the potential to influence the future direction of the field.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2011.08.003}, author = {Keller, Philipp J and Dodt, Hans-Ulrich} } @article {6290, title = {Lineage analysis of Drosophila lateral antennal lobe neurons reveals notch-dependent binary temporal fate decisions.}, journal = {PLoS Biology}, volume = {10}, year = {2012}, month = {2012 Nov 20}, pages = {e1001425}, abstract = {

Binary cell fate decisions allow the production of distinct sister neurons from an intermediate precursor. Neurons are further diversified based on the birth order of intermediate precursors. Here we examined the interplay between binary cell fate and birth-order-dependent temporal fate in the Drosophila lateral antennal lobe (lAL) neuronal lineage. Single-cell mapping of the lAL lineage by twin-spot mosaic analysis with repressible cell markers (ts-MARCM) revealed that projection neurons (PNs) and local interneurons (LNs) are made in pairs through binary fate decisions. Forty-five types of PNs innervating distinct brain regions arise in a stereotyped sequence; however, the PNs with similar morphologies are not necessarily born in a contiguous window. The LNs are morphologically less diverse than the PNs, and the sequential morphogenetic changes in the two pairs occur independently. Sanpodo-dependent Notch activity promotes and patterns the LN fates. By contrast, Notch diversifies PN temporal fates in a Sanpodo-dispensable manner. These pleiotropic Notch actions underlie the differential temporal fate specification of twin neurons produced by common precursors within a lineage, possibly by modulating postmitotic neurons{\textquoteright} responses to Notch-independent transcriptional cascades.

}, keywords = {Animals, Biological Markers, Brain, Cell Division, Cell Lineage, Cellular, Developmental, Drosophila, Drosophila Proteins, Embryo, Gene Expression Regulation, Genes, Immunohistochemistry, Insect, Larva, Mechanotransduction, Nerve Tissue Proteins, Neurogenesis, Neurons, Nonmammalian, Notch, Receptors, Single-Cell Analysis}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1001425}, author = {Lin, Suewei and Kao, Chih-Fei and Yu, Hung-Hsiang and Huang, Yaling and Lee, Tzumin} } @article {46607, title = {Lmo4 in the basolateral complex of the amygdala modulates fear learning.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012 Apr 3}, pages = {e34559}, abstract = {

Pavlovian fear conditioning is an associative learning paradigm in which mice learn to associate a neutral conditioned stimulus with an aversive unconditioned stimulus. In this study, we demonstrate a novel role for the transcriptional regulator Lmo4 in fear learning. LMO4 is predominantly expressed in pyramidal projection neurons of the basolateral complex of the amygdala (BLC). Mice heterozygous for a genetrap insertion in the Lmo4 locus (Lmo4gt/+), which express 50\% less Lmo4 than their wild type (WT) counterparts display enhanced freezing to both the context and the cue in which they received the aversive stimulus. Small-hairpin RNA-mediated knockdown of Lmo4 in the BLC, but not the dentate gyrus region of the hippocampus recapitulated this enhanced conditioning phenotype, suggesting an adult- and brain region-specific role for Lmo4 in fear learning. Immunohistochemical analyses revealed an increase in the number of c-Fos positive puncta in the BLC of Lmo4gt/+ mice in comparison to their WT counterparts after fear conditioning. Lastly, we measured anxiety-like behavior in Lmo4gt/+ mice and in mice with BLC-specific downregulation of Lmo4 using the elevated plus maze, open field, and light/dark box tests. Global or BLC-specific knockdown of Lmo4 did not significantly affect anxiety-like behavior. These results suggest a selective role for LMO4 in the BLC in modulating learned but not unlearned fear.

}, keywords = {Adaptor Proteins, Signal Transducing, Amygdala, Animals, Behavior, Animal, Conditioning (Psychology), Cues, Fear, Gene Knockdown Techniques, LIM Domain Proteins, Male, Mice, Mice, Inbred C57BL, Neurons, Protein Transport}, issn = {1932-6203}, doi = {10.1371/journal.pone.0034559}, author = {Maiya, Rajani and Kharazia, Viktor and Lasek, Amy W and Heberlein, Ulrike} } @article {6503, title = {Making your database available through Wikipedia: the pros and cons.}, journal = {Nucleic Acids Research}, volume = {40}, year = {2012}, month = {2012 Jan}, pages = {D9-12}, abstract = {

Wikipedia, the online encyclopedia, is the most famous wiki in use today. It contains over 3.7 million pages of content; with many pages written on scientific subject matters that include peer-reviewed citations, yet are written in an accessible manner and generally reflect the consensus opinion of the community. In this, the 19th Annual Database Issue of Nucleic Acids Research, there are 11 articles that describe the use of a wiki in relation to a biological database. In this commentary, we discuss how biological databases can be integrated with Wikipedia, thereby utilising the pre-existing infrastructure, tools and above all, large community of authors (or Wikipedians). The limitations to the content that can be included in Wikipedia are highlighted, with examples drawn from articles found in this issue and other wiki-based resources, indicating why other wiki solutions are necessary. We discuss the merits of using open wikis, like Wikipedia, versus other models, with particular reference to potential vandalism. Finally, we raise the question about the future role of dedicated database biocurators in context of the thousands of crowdsourced, community annotations that are now being stored in wikis.

}, keywords = {Databases, Encyclopedias as Topic, Factual, Internet, Systems Integration}, issn = {1362-4962}, doi = {10.1093/nar/gkr1195}, author = {Finn, Robert D and Gardner, Paul P and Bateman, Alex} } @article {6326, title = {Maturation in action: CryoEM study of a viral capsid caught during expansion.}, journal = {Structure}, volume = {20}, year = {2012}, month = {2012 Aug 8}, pages = {1384-90}, abstract = {

Bacteriophage HK97 maturation involves discrete intermediate particle forms, comparable to transitional states in protein folding, before reaching its mature form. The process starts by formation of a metastable prohead, poised for exothermic expansion triggered by DNA packaging. During maturation, the capsid subunit transitions from a strained to a canonical tertiary conformation and this has been postulated to be the driving mechanism for initiating expansion via switching hexameric capsomer architecture from skewed to 6-fold symmetric. We report the subnanometer electron-cryomicroscopy reconstruction of the HK97 first expansion intermediate before any crosslink formation. This form displays 6-fold symmetric hexamers, but capsid subunit tertiary structures exhibit distortions comparable to the prohead forms. We propose that coat subunit strain release acts in synergy with the first crosslinks to drive forward maturation. Finally, we speculate that the energetic features of this transition may result from increased stability of intermediates during maturation via enhanced inter-subunit interactions.

}, keywords = {Amino Acid Substitution, Bacteriophages, Capsid, Capsid Proteins, Cryoelectron Microscopy, Protein Structure, Protein Subunits, Quaternary, Secondary, Tertiary, Virus Assembly}, issn = {1878-4186}, doi = {10.1016/j.str.2012.05.011}, author = {Veesler, David and Quispe, Joel and Grigorieff, Nikolaus and Potter, Clinton S and Carragher, Bridget and Johnson, John E} } @article {46048, title = {The mechanisms of repetitive spike generation in an axonless retinal interneuron.}, journal = {Cell Reports}, volume = {1}, year = {2012}, month = {2012 Feb 23}, pages = {155-66}, abstract = {

Several types of retinal interneurons exhibit spikes but lack axons. One such neuron is the AII amacrine cell, in which spikes recorded at the soma exhibit small amplitudes (\<10 mV) and broad time courses (\>5 ms). Here, we used electrophysiological recordings and computational analysis to examine the mechanisms underlying this atypical spiking. We found that somatic spikes likely represent large, brief action potential-like events initiated in a single, electrotonically distal dendritic compartment. In this same compartment, spiking undergoes slow modulation, likely by an M-type K conductance. The structural correlate of this compartment is a thin neurite that extends from the primary dendritic tree: local application of TTX to this neurite, or excision of it, eliminates spiking. Thus, the physiology of the axonless AII is much more complex than would be anticipated from morphological descriptions and somatic recordings; in particular, the AII possesses a single dendritic structure that controls its firing pattern.

}, keywords = {Action Potentials, Amacrine Cells, Animals, Axons, Female, Interneurons, Ion Channel Gating, Mice, Mice, Inbred C57BL, Models, Neurological, Potassium Channels, Retina, Time Factors}, issn = {2211-1247}, doi = {10.1016/j.celrep.2011.12.006}, author = {Cembrowski, Mark S and Logan, Stephen M and Tian, Miao and Jia, Li and Li, Wei and Kath, William L and Riecke, Hermann and Singer, Joshua H} } @article {5661, title = {A mechanistic model of early sensory processing based on subtracting sparse representations.}, journal = {Advances in Neural Information Processing Systems}, volume = {25}, year = {2012}, month = {2012}, pages = {1979-87}, abstract = {

Early stages of sensory systems face the challenge of compressing information from numerous receptors onto a much smaller number of projection neurons, a so called communication bottleneck. To make more efficient use of limited bandwidth, compression may be achieved using predictive coding, whereby predictable, or redundant, components of the stimulus are removed. In the case of the retina, Srinivasan et al. (1982) suggested that feedforward inhibitory connections subtracting a linear prediction generated from nearby receptors implement such compression, resulting in biphasic center-surround receptive fields. However, feedback inhibitory circuits are common in early sensory circuits and furthermore their dynamics may be nonlinear. Can such circuits implement predictive coding as well? Here, solving the transient dynamics of nonlinear reciprocal feedback circuits through analogy to a signal-processing algorithm called linearized Bregman iteration we show that nonlinear predictive coding can be implemented in an inhibitory feedback circuit. In response to a step stimulus, interneuron activity in time constructs progressively less sparse but more accurate representations of the stimulus, a temporally evolving prediction. This analysis provides a powerful theoretical framework to interpret and understand the dynamics of early sensory processing in a variety of physiological experiments and yields novel predictions regarding the relation between activity and stimulus statistics.

}, author = {Druckmann, Shaul and Hu, T and Chklovskii, D} } @article {4487, title = {mGRASP enables mapping mammalian synaptic connectivity with light microscopy.}, journal = {Nature Methods}, volume = {9}, year = {2012}, month = {2012 Jan}, pages = {96-102}, abstract = {

The GFP reconstitution across synaptic partners (GRASP) technique, based on functional complementation between two nonfluorescent GFP fragments, can be used to detect the location of synapses quickly, accurately and with high spatial resolution. The method has been previously applied in the nematode and the fruit fly but requires substantial modification for use in the mammalian brain. We developed mammalian GRASP (mGRASP) by optimizing transmembrane split-GFP carriers for mammalian synapses. Using in silico protein design, we engineered chimeric synaptic mGRASP fragments that were efficiently delivered to synaptic locations and reconstituted GFP fluorescence in vivo. Furthermore, by integrating molecular and cellular approaches with a computational strategy for the three-dimensional reconstruction of neurons, we applied mGRASP to both long-range circuits and local microcircuits in the mouse hippocampus and thalamocortical regions, analyzing synaptic distribution in single neurons and in dendritic compartments.

}, issn = {1548-7105}, doi = {10.1038/nmeth.1784}, author = {Kim, Jinhyun and Zhao, Ting and Petralia, Ronald S and Yu, Yang and Peng, Hanchuan and Myers, Eugene and Magee, Jeffrey C} } @article {6171, title = {Minimizing manual image segmentation turn-around time for neuronal reconstruction by embracing uncertainty.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012}, pages = {e44448}, abstract = {

The ability to automatically segment an image into distinct regions is a critical aspect in many visual processing applications. Because inaccuracies often exist in automatic segmentation, manual segmentation is necessary in some application domains to correct mistakes, such as required in the reconstruction of neuronal processes from microscopic images. The goal of the automated segmentation tool is traditionally to produce the highest-quality segmentation, where quality is measured by the similarity to actual ground truth, so as to minimize the volume of manual correction necessary. Manual correction is generally orders-of-magnitude more time consuming than automated segmentation, often making handling large images intractable. Therefore, we propose a more relevant goal: minimizing the turn-around time of automated/manual segmentation while attaining a level of similarity with ground truth. It is not always necessary to inspect every aspect of an image to generate a useful segmentation. As such, we propose a strategy to guide manual segmentation to the most uncertain parts of segmentation. Our contributions include 1) a probabilistic measure that evaluates segmentation without ground truth and 2) a methodology that leverages these probabilistic measures to significantly reduce manual correction while maintaining segmentation quality.

}, keywords = {Animals, Automated, Computer-Assisted, Humans, Image Processing, Models, Neurons, Pattern Recognition, Theoretical, Uncertainty}, issn = {1932-6203}, doi = {10.1371/journal.pone.0044448}, author = {Plaza, Stephen M and Scheffer, Louis K and Saunders, Mathew} } @article {5327, title = {Molecular diversity of Dscam and self-recognition.}, journal = {Advances in Experimental Medicine and Biology}, volume = {739}, year = {2012}, month = {2012}, pages = {262-75}, abstract = {

Cell recognition requires interactions through molecules located on cell surface. The insect homolog of Down syndrome cell adhesion molecule (Dscam) manifests huge molecular diversity in its extracellular domain. High-affinity Dscam-Dscam interactions only occur between isoforms that carry identical extracellular domains. Homophilic Dscam signaling can, thus, vary in strength depending on the compositions of Dscams present on the opposing cell surfaces. Dscam abundantly exists in the developing nervous system and governs arborization and proper elaboration of neurites. Notably, individual neurons may stochastically and dynamically express a small subset of Dscam isoforms such that any given neurite can be endowed with a unique repertoire of Dscams. This allows individual neurites to recognize their sister branches. Self-recognition leads to self-repulsion, ensuring divergent migration of sister processes. By contrast, weak homophilic Dscam interactions may promote fasciculation of neurites that express analogous, but not identical, Dscams. Differential Dscam binding may provide graded cell recognition that in turn governs complex neuronal morphogenesis.

}, keywords = {Animals, Cell Adhesion Molecules, Cell Communication, Drosophila Proteins, Gene Expression Regulation, Neurons, Protein Isoforms}, issn = {0065-2598}, doi = {10.1007/978-1-4614-1704-0_17}, author = {Shi, Lei and Lee, Tzumin} } @article {6319, title = {Movies of ice-embedded particles enhance resolution in electron cryo-microscopy.}, journal = {Structure}, volume = {20}, year = {2012}, month = {2012 Nov 7}, pages = {1823-8}, abstract = {

Low-dose images obtained by electron cryo-microscopy (cryo-EM) are often affected by blurring caused by sample motion during electron beam exposure, degrading signal especially at high resolution. We show here that we can align frames of movies, recorded with a direct electron detector during beam exposure of rotavirus double-layered particles, thereby greatly reducing image blurring caused by beam-induced motion and sample stage instabilities. This procedure increases the efficiency of cryo-EM imaging and enhances the resolution obtained in three-dimensional reconstructions of the particle. Using movies in this way is generally applicable to all cryo-EM samples and should also improve the performance of midrange electron microscopes that may have limited mechanical stability and beam coherence.

}, keywords = {Cryoelectron Microscopy, Ice, Rotavirus}, issn = {1878-4186}, doi = {10.1016/j.str.2012.08.026}, author = {Campbell, Melody G and Cheng, Anchi and Brilot, Axel F and Moeller, Arne and Lyumkis, Dmitry and Veesler, David and Pan, Junhua and Harrison, Stephen C and Potter, Clinton S and Carragher, Bridget and Grigorieff, Nikolaus} } @article {4761, title = {Multiple dynamic representations in the motor cortex during sensorimotor learning.}, journal = {Nature}, volume = {484}, year = {2012}, month = {2012 Apr 26}, pages = {473-8}, abstract = {

The mechanisms linking sensation and action during learning are poorly understood. Layer 2/3 neurons in the motor cortex might participate in sensorimotor integration and learning; they receive input from sensory cortex and excite deep layer neurons, which control movement. Here we imaged activity in the same set of layer 2/3 neurons in the motor cortex over weeks, while mice learned to detect objects with their whiskers and report detection with licking. Spatially intermingled neurons represented sensory (touch) and motor behaviours (whisker movements and licking). With learning, the population-level representation of task-related licking strengthened. In trained mice, population-level representations were redundant and stable, despite dynamism of single-neuron representations. The activity of a subpopulation of neurons was consistent with touch driving licking behaviour. Our results suggest that ensembles of motor cortex neurons couple sensory input to multiple, related motor programs during learning.

}, issn = {1476-4687}, doi = {10.1038/nature11039}, author = {Huber, D and Gutnisky, D A and Peron, S and O{\textquoteright}Connor, D H and Wiegert, J S and Tian, L and Oertner, T G and Looger, LL and Svoboda, K} } @article {47648, title = {Multiscale diffusion in the mitotic Drosophila melanogaster syncytial blastoderm.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 May 29}, pages = {8588-93}, abstract = {

Despite the fundamental importance of diffusion for embryonic morphogen gradient formation in the early Drosophila melanogaster embryo, there remains controversy regarding both the extent and the rate of diffusion of well-characterized morphogens. Furthermore, the recent observation of diffusional "compartmentalization" has suggested that diffusion may in fact be nonideal and mediated by an as-yet-unidentified mechanism. Here, we characterize the effects of the geometry of the early syncytial Drosophila embryo on the effective diffusivity of cytoplasmic proteins. Our results demonstrate that the presence of transient mitotic membrane furrows results in a multiscale diffusion effect that has a significant impact on effective diffusion rates across the embryo. Using a combination of live-cell experiments and computational modeling, we characterize these effects and relate effective bulk diffusion rates to instantaneous diffusion coefficients throughout the syncytial blastoderm nuclear cycle phase of the early embryo. This multiscale effect may be related to the effect of interphase nuclei on effective diffusion, and thus we propose that an as-yet-unidentified role of syncytial membrane furrows is to temporally regulate bulk embryonic diffusion rates to balance the multiscale effect of interphase nuclei, which ultimately stabilizes the shapes of various morphogen gradients.

}, keywords = {Algorithms, Animals, Animals, Genetically Modified, Blastoderm, Cell Compartmentation, Cell Membrane, Computer Simulation, Cytoplasm, Diffusion, Drosophila melanogaster, Embryo, Nonmammalian, Fluorescence Recovery After Photobleaching, Giant Cells, Green Fluorescent Proteins, Kinetics, Microscopy, Fluorescence, Mitosis, Models, Biological}, issn = {1091-6490}, doi = {10.1073/pnas.1204270109}, author = {Daniels, Brian R and Rikhy, Richa and Renz, Malte and Dobrowsky, Terrence M and Lippincott-Schwartz, Jennifer} } @article {46733, title = {Multiscale dynamics in nucleocytoplasmic transport.}, journal = {Current Opinion in Cell Biology}, volume = {24}, year = {2012}, month = {2012 Feb}, pages = {100-6}, abstract = {

The nuclear pore complex (NPC) has long been viewed as a point-like entry and exit channel between the nucleus and the cytoplasm. New data support a different view whereby the complex displays distinct spatial dynamics of variable duration ranging from milliseconds to events spanning the entire cell cycle. Discrete interaction sites outside the central channel become apparent, and transport regulation at these sites seems to be of greater importance than currently thought. Nuclear pore components are highly active outside the NPC or impact the fate of cargo transport away from the nuclear pore. The NPC is a highly dynamic, crowded environment-constantly loaded with cargo while providing selectivity based on unfolded proteins. Taken together, this comprises a new paradigm in how we view import/export dynamics and emphasizes the multiscale nature of NPC-mediated cellular transport.

}, keywords = {Active Transport, Cell Nucleus, Animals, Biological Transport, Cell Nucleus, Cytoplasm, Eukaryotic Cells, Models, Biological, Nuclear Pore, Nuclear Pore Complex Proteins}, issn = {1879-0410}, doi = {10.1016/j.ceb.2011.11.011}, author = {Grunwald, David and Singer, Robert H} } @article {5153, title = {The Ndc80 kinetochore complex directly modulates microtubule dynamics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 Aug 20}, pages = {16113-8}, abstract = {

The conserved Ndc80 complex is an essential microtubule-binding component of the kinetochore. Recent findings suggest that the Ndc80 complex influences microtubule dynamics at kinetochores in vivo. However, it was unclear if the Ndc80 complex mediates these effects directly, or by affecting other factors localized at the kinetochore. Using a reconstituted system in vitro, we show that the human Ndc80 complex directly stabilizes the tips of disassembling microtubules and promotes rescue (the transition from microtubule shortening to growth). In vivo, an N-terminal domain in the Ndc80 complex is phosphorylated by the Aurora B kinase. Mutations that mimic phosphorylation of the Ndc80 complex prevent stable kinetochore-microtubule attachment, and mutations that block phosphorylation damp kinetochore oscillations. We find that the Ndc80 complex with Aurora B phosphomimetic mutations is defective at promoting microtubule rescue, even when robustly coupled to disassembling microtubule tips. This impaired ability to affect dynamics is not simply because of weakened microtubule binding, as an N-terminally truncated complex with similar binding affinity is able to promote rescue. Taken together, these results suggest that in addition to regulating attachment stability, Aurora B controls microtubule dynamics through phosphorylation of the Ndc80 complex.

}, issn = {1091-6490}, doi = {10.1073/pnas.1209615109}, author = {Umbreit, Neil T and Gestaut, Daniel R and Tien, Jerry F and Vollmar, Breanna S and Gonen, Tamir and Asbury, Charles L and Davis, Trisha N} } @article {6220, title = {A network of spiking neurons for computing sparse representations in an energy-efficient way.}, journal = {Neural computation}, volume = {24}, year = {2012}, month = {2012 Nov}, pages = {2852-72}, abstract = {Computing sparse redundant representations is an important problem in both applied mathematics and neuroscience. In many applications, this problem must be solved in an energy-efficient way. Here, we propose a hybrid distributed algorithm (HDA), which solves this problem on a network of simple nodes communicating by low-bandwidth channels. HDA nodes perform both gradient-descent-like steps on analog internal variables and coordinate-descent-like steps via quantized external variables communicated to each other. Interestingly, the operation is equivalent to a network of integrate-and-fire neurons, suggesting that HDA may serve as a model of neural computation. We show that the numerical performance of HDA is on par with existing algorithms. In the asymptotic regime, the representation error of HDA decays with time, t, as 1/t. HDA is stable against time-varying noise; specifically, the representation error decays as 1/√t for gaussian white noise.}, keywords = {Action Potentials, Algorithms, Models, Neural Networks (Computer), Neurological, Neurons}, issn = {1530-888X}, doi = {10.1162/NECO_a_00353}, author = {Hu, Tao and Genkin, Alexander and Chklovskii, Dmitri B} } @article {5710, title = {Network resets in medial prefrontal cortex mark the onset of behavioral uncertainty.}, journal = {Science}, volume = {338}, year = {2012}, month = {2012 Oct 5}, pages = {135-9}, abstract = {

Regions within the prefrontal cortex are thought to process beliefs about the world, but little is known about the circuit dynamics underlying the formation and modification of these beliefs. Using a task that permits dissociation between the activity encoding an animal{\textquoteright}s internal state and that encoding aspects of behavior, we found that transient increases in the volatility of activity in the rat medial prefrontal cortex accompany periods when an animal{\textquoteright}s belief is modified after an environmental change. Activity across the majority of sampled neurons underwent marked, abrupt, and coordinated changes when prior belief was abandoned in favor of exploration of alternative strategies. These dynamics reflect network switches to a state of instability, which diminishes over the period of exploration as new stable representations are formed.

}, keywords = {Animal, Animals, Behavior, Long-Evans, Male, Nerve Net, Neurons, Prefrontal Cortex, Rats, Rejection (Psychology), Reward, Uncertainty}, issn = {1095-9203}, doi = {10.1126/science.1226518}, author = {Karlsson, Mattias P and Tervo, Dougal G R and Karpova, Alla Y} } @article {5161, title = {Neural activity imaging with genetically encoded calcium indicators.}, journal = {Progress in Brain Research}, volume = {196}, year = {2012}, month = {2012}, pages = {79-94}, abstract = {

Genetically encoded calcium indicators (GECIs), together with modern microscopy, allow repeated activity measurement, in real time and with cellular resolution, of defined cellular populations. Recent efforts in protein engineering have yielded several high-quality GECIs that facilitate new applications in neuroscience. Here, we summarize recent progress in GECI design, optimization, and characterization, and provide guidelines for selecting the appropriate GECI for a given biological application. We focus on the unique challenges associated with imaging in behaving animals.

}, keywords = {Animals, Calcium, Calcium Signaling, Molecular Imaging, Neurons}, issn = {1875-7855}, doi = {10.1016/B978-0-444-59426-6.00005-7}, author = {Tian, Lin and Akerboom, Jasper and Schreiter, Eric R and Looger, Loren L} } @article {4600, title = {Neuron transplantation partially reverses an obesity disorder in mice.}, journal = {Cell Metabolism}, volume = {15}, year = {2012}, month = {2012 Feb 8}, pages = {133-4}, abstract = {

Mice lacking leptin receptors are grossly obese and diabetic, in part due to dysfunction in brain circuits important for energy homeostasis. Transplantation of leptin receptor-expressing hypothalamic progenitor neurons into the brains of leptin receptor deficient mice led to integration into neural circuits, reduced obesity, and normalized circulating glucose levels.

}, issn = {1932-7420}, doi = {10.1016/j.cmet.2012.01.011}, author = {Sternson, Scott M} } @article {5658, title = {Neuronal circuits underlying persistent representations despite time varying activity.}, journal = {Current Biology}, volume = {22}, year = {2012}, month = {2012 Nov 20}, pages = {2095-103}, abstract = {

Our brains are capable of remarkably stable stimulus representations despite time-varying neural activity. For instance, during delay periods in working memory tasks, while stimuli are represented in working memory, neurons in the prefrontal cortex, thought to support the memory representation, exhibit time-varying neuronal activity. Since neuronal activity encodes the stimulus, its time-varying dynamics appears to be paradoxical and incompatible with stable network stimulus representations. Indeed, this finding raises a fundamental question: can stable representations only be encoded with stable neural activity, or, its corollary, is every change in activity a sign of change in stimulus representation?

}, issn = {1879-0445}, doi = {10.1016/j.cub.2012.08.058}, author = {Druckmann, S and Chklovskii, Dmitri B} } @article {5435, title = {Neuronal spike generation mechanism as an oversampling, noise-shaping A-to-D converter.}, journal = {Advances in Neural Information Processing Systems}, volume = {24}, year = {2012}, month = {2012}, pages = {503-11}, abstract = {

We explore the hypothesis that the neuronal spike generation mechanism is an analog-to-digital converter, which rectifies low-pass filtered summed synaptic currents and encodes them into spike trains linearly decodable in post-synaptic neurons. To digitally encode an analog current waveform, the sampling rate of the spike generation mechanism must exceed its Nyquist rate. Such oversampling is consistent with the experimental observation that the precision of the spike-generation mechanism is an order of magnitude greater than the cut-off frequency of dendritic low-pass filtering. To achieve additional reduction in the error of analog-to-digital conversion, electrical engineers rely on noise-shaping. If noise-shaping were used in neurons, it would introduce correlations in spike timing to reduce low-frequency (up to Nyquist) transmission error at the cost of high-frequency one (from Nyquist to sampling rate). Using experimental data from three different classes of neurons, we demonstrate that biological neurons utilize noise-shaping. We also argue that rectification by the spike-generation mechanism may improve energy efficiency and carry out de-noising. Finally, the zoo of ion channels in neurons may be viewed as a set of predictors, various subsets of which are activated depending on the statistics of the input current.

}, author = {Chklovskii, Dmitri B and Soudry, Daniel} } @article {5205, title = {Neuroscience. The mind of a male?}, journal = {Science}, volume = {337}, year = {2012}, month = {2012 Jul 27}, pages = {416-7}, keywords = {Animal, Animals, Caenorhabditis elegans, Male, Nerve Net, Neurons, Sexual Behavior, Synapses}, issn = {1095-9203}, doi = {10.1126/science.1225853}, author = {Chklovskii, Dmitri B and Bargmann, Cornelia I} } @article {6293, title = {Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens.}, journal = {Cell}, volume = {151}, year = {2012}, month = {2012 Dec 7}, pages = {1370-85}, abstract = {

Optical imaging of the dynamics of living specimens involves tradeoffs between spatial resolution, temporal resolution, and phototoxicity, made more difficult in three dimensions. Here, however, we report that rapid three-dimensional (3D) dynamics can be studied beyond the diffraction limit in thick or densely fluorescent living specimens over many time points by combining ultrathin planar illumination\ produced by scanned Bessel beams with super-resolution structured illumination microscopy. We demonstrate in\ vivo karyotyping of chromosomes during mitosis and identify different dynamics for the actin cytoskeleton at the dorsal and ventral surfaces of fibroblasts. Compared to spinning disk confocal microscopy, we\ demonstrate substantially reduced photodamage when imaging rapid morphological changes in D.\ discoideum cells, as well as improved contrast and resolution at depth within developing C.\ elegans embryos. Bessel beam structured plane illumination thus promises new insights into complex biological phenomena that require 4D subcellular spatiotemporal detail in either a single or multicellular context.

}, keywords = {Animals, Brain, Caenorhabditis elegans, Cell Line, Dermatitis, Dictyostelium, Drosophila melanogaster, Fibroblasts, Fluorescence, Humans, Imaging, Karyotyping, Larva, Microscopy, Mitosis, Optical Imaging, Phototoxic, Three-Dimensional, Tumor}, issn = {1097-4172}, doi = {10.1016/j.cell.2012.10.008}, author = {Gao, Liang and Shao, Lin and Higgins, Christopher D and Poulton, John S and Peifer, Mark and Davidson, Michael W and Wu, Xufeng and Goldstein, Bob and Betzig, Eric} } @article {6294, title = {Nonlinear dendritic integration of sensory and motor input during an active sensing task.}, journal = {Nature}, volume = {492}, year = {2012}, month = {2012 Dec 13}, pages = {247-51}, abstract = {

Active dendrites provide neurons with powerful processing capabilities. However, little is known about the role of neuronal dendrites in behaviourally related circuit computations. Here we report that a novel global dendritic nonlinearity is involved in the integration of sensory and motor information within layer 5 pyramidal neurons during an active sensing behaviour. Layer 5 pyramidal neurons possess elaborate dendritic arborizations that receive functionally distinct inputs, each targeted to spatially separate regions. At the cellular level, coincident input from these segregated pathways initiates regenerative dendritic electrical events that produce bursts of action potential output and circuits featuring this powerful dendritic nonlinearity can implement computations based on input correlation. To examine this in vivo we recorded dendritic activity in layer 5 pyramidal neurons in the barrel cortex using two-photon calcium imaging in mice performing an object-localization task. Large-amplitude, global calcium signals were observed throughout the apical tuft dendrites when active touch occurred at particular object locations or whisker angles. Such global calcium signals are produced by dendritic plateau potentials that require both vibrissal sensory input and primary motor cortex activity. These data provide direct evidence of nonlinear dendritic processing of correlated sensory and motor information in the mammalian neocortex during active sensation.

}, keywords = {Animal, Animals, Behavior, Calcium, Dendrites, Inbred C57BL, Male, Mice, Motor Activity, Patch-Clamp Techniques, Pyramidal Cells, Sensation, Signal Transduction}, issn = {1476-4687}, doi = {10.1038/nature11601}, author = {Xu, Ning-long and Harnett, Mark T and Williams, Stephen R and Huber, Daniel and O{\textquoteright}Connor, Daniel H and Svoboda, Karel and Magee, Jeffrey C} } @article {4489, title = {Nonlinear structured-illumination microscopy with a photoswitchable protein reveals cellular structures at 50-nm resolution.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 Jan 17}, pages = {E135-43}, abstract = {

Using ultralow light intensities that are well suited for investigating biological samples, we demonstrate whole-cell superresolution imaging by nonlinear structured-illumination microscopy. Structured-illumination microscopy can increase the spatial resolution of a wide-field light microscope by a factor of two, with greater resolution extension possible if the emission rate of the sample responds nonlinearly to the illumination intensity. Saturating the fluorophore excited state is one such nonlinear response, and a realization of this idea, saturated structured-illumination microscopy, has achieved approximately 50-nm resolution on dye-filled polystyrene beads. Unfortunately, because saturation requires extremely high light intensities that are likely to accelerate photobleaching and damage even fixed tissue, this implementation is of limited use for studying biological samples. Here, reversible photoswitching of a fluorescent protein provides the required nonlinearity at light intensities six orders of magnitude lower than those needed for saturation. We experimentally demonstrate approximately 40-nm resolution on purified microtubules labeled with the fluorescent photoswitchable protein Dronpa, and we visualize cellular structures by imaging the mammalian nuclear pore and actin cytoskeleton. As a result, nonlinear structured-illumination microscopy is now a biologically compatible superresolution imaging method.

}, issn = {1091-6490}, doi = {10.1073/pnas.1107547108}, author = {Rego, E Hesper and Shao, Lin and Macklin, John J and Winoto, Lukman and Johansson, G{\"o}ran A and Kamps-Hughes, Nicholas and Davidson, Michael W and Gustafsson, Mats G L} } @article {46719, title = {Nuclear pore component Nup98 is a potential tumor suppressor and regulates posttranscriptional expression of select p53 target genes.}, journal = {Molecular Cell}, volume = {48}, year = {2012}, month = {2012 Dec 14}, pages = {799-810}, abstract = {

The p53 tumor suppressor utilizes multiple mechanisms to selectively regulate its myriad target genes, which in turn mediate diverse cellular processes. Here, using conventional and single-molecule mRNA analyses, we demonstrate that the nucleoporin Nup98 is required for full expression of p21, a key effector of the p53 pathway, but not several other p53 target genes. Nup98 regulates p21 mRNA levels by a posttranscriptional mechanism in which a complex containing Nup98 and the p21 mRNA 3{\textquoteright}UTR protects p21 mRNA from degradation by the exosome. An in silico approach revealed another p53 target (14-3-3σ) to be similarly regulated by Nup98. The expression of Nup98 is reduced in murine and human hepatocellular carcinomas (HCCs) and correlates with p21 expression in HCC patients. Our study elucidates a previously unrecognized function of wild-type Nup98 in regulating select p53 target genes that is distinct from the well-characterized oncogenic properties of Nup98 fusion proteins.

}, keywords = {14-3-3 Proteins, 3{\textquoteright} Untranslated Regions, Animals, Antineoplastic Agents, Phytogenic, Apoptosis, Binding Sites, Camptothecin, Carcinoma, Hepatocellular, Cell Aging, Cyclin-Dependent Kinase Inhibitor p21, Exosomes, Gene Expression Regulation, Neoplastic, Hep G2 Cells, Humans, Liver Neoplasms, Male, Mice, Mice, Knockout, Nuclear Pore Complex Proteins, P-Glycoproteins, RNA Interference, RNA Processing, Post-Transcriptional, RNA Stability, RNA, Messenger, Time Factors, Transfection, Tumor Suppressor Protein p53}, issn = {1097-4164}, doi = {10.1016/j.molcel.2012.09.020}, author = {Singer, Stephan and Zhao, Ruiying and Barsotti, Anthony M and Ouwehand, Anette and Fazollahi, Mina and Coutavas, Elias and Breuhahn, Kai and Neumann, Olaf and Longerich, Thomas and Pusterla, Tobias and Powers, Maureen A and Giles, Keith M and Leedman, Peter J and Hess, Jochen and Grunwald, David and Bussemaker, Harmen J and Singer, Robert H and Schirmacher, Peter and Prives, Carol} } @article {6329, title = {Nucleotide excision repair (NER) machinery recruitment by the transcription-repair coupling factor involves unmasking of a conserved intramolecular interface.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 Feb 28}, pages = {3353-8}, abstract = {

Transcription-coupled DNA repair targets DNA lesions that block progression of elongating RNA polymerases. In bacteria, the transcription-repair coupling factor (TRCF; also known as Mfd) SF2 ATPase recognizes RNA polymerase stalled at a site of DNA damage, removes the enzyme from the DNA, and recruits the Uvr(A)BC nucleotide excision repair machinery via UvrA binding. Previous studies of TRCF revealed a molecular architecture incompatible with UvrA binding, leaving its recruitment mechanism unclear. Here, we examine the UvrA recognition determinants of TRCF using X-ray crystallography of a core TRCF-UvrA complex and probe the conformational flexibility of TRCF in the absence and presence of nucleotides using small-angle X-ray scattering. We demonstrate that the C-terminal domain of TRCF is inhibitory for UvrA binding, but not RNA polymerase release, and show that nucleotide binding induces concerted multidomain motions. Our studies suggest that autoinhibition of UvrA binding in TRCF may be relieved only upon engaging the DNA damage.

}, keywords = {Adenosine Triphosphatases, Adenosine Triphosphate, Amino Acid Sequence, Bacterial, Bacterial Proteins, Crystallography, DNA, DNA Damage, DNA Helicases, DNA Repair, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Hydrolysis, Models, Molecular, Molecular Sequence Data, Protein Binding, Protein Conformation, Protein Interaction Mapping, Protein Structure, RNA Polymerase I, Tertiary, Transcription Factors, X-Ray}, issn = {1091-6490}, doi = {10.1073/pnas.1115105109}, author = {Deaconescu, Alexandra M and Sevostyanova, Anastasia and Artsimovitch, Irina and Grigorieff, Nikolaus} } @article {65017, title = {An olfactory subsystem that mediates high-sensitivity detection of volatile amines.}, journal = {Cell Rep}, volume = {2}, year = {2012}, month = {2012 Jul 26}, pages = {76-88}, abstract = {

Olfactory stimuli are detected by over 1,000 odorant receptors in mice, with each receptor being mapped to specific glomeruli in the olfactory bulb. The trace amine-associated receptors (TAARs) are a small family of evolutionarily conserved olfactory receptors whose contribution to olfaction remains enigmatic. Here, we show that a majority of the TAARs are mapped to a discrete subset of glomeruli in the dorsal olfactory bulb of the mouse. This TAAR projection is distinct from the previously described class I and class II domains, and is formed by a sensory neuron population that is restricted to express TAAR genes prior to choice. We also show that the dorsal TAAR glomeruli are selectively activated by amines at low concentrations. Our data uncover a hard-wired, parallel input stream in the main olfactory pathway that is specialized for the detection of volatile amines.

}, keywords = {Amines, Animals, Female, Gene Targeting, Mice, Mice, Inbred C57BL, Mice, Transgenic, Models, Biological, Multigene Family, Olfactory Pathways, Olfactory Perception, Olfactory Receptor Neurons, Receptors, Cell Surface, Receptors, G-Protein-Coupled, Substrate Specificity, Volatile Organic Compounds, Volatilization}, issn = {2211-1247}, doi = {10.1016/j.celrep.2012.06.006}, author = {Pacifico, Rodrigo and Dewan, Adam and Cawley, Dillon and Guo, Caiying and Bozza, Thomas} } @article {6328, title = {Optimal noise reduction in 3D reconstructions of single particles using a volume-normalized filter.}, journal = {Journal of Structural Biology}, volume = {180}, year = {2012}, month = {2012 Oct}, pages = {26-38}, abstract = {

The high noise level found in single-particle electron cryo-microscopy (cryo-EM) image data presents a special challenge for three-dimensional (3D) reconstruction of the imaged molecules. The spectral signal-to-noise ratio (SSNR) and related Fourier shell correlation (FSC) functions are commonly used to assess and mitigate the noise-generated error in the reconstruction. Calculation of the SSNR and FSC usually includes the noise in the solvent region surrounding the particle and therefore does not accurately reflect the signal in the particle density itself. Here we show that the SSNR in a reconstructed 3D particle map is linearly proportional to the fractional volume occupied by the particle. Using this relationship, we devise a novel filter (the "single-particle Wiener filter") to minimize the error in a reconstructed particle map, if the particle volume is known. Moreover, we show how to approximate this filter even when the volume of the particle is not known, by optimizing the signal within a representative interior region of the particle. We show that the new filter improves on previously proposed error-reduction schemes, including the conventional Wiener filter as well as figure-of-merit weighting, and quantify the relationship between all of these methods by theoretical analysis as well as numeric evaluation of both simulated and experimentally collected data. The single-particle Wiener filter is applicable across a broad range of existing 3D reconstruction techniques, but is particularly well suited to the Fourier inversion method, leading to an efficient and accurate implementation.

}, keywords = {Algorithms, Capsid, Cryoelectron Microscopy, Data Interpretation, Fourier Analysis, Imaging, Kinesin, Models, Molecular, Papillomaviridae, Protein Structure, Quaternary, Signal-To-Noise Ratio, Software, Statistical, Tertiary, Three-Dimensional}, issn = {1095-8657}, doi = {10.1016/j.jsb.2012.05.005}, author = {Sindelar, Charles V and Grigorieff, Nikolaus} } @article {5164, title = {Optimization of a GCaMP calcium indicator for neural activity imaging.}, journal = {The Journal of Neuroscience}, volume = {32}, year = {2012}, month = {2012 Oct 3}, pages = {13819-40}, chapter = {13819}, abstract = {

Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Recent efforts in protein engineering have significantly increased the performance of GECIs. The state-of-the art single-wavelength GECI, GCaMP3, has been deployed in a number of model organisms and can reliably detect three or more action potentials in short bursts in several systems in vivo . Through protein structure determination, targeted mutagenesis, high-throughput screening, and a battery of in vitro assays, we have increased the dynamic range of GCaMP3 by severalfold, creating a family of {\textquotedblleft}GCaMP5{\textquotedblright} sensors. We tested GCaMP5s in several systems: cultured neurons and astrocytes, mouse retina, and in vivo in Caenorhabditis chemosensory neurons, Drosophila larval neuromuscular junction and adult antennal lobe, zebrafish retina and tectum, and mouse visual cortex. Signal-to-noise ratio was improved by at least 2- to 3-fold. In the visual cortex, two GCaMP5 variants detected twice as many visual stimulus-responsive cells as GCaMP3. By combining in vivo imaging with electrophysiology we show that GCaMP5 fluorescence provides a more reliable measure of neuronal activity than its predecessor GCaMP3.GCaMP5allows more sensitive detection of neural activity in vivo andmayfind widespread applications for cellular imaging in general.

}, doi = {10.1523/​JNEUROSCI.2601-12.2012}, author = {Akerboom, Jasper and Chen, Tsai-Wen and Wardill, Trevor J. and Marvin, Jonathan S and Mutlu, Sevinc and Carreras Caldero, Nicole and Esposti, Federico and Borghuis, Bart G and Sun, Xiaonan Richard and Gordus, Andrew and Orger, Michael B. and Portugues, Ruben and Engert, Florian and Macklin, John J and Filosa, Alessandro and Aggarwal, Aman and Kerr, Rex and Takagi, Ryousuke and Kracun, Sebastian and Shigetomi, Eiji and Khakh, Baljit S. and Baier, Herwig and Lagnado, Leon and Wang, Samuel S-H and Bargmann, Cornelia and Kimmel, Bruce and Jayaraman, Vivek and Svoboda, Karel and Kim, Douglas S. and Schreiter, Eric R and Looger, Loren L} } @article {5329, title = {Optogenetic analysis of a nociceptor neuron and network reveals ion channels acting downstream of primary sensors.}, journal = {Current Biology}, volume = {22}, year = {2012}, month = {2012 May 8}, pages = {743-52}, abstract = {

Nociception generally evokes rapid withdrawal behavior in order to protect the tissue from harmful insults. Most nociceptive neurons responding to mechanical insults display highly branched dendrites, an anatomy shared by Caenorhabditis elegans FLP and PVD neurons, which mediate harsh touch responses. Although several primary molecular nociceptive sensors have been characterized, less is known about modulation and amplification of noxious signals within nociceptor neurons. First, we analyzed the FLP/PVD network by optogenetics and studied integration of signals from these cells in downstream interneurons. Second, we investigated which genes modulate PVD function, based on prior single-neuron mRNA profiling of PVD.

}, keywords = {Ion Channels, Neurons}, issn = {1879-0445}, doi = {10.1016/j.cub.2012.02.066}, author = {Husson, Steven J and Costa, Wagner Steuer and Wabnig, Sebastian and Stirman, Jeffrey N and Watson, Joseph D and Spencer, W Clay and Akerboom, Jasper and Looger, Loren L and Treinin, Millet and Miller, David M and Lu, Hang and Gottschalk, Alexander} } @article {6501, title = {Organization and metamorphosis of glia in the Drosophila visual system.}, journal = {The Journal of Comparative Neurology}, volume = {520}, year = {2012}, month = {2012 Jul 1}, pages = {2067-85}, abstract = {

The visual system of Drosophila is an excellent model for determining the interactions that direct the differentiation of the nervous system{\textquoteright}s many unique cell types. Glia are essential not only in the development of the nervous system, but also in the function of those neurons with which they become associated in the adult. Given their role in visual system development and adult function we need to both accurately and reliably identify the different subtypes of glia, and to relate the glial subtypes in the larval brain to those previously described for the adult. We viewed driver expression in subsets of larval eye disc glia through the earliest stages of pupal development to reveal the counterparts of these cells in the adult. Two populations of glia exist in the lamina, the first neuropil of the adult optic lobe: those that arise from precursors in the eye-disc/optic stalk and those that arise from precursors in the brain. In both cases, a single larval source gives rise to at least three different types of adult glia. Furthermore, analysis of glial cell types in the second neuropil, the medulla, has identified at least four types of astrocyte-like (reticular) glia. Our clarification of the lamina{\textquoteright}s adult glia and identification of their larval origins, particularly the respective eye disc and larval brain contributions, begin to define developmental interactions which establish the different subtypes of glia.

}, keywords = {Animals, Biological, Drosophila, Drosophila Proteins, Electron, Eye, Genetically Modified, Green Fluorescent Proteins, Horseradish Peroxidase, Metamorphosis, Microscopy, Neuroglia, Neuropil, Nonmammalian, Optic Chiasm, Optic Lobe, Transmission, Visual Pathways}, issn = {1096-9861}, doi = {10.1002/cne.23071}, author = {Edwards, Tara N and Nuschke, Andrea C and Nern, Aljoscha and Meinertzhagen, Ian A.} } @article {6330, title = {Outcome of the first electron microscopy validation task force meeting.}, journal = {Structure}, volume = {20}, year = {2012}, month = {2012 Feb 8}, pages = {205-14}, abstract = {

This Meeting Review describes the proceedings and conclusions from the inaugural meeting of the Electron Microscopy Validation Task Force organized by the Unified Data Resource for 3DEM (http://www.emdatabank.org) and held at Rutgers University in New Brunswick, NJ on September 28 and 29, 2010. At the workshop, a group of scientists involved in collecting electron microscopy data, using the data to determine three-dimensional electron microscopy (3DEM) density maps, and building molecular models into the maps explored how to assess maps, models, and other data that are deposited into the Electron Microscopy Data Bank and Protein Data Bank public data archives. The specific recommendations resulting from the workshop aim to increase the impact of 3DEM in biology and medicine.

}, keywords = {Animals, Databases, Electron, Factual, Guidelines as Topic, Humans, Information Storage and Retrieval, Macromolecular Substances, Microscopy, Models, Molecular, Molecular Conformation, Molecular Sequence Annotation}, issn = {1878-4186}, doi = {10.1016/j.str.2011.12.014}, author = {Henderson, Richard and Sali, Andrej and Baker, Matthew L and Carragher, Bridget and Devkota, Batsal and Downing, Kenneth H and Egelman, Edward H and Feng, Zukang and Frank, Joachim and Grigorieff, Nikolaus and Jiang, Wen and Ludtke, Steven J and Medalia, Ohad and Penczek, Pawel A and Rosenthal, Peter B and Rossmann, Michael G and Schmid, Michael F and Schr{\"o}der, Gunnar F and Steven, Alasdair C and Stokes, David L and Westbrook, John D and Wriggers, Willy and Yang, Huanwang and Young, Jasmine and Berman, Helen M and Chiu, Wah and Kleywegt, Gerard J and Lawson, Catherine L} } @article {5389, title = {Parallel wavefront measurements in ultrasound pulse guided digital phase conjugation.}, journal = {Optics Express}, volume = {20}, year = {2012}, month = {2012 Oct 22}, pages = {24827-34}, abstract = {

Ultrasound pulse guided digital phase conjugation has emerged to realize fluorescence imaging inside random scattering media. Its major limitation is the slow imaging speed, as a new wavefront needs to be measured for each voxel. Therefore 3D or even 2D imaging can be time consuming. For practical applications on biological systems, we need to accelerate the imaging process by orders of magnitude. Here we propose and experimentally demonstrate a parallel wavefront measurement scheme towards such a goal. Multiple focused ultrasound pulses of different carrier frequencies can be simultaneously launched inside a scattering medium. Heterodyne interferometry is used to measure all of the wavefronts originating from every sound focus in parallel. We use these wavefronts in sequence to rapidly excite fluorescence at all the voxels defined by the focused ultrasound pulses. In this report, we employed a commercially available sound transducer to generate two sound foci in parallel, doubled the wavefront measurement speed, and reduced the mechanical scanning steps of the sound transducer to half.

}, issn = {1094-4087}, doi = {http://dx.doi.org/10.1364/OE.20.024827}, author = {Fiolka, Reto and Si, Ke and Cui, Meng} } @article {66011, title = {Pediatric epilepsy surgery: long-term 5-year seizure remission and medication use}, journal = {Neurosurgery}, volume = {71}, year = {2012}, month = {Feb-08-2013}, pages = {985 - 993}, abstract = {

Background:\ It is unclear whether long-term seizure outcomes in children are similar to those in adult epilepsy surgery patients.

Objective:\ To determine 5-year outcomes and antiepilepsy drug (AED) use in pediatric epilepsy surgery patients from a single institution.

Methods:\ The cohort consisted of children younger than 18 years of age whose 5-year outcome data would have been available by 2010. Comparisons were made between patients with and without 5-year data (n = 338), patients with 5-year data for seizure outcome (n = 257), and seizure-free patients on and off AEDs (n = 137).

Results:\ Five-year data were available from 76\% of patients. More seizure-free patients with focal resections for hippocampal sclerosis and tumors lacked 5-year data compared with other cases. Of those with 5-year data, 53\% were continuously seizure free, 18\% had late seizure recurrence, 3\% became seizure free after initial failure, and 25\% were never seizure free. Patients were more likely to be continuously seizure free if their surgery was performed during the period 2001 to 2005 (68\%) compared with surgery performed from 1996 to 2000 (61\%), 1991 to 1995 (36\%), and 1986 to 1990 (46\%). More patients had 1 or fewer seizures per month in the late seizure recurrence (47\%) compared with the not seizure-free group (20\%). Four late deaths occurred in the not seizure-free group compared with 1 in the seizure-free group. Of patients who were continuously seizure free, 55\% were not taking AEDs, and more cortical dysplasia patients (74\%) had stopped taking AEDs compared with hemimegalencephaly patients (18\%).

Conclusion:\ In children, 5-year outcomes improved over 20 years of clinical experience. Our results are similar to those of adult epilepsy surgery patients despite mostly extratemporal and hemispheric operations for diverse developmental etiologies.

}, issn = {0148-396X}, doi = {10.1227/NEU.0b013e31826cdd5a}, url = {https://academic.oup.com/neurosurgery/article/71/5/985/2595469http://academic.oup.com/neurosurgery/article-pdf/71/5/985/32585196/00006123-201211000-00011.pdfhttp://academic.oup.com/neurosurgery/article-pdf/71/5/985/32585196/00006123-201211000-00011.pdf}, author = {Hauptman, Jason S. and Pedram, Kayvon and Sison, Christia Angela and Sankar, Raman and Salamon, Noriko and Vinters, Harry V. and Mathern, Gary W.} } @article {6296, title = {The Pfam protein families database.}, journal = {Nucleic acids research}, volume = {40}, year = {2012}, month = {2012 Jan}, pages = {D290-301}, abstract = {

Pfam is a widely used database of protein families, currently containing more than 13,000 manually curated protein families as of release 26.0. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/). Here, we report on changes that have occurred since our 2010 NAR paper (release 24.0). Over the last 2 years, we have generated 1840 new families and increased coverage of the UniProt Knowledgebase (UniProtKB) to nearly 80\%. Notably, we have taken the step of opening up the annotation of our families to the Wikipedia community, by linking Pfam families to relevant Wikipedia pages and encouraging the Pfam and Wikipedia communities to improve and expand those pages. We continue to improve the Pfam website and add new visualizations, such as the {\textquoteright}sunburst{\textquoteright} representation of taxonomic distribution of families. In this work we additionally address two topics that will be of particular interest to the Pfam community. First, we explain the definition and use of family-specific, manually curated gathering thresholds. Second, we discuss some of the features of domains of unknown function (also known as DUFs), which constitute a rapidly growing class of families within Pfam.

}, keywords = {Amino Acid, Databases, Encyclopedias as Topic, Internet, Protein, Protein Structure, Proteins, Sequence Homology, Tertiary}, issn = {1362-4962}, doi = {10.1093/nar/gkr1065}, author = {Punta, Marco and Coggill, Penny C and Eberhardt, Ruth Y and Mistry, Jaina and Tate, John and Boursnell, Chris and Pang, Ningze and Forslund, Kristoffer and Ceric, Goran and Clements, Jody and Heger, Andreas and Holm, Liisa and Sonnhammer, Erik L L and Sean R. Eddy and Bateman, Alex and Finn, Robert D} } @article {47646, title = {Plasticity of the asialoglycoprotein receptor deciphered by ensemble FRET imaging and single-molecule counting PALM imaging.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 Oct 30}, pages = {E2989-97}, abstract = {

The stoichiometry and composition of membrane protein receptors are critical to their function. However, the inability to assess receptor subunit stoichiometry in situ has hampered efforts to relate receptor structures to functional states. Here, we address this problem for the asialoglycoprotein receptor using ensemble FRET imaging, analytical modeling, and single-molecule counting with photoactivated localization microscopy (PALM). We show that the two subunits of asialoglycoprotein receptor [rat hepatic lectin 1 (RHL1) and RHL2] can assemble into both homo- and hetero-oligomeric complexes, displaying three forms with distinct ligand specificities that coexist on the plasma membrane: higher-order homo-oligomers of RHL1, higher-order hetero-oligomers of RHL1 and RHL2 with two-to-one stoichiometry, and the homo-dimer RHL2 with little tendency to further homo-oligomerize. Levels of these complexes can be modulated in the plasma membrane by exogenous ligands. Thus, even a simple two-subunit receptor can exhibit remarkable plasticity in structure, and consequently function, underscoring the importance of deciphering oligomerization in single cells at the single-molecule level.

}, keywords = {Asialoglycoprotein Receptor, Fluorescence Resonance Energy Transfer, Ligands, Microscopy, Confocal}, issn = {1091-6490}, doi = {10.1073/pnas.1211753109}, author = {Renz, Malte and Daniels, Brian R and V{\'a}mosi, Gy{\"o}rgy and Arias, Irwin M and Lippincott-Schwartz, Jennifer} } @article {47656, title = {Plasticity of the asialoglycoprotein receptor deciphered by ensemble FRET imaging and single-molecule counting PALM imaging.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 Oct 30}, pages = {E2989-97}, abstract = {

The stoichiometry and composition of membrane protein receptors are critical to their function. However, the inability to assess receptor subunit stoichiometry in situ has hampered efforts to relate receptor structures to functional states. Here, we address this problem for the asialoglycoprotein receptor using ensemble FRET imaging, analytical modeling, and single-molecule counting with photoactivated localization microscopy (PALM). We show that the two subunits of asialoglycoprotein receptor [rat hepatic lectin 1 (RHL1) and RHL2] can assemble into both homo- and hetero-oligomeric complexes, displaying three forms with distinct ligand specificities that coexist on the plasma membrane: higher-order homo-oligomers of RHL1, higher-order hetero-oligomers of RHL1 and RHL2 with two-to-one stoichiometry, and the homo-dimer RHL2 with little tendency to further homo-oligomerize. Levels of these complexes can be modulated in the plasma membrane by exogenous ligands. Thus, even a simple two-subunit receptor can exhibit remarkable plasticity in structure, and consequently function, underscoring the importance of deciphering oligomerization in single cells at the single-molecule level.

}, keywords = {Asialoglycoprotein Receptor, Fluorescence Resonance Energy Transfer, Ligands, Microscopy, Confocal}, issn = {1091-6490}, doi = {10.1073/pnas.1211753109}, author = {Renz, Malte and Daniels, Brian R and V{\'a}mosi, Gy{\"o}rgy and Arias, Irwin M and Lippincott-Schwartz, Jennifer} } @article {45730, title = {Preparation and mounting of adult Drosophila structures in Canada balsam.}, journal = {Cold Spring Harb Protoc}, volume = {2012}, year = {2012}, month = {2012 Mar}, pages = {373-5}, abstract = {

The Drosophila cuticle carries a rich array of morphological details. Thus, cuticle examination has had a central role in the history of genetics. To prepare fine "museum-quality," permanent slides, it is best to mount specimens in Canada Balsam. It is difficult to give precise recipes for Canada Balsam, because every user seems to prefer a slightly different viscosity. Dilute solutions spread easily and do not dry too rapidly while mounting specimens. The disadvantage is that there is actually less Balsam in a "drop" of the solution, and when dried, it can contract from the sides of the coverslip, sometimes disturbing the specimen. Unfortunately, there is no substitute for experience when using Canada Balsam. This protocol describes a procedure for mounting adult cuticles in Canada Balsam.

}, keywords = {Animals, Balsams, Drosophila, Microscopy, Preservation, Biological, Specimen Handling}, issn = {1559-6095}, doi = {10.1101/pdb.prot067389}, author = {Stern, David L and Sucena, Elio} } @article {5460, title = {Proprioceptive coupling within motor neurons drives C. elegans forward locomotion.}, journal = {Neuron}, volume = {76}, year = {2012}, month = {2012 Nov 21}, pages = {750-61}, abstract = {

Locomotion requires coordinated motor activity throughout an animal{\textquoteright}s body. In both vertebrates and invertebrates, chains of coupled central pattern generators (CPGs) are commonly evoked to explain local rhythmic behaviors. In C.\ elegans, we report that proprioception within the motor circuit is responsible for propagating and coordinating rhythmic undulatory waves from head to tail during forward movement. Proprioceptive coupling between adjacent body regions transduces rhythmic movement initiated near the head into bending waves driven along the body by a chain of reflexes. Using optogenetics and calcium imaging to manipulate and monitor motor circuit activity of moving C.\ elegans held in microfluidic devices, we found that the B-type cholinergic motor neurons transduce the proprioceptive signal. In C.\ elegans, a sensorimotor feedback loop operating within a specific type of motor neuron both drives and organizes body movement.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2012.08.039}, author = {Wen, Quan and Po, Michelle D. and Hulme, Elizabeth and Chen, Sway and Liu, Xinyu and Kwok, Sen Wai and Gershow, Marc and Leifer, Andrew M. and Butler, Victoria and Fang-Yen, Christopher and Kawano, Taizo and Schafer, William R and Whitesides, George and Wyart, Matthieu and Chklovskii, Dmitri B and Samuel, Aravinthan D. T.} } @article {4900, title = {Pupil-segmentation-based adaptive optical correction of a high-numerical-aperture gradient refractive index lens for two-photon fluorescence endoscopy.}, journal = {Optics Letters}, volume = {37}, year = {2012}, month = {2012 Jun}, pages = {2001-3}, abstract = {

The intrinsic aberrations of high-NA gradient refractive index (GRIN) lenses limit their image quality as well as field of view. Here we used a pupil-segmentation-based adaptive optical approach to correct the inherent aberrations in a two-photon fluorescence endoscope utilizing a 0.8\ NA GRIN lens. By correcting the field-dependent aberrations, we recovered diffraction-limited performance across a large imaging field. The consequent improvements in imaging signal and resolution allowed us to detect fine structures that were otherwise invisible inside mouse brain slices.

}, doi = {10.1364/OL.37.002001}, url = {http://dx.doi.org/10.1364/OL.37.002001}, author = {Wang, Chan and Ji, Na} } @article {47651, title = {Quantitative analysis of photoactivated localization microscopy (PALM) datasets using pair-correlation analysis.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {34}, year = {2012}, month = {2012 May}, pages = {396-405}, abstract = {

Pointillistic based super-resolution techniques, such as photoactivated localization microscopy (PALM), involve multiple cycles of sequential activation, imaging, and precise localization of single fluorescent molecules. A super-resolution image, having nanoscopic structural information, is then constructed by compiling all the image sequences. Because the final image resolution is determined by the localization precision of detected single molecules and their density, accurate image reconstruction requires imaging of biological structures labeled with fluorescent molecules at high density. In such image datasets, stochastic variations in photon emission and intervening dark states lead to uncertainties in identification of single molecules. This, in turn, prevents the proper utilization of the wealth of information on molecular distribution and quantity. A recent strategy for overcoming this problem is pair-correlation analysis applied to PALM. Using rigorous statistical algorithms to estimate the number of detected proteins, this approach allows the spatial organization of molecules to be quantitatively described.

}, keywords = {Algorithms, Animals, Cell Membrane, Cercopithecus aethiops, COS Cells, Green Fluorescent Proteins, Humans, Image Processing, Computer-Assisted, Microscopy, Fluorescence, Photons, Proteins}, issn = {1521-1878}, doi = {10.1002/bies.201200022}, author = {Sengupta, Prabuddha and Lippincott-Schwartz, Jennifer} } @article {4898, title = {Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy.}, journal = {Nature Methods}, volume = {9}, year = {2012}, month = {2012 Jun 3}, pages = {755-63}, abstract = {

Live imaging of large biological specimens is fundamentally limited by the short optical penetration depth of light microscopes. To maximize physical coverage, we developed the SiMView technology framework for high-speed in vivo imaging, which records multiple views of the specimen simultaneously. SiMView consists of a light-sheet microscope with four synchronized optical arms, real-time electronics for long-term sCMOS-based image acquisition at 175 million voxels per second, and computational modules for high-throughput image registration, segmentation, tracking and real-time management of the terabytes of multiview data recorded per specimen. We developed one-photon and multiphoton SiMView implementations and recorded cellular dynamics in entire Drosophila melanogaster embryos with 30-s temporal resolution throughout development. We furthermore performed high-resolution long-term imaging of the developing nervous system and followed neuroblast cell lineages in vivo. SiMView data sets provide quantitative morphological information even for fast global processes and enable accurate automated cell tracking in the entire early embryo.

High-resolution movies in the Digital Embryo repository
Nature News: "Fruitfly development, cell by cell" by Lauren Gravitz
Nature Methods Technology Feature: "Faster frames, clearer pictures" by Monya Baker
Andor Insight Awards: Life Sciences Winner

}, issn = {1548-7105}, doi = {10.1038/nmeth.2062}, author = {Tomer, Raju and Khairy, Khaled and Amat, Fernando and Keller, Philipp J} } @article {6297, title = {Quantitative semi-automated analysis of morphogenesis with single-cell resolution in complex embryos.}, journal = {Development}, volume = {139}, year = {2012}, month = {2012 Nov}, pages = {4271-9}, abstract = {

A quantitative understanding of tissue morphogenesis requires description of the movements of individual cells in space and over time. In transparent embryos, such as C. elegans, fluorescently labeled nuclei can be imaged in three-dimensional time-lapse (4D) movies and automatically tracked through early cleavage divisions up to \ 350 nuclei. A similar analysis of later stages of C. elegans development has been challenging owing to the increased error rates of automated tracking of large numbers of densely packed nuclei. We present Nucleitracker4D, a freely available software solution for tracking nuclei in complex embryos that integrates automated tracking of nuclei in local searches with manual curation. Using these methods, we have been able to track \>99\% of all nuclei generated in the C. elegans embryo. Our analysis reveals that ventral enclosure of the epidermis is accompanied by complex coordinated migration of the neuronal substrate. We can efficiently track large numbers of migrating nuclei in 4D movies of zebrafish cardiac morphogenesis, suggesting that this approach is generally useful in situations in which the number, packing or dynamics of nuclei present challenges for automated tracking.

}, keywords = {Animals, Caenorhabditis elegans, Cell Differentiation, Cell Division, Cell Movement, Cell Nucleus, Computer-Assisted, Computers, Embryo, Epidermis, Image Processing, Morphogenesis, Nonmammalian, Single-Cell Analysis, Software, Statistics as Topic, Zebrafish}, issn = {1477-9129}, doi = {10.1242/dev.086256}, author = {Giurumescu, Claudiu A and Kang, Sukryool and Planchon, Thomas A and Betzig, Eric and Bloomekatz, Joshua and Yelon, Deborah and Cosman, Pamela and Chisholm, Andrew D} } @article {47647, title = {Rab10 and myosin-Va mediate insulin-stimulated GLUT4 storage vesicle translocation in adipocytes.}, journal = {The Journal of cell biology}, volume = {198}, year = {2012}, month = {2012 Aug 20}, pages = {545-60}, abstract = {

Rab proteins are important regulators of insulin-stimulated GLUT4 translocation to the plasma membrane (PM), but the precise steps in GLUT4 trafficking modulated by particular Rab proteins remain unclear. Here, we systematically investigate the involvement of Rab proteins in GLUT4 trafficking, focusing on Rab proteins directly mediating GLUT4 storage vesicle (GSV) delivery to the PM. Using dual-color total internal reflection fluorescence (TIRF) microscopy and an insulin-responsive aminopeptidase (IRAP)-pHluorin fusion assay, we demonstrated that Rab10 directly facilitated GSV translocation to and docking at the PM. Rab14 mediated GLUT4 delivery to the PM via endosomal compartments containing transferrin receptor (TfR), whereas Rab4A, Rab4B, and Rab8A recycled GLUT4 through the endosomal system. Myosin-Va associated with GSVs by interacting with Rab10, positioning peripherally recruited GSVs for ultimate fusion. Thus, multiple Rab proteins regulate the trafficking of GLUT4, with Rab10 coordinating with myosin-Va to mediate the final steps of insulin-stimulated GSV translocation to the PM.

}, keywords = {3T3-L1 Cells, Adipocytes, Animals, Cell Membrane, Cytoplasmic Vesicles, Glucose Transporter Type 4, Insulin, Mice, Myosin Heavy Chains, Myosin Type V, Protein Transport, rab GTP-Binding Proteins}, issn = {1540-8140}, doi = {10.1083/jcb.201111091}, author = {Chen, Yu and Wang, Yan and Zhang, Jinzhong and Deng, Yongqiang and Jiang, Li and Song, Eli and Wu, Xufeng S and Hammer, John A and Xu, Tao and Lippincott-Schwartz, Jennifer} } @article {4597, title = {A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more.}, journal = {RNA}, volume = {18}, year = {2012}, month = {2012 Feb}, pages = {193-212}, abstract = {

The standard approach for single-sequence RNA secondary structure prediction uses a nearest-neighbor thermodynamic model with several thousand experimentally determined energy parameters. An attractive alternative is to use statistical approaches with parameters estimated from growing databases of structural RNAs. Good results have been reported for discriminative statistical methods using complex nearest-neighbor models, including CONTRAfold, Simfold, and ContextFold. Little work has been reported on generative probabilistic models (stochastic context-free grammars [SCFGs]) of comparable complexity, although probabilistic models are generally easier to train and to use. To explore a range of probabilistic models of increasing complexity, and to directly compare probabilistic, thermodynamic, and discriminative approaches, we created TORNADO, a computational tool that can parse a wide spectrum of RNA grammar architectures (including the standard nearest-neighbor model and more) using a generalized super-grammar that can be parameterized with probabilities, energies, or arbitrary scores. By using TORNADO, we find that probabilistic nearest-neighbor models perform comparably to (but not significantly better than) discriminative methods. We find that complex statistical models are prone to overfitting RNA structure and that evaluations should use structurally nonhomologous training and test data sets. Overfitting has affected at least one published method (ContextFold). The most important barrier to improving statistical approaches for RNA secondary structure prediction is the lack of diversity of well-curated single-sequence RNA secondary structures in current RNA databases.

}, issn = {1469-9001}, doi = {10.1261/rna.030049.111}, author = {Rivas, Elena and Lang, Raymond and Eddy, Sean R.} } @article {45731, title = {Rapid mounting of adult Drosophila structures in Hoyer{\textquoteright}s medium.}, journal = {Cold Spring Harb Protoc}, volume = {2012}, year = {2012}, month = {2012 Jan}, pages = {107-9}, abstract = {

The Drosophila cuticle carries a rich array of morphological details. Thus, cuticle examination has had a central role in the history of genetics. This protocol describes a procedure for mounting adult cuticles in Hoyer{\textquoteright}s medium, a useful mountant for both larval and adult cuticles. The medium digests soft tissues rapidly, leaving the cuticle cleared for observation. In addition, samples can be transferred directly from water to Hoyer{\textquoteright}s medium. However, specimens mounted in Hoyer{\textquoteright}s medium degrade over time. For example, the fine denticles on the larval dorsum are best observed soon after mounting; they begin to fade after 1 week, and can disappear completely after several months. More robust features, such as the ventral denticle belts, will persist for a longer period of time. Because adults cannot profitably be mounted whole in Hoyer{\textquoteright}s medium, some dissection is necessary.

}, keywords = {Animals, Drosophila, Integumentary System, Specimen Handling}, issn = {1559-6095}, doi = {10.1101/pdb.prot067371}, author = {Stern, David L and Sucena, Elio} } @article {4840, title = {Real neuroscience in virtual worlds.}, journal = {Current Opinion in Neurobiology}, volume = {22}, year = {2012}, month = {2012 Feb}, pages = {3-10}, abstract = {

Virtual reality (VR) holds great promise as a tool to study the neural circuitry underlying animal behaviors. Here, we discuss the advantages of VR and the experimental paradigms and technologies that enable closed loop behavioral experiments. We review recent results from VR research in genetic model organisms where the potential combination of rich behaviors, genetic tools and cutting edge neural recording techniques are leading to breakthroughs in our understanding of the neural basis of behavior. We also discuss several key issues to consider when performing VR experiments and provide an outlook for the future of this exciting experimental toolkit.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2011.10.015}, author = {Dombeck, Daniel A and Reiser, Michael B} } @article {4593, title = {Reduced release probability prevents vesicle depletion and transmission failure at dynamin mutant synapses.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 Feb 21}, pages = {E515-23}, abstract = {

Endocytic recycling of synaptic vesicles after exocytosis is critical for nervous system function. At synapses of cultured neurons that lack the two "neuronal" dynamins, dynamin 1 and 3, smaller excitatory postsynaptic currents are observed due to an impairment of the fission reaction of endocytosis that results in an accumulation of arrested clathrin-coated pits and a greatly reduced synaptic vesicle number. Surprisingly, despite a smaller readily releasable vesicle pool and fewer docked vesicles, a strong facilitation, which correlated with lower vesicle release probability, was observed upon action potential stimulation at such synapses. Furthermore, although network activity in mutant cultures was lower, Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) activity was unexpectedly increased, consistent with the previous report of an enhanced state of synapsin 1 phosphorylation at CaMKII-dependent sites in such neurons. These changes were partially reversed by overnight silencing of synaptic activity with tetrodotoxin, a treatment that allows progression of arrested endocytic pits to synaptic vesicles. Facilitation was also counteracted by CaMKII inhibition. These findings reveal a mechanism aimed at preventing synaptic transmission failure due to vesicle depletion when recycling vesicle traffic is backed up by a defect in dynamin-dependent endocytosis and provide new insight into the coupling between endocytosis and exocytosis.

}, issn = {1091-6490}, doi = {10.1073/pnas.1121626109}, author = {Lou, Xuelin and Fan, Fan and Messa, Mirko and Raimondi, Andrea and Wu, Yumei and Looger, Loren L and Ferguson, Shawn M and De Camilli, Pietro} } @article {4589, title = {Regular spiking and intrinsic bursting pyramidal cells show orthogonal forms of experience-dependent plasticity in layer V of barrel cortex.}, journal = {Neuron}, volume = {73}, year = {2012}, month = {2012 Jan 26}, pages = {391-404}, abstract = {

Most functional plasticity studies in the cortex have focused on layers (L) II/III and IV, whereas relatively little is known of LV. Structural measurements of dendritic spines in\ vivo suggest some specialization among LV cell subtypes. We therefore studied experience-dependent plasticity in the barrel cortex using intracellular recordings to distinguish regular spiking (RS) and intrinsic bursting (IB) subtypes. Postsynaptic potentials and suprathreshold responses in\ vivo revealed a remarkable dichotomy in RS and IB cell plasticity; spared whisker potentiation occurred in IB but not RS cells while deprived whisker depression occurred in RS but not IB cells. Similar RS/IB differences were found in the LII/III to V connections in brain slices. Modeling studies showed that subthreshold changes predicted the suprathreshold changes. These studies demonstrate the major functional partition of plasticity within a single cortical layer and reveal the LII/III to LV connection as a major excitatory locus of cortical plasticity.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.11.034}, author = {Jacob, Vincent and Petreanu, Leopoldo and Wright, Nick and Svoboda, Karel and Fox, Kevin} } @article {46730, title = {Regulation of local expression of cell adhesion and motility-related mRNAs in breast cancer cells by IMP1/ZBP1.}, journal = {The Journal of Cell Science}, volume = {125}, year = {2012}, month = {2012 Jan 1}, pages = {81-91}, abstract = {

Metastasis involves tumor cell detachment from the primary tumor, and acquisition of migratory and invasive capabilities. These capabilities are mediated by multiple events, including loss of cell-cell contact, an increase in focal adhesion turnover and failure to maintain a normal cell polarity. We have previously reported that silencing of the expression of the zipcode-binding protein IMP1/ZBP1 in breast tumor patients is associated with metastasis. IMP1/ZBP1 selectively binds to a group of mRNAs that encode important mediators for cell adhesion and motility. Here, we show that in both T47D and MDA231 human breast carcinoma cells IMP1/ZBP1 functions to suppress cell invasion. Binding of ZBP1 to the mRNAs encoding E-cadherin, β-actin, α-actinin and the Arp2/3 complex facilitates localization of the mRNAs, which stabilizes cell-cell connections and focal adhesions. Our studies suggest a novel mechanism through which IMP1/ZBP1 simultaneously regulates the local expression of many cell-motility-related mRNAs to maintain cell adherence and polarity, decrease focal adhesion turnover and maintain a persistent and directional motility.

}, keywords = {Actin-Related Protein 2-3 Complex, Actinin, Actins, Breast Neoplasms, Cadherins, Cell Adhesion, Cell Line, Tumor, Cell Movement, Focal Adhesions, Gene Expression Regulation, Neoplastic, Humans, Neoplasm Invasiveness, Neoplasm Metastasis, RNA, Messenger, RNA, Neoplasm, RNA-Binding Proteins}, issn = {1477-9137}, doi = {10.1242/jcs.086132}, author = {Gu, Wei and Katz, Zachary and Wu, Bin and Park, Hye Yoon and Li, Deling and Lin, Stanley and Wells, Amber L and Singer, Robert H} } @article {4594, title = {Regulation of neuronal input transformations by tunable dendritic inhibition.}, journal = {Nature Neuroscience}, volume = {15}, year = {2012}, month = {2012 Jan 15}, pages = {423-30}, abstract = {

Transforming synaptic input into action potential output is a fundamental function of neurons. The pattern of action potential output from principal cells of the mammalian hippocampus encodes spatial and nonspatial information, but the cellular and circuit mechanisms by which neurons transform their synaptic input into a given output are unknown. Using a combination of optical activation and cell type-specific pharmacogenetic silencing in vitro, we found that dendritic inhibition is the primary regulator of input-output transformations in mouse hippocampal CA1 pyramidal cells, and acts by gating the dendritic electrogenesis driving burst spiking. Dendrite-targeting interneurons are themselves modulated by interneurons targeting pyramidal cell somata, providing a synaptic substrate for tuning pyramidal cell output through interactions in the local inhibitory network. These results provide evidence for a division of labor in cortical circuits, where distinct computational functions are implemented by subtypes of local inhibitory neurons.

}, issn = {1546-1726}, doi = {10.1038/nn.3024}, author = {Lovett-Barron, Matthew and Turi, Gergely F and Kaifosh, Patrick and Lee, Peter H and Bolze, Fr{\'e}d{\'e}ric and Sun, Xiao-Hua and Nicoud, Jean-Fran\c cois and Zemelman, Boris V and Sternson, Scott M and Losonczy, Attila} } @article {6515, title = {A resource for manipulating gene expression and analyzing cis-regulatory modules in the Drosophila CNS.}, journal = {Cell Reports}, volume = {2}, year = {2012}, month = {2012 Oct 25}, pages = {1002-13}, abstract = {

Here, we describe the embryonic central nervous system expression of 5,000 GAL4 lines made using molecularly defined cis-regulatory DNA inserted into a single attP genomic location. We document and annotate the patterns in early embryos when neurogenesis is at its peak, and in older embryos where there is maximal neuronal diversity and the first neural circuits are established. We note expression in other tissues, such as the lateral body wall (muscle, sensory neurons, and trachea) and viscera. Companion papers report on the adult brain and larval imaginal discs, and the integrated data sets\ are available online (http://www.janelia.org/gal4-gen1). This collection of embryonically expressed GAL4 lines will be valuable for determining neuronal morphology and function. The 1,862 lines expressed in small subsets of neurons (\<20/segment) will be especially valuable for characterizing\ interneuronal diversity and function, because although interneurons comprise the majority of all central nervous system neurons, their gene expression profile and function remain virtually unexplored.

}, keywords = {Animals, Central Nervous System, Databases, Drosophila, Drosophila Proteins, Embryo, Factual, Female, Gene Expression, Genes, Genetically Modified, Internet, Male, Nonmammalian, Regulatory Elements, Reporter, Transcription Factors, Transcriptional}, issn = {2211-1247}, doi = {10.1016/j.celrep.2012.09.009}, author = {Manning, Laurina and Heckscher, Ellie S and Purice, Maria D and Roberts, Jourdain and Bennett, Alysha L and Kroll, Jason R and Pollard, Jill L and Strader, Marie E and Lupton, Josh R and Dyukareva, Anna V and Doan, Phuong Nam and Bauer, David M and Wilbur, Allison N and Tanner, Stephanie and Kelly, Jimmy J and Lai, Sen-Lin and Tran, Khoa D and Kohwi, Minoree and Laverty, Todd R and Pearson, Joseph C and Crews, Stephen T and Rubin, Gerald M and Doe, Chris Q} } @article {5159, title = {Running in reverse: rhodopsins sense voltage.}, journal = {Nature Methods}, volume = {9}, year = {2012}, month = {2012 Jan}, pages = {43-4}, keywords = {Action Potentials, Animals, Halorhodopsins, Humans, Neurons}, issn = {1548-7105}, doi = {10.1038/nmeth.1817}, author = {Looger, Loren L} } @article {5160, title = {Selective esterase-ester pair for targeting small molecules with cellular specificity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 Mar 27}, pages = {4756-61}, abstract = {

Small molecules are important tools to measure and modulate intracellular signaling pathways. A longstanding limitation for using chemical compounds in complex tissues has been the inability to target bioactive small molecules to a specific cell class. Here, we describe a generalizable esterase-ester pair capable of targeted delivery of small molecules to living cells and tissue with cellular specificity. We used fluorogenic molecules to rapidly identify a small ester masking motif that is stable to endogenous esterases, but is efficiently removed by an exogenous esterase. This strategy allows facile targeting of dyes and drugs in complex biological environments to label specific cell types, illuminate gap junction connectivity, and pharmacologically perturb distinct subsets of cells. We expect this approach to have general utility for the specific delivery of many small molecules to defined cellular populations.

}, keywords = {Animals, Astrocytes, Biocatalysis, Cell Survival, Cells, Coculture Techniques, Esterases, Esters, Fluorescence, Fluorescent Dyes, Gap Junctions, Hela Cells, Hippocampus, Humans, Hydrolysis, Mice, Microscopy, Neurons, Organ Specificity, Permeability, Rats, Small Molecule Libraries}, issn = {1091-6490}, doi = {10.1073/pnas.1111943109}, author = {Tian, Lin and Yang, Yunlei and Wysocki, Laura M and Arnold, Alma C and Hu, Amy and Ravichandran, Balaji and Sternson, Scott M and Looger, Loren L and Lavis, Luke D} } @article {5480, title = {Sexual deprivation increases ethanol intake in Drosophila.}, journal = {Science}, volume = {335}, year = {2012}, month = {2012 Mar 16}, pages = {1351-5}, abstract = {

The brain{\textquoteright}s reward systems reinforce behaviors required for species survival, including sex, food consumption, and social interaction. Drugs of abuse co-opt these neural pathways, which can lead to addiction. Here, we used Drosophila melanogaster to investigate the relationship between natural and drug rewards. In males, mating increased, whereas sexual deprivation reduced, neuropeptide F (NPF) levels. Activation or inhibition of the NPF system in turn reduced or enhanced ethanol preference. These results thus link sexual experience, NPF system activity, and ethanol consumption. Artificial activation of NPF neurons was in itself rewarding and precluded the ability of ethanol to act as a reward. We propose that activity of the NPF-NPF receptor axis represents the state of the fly reward system and modifies behavior accordingly.

}, keywords = {Acetates, Addictive, Alcohol Drinking, Animal, Animals, Behavior, Cohort Studies, Conditioning (Psychology), Cues, Drosophila melanogaster, Drosophila Proteins, Ethanol, Female, Male, Neurons, Neuropeptide, Neuropeptides, Oleic Acids, Pheromones, Receptors, Reward, Sexual Behavior, TRPC Cation Channels}, issn = {1095-9203}, doi = {10.1126/science.1215932}, author = {Shohat-Ophir, G. and Kaun, K.R. and Azanchi, R. and Mohammed, H and Heberlein, U} } @article {4521, title = {Sexual experience affects ethanol intake in Drosophila through Neuropeptide F.}, journal = {Science}, volume = {335}, year = {2012}, month = {03/2012}, pages = {1351-5}, abstract = {

The brain{\textquoteright}s reward systems reinforce behaviors required for species survival, including sex, food consumption, and social interaction. Drugs of abuse co-opt these neural pathways, which can lead to addiction. Here, we used Drosophila melanogaster to investigate the relationship between natural and drug rewards. In males, mating increased, whereas sexual deprivation reduced, neuropeptide F (NPF) levels. Activation or inhibition of the NPF system in turn reduced or enhanced ethanol preference. These results thus link sexual experience, NPF system activity, and ethanol consumption. Artificial activation of NPF neurons was in itself rewarding and precluded the ability of ethanol to act as a reward. We propose that activity of the NPF{\textendash}NPF receptor axis represents the state of the fly reward system and modifies behavior accordingly.

}, doi = {10.1126/science.1215932 }, author = {Shohat-Ophir, G. and Kaun, K.R. and Azanchi, R. and Heberlein, U} } @article {68361, title = {Sexually Dimorphic BDNF Signaling Directs Sensory Innervation of the Mammary Gland}, journal = {Science}, volume = {338}, year = {2012}, month = {12/2012}, pages = {1357-1360}, abstract = {

Male and female mice differ in the neuronal patterns that serve the mammary glands. Yin Liu et al. (p. 1357) now describe how gonadal hormones drive development of distinct male and female sensory innervations. Although both male and female mammary glands develop their sensory innervation similarly in early embryogenesis, once the androgens take effect, the developmental trajectories diverge. By birth, the rich network of sensory neurons present in the female is absent in the male. Androgens cause a switch from expression of the full-length neurotrophin receptor TrkB to its truncated form, TrkB.T1, both of which are expressed on the neurons. In males, truncated TrkB.T1 sequesters brain-derived neurotrophic factor (BDNF) from further activity, whereas in females, full-length TrkB binds BDNF and supports neuronal development. Androgen-driven changes in receptor expression disrupt a neuronal signaling pathway and de-innervation. How neural circuits associated with sexually dimorphic organs are differentially assembled during development is unclear. Here, we report a sexually dimorphic pattern of mouse mammary gland sensory innervation and the mechanism of its formation. Brain-derived neurotrophic factor (BDNF), emanating from mammary mesenchyme and signaling through its receptor TrkB on sensory axons, is required for establishing mammary gland sensory innervation of both sexes at early developmental stages. Subsequently, in males, androgens promote mammary mesenchymal expression of a truncated form of TrkB, which prevents BDNF-TrkB signaling in sensory axons and leads to a rapid loss of mammary gland innervation independent of neuronal apoptosis. Thus, sex hormone regulation of a neurotrophic factor signal directs sexually dimorphic axonal growth and maintenance, resulting in generation of a sex-specific neural circuit.

}, doi = {10.1126/science.1228258}, url = {https://www.science.org/doi/abs/10.1126/science.1228258}, author = {Yin Liu and Michael Rutlin and Siyi Huang and Colleen A. Barrick and Fan Wang and Kevin R. Jones and Lino Tessarollo and David D. Ginty} } @article {5036, title = {A simple strategy for detecting moving objects during locomotion revealed by animal-robot interactions.}, journal = {Current Biology}, volume = {22}, year = {2012}, month = {2012 Jun 20}, pages = {1344-50}, abstract = {

An important role of visual systems is to detect nearby predators, prey, and potential mates [1], which may be distinguished in part by their motion. When an animal is at rest, an object moving in any direction may easily be detected by motion-sensitive visual circuits [2, 3]. During locomotion,\ however, this strategy is compromised because the observer must detect a moving object within the pattern of\ optic flow created by its own motion through the stationary\ background. However, objects that move creating back-to-front (regressive) motion may be unambiguously distinguished from stationary objects because forward locomotion creates only front-to-back (progressive) optic flow. Thus, moving animals should exhibit an enhanced sensitivity to regressively moving objects. We explicitly tested this hypothesis by constructing a simple fly-sized robot that was programmed to interact with a real fly. Our measurements indicate that whereas walking female flies freeze in response to a regressively moving object, they ignore a progressively moving one. Regressive motion salience also explains observations of behaviors exhibited by pairs of walking flies. Because the assumptions underlying the regressive motion salience hypothesis are general, we suspect that the behavior we have observed in Drosophila may be widespread among eyed, motile organisms.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2012.05.024}, author = {Zabala, Francisco and Polidoro, Peter and Robie, Alice A and Branson, Kristin and Perona, Pietro and Dickinson, Michael H} } @article {67279, title = {Simplified models for LHC new physics searches}, journal = {Journal of Physics G: Nuclear and Particle Physics}, volume = {39}, year = {2012}, month = {Jan-10-2012}, pages = {105005}, abstract = {

This document proposes a collection of simplified models relevant to the design of new-physics searches at the Large Hadron Collider (LHC) and the characterization of their results. Both ATLAS and CMS have already presented some results in terms of simplified models, and we encourage them to continue and expand this effort, which supplements both signature-based results and benchmark model interpretations. A simplified model is defined by an effective Lagrangian describing the interactions of a small number of new particles. Simplified models can equally well be described by a small number of masses and cross-sections. These parameters are directly related to collider physics observables, making simplified models a particularly effective framework for evaluating searches and a useful starting point for characterizing positive signals of new physics. This document serves as an official summary of the results from the {\textquoteright}Topologies for Early LHC Searches{\textquoteright} workshop, held at SLAC in September of 2010, the purpose of which was to develop a set of representative models that can be used to cover all relevant phase space in experimental searches. Particular emphasis is placed on searches relevant for the first ~50{\textendash}500 pb-1\ of data and those motivated by supersymmetric models. This note largely summarizes material posted at\ http://lhcnewphysics.org/, which includes simplified model definitions, Monte Carlo material, and supporting contacts within the theory community. We also comment on future developments that may be useful as more data is gathered and analyzed by the experiments.

}, issn = {0954-3899}, doi = {10.1088/0954-3899/39/10/105005}, url = {https://iopscience.iop.org/article/10.1088/0954-3899/39/10/105005}, author = {Alves, Daniele and Arkani-Hamed, Nima and Arora, Sanjay and Bai, Yang and Baumgart, Matthew and Berger, Joshua and Buckley, Matthew and Butler, Bart and Chang, Spencer and Cheng, Hsin-Chia and Cheung, Clifford and Chivukula, R Sekhar and Cho, Won Sang and Cotta, Randy and D{\textquoteright}Alfonso, Mariarosaria and Hedri, Sonia El and Essig, Rouven and Evans, Jared A and Fitzpatrick, Liam and Fox, Patrick and Franceschini, Roberto and Freitas, Ayres and Gainer, James S and Gershtein, Yuri and Gray, Richard and Gregoire, Thomas and Gripaios, Ben and Gunion, Jack and Han, Tao and Haas, Andy and Hansson, Per and Hewett, JoAnne and Hits, Dmitry and Hubisz, Jay and Izaguirre, Eder and Kaplan, Jared and Katz, Emanuel and Kilic, Can and Kim, Hyung-Do and Kitano, Ryuichiro and Koay, Sue Ann and Ko, Pyungwon and Krohn, David and Kuflik, Eric and Lewis, Ian and Lisanti, Mariangela and Liu, Tao and Liu, Zhen and Lu, Ran and Luty, Markus and Meade, Patrick and Morrissey, David and Mrenna, Stephen and Nojiri, Mihoko and Okui, Takemichi and Padhi, Sanjay and Papucci, Michele and Park, Michael and Park, Myeonghun and Perelstein, Maxim and Peskin, Michael and Phalen, Daniel and Rehermann, Keith and Rentala, Vikram and Roy, Tuhin and Ruderman, Joshua T and Sanz, Veronica and Schmaltz, Martin and Schnetzer, Stephen and Schuster, Philip and Schwaller, Pedro and Schwartz, Matthew D and Schwartzman, Ariel and Shao, Jing and Shelton, Jessie and Shih, David and Shu, Jing and Silverstein, Daniel and Simmons, Elizabeth and Somalwar, Sunil and Spannowsky, Michael and Spethmann, Christian and Strassler, Matthew and Su, Shufang and Tait, Tim and Thomas, Brooks and Thomas, Scott and Toro, Natalia and Volansky, Tomer and Wacker, Jay and Waltenberger, Wolfgang and Yavin, Itay and Yu, Felix and Zhao, Yue and Zurek, Kathryn} } @article {46725, title = {Single-mRNA counting using fluorescent in situ hybridization in budding yeast.}, journal = {Nature Protocols}, volume = {7}, year = {2012}, month = {2012 Feb 2}, pages = {408-19}, abstract = {

Fluorescent in situ hybridization (FISH) allows the quantification of single mRNAs in budding yeast using fluorescently labeled single-stranded DNA probes, a wide-field epifluorescence microscope and a spot-detection algorithm. Fixed yeast cells are attached to coverslips and hybridized with a mixture of FISH probes, each conjugated to several fluorescent dyes. Images of cells are acquired in 3D and maximally projected for single-molecule analysis. Diffraction-limited labeled mRNAs are observed as bright fluorescent spots and can be quantified using a spot-detection algorithm. FISH preserves the spatial distribution of cellular RNA distribution within the cell and the stochastic fluctuations in individual cells that can lead to phenotypic differences within a clonal population. This information, however, is lost if the RNA content is measured on a population of cells by using reverse transcriptase PCR, microarrays or high-throughput sequencing. The FISH procedure and image acquisition described here can be completed in 3 d.

}, keywords = {Algorithms, Antisense Elements (Genetics), In Situ Hybridization, Fluorescence, RNA, Fungal, RNA, Messenger, Saccharomyces cerevisiae}, issn = {1750-2799}, doi = {10.1038/nprot.2011.451}, author = {Trcek, Tatjana and Chao, Jeffrey A and Larson, Daniel R and Park, Hye Yoon and Zenklusen, Daniel and Shenoy, Shailesh M and Singer, Robert H} } @article {68485, title = {SnapShot: Optical control and imaging of brain activity.}, journal = {Cell}, volume = {149}, year = {2012}, month = {06/2012}, pages = {1650-1650.e2}, abstract = {

No abstract available.

}, keywords = {Animals, Brain, Microscopy, Fluorescence, Molecular Imaging, Optics and Photonics}, issn = {1097-4172}, doi = {10.1016/j.cell.2012.06.009}, author = {Richard Sun, X and Giovannucci, Andrea and Sgro, Allyson E and Wang, Samuel S-H} } @article {6504, title = {Solitary and gregarious locusts differ in circadian rhythmicity of a visual output neuron.}, journal = {Journal of BiologicalRrhythms}, volume = {27}, year = {2012}, month = {2012 Jun}, pages = {196-205}, abstract = {

Locusts demonstrate remarkable phenotypic plasticity driven by changes in population density. This density dependent phase polyphenism is associated with many physiological, behavioral, and morphological changes, including observations that cryptic solitarious (solitary-reared) individuals start to fly at dusk, whereas gregarious (crowd-reared) individuals are day-active. We have recorded for 24-36 h, from an identified visual output neuron, the descending contralateral movement detector (DCMD) of Schistocerca gregaria in solitarious and gregarious animals. DCMD signals impending collision and participates in flight avoidance maneuvers. The strength of DCMD{\textquoteright}s response to looming stimuli, characterized by the number of evoked spikes and peak firing rate, varies approximately sinusoidally with a period close to 24 h under constant light in solitarious locusts. In gregarious individuals the 24-h pattern is more complex, being modified by secondary ultradian rhythms. DCMD{\textquoteright}s strongest responses occur around expected dusk in solitarious locusts but up to 6 h earlier in gregarious locusts, matching the times of day at which locusts of each type are most active. We thus demonstrate a neuronal correlate of a temporal shift in behavior that is observed in gregarious locusts. Our ability to alter the nature of a circadian rhythm by manipulating the rearing density of locusts under identical light-dark cycles may provide important tools to investigate further the mechanisms underlying diurnal rhythmicity.

}, keywords = {Animal, Animals, Behavior, Biological, Circadian Rhythm, Female, Grasshoppers, Habituation, Male, Models, Neurons, Ocular, Phenotype, Psychophysiologic, Sense Organs, Social Behavior, Time Factors, Vision, Visual Fields}, issn = {1552-4531}, doi = {10.1177/0748730412440860}, author = {Gaten, Edward and Huston, Stephen J and Dowse, Harold B and Matheson, Tom} } @article {46732, title = {Spatial arrangement of an RNA zipcode identifies mRNAs under post-transcriptional control.}, journal = {Genes \& Development}, volume = {26}, year = {2012}, month = {2012 Jan 1}, pages = {43-53}, abstract = {

How RNA-binding proteins recognize specific sets of target mRNAs remains poorly understood because current approaches depend primarily on sequence information. In this study, we demonstrate that specific recognition of messenger RNAs (mRNAs) by RNA-binding proteins requires the correct spatial positioning of these sequences. We characterized both the cis-acting sequence elements and the spatial restraints that define the mode of RNA binding of the zipcode-binding protein 1 (ZBP1/IMP1/IGF2BP1) to the β-actin zipcode. The third and fourth KH (hnRNP K homology) domains of ZBP1 specifically recognize a bipartite RNA element comprised of a 5{\textquoteright} element (CGGAC) followed by a variable 3{\textquoteright} element (C/A-CA-C/U) that must be appropriately spaced. Remarkably, the orientation of these elements is interchangeable within target transcripts bound by ZBP1. The spatial relationship of this consensus binding site identified conserved transcripts that were verified to associate with ZBP1 in vivo. The dendritic localization of one of these transcripts, spinophilin, was found to be dependent on both ZBP1 and the RNA elements recognized by ZBP1 KH34.

}, keywords = {Actins, Animals, Base Sequence, Cells, Cultured, Consensus Sequence, Dendrites, Gene Expression Regulation, Glycoproteins, Humans, Ligands, Mice, Microfilament Proteins, Models, Molecular, Molecular Sequence Data, Nerve Tissue Proteins, Protein Binding, Protein Structure, Tertiary, RNA, Messenger}, issn = {1549-5477}, doi = {10.1101/gad.177428.111}, author = {Patel, Vivek L and Mitra, Somdeb and Harris, Richard and Buxbaum, Adina R and Lionnet, Timoth{\'e}e and Brenowitz, Michael and Girvin, Mark and Levy, Matthew and Almo, Steven C and Singer, Robert H and Chao, Jeffrey A} } @article {6299, title = {The structural basis for the narrow substrate specificity of an acetyl esterase from Thermotoga maritima.}, journal = {Biochimica et Biophysica Acta}, volume = {1824}, year = {2012}, month = {2012 Sep}, pages = {1024-30}, abstract = {

Acetyl esterases from carbohydrate esterase family 7 exhibit unusual substrate specificity. These proteins catalyze the cleavage of disparate acetate esters with high efficiency, but are unreactive to larger acyl groups. The structural basis for this distinct selectivity profile is unknown. Here, we investigate a thermostable acetyl esterase (TM0077) from Thermotoga maritima using evolutionary relationships, structural information, fluorescent kinetic measurements, and site directed mutagenesis. We measured the kinetic and structural determinants for this specificity using a diverse series of small molecule enzyme substrates, including novel fluorogenic esters. These experiments identified two hydrophobic plasticity residues (Pro228, and Ile276) surrounding the nucleophilic serine that impart this specificity of TM0077 for small, straight-chain esters. Substitution of these residues with alanine imparts broader specificity to TM0077 for the hydrolysis of longer and bulkier esters. Our results suggest the specificity of acetyl esterases have been finely tuned by evolution to catalyze the removal of acetate groups from diverse substrates, but can be modified by focused amino acid substitutions to yield enzymes capable of cleaving larger ester functionalities.

}, keywords = {Acetylesterase, Bacterial Proteins, Binding Sites, Catalysis, Esters, Fluoresceins, Fluorescent Dyes, Hydrolysis, Kinetics, Models, Molecular, Mutagenesis, Site-Directed, Substrate Specificity, Thermotoga maritima}, issn = {0006-3002}, doi = {10.1016/j.bbapap.2012.05.009}, author = {Hedge, Matthew K and Gehring, Alexandra M and Adkins, Chinessa T and Weston, Leigh A and Lavis, Luke D and Johnson, R Jeremy} } @article {5149, title = {The structure of purified kinetochores reveals multiple microtubule-attachment sites.}, journal = {Nature Structural \& Molecular Biology}, volume = {19}, year = {2012}, month = {2012 Aug 12}, pages = {925-9}, abstract = {

Chromosomes must be accurately partitioned to daughter cells to prevent aneuploidy, a hallmark of many tumors and birth defects. Kinetochores are the macromolecular machines that segregate chromosomes by maintaining load-bearing attachments to the dynamic tips of microtubules. Here, we present the structure of isolated budding-yeast kinetochore particles, as visualized by EM and electron tomography of negatively stained preparations. The kinetochore appears as an \ 126-nm particle containing a large central hub surrounded by multiple outer globular domains. In the presence of microtubules, some particles also have a ring that encircles the microtubule. Our data, showing that kinetochores bind to microtubules via multivalent attachments, lay the foundation to uncover the key mechanical and regulatory mechanisms by which kinetochores control chromosome segregation and cell division.

}, issn = {1545-9985}, doi = {10.1038/nsmb.2358}, author = {Gonen, Shane and Akiyoshi, Bungo and Iadanza, Matthew G and Shi, Dan and Duggan, Nicole and Biggins, Sue and Gonen, Tamir} } @article {6300, title = {A subset of dopamine neurons signals reward for odour memory in Drosophila.}, journal = {Nature}, volume = {488}, year = {2012}, month = {2012 Aug 23}, pages = {512-6}, abstract = {

Animals approach stimuli that predict a pleasant outcome. After the paired presentation of an odour and a reward, Drosophila melanogaster can develop a conditioned approach towards that odour. Despite recent advances in understanding the neural circuits for associative memory and appetitive motivation, the cellular mechanisms for reward processing in the fly brain are unknown. Here we show that a group of dopamine neurons in the protocerebral anterior medial (PAM) cluster signals sugar reward by transient activation and inactivation of target neurons in intact behaving flies. These dopamine neurons are selectively required for the reinforcing property of, but not a reflexive response to, the sugar stimulus. In vivo calcium imaging revealed that these neurons are activated by sugar ingestion and the activation is increased on starvation. The output sites of the PAM neurons are mainly localized to the medial lobes of the mushroom bodies (MBs), where appetitive olfactory associative memory is formed. We therefore propose that the PAM cluster neurons endow a positive predictive value to the odour in the MBs. Dopamine in insects is known to mediate aversive reinforcement signals. Our results highlight the cellular specificity underlying the various roles of dopamine and the importance of spatially segregated local circuits within the MBs.

}, keywords = {Animals, Appetitive Behavior, Calcium Signaling, Dendrites, Dopamine, Dopaminergic Neurons, Drosophila melanogaster, Memory, Mushroom Bodies, Odors, Reward, Smell}, issn = {1476-4687}, doi = {10.1038/nature11304}, author = {Liu, Chang and Placais, Pierre-Yves and Yamagata, Nobuhiro and Pfeiffer, Barret D and Aso, Yoshinori and Friedrich, Anja B and Siwanowicz, Igor and Rubin, Gerald M and Preat, Thomas and Tanimoto, Hiromu} } @article {4892, title = {Superpenetration optical microscopy by iterative multiphoton adaptive compensation technique.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 May 29}, pages = {8434-9}, abstract = {

Biological tissues are rarely transparent, presenting major challenges for deep tissue optical microscopy. The achievable imaging depth is fundamentally limited by wavefront distortions caused by aberration and random scattering. Here, we report an iterative wavefront compensation technique that takes advantage of the nonlinearity of multiphoton signals to determine and compensate for these distortions and to focus light inside deep tissues. Different from conventional adaptive optics methods, this technique can rapidly measure highly complicated wavefront distortions encountered in deep tissue imaging and provide compensations for not only aberration but random scattering. The technique is tested with a variety of highly heterogeneous biological samples including mouse brain tissue, skull, and lymph nodes. We show that high quality three-dimensional imaging can be realized at depths beyond the reach of conventional multiphoton microscopy and adaptive optics methods, albeit over restricted distances for a given correction. Moreover, the required laser excitation power can be greatly reduced in deep tissues, deviating from the power requirement of ballistic light excitation and thus significantly reducing photo damage to the biological tissue.

}, issn = {1091-6490}, doi = {10.1073/pnas.1119590109}, author = {Tang, Jianyong and Germain, Ronald N and Cui, Meng} } @article {6175, title = {Super-resolution using sparse representations over learned dictionaries: reconstruction of brain structure using electron microscopy.}, journal = {arXiv.org }, year = {2012}, month = {2012 Oct}, abstract = {

A central problem in neuroscience is reconstructing neuronal circuits on the synapse level. Due to a wide range of scales in brain architecture such reconstruction requires imaging that is both high-resolution and high-throughput. Existing electron microscopy (EM) techniques possess required resolution in the lateral plane and either high-throughput or high depth resolution but not both. Here, we exploit recent advances in unsupervised learning and signal processing to obtain high depth-resolution EM images computationally without sacrificing throughput. First, we show that the brain tissue can be represented as a sparse linear combination of localized basis functions that are learned using high-resolution datasets. We then develop compressive sensing-inspired techniques that can reconstruct the brain tissue from very few (typically 5) tomographic views of each section. This enables tracing of neuronal processes and, hence, high throughput reconstruction of neural circuits on the level of individual synapses.

}, author = {Hu, T and Nunez-Iglesias, J and Vitaladevuni, S. and Scheffer, L. and Xu, S and Bolorizadeh, M and Hess, H and Fetter, R and Chklovskii, D} } @article {6506, title = {A survey of 6,300 genomic fragments for cis-regulatory activity in the imaginal discs of Drosophila melanogaster.}, journal = {Cell Reports}, volume = {2}, year = {2012}, month = {2012 Oct 25}, pages = {1014-24}, abstract = {

Over 6,000 fragments from the genome of Drosophila melanogaster were analyzed for their ability to drive expression of GAL4 reporter genes in the third-instar larval imaginal discs. About 1,200 reporter genes drove expression in the eye, antenna, leg, wing, haltere, or genital imaginal discs. The patterns ranged from large regions to individual cells. About 75\% of the active fragments drove expression in multiple discs; 20\% were expressed in ventral, but not dorsal, discs (legs, genital, and antenna), whereas \~{}23\% were expressed in dorsal but not ventral discs (wing, haltere, and eye). Several patterns, for example, within the leg chordotonal organ, appeared a surprisingly large\ number of times. Unbiased searches for DNA sequence motifs suggest candidate transcription factors that may regulate enhancers with shared activities. Together, these expression patterns provide a valuable resource to the community and offer a broad overview of how transcriptional regulatory information is distributed in the Drosophila genome.

}, keywords = {Animals, Arthropod Antennae, Blastodisc, Databases, Drosophila melanogaster, Drosophila Proteins, Eye, Factual, Genes, Genetically Modified, Genome, Imaginal Discs, Regulatory Elements, Reporter, Transcription Factors, Transcriptional, Wing}, issn = {2211-1247}, doi = {10.1016/j.celrep.2012.09.010}, author = {Jory, Aur{\'e}lie and Estella, Carlos and Giorgianni, Matt W and Slattery, Matthew and Laverty, Todd R and Rubin, Gerald M and Mann, Richard S} } @article {5922, title = {Synaptic amplification by dendritic spines enhances input cooperativity.}, journal = {Nature}, volume = {491}, year = {2012}, month = {2012 Nov 22}, pages = {599-602}, abstract = {

Dendritic spines are the nearly ubiquitous site of excitatory synaptic input onto neurons and as such are critically positioned to influence diverse aspects of neuronal signalling. Decades of theoretical studies have proposed that spines may function as highly effective and modifiable chemical and electrical compartments that regulate synaptic efficacy, integration and plasticity. Experimental studies have confirmed activity-dependent structural dynamics and biochemical compartmentalization by spines. However, there is a longstanding debate over the influence of spines on the electrical aspects of synaptic transmission and dendritic operation. Here we measure the amplitude ratio of spine head to parent dendrite voltage across a range of dendritic compartments and calculate the associated spine neck resistance (R(neck)) for spines at apical trunk dendrites in rat hippocampal CA1 pyramidal neurons. We find that R(neck) is large enough (\ 500 MΩ) to amplify substantially the spine head depolarization associated with a unitary synaptic input by \ 1.5- to \ 45-fold, depending on parent dendritic impedance. A morphologically realistic compartmental model capable of reproducing the observed spatial profile of the amplitude ratio indicates that spines provide a consistently high-impedance input structure throughout the dendritic arborization. Finally, we demonstrate that the amplification produced by spines encourages electrical interaction among coactive inputs through an R(neck)-dependent increase in spine head voltage-gated conductance activation. We conclude that the electrical properties of spines promote nonlinear dendritic processing and associated forms of plasticity and storage, thus fundamentally enhancing the computational capabilities of neurons.

}, keywords = {Animals, Dendritic Spines, Electric Impedance, Excitatory Postsynaptic Potentials, Male, Models, Neurological, Pyramidal Cells, Rats, Sprague-Dawley, Synapses, Wistar}, issn = {1476-4687}, doi = {10.1038/nature11554}, author = {Harnett, Mark T and Makara, Judit K and Spruston, Nelson and Kath, William L and Magee, Jeffrey C} } @article {46051, title = {Synaptic plasticity of NMDA receptors: mechanisms and functional implications.}, journal = {Current Opinion in Neurobiology}, volume = {22}, year = {2012}, month = {2012 Jun}, pages = {496-508}, abstract = {

Beyond their well-established role as triggers for LTP and LTD of fast synaptic transmission mediated by AMPA receptors, an expanding body of evidence indicates that NMDA receptors (NMDARs) themselves are also dynamically regulated and subject to activity-dependent long-term plasticity. NMDARs can significantly contribute to information transfer at synapses particularly during periods of repetitive activity. It is also increasingly recognized that NMDARs participate in dendritic synaptic integration and are critical for generating persistent activity of neural assemblies. Here we review recent advances on the mechanisms and functional consequences of NMDAR plasticity. Given the unique biophysical properties of NMDARs, synaptic plasticity of NMDAR-mediated transmission emerges as a particularly powerful mechanism for the fine tuning of information encoding and storage throughout the brain.

}, keywords = {Animals, Biophysics, Neuronal Plasticity, Receptors, N-Methyl-D-Aspartate, Synapses, Synaptic Transmission}, issn = {1873-6882}, doi = {10.1016/j.conb.2012.01.007}, author = {Hunt, David L and Castillo, Pablo E} } @article {5335, title = {Synergistic actions of metabotropic acetylcholine and glutamate receptors on the excitability of hippocampal CA1 pyramidal neurons.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {32}, year = {2012}, month = {2012 May 2}, pages = {6081-91}, abstract = {

A variety of neurotransmitters are responsible for regulating neural activity during different behavioral states. Unique responses to combinations of neurotransmitters provide a powerful mechanism by which neural networks could be differentially activated during a broad range of behaviors. Here, we show, using whole-cell recordings in rat hippocampal slices, that group I metabotropic glutamate receptors (mGluRs) and muscarinic acetylcholine receptors (mAChRs) synergistically increase the excitability of hippocampal CA1 pyramidal neurons by converting the post-burst afterhyperpolarization to an afterdepolarization via a rapidly reversible upregulation of Ca(v)2.3 R-type calcium channels. Coactivation of mAChRs and mGluRs also induced a long-lasting enhancement of the responses mediated by each receptor type. These results suggest that cooperative signaling via mAChRs and group I mGluRs could provide a mechanism by which cognitive processes may be modulated by conjoint activation of two separate neurotransmitter systems.

}, keywords = {Action Potentials, Animals, Calcium Channels, Cation Transport Proteins, Inbred C57BL, Knockout, Male, Metabotropic Glutamate, Mice, Muscarinic, Pyramidal Cells, R-Type, Rats, Receptors, Wistar}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.6519-11.2012}, author = {Park, Jin-Yong and Spruston, Nelson} } @article {43051, title = {Tandem fluorescent protein timers for in vivo analysis of protein dynamics.}, journal = {Nature Biotechnology}, volume = {30}, year = {2012}, month = {2012 Jun 24}, pages = {708-14}, abstract = {

The functional state of a cell is largely determined by the spatiotemporal organization of its proteome. Technologies exist for measuring particular aspects of protein turnover and localization, but comprehensive analysis of protein dynamics across different scales is possible only by combining several methods. Here we describe tandem fluorescent protein timers (tFTs), fusions of two single-color fluorescent proteins that mature with different kinetics, which we use to analyze protein turnover and mobility in living cells. We fuse tFTs to proteins in yeast to study the longevity, segregation and inheritance of cellular components and the mobility of proteins between subcellular compartments; to measure protein degradation kinetics without the need for time-course measurements; and to conduct high-throughput screens for regulators of protein turnover. Our experiments reveal the stable nature and asymmetric inheritance of nuclear pore complexes and identify regulators of N-end rule{\textendash}mediated protein degradation.

}, keywords = {Green Fluorescent Proteins, High-Throughput Screening Assays, Kinetics, Nuclear Pore, Protein Stability, Proteins, Proteolysis, Saccharomyces cerevisiae, Subcellular Fractions}, issn = {1546-1696}, doi = {10.1038/nbt.2281}, author = {Khmelinskii, Anton and Keller, Philipp J and Bartosik, Anna and Meurer, Matthias and Barry, Joseph D and Mardin, Balca R and Kaufmann, Andreas and Trautmann, Susanne and Wachsmuth, Malte and Pereira, Gislene and Huber, Wolfgang and Schiebel, Elmar and Knop, Michael} } @article {6778, title = {Target-specific output patterns are predicted by the distribution of regular-spiking and bursting pyramidal neurons in the subiculum.}, journal = {Hippocampus}, volume = {22}, year = {2012}, month = {2012 Apr}, pages = {693-706}, abstract = {

Pyramidal neurons in the subiculum project to a variety of cortical and subcortical areas in the brain to convey information processed in the hippocampus. Previous studies have shown that two groups of subicular pyramidal neurons{\textendash}regular-spiking and bursting neurons{\textendash}are distributed in an organized fashion along the proximal-distal axis, with more regular-spiking neurons close to CA1 (proximal) and more bursting neurons close to presubiculum (distal). Anatomically, neurons projecting to some targets are located more proximally along this axis, while others are located more distally. However, the relationship between the firing properties and the targets of subicular pyramidal neurons is not known. To study this relationship, we used in vivo injections of retrogradely transported fluorescent beads into each of nine different regions and conducted whole-cell current-clamp recordings from the bead-containing subicular neurons in acute brain slices. We found that subicular projections to each area were composed of a mixture of regular-spiking and bursting neurons. Neurons projecting to amygdala, lateral entorhinal cortex, nucleus accumbens, and medial/ventral orbitofrontal cortex were located primarily in the proximal subiculum and consisted mostly of regular-spiking neurons (\~{}80\%). By contrast, neurons projecting to medial EC, presubiculum, retrosplenial cortex, and ventromedial hypothalamus were located primarily in the distal subiculum and consisted mostly of bursting neurons (\~{}80\%). Neurons projecting to a thalamic nucleus were located in the middle portion of subiculum, and their probability of bursting was close to 50\%. Thus, the fraction of bursting neurons projecting to each target region was consistent with the known distribution of regular-spiking and bursting neurons along the proximal-distal axis of the subiculum. Variation in the distribution of regular-spiking and bursting neurons suggests that different types of information are conveyed from the subiculum to its various targets.

}, keywords = {Action Potentials, Animals, Biophysical Phenomena, CA1 Region, CA3 Region, Efferent Pathways, Electrophysiological Phenomena, Hippocampal, Hippocampus, Male, Patch-Clamp Techniques, Pyramidal Cells, Rats, Wistar}, issn = {1098-1063}, doi = {10.1002/hipo.20931}, author = {Kim, Yujin and Spruston, Nelson} } @article {4632, title = {Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 Apr 3}, pages = {5311-5}, abstract = {

Previous implementations of structured-illumination microscopy (SIM) were slow or designed for one-color excitation, sacrificing two unique and extremely beneficial aspects of light microscopy: live-cell imaging in multiple colors. This is especially unfortunate because, among the resolution-extending techniques, SIM is an attractive choice for live-cell imaging; it requires no special fluorophores or high light intensities to achieve twice diffraction-limited resolution in three dimensions. Furthermore, its wide-field nature makes it light-efficient and decouples the acquisition speed from the size of the lateral field of view, meaning that high frame rates over large volumes are possible. Here, we report a previously undescribed SIM setup that is fast enough to record 3D two-color datasets of living whole cells. Using rapidly programmable liquid crystal devices and a flexible 2D grid pattern algorithm to switch between excitation wavelengths quickly, we show volume rates as high as 4 s in one color and 8.5 s in two colors over tens of time points. To demonstrate the capabilities of our microscope, we image a variety of biological structures, including mitochondria, clathrin-coated vesicles, and the actin cytoskeleton, in either HeLa cells or cultured neurons.

}, issn = {1091-6490}, doi = {10.1073/pnas.1119262109}, author = {Fiolka, Reto and Shao, Lin and Rego, E Hesper and Davidson, Michael W and Gustafsson, Mats G L} } @article {5482, title = {Tissue-specific activation of a single gustatory receptor produces opposing behavioral responses in Drosophila.}, journal = {Genetics}, volume = {192}, year = {2012}, month = {2012 Oct}, pages = {521-32}, abstract = {

Understanding sensory systems that perceive environmental inputs and neural circuits that select appropriate motor outputs is essential for studying how organisms modulate behavior and make decisions necessary for survival. Drosophila melanogaster oviposition is one such important behavior, in which females evaluate their environment and choose to lay eggs on substrates they may find aversive in other contexts. We employed neurogenetic techniques to characterize neurons that influence the choice between repulsive positional and attractive egg-laying responses toward the bitter-tasting compound lobeline. Surprisingly, we found that neurons expressing Gr66a, a gustatory receptor normally involved in avoidance behaviors, receive input for both attractive and aversive preferences. We hypothesized that these opposing responses may result from activation of distinct Gr66a-expressing neurons. Using tissue-specific rescue experiments, we found that Gr66a-expressing neurons on the legs mediate positional aversion. In contrast, pharyngeal taste cells mediate the egg-laying attraction to lobeline, as determined by analysis of mosaic flies in which subsets of Gr66a neurons were silenced. Finally, inactivating mushroom body neurons disrupted both aversive and attractive responses, suggesting that this brain structure is a candidate integration center for decision-making during Drosophila oviposition. We thus define sensory and central neurons critical to the process by which flies decide where to lay an egg. Furthermore, our findings provide insights into the complex nature of gustatory perception in Drosophila. We show that tissue-specific activation of bitter-sensing Gr66a neurons provides one mechanism by which the gustatory system differentially encodes aversive and attractive responses, allowing the female fly to modulate her behavior in a context-dependent manner.

}, issn = {1943-2631}, doi = {10.1534/genetics.112.142455}, author = {Joseph, Ryan M and Heberlein, Ulrike} } @article {6301, title = {A toolbox of Cre-dependent optogenetic transgenic mice for light-induced activation and silencing.}, journal = {Nature Neuroscience}, volume = {15}, year = {2012}, month = {2012 May}, pages = {793-802}, abstract = {

Cell type-specific expression of optogenetic molecules allows temporally precise manipulation of targeted neuronal activity. Here we present a toolbox of four knock-in mouse lines engineered for strong, Cre-dependent expression of channelrhodopsins ChR2-tdTomato and ChR2-EYFP, halorhodopsin eNpHR3.0 and archaerhodopsin Arch-ER2. All four transgenes mediated Cre-dependent, robust activation or silencing of cortical pyramidal neurons in vitro and in vivo upon light stimulation, with ChR2-EYFP and Arch-ER2 demonstrating light sensitivity approaching that of in utero or virally transduced neurons. We further show specific photoactivation of parvalbumin-positive interneurons in behaving ChR2-EYFP reporter mice. The robust, consistent and inducible nature of our ChR2 mice represents a significant advance over previous lines, and the Arch-ER2 and eNpHR3.0 mice are to our knowledge the first demonstration of successful conditional transgenic optogenetic silencing. When combined with the hundreds of available Cre driver lines, this optimized toolbox of reporter mice will enable widespread investigations of neural circuit function with unprecedented reliability and accuracy.

}, keywords = {Action Potentials, Animals, Archaeal Proteins, Brain, Electroporation, Halorhodopsins, Integrases, Light, Luminescent Proteins, Mice, Neurogenesis, Neurons, Optics and Photonics, Proteins, Rhodopsin, Transgenic, Wakefulness}, issn = {1546-1726}, doi = {10.1038/nn.3078}, author = {Madisen, Linda and Mao, Tianyi and Koch, Henner and Zhuo, Jia-min and Berenyi, Antal and Fujisawa, Shigeyoshi and Hsu, Yun-Wei A and Garcia, Alfredo J and Gu, Xuan and Zanella, Sebastien and Kidney, Jolene and Gu, Hong and Mao, Yimei and Hooks, Bryan M and Boyden, Edward S and Buzs{\'a}ki, Gy{\"o}rgy and Ramirez, Jan Marino and Jones, Allan R and Svoboda, Karel and Han, Xue and Turner, Eric E and Zeng, Hongkui} } @article {46785, title = {TrakEM2 software for neural circuit reconstruction.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012}, pages = {e38011}, abstract = {

A key challenge in neuroscience is the expeditious reconstruction of neuronal circuits. For model systems such as Drosophila and C. elegans, the limiting step is no longer the acquisition of imagery but the extraction of the circuit from images. For this purpose, we designed a software application, TrakEM2, that addresses the systematic reconstruction of neuronal circuits from large electron microscopical and optical image volumes. We address the challenges of image volume composition from individual, deformed images; of the reconstruction of neuronal arbors and annotation of synapses with fast manual and semi-automatic methods; and the management of large collections of both images and annotations. The output is a neural circuit of 3d arbors and synapses, encoded in NeuroML and other formats, ready for analysis.

}, keywords = {Animals, Models, Neurological, Nerve Net, Neuroimaging, Neurons, Software, Synapses, Synaptic Transmission}, issn = {1932-6203}, doi = {10.1371/journal.pone.0038011}, author = {Cardona, Albert and Saalfeld, Stephan and Schindelin, Johannes and Arganda-Carreras, Ignacio and Preibisch, Stephan and Longair, Mark and Tomancak, Pavel and Hartenstein, Volker and Douglas, Rodney J} } @article {5684, title = {TrakEM2 software for neural circuit reconstruction.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012}, pages = {e38011}, abstract = {

A key challenge in neuroscience is the expeditious reconstruction of neuronal circuits. For model systems such as Drosophila and C. elegans, the limiting step is no longer the acquisition of imagery but the extraction of the circuit from images. For this purpose, we designed a software application, TrakEM2, that addresses the systematic reconstruction of neuronal circuits from large electron microscopical and optical image volumes. We address the challenges of image volume composition from individual, deformed images; of the reconstruction of neuronal arbors and annotation of synapses with fast manual and semi-automatic methods; and the management of large collections of both images and annotations. The output is a neural circuit of 3d arbors and synapses, encoded in NeuroML and other formats, ready for analysis.

}, keywords = {Animals, Models, Nerve Net, Neuroimaging, Neurological, Neurons, Software, Synapses, Synaptic Transmission}, issn = {1932-6203}, doi = {10.1371/journal.pone.0038011}, author = {Cardona, Albert and Saalfeld, Stephan and Schindelin, Johannes and Arganda-Carreras, Ignacio and Preibisch, Stephan and Longair, Mark and Tomancak, Pavel and Hartenstein, Volker and Douglas, Rodney J} } @article {46724, title = {Transcription goes digital.}, journal = {EMBO Reports}, volume = {13}, year = {2012}, month = {2012 Apr 2}, pages = {313-21}, abstract = {

Transcription is a complex process that integrates the state of the cell and its environment to generate adequate responses for cell fitness and survival. Recent microscopy experiments have been able to monitor transcription from single genes in individual cells. These observations have revealed two striking features: transcriptional activity can vary markedly from one cell to another, and is subject to large changes over time, sometimes within minutes. How the chromatin structure, transcription machinery assembly and signalling networks generate such patterns is still unclear. In this review, we present the techniques used to investigate transcription from single genes, introduce quantitative modelling tools, and discuss transcription mechanisms and their implications for gene expression regulation.

}, keywords = {Animals, Gene Expression Regulation, Genes, Humans, Models, Genetic, Stochastic Processes, Transcription, Genetic}, issn = {1469-3178}, doi = {10.1038/embor.2012.31}, author = {Lionnet, Timoth{\'e}e and Singer, Robert H} } @article {6518, title = {Transcription initiation by human RNA polymerase II visualized at single-molecule resolution.}, journal = {Genes \& Development}, volume = {26}, year = {2012}, month = {2012 Aug 1}, pages = {1691-702}, abstract = {

Forty years of classical biochemical analysis have identified the molecular players involved in initiation of transcription by eukaryotic RNA polymerase II (Pol II) and largely assigned their functions. However, a dynamic picture of Pol II transcription initiation and an understanding of the mechanisms of its regulation have remained elusive due in part to inherent limitations of conventional ensemble biochemistry. Here we have begun to dissect promoter-specific transcription initiation directed by a reconstituted human Pol II system at single-molecule resolution using fluorescence video-microscopy. We detected several stochastic rounds of human Pol II transcription from individual DNA templates, observed attenuation of transcription by promoter mutations, observed enhancement of transcription by activator Sp1, and correlated the transcription signals with real-time interactions of holo-TFIID molecules at individual DNA templates. This integrated single-molecule methodology should be applicable to studying other complex biological processes.

}, keywords = {Fluorescence, Genetic, Humans, Microscopy, Molecular Imaging, Mutation, Promoter Regions, RNA Polymerase II, Sp1 Transcription Factor, Transcription, Transcription Factor TFIID, Video}, issn = {1549-5477}, doi = {10.1101/gad.194936.112}, author = {Revyakin, Andrey and Zhang, Zhengjian and Coleman, Robert A and Li, Yan and Inouye, Carla and Lucas, Julian K and Park, Sang-Ryul and Chu, Steven and Tjian, Robert} } @article {5339, title = {Transcriptional control of cell fate specification: lessons from the fly retina.}, journal = {Current Topics in Developmental Biology}, volume = {98}, year = {2012}, month = {2012}, pages = {259-76}, abstract = {

It is now widely recognized that as cells of developing tissues transition through successive states of decreasing pluripotency into a state of terminal differentiation, they undergo significant changes in their gene expression profiles. Interestingly, these successive states of increasing differentiation are marked by the spatially and temporally restricted expression of sets of transcription factors. Each wave of transcription factors not only signals the arrival of a given stage in cellular differentiation, but it is also necessary for the activation of the next set of transcription factors, creating the appearance of a smooth, directed, and deterministic genetic program of cellular differentiation. Until recently, however, it was largely unknown which genes, besides each other, these transcription factors were activating. Thus, the molecular definition of any given step of differentiation, and how it gave rise to the following step remained unclear. Recent advances in transcriptomics, bioinformatics, and molecular genetics resulted in the identification of numerous transcription factor target genes (TGs). These advances have opened the door to using similar approaches in developmental biology to understand what the transcriptional cascades of cellular differentiation might be. Using the development of the Drosophila eye as a model system, we discuss the role of transcription factors and their TGs in cell fate specification and terminal differentiation.

}, keywords = {Animals, Cell Lineage, Developmental, Drosophila melanogaster, Gene Expression Regulation, Genetic, Humans, Retina, Signal Transduction, Transcription}, issn = {1557-8933}, doi = {10.1016/B978-0-12-386499-4.00010-0}, author = {Quan, Xiao-jiang and Ramaekers, Ariane and Hassan, Bassem A} } @article {68820, title = {Transcriptional signature of accessory cells in the lateral line, using the Tnk1bp1:EGFP transgenic zebrafish line}, journal = {BMC developmental biology}, volume = {12}, year = {2012}, month = {01/2012}, pages = {6}, abstract = {

Background:\ Because of the structural and molecular similarities between the two systems, the lateral line, a fish and amphibian specific sensory organ, has been widely used in zebrafish as a model to study the development/biology of neuroepithelia of the inner ear. Both organs have hair cells, which are the mechanoreceptor cells, and supporting cells providing other functions to the epithelium. In most vertebrates (excluding mammals), supporting cells comprise a pool of progenitors that replace damaged or dead hair cells. However, the lack of regenerative capacity in mammals is the single leading cause for acquired hearing disorders in humans.

Results:\ In an effort to understand the regenerative process of hair cells in fish, we characterized and cloned an egfp transgenic stable fish line that trapped tnks1bp1, a highly conserved gene that has been implicated in the maintenance of telomeres{\textquoteright} length. We then used this Tg(tnks1bp1:EGFP) line in a FACsorting strategy combined with microarrays to identify new molecular markers for supporting cells.

Conclusions:\ We present a Tg(tnks1bp1:EGFP) stable transgenic line, which we used to establish a transcriptional profile of supporting cells in the zebrafish lateral line. Therefore we are providing a new set of markers specific for supporting cells as well as candidates for functional analysis of this important cell type. This will prove to be a valuable tool for the study of regeneration in the lateral line of zebrafish in particular and for regeneration of neuroepithelia in general.

}, doi = {10.1186/1471-213X-12-6}, author = {Behra, Martine and Gallardo, Viviana and Bradsher, John and Torrado, Aranza and Elkahloun, Abdel and Idol, Jennifer and Sheehy, Jessica and Zonies, Seth and Xu, Lisha and Shaw, Kenna and Satou, Chie and Higashijima, Shin-Ichi and Weinstein, Brant and Burgess, Shawn} } @article {46731, title = {Transgenic expression of ZBP1 in neurons suppresses cocaine-associated conditioning.}, journal = {Learning \& Memory}, volume = {19}, year = {2012}, month = {2012 Feb}, pages = {35-42}, abstract = {

To directly address whether regulating mRNA localization can influence animal behavior, we created transgenic mice that conditionally express Zipcode Binding Protein 1 (ZBP1) in a subset of neurons in the brain. ZBP1 is an RNA-binding protein that regulates the localization, as well as translation and stability of target mRNAs in the cytoplasm. We took advantage of the absence of ZBP1 expression in the mature brain to examine the effect of expressing ZBP1 on animal behavior. We constructed a transgene conditionally expressing a GFP-ZBP1 fusion protein in a subset of forebrain neurons and compared cocaine-cued place conditioning in these mice versus noninduced littermates. Transgenic ZBP1 expression resulted in impaired place conditioning relative to nonexpressing littermates, and acutely repressing expression of the transgene restored normal cocaine conditioning. To gain insight into the molecular changes that accounted for this change in behavior, we identified mRNAs that specifically immunoprecipitated with transgenic ZBP1 protein from the brains of these mice. These data suggest that RNA-binding proteins can be used as a tool to identify the post-transcriptional regulation of gene expression in the establishment and function of neural circuits involved in addiction behaviors.

}, keywords = {Animals, Brain, Cocaine, Conditioning (Psychology), Cues, DNA-Binding Proteins, Dopamine Uptake Inhibitors, Doxycycline, Gene Expression Regulation, Green Fluorescent Proteins, Immunoprecipitation, Male, Mice, Mice, Transgenic, Microarray Analysis, Neurons, RNA, Messenger, RNA-Binding Proteins}, issn = {1549-5485}, doi = {10.1101/lm.024471.111}, author = {Lapidus, Kyle A B and Nwokafor, Chiso and Scott, Daniel and Baroni, Timothy E and Tenenbaum, Scott A and Hiroi, Noboru and Singer, Robert H and Czaplinski, Kevin} } @article {4973, title = {Transvection is common throughout the Drosophila genome.}, journal = {Genetics}, volume = {191}, year = {2012}, month = {2012 May 29}, pages = {1129-41}, abstract = {

Higher-order genome organization plays an important role in transcriptional regulation. In Drosophila, somatic pairing of homologous chromosomes can lead to transvection, by which the regulatory region of a gene can influence transcription in trans. We observe transvection between transgenes inserted at commonly used phiC31 integration sites in the Drosophila genome. When two transgenes that carry endogenous regulatory elements driving the expression of either LexA or GAL4 are inserted at the same integration site and paired, the enhancer of one transgene can drive or repress expression of the paired transgene. These transvection effects depend on compatibility between regulatory elements and are often restricted to a subset of cell types within a given expression pattern. We further show that activated UAS-transgenes can also drive transcription in trans. We discuss the implication of these findings for 1) understanding the molecular mechanisms that underlie transvection and 2) the design of experiments that utilize site-specific integration.

}, issn = {1943-2631}, doi = {10.1534/genetics.112.140475}, author = {Mellert, David J and Truman, James W} } @article {4598, title = {Triggering a cell shape change by exploiting preexisting actomyosin contractions.}, journal = {Science}, volume = {335}, year = {2012}, month = {2012 Mar 9}, pages = {1232-5}, abstract = {

Apical constriction changes cell shapes, driving critical morphogenetic events, including gastrulation in diverse organisms and neural tube closure in vertebrates. Apical constriction is thought to be triggered by contraction of apical actomyosin networks. We found that apical actomyosin contractions began before cell shape changes in both Caenorhabitis elegans and Drosophila. In C. elegans, actomyosin networks were initially dynamic, contracting and generating cortical tension without substantial shrinking of apical surfaces. Apical cell-cell contact zones and actomyosin only later moved increasingly in concert, with no detectable change in actomyosin dynamics or cortical tension. Thus, apical constriction appears to be triggered not by a change in cortical tension, but by dynamic linking of apical cell-cell contact zones to an already contractile apical cortex.

}, issn = {1095-9203}, doi = {10.1126/science.1217869}, author = {Roh-Johnson, Minna and Shemer, Gidi and Higgins, Christopher D and McClellan, Joseph H and Werts, Adam D and Tulu, U Serdar and Gao, Liang and Betzig, Eric and Kiehart, Daniel P and Goldstein, Bob} } @article {6302, title = {Ultrabithorax confers spatial identity in a context-specific manner in the Drosophila postembryonic ventral nervous system.}, journal = {Neural Development}, volume = {7}, year = {2012}, month = {2012 Sep 11}, pages = {31}, abstract = {

BACKGROUND: In holometabolous insects such as Drosophila melanogaster, neuroblasts produce an initial population of diverse neurons during embryogenesis and a much larger set of adult-specific neurons during larval life. In the ventral CNS, many of these secondary neuronal lineages differ significantly from one body segment to another, suggesting a role for anteroposterior patterning genes. RESULTS: Here we systematically characterize the expression pattern and function of the Hox gene Ultrabithorax (Ubx) in all 25 postembryonic lineages. We find that Ubx is expressed in a segment-, lineage-, and hemilineage-specific manner in the thoracic and anterior abdominal segments. When Ubx is removed from neuroblasts via mitotic recombination, neurons in these segments exhibit the morphologies and survival patterns of their anterior thoracic counterparts. Conversely, when Ubx is ectopically expressed in anterior thoracic segments, neurons exhibit complementary posterior transformation phenotypes. CONCLUSION: Our findings demonstrate that Ubx plays a critical role in conferring segment-appropriate morphology and survival on individual neurons in the adult-specific ventral CNS. Moreover, while always conferring spatial identity in some sense, Ubx has been co-opted during evolution for distinct and even opposite functions in different neuronal hemilineages.

}, keywords = {Animals, Cell Death, Developmental, Drosophila, Drosophila melanogaster, Drosophila Proteins, Gene Expression Regulation, Genetically Modified, Homeodomain Proteins, Larva, Nervous System, Transcription Factors}, issn = {1749-8104}, doi = {10.1186/1749-8104-7-31}, author = {Marin, Elizabeth C and Dry, Katie E and Alaimo, Danielle R and Rudd, Kirstin T and Cillo, Anthony R and Clenshaw, Michael E and Negre, Nicolas and White, Kevin P and Truman, James W} } @article {46722, title = {An unbiased analysis method to quantify mRNA localization reveals its correlation with cell motility.}, journal = {Cell Reports}, volume = {1}, year = {2012}, month = {2012 Feb 23}, pages = {179-84}, abstract = {

Localization of mRNA is a critical mechanism used by a large fraction of transcripts to restrict its translation to specific cellular regions. Although current high-resolution imaging techniques provide ample information, the analysis methods for localization have either been qualitative or employed quantification in nonrandomly selected regions of interest. Here, we describe an analytical method for objective quantification of mRNA localization using a combination of two characteristics of its molecular distribution, polarization and dispersion. The validity of the method is demonstrated using single-molecule FISH images of budding yeast and fibroblasts. Live-cell analysis of endogenous β-actin mRNA in mouse fibroblasts reveals that mRNA polarization has a half-life of ~16 min and is cross-correlated with directed cell migration. This novel approach provides insights into the dynamic regulation of mRNA localization and its physiological roles.

}, keywords = {Actins, Animals, Cell Movement, Chick Embryo, Computer Simulation, Embryo, Mammalian, Fibroblasts, Green Fluorescent Proteins, Imaging, Three-Dimensional, In Situ Hybridization, Mice, Monte Carlo Method, RNA Transport, RNA, Messenger, Saccharomyces cerevisiae}, issn = {2211-1247}, doi = {10.1016/j.celrep.2011.12.009}, author = {Park, Hye Yoon and Trcek, Tatjana and Wells, Amber L and Chao, Jeffrey A and Singer, Robert H} } @article {4486, title = {Use of a Drosophila genome-wide conserved sequence database to identify functionally related cis-regulatory enhancers.}, journal = {Developmental Dynamics: An Official Publication of the American Association of Anatomists}, volume = {241}, year = {2012}, month = {2012 Jan}, pages = {169-89}, abstract = {

Phylogenetic footprinting has revealed that cis-regulatory enhancers consist of conserved DNA sequence clusters (CSCs). Currently, there is no systematic approach for enhancer discovery and analysis that takes full-advantage of the sequence information within enhancer CSCs.

}, issn = {1097-0177}, doi = {10.1002/dvdy.22728}, author = {Brody, Thomas and Yavatkar, Amarendra S and Kuzin, Alexander and Kundu, Mukta and Tyson, Leonard J and Ross, Jermaine and Lin, Tzu-Yang and Lee, Chi-Hon and Awasaki, Takeshi and Lee, Tzumin and Odenwald, Ward F} } @article {4629, title = {Using translational enhancers to increase transgene expression in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 Apr 9}, pages = {6626-31}, abstract = {

The ability to specify the expression levels of exogenous genes inserted in the genomes of transgenic animals is critical for the success of a wide variety of experimental manipulations. Protein production can be regulated at the level of transcription, mRNA transport, mRNA half-life, or translation efficiency. In this report, we show that several well-characterized sequence elements derived from plant and insect viruses are able to function in Drosophila to increase the apparent translational efficiency of mRNAs by as much as 20-fold. These increases render expression levels sufficient for genetic constructs previously requiring multiple copies to be effective in single copy, including constructs expressing the temperature-sensitive inactivator of neuronal function Shibire(ts1), and for the use of cytoplasmic GFP to image the fine processes of neurons.

}, issn = {1091-6490}, doi = {10.1073/pnas.1204520109}, author = {Pfeiffer, Barret D and Truman, James W and Rubin, Gerald M} } @article {5831, title = {Visual neuroscience: a moving story of neuromodulation.}, journal = {Current Biology}, volume = {22}, year = {2012}, month = {2012 Dec 18}, pages = {R1057-9}, abstract = {

The visual neurons of many animals process sensory input differently depending on the animal{\textquoteright}s state of locomotion. Now, new work in Drosophila melanogaster shows that neuromodulatory neurons active during flight boost responses of neurons in the visual system.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2012.11.041}, author = {Jayaraman, Vivek} } @article {4975, title = {Visualization and analysis of 3D microscopic images.}, journal = {PLoS Computational Biology}, volume = {8}, year = {2012}, month = {2012 Jun}, pages = {e1002519}, abstract = {

In a wide range of biological studies, it is highly desirable to visualize and analyze three-dimensional (3D) microscopic images. In this primer, we first introduce several major methods for visualizing typical 3D images and related multi-scale, multi-time-point, multi-color data sets. Then, we discuss three key categories of image analysis tasks, namely segmentation, registration, and annotation. We demonstrate how to pipeline these visualization and analysis modules using examples of profiling the single-cell gene-expression of C. elegans and constructing a map of stereotyped neurite tracts in a fruit fly brain.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1002519}, author = {Long, Fuhui and Zhou, Jianlong and Peng, Hanchuan} } @article {47654, title = {Visualization of live primary cilia dynamics using fluorescence microscopy.}, journal = {Current protocols in cell biology / editorial board, Juan S. Bonifacino ... [et al.]}, volume = {Chapter 4}, year = {2012}, month = {2012 Dec}, pages = {Unit 4.26}, abstract = {

Methods useful for exploring the formation and functions of primary cilia in living cells are described here. First, multiple protocols for visualizing solitary cilia that extend away from the cell body are described. Primary cilia collect, synthesize, and transmit information about the extracellular space into the cell body to promote critical cellular responses. Problems with cilia formation or function can lead to dramatic changes in cell physiology. These methods can be used to assess cilia formation and length, the location of the cilium relative to other cellular structures, and localization of specific proteins to the cilium. The subsequent protocols describe how to quantify movement of fluorescent molecules within the cilium using kymographs, photobleaching, and photoconversion. The microtubules that form the structural scaffold of the cilium are also critical avenues for kinesin and dynein-mediated movement of proteins within the cilium. Assessing intraflagellar dynamics can provide insight into mechanisms of ciliary-mediated signal perception and transmission.

}, keywords = {Animals, Bodily Secretions, Cilia, Dyneins, Epithelial Cells, Flagella, Humans, Kinesin, Kymography, Microscopy, Fluorescence, Microtubules, Photobleaching, Primary Cell Culture, Signal Transduction}, issn = {1934-2616}, doi = {10.1002/0471143030.cb0426s57}, author = {Ott, Carolyn and Lippincott-Schwartz, Jennifer} } @article {47645, title = {Visualization of live primary cilia dynamics using fluorescence microscopy.}, journal = {Current protocols in cell biology / editorial board, Juan S. Bonifacino ... [et al.]}, volume = {Chapter 4}, year = {2012}, month = {2012 Dec}, pages = {Unit 4.26}, abstract = {

Methods useful for exploring the formation and functions of primary cilia in living cells are described here. First, multiple protocols for visualizing solitary cilia that extend away from the cell body are described. Primary cilia collect, synthesize, and transmit information about the extracellular space into the cell body to promote critical cellular responses. Problems with cilia formation or function can lead to dramatic changes in cell physiology. These methods can be used to assess cilia formation and length, the location of the cilium relative to other cellular structures, and localization of specific proteins to the cilium. The subsequent protocols describe how to quantify movement of fluorescent molecules within the cilium using kymographs, photobleaching, and photoconversion. The microtubules that form the structural scaffold of the cilium are also critical avenues for kinesin and dynein-mediated movement of proteins within the cilium. Assessing intraflagellar dynamics can provide insight into mechanisms of ciliary-mediated signal perception and transmission.

}, keywords = {Animals, Bodily Secretions, Cilia, Dyneins, Epithelial Cells, Flagella, Humans, Kinesin, Kymography, Microscopy, Fluorescence, Microtubules, Photobleaching, Primary Cell Culture, Signal Transduction}, issn = {1934-2616}, doi = {10.1002/0471143030.cb0426s57}, author = {Ott, Carolyn and Lippincott-Schwartz, Jennifer} } @article {47655, title = {Visualizing cell structure and function with point-localization superresolution imaging.}, journal = {Developmental cell}, volume = {23}, year = {2012}, month = {2012 Dec 11}, pages = {1092-102}, abstract = {

Fundamental to the success of cell and developmental biology is the ability to tease apart molecular organization in cells and tissues by localizing specific proteins with respect to one another in a native cellular context. However, many key cellular structures (from mitochondrial cristae to nuclear pores) lie below the diffraction limit of visible light, precluding analysis of their organization by conventional approaches. Point-localization superresolution microscopy techniques, such as PALM and STORM, are poised to resolve, with unprecedented clarity, the organizational principles of macromolecular complexes within cells, thus leading to deeper insights into cellular function in both health and disease.

}, keywords = {Cell Physiological Phenomena, Cells, Cellular Structures, Fluorescent Dyes, Imaging, Three-Dimensional, Microscopy, Microscopy, Fluorescence, Mitochondrial Membranes}, issn = {1878-1551}, doi = {10.1016/j.devcel.2012.09.022}, author = {Sengupta, Prabuddha and van Engelenburg, Schuyler and Lippincott-Schwartz, Jennifer} } @article {5341, title = {Volume electron microscopy for neuronal circuit reconstruction.}, journal = {Current Opinion in Neurobiology}, volume = {22}, year = {2012}, month = {2012 Feb}, pages = {154-61}, abstract = {

The last decade has seen a rapid increase in the number of tools to acquire volume electron microscopy (EM) data. Several new scanning EM (SEM) imaging methods have emerged, and classical transmission EM (TEM) methods are being scaled up and automated. Here we summarize the new methods for acquiring large EM volumes, and discuss the tradeoffs in terms of resolution, acquisition speed, and reliability. We then assess each method{\textquoteright}s applicability to the problem of reconstructing anatomical connectivity between neurons, considering both the current capabilities and future prospects of the method. Finally, we argue that neuronal {\textquoteright}wiring diagrams{\textquoteright} are likely necessary, but not sufficient, to understand the operation of most neuronal circuits: volume EM imaging will likely find its best application in combination with other methods in neuroscience, such as molecular biology, optogenetics, and physiology.

}, keywords = {Animals, Brain, Computer-Assisted, Electron, Humans, Image Processing, Microscopy, Neural Pathways}, issn = {1873-6882}, doi = {10.1016/j.conb.2011.10.022}, author = {Briggman, Kevin L and Bock, Davi D} } @article {46721, title = {β-Actin mRNA compartmentalization enhances focal adhesion stability and directs cell migration.}, journal = {Genes \& Development}, volume = {26}, year = {2012}, month = {2012 Sep 1}, pages = {1885-90}, abstract = {

Directed cell motility is at the basis of biological phenomena such as development, wound healing, and metastasis. It has been shown that substrate attachments mediate motility by coupling the cell{\textquoteright}s cytoskeleton with force generation. However, it has been unclear how the persistence of cell directionality is facilitated. We show that mRNA localization plays an important role in this process, but the mechanism of action is still unknown. In this study, we show that the zipcode-binding protein 1 transports β-actin mRNA to the focal adhesion compartment, where it dwells for minutes, suggesting a means for associating its localization with motility through the formation of stable connections between adhesions and newly synthesized actin filaments. In order to demonstrate this, we developed an approach for assessing the functional consequences of β-actin mRNA and protein localization by tethering the mRNA to a specific location-in this case, the focal adhesion complex. This approach will have a significant impact on cell biology because it is now possible to forcibly direct any mRNA and its cognate protein to specific locations in the cell. This will reveal the importance of localized protein translation on various cellular processes.

}, keywords = {Actins, Animals, Cell Compartmentation, Cell Line, Cell Movement, Cells, Cultured, Fibroblasts, Focal Adhesions, Glycoproteins, Mice, Mice, Knockout, RNA, Messenger}, issn = {1549-5477}, doi = {10.1101/gad.190413.112}, author = {Katz, Zachary B and Wells, Amber L and Park, Hye Yoon and Wu, Bin and Shenoy, Shailesh M and Singer, Robert H} } @article {46346, title = {β-secretase cleavage of the fly amyloid precursor protein is required for glial survival.}, journal = {Journal of Neuroscience}, volume = {32}, year = {2012}, month = {2012 Nov 14}, pages = {16181-92}, abstract = {

β-secretase (or BACE1) is the key enzyme in the production of β-amyloid (Aβ), which accumulates in the senile plaques characteristic for Alzheimer{\textquoteright}s disease. Consequently, the lack of BACE1 prevents β-processing of the amyloid precursor protein and Aβ production, which made it a promising target for drug development. However, the loss of BACE1 is also detrimental, leading to myelination defects and altered neuronal activity, functions that have been associated with the cleavage of Neuregulin and a voltage-gated sodium channel subunit. Here we show that the Drosophila ortholog of BACE, dBACE, is required for glial survival. Cell-specific knockdown experiments reveal that this is a non-cell autonomous function, as a knockdown of dBACE in photoreceptor neurons leads to progressive degeneration of glia in their target zone, the lamina. Interestingly, this phenotype is suppressed by the loss of the fly amyloid precursor protein (APPL), whereas a secretion-deficient form of APPL enhances the degeneration. This shows that full-length APPL in neurons promotes the death of neighboring glial cells and that β-processing of APPL is needed to prevent glial death. These results therefore not only demonstrate a novel function for an APP protein in glia, but they also show this function specifically requires regulation by β-cleavage.

}, keywords = {Amyloid beta-Protein Precursor, Amyloid Precursor Protein Secretases, Animals, Axons, Blotting, Western, Cell Death, Cell Movement, Cell Survival, Drosophila, Immunohistochemistry, Microscopy, Electron, Neuregulins, Neuroglia, Polymerase Chain Reaction, Retina, RNA, RNA Interference, Vacuoles}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0228-12.2012}, author = {Bolkan, Bonnie J and Triphan, Tilman and Kretzschmar, Doris} } @article {46614, title = {Abnormal behavior in mice mutant for the Disc1 binding partner, Dixdc1.}, journal = {Translational Psychiatry}, volume = {1}, year = {2011}, month = {2011}, pages = {e43}, abstract = {

Disrupted-in-Schizophrenia-1 (DISC1) is a genetic susceptibility locus for major mental illness, including schizophrenia and depression. The Disc1 protein was recently shown to interact with the Wnt signaling protein, DIX domain containing 1 (Dixdc1). Both proteins participate in neural progenitor proliferation dependent on Wnt signaling, and in neural migration independently of Wnt signaling. Interestingly, their effect on neural progenitor proliferation is additive. By analogy to Disc1, mutations in Dixdc1 may lead to abnormal behavior in mice, and to schizophrenia or depression in humans. To explore this hypothesis further, we generated mice mutant at the Dixdc1 locus and analyzed their behavior. Dixdc1(-/-) mice had normal prepulse inhibition, but displayed decreased spontaneous locomotor activity, abnormal behavior in the elevated plus maze and deficits in startle reactivity. Our results suggest that Dixdc1(-/-) mice will be a useful tool to elucidate molecular pathophysiology involving Disc1 in major mental illnesses.

}, keywords = {Animals, Behavior, Animal, Epistasis, Genetic, Humans, Intracellular Signaling Peptides and Proteins, Male, Mice, Mice, 129 Strain, Mice, Mutant Strains, Mice, Transgenic, Microfilament Proteins, Nerve Tissue Proteins}, issn = {2158-3188}, doi = {10.1038/tp.2011.41}, author = {Kivim{\"a}e, S and Martin, P-M and Kapfhamer, D and Ruan, Y and Heberlein, U and Rubenstein, J L R and Cheyette, B N R} } @article {5271, title = {Accelerated profile HMM searches.}, journal = {PLoS Computational Biology}, volume = {7}, year = {2011}, month = {2011 Oct}, pages = {e1002195}, abstract = {

Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been hindered by the computational expense of existing software implementations. Here I describe an acceleration heuristic for profile HMMs, the "multiple segment Viterbi" (MSV) algorithm. The MSV algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. MSV scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an MSV score and thus facilitating its use as a heuristic filter. I also describe a 20-fold acceleration of the standard profile HMM Forward/Backward algorithms using a method I call "sparse rescaling". These methods are assembled in a pipeline in which high-scoring MSV hits are passed on for reanalysis with the full HMM Forward/Backward algorithm. This accelerated pipeline is implemented in the freely available HMMER3 software package. Performance benchmarks show that the use of the heuristic MSV filter sacrifices negligible sensitivity compared to unaccelerated profile HMM searches. HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches.

}, keywords = {Algorithms, Computational Biology, Databases, Information Storage and Retrieval, Markov Chains, Protein, Sequence Alignment, Software}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1002195}, author = {Eddy, Sean R.} } @article {6331, title = {An adaptation of the Wiener filter suitable for analyzing images of isolated single particles.}, journal = {Journal of Structural Biology}, volume = {176}, year = {2011}, month = {2011 Oct}, pages = {60-74}, abstract = {

The Wiener filter is a standard means of optimizing the signal in sums of aligned, noisy images obtained by electron cryo-microscopy (cryo-EM). However, estimation of the resolution-dependent ("spectral") signal-to-noise ratio (SSNR) from the input data has remained problematic, and error reduction due to specific application of the SSNR term within a Wiener filter has not been reported. Here we describe an adjustment to the Wiener filter for optimal summation of images of isolated particles surrounded by large regions of featureless background, as is typically the case in single-particle cryo-EM applications. We show that the density within the particle area can be optimized, in the least-squares sense, by scaling the SSNR term found in the conventional Wiener filter by a factor that reflects the fraction of the image field occupied by the particle. We also give related expressions that allow the SSNR to be computed for application in this new filter, by incorporating a masking step into a Fourier Ring Correlation (FRC), a standard resolution measure. Furthermore, we show that this masked FRC estimation scheme substantially improves on the accuracy of conventional SSNR estimation methods. We demonstrate the validity of our new approach in numeric tests with simulated data corresponding to realistic cryo-EM imaging conditions. This variation of the Wiener filter and accompanying derivation should prove useful for a variety of single-particle cryo-EM applications, including 3D reconstruction.

}, keywords = {Algorithms, Computer-Assisted, Cryoelectron Microscopy, Fourier Analysis, Image Processing, Models, Molecular, Protein Conformation, Signal-To-Noise Ratio}, issn = {1095-8657}, doi = {10.1016/j.jsb.2011.06.010}, author = {Sindelar, Charles V and Grigorieff, Nikolaus} } @article {2181, title = {Adeno-associated viral vectors for mapping, monitoring, and manipulating neural circuits.}, journal = {Human Gene Therapy}, volume = {22}, year = {2011}, month = {2011 Feb 14}, pages = {669-77}, abstract = {

Understanding the structure and function of neural circuits are central questions in neuroscience research. To address these questions, new genetically encoded tools have been developed for mapping, monitoring, and manipulating neurons. Essential to implementation of these tools is their selective delivery to defined neuronal populations in the brain. This has been facilitated by recent improvements in cell type-specific transgene expression using recombinant adeno-associated viral vectors. Here, we highlight these developments and discuss areas for improvement that could further expand capabilities for neural circuit analysis.

}, issn = {1557-7422}, doi = {10.1089/hum.2010.204}, author = {Sternson, Scott and Betley, J Nicholas} } @article {4935, title = {Advances in structural and functional analysis of membrane proteins by electron crystallography.}, journal = {Structure}, volume = {19}, year = {2011}, month = {2011 Oct 12}, pages = {1381-93}, abstract = {

Electron crystallography is a powerful technique for the study of membrane protein structure and function in the lipid environment. When well-ordered two-dimensional crystals are obtained the structure of both protein and lipid can be determined and lipid-protein interactions analyzed. Protons and ionic charges can be visualized by electron crystallography and the protein of interest can be captured for structural analysis in a variety of physiologically distinct states. This review highlights the strengths of electron crystallography and the momentum that is building up in automation and the development of high throughput tools and methods for structural and functional analysis of membrane proteins by electron crystallography.

}, keywords = {Aquaporin 1, Archaea, Automatic Data Processing, Bacteriorhodopsins, Cell Membrane, Computer-Assisted, Cryoelectron Microscopy, Crystallography, Detergents, Dialysis, Humans, Image Processing, Lipid Bilayers, Membrane Proteins, Membrane Transport Proteins, Protein Conformation, Static Electricity}, issn = {1878-4186}, doi = {10.1016/j.str.2011.09.001}, author = {Wisedchaisri, Goragot and Reichow, Steve L and Gonen, Tamir} } @article {4497, title = {Advances in the chemistry of small molecule fluorescent probes.}, journal = {Current Opinion in Chemical Biology}, volume = {15}, year = {2011}, month = {2011 Dec}, pages = {752-9}, abstract = {

Small molecule fluorophores are essential tools for chemical biology. A benefit of synthetic dyes is the ability to employ chemical approaches to control the properties and direct the position of the fluorophore. Applying modern synthetic organic chemistry strategies enables efficient tailoring of the chemical structure to obtain probes for specific biological experiments. Chemistry can also be used to activate fluorophores; new fluorogenic enzyme substrates and photoactivatable compounds with improved properties have been prepared that facilitate advanced imaging experiments with low background fluorescence. Finally, chemical reactions in live cells can be used to direct the spatial distribution of the fluorophore, allowing labeling of defined cellular regions with synthetic dyes.

}, issn = {1879-0402}, doi = {10.1016/j.cbpa.2011.10.013}, author = {Wysocki, Laura M and Lavis, Luke D} } @article {3309, title = {AGRP neurons are sufficient to orchestrate feeding behavior rapidly and without training.}, journal = {Nature Neuroscience}, volume = {14}, year = {2011}, month = {2011 Mar}, pages = {351-5}, abstract = {

Two intermingled hypothalamic neuron populations specified by expression of agouti-related peptide (AGRP) or pro-opiomelanocortin (POMC) positively and negatively influence feeding behavior, respectively, possibly by reciprocally regulating downstream melanocortin receptors. However, the sufficiency of these neurons to control behavior and the relationship of their activity to the magnitude and dynamics of feeding are unknown. To measure this, we used channelrhodopsin-2 for cell type-specific photostimulation. Activation of only 800 AGRP neurons in mice evoked voracious feeding within minutes. The behavioral response increased with photoexcitable neuron number, photostimulation frequency and stimulus duration. Conversely, POMC neuron stimulation reduced food intake and body weight, which required melanocortin receptor signaling. However, AGRP neuron-mediated feeding was not dependent on suppressing this melanocortin pathway, indicating that AGRP neurons directly engage feeding circuits. Furthermore, feeding was evoked selectively over drinking without training or prior photostimulus exposure, which suggests that AGRP neurons serve a dedicated role coordinating this complex behavior.

}, keywords = {Agouti-Related Protein, Animal, Animals, Behavior, Classical, Conditioning, Eating, Feeding Behavior, Hypothalamus, Melanocortins, Mice, Neurons, Photic Stimulation, Pro-Opiomelanocortin, Recombinant Fusion Proteins, Rhodopsin}, issn = {1546-1726}, doi = {10.1038/nn.2739}, author = {Aponte, Yexica and Atasoy, Deniz and Sternson, Scott M} } @article {5483, title = {Alk is a transcriptional target of LMO4 and ERα that promotes cocaine sensitization and reward.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {31}, year = {2011}, month = {2011 Oct 5}, pages = {14134-41}, abstract = {

Previously, we showed that the mouse LIM-domain only 4 (Lmo4) gene, which encodes a protein containing two zinc-finger LIM domains that interact with various DNA-binding transcription factors, attenuates behavioral sensitivity to repeated cocaine administration. Here we show that transcription of anaplastic lymphoma kinase (Alk) is repressed by LMO4 in the striatum and that Alk promotes the development of cocaine sensitization and conditioned place preference, a measure of cocaine reward. Since LMO4 is known to interact with estrogen receptor α (ERα) at the promoters of target genes, we investigated whether Alk expression might be controlled by a similar mechanism. We found that LMO4 and ERα are associated with the Alk promoter by chromatin immunoprecipitation and that Alk is an estrogen-responsive gene in the striatum. Moreover, we show that ERα knock-out mice exhibit enhanced cocaine sensitization and conditioned place preference and an increase in Alk expression in the nucleus accumbens. These data define a novel regulatory network involved in behavioral responses to cocaine. Interestingly, sex differences in several behavioral responses to cocaine in humans and rodents have been described, and estrogen is thought to mediate some of these differences. Our data suggest that estrogen regulation of Alk may be one mechanism responsible for sexually dimorphic responses to cocaine.

}, keywords = {Adaptor Proteins, Animals, Cells, Cocaine, Cultured, Estrogen Receptor alpha, Gene Targeting, Genetic, HEK293 Cells, Humans, Inbred C57BL, Knockout, LIM Domain Proteins, Male, Mice, Motor Activity, Newborn, Receptor Protein-Tyrosine Kinases, Reward, Signal Transducing, Transcription}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3415-11.2011}, author = {Lasek, Amy W and Gesch, Julie and Giorgetti, Francesco and Kharazia, Viktor and Heberlein, Ulrike} } @article {4310, title = {Anisotropic path searching for automatic neuron reconstruction.}, journal = {Medical Image Analysis}, volume = {15}, year = {2011}, month = {2011 Oct}, pages = {680-9}, abstract = {

Full reconstruction of neuron morphology is of fundamental interest for the analysis and understanding of their functioning. We have developed a novel method capable of automatically tracing neurons in three-dimensional microscopy data. In contrast to template-based methods, the proposed approach makes no assumptions about the shape or appearance of neurite structure. Instead, an efficient seeding approach is applied to capture complex neuronal structures and the tracing problem is solved by computing the optimal reconstruction with a weighted graph. The optimality is determined by the cost function designed for the path between each pair of seeds and by topological constraints defining the component interrelations and completeness. In addition, an automated neuron comparison method is introduced for performance evaluation and structure analysis. The proposed algorithm is computationally efficient and has been validated using different types of microscopy data sets including Drosophila{\textquoteright}s projection neurons and fly neurons with presynaptic sites. In all cases, the approach yielded promising results.

}, issn = {1361-8423}, doi = {10.1016/j.media.2011.05.013}, author = {Xie, Jun and Zhao, Ting and Lee, Tzumin and Myers, Eugene and Peng, Hanchuan} } @article {4523, title = {Arouser reveals a role for synapse number in the regulation of ethanol sensitivity.}, journal = {Neuron}, volume = {70}, year = {2011}, month = {2011 Jun 9}, pages = {979-90}, abstract = {

A reduced sensitivity to the sedating effects of alcohol is a characteristic associated with alcohol use disorders (AUDs). A genetic screen for ethanol sedation mutants in Drosophila identified arouser (aru), which functions in developing neurons to reduce ethanol sensitivity. Genetic evidence suggests that aru regulates ethanol sensitivity through its activation by Egfr/Erk signaling and its inhibition by PI3K/Akt signaling. The aru mutant also has an increased number of synaptic terminals in the larva and adult fly. Both the increased ethanol sensitivity and synapse number of the aru mutant are restored upon adult social isolation, suggesting a causal relationship between synapse number and ethanol sensitivity. We thus show that a developmental abnormality affecting synapse number and ethanol sensitivity is not permanent and can be reversed by manipulating the environment of the adult fly.

}, keywords = {Adaptor Proteins, Animal, Animals, Arabidopsis Proteins, Behavior, Brain, Central Nervous System Depressants, Developmental, Drosophila, Drosophila Proteins, Epidermal Growth Factor, Ethanol, Gene Expression Regulation, Genetically Modified, Green Fluorescent Proteins, Invertebrate Peptide, Larva, Mutation, Neuromuscular Junction, Neurons, Phosphatidylinositol 3-Kinases, Receptor, Receptors, Reflex, RNA Interference, Signal Transducing, Signal Transduction, Social Isolation, Synapses}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.03.030}, author = {Eddison, Mark and Guarnieri, Douglas J and Cheng, Ling and Liu, Che-Hsiung and Moffat, Kevin G and Davis, Graeme and Heberlein, Ulrike} } @article {46345, title = {Associative learning between odorants and mechanosensory punishment in larval Drosophila.}, journal = {Journal of Expiremental Biology}, volume = {214}, year = {2011}, month = {2011 Dec 1}, pages = {3897-905}, abstract = {

We tested whether Drosophila larvae can associate odours with a mechanosensory disturbance as a punishment, using substrate vibration conveyed by a loudspeaker (buzz:). One odour (A) was presented with the buzz, while another odour (B) was presented without the buzz (A/B training). Then, animals were offered the choice between A and B. After reciprocal training (A/B), a second experimental group was tested in the same way. We found that larvae show conditioned escape from the previously punished odour. We further report an increase of associative performance scores with the number of punishments, and an increase according to the number of training cycles. Within the range tested (between 50 and 200 Hz), however, the pitch of the buzz does not apparently impact associative success. Last, but not least, we characterized odour-buzz memories with regard to the conditions under which they are behaviourally expressed--or not. In accordance with what has previously been found for associative learning between odours and bad taste (such as high concentration salt or quinine), we report that conditioned escape after odour-buzz learning is disabled if escape is not warranted, i.e. if no punishment to escape from is present during testing. Together with the already established paradigms for the association of odour and bad taste, the present assay offers the prospect of analysing how a relatively simple brain orchestrates memory and behaviour with regard to different kinds of {\textquoteright}bad{\textquoteright} events.

}, keywords = {Animals, Association Learning, Behavior, Animal, Conditioning (Psychology), Drosophila melanogaster, Larva, Mechanotransduction, Cellular, Memory, Odors, Punishment, Sound}, issn = {1477-9145}, doi = {10.1242/jeb.060533}, author = {Eschbach, Claire and Cano, Carmen and Haberkern, Hannah and Schraut, Karla and Guan, Chonglin and Triphan, Tilman and Gerber, Bertram} } @article {6335, title = {Atomic model of an infectious rotavirus particle.}, journal = {The EMBO Journal}, volume = {30}, year = {2011}, month = {2011 Jan 19}, pages = {408-16}, abstract = {

Non-enveloped viruses of different types have evolved distinct mechanisms for penetrating a cellular membrane during infection. Rotavirus penetration appears to occur by a process resembling enveloped-virus fusion: membrane distortion linked to conformational changes in a viral protein. Evidence for such a mechanism comes from crystallographic analyses of fragments of VP4, the rotavirus-penetration protein, and infectivity analyses of structure-based VP4 mutants. We describe here the structure of an infectious rotavirus particle determined by electron cryomicroscopy (cryoEM) and single-particle analysis at about 4.3 {\r A} resolution. The cryoEM image reconstruction permits a nearly complete trace of the VP4 polypeptide chain, including the positions of most side chains. It shows how the two subfragments of VP4 (VP8(*) and VP5(*)) retain their association after proteolytic cleavage, reveals multiple structural roles for the β-barrel domain of VP5(*), and specifies interactions of VP4 with other capsid proteins. The virion model allows us to integrate structural and functional information into a coherent mechanism for rotavirus entry.

}, keywords = {Capsid Proteins, Cell Membrane, Cryoelectron Microscopy, Crystallography, Models, Molecular, Protein Structure, Rotavirus, Secondary, Virion, Virus Internalization}, issn = {1460-2075}, doi = {10.1038/emboj.2010.322}, author = {Settembre, Ethan C and Chen, James Z and Dormitzer, Philip R and Grigorieff, Nikolaus and Harrison, Stephen C} } @article {5375, title = {Automated high speed stitching of large 3D microscopic images.}, journal = {2011 8TH IEEE International Symposium on Biomedical Imaging: From Nano to Macro}, year = {2011}, month = {2011 Mar 30}, pages = {238-41}, abstract = {

High-resolution microscopic imaging of biological samples often produces multiple 3D image tiles to cover a large field of view of specimen. Usually each tile has a large size, in the range of hundreds of megabytes to several gigabytes. For many of our image data sets, existing software tools are often unable to stitch those 3D tiles into a panoramic view, thus impede further data analysis. We propose a simple, but accurate, robust, and automatic method to stitch a group of image tiles without a priori adjacency information of them. We first use a multiscale strategy to register a pair of 3D image tiles rapidly, achieving about 8~10 times faster speed and 10 times less memory requirement compared to previous methods. Then we design a minimum-spanning-tree based method to determine the optimal adjacency of tiles. We have successfully stitched large image stacks of model animals including C. elegans, fruit fly, dragonfly, and mouse, which could not be stitched by several existing methods.

}, issn = {1945-7928}, doi = {10.1109/isbi.2011.5872396}, author = {Yu, Yang and Peng, Hanchuan} } @article {2700, title = {Automated reconstruction of neuronal morphology based on local geometrical and global structural models.}, journal = {Neuroinformatics}, volume = {9}, year = {2011}, month = {2011 May 6}, pages = {247-61}, abstract = {

Digital reconstruction of neurons from microscope images is an important and challenging problem in neuroscience. In this paper, we propose a model-based method to tackle this problem. We first formulate a model structure, then develop an algorithm for computing it by carefully taking into account morphological characteristics of neurons, as well as the image properties under typical imaging protocols. The method has been tested on the data sets used in the DIADEM competition and produced promising results for four out of the five data sets.

}, issn = {1559-0089}, doi = {10.1007/s12021-011-9120-3}, author = {Zhao, Ting and Xie, Jun and Amat, Fernando and Clack, Nathan and Ahammad, Parvez and Peng, Hanchuan and Long, Fuhui and Myers, Eugene} } @conference {2721, title = {Automatic 3D neuron tracing using all-paths pruning.}, booktitle = {Conference on Intelligent Systems for Molecular Biology}, year = {2011}, month = {2011}, address = {Vienna}, abstract = {

Motivation: Digital reconstruction, or tracing, of 3D neuron structures is critical toward reverse engineering the wiring and functions of a brain. However, despite a number of existing studies, this task is still challenging, especially when a 3D microscopic image has low signal-to-noise ratio (SNR) and fragmented neuron segments. Published work can handle these hard situations only by introducing global prior information, such as where a neurite segment starts and terminates. However, manual incorporation of such global information can be very time consuming. Thus, a completely automatic approach for these hard situations is highly desirable.

Results: We have developed an automatic graph algorithm, called the all-path pruning (APP), to trace the 3D structure of a neuron. To avoid potential mis-tracing of some parts of a neuron, an APP first produces an initial over-reconstruction, by tracing the optimal geodesic shortest path from the seed location to every possible destination voxel/pixel location in the image. Since the initial reconstruction contains all the possible paths and thus could contain redundant structural components (SC), we simplify the entire reconstruction without compromising its connectedness by pruning the redundant structural elements, using a new maximal-covering minimal-redundant (MCMR) subgraph algorithm. We show that MCMR has a linear computational complexity and will converge. We examined the performance of our method using challenging 3D neuronal image datasets of model organisms (e.g. fruit fly).

}, author = {Long, Fuhui and Peng, Hanchuan and Myers, Eugene} } @article {47674, title = {Bile acid stimulates hepatocyte polarization through a cAMP-Epac-MEK-LKB1-AMPK pathway.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Jan 25}, pages = {1403-8}, abstract = {

This study describes a unique function of taurocholate in bile canalicular formation involving signaling through a cAMP-Epac-MEK-Rap1-LKB1-AMPK pathway. In rat hepatocyte sandwich cultures, polarization was manifested by sequential progression of bile canaliculi from small structures to a fully branched network. Taurocholate accelerated canalicular network formation and concomitantly increased cAMP, which were prevented by adenyl cyclase inhibitor. The cAMP-dependent PKA inhibitor did not prevent the taurocholate effect. In contrast, activation of Epac, another cAMP downstream kinase, accelerated canalicular network formation similar to the effect of taurocholate. Inhibition of Epac downstream targets, Rap1 and MEK, blocked the taurocholate effect. Taurocholate rapidly activated MEK, LKB1, and AMPK, which were prevented by inhibition of adenyl cyclase or MEK. Our previous study showed that activated-LKB1 and AMPK participate in canalicular network formation. Linkage between bile acid synthesis, hepatocyte polarization, and regulation of energy metabolism is likely important in normal hepatocyte development and disease.

}, keywords = {Adenylate Kinase, Animals, Bile Acids and Salts, Blotting, Western, Cell Polarity, Cells, Cultured, Chenodeoxycholic Acid, Cholagogues and Choleretics, Cyclic AMP, Dose-Response Relationship, Drug, Green Fluorescent Proteins, Guanine Nucleotide Exchange Factors, Hepatocytes, Imines, Microscopy, Confocal, Mitogen-Activated Protein Kinase Kinases, Models, Biological, Protein-Serine-Threonine Kinases, rap1 GTP-Binding Proteins, Rats, Rats, Sprague-Dawley, Signal Transduction, Taurocholic Acid, Ursodeoxycholic Acid}, issn = {1091-6490}, doi = {10.1073/pnas.1018376108}, author = {Fu, Dong and Wakabayashi, Yoshiyuki and Lippincott-Schwartz, Jennifer and Arias, Irwin M} } @article {4928, title = {The binding of cholera toxin to the periplasmic vestibule of the type II secretion channel.}, journal = {Channels}, volume = {5}, year = {2011}, month = {2011 May-Jun}, pages = {215-8}, abstract = {

The type II secretion system (T2SS) is a large macromolecular complex spanning the inner and outer membranes of many gram-negative bacteria. The T2SS is responsible for the secretion of virulence factors such as cholera toxin (CT) and heat-labile enterotoxin (LT) from Vibrio cholerae and enterotoxigenic Escherichia coli, respectively. CT and LT are closely related AB5 heterohexamers, composed of one A subunit and a B-pentamer. Both CT and LT are translocated, as folded protein complexes, from the periplasm across the outer membrane through the type II secretion channel, the secretin GspD. We recently published the 19 {\r A} structure of the V. cholerae secretin (VcGspD) in its closed state and showed by SPR measurements that the periplasmic domain of GspD interacts with the B-pentamer complex. Here we extend these studies by characterizing the binding of the cholera toxin B-pentamer to VcGspD using electron microscopy of negatively stained preparations. Our studies indicate that the pentamer is captured within the large periplasmic vestibule of VcGspD. These new results agree well with our previously published studies and are in accord with a piston-driven type II secretion mechanism.

}, keywords = {Bacterial Proteins, Bacterial Secretion Systems, Cholera Toxin, Periplasm, Porins, Protein Folding, Protein Structure, Protein Subunits, Protein Transport, Quaternary, Tertiary, Vibrio cholerae}, issn = {1933-6969}, author = {Reichow, Steve L and Korotkov, Konstantin V and Gonen, Melissa and Sun, Ji and Delarosa, Jaclyn R and Hol, Wim G J and Gonen, Tamir} } @article {47660, title = {Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Dec 27}, pages = {21081-6}, abstract = {

Superresolution imaging techniques based on the precise localization of single molecules, such as photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM), achieve high resolution by fitting images of single fluorescent molecules with a theoretical Gaussian to localize them with a precision on the order of tens of nanometers. PALM/STORM rely on photoactivated proteins or photoswitching dyes, respectively, which makes them technically challenging. We present a simple and practical way of producing point localization-based superresolution images that does not require photoactivatable or photoswitching probes. Called bleaching/blinking assisted localization microscopy (BaLM), the technique relies on the intrinsic bleaching and blinking behaviors characteristic of all commonly used fluorescent probes. To detect single fluorophores, we simply acquire a stream of fluorescence images. Fluorophore bleach or blink-off events are detected by subtracting from each image of the series the subsequent image. Similarly, blink-on events are detected by subtracting from each frame the previous one. After image subtractions, fluorescence emission signals from single fluorophores are identified and the localizations are determined by fitting the fluorescence intensity distribution with a theoretical Gaussian. We also show that BaLM works with a spectrum of fluorescent molecules in the same sample. Thus, BaLM extends single molecule-based superresolution localization to samples labeled with multiple conventional fluorescent probes.

}, keywords = {Animals, Cercopithecus aethiops, COS Cells, Fluorescent Dyes, Green Fluorescent Proteins, Image Interpretation, Computer-Assisted, Microscopy, Fluorescence, Photobleaching, Software}, issn = {1091-6490}, doi = {10.1073/pnas.1117430109}, author = {Burnette, Dylan T and Sengupta, Prabuddha and Dai, Yuhai and Lippincott-Schwartz, Jennifer and Kachar, Bechara} } @article {4157, title = {BrainAligner: 3D registration atlases of Drosophila brains.}, journal = {Nature Methods}, volume = {8}, year = {2011}, month = {2011 Jun}, pages = {493-500}, abstract = {

Analyzing Drosophila melanogaster neural expression patterns in thousands of three-dimensional image stacks of individual brains requires registering them into a canonical framework based on a fiducial reference of neuropil morphology. Given a target brain labeled with predefined landmarks, the BrainAligner program automatically finds the corresponding landmarks in a subject brain and maps it to the coordinate system of the target brain via a deformable warp. Using a neuropil marker (the antibody nc82) as a reference of the brain morphology and a target brain that is itself a statistical average of data for 295 brains, we achieved a registration accuracy of 2 μm on average, permitting assessment of stereotypy, potential connectivity and functional mapping of the adult fruit fly brain. We used BrainAligner to generate an image pattern atlas of 2954 registered brains containing 470 different expression patterns that cover all the major compartments of the fly brain.

}, keywords = {Algorithms, Animals, Brain, Computer-Assisted, Drosophila melanogaster, Drosophila Proteins, Gene Expression, Genetically Modified, Green Fluorescent Proteins, Image Processing, Neuropil, Recombinant Proteins, Software, Transcription Factors}, issn = {1548-7105}, doi = {10.1038/nmeth.1602}, author = {Peng, Hanchuan and Chung, Phuong and Long, Fuhui and Qu, Lei and Jenett, Arnim and Seeds, Andrew M and Myers, Eugene W and Simpson, Julie H} } @article {47668, title = {Bridging structure and process in developmental biology through new imaging technologies.}, journal = {Developmental cell}, volume = {21}, year = {2011}, month = {2011 Jul 19}, pages = {5-10}, abstract = {

Many unexpected discoveries in developmental biology have depended on advancement of imaging technologies to visualize developmental processes as they unfold across multiple spatial and temporal scales. This essay surveys the recent advances in imaging, highlighting emerging capabilities with an eye toward those poised to have the greatest impact on developmental biology.

}, keywords = {Animals, Cell Biology, Cells, Developmental Biology, Green Fluorescent Proteins, Microscopy}, issn = {1878-1551}, doi = {10.1016/j.devcel.2011.06.030}, author = {Lippincott-Schwartz, Jennifer} } @article {5311, title = {The BTB/POZ zinc finger protein Broad-Z3 promotes dendritic outgrowth during metamorphic remodeling of the peripheral stretch receptor dbd.}, journal = {Neural Development}, volume = {6}, year = {2011}, month = {2011 Dec 12}, pages = {39}, abstract = {

Various members of the family of BTB/POZ zinc-finger transcription factors influence patterns of dendritic branching. One such member, Broad, is notable because its BrZ3 isoform is widely expressed in Drosophila in immature neurons around the time of arbor outgrowth. We used the metamorphic remodeling of an identified sensory neuron, the dorsal bipolar dendrite sensory neuron (dbd), to examine the effects of BrZ3 expression on the extent and pattern of dendrite growth during metamorphosis.

}, keywords = {Animals, Biological, Dendrites, Drosophila, Drosophila Proteins, Growth Cones, Mechanoreceptors, Metamorphosis, Neurons, Transcription Factors, Zinc Fingers}, issn = {1749-8104}, doi = {10.1186/1749-8104-6-39}, author = {Scott, Janet A and Williams, Darren W and Truman, James W} } @article {2341, title = {Cell assembly sequences arising from spike threshold adaptation keep track of time in the hippocampus.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {31}, year = {2011}, month = {2011 Feb 23}, pages = {2828-34}, abstract = {

Hippocampal neurons can display reliable and long-lasting sequences of transient firing patterns, even in the absence of changing external stimuli. We suggest that time-keeping is an important function of these sequences, and propose a network mechanism for their generation. We show that sequences of neuronal assemblies recorded from rat hippocampal CA1 pyramidal cells can reliably predict elapsed time (15-20 s) during wheel running with a precision of 0.5 s. In addition, we demonstrate the generation of multiple reliable, long-lasting sequences in a recurrent network model. These sequences are generated in the presence of noisy, unstructured inputs to the network, mimicking stationary sensory input. Identical initial conditions generate similar sequences, whereas different initial conditions give rise to distinct sequences. The key ingredients responsible for sequence generation in the model are threshold-adaptation and a Mexican-hat-like pattern of connectivity among pyramidal cells. This pattern may arise from recurrent systems such as the hippocampal CA3 region or the entorhinal cortex. We hypothesize that mechanisms that evolved for spatial navigation also support tracking of elapsed time in behaviorally relevant contexts.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3773-10.2011}, author = {Itskov, Vladimir and Curto, Carina and Pastalkova, Eva and Buzs{\'a}ki, Gy{\"o}rgy} } @article {47666, title = {Cell biology. SevERing mitochondria.}, journal = {Science (New York, N.Y.)}, volume = {334}, year = {2011}, month = {2011 Oct 14}, pages = {186-7}, keywords = {Cytosol, Dynamins, Endoplasmic Reticulum, Membrane Proteins, Mitochondria, Mitochondrial Proteins, Models, Biological, Yeasts}, issn = {1095-9203}, doi = {10.1126/science.1214059}, author = {Rambold, Angelika S and Lippincott-Schwartz, Jennifer} } @article {47657, title = {Cellular mechanism of bile acid-accelerated hepatocyte polarity.}, journal = {Small GTPases}, volume = {2}, year = {2011}, month = {2011 Nov 1}, pages = {314-317}, abstract = {

We recently discovered that the major mammalian bile acid, taurocholate, accelerated polarity in primary rat hepatocytes. Taurocholate increased cellular cAMP and signals through an Epac-Rap1-MEK-LKB1-AMPK pathway for its polarity effect. This review discusses possible mechanisms for how taurocholate affects different cell polarity factors, particularly AMPK, and thereby regulates events that generate polarity. These include tight junction formation, apical trafficking, recycling endosome dynamics, and cytoskeleton rearrangement. We also discuss whether the effects of taurocholate are mediated by other LKB1 downstream kinases, such as Par1 and NUAK1.

}, issn = {2154-1256}, doi = {10.4161/sgtp.18087}, author = {Fu, Dong and Lippincott-Schwartz, Jennifer and Arias, Irwin M} } @article {47221, title = {Cellular-resolution population imaging reveals robust sparse coding in the Drosophila mushroom body.}, journal = {The Journal of Neuroscience : the official journal of the Society for Neuroscience}, volume = {31}, year = {2011}, month = {2011 Aug 17}, pages = {11772-85}, abstract = {

Sensory stimuli are represented in the brain by the activity of populations of neurons. In most biological systems, studying population coding is challenging since only a tiny proportion of cells can be recorded simultaneously. Here we used two-photon imaging to record neural activity in the relatively simple Drosophila mushroom body (MB), an area involved in olfactory learning and memory. Using the highly sensitive calcium indicator GCaMP3, we simultaneously monitored the activity of \>100 MB neurons in vivo (\~{}5\% of the total population). The MB is thought to encode odors in sparse patterns of activity, but the code has yet to be explored either on a population level or with a wide variety of stimuli. We therefore imaged responses to odors chosen to evaluate the robustness of sparse representations. Different odors activated distinct patterns of MB neurons; however, we found no evidence for spatial organization of neurons by either response probability or odor tuning within the cell body layer. The degree of sparseness was consistent across a wide range of stimuli, from monomolecular odors to artificial blends and even complex natural smells. Sparseness was mainly invariant across concentrations, largely because of the influence of recent odor experience. Finally, in contrast to sensory processing in other systems, no response features distinguished natural stimuli from monomolecular odors. Our results indicate that the fundamental feature of odor processing in the MB is to create sparse stimulus representations in a format that facilitates arbitrary associations between odor and punishment or reward.

}, keywords = {Animals, Animals, Genetically Modified, Diagnostic Imaging, Drosophila, Microscopy, Fluorescence, Multiphoton, Mushroom Bodies, Odors, Olfactory Pathways, Olfactory Receptor Neurons, Random Allocation, Smell}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.1099-11.2011}, author = {Honegger, Kyle S and Campbell, Robert A A and Turner, Glenn C} } @article {3977, title = {Chemical and genetic engineering of selective ion channel-ligand interactions.}, journal = {Science}, volume = {333}, year = {2011}, month = {2011 Sep 2}, pages = {1292-6}, abstract = {

Ionic flux mediates essential physiological and behavioral functions in defined cell populations. Cell type-specific activators of diverse ionic conductances are needed for probing these effects. We combined chemistry and protein engineering to enable the systematic creation of a toolbox of ligand-gated ion channels (LGICs) with orthogonal pharmacologic selectivity and divergent functional properties. The LGICs and their small-molecule effectors were able to activate a range of ionic conductances in genetically specified cell types. LGICs constructed for neuronal perturbation could be used to selectively manipulate neuron activity in mammalian brains in vivo. The diversity of ion channel tools accessible from this approach will be useful for examining the relationship between neuronal activity and animal behavior, as well as for cell biological and physiological applications requiring chemical control of ion conductance.

}, keywords = {5-HT3, Animals, Benzamides, Bicyclo Compounds, Brain, Feeding Behavior, Female, Glycine, HEK293 Cells, Humans, Inbred C57BL, Ion Channel Gating, Ligand-Gated Ion Channels, Ligands, Membrane Potentials, Mice, Mutagenesis, Neurons, Nicotinic, Patch-Clamp Techniques, Protein Binding, Protein Engineering, Protein Structure, Quinuclidines, Receptors, Recombinant Fusion Proteins, Serotonin, Small Molecule Libraries, Stereoisomerism, Tertiary}, issn = {1095-9203}, doi = {10.1126/science.1206606}, author = {Magnus, Christopher J and Lee, Peter H and Atasoy, Deniz and Su, Helen H and Looger, Loren L and Sternson, Scott M} } @article {3294, title = {Coding of image feature descriptors for distributed rate-efficient visual correspondences.}, journal = {International Journal of Computer Vision}, volume = {94}, year = {2011}, month = {2011 Sep}, pages = {267-81}, abstract = {

Establishing visual correspondences is a critical step in many computer vision tasks involving multiple views of a scene. In a dynamic environment and when cameras are mobile, visual correspondences need to be updated on a recurring basis. At the same time, the use of wireless links between camera motes imposes tight rate constraints. This combination of issues motivates us to consider the problem of establishing visual correspondences in a distributed fashion between cameras operating under rate constraints. We propose a solution based on constructing distance preserving hashes using binarized random projections. By exploiting the fact that descriptors of regions in correspondence are highly correlated, we propose a novel use of distributed source coding via linear codes on the binary hashes to more efficiently exchange feature descriptors for establishing correspondences across multiple camera views. A systematic approach is used to evaluate rate vs visual correspondences retrieval performance; under a stringent matching criterion, our proposed methods demonstrate superior performance to a baseline scheme employing transform coding of descriptors.

}, issn = {0920-5691}, doi = {10.1007/s11263-011-0427-1}, author = {Ahammad, Parvez and Yeo, C and Ramchandran, K} } @article {1766, title = {The coding of temperature in the Drosophila brain.}, journal = {Cell}, volume = {144}, year = {2011}, month = {2011 Feb 18}, pages = {614-24}, abstract = {

Thermosensation is an indispensable sensory modality. Here, we study temperature coding in Drosophila, and show that temperature is represented by a spatial map of activity in the brain. First, we identify TRP channels that function in the fly antenna to mediate the detection of cold stimuli. Next, we identify the hot-sensing neurons and show that hot and cold antennal receptors project onto distinct, but adjacent glomeruli in the Proximal-Antennal-Protocerebrum (PAP) forming a thermotopic map in the brain. We use two-photon imaging to reveal the functional segregation of hot and cold responses in the PAP, and show that silencing the hot- or cold-sensing neurons produces animals with distinct and discrete deficits in their behavioral responses to thermal stimuli. Together, these results demonstrate that dedicated populations of cells orchestrate behavioral responses to different temperature stimuli, and reveal a labeled-line logic for the coding of temperature information in the brain.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2011.01.028}, author = {Gallio, Marco and Ofstad, Tyler A and Macpherson, Lindsey J and Wang, Jing W and Zuker, Charles S} } @article {2755, title = {A combinatorial semaphorin code instructs the initial steps of sensory circuit assembly in the Drosophila CNS.}, journal = {Neuron}, volume = {70}, year = {2011}, month = {2011 Apr 28}, pages = {281-98}, abstract = {

Longitudinal axon fascicles within the Drosophila embryonic CNS provide connections between body segments and are required for coordinated neural signaling along the anterior-posterior axis. We show here that establishment of select CNS longitudinal tracts and formation of precise mechanosensory afferent innervation to the same CNS region are coordinately regulated by the secreted semaphorins Sema-2a and Sema-2b. Both Sema-2a and Sema-2b utilize the same neuronal receptor, plexin B (PlexB), but serve distinct guidance functions. Localized Sema-2b attraction promotes the initial assembly of a subset of CNS longitudinal projections and subsequent targeting of chordotonal sensory afferent axons to these same longitudinal connectives, whereas broader Sema-2a repulsion serves to prevent aberrant innervation. In the absence of Sema-2b or PlexB, chordotonal afferent connectivity within the CNS is severely disrupted, resulting in specific larval behavioral deficits. These results reveal that distinct semaphorin-mediated guidance functions converge at PlexB and are critical for functional neural circuit assembly.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.02.050}, author = {Wu, Zhuhao and Sweeney, Lora B and Ayoob, Joseph C and Chak, Kayam and Andreone, Benjamin J and Ohyama, Tomoko and Kerr, Rex and Luo, Liqun and Zlatic, Marta and Kolodkin, Alex L} } @article {68821, title = {Compartmentalized Notch signaling sustains epithelial mirror symmetry}, journal = {Development}, volume = {138}, year = {2011}, month = {03/2011}, pages = {1143-1152}, abstract = {

Bilateral symmetric tissues must interpret axial references to maintain their global architecture during growth or repair. The regeneration of hair cells in the zebrafish lateral line, for example, forms a vertical midline that bisects the neuromast epithelium into perfect mirror-symmetric plane-polarized halves. Each half contains hair cells of identical planar orientation but opposite to that of the confronting half. The establishment of bilateral symmetry in this organ is poorly understood. Here, we show that hair-cell regeneration is strongly directional along an axis perpendicular to that of epithelial planar polarity. We demonstrate compartmentalized Notch signaling in neuromasts, and show that directional regeneration depends on the development of hair-cell progenitors in polar compartments that have low Notch activity. High-resolution live cell tracking reveals a novel process of planar cell inversions whereby sibling hair cells invert positions immediately after progenitor cytokinesis, demonstrating that oriented progenitor divisions are dispensable for bilateral symmetry. Notwithstanding the invariably directional regeneration, the planar polarization of the epithelium eventually propagates symmetrically because mature hair cells move away from the midline towards the periphery of the neuromast. We conclude that a strongly anisotropic regeneration process that relies on the dynamic stabilization of progenitor identity in permissive polar compartments sustains bilateral symmetry in the lateral line.

}, issn = {0950-1991}, doi = {10.1242/dev.060566}, url = {https://doi.org/10.1242/dev.060566}, author = {Wibowo, Indra and Pinto-Teixeira, Filipe and Satou, Chie and Higashijima, Shin-Ichi and L{\'o}pez-Schier, Hern{\'a}n} } @article {4070, title = {A computational statistics approach for estimating the spatial range of morphogen gradients.}, journal = {Development}, volume = {138}, year = {2011}, month = {2011 Nov}, pages = {4867-74}, abstract = {

A crucial issue in studies of morphogen gradients relates to their range: the distance over which they can act as direct regulators of cell signaling, gene expression and cell differentiation. To address this, we present a straightforward statistical framework that can be used in multiple developmental systems. We illustrate the developed approach by providing a point estimate and confidence interval for the spatial range of the graded distribution of nuclear Dorsal, a transcription factor that controls the dorsoventral pattern of the Drosophila embryo.

}, issn = {1477-9129}, doi = {10.1242/dev.071571}, author = {Kanodia, Jitendra S and Kim, Yoosik and Tomer, Raju and Khan, Zia and Chung, Kwanghun and Storey, John D and Lu, Hang and Keller, Philipp J and Shvartsman, Stansilas Y} } @article {5411, title = {Control of embryonic stem cell lineage commitment by core promoter factor, TAF3.}, journal = {Cell}, volume = {146}, year = {2011}, month = {2011 Sep 2}, pages = {720-31}, abstract = {

Deciphering the molecular basis of pluripotency is fundamental to our understanding of development and embryonic stem cell function. Here, we report that TAF3, a TBP-associated core promoter factor, is highly enriched in ES cells. In this context, TAF3 is required for endoderm lineage differentiation and prevents premature specification of neuroectoderm and mesoderm. In addition to its role in the core promoter recognition complex TFIID, genome-wide binding studies reveal that TAF3 localizes to a subset of chromosomal regions bound by CTCF/cohesin that are selectively associated with genes upregulated by TAF3. Notably, CTCF directly recruits TAF3 to promoter distal sites and TAF3-dependent DNA looping is observed between the promoter distal sites and core promoters occupied by TAF3/CTCF/cohesin. Together, our findings support a new role of TAF3 in mediating long-range chromatin regulatory interactions that safeguard the finely-balanced transcriptional programs underlying pluripotency.

}, keywords = {Animals, Cell Cycle Proteins, Cell Proliferation, Chromosomal Proteins, Developmental, Embryonic Stem Cells, Endoderm, Gene Expression Regulation, Genetic, Homeodomain Proteins, Humans, Mice, Non-Histone, Promoter Regions, Repressor Proteins, Teratoma, Transcription, Transcription Factor TFIID}, issn = {1097-4172}, doi = {10.1016/j.cell.2011.08.005}, author = {Liu, Zhe and Scannell, Devin R and Eisen, Michael B and Tjian, Robert} } @article {2384, title = {Core promoter recognition complex changes accompany liver development.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Mar 8}, pages = {3906-11}, abstract = {

Recent studies of several key developmental transitions have brought into question the long held view of the basal transcriptional apparatus as ubiquitous and invariant. In an effort to better understand the role of core promoter recognition and coactivator complex switching in cellular differentiation, we have examined changes in transcription factor IID (TFIID) and cofactor required for Sp1 activation/Mediator during mouse liver development. Here we show that the differentiation of fetal liver progenitors to adult hepatocytes involves a wholesale depletion of canonical cofactor required for Sp1 activation/Mediator and TFIID complexes at both the RNA and protein level, and that this alteration likely involves silencing of transcription factor promoters as well as protein degradation. It will be intriguing for future studies to determine if a novel and as yet unknown core promoter recognition complex takes the place of TFIID in adult hepatocytes and to uncover the mechanisms that down-regulate TFIID during this critical developmental transition.

}, issn = {1091-6490}, doi = {10.1073/pnas.1100640108}, author = {D{\textquoteright}Alessio, Joseph A and Ng, Raymond and Willenbring, Holger and Tjian, Robert} } @article {46736, title = {Cotranscriptional effect of a premature termination codon revealed by live-cell imaging.}, journal = {RNA}, volume = {17}, year = {2011}, month = {2011 Dec}, pages = {2094-107}, abstract = {

Aberrant mRNAs with premature translation termination codons (PTCs) are recognized and eliminated by the nonsense-mediated mRNA decay (NMD) pathway in eukaryotes. We employed a novel live-cell imaging approach to investigate the kinetics of mRNA synthesis and release at the transcription site of PTC-containing (PTC+) and PTC-free (PTC-) immunoglobulin-μ reporter genes. Fluorescence recovery after photobleaching (FRAP) and photoconversion analyses revealed that PTC+ transcripts are specifically retained at the transcription site. Remarkably, the retained PTC+ transcripts are mainly unspliced, and this RNA retention is dependent upon two important NMD factors, UPF1 and SMG6, since their depletion led to the release of the PTC+ transcripts. Finally, ChIP analysis showed a physical association of UPF1 and SMG6 with both the PTC+ and the PTC- reporter genes in vivo. Collectively, our data support a mechanism for regulation of PTC+ transcripts at the transcription site.

}, keywords = {Cell Line, Codon, Nonsense, Cytoplasm, Gene Expression Regulation, Gene Order, Gene Silencing, Humans, Immunoglobulin mu-Chains, In Situ Hybridization, Fluorescence, Nonsense Mediated mRNA Decay, RNA Splicing, RNA, Messenger, Telomerase, Trans-Activators, Transcription, Genetic}, issn = {1469-9001}, doi = {10.1261/rna.02918111}, author = {de Turris, Valeria and Nicholson, Pamela and Orozco, Rodolfo Zamudio and Singer, Robert H and M{\"u}hlemann, Oliver} } @article {6524, title = {A critical role of mitochondrial phosphatase Ptpmt1 in embryogenesis reveals a mitochondrial metabolic stress-induced differentiation checkpoint in embryonic stem cells.}, journal = {Molecular and Cellular Biology}, volume = {31}, year = {2011}, month = {2011 Dec}, pages = {4902-16}, abstract = {

Mitochondria are highly dynamic organelles that play multiple roles in cells. How mitochondria cooperatively modulate embryonic stem (ES) cell function during development is not fully understood. Global disruption of Ptpmt1, a mitochondrial Pten-like phosphatidylinositol phosphate (PIP) phosphatase, resulted in developmental arrest and postimplantation lethality. Ptpmt1(-/-) blastocysts failed to outgrow, and inner-cell-mass cells failed to thrive. Depletion of Ptpmt1 in conditional knockout ES cells decreased proliferation without affecting energy homeostasis or cell survival. Differentiation of Ptpmt1-depleted ES cells was essentially blocked. This was accompanied by upregulation of cyclin-dependent kinase inhibitors and a significant cell cycle delay. Reintroduction of wild-type but not of catalytically deficient Ptpmt1 C132S or truncated Ptpmt1 lacking the mitochondrial localization signal restored the differentiation capabilities of Ptpmt1 knockout ES cells. Intriguingly, Ptpmt1 is specifically important for stem cells, as ablation of Ptpmt1 in differentiated embryonic fibroblasts did not disturb cellular function. Further analyses demonstrated that oxygen consumption of Ptpmt1-depleted cells was decreased, while glycolysis was concomitantly enhanced. In addition, mitochondrial fusion/dynamics were compromised in Ptpmt1 knockout cells due to accumulation of PIPs. These studies, while establishing a crucial role for Ptpmt1 phosphatase in embryogenesis, reveal a mitochondrial metabolic stress-activated checkpoint in the control of ES cell differentiation.

}, keywords = {Alleles, Animals, Apoptosis, Cell Cycle Checkpoints, Cell Differentiation, Cell Proliferation, Cloning, Confocal, Embryonic Development, Embryonic Stem Cells, Fibroblasts, Glycolysis, Immunohistochemistry, In Situ Nick-End Labeling, Knockout, Mice, Microscopy, Mitochondria, Molecular, Phosphatidylinositol Phosphates, Physiological, PTEN Phosphohydrolase, Reactive Oxygen Species, Stress}, issn = {1098-5549}, doi = {10.1128/MCB.05629-11}, author = {Shen, Jinhua and Liu, Xia and Yu, Wen-Mei and Liu, Jie and Nibbelink, Milou Groot and Guo, Caiying and Finkel, Toren and Qu, Cheng-Kui} } @article {46735, title = {A date with telomerase: pick you up at S phase.}, journal = {Molecular Cell}, volume = {44}, year = {2011}, month = {2011 Dec 9}, pages = {685-6}, abstract = {

Using the MS2 system for labeling mRNA, in this issue, Gallardo et al. (2011) find that telomere lengthening depends on a stable accumulation of multiple telomerase complexes in late S phase and that this process is temporally regulated by Rif1/2 proteins.

}, issn = {1097-4164}, doi = {10.1016/j.molcel.2011.11.013}, author = {Hocine, S and Singer, R H} } @article {6874, title = {Deletion of the betaine-GABA transporter (BGT1; slc6a12) gene does not affect seizure thresholds of adult mice.}, journal = {Epilepsy Research}, volume = {95}, year = {2011}, month = {2011 Jun}, pages = {70-81}, abstract = {

Gamma-aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the mammalian brain. Once released, it is removed from the extracellular space by cellular uptake catalyzed by GABA transporter proteins. Four GABA transporters (GAT1, GAT2, GAT3 and BGT1) have been identified. Inhibition of the GAT1 by the clinically available anti-epileptic drug tiagabine has been an effective strategy for the treatment of some patients with partial seizures. Recently, the investigational drug EF1502, which inhibits both GAT1 and BGT1, was found to exert an anti-convulsant action synergistic to that of tiagabine, supposedly due to inhibition of BGT1. The present study addresses the role of BGT1 in seizure control and the effect of EF1502 by developing and exploring a new mouse line lacking exons 3-5 of the BGT1 (slc6a12) gene. The deletion of this sequence abolishes the expression of BGT1 mRNA. However, homozygous BGT1-deficient mice have normal development and show seizure susceptibility indistinguishable from that in wild-type mice in a variety of seizure threshold models including: corneal kindling, the minimal clonic and minimal tonic extension seizure threshold tests, the 6Hz seizure threshold test, and the i.v. pentylenetetrazol threshold test. We confirm that BGT1 mRNA is present in the brain, but find that the levels are several hundred times lower than those of GAT1 mRNA; possibly explaining the apparent lack of phenotype. In conclusion, the present results do not support a role for BGT1 in the control of seizure susceptibility and cannot provide a mechanistic understanding of the synergism that has been previously reported with tiagabine and EF1502.

}, keywords = {Animals, Anticonvulsants, Convulsants, Crosses, Dose-Response Relationship, Drug, Electroshock, Exons, Female, GABA Plasma Membrane Transport Proteins, Genetic, Inbred C57BL, Isoxazoles, Kindling, Knockout, Male, Messenger, Mice, Neurologic, Nipecotic Acids, Pentylenetetrazole, RNA, Seizures}, issn = {1872-6844}, doi = {10.1016/j.eplepsyres.2011.02.014}, author = {Lehre, A C and Rowley, N M and Zhou, Y. and Holmseth, S and Guo, C and Holen, T and Hua, R and Laake, P and Olofsson, A M and Poblete-Naredo, I and Rusakov, D A and Madsen, K K and Clausen, R P and Schousboe, A and White, H S and Danbolt, N C} } @article {6517, title = {Development and characterization of a mouse with profound biotinidase deficiency: a biotin-responsive neurocutaneous disorder.}, journal = {Molecular Genetics and Metabolism}, volume = {102}, year = {2011}, month = {2011 Feb}, pages = {161-9}, abstract = {

Biotinidase deficiency is the primary enzymatic defect in biotin-responsive, late-onset multiple carboxylase deficiency. Untreated children with profound biotinidase deficiency usually exhibit neurological symptoms including lethargy, hypotonia, seizures, developmental delay, sensorineural hearing loss and optic atrophy; and cutaneous symptoms including skin rash, conjunctivitis and alopecia. Although the clinical features of the disorder markedly improve or are prevented with biotin supplementation, some symptoms, once they occur, such as developmental delay, hearing loss and optic atrophy, are usually irreversible. To prevent development of symptoms, the disorder is screened for in the newborn period in essentially all states and in many countries. In order to better understand many aspects of the pathophysiology of the disorder, we have developed a transgenic biotinidase-deficient mouse. The mouse has a null mutation that results in no detectable serum biotinidase activity or cross-reacting material to antibody prepared against biotinidase. When fed a biotin-deficient diet these mice develop neurological and cutaneous symptoms, carboxylase deficiency, mild hyperammonemia, and exhibit increased urinary excretion of 3-hydroxyisovaleric acid and biotin and biotin metabolites. The clinical features are reversed with biotin supplementation. This biotinidase-deficient animal can be used to study systematically many aspects of the disorder and the role of biotinidase, biotin and biocytin in normal and in enzyme-deficient states.

}, keywords = {Animal, Animals, Behavior, Biotin, Biotinidase, Biotinidase Deficiency, Body Weight, Diet, Disease Models, Enzymologic, Female, Gene Expression Regulation, Inbred C57BL, Knockout, Liver, Male, Mice, Neurocutaneous Syndromes, Vitamin B Complex}, issn = {1096-7206}, doi = {10.1016/j.ymgme.2010.10.005}, author = {Pindolia, Kirit and Jordan, Megan and Guo, Caiying and Matthews, Nell and Mock, Donald M and Strovel, Erin and Blitzer, Miriam and Wolf, Barry} } @article {5379, title = {DIADEMchallenge.org: a compendium of resources fostering the continuous development of automated neuronal reconstruction.}, journal = {Neuroinformatics}, volume = {9}, year = {2011}, month = {2011 Sep}, pages = {303-4}, abstract = {

Concomitant with the publication of this Special Issue of Neuroinformatics, a substantially updated version of the DIADEM web site has been released at http://diademchallenge.org. This web site was originally designed to host the challenge for automating the digital reconstruction of axonal and dendritic morphology (hence the DIADEM acronym). This post-competition version features additional content for continued use as the access point for DIADEM-related material. From the very beginning, one of the spirits of DIADEM has been to share data and resources with the neuroscience research community at large. The resources available from or linked to the DIADEM website constitute a substantial scientific legacy of the 2009/2010 competition. The new content includes finalist algorithms, image stack data, gold standard reconstructions, an updated DIADEM metric, and a retrospective on the competition in text and images.

}, doi = {10.1007/s12021-011-9104-3}, author = {Gillette, Todd A. and Brown, Kerry M. and Svoboda, Karel and Liu, Yuan and Ascoli, Giorgio A.} } @article {4071, title = {Digital scanned laser light-sheet fluorescence microscopy (DSLM) of zebrafish and Drosophila embryonic development.}, journal = {Cold Spring Harbor Protocols}, volume = {2011}, year = {2011}, month = {2011 Oct}, pages = {1235-43}, abstract = {

Embryonic development is one of the most complex processes encountered in biology. In vertebrates and higher invertebrates, a single cell transforms into a fully functional organism comprising several tens of thousands of cells, arranged in tissues and organs that perform impressive tasks. In vivo observation of this biological process at high spatiotemporal resolution and over long periods of time is crucial for quantitative developmental biology. Importantly, such recordings must be realized without compromising the physiological development of the specimen. In digital scanned laser light-sheet fluorescence microscopy (DSLM), a specimen is rapidly scanned with a thin sheet of light while fluorescence is recorded perpendicular to the axis of illumination with a camera. Combining light-sheet technology and fast laser scanning, DSLM delivers quantitative data for entire embryos at high spatiotemporal resolution. Compared with confocal and two-photon fluorescence microscopy, DSLM exposes the embryo to at least three orders of magnitude less light energy, but still provides up to 50 times faster imaging speeds and a 10{\textendash}100-fold higher signal-to-noise ratio. By using automated image processing algorithms, DSLM images of embryogenesis can be converted into a digital representation. These digital embryos permit following cells as a function of time, revealing cell fate as well as cell origin. By means of such analyses, developmental building plans of tissues and organs can be determined in a whole-embryo context. This article presents a sample preparation and imaging protocol for studying the development of whole zebrafish and Drosophila embryos using DSLM.

}, issn = {1559-6095}, doi = {10.1101/pdb.prot065839}, author = {Keller, Philipp J and Schmidt, Annette D and Wittbrodt, Jochen and Stelzer, Ernst H K} } @article {3358, title = {Direct targets of the D. melanogaster DSXF protein and the evolution of sexual development.}, journal = {Development}, volume = {138}, year = {2011}, month = {2011 Jul}, pages = {2761-71}, abstract = {

Uncovering the direct regulatory targets of doublesex (dsx) and fruitless (fru) is crucial for an understanding of how they regulate sexual development, morphogenesis, differentiation and adult functions (including behavior) in Drosophila melanogaster. Using a modified DamID approach, we identified 650 DSX-binding regions in the genome from which we then extracted an optimal palindromic 13 bp DSX-binding sequence. This sequence is functional in vivo, and the base identity at each position is important for DSX binding in vitro. In addition, this sequence is enriched in the genomes of D. melanogaster (58 copies versus approximately the three expected from random) and in the 11 other sequenced Drosophila species, as well as in some other Dipterans. Twenty-three genes are associated with both an in vivo peak in DSX binding and an optimal DSX-binding sequence, and thus are almost certainly direct DSX targets. The association of these 23 genes with optimum DSX binding sites was used to examine the evolutionary changes occurring in DSX and its targets in insects.

}, issn = {1477-9129}, doi = {10.1242/dev.065227}, author = {Luo, Shengzhan D and Shi, Guang W and Baker, Bruce S} } @article {46042, title = {Disruption of circadian clocks has ramifications for metabolism, brain, and behavior.}, journal = {Proceedings of the National Academy of Sciences USA}, volume = {108}, year = {2011}, month = {2011 Jan 25}, pages = {1657-62}, abstract = {

Circadian (daily) rhythms are present in almost all plants and animals. In mammals, a brain clock located in the hypothalamic suprachiasmatic nucleus maintains synchrony between environmental light/dark cycles and physiology and behavior. Over the past 100 y, especially with the advent of electric lighting, modern society has resulted in a round-the-clock lifestyle, in which natural connections between rest/activity cycles and environmental light/dark cycles have been degraded or even broken. Instances in which rapid changes to sleep patterns are necessary, such as transmeridian air travel, demonstrate negative effects of acute circadian disruption on physiology and behavior. However, the ramifications of chronic disruption of the circadian clock for mental and physical health are not yet fully understood. By housing mice in 20-h light/dark cycles, incongruous with their endogenous \~{}24-h circadian period, we were able to model the effects of chronic circadian disruption noninvasively. Housing in these conditions results in accelerated weight gain and obesity, as well as changes in metabolic hormones. In the brain, circadian-disrupted mice exhibit a loss of dendritic length and decreased complexity of neurons in the prelimbic prefrontal cortex, a brain region important in executive function and emotional control. Disrupted animals show decreases in cognitive flexibility and changes in emotionality consistent with the changes seen in neural architecture. How our findings translate to humans living and working in chronic circadian disruption is unknown, but we believe that this model can provide a foundation to understand how environmental disruption of circadian rhythms impacts the brain, behavior, and physiology.

}, keywords = {Animals, Behavior, Animal, Biological Clocks, Blood Glucose, Body Temperature, Brain, Circadian Clocks, Circadian Rhythm, Energy Metabolism, Humans, Insulin, Leptin, Male, Maze Learning, Mice, Mice, Inbred C57BL, Motor Activity, Neurons, Photoperiod, Prefrontal Cortex, Weight Gain}, issn = {1091-6490}, doi = {10.1073/pnas.1018375108}, author = {Karatsoreos, Ilia N and Bhagat, Sarah and Bloss, Erik B and Morrison, John H and McEwen, Bruce S} } @article {46050, title = {Distinct functions of kainate receptors in the brain are determined by the auxiliary subunit Neto1.}, journal = {Nature Neuroscience}, volume = {14}, year = {2011}, month = {2011 Jul}, pages = {866-73}, abstract = {

Ionotropic glutamate receptors principally mediate fast excitatory transmission in the brain. Among the three classes of ionotropic glutamate receptors, kainate receptors (KARs) have a unique brain distribution, which has been historically defined by (3)H-radiolabeled kainate binding. Compared with recombinant KARs expressed in heterologous cells, synaptic KARs exhibit characteristically slow rise-time and decay kinetics. However, the mechanisms responsible for these distinct KAR properties remain unclear. We found that both the high-affinity binding pattern in the mouse brain and the channel properties of native KARs are determined by the KAR auxiliary subunit Neto1. Through modulation of agonist binding affinity and off-kinetics of KARs, but not trafficking of KARs, Neto1 determined both the KAR high-affinity binding pattern and the distinctively slow kinetics of postsynaptic KARs. By regulating KAR excitatory postsynaptic current kinetics, Neto1 can control synaptic temporal summation, spike generation and fidelity.

}, keywords = {Animals, Animals, Newborn, Biophysical Phenomena, Biophysics, CA1 Region, Hippocampal, Cell Line, Transformed, Cerebellum, Dizocilpine Maleate, Dose-Response Relationship, Drug, Drug Interactions, Electric Stimulation, Excitatory Amino Acid Agonists, Excitatory Amino Acid Antagonists, Excitatory Postsynaptic Potentials, Gene Expression Regulation, Green Fluorescent Proteins, Guanylate Kinase, Humans, Immunoprecipitation, In Vitro Techniques, Intracellular Signaling Peptides and Proteins, Kainic Acid, Lipoproteins, LDL, Membrane Potentials, Membrane Proteins, Mice, Mice, Knockout, Neurons, Patch-Clamp Techniques, Presynaptic Terminals, Protein Binding, Protein Subunits, Receptors, Kainic Acid, Synaptophysin, Transfection, Tritium}, issn = {1546-1726}, doi = {10.1038/nn.2837}, author = {Straub, Christoph and Hunt, David L and Yamasaki, Miwako and Kim, Kwang S and Watanabe, Masahiko and Castillo, Pablo E and Tomita, Susumu} } @article {1513, title = {Drosophila brainbow: a recombinase-based fluorescence labeling technique to subdivide neural expression patterns.}, journal = {Nature Methods}, volume = {8}, year = {2011}, month = {2011 Mar}, pages = {253-9}, abstract = {

We developed a multicolor neuron labeling technique in Drosophila melanogaster that combines the power to specifically target different neural populations with the label diversity provided by stochastic color choice. This adaptation of vertebrate Brainbow uses recombination to select one of three epitope-tagged proteins detectable by immunofluorescence. Two copies of this construct yield six bright, separable colors. We used Drosophila Brainbow to study the innervation patterns of multiple antennal lobe projection neuron lineages in the same preparation and to observe the relative trajectories of individual aminergic neurons. Nerve bundles, and even individual neurites hundreds of micrometers long, can be followed with definitive color labeling. We traced motor neurons in the subesophageal ganglion and correlated them to neuromuscular junctions to identify their specific proboscis muscle targets. The ability to independently visualize multiple lineage or neuron projections in the same preparation greatly advances the goal of mapping how neurons connect into circuits.

}, issn = {1548-7105}, doi = {10.1038/nmeth.1566}, author = {Hampel, Stefanie and Chung, Phuong and McKellar, Claire E and Hall, Donald and Looger, Loren L and Simpson, Julie H} } @article {5686, title = {The Drosophila larval visual system: high-resolution analysis of a simple visual neuropil.}, journal = {Developmental Biology}, volume = {358}, year = {2011}, month = {2011 Oct 1}, pages = {33-43}, abstract = {

The task of the visual system is to translate light into neuronal encoded information. This translation of photons into neuronal signals is achieved by photoreceptor neurons (PRs), specialized sensory neurons, located in the eye. Upon perception of light the PRs will send a signal to target neurons, which represent a first station of visual processing. Increasing complexity of visual processing stems from the number of distinct PR subtypes and their various types of target neurons that are contacted. The visual system of the fruit fly larva represents a simple visual system (larval optic neuropil, LON) that consists of 12 PRs falling into two classes: blue-senstive PRs expressing Rhodopsin 5 (Rh5) and green-sensitive PRs expressing Rhodopsin 6 (Rh6). These afferents contact a small number of target neurons, including optic lobe pioneers (OLPs) and lateral clock neurons (LNs). We combine the use of genetic markers to label both PR subtypes and the distinct, identifiable sets of target neurons with a serial EM reconstruction to generate a high-resolution map of the larval optic neuropil. We find that the larval optic neuropil shows a clear bipartite organization consisting of one domain innervated by PRs and one devoid of PR axons. The topology of PR projections, in particular the relationship between Rh5 and Rh6 afferents, is maintained from the nerve entering the brain to the axon terminals. The target neurons can be subdivided according to neurotransmitter or neuropeptide they use as well as the location within the brain. We further track the larval optic neuropil through development from first larval instar to its location in the adult brain as the accessory medulla.

}, keywords = {Animals, Confocal, Drosophila, Drosophila Proteins, Electron, Immunohistochemistry, Invertebrate, Larva, Microscopy, Neuropil, Ocular, Photoreceptor Cells, Rhodopsin, Synapses, Transmission, Vision}, issn = {1095-564X}, doi = {10.1016/j.ydbio.2011.07.006}, author = {Sprecher, Simon G and Cardona, Albert and Hartenstein, Volker.} } @article {4524, title = {A Drosophila model for alcohol reward.}, journal = {Nature Neuroscience}, volume = {14}, year = {2011}, month = {2011 May}, pages = {612-9}, abstract = {

The rewarding properties of drugs contribute to the development of abuse and addiction. We developed a new assay for investigating the motivational properties of ethanol in the genetically tractable model Drosophila melanogaster. Flies learned to associate cues with ethanol intoxication and, although transiently aversive, the experience led to a long-lasting attraction for the ethanol-paired cue, implying that intoxication is rewarding. Temporally blocking transmission in dopaminergic neurons revealed that flies require activation of these neurons to express, but not develop, conditioned preference for ethanol-associated cues. Moreover, flies acquired, consolidated and retrieved these rewarding memories using distinct sets of neurons in the mushroom body. Finally, mutations in scabrous, encoding a fibrinogen-related peptide that regulates Notch signaling, disrupted the formation of memories for ethanol reward. Our results thus establish that Drosophila can be useful for understanding the molecular, genetic and neural mechanisms underling the rewarding properties of ethanol.

}, keywords = {Alcohol-Related Disorders, Alcohols, Analysis of Variance, Animal, Animals, Behavior, Chromatography, Conditioning (Psychology), Disease Models, Dopamine, Drosophila, Drosophila Proteins, Electric Stimulation, Ethanol, Food Preferences, Genetically Modified, Green Fluorescent Proteins, High Pressure Liquid, Male, Maze Learning, Mushroom Bodies, Neurons, Odors, Reward, Synaptic Transmission, Time Factors, Tyrosine 3-Monooxygenase}, issn = {1546-1726}, doi = {10.1038/nn.2805}, author = {Kaun, Karla R and Azanchi, Reza and Maung, Zaw and Hirsh, Jay and Heberlein, Ulrike} } @article {5484, title = {A Drosophila model for fetal alcohol syndrome disorders: role for the insulin pathway.}, journal = {Disease Models \& Mechanisms}, volume = {4}, year = {2011}, month = {2011 May}, pages = {335-46}, abstract = {

Prenatal exposure to ethanol in humans results in a wide range of developmental abnormalities, including growth deficiency, developmental delay, reduced brain size, permanent neurobehavioral abnormalities and fetal death. Here we describe the use of Drosophila melanogaster as a model for exploring the effects of ethanol exposure on development and behavior. We show that developmental ethanol exposure causes reduced viability, developmental delay and reduced adult body size. We find that flies reared on ethanol-containing food have smaller brains and imaginal discs, which is due to reduced cell division rather than increased apoptosis. Additionally, we show that, as in mammals, flies reared on ethanol have altered responses to ethanol vapor exposure as adults, including increased locomotor activation, resistance to the sedating effects of the drug and reduced tolerance development upon repeated ethanol exposure. We have found that the developmental and behavioral defects are largely due to the effects of ethanol on insulin signaling; specifically, a reduction in Drosophila insulin-like peptide (Dilp) and insulin receptor expression. Transgenic expression of Dilp proteins in the larval brain suppressed both the developmental and behavioral abnormalities displayed by ethanol-reared adult flies. Our results thus establish Drosophila as a useful model system to uncover the complex etiology of fetal alcohol syndrome.

}, keywords = {Adaptation, Animal, Animals, Apoptosis, Behavior, Brain, Cell Proliferation, Disease Models, Drosophila melanogaster, Drosophila Proteins, Ethanol, Eye, Female, Fetal Alcohol Syndrome, Humans, Insulin, Larva, Physiological, Pregnancy, Receptor, Signal Transduction, Survival Analysis}, issn = {1754-8411}, doi = {10.1242/dmm.006411}, author = {McClure, Kimberly D and French, Rachael L and Heberlein, Ulrike} } @article {4525, title = {Drosophila tao controls mushroom body development and ethanol-stimulated behavior through par-1.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {31}, year = {2011}, month = {2011 Jan 19}, pages = {1139-48}, abstract = {

In both mammalian and insect models of ethanol-induced behavior, low doses of ethanol stimulate locomotion. However, the mechanisms of the stimulant effects of ethanol on the CNS are mostly unknown. We have identified tao, encoding a serine-threonine kinase of the Ste20 family, as a gene necessary for ethanol-induced locomotor hyperactivity in Drosophila. Mutations in tao also affect behavioral responses to cocaine and nicotine, making flies resistant to the effects of both drugs. We show that tao function is required during the development of the adult nervous system and that tao mutations cause defects in the development of central brain structures, including the mushroom body. Silencing of a subset of mushroom body neurons is sufficient to reduce ethanol-induced hyperactivity, revealing the mushroom body as an important locus mediating the stimulant effects of ethanol. We also show that mutations in par-1 suppress both the mushroom body morphology and behavioral phenotypes of tao mutations and that the phosphorylation state of the microtubule-binding protein Tau can be altered by RNA interference knockdown of tao, suggesting that tao and par-1 act in a pathway to control microtubule dynamics during neural development.

}, keywords = {Analysis of Variance, Animal, Animals, Behavior, Biological, Blotting, Drosophila, Drosophila Proteins, Ethanol, Hyperkinesis, Immunohistochemistry, Metamorphosis, Motor Activity, Mushroom Bodies, Neurons, Protein-Serine-Threonine Kinases, Western}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4416-10.2011}, author = {King, Ian and Tsai, Linus T-Y and Pflanz, Ralf and Voigt, Aaron and Lee, Seongsoo and J{\"a}ckle, Herbert and Lu, Bingwei and Heberlein, Ulrike} } @article {47672, title = {Dynamics of endosomal sorting complex required for transport (ESCRT) machinery during cytokinesis and its role in abscission.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Mar 22}, pages = {4846-51}, abstract = {

The final stage of cytokinesis is abscission, the cutting of the narrow membrane bridge connecting two daughter cells. The endosomal sorting complex required for transport (ESCRT) machinery is required for cytokinesis, and ESCRT-III has membrane scission activity in vitro, but the role of ESCRTs in abscission has been undefined. Here, we use structured illumination microscopy and time-lapse imaging to dissect the behavior of ESCRTs during abscission. Our data reveal that the ESCRT-I subunit tumor-susceptibility gene 101 (TSG101) and the ESCRT-III subunit charged multivesicular body protein 4b (CHMP4B) are sequentially recruited to the center of the intercellular bridge, forming a series of cortical rings. Late in cytokinesis, however, CHMP4B is acutely recruited to the narrow constriction site where abscission occurs. The ESCRT disassembly factor vacuolar protein sorting 4 (VPS4) follows CHMP4B to this site, and cell separation occurs immediately. That arrival of ESCRT-III and VPS4 correlates both spatially and temporally with the abscission event suggests a direct role for these proteins in cytokinetic membrane abscission.

}, keywords = {Animals, Cell Line, Cytokinesis, DNA-Binding Proteins, Dogs, Endosomal Sorting Complexes Required for Transport, Endosomes, Humans, Transcription Factors}, issn = {1091-6490}, doi = {10.1073/pnas.1102714108}, author = {Elia, Natalie and Sougrat, Rachid and Spurlin, Tighe A and Hurley, James H and Lippincott-Schwartz, Jennifer} } @article {5660, title = {Effective stimuli for constructing reliable neuron models.}, journal = {PLoS Computational Biology}, volume = {7}, year = {2011}, month = {2011 Aug}, pages = {e1002133}, abstract = {

The rich dynamical nature of neurons poses major conceptual and technical challenges for unraveling their nonlinear membrane properties. Traditionally, various current waveforms have been injected at the soma to probe neuron dynamics, but the rationale for selecting specific stimuli has never been rigorously justified. The present experimental and theoretical study proposes a novel framework, inspired by learning theory, for objectively selecting the stimuli that best unravel the neuron{\textquoteright}s dynamics. The efficacy of stimuli is assessed in terms of their ability to constrain the parameter space of biophysically detailed conductance-based models that faithfully replicate the neuron{\textquoteright}s dynamics as attested by their ability to generalize well to the neuron{\textquoteright}s response to novel experimental stimuli. We used this framework to evaluate a variety of stimuli in different types of cortical neurons, ages and animals. Despite their simplicity, a set of stimuli consisting of step and ramp current pulses outperforms synaptic-like noisy stimuli in revealing the dynamics of these neurons. The general framework that we propose paves a new way for defining, evaluating and standardizing effective electrical probing of neurons and will thus lay the foundation for a much deeper understanding of the electrical nature of these highly sophisticated and non-linear devices and of the neuronal networks that they compose.

}, keywords = {Action Potentials, Algorithms, Animals, Computational Biology, Electric Conductivity, Electrophysiology, Interneurons, Mice, Models, Neurological, Neurons, Patch-Clamp Techniques, Pyramidal Cells, Rats, Wistar}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1002133}, author = {Druckmann, Shaul and Berger, Thomas K and Sch{\"u}rmann, Felix and Hill, Sean and Markram, Henry and Segev, Idan} } @article {4228, title = {Electrical synaptic input to ganglion cells underlies differences in the output and absolute sensitivity of parallel retinal circuits.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {31}, year = {2011}, month = {2011 Aug 24}, pages = {12218-28}, abstract = {

Parallel circuits throughout the CNS exhibit distinct sensitivities and responses to sensory stimuli. Ambiguities in the source and properties of signals elicited by physiological stimuli, however, frequently obscure the mechanisms underlying these distinctions. We found that differences in the degree to which activity in two classes of Off retinal ganglion cell (RGC) encode information about light stimuli near detection threshold were not due to obvious differences in the cells{\textquoteright} intrinsic properties or the chemical synaptic input the cells received; indeed, differences in the cells{\textquoteright} light responses were largely insensitive to block of fast ionotropic glutamate receptors. Instead, the distinct responses of the two types of RGCs likely reflect differences in light-evoked electrical synaptic input. These results highlight a surprising strategy by which the retina differentially processes and routes visual information and provide new insight into the circuits that underlie responses to stimuli near detection threshold.

}, keywords = {Animals, Cell Communication, Electrical Synapses, Inbred C57BL, Ionotropic Glutamate, Mice, Neural Pathways, Ocular, Organ Culture Techniques, Photic Stimulation, Receptors, Retina, Retinal Ganglion Cells, Sensitivity and Specificity, Sensory Thresholds, Synaptic Transmission, Vision, Visual Pathways}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3241-11.2011}, author = {Murphy, Gabe J and Rieke, Fred} } @article {2906, title = {Electro-optical pockels scattering from a single nanocrystal.}, journal = {Optics Express}, volume = {19}, year = {2011}, month = {2011 May 9}, pages = {9000-7}, abstract = {

The electro-optical Pockels response from a single non-centrosymmetric nanocrystal is reported. High sensitivity to the weak electric-field dependent nonlinear scattering is achieved through a dedicated imaging interferometric microscope and the linear dependence of electro-optical signal upon the applied field is checked. Using different incident light polarization states, a priori random spatial orientation of the crystal can be inferred. The electro-optical response from a nanocrystal provides local subwavelength sensor of quasi-static electric fields with potential applications in physics and biology. It also leads to a new sub-wavelength microscopy towards the nanoscale investigation of interesting phenomena such as nanoferroelectricity.

}, issn = {1094-4087}, doi = {10.1364/OE.19.009000}, author = {Hajj, Bassam and Perruchas, Sandrine and Lautru, Joseph and Dantelle, G{\'e}raldine and Gacoin, Thierry and Zyss, Joseph and Chauvat, Dominique} } @article {47670, title = {Emerging in vivo analyses of cell function using fluorescence imaging (*).}, journal = {Annual review of biochemistry}, volume = {80}, year = {2011}, month = {2011}, pages = {327-32}, abstract = {

Understanding how cells of all types sense external and internal signals and how these signals are processed to yield particular responses is a major goal of biology. Genetically encoded fluorescent proteins (FPs) and fluorescent sensors are playing an important role in achieving this comprehensive knowledge base of cell function. Providing high sensitivity and immense versatility while being minimally perturbing to a biological specimen, the probes can be used in different microscopy techniques to visualize cellular processes on many spatial scales. Three review articles in this volume discuss recent advances in probe design and applications. These developments help expand the range of biochemical processes in living systems suitable for study. They provide researchers with exciting new tools to explore how cellular processes are organized and their activity regulated in vivo.

}, keywords = {Cell Physiological Phenomena, Fluorescence Resonance Energy Transfer, Luminescent Proteins, Microscopy, Fluorescence, Nitric Oxide, Signal Transduction, Zinc}, issn = {1545-4509}, doi = {10.1146/annurev-biochem-121010-125553}, author = {Lippincott-Schwartz, Jennifer} } @article {46043, title = {Evidence for reduced experience-dependent dendritic spine plasticity in the aging prefrontal cortex.}, journal = {Journal of Neuroscience}, volume = {31}, year = {2011}, month = {2011 May 25}, pages = {7831-9}, abstract = {

Cognitive functions that require the prefrontal cortex are highly sensitive to aging in humans, nonhuman primates, and rodents, although the neurobiological correlates of this vulnerability remain largely unknown. It has been proposed that dendritic spines represent the primary site of structural plasticity in the adult brain, and recent data have supported the hypothesis that aging is associated with alterations of dendritic spine morphology and plasticity in prefrontal cortex. However, no study to date has directly examined whether aging alters the capacity for experience-dependent spine plasticity in aging prefrontal neurons. To address this possibility, we used young, middle-aged, and aged rats in a behavioral stress paradigm known to produce spine remodeling in prefrontal cortical neurons. In young rats, stress resulted in dendritic spine loss and altered patterns of spine morphology; in contrast, spines from middle-aged and aged animals were remarkably stable and did not show evidence of remodeling. The loss of stress-induced spine plasticity observed in aging rats occurred alongside robust age-related reductions in spine density and shifts in remaining spine morphology. Together, the data presented here provide the first evidence that experience-dependent spine plasticity is altered by aging in prefrontal cortex, and support a model in which dendritic spines become progressively less plastic in the aging brain.

}, keywords = {Aging, Animals, Cognition, Dendritic Spines, Learning, Male, Neuronal Plasticity, Prefrontal Cortex, Rats, Rats, Sprague-Dawley}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0839-11.2011}, author = {Bloss, Erik B and Janssen, William G and Ohm, Daniel T and Yuk, Frank J and Wadsworth, Shannon and Saardi, Karl M and McEwen, Bruce S and Morrison, John H} } @article {46610, title = {An evolutionary conserved role for anaplastic lymphoma kinase in behavioral responses to ethanol.}, journal = {PLoS One}, volume = {6}, year = {2011}, month = {2011 Jul 22}, pages = {e22636}, abstract = {

Anaplastic lymphoma kinase (Alk) is a gene expressed in the nervous system that encodes a receptor tyrosine kinase commonly known for its oncogenic function in various human cancers. We have determined that Alk is associated with altered behavioral responses to ethanol in the fruit fly Drosophila melanogaster, in mice, and in humans. Mutant flies containing transposon insertions in dAlk demonstrate increased resistance to the sedating effect of ethanol. Database analyses revealed that Alk expression levels in the brains of recombinant inbred mice are negatively correlated with ethanol-induced ataxia and ethanol consumption. We therefore tested Alk gene knockout mice and found that they sedate longer in response to high doses of ethanol and consume more ethanol than wild-type mice. Finally, sequencing of human ALK led to the discovery of four polymorphisms associated with a low level of response to ethanol, an intermediate phenotype that is predictive of future alcohol use disorders (AUDs). These results suggest that Alk plays an evolutionary conserved role in ethanol-related behaviors. Moreover, ALK may be a novel candidate gene conferring risk for AUDs as well as a potential target for pharmacological intervention.

}, keywords = {Alcohol Drinking, Alcoholics, Animals, Behavior, Animal, Conscious Sedation, Drosophila melanogaster, Drosophila Proteins, Ethanol, Evolution, Molecular, Female, Gene Expression Regulation, Enzymologic, Homeodomain Proteins, Humans, Male, Mice, Polymorphism, Genetic, Receptor Protein-Tyrosine Kinases}, issn = {1932-6203}, doi = {10.1371/journal.pone.0022636}, author = {Lasek, Amy W and Lim, Jana and Kliethermes, Christopher L and Berger, Karen H and Joslyn, Geoff and Brush, Gerry and Xue, Liquan and Robertson, Margaret and Moore, Monica S and Vranizan, Karen and Morris, Stephan W and Schuckit, Marc A and White, Raymond L and Heberlein, Ulrike} } @article {47664, title = {An evolving paradigm for the secretory pathway?}, journal = {Molecular biology of the cell}, volume = {22}, year = {2011}, month = {2011 Nov}, pages = {3929-32}, abstract = {

The paradigm that the secretory pathway consists of a stable endoplasmic reticulum and Golgi apparatus, using discrete transport vesicles to exchange their contents, gained important support from groundbreaking biochemical and genetic studies during the 1980s. However, the subsequent development of new imaging technologies with green fluorescent protein introduced data on dynamic processes not fully accounted for by the paradigm. As a result, we may be seeing an example of how a paradigm is evolving to account for the results of new technologies and their new ways of describing cellular processes.

}, keywords = {Animals, Awards and Prizes, Cells, Cultured, Fluorescence Recovery After Photobleaching, Green Fluorescent Proteins, Humans, Microscopy, Electron, Microscopy, Video, Models, Biological, Protein Transport, Proteins, Secretory Vesicles}, issn = {1939-4586}, doi = {10.1091/mbc.E11-05-0452}, author = {Lippincott-Schwartz, Jennifer} } @article {6507, title = {Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes.}, journal = {Nucleic Acids Research}, volume = {39}, year = {2011}, month = {2011 Sep 1}, pages = {7529-47}, abstract = {

We took advantage of the unusual genomic organization of the ciliate Oxytricha trifallax to screen for eukaryotic non-coding RNA (ncRNA) genes. Ciliates have two types of nuclei: a germ line micronucleus that is usually transcriptionally inactive, and a somatic macronucleus that contains a reduced, fragmented and rearranged genome that expresses all genes required for growth and asexual reproduction. In some ciliates including Oxytricha, the macronuclear genome is particularly extreme, consisting of thousands of tiny {\textquoteright}nanochromosomes{\textquoteright}, each of which usually contains only a single gene. Because the organism itself identifies and isolates most of its genes on single-gene nanochromosomes, nanochromosome structure could facilitate the discovery of unusual genes or gene classes, such as ncRNA genes. Using a draft Oxytricha genome assembly and a custom-written protein-coding genefinding program, we identified a subset of nanochromosomes that lack any detectable protein-coding gene, thereby strongly enriching for nanochromosomes that carry ncRNA genes. We found only a small proportion of non-coding nanochromosomes, suggesting that Oxytricha has few independent ncRNA genes besides homologs of already known RNAs. Other than new members of known ncRNA classes including C/D and H/ACA snoRNAs, our screen identified one new family of small RNA genes, named the Arisong RNAs, which share some of the features of small nuclear RNAs.

}, keywords = {Base Sequence, Chromosomes, Conserved Sequence, Genes, Genome, Genomics, Introns, Oxytricha, Protozoan, RNA, Small Nuclear, Small Nucleolar, Untranslated}, issn = {1362-4962}, doi = {10.1093/nar/gkr501}, author = {Jung, Seolkyoung and Swart, Estienne C and Minx, Patrick J and Magrini, Vincent and Mardis, Elaine R and Landweber, Laura F and Eddy, Sean R.} } @article {4389, title = {Facile and general synthesis of photoactivatable xanthene dyes.}, journal = {Angewandte Chemie}, volume = {50}, year = {2011}, month = {2011 Nov 18}, pages = {11206-9}, abstract = {

Despite the apparent simplicity of the xanthene fluorophores, the preparation of caged derivatives with free carboxy groups remains a synthetic challenge. A straightforward and flexible strategy for preparing rhodamine and fluorescein derivatives was developed using reduced, {\textquotedblleft}leuco{\textquotedblright} intermediates.

}, issn = {1521-3773}, doi = {10.1002/anie.201104571}, author = {Wysocki, Laura M and Grimm, Jonathan B and Tkachuk, Ariana N and Brown, Timothy A and Betzig, Eric and Lavis, Luke D} } @article {5280, title = {Fast filtering for RNA homology search.}, journal = {Bioinformatics}, volume = {27}, year = {2011}, month = {2011 Nov 15}, pages = {3102-9}, abstract = {

MOTIVATION: Homology search for RNAs can use secondary structure information to increase power by modeling base pairs, as in covariance models, but the resulting computational costs are high. Typical acceleration strategies rely on at least one filtering stage using sequence-only search. RESULTS: Here we present the multi-segment CYK (MSCYK) filter, which implements a heuristic of ungapped structural alignment for RNA homology search. Compared to gapped alignment, this approximation has lower computation time requirements (O(N$^{4}$) reduced to O(N{\textthreesuperior}), and space requirements (O(N{\textthreesuperior}) reduced to O(N{\texttwosuperior}). A vector-parallel implementation of this method gives up to 100-fold speed-up; vector-parallel implementations of standard gapped alignment at two levels of precision give 3- and 6-fold speed-ups. These approaches are combined to create a filtering pipeline that scores RNA secondary structure at all stages, with results that are synergistic with existing methods.

}, keywords = {Algorithms, Base Sequence, Consensus Sequence, Humans, Nucleic Acid, Nucleic Acid Conformation, RNA, Sequence Alignment, Sequence Analysis, Sequence Homology, Software}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btr545}, author = {Kolbe, Diana L and Eddy, Sean R.} } @article {65016, title = {Flip-flop memory circuit uses a synaptic AMPK-dependent positive feedback loop and is switched by hunger state.}, journal = {Appetite}, volume = {57}, year = {2011}, month = {2011 Jul 01}, pages = {47}, abstract = {

Synaptic plasticity\ in response to changes in physiologic state is coordinated by hormonal signals across multiple neuronal cell types, but the significance and underlying mechanisms are unclear. Here, we combine cell type-specific electrophysiological, pharmacological, and optogenetic techniques to dissect neural circuits and molecular pathways controlling synaptic plasticity onto AGRP neurons, a population that regulates feeding. We find that food deprivation elevates excitatory synaptic input, which is mediated by a presynaptic positive feedback loop involving AMP-activated protein kinase. Potentiation of glutamate release was triggered by the orexigenic hormone ghrelin and exhibited hysteresis, persisting for hours after ghrelin removal. Persistent activity was reversed by the anorexigenic hormone leptin, and optogenetic photostimulation demonstrated involvement of opioid release from POMC neurons. Based on these experiments, we propose a memory storage device for physiological state constructed from bistable synapses that are flipped between two sustained activity states by transient exposure to hormones signaling energy levels. Supported by: Howard Hughes Medical Institute.

}, doi = {10.1016/j.appet.2011.05.296}, author = {Y.Yang and D.Atasoy and S.Sternson} } @article {4925, title = {Fragment-based phase extension for three-dimensional structure determination of membrane proteins by electron crystallography.}, journal = {Structure}, volume = {19}, year = {2011}, month = {2011 Jul 13}, pages = {976-87}, abstract = {

In electron crystallography, membrane protein structure is determined from two-dimensional crystals where the protein is embedded in a membrane. Once large and well-ordered 2D crystals are grown, one of the bottlenecks in electron crystallography is the collection of image data to directly provide experimental phases to high resolution. Here, we describe an approach to bypass this bottleneck, eliminating the need for high-resolution imaging. We use the strengths of electron crystallography in rapidly obtaining accurate experimental phase information from low-resolution images and accurate high-resolution amplitude information from electron diffraction. The low-resolution experimental phases were used for the placement of α helix fragments and extended to high resolution using phases from the fragments. Phases were further improved by density modifications followed by fragment expansion and structure refinement against the high-resolution diffraction data. Using this approach, structures of three membrane proteins were determined rapidly and accurately to atomic resolution without high-resolution image data.

}, keywords = {Crystallization, Crystallography, Electrons, Ligands, Membrane Proteins, Models, Molecular, Molecular Imaging, Peptide Fragments, Protein Conformation, X-Ray}, issn = {1878-4186}, doi = {10.1016/j.str.2011.04.008}, author = {Wisedchaisri, Goragot and Gonen, Tamir} } @article {4307, title = {From cudgel to scalpel: toward precise neural control with optogenetics.}, journal = {Nature Methods}, volume = {8}, year = {2011}, month = {2011 Jan}, pages = {30-4}, abstract = {

Optogenetics is routinely used to activate and inactivate genetically defined neuronal populations in vivo. A second optogenetic revolution will occur when spatially distributed and sparse neural assemblies can be precisely manipulated in behaving animals.

}, keywords = {Animals, Gene Expression Regulation, Genetic Techniques, Light, Neurons, Organ Specificity, Photic Stimulation}, issn = {1548-7105}, doi = {10.1038/nmeth.f.325}, author = {Peron, Simon and Svoboda, Karel} } @article {47903, title = {Frozen tissue can provide reproducible proteomic results of subcellular fractionation.}, journal = {Analytical biochemistry}, volume = {418}, year = {2011}, month = {2011 Nov 1}, pages = {78-84}, abstract = {

Differential detergent fractionation (DDF) is frequently used to partition fresh cells and tissues into distinct compartments. We have tested whether DDF can reproducibly extract and fractionate cellular protein components from frozen tissues. Frozen kidneys were sequentially extracted with three different buffer systems. Analysis of the three fractions with liquid chromatography-tandem mass spectrometry (LC-MS/MS) identified 1693 proteins, some of which were common to all fractions and others of which were unique to specific fractions. Normalized spectral index (SI(N)) values obtained from these data were compared to evaluate both the reproducibility of the method and the efficiency of enrichment. SI(N) values between replicate fractions demonstrated a high correlation, confirming the reproducibility of the method. Correlation coefficients across the three fractions were significantly lower than those for the replicates, supporting the capability of DDF to differentially fractionate proteins into separate compartments. Subcellular annotation of the proteins identified in each fraction demonstrated a significant enrichment of cytoplasmic, cell membrane, and nuclear proteins in the three respective buffer system fractions. We conclude that DDF can be applied to frozen tissue to generate reproducible proteome coverage discriminating subcellular compartments. This demonstrates the feasibility of analyzing cellular compartment-specific proteins in archived tissue samples with the simple DDF method.

}, keywords = {Animals, Cell Fractionation, Detergents, Freezing, Frozen Sections, Mice, Mice, Inbred C57BL, Proteome, Proteomics, Subcellular Fractions, Tandem Mass Spectrometry}, issn = {1096-0309}, doi = {10.1016/j.ab.2011.06.045}, author = {Lim, Jihyeon and Menon, Vilas and Bitzer, Markus and Miller, Leah M and Madrid-Aliste, Carlos and Weiss, Louis M and Fiser, Andras and Angeletti, Ruth H} } @article {3359, title = {Functional dissection of the neural substrates for sexual behaviors in Drosophila melanogaster.}, journal = {Genetics}, volume = {189}, year = {2011}, month = {2011 Jun 24}, pages = {195-211}, abstract = {

The male-specific Fruitless proteins (Fru(M)) act to establish the potential for male courtship behavior in Drosophila melanogaster and are expressed in small groups of neurons throughout the nervous system. We screened \ 1000 GAL4 lines, using assays for general courtship, male-male interactions, and male fertility to determine the phenotypes resulting from the GAL4 driven inhibition of Fru(M) expression in subsets of these neurons. A battery of secondary assays showed that the phenotypic classes of GAL4 lines could be divided into subgroups based on additional neurobiological and behavioral criteria. For example, in some lines restoration of Fru(M) expression in cholinergic neurons restores fertility or reduces male-male courtship. Persistent chains of males courting each other in some lines results from males courting both sexes indiscriminately whereas in other lines this phenotype result from apparent habituation deficits. Inhibition of ectopic Fru(M) expression in females, in populations of neurons where Fru(M) is necessary for male fertility, can rescue female infertility. To identify the neurons responsible for some of the observed behavioral alterations, we determined the overlap between the identified GAL4 lines and endogenous Fru(M) expression in lines with fertility defects. The GAL4 lines causing fertility defects generally had widespread overlap with Fru(M) expression in many regions of the nervous system suggesting likely redundant Fru(M)-expressing neuronal pathways capable of conferring male fertility. From associations between the screened behaviors, we propose a functional model for courtship initiation.

}, issn = {1943-2631}, doi = {10.1534/genetics.111.129940}, author = {Meissner, Geoffrey W and Manoli, Devanand S and Chavez, Jose F and Knapp, Jon-Michael and Lin, Tasha L and Stevens, Robin J and Mellert, David J and Tran, David H and Baker, Bruce S} } @article {47663, title = {Functional nanoscale organization of signaling molecules downstream of the T cell antigen receptor.}, journal = {Immunity}, volume = {35}, year = {2011}, month = {2011 Nov 23}, pages = {705-20}, abstract = {

Receptor-regulated cellular signaling often is mediated by formation of transient, heterogeneous protein complexes of undefined structure. We used single and two-color photoactivated localization microscopy to study complexes downstream of the T cell antigen receptor (TCR) in single-molecule detail at the plasma membrane of intact T cells. The kinase ZAP-70 distributed completely with the TCRζ chain and both partially mixed with the adaptor LAT in activated cells, thus showing localized activation of LAT by TCR-coupled ZAP-70. In resting and activated cells, LAT primarily resided in nanoscale clusters as small as dimers whose formation depended on protein-protein and protein-lipid interactions. Surprisingly, the adaptor SLP-76 localized to the periphery of LAT clusters. This nanoscale structure depended on polymerized actin and its disruption affected TCR-dependent cell function. These results extend our understanding of the mechanism of T cell activation and the formation and organization of TCR-mediated signaling complexes, findings also relevant to other receptor systems.

}, keywords = {Actins, Adaptor Proteins, Signal Transducing, Cell Line, Tumor, Cells, Cultured, Humans, Jurkat Cells, Lymphocyte Activation, Membrane Proteins, Phospholipase C gamma, Phosphoproteins, Phosphorylation, Protein Binding, Protein Multimerization, Protein Transport, Receptors, Antigen, T-Cell, Receptors, Antigen, T-Cell, gamma-delta, Signal Transduction, T-Lymphocytes, ZAP-70 Protein-Tyrosine Kinase}, issn = {1097-4180}, doi = {10.1016/j.immuni.2011.10.004}, author = {Sherman, Eilon and Barr, Valarie and Manley, Suliana and Patterson, George and Balagopalan, Lakshmi and Akpan, Itoro and Regan, Carole K and Merrill, Robert K and Sommers, Connie L and Lippincott-Schwartz, Jennifer and Samelson, Lawrence E} } @article {47658, title = {Fuse or die: Shaping mitochondrial fate during starvation.}, journal = {Communicative \& integrative biology}, volume = {4}, year = {2011}, month = {2011 Nov 1}, pages = {752-4}, abstract = {

Mitochondria continuously change their shape and thereby influence different cellular processes like cell death or development. Recently, we showed that during starvation mitochondria fuse into a highly connected network. The change in mitochondrial shape was dependent on inactivation of the fission protein Drp1, through targeting of two different phosphorylation sites. This rapid inhibition of mitochondrial fission led to unopposed fusion, protecting mitochondria from starvation-induced degradation and enabling the cell to survive nutrient scarce conditions.

}, issn = {1942-0889}, author = {Rambold, Angelika S and Kostelecky, Brenda and Lippincott-Schwartz, Jennifer} } @article {4156, title = {Genetic manipulation of genes and cells in the nervous system of the fruit fly.}, journal = {Neuron}, volume = {72}, year = {2011}, month = {2011 Oct 20}, pages = {202-30}, abstract = {

Research in the fruit fly Drosophila melanogaster has led to insights in neural development, axon guidance, ion channel function, synaptic transmission, learning and memory, diurnal rhythmicity, and neural disease that have had broad implications for neuroscience. Drosophila is currently the eukaryotic model organism that permits the most sophisticated in\ vivo manipulations to address the function of neurons and neuronally expressed genes. Here, we summarize many of the techniques that help assess the role of specific neurons by labeling, removing, or altering their activity. We also survey genetic manipulations to identify and characterize neural genes by mutation, overexpression, and protein labeling. Here, we attempt to acquaint the reader with available options and contexts to apply these methods.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.09.021}, author = {Venken, Koen J T and Simpson, Julie H and Bellen, Hugo J} } @article {46611, title = {The genetic relationships between ethanol preference, acute ethanol sensitivity, and ethanol tolerance in Drosophila melanogaster.}, journal = {Fly (Austin)}, volume = {5}, year = {2011}, month = {2011 Jul-Sep}, pages = {191-9}, abstract = {

The relationship between alcohol consumption, sensitivity, and tolerance is an important question that has been addressed in humans and rodent models. Studies have shown that alcohol consumption and risk of abuse may correlate with (1) increased sensitivity to the stimulant effects of alcohol, (2) decreased sensitivity to the depressant effects of alcohol, and (3) increased alcohol tolerance. However, many conflicting results have been observed. To complement these studies, we utilized a different organism and approach to analyze the relationship between ethanol consumption and other ethanol responses. Using a set of 20 Drosophila melanogaster mutants that were isolated for altered ethanol sensitivity, we measured ethanol-induced hyperactivity, ethanol sedation, sedation tolerance, and ethanol consumption preference. Ethanol preference showed a strong positive correlation with ethanol tolerance, consistent with some rodent and human studies, but not with ethanol hyperactivity or sedation. No pairwise correlations were observed between ethanol hyperactivity, sedation, and tolerance. The evolutionary conservation of the relationship between tolerance and ethanol consumption in flies, rodents, and humans indicates that there are fundamental biological mechanisms linking specific ethanol responses.

}, keywords = {Alcohol Drinking, Alcoholic Intoxication, Animals, Central Nervous System Depressants, Drosophila melanogaster, Drosophila Proteins, Ethanol, Food Preferences, Hyperkinesis, Male, Transcription Factors}, issn = {1933-6942}, author = {Devineni, Anita V and McClure, Kimberly D and Guarnieri, Douglas J and Corl, Ammon B and Wolf, Fred W and Eddison, Mark and Heberlein, Ulrike} } @article {4371, title = {A genetically encoded, high-signal-to-noise maltose sensor.}, journal = {Proteins}, volume = {79}, year = {2011}, month = {2011 Nov}, pages = {3025-36}, abstract = {

We describe the generation of a family of high-signal-to-noise single-wavelength genetically encoded indicators for maltose. This was achieved by insertion of circularly permuted fluorescent proteins into a bacterial periplasmic binding protein (PBP), Escherichia coli maltodextrin-binding protein, resulting in a four-color family of maltose indicators. The sensors were iteratively optimized to have sufficient brightness and maltose-dependent fluorescence increases for imaging, under both one- and two-photon illumination. We demonstrate that maltose affinity of the sensors can be tuned in a fashion largely independent of the fluorescent readout mechanism. Using literature mutations, the binding specificity could be altered to moderate sucrose preference, but with a significant loss of affinity. We use the soluble sensors in individual E. coli bacteria to observe rapid maltose transport across the plasma membrane, and membrane fusion versions of the sensors on mammalian cells to visualize the addition of maltose to extracellular media. The PBP superfamily includes scaffolds specific for a number of analytes whose visualization would be critical to the reverse engineering of complex systems such as neural networks, biosynthetic pathways, and signal transduction cascades. We expect the methodology outlined here to be useful in the development of indicators for many such analytes.

}, issn = {1097-0134}, doi = {10.1002/prot.23118}, author = {Marvin, Jonathan S and Schreiter, Eric R and Echevarr{\'\i}a, Ileabett M and Looger, Loren L} } @article {46613, title = {Genome-wide association and genetic functional studies identify autism susceptibility candidate 2 gene (AUTS2) in the regulation of alcohol consumption.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Apr 26}, pages = {7119-24}, abstract = {

Alcohol consumption is a moderately heritable trait, but the genetic basis in humans is largely unknown, despite its clinical and societal importance. We report a genome-wide association study meta-analysis of \~{}2.5 million directly genotyped or imputed SNPs with alcohol consumption (gram per day per kilogram body weight) among 12 population-based samples of European ancestry, comprising 26,316 individuals, with replication genotyping in an additional 21,185 individuals. SNP rs6943555 in autism susceptibility candidate 2 gene (AUTS2) was associated with alcohol consumption at genome-wide significance (P = 4 {\texttimes} 10(-8) to P = 4 {\texttimes} 10(-9)). We found a genotype-specific expression of AUTS2 in 96 human prefrontal cortex samples (P = 0.026) and significant (P \< 0.017) differences in expression of AUTS2 in whole-brain extracts of mice selected for differences in voluntary alcohol consumption. Down-regulation of an AUTS2 homolog caused reduced alcohol sensitivity in Drosophila (P \< 0.001). Our finding of a regulator of alcohol consumption adds knowledge to our understanding of genetic mechanisms influencing alcohol drinking behavior.

}, keywords = {Alcohol Drinking, Animals, Drosophila melanogaster, European Continental Ancestry Group, Female, Gene Expression Regulation, Genome-Wide Association Study, Genotype, Humans, Male, Mice, Nuclear Proteins, Polymorphism, Single Nucleotide, Proteins, Quantitative Trait, Heritable}, issn = {1091-6490}, doi = {10.1073/pnas.1017288108}, author = {Schumann, Gunter and Coin, Lachlan J and Lourdusamy, Anbarasu and Charoen, Pimphen and Berger, Karen H and Stacey, David and Desrivi{\`e}res, Sylvane and Aliev, Fazil A and Khan, Anokhi A and Amin, Najaf and Aulchenko, Yurii S and Bakalkin, Georgy and Bakker, Stephan J and Balkau, Beverley and Beulens, Joline W and Bilbao, Ainhoa and de Boer, Rudolf A and Beury, Delphine and Bots, Michiel L and Breetvelt, Elemi J and Cauchi, St{\'e}phane and Cavalcanti-Proen{\c c}a, Christine and Chambers, John C and Clarke, Toni-Kim and Dahmen, Norbert and de Geus, Eco J and Dick, Danielle and Ducci, Francesca and Easton, Alanna and Edenberg, Howard J and Esko, T{\~o}nu and Esk, T{\~o}nu and Fern{\'a}ndez-Medarde, Alberto and Foroud, Tatiana and Freimer, Nelson B and Girault, Jean-Antoine and Grobbee, Diederick E and Guarrera, Simonetta and Gudbjartsson, Daniel F and Hartikainen, Anna-Liisa and Heath, Andrew C and Hesselbrock, Victor and Hofman, Albert and Hottenga, Jouke-Jan and Isohanni, Matti K and Kaprio, Jaakko and Khaw, Kay-Tee and Kuehnel, Brigitte and Laitinen, Jaana and Lobbens, St{\'e}phane and Luan, Jian{\textquoteright}an and Mangino, Massimo and Maroteaux, Matthieu and Matullo, Giuseppe and McCarthy, Mark I and Mueller, Christian and Navis, Gerjan and Numans, Mattijs E and N{\'u}{\~n}ez, Alejandro and Nyholt, Dale R and Onland-Moret, Charlotte N and Oostra, Ben A and O{\textquoteright}Reilly, Paul F and Palkovits, Miklos and Penninx, Brenda W and Polidoro, Silvia and Pouta, Anneli and Prokopenko, Inga and Ricceri, Fulvio and Santos, Eugenio and Smit, Johannes H and Soranzo, Nicole and Song, Kijoung and Sovio, Ulla and Stumvoll, Michael and Surakk, Ida and Thorgeirsson, Thorgeir E and Thorsteinsdottir, Unnur and Troakes, Claire and Tyrfingsson, Thorarinn and T{\"o}njes, Anke and Uiterwaal, Cuno S and Uitterlinden, Andre G and van der Harst, Pim and van der Schouw, Yvonne T and Staehlin, Oliver and Vogelzangs, Nicole and Vollenweider, Peter and Waeber, Gerard and Wareham, Nicholas J and Waterworth, Dawn M and Whitfield, John B and Wichmann, Erich H and Willemsen, Gonneke and Witteman, Jacqueline C and Yuan, Xin and Zhai, Guangju and Zhao, Jing H and Zhang, Weihua and Martin, Nicholas G and Metspalu, Andres and Doering, Angela and Scott, James and Spector, Tim D and Loos, Ruth J and Boomsma, Dorret I and Mooser, Vincent and Peltonen, Leena and Stefansson, Kari and van Duijn, Cornelia M and Vineis, Paolo and Sommer, Wolfgang H and Kooner, Jaspal S and Spanagel, Rainer and Heberlein, Ulrike A and Jarvelin, Marjo-Riitta and Elliott, Paul} } @article {4300, title = {Glia instruct developmental neuronal remodeling through TGF-β signaling.}, journal = {Nature Neuroscience}, volume = {14}, year = {2011}, month = {2011 Jun 19}, pages = {821-3}, abstract = {

We found that glia secrete myoglianin, a TGF-β ligand, to instruct developmental neural remodeling in Drosophila. Glial myoglianin upregulated neuronal expression of an ecdysone nuclear receptor that triggered neurite remodeling following the late-larval ecdysone peak. Thus glia orchestrate developmental neural remodeling not only by engulfment of unwanted neurites but also by enabling neuron remodeling.

}, keywords = {Animals, Developmental, Double-Stranded, Drosophila, Drosophila Proteins, Gene Expression Regulation, Genetically Modified, Green Fluorescent Proteins, MicroRNAs, Models, Mushroom Bodies, Mutation, Neurogenesis, Neuroglia, Neurological, RNA, Signal Transduction, Transforming Growth Factor beta}, issn = {1546-1726}, doi = {10.1038/nn.2833}, author = {Awasaki, Takeshi and Huang, Yaling and O{\textquoteright}Connor, Michael B and Lee, Tzumin} } @article {46425, title = {Glial-derived prodegenerative signaling in the Drosophila neuromuscular system.}, journal = {Neuron}, volume = {72}, year = {2011}, month = {2011 Dec 8}, pages = {760-75}, abstract = {

We provide evidence for a prodegenerative, glial-derived signaling framework in the Drosophila neuromuscular system that includes caspase and mitochondria-dependent signaling. We demonstrate that Drosophila TNF-α (eiger) is expressed in a subset of peripheral glia, and the TNF-α receptor (TNFR), Wengen, is expressed in motoneurons. NMJ degeneration caused by disruption of the spectrin/ankyrin skeleton is suppressed by an eiger mutation or by eiger knockdown within a subset of peripheral glia. Loss of wengen in motoneurons causes a similar suppression providing evidence for glial-derived prodegenerative TNF-α signaling. Neither JNK nor NFκβ is required for prodegenerative signaling. However, we provide evidence for the involvement of both an initiator and effector caspase, Dronc and Dcp-1, and mitochondrial-dependent signaling. Mutations that deplete the axon and nerve terminal of mitochondria suppress degeneration as do mutations in Drosophila Bcl-2 (debcl), a mitochondria-associated protein, and Apaf-1 (dark), which links mitochondrial signaling with caspase activity in other systems.

}, keywords = {Animals, Animals, Genetically Modified, Apoptotic Protease-Activating Factor 1, Caspases, Disease Models, Animal, Drosophila, Drosophila Proteins, Excitatory Postsynaptic Potentials, Fluorescence Recovery After Photobleaching, Green Fluorescent Proteins, Mitochondria, Motor Neuron Disease, Mutation, Nerve Degeneration, Nerve Tissue Proteins, Neuroglia, Neuromuscular Junction, Proto-Oncogene Proteins, Receptors, Tumor Necrosis Factor, RNA Interference, Signal Transduction}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.09.031}, author = {Keller, Lani C and Cheng, Ling and Locke, Cody J and M{\"u}ller, Martin and Fetter, Richard D and Davis, Graeme W} } @article {4385, title = {A gustotopic map of taste qualities in the mammalian brain.}, journal = {Science}, volume = {333}, year = {2011}, month = {2011 Sep 2}, pages = {1262-6}, abstract = {

The taste system is one of our fundamental senses, responsible for detecting and responding to sweet, bitter, umami, salty, and sour stimuli. In the tongue, the five basic tastes are mediated by separate classes of taste receptor cells each finely tuned to a single taste quality. We explored the logic of taste coding in the brain by examining how sweet, bitter, umami, and salty qualities are represented in the primary taste cortex of mice. We used in vivo two-photon calcium imaging to demonstrate topographic segregation in the functional architecture of the gustatory cortex. Each taste quality is represented in its own separate cortical field, revealing the existence of a gustotopic map in the brain. These results expose the basic logic for the central representation of taste.

}, keywords = {Afferent Pathways, Animals, Brain Mapping, Cerebral Cortex, Cycloheximide, Inbred C57BL, Knockout, Mice, Molecular Imaging, Neurons, Sodium Chloride, Sodium Glutamate, Sweetening Agents, Taste, Taste Buds}, issn = {1095-9203}, doi = {10.1126/science.1204076}, author = {Chen, Xiaoke and Gabitto, Mariano and Peng, Yueqing and Ryba, Nicholas J P and Zuker, Charles S} } @article {47905, title = {Hallmarks of molecular action of microtubule stabilizing agents: effects of epothilone B, ixabepilone, peloruside A, and laulimalide on microtubule conformation.}, journal = {The Journal of biological chemistry}, volume = {286}, year = {2011}, month = {2011 Apr 1}, pages = {11765-78}, abstract = {

Microtubule stabilizing agents (MSAs) comprise a class of drugs that bind to microtubule (MT) polymers and stabilize them against disassembly. Several of these agents are currently in clinical use as anticancer drugs, whereas others are in various stages of development. Nonetheless, there is insufficient knowledge about the molecular modes of their action. Recent studies from our laboratory utilizing hydrogen-deuterium exchange in combination with mass spectrometry (MS) provide new information on the conformational effects of Taxol and discodermolide on microtubules isolated from chicken erythrocytes (CET). We report here a comprehensive analysis of the effects of epothilone B, ixabepilone (IXEMPRA(TM)), laulimalide, and peloruside A on CET conformation. The results of our comparative hydrogen-deuterium exchange MS studies indicate that all MSAs have significant conformational effects on the C-terminal H12 helix of α-tubulin, which is a likely molecular mechanism for the previously observed modulations of MT interactions with microtubule-associated and motor proteins. More importantly, the major mode of MT stabilization by MSAs is the tightening of the longitudinal interactions between two adjacent αβ-tubulin heterodimers at the interdimer interface. In contrast to previous observations reported with bovine brain tubulin, the lateral interactions between the adjacent protofilaments in CET are particularly strongly stabilized by peloruside A and laulimalide, drugs that bind outside the taxane site. This not only highlights the significance of tubulin isotype composition in modulating drug effects on MT conformation and stability but also provides a potential explanation for the synergy observed when combinations of taxane and alternative site binding drugs are used.

}, keywords = {Animals, Bicyclo Compounds, Heterocyclic, Binding Sites, Brain, Brain Chemistry, Cattle, Epothilones, Lactones, Macrolides, Mass Spectrometry, Microtubules, Nerve Tissue Proteins, Protein Structure, Secondary, Tubulin, Tubulin Modulators}, issn = {1083-351X}, doi = {10.1074/jbc.M110.162214}, author = {Khrapunovich-Baine, Marina and Menon, Vilas and Yang, Chia-Ping Huang and Northcote, Peter T and Miller, John H and Angeletti, Ruth Hogue and Fiser, Andras and Horwitz, Susan Band and Xiao, Hui} } @article {47222, title = {Heterotypic gap junctions between two neurons in the drosophila brain are critical for memory.}, journal = {Current Biology : CB}, volume = {21}, year = {2011}, month = {2011 May 24}, pages = {848-54}, abstract = {

Gap junctions play an important role in the regulation of neuronal metabolism and homeostasis by serving as connections that enable small molecules to pass between cells and synchronize activity between cells. Although recent studies have linked gap junctions to memory formation, it remains unclear how they contribute to this process. Gap junctions are hexameric hemichannels formed from the connexin and pannexin gene families in chordates and the innexin (inx) gene family in invertebrates. Here we show that two modulatory neurons, the anterior paired lateral (APL) neuron and the dorsal paired medial (DPM) neuron, form heterotypic gap junctions within the mushroom body (MB), a learning and memory center in the Drosophila brain. Using RNA interference-mediated knockdowns of inx7 and inx6 in the APL and DPM neurons, respectively, we found that flies showed normal olfactory associative learning and intact anesthesia-resistant memory (ARM) but failed to form anesthesia-sensitive memory (ASM). Our results reveal that the heterotypic gap junctions between the APL and DPM neurons are an essential part of the MB circuitry for memory formation, potentially constituting a recurrent neural network to stabilize ASM.

}, keywords = {Anesthesia, Animals, Animals, Genetically Modified, Connexins, Drosophila, Drosophila Proteins, Gap Junctions, Memory, Mushroom Bodies, Neurons, RNA Interference, Smell}, issn = {1879-0445}, doi = {10.1016/j.cub.2011.02.041}, author = {Wu, Chia-Lin and Shih, Meng-Fu Maxwell and Lai, Jason Sih-Yu and Yang, Hsun-Ti and Turner, Glenn C and Chen, Linyi and Chiang, Ann-Shyn} } @article {4325, title = {High resolution segmentation of neuronal tissues from low depth-resolution EM imagery.}, journal = {8th International Conference of Energy Minimization Methods in Computer Vision and Pattern Recognition Energy Minimization Methods in Computer Vision and Pattern Recognition}, volume = {6819}, year = {2011}, month = {2011}, pages = {261-72}, abstract = {

The challenge of recovering the topology of massive neuronal circuits can potentially be met by high throughput Electron Microscopy (EM) imagery. Segmenting a 3-dimensional stack of EM images into the individual neurons is difficult, due to the low depth-resolution in existing high-throughput EM technology, such as serial section Transmission EM (ssTEM). In this paper we propose methods for detecting the high resolution locations of membranes from low depth-resolution images. We approach this problem using both a method that learns a discriminative, over-complete dictionary and a kernel SVM. We test this approach on tomographic sections produced in simulations from high resolution Focused Ion Beam (FIB) images and on low depth-resolution images acquired with ssTEM and evaluate our results by comparing it to manual labeling of this data.

}, issn = {978-3-642-23093-6}, author = {Glasner, Daniel and Hu, Tao and Nunez-Iglesias, Juan and Scheffer, Lou and Xu, CS and Hess, Harald and Fetter, Richard and Chklovskii, Dmitri and Basri, Ronen} } @article {2474, title = {A high speed wavefront determination method based on spatial frequency modulations for focusing light through random scattering media.}, journal = {Optics Express}, volume = {19}, year = {2011}, month = {2011 Feb 14}, pages = {2989-95}, abstract = {

A large number of degrees of freedom are required to produce a high quality focus through random scattering media. Previous demonstrations based on spatial phase modulations suffer from either a slow speed or a small number of degrees of freedom. In this work, a high speed wavefront determination technique based on spatial frequency domain wavefront modulations is proposed and experimentally demonstrated, which is capable of providing both a high operation speed and a large number of degrees of freedom. The technique was employed to focus light through a strongly scattering medium and the entire wavefront was determined in 400 milliseconds, \ three orders of magnitude faster than the previous report.

}, issn = {1094-4087}, doi = {10.1364/OE.19.002989}, author = {Cui, Meng} } @article {6135, title = {High-throughput behavioral analysis in C. elegans.}, journal = {Nature Methods}, volume = {8}, year = {2011}, month = {2011 Jun 5}, pages = {592-8}, abstract = {

We designed a real-time computer vision system, the Multi-Worm Tracker (MWT), which can simultaneously quantify the behavior of dozens of Caenorhabditis elegans on a Petri plate at video rates. We examined three traditional behavioral paradigms using this system: spontaneous movement on food, where the behavior changes over tens of minutes; chemotaxis, where turning events must be detected accurately to determine strategy; and habituation of response to tap, where the response is stochastic and changes over time. In each case, manual analysis or automated single-worm tracking would be tedious and time-consuming, but the MWT system allowed rapid quantification of behavior with minimal human effort. Thus, this system will enable large-scale forward and reverse genetic screens for complex behaviors.

}, keywords = {Animal, Animals, Behavior, Caenorhabditis elegans, Chemotaxis, Computer-Assisted, Image Processing, Movement, Software, Stochastic Processes, Time Factors}, issn = {1548-7105}, doi = {10.1038/nmeth.1625}, author = {Swierczek, Nicholas A and Giles, Andrew C and Rankin, Catharine H and Kerr, Rex A} } @article {68486, title = {A high-throughput method for generating uniform microislands for autaptic neuronal cultures.}, journal = {J Neurosci Methods}, volume = {198}, year = {2011}, month = {06/2011}, pages = {230-5}, abstract = {

Generating microislands of culture substrate on coverslips by spray application of poly-d lysine is a commonly used method for culturing isolated neurons that form self (autaptic) synapses. This preparation has multiple advantages for studying synaptic transmission in isolation; however, generating microislands by spraying produces islands of non-uniform size and thus cultures vary widely in the number of islands containing single neurons. To address these problems, we developed a high-throughput method for reliably generating uniformly shaped microislands of culture substrate. Stamp molds formed of poly(dimethylsiloxane) (PDMS) were fabricated with arrays of circles and used to generate stamps made of 9.2\% agarose. The agarose stamps were capable of loading sufficient poly D-lysine and collagen dissolved in acetic acid to rapidly generate coverslips containing at least 64 microislands per coverslip. When hippocampal neurons were cultured on these coverslips, there were significantly more single-neuron islands per coverslip. We noted that single neurons tended to form one of three distinct neurite-arbor morphologies, which varied with island size and the location of the cell body on the island. To our surprise, the number of synapses per autaptic neuron did not correlate with arbor shape or island size, suggesting that other factors regulate the number of synapses formed by isolated neurons. The stamping method we report can be used to increase the number of single-neuron islands per culture and aid in the rapid visualization of microislands.

}, keywords = {Animals, Cell Communication, Cell Culture Techniques, Cells, Cultured, Dendrites, Hippocampus, Mice, Neurons, Synapses, Synaptic Transmission}, issn = {1872-678X}, doi = {10.1016/j.jneumeth.2011.04.012}, author = {Sgro, Allyson E and Nowak, Amy L and Austin, Naola S and Custer, Kenneth L and Allen, Peter B and Chiu, Daniel T and Bajjalieh, Sandra M} } @article {1093, title = {Histochemistry: live and in color.}, journal = {The Journal of Histochemistry and Cytochemistry: Official Journal of the Histochemistry Society}, volume = {59}, year = {2011}, month = {2011 Feb}, pages = {139-45}, abstract = {

Histochemistry (chemistry in the context of biological tissue) is an invaluable set of techniques used to visualize biological structures. This field lies at the interface of organic chemistry, biochemistry, and biology. Integration of these disciplines over the past century has permitted the imaging of cells and tissues using microscopy. Today, by exploiting the unique chemical environments within cells, heterologous expression techniques, and enzymatic activity, histochemical methods can be used to visualize structures in living matter. This review focuses on the labeling techniques and organic fluorophores used in live cells.

}, issn = {1551-5044}, doi = {10.1369/0022155410395760}, author = {Lavis, Luke D} } @article {4302, title = {HMMER web server: interactive sequence similarity searching.}, journal = {Nucleic Acids Research}, volume = {39}, year = {2011}, month = {2011 Jul}, pages = {W29-37}, abstract = {

HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain relative to previous versions. It is now feasible to make efficient profile hidden Markov model (profile HMM) searches via the web. A HMMER web server (http://hmmer.janelia.org) has been designed and implemented such that most protein database searches return within a few seconds. Methods are available for searching either a single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence database, and for searching a protein sequence against Pfam. The web server is designed to cater to a range of different user expertise and accepts batch uploading of multiple queries at once. All search methods are also available as RESTful web services, thereby allowing them to be readily integrated as remotely executed tasks in locally scripted workflows. We have focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them.

}, keywords = {Internet, Protein, Sequence Alignment, Sequence Analysis, Software}, issn = {1362-4962}, doi = {10.1093/nar/gkr367}, author = {Finn, Robert D and Clements, Jody and Eddy, Sean R.} } @article {6358, title = {Hox gene Ultrabithorax regulates distinct sets of target genes at successive stages of Drosophila haltere morphogenesis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Feb 15}, pages = {2855-60}, abstract = {

Hox genes encode highly conserved transcription factors that regionalize the animal body axis by controlling complex developmental processes. Although they are known to operate in multiple cell types and at different stages, we are still missing the batteries of genes targeted by any one Hox gene over the course of a single developmental process to achieve a particular cell and organ morphology. The transformation of wings into halteres by the Hox gene Ultrabithorax (Ubx) in Drosophila melanogaster presents an excellent model system to study the Hox control of transcriptional networks during successive stages of appendage morphogenesis and cell differentiation. We have used an inducible misexpression system to switch on Ubx in the wing epithelium at successive stages during metamorphosis{\textendash}in the larva, prepupa, and pupa. We have then used extensive microarray expression profiling and quantitative RT-PCR to identify the primary transcriptional responses to Ubx. We find that Ubx targets range from regulatory genes like transcription factors and signaling components to terminal differentiation genes affecting a broad repertoire of cell behaviors and metabolic reactions. Ubx up- and down-regulates hundreds of downstream genes at each stage, mostly in a subtle manner. Strikingly, our analysis reveals that Ubx target genes are largely distinct at different stages of appendage morphogenesis, suggesting extensive interactions between Hox genes and hormone-controlled regulatory networks to orchestrate complex genetic programs during metamorphosis.

}, keywords = {Animals, Cluster Analysis, Developmental, Drosophila, Drosophila Proteins, Fluorescent Antibody Technique, Gene Expression Regulation, Gene Regulatory Networks, Homeodomain Proteins, In Situ Hybridization, Life Cycle Stages, Microarray Analysis, Morphogenesis, Reverse Transcriptase Polymerase Chain Reaction, Transcription Factors, Wing}, issn = {1091-6490}, doi = {10.1073/pnas.1015077108}, author = {Pavlopoulos, Anastasios and Akam, Michael} } @article {46424, title = {Hts/Adducin controls synaptic elaboration and elimination.}, journal = {Neuron}, volume = {69}, year = {2011}, month = {2011 Mar 24}, pages = {1114-31}, abstract = {

Neural development requires both synapse elaboration and elimination, yet relatively little is known about how these opposing activities are coordinated. Here, we provide evidence Hts/Adducin can serve this function. We show that Drosophila Hts/Adducin is enriched both pre- and postsynaptically at the NMJ. We then demonstrate that presynaptic Hts/Adducin is necessary and sufficient to control two opposing processes associated with synapse remodeling: (1) synapse stabilization as determined by light level and ultrastructural and electrophysiological assays and (2) the elaboration of actin-based, filopodia-like protrusions that drive synaptogenesis and growth. Synapse remodeling is sensitive to Hts/Adducin levels, and we provide evidence that the synaptic localization of Hts/Adducin is controlled via phosphorylation. Mechanistically, Drosophila Hts/Adducin protein has actin-capping activity. We propose that phosphorylation-dependent regulation of Hts/Adducin controls the level, localization, and activity of Hts/Adducin, influencing actin-based synapse elaboration and spectrin-based synapse stabilization. Hts/Adducin may define a mechanism to switch between synapse stability and dynamics.

}, keywords = {Actins, Animals, Animals, Genetically Modified, Biological Transport, Blotting, Western, Calmodulin-Binding Proteins, Cytoskeleton, Drosophila, Drosophila Proteins, Electrophysiology, Immunohistochemistry, Microscopy, Electron, Transmission, Phosphorylation, Spectrin, Synapses, Synaptic Transmission}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.02.007}, author = {Pielage, Jan and Bulat, Victoria and Zuchero, J Bradley and Fetter, Richard D and Davis, Graeme W} } @article {3975, title = {Hunger states switch a flip-flop memory circuit via a synaptic AMPK-dependent positive feedback loop.}, journal = {Cell}, volume = {146}, year = {2011}, month = {2011 Sep 16}, pages = {992-1003}, abstract = {

Synaptic plasticity in response to changes in physiologic state is coordinated by hormonal signals across multiple neuronal cell types. Here, we combine cell-type-specific electrophysiological, pharmacological, and optogenetic techniques to dissect neural circuits and molecular pathways controlling synaptic plasticity onto AGRP neurons, a population that regulates feeding. We find that food deprivation elevates excitatory synaptic input, which is mediated by\ a presynaptic positive feedback loop involving AMP-activated protein kinase. Potentiation of glutamate release was triggered by the orexigenic hormone ghrelin and exhibited hysteresis, persisting for hours after ghrelin removal. Persistent activity was reversed by the anorexigenic hormone leptin, and optogenetic photostimulation demonstrated involvement of opioid release from POMC neurons. Based on these experiments, we propose a memory storage device for physiological state constructed from bistable synapses that are flipped between two sustained activity states by transient exposure to hormones signaling energy levels.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2011.07.039}, author = {Yang, Yunlei and Atasoy, Deniz and Su, Helen H and Sternson, Scott M} } @article {3930, title = {Imaging light responses of targeted neuron populations in the rodent retina.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {31}, year = {2011}, month = {2011 Feb 23}, pages = {2855-67}, abstract = {

Decoding the wiring diagram of the retina requires simultaneous observation of activity in identified neuron populations. Available recording methods are limited in their scope: electrodes can access only a small fraction of neurons at once, whereas synthetic fluorescent indicator dyes label tissue indiscriminately. Here, we describe a method for studying retinal circuitry at cellular and subcellular levels combining two-photon microscopy and a genetically encoded calcium indicator. Using specific viral and promoter constructs to drive expression of GCaMP3, we labeled all five major neuron classes in the adult mouse retina. Stimulus-evoked GCaMP3 responses as imaged by two-photon microscopy permitted functional cell type annotation. Fluorescence responses were similar to those measured with the small molecule dye OGB-1. Fluorescence intensity correlated linearly with spike rates \>10 spikes/s, and a significant change in fluorescence always reflected a significant change in spike firing rate. GCaMP3 expression had no apparent effect on neuronal function. Imaging at subcellular resolution showed compartment-specific calcium dynamics in multiple identified cell types.

}, keywords = {Action Potentials, Animals, Female, Inbred C57BL, Male, Mice, Neurons, Ocular, Organ Culture Techniques, Retina, Vision, Voltage-Sensitive Dye Imaging}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.6064-10.2011}, author = {Borghuis, Bart G and Tian, Lin and Xu, Ying and Nikonov, Sergei S and Vardi, Noga and Zemelman, Boris V and Looger, Loren L} } @article {3522, title = {In search of the structure of human olfactory space.}, journal = {Frontiers in Systems Neuroscience}, volume = {5}, year = {2011}, month = {2011 Jun 2}, pages = {65}, abstract = {

We analyze the responses of human observers to an ensemble of monomolecular odorants. Each odorant is characterized by a set of 146 perceptual descriptors obtained from a database of odor character profiles. Each odorant is therefore represented by a point in a highly multidimensional sensory space. In this work we study the arrangement of odorants in this perceptual space. We argue that odorants densely sample a two-dimensional curved surface embedded in the multidimensional sensory space. This surface can account for more than half of the variance of the perceptual data. We also show that only 12\% of experimental variance cannot be explained by curved surfaces of substantially small dimensionality (\<10). We suggest that these curved manifolds represent the relevant spaces sampled by the human olfactory system, thereby providing surrogates for olfactory sensory space. For the case of 2D approximation, we relate the two parameters on the curved surface to the physico-chemical parameters of odorant molecules. We show that one of the dimensions is related to eigenvalues of molecules{\textquoteright} connectivity matrix, while the other is correlated with measures of molecules{\textquoteright} polarity. We discuss the behavioral significance of these findings.

}, author = {Koulakov, Alexei and Kolterman, Brian E. and Enikolopov, Armen and Rinberg, Dmitry} } @article {2311, title = {Inputs to the dorsal striatum of the mouse reflect the parallel circuit architecture of the forebrain.}, journal = {Frontiers in Neuroanatomy}, volume = {4}, year = {2011}, month = {2011}, pages = {147}, abstract = {

The basal ganglia play a critical role in the regulation of voluntary action in vertebrates. Our understanding of the function of the basal ganglia relies heavily upon anatomical information, but continued progress will require an understanding of the specific functional roles played by diverse cell types and their connectivity. An increasing number of mouse lines allow extensive identification, characterization, and manipulation of specified cell types in the basal ganglia. Despite the promise of genetically modified mice for elucidating the functional roles of diverse cell types, there is relatively little anatomical data obtained directly in the mouse. Here we have characterized the retrograde labeling obtained from a series of tracer injections throughout the dorsal striatum of adult mice. We found systematic variations in input along both the medial-lateral and anterior-posterior neuraxes in close agreement with canonical features of basal ganglia anatomy in the rat. In addition to the canonical features we have provided experimental support for the importance of non-canonical inputs to the striatum from the raphe nuclei and the amygdala. To look for organization at a finer scale we have analyzed the correlation structure of labeling intensity across our entire dataset. Using this analysis we found substantial local heterogeneity within the large-scale order. From this analysis we conclude that individual striatal sites receive varied combinations of cortical and thalamic input from multiple functional areas, consistent with some earlier studies in the rat that have suggested the presence of a combinatorial map.

}, issn = {1662-5129}, doi = {10.3389/fnana.2010.00147}, author = {Pan, Weixing X and Mao, Tianyi and Dudman, Joshua T} } @article {46608, title = {Insulin attenuates the acquisition and expression of ethanol-induced locomotor sensitization in DBA/2J mice.}, journal = {Life Sciences}, volume = {89}, year = {2011}, month = {2011 Dec 19}, pages = {968-74}, abstract = {

AIM: Ethanol-induced locomotor sensitization is a behavioral manifestation of physiological responses to repeated ethanol exposures. While ethanol exerts direct effects on multiple neurotransmitter systems in the brain, ethanol-induced changes in metabolic state, including acute hyperglycemia and inhibition of insulin signaling, also have plausible roles in the expression of ethanol-related behaviors through direct and indirect effects on brain function. The current experiments examined whether insulin administration or the resultant hypoglycemia might attenuate the development of sensitization to the locomotor stimulant effect of ethanol.

MAIN METHODS: Male and female DBA/2J mice received daily injections of 5 or 10 IU/kg insulin before or after a stimulating dose of ethanol and subsequent testing in an automated activity monitor. Blood glucose levels were determined upon the completion of the experiments.

KEY FINDINGS: Insulin injected prior to ethanol blunted the acute stimulant response as well as the acquisition and expression of locomotor sensitization, while insulin given after ethanol did not affect the development of the sensitized response. In a separate experiment, mice given glucose concurrently with insulin developed ethanol-induced locomotor sensitization normally.

SIGNIFICANCE: These experiments suggest that insulin attenuates the development of ethanol-induced locomotor sensitization, and that blood glucose levels can largely account for this effect. Further studies of the role of ethanol-induced metabolic states should provide novel information on the expression of ethanol-related behaviors.

}, keywords = {Animals, Behavior, Animal, Blood Glucose, Central Nervous System Depressants, Dose-Response Relationship, Drug, Ethanol, Female, Glucose, Hypoglycemia, Hypoglycemic Agents, Insulin, Male, Mice, Mice, Inbred DBA, Motor Activity}, issn = {1879-0631}, doi = {10.1016/j.lfs.2011.10.011}, author = {Kliethermes, Christopher L and Heberlein, Ulrike} } @article {2694, title = {Intracellular determinants of hippocampal CA1 place and silent cell activity in a novel environment.}, journal = {Neuron}, volume = {70}, year = {2011}, month = {2011 Apr 14}, pages = {109-20}, abstract = {

For each environment a rodent has explored, its hippocampus contains a map consisting of a unique subset of neurons, called place cells, that have spatially tuned spiking there, with the remaining neurons being essentially silent. Using whole-cell recording in freely moving rats exploring a novel maze, we observed differences in intrinsic cellular properties and input-based subthreshold membrane potential levels underlying this division into place and silent cells. Compared to silent cells, place cells had lower spike thresholds and peaked versus flat subthreshold membrane potentials as a function of animal location. Both differences were evident from the beginning of exploration. Additionally, future place cells exhibited higher burst propensity before exploration. Thus, internal settings appear to predetermine which cells will represent the next novel environment encountered. Furthermore, place cells fired spatially tuned bursts with large, putatively calcium-mediated depolarizations that could trigger plasticity and stabilize the new map for long-term storage. Our results provide new insight into hippocampal memory formation.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.03.006}, author = {Epsztein, J{\'e}r{\^o}me and Brecht, Michael and Lee, Albert K} } @article {46300, title = {Intracellular dynamics of virtual place cells.}, journal = {Neural Computation}, volume = {23}, year = {2011}, month = {2011 Mar}, pages = {651-5}, abstract = {

The pattern of spikes recorded from place cells in the rodent hippocampus is strongly modulated by both the spatial location in the environment and the theta rhythm. The phases of the spikes in the theta cycle advance during movement through the place field. Recently intracellular recordings from hippocampal neurons (Harvey, Collman, Dombeck, \& Tank, 2009 ) showed an increase in the amplitude of membrane potential oscillations inside the place field, which was interpreted as evidence that an intracellular mechanism caused phase precession. Here we show that an existing network model of the hippocampus (Tsodyks, Skaggs, Sejnowski, \& McNaughton, 1996 ) can equally reproduce this and other aspects of the intracellular recordings, which suggests that new experiments are needed to distinguish the contributions of intracellular and network mechanisms to phase precession.

}, issn = {1530-888X}, doi = {10.1162/NECO_a_00087}, author = {Romani, Sandro and Sejnowski, Terrence J and Tsodyks, Misha} } @article {4303, title = {Laminar analysis of excitatory local circuits in vibrissal motor and sensory cortical areas.}, journal = {PLoS Biology}, volume = {9}, year = {2011}, month = {2011 Jan 4}, pages = {e1000572}, abstract = {

Rodents move their whiskers to locate and identify objects. Cortical areas involved in vibrissal somatosensation and sensorimotor integration include the vibrissal area of the primary motor cortex (vM1), primary somatosensory cortex (vS1; barrel cortex), and secondary somatosensory cortex (S2). We mapped local excitatory pathways in each area across all cortical layers using glutamate uncaging and laser scanning photostimulation. We analyzed these maps to derive laminar connectivity matrices describing the average strengths of pathways between individual neurons in different layers and between entire cortical layers. In vM1, the strongest projection was L2/3{\textrightarrow}L5. In vS1, strong projections were L2/3{\textrightarrow}L5 and L4{\textrightarrow}L3. L6 input and output were weak in both areas. In S2, L2/3{\textrightarrow}L5 exceeded the strength of the ascending L4{\textrightarrow}L3 projection, and local input to L6 was prominent. The most conserved pathways were L2/3{\textrightarrow}L5, and the most variable were L4{\textrightarrow}L2/3 and pathways involving L6. Local excitatory circuits in different cortical areas are organized around a prominent descending pathway from L2/3{\textrightarrow}L5, suggesting that sensory cortices are elaborations on a basic motor cortex-like plan.

}, keywords = {Animals, Brain Mapping, Mice, Motor Cortex, Nerve Net, Presynaptic Terminals, Somatosensory Cortex, Vibrissae}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1000572}, author = {Hooks, B M and Hires, S Andrew and Zhang, Ying-Xin and Huber, Daniel and Petreanu, Leopoldo and Svoboda, Karel and Shepherd, Gordon M G} } @article {4326, title = {Large-scale automated histology in the pursuit of connectomes.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {31}, year = {2011}, month = {2011 Nov 9}, pages = {16125-38}, abstract = {

How does the brain compute? Answering this question necessitates neuronal connectomes, annotated graphs of all synaptic connections within defined brain areas. Further, understanding the energetics of the brain{\textquoteright}s computations requires vascular graphs. The assembly of a connectome requires sensitive hardware tools to measure neuronal and neurovascular features in all three dimensions, as well as software and machine learning for data analysis and visualization. We present the state of the art on the reconstruction of circuits and vasculature that link brain anatomy and function. Analysis at the scale of tens of nanometers yields connections between identified neurons, while analysis at the micrometer scale yields probabilistic rules of connection between neurons and exact vascular connectivity.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4077-11.2011}, author = {Kleinfeld, David and Bharioke, Arjun and Blinder, Pablo and Bock, Davi D and Briggman, Kevin L and Chklovskii, Dmitri B and Denk, Winfried and Helmstaedter, Moritz and Kaufhold, John P and Lee, Wei-Chung Allen and Meyer, Hanno S and Micheva, Kristina D and Oberlaender, Marcel and Prohaska, Steffen and Reid, R Clay and Smith, Stephen J and Takemura, Shinya and Tsai, Philbert S and Sakmann, Bert} } @article {47706, title = {Learning, memory, and the role of neural network architecture.}, journal = {PLoS computational biology}, volume = {7}, year = {2011}, month = {2011 Jun}, pages = {e1002063}, abstract = {

The performance of information processing systems, from artificial neural networks to natural neuronal ensembles, depends heavily on the underlying system architecture. In this study, we compare the performance of parallel and layered network architectures during sequential tasks that require both acquisition and retention of information, thereby identifying tradeoffs between learning and memory processes. During the task of supervised, sequential function approximation, networks produce and adapt representations of external information. Performance is evaluated by statistically analyzing the error in these representations while varying the initial network state, the structure of the external information, and the time given to learn the information. We link performance to complexity in network architecture by characterizing local error landscape curvature. We find that variations in error landscape structure give rise to tradeoffs in performance; these include the ability of the network to maximize accuracy versus minimize inaccuracy and produce specific versus generalizable representations of information. Parallel networks generate smooth error landscapes with deep, narrow minima, enabling them to find highly specific representations given sufficient time. While accurate, however, these representations are difficult to generalize. In contrast, layered networks generate rough error landscapes with a variety of local minima, allowing them to quickly find coarse representations. Although less accurate, these representations are easily adaptable. The presence of measurable performance tradeoffs in both layered and parallel networks has implications for understanding the behavior of a wide variety of natural and artificial learning systems.

}, keywords = {Computational Biology, Humans, Learning, Memory, Models, Neurological, Nerve Net, Neural Networks (Computer)}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1002063}, author = {Hermundstad, Ann M and Brown, Kevin S and Bassett, Danielle S and Carlson, Jean M} } @proceedings {46351, title = {Learning to Agglomerate Superpixel Hierarchies}, volume = {24}, year = {2011}, month = {12/2011}, publisher = {MIT Press}, address = {Granada, Spain}, abstract = {

An agglomerative clustering algorithm merges the most similar pair of clusters at every iteration. The function that evaluates similarity is traditionally hand- designed, but there has been recent interest in supervised or semisupervised settings in which ground-truth clustered data is available for training. Here we show how to train a similarity function by regarding it as the action-value function of a reinforcement learning problem. We apply this general method to segment images by clustering superpixels, an application that we call Learning to Agglomerate Superpixel Hierarchies (LASH). When applied to a challenging dataset of brain images from serial electron microscopy, LASH dramatically improved segmentation accuracy when clustering supervoxels generated by state of the boundary detection algorithms. The naive strategy of directly training only supervoxel similarities and applying single linkage clustering produced less improvement.

}, author = {Viren Jain and Srinivas C. Turaga and K Briggman and Moritz N. Helmstaedter and Winfried Denk and H. S. Seung} } @article {3846, title = {Learning to agglomerate superpixel hierarchies.}, journal = {Neural Information Processing Systems}, volume = {24}, year = {2011}, month = {2011}, pages = {648-56}, abstract = {

An agglomerative clustering algorithm merges the most similar pair of clusters at every iteration. The function that evaluates similarity is traditionally handdesigned, but there has been recent interest in supervised or semisupervised settings in which ground-truth clustered data is available for training. Here we show how to train a similarity function by regarding it as the action-value function of a reinforcement learning problem. We apply this general method to segment images by clustering superpixels, an application that we call Learning to Agglomerate Superpixel Hierarchies (LASH). When applied to a challenging dataset of brain images from serial electron microscopy, LASH dramatically improved segmentation accuracy when clustering supervoxels generated by state of the boundary detection algorithms. The naive strategy of directly training only supervoxel similarities and applying single linkage clustering produced less improvement.

}, author = {Jain, Viren and Turaga, Srinivas and Briggman, Kevin and Helmstaedter, Moritz N. and Denk, Winfried and Seung, Sebastian} } @article {2720, title = {Limiting amounts of centrosome material set centrosome size in C.elegans embryos.}, journal = {Current Biology}, volume = {21}, year = {2011}, month = {2011 Aug 9}, pages = {1259-67}, abstract = {

The ways in which cells set the size of intracellular structures is an important but largely unsolved problem [1]. Early embryonic divisions pose special problems in this regard. Many checkpoints common in somatic cells are missing from these divisions, which are characterized by rapid reductions in cell size and short cell cycles [2]. Embryonic cells must therefore possess simple and robust mechanisms that allow the size of many of their intracellular structures to rapidly scale with cell size.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2011.06.002}, author = {Decker, Markus and Jaensch, Steffen and Pozniakovsky, A and Zinke, A and O{\textquoteright}Connell, K F and Zachariae, W and Myers, Eugene and Hyman, Anthony A} } @article {65011, title = {Lineage-based analysis of the development of the central complex of the Drosophila brain.}, journal = {J Comp Neurol}, volume = {519}, year = {2011}, month = {2011 Mar 01}, pages = {661-89}, abstract = {

Most neurons of the central complex belong to 10 secondary (larvally produced) lineages. In the late larva, undifferentiated axon tracts of these lineages form a primordium in which all of the compartments of the central complex can be recognized as discrete entities. Four posterior lineages (DPMm1, DPMpm1, DPMpm2, and CM4) generate the classes of small-field neurons that interconnect the protocerebral bridge, fan-shaped body, noduli, and ellipsoid body. Three lineages located in the anterior brain, DALv2, BAmv1, and DALcl2, form the large-field neurons of the ellipsoid body and fan-shaped body, respectively. These lineages provide an input channel from the optic tubercle and connect the central complex with adjacent anterior brain compartments. Three lineages in the posterior cortex, CM3, CP2, and DPMpl2, connect the posterior brain neuropil with specific layers of the fan-shaped body. Even though all of the compartments of the central complex are prefigured in the late larval brain by the axon tracts of the above-mentioned lineages, the neuropil differentiates during the first 2 days of the pupal period when terminal branches and synapses of secondary neurons are formed. During this phase the initially straight horizontal layers of the central complex bend in the frontal plane, which produces the characteristic shape of the fan-shaped and ellipsoid body. Our analysis provides a comprehensive picture of the lineages that form the central complex, and will facilitate future studies that address the structure or function of the central complex at the single cell level.

}, keywords = {Animals, Brain, Cell Lineage, Drosophila melanogaster, Drosophila Proteins, Metamorphosis, Biological, Morphogenesis, Neurons}, issn = {1096-9861}, doi = {10.1002/cne.22542}, author = {Pereanu, Wayne and Younossi-Hartenstein, Amelia and Lovick, Jennifer and Spindler, Shana and Hartenstein, Volker} } @article {46612, title = {Lmo genes regulate behavioral responses to ethanol in Drosophila melanogaster and the mouse.}, journal = {Alcoholism, Clinical and Experimental Research}, volume = {35}, year = {2011}, month = {2011 Sep}, pages = {1600-6}, abstract = {

BACKGROUND: Previous work from our laboratory demonstrated a role for the Drosophila Lim-only (dLmo) gene in regulating behavioral responses to cocaine. Herein, we examined whether dLmo influences the flies{\textquoteright} sensitivity to ethanol{\textquoteright}s sedating effects. We also investigated whether 1 of the mammalian homologs of dLmo, Lmo3, is involved in behavioral responses to ethanol in mice.

METHODS: To examine dLmo function in ethanol-induced sedation, mutant flies with reduced or increased dLmo expression were tested using the loss of righting (LOR) assay. To determine whether mouse Lmo3 regulates behavioral responses to ethanol, we generated transgenic mice expressing a short-hairpin RNA targeting Lmo3 for RNA interference-mediated knockdown by lentiviral infection of single cell embryos. Adult founder mice, expressing varying amounts of Lmo3 in the brain, were tested using ethanol loss-of-righting-reflex (LORR) and 2-bottle choice ethanol consumption assays.

RESULTS: We found that in flies, reduced dLmo activity increased sensitivity to ethanol-induced sedation, whereas increased expression of dLmo led to increased resistance to ethanol-induced sedation. In mice, reduced levels of Lmo3 were correlated with increased sedation time in the LORR test and decreased ethanol consumption in the 2-bottle choice protocol.

CONCLUSIONS: These data describe a novel and conserved role for Lmo genes in flies and mice in behavioral responses to ethanol. These studies also demonstrate the feasibility of rapidly translating findings from invertebrate systems to mammalian models of alcohol abuse by combining RNA interference in transgenic mice and behavioral testing.

}, keywords = {Adaptor Proteins, Signal Transducing, Animals, Behavior, Animal, Brain, Central Nervous System Depressants, Disease Models, Animal, Drosophila melanogaster, Drosophila Proteins, Ethanol, Female, Genotype, Green Fluorescent Proteins, Homeodomain Proteins, Hypnotics and Sedatives, LIM Domain Proteins, Male, Mice, Mice, Inbred C57BL, Mice, Transgenic, RNA, Small Interfering}, issn = {1530-0277}, doi = {10.1111/j.1530-0277.2011.01506.x}, author = {Lasek, Amy W and Giorgetti, Francesco and Berger, Karen H and Tayor, Stacy and Heberlein, Ulrike} } @article {5283, title = {Long-range neuronal circuits underlying the interaction between sensory and motor cortex.}, journal = {Neuron}, volume = {72}, year = {2011}, month = {2011 Oct 6}, pages = {111-23}, abstract = {

In the rodent vibrissal system, active sensation and sensorimotor integration are mediated in part by connections between barrel cortex and vibrissal motor cortex. Little is known about how these structures interact at the level of neurons. We used Channelrhodopsin-2 (ChR2) expression, combined with anterograde and retrograde labeling, to map connections between barrel cortex and pyramidal neurons in mouse motor cortex. Barrel cortex axons preferentially targeted upper layer (L2/3, L5A) neurons in motor cortex; input to neurons projecting back to barrel cortex was particularly strong. Barrel cortex input to deeper layers (L5B, L6) of motor cortex, including neurons projecting to the brainstem, was weak, despite pronounced geometric overlap of dendrites with axons from barrel cortex. Neurons in different layers received barrel cortex input within stereotyped dendritic domains. The cortico-cortical neurons in superficial layers of motor cortex thus couple motor and sensory signals and might mediate sensorimotor integration and motor learning.

}, keywords = {Animals, Inbred C57BL, Membrane Potentials, Mice, Molecular Imaging, Motor Cortex, Neural Pathways, Neuroanatomical Tract-Tracing Techniques, Neurons, Somatosensory Cortex, Vibrissae}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.07.029}, author = {Mao, Tianyi and Kusefoglu, Deniz and Hooks, Bryan M and Huber, Daniel and Petreanu, Leopoldo and Svoboda, Karel} } @article {6445, title = {Mapping a sensory-motor network onto a structural and functional ground plan in the hindbrain.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Jan 18}, pages = {1170-5}, abstract = {

The hindbrain of larval zebrafish contains a relatively simple ground plan in which the neurons throughout it are arranged into stripes that represent broad neuronal classes that differ in transmitter identity, morphology, and transcription factor expression. Within the stripes, neurons are stacked continuously according to age as well as structural and functional properties, such as axonal extent, input resistance, and the speed at which they are recruited during movements. Here we address the question of how particular networks among the many different sensory-motor networks in hindbrain arise from such an orderly plan. We use a combination of transgenic lines and pairwise patch recording to identify excitatory and inhibitory interneurons in the hindbrain network for escape behaviors initiated by the Mauthner cell. We map this network onto the ground plan to show that an individual hindbrain network is built by drawing components in predictable ways from the underlying broad patterning of cell types stacked within stripes according to their age and structural and functional properties. Many different specialized hindbrain networks may arise similarly from a simple early patterning.

}, keywords = {Animals, Body Patterning, Brain Mapping, Computer-Assisted, Electrophysiology, Escape Reaction, Genetically Modified, Image Processing, Immunohistochemistry, Interneurons, Larva, Nerve Net, Patch-Clamp Techniques, Psychomotor Performance, Rhombencephalon, Zebrafish}, issn = {1091-6490}, doi = {10.1073/pnas.1012189108}, author = {Koyama, Minoru and Kinkhabwala, Amina and Satou, Chie and Higashijima, Shin-Ichi and Fetcho, Joseph} } @article {47662, title = {Mechanisms of mitochondria and autophagy crosstalk.}, journal = {Cell cycle (Georgetown, Tex.)}, volume = {10}, year = {2011}, month = {2011 Dec 1}, pages = {4032-8}, abstract = {

Autophagy is a cellular survival pathway that recycles intracellular components to compensate for nutrient depletion and ensures the appropriate degradation of organelles. Mitochondrial number and health are regulated by mitophagy, a process by which excessive or damaged mitochondria are subjected to autophagic degradation. Autophagy is thus a key determinant for mitochondrial health and proper cell function. Mitophagic malfunction has been recently proposed to contribute to progressive neuronal loss in Parkinson{\textquoteright}s disease. In addition to autophagy{\textquoteright}s significance in mitochondrial integrity, several lines of evidence suggest that mitochondria can also substantially influence the autophagic process. The mitochondria{\textquoteright}s ability to influence and be influenced by autophagy places both elements (mitochondria and autophagy) in a unique position where defects in one or the other system could increase the risk to various metabolic and autophagic related diseases.

}, keywords = {Animals, Apoptosis, Autophagy, DNA Replication, DNA, Mitochondrial, Humans, Mammals, Metabolic Diseases, Microtubule-Associated Proteins, Mitochondria, Mitochondrial Membranes, Mitochondrial Proteins, Stress, Physiological}, issn = {1551-4005}, doi = {10.4161/cc.10.23.18384}, author = {Rambold, Angelika S and Lippincott-Schwartz, Jennifer} } @article {6393, title = {Met and gce are functionally redundant in transducing the {\textquotedblleft}status quo{\textquotedblright} action of juvenile hormone in Drosophila.}, journal = {Insect Biochemistry and Molecular Biology}, volume = {41}, year = {2011}, month = {2011 Dec}, pages = {938-45}, abstract = {

The Drosophila Methoprene-tolerant (Met) and Germ cell-expressed (Gce) bHLH-PAS transcription factors are products of two paralogous genes. Both proteins potentially mediate the effect of juvenile hormone (JH) as candidate JH receptors. Here we report that Met and Gce are partially redundant in transducing JH action. Both Met and gce null single mutants are fully viable, but the Met gce double mutant, Met(27) gce(2.5k), dies during the larval-pupal transition. Precocious and enhanced caspase-dependent programmed cell death (PCD) appears in fat body cells of Met(27) gce(2.5k) during the early larval stages. Expression of Kr-h1, a JH response gene that inhibits 20-hydroxyecdysone (20E)-induced broad (br) expression, is abolished in Met(27) gce(2.5k) during larval molts. Consequently, expression of br occurs precociously in Met(27) gce(2.5k), which may cause precocious caspase-dependent PCD during the early larval stages. Defective phenotypes and gene expression changes in Met(27) gce(2.5k) double mutants are similar to those found in JH-deficient animals. Importantly, exogenous application of JH agonists rescued the JH-deficient animals but not the Met(27) gce(2.5k) mutants. Our data suggest a model in which Drosophila Met and Gce redundantly transduce JH action to prevent 20E-induced caspase-dependent PCD during larval molts by induction of Kr-h1 expression and inhibition of br expression.

}, issn = {1879-0240}, doi = {10.1016/j.ibmb.2011.09.003}, author = {Abdou, M and He, Q and Wen, D and Zyaan, O and Wang, J and Xu, J and Baumann, Aaron and Joseph, J and WIlson, TG and Li, S and Wang, J} } @article {3976, title = {Metabolism: let them eat fat.}, journal = {Nature}, volume = {477}, year = {2011}, month = {2011 Sep 8}, pages = {166-7}, abstract = {

A specialist neuron uses an intriguing process to help control the body{\textquoteright}s response to hunger. A lipid pathway involving the breakdown of cellular components regulates the expression of a neuropeptide that affects feeding and body weight.

}, issn = {1476-4687}, doi = {10.1038/477166a}, author = {Sternson, Scott M} } @article {5381, title = {Minimum-energy vesicle and cell shapes calculated using spherical harmonics parameterization.}, journal = {Soft Matter}, volume = {7}, year = {2011}, month = {2011 Jan 21}, pages = {2138-43}, abstract = {

An important open question in biophysics is to understand how mechanical forces shape membrane-bounded cells and their organelles. A general solution to this problem is to calculate the bending energy of an arbitrarily shaped membrane surface, which can include both lipids and cytoskeletal proteins, and minimize the energy subject to all mechanical constraints. However, the calculations are difficult to perform, especially for shapes that do not possess axial symmetry. We show that the spherical harmonics parameterization (SHP) provides an analytic description of shape that can be used to quickly and reliably calculate minimum energy shapes of both symmetric and asymmetric surfaces. Using this method, we probe the entire set of shapes predicted by the bilayer couple model, unifying work based on different computational approaches, and providing additional details of the transitions between different shape classes. In addition, we present new minimum-energy morphologies based on non-linear models of membrane skeletal elasticity that closely mimic extreme shapes of red blood cells. The SHP thus provides a versatile shape description that can be used to investigate forces that shape cells.

}, doi = {10.1039/c0sm01193b}, author = {Khairy, Khaled and Howard, Jonathon} } @inbook {6395, title = {Molecular evolution of juvenile hormone signaling.}, booktitle = {Gene Duplication: Book 2}, year = {2011}, chapter = {18}, author = {Baumann, Aaron and WIlson, TG}, editor = {Friedberg, F} } @article {4650, title = {Morphological evolution caused by many subtle-effect substitutions in regulatory DNA.}, journal = {Nature}, volume = {474}, year = {2011}, month = {2011 Jun 30}, pages = {598-603}, abstract = {

Morphology evolves often through changes in developmental genes, but the causal mutations, and their effects, remain largely unknown. The evolution of naked cuticle on larvae of Drosophila sechellia resulted from changes in five transcriptional enhancers of shavenbaby (svb), a transcript of the ovo locus that encodes a transcription factor that governs morphogenesis of microtrichiae, hereafter called {\textquoteright}trichomes{\textquoteright}. Here we show that the function of one of these enhancers evolved through multiple single-nucleotide substitutions that altered both the timing and level of svb expression. The consequences of these nucleotide substitutions on larval morphology were quantified with a novel functional assay. We found that each substitution had a relatively small phenotypic effect, and that many nucleotide changes account for this large morphological difference. In addition, we observed that the substitutions had non-additive effects. These data provide unprecedented resolution of the phenotypic effects of substitutions and show how individual nucleotide changes in a transcriptional enhancer have caused morphological evolution.

}, keywords = {Animals, Base Sequence, Biological Evolution, Developmental, DNA-Binding Proteins, Drosophila, Drosophila melanogaster, Drosophila Proteins, Embryo, Enhancer Elements, Female, Gene Expression Regulation, Genetic, Larva, Male, Nonmammalian, Nucleic Acid, Phenotype, Sequence Alignment, Sequence Homology, Transcription Factors}, issn = {1476-4687}, doi = {10.1038/nature10200}, author = {Frankel, Nicol{\'a}s and Erezyilmaz, Deniz F and McGregor, Alistair P and Wang, Shu and Payre, Fran\c cois and Stern, David L} } @article {2161, title = {Multi-camera real-time three-dimensional tracking of multiple flying animals.}, journal = {Journal of the Royal Society, Interface}, volume = {8}, year = {2011}, month = {2011 Mar 6}, pages = {395-409}, abstract = {

Automated tracking of animal movement allows analyses that would not otherwise be possible by providing great quantities of data. The additional capability of tracking in real time{\textendash}with minimal latency{\textendash}opens up the experimental possibility of manipulating sensory feedback, thus allowing detailed explorations of the neural basis for control of behaviour. Here, we describe a system capable of tracking the three-dimensional position and body orientation of animals such as flies and birds. The system operates with less than 40 ms latency and can track multiple animals simultaneously. To achieve these results, a multi-target tracking algorithm was developed based on the extended Kalman filter and the nearest neighbour standard filter data association algorithm. In one implementation, an 11-camera system is capable of tracking three flies simultaneously at 60 frames per second using a gigabit network of nine standard Intel Pentium 4 and Core 2 Duo computers. This manuscript presents the rationale and details of the algorithms employed and shows three implementations of the system. An experiment was performed using the tracking system to measure the effect of visual contrast on the flight speed of Drosophila melanogaster. At low contrasts, speed is more variable and faster on average than at high contrasts. Thus, the system is already a useful tool to study the neurobiology and behaviour of freely flying animals. If combined with other techniques, such as {\textquoteright}virtual reality{\textquoteright}-type computer graphics or genetic manipulation, the tracking system would offer a powerful new way to investigate the biology of flying animals.

}, issn = {1742-5662}, doi = {10.1098/rsif.2010.0230}, author = {Straw, Andrew D and Branson, Kristin and Neumann, Titus R and Dickinson, Michael H} } @conference {6449, title = {Multiple instance learning with manifold bags.}, booktitle = {International Conference on Machine Learning}, year = {2011}, month = {2011}, abstract = {

In many machine learning applications, labeling every instance of data is burdensome. Multiple Instance Learning (MIL), in which training data is provided in the form of labeled bags rather than labeled instances, is one approach for a more relaxed form of supervised learning. Though much progress has been made in analyzing MIL problems, existing work considers bags that have a finite number of instances. In this paper we argue that in many applications of MIL (e.g. image, audio, etc.) the bags are better modeled as low dimensional manifolds in high dimensional feature space. We show that the geometric structure of such manifold bags affects PAC-learnability. We discuss how a learning algorithm that is designed for finite sized bags can be adapted to learn from manifold bags. Furthermore, we propose a simple heuristic that reduces the memory requirements of such algorithms. Our experiments on real-world data validate our analysis and show that our approach works well.

}, author = {Babenko, B and Verma, N and Dollar, P and Belongie, S} } @article {3892, title = {Multiple new site-specific recombinases for use in manipulating animal genomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Aug 23}, pages = {14198-203}, abstract = {

Site-specific recombinases have been used for two decades to manipulate the structure of animal genomes in highly predictable ways and have become major research tools. However, the small number of recombinases demonstrated to have distinct specificities, low toxicity, and sufficient activity to drive reactions to completion in animals has been a limitation. In this report we show that four recombinases derived from yeast-KD, B2, B3, and R-are highly active and nontoxic in Drosophila and that KD, B2, B3, and the widely used FLP recombinase have distinct target specificities. We also show that the KD and B3 recombinases are active in mice.

}, issn = {1091-6490}, doi = {10.1073/pnas.1111704108}, author = {Nern, Aljoscha and Pfeiffer, Barret D and Svoboda, Karel and Rubin, Gerald M} } @article {3565, title = {Multiplexed shotgun genotyping for rapid and efficient genetic mapping.}, journal = {Genome Research}, volume = {21}, year = {2011}, month = {2011 Apr}, pages = {610-7}, abstract = {

We present a new approach to genotyping based on multiplexed shotgun sequencing that can identify recombination breakpoints in a large number of individuals simultaneously at a resolution sufficient for most mapping purposes, such as quantitative trait locus (QTL) mapping and mapping of induced mutations. We first describe a simple library construction protocol that uses just 10 ng of genomic DNA per individual and makes the approach accessible to any laboratory with standard molecular biology equipment. Sequencing this library results in a large number of sequence reads widely distributed across the genomes of multiplexed bar-coded individuals. We develop a Hidden Markov Model to estimate ancestry at all genomic locations in all individuals using these data. We demonstrate the utility of the approach by mapping a dominant marker allele in D. simulans to within 105 kb of its true position using 96 F1-backcross individuals genotyped in a single lane on an Illumina Genome Analyzer. We further demonstrate the utility of our method by genetically mapping more than 400 previously unassembled D. simulans contigs to linkage groups and by evaluating the quality of targeted introgression lines. At this level of multiplexing and divergence between strains, our method allows estimation of recombination breakpoints to a median of 38-kb intervals. Our analysis suggests that higher levels of multiplexing and/or use of strains with lower levels of divergence are practicable.

}, keywords = {Animals, Chromosome Breakpoints, Chromosome Mapping, Computational Biology, DNA, Dominant, Drosophila, Female, Genes, Genetic, Genetic Markers, Genotype, Male, Molecular Typing, Phenotype, Quantitative Trait Loci, Recombination, Research Design, Sequence Analysis}, issn = {1549-5469}, doi = {10.1101/gr.115402.110}, author = {Andolfatto, Peter and Davison, Dan and Erezyilmaz, Deniz and Hu, Tina T and Mast, Joshua and Sunayama-Morita, Tomoko and Stern, David L} } @article {47904, title = {Multi-scale correlation structure of gene expression in the brain.}, journal = {Neural networks : the official journal of the International Neural Network Society}, volume = {24}, year = {2011}, month = {2011 Nov}, pages = {933-42}, abstract = {

The mammalian brain is best understood as a multi-scale hierarchical neural system, in the sense that connection and function occur on multiple scales from micro to macro. Modern genomic-scale expression profiling can provide insight into methodologies that elucidate this architecture. We present a methodology for understanding the relationship of gene expression and neuroanatomy based on correlation between gene expression profiles across tissue samples. A resulting tool, NeuroBlast, can identify networks of genes co-expressed within or across neuroanatomic structures. The method applies to any data modality that can be mapped with sufficient spatial resolution, and provides a computation technique to elucidate neuroanatomy via patterns of gene expression on spatial and temporal scales. In addition, from the perspective of spatial location, we discuss a complementary technique that identifies gene classes that contribute to defining anatomic patterns.

}, keywords = {Algorithms, Animals, Atlases as Topic, Brain, Brain Chemistry, Data Mining, Databases, Genetic, Gene Expression, Mice, Mice, Inbred C57BL, Nerve Tissue Proteins, Tryptophan Hydroxylase}, issn = {1879-2782}, doi = {10.1016/j.neunet.2011.06.012}, author = {Hawrylycz, Mike and Ng, Lydia and Page, Damon and Morris, John and Lau, Chris and Faber, Sky and Faber, Vance and Sunkin, Susan and Menon, Vilas and Lein, Ed and Jones, Allan} } @article {5291, title = {Mushroom body efferent neurons responsible for aversive olfactory memory retrieval in Drosophila.}, journal = {Nature Neuroscience}, volume = {14}, year = {2011}, month = {2011 Jun 19}, pages = {903-10}, abstract = {

Aversive olfactory memory is formed in the mushroom bodies in Drosophila melanogaster. Memory retrieval requires mushroom body output, but the manner in which a memory trace in the mushroom body drives conditioned avoidance of a learned odor remains unknown. To identify neurons that are involved in olfactory memory retrieval, we performed an anatomical and functional screen of defined sets of mushroom body output neurons. We found that MB-V2 neurons were essential for retrieval of both short- and long-lasting memory, but not for memory formation or memory consolidation. MB-V2 neurons are cholinergic efferent neurons that project from the mushroom body vertical lobes to the middle superiormedial protocerebrum and the lateral horn. Notably, the odor response of MB-V2 neurons was modified after conditioning. As the lateral horn has been implicated in innate responses to repellent odorants, we propose that MB-V2 neurons recruit the olfactory pathway involved in innate odor avoidance during memory retrieval.

}, keywords = {Afferent Pathways, Analysis of Variance, Animal, Animals, Antigens, Avoidance Learning, Behavior, Biological, CD8, Choline O-Acetyltransferase, Conditioning (Psychology), Drosophila melanogaster, Drosophila Proteins, Gene Expression Regulation, Genetically Modified, Glutamate Decarboxylase, Green Fluorescent Proteins, Memory, Mental Recall, Models, Motor Neurons, Mushroom Bodies, Odors, Olfactory Pathways, Short-Term, Smell, Synapsins, Temperature, Time Factors, Transcription Factors, Tyrosine 3-Monooxygenase, Vesicular Glutamate Transport Proteins}, issn = {1546-1726}, doi = {10.1038/nn.2846}, author = {S{\'e}journ{\'e}, Julien and Placais, Pierre-Yves and Aso, Yoshinori and Siwanowicz, Igor and Trannoy, S{\'e}verine and Thoma, Vladimiros and Tedjakumala, Stevanus R and Rubin, Gerald M and Tch{\'e}nio, Paul and Ito, Kei and Isabel, Guillaume and Tanimoto, Hiromu and Preat, Thomas} } @article {6321, title = {Near-atomic resolution reconstructions of icosahedral viruses from electron cryo-microscopy.}, journal = {Current Opinion in Structural Biology}, volume = {21}, year = {2011}, month = {2011 Apr}, pages = {265-73}, abstract = {

Nine different near-atomic resolution structures of icosahedral viruses, determined by electron cryo-microscopy and published between early 2008 and late 2010, fulfil predictions made 15 years ago that single-particle cryo-EM techniques could visualize molecular detail at 3-4A resolution. This review summarizes technical developments, both in instrumentation and in computation, that have led to the new structures, which advance our understanding of virus assembly and cell entry.

}, keywords = {Computer Simulation, Computer-Assisted, Cryoelectron Microscopy, Image Processing, Models, Molecular, Virus Assembly, Viruses}, issn = {1879-033X}, doi = {10.1016/j.sbi.2011.01.008}, author = {Grigorieff, Nikolaus and Harrison, Stephen C} } @article {2164, title = {Network anatomy and in vivo physiology of visual cortical neurons.}, journal = {Nature}, volume = {471}, year = {2011}, month = {2011 Mar 10}, pages = {177-82}, abstract = {

In the cerebral cortex, local circuits consist of tens of thousands of neurons, each of which makes thousands of synaptic connections. Perhaps the biggest impediment to understanding these networks is that we have no wiring diagrams of their interconnections. Even if we had a partial or complete wiring diagram, however, understanding the network would also require information about each neuron{\textquoteright}s function. Here we show that the relationship between structure and function can be studied in the cortex with a combination of in vivo physiology and network anatomy. We used two-photon calcium imaging to characterize a functional property{\textendash}the preferred stimulus orientation{\textendash}of a group of neurons in the mouse primary visual cortex. Large-scale electron microscopy of serial thin sections was then used to trace a portion of these neurons{\textquoteright} local network. Consistent with a prediction from recent physiological experiments, inhibitory interneurons received convergent anatomical input from nearby excitatory neurons with a broad range of preferred orientations, although weak biases could not be rejected.

}, keywords = {Animals, Calcium Signaling, Electron, Fluorescence, Interneurons, Male, Mice, Microscopy, Microtomy, Nerve Net, Neural Inhibition, Neurons, Pyramidal Cells, Synapses, Transmission, Visual Cortex}, issn = {1476-4687}, doi = {10.1038/nature09802}, author = {Bock, Davi D and Lee, Wei-Chung Allen and Kerlin, Aaron M and Andermann, Mark L and Hood, Greg and Wetzel, Arthur W and Yurgenson, Sergey and Soucy, Edward R and Kim, Hyon Suk and Reid, R Clay} } @article {3867, title = {Neural correlates of illusory motion perception in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Jun 7}, pages = {9685-90}, abstract = {

When the contrast of an image flickers as it moves, humans perceive an illusory reversal in the direction of motion. This classic illusion, called reverse-phi motion, has been well-characterized using psychophysics, and several models have been proposed to account for its effects. Here, we show that Drosophila melanogaster also respond behaviorally to the reverse-phi illusion and that the illusion is present in dendritic calcium signals of motion-sensitive neurons in the fly lobula plate. These results closely match the predictions of the predominant model of fly motion detection. However, high flicker rates cause an inversion of the reverse-phi behavioral response that is also present in calcium signals of lobula plate tangential cell dendrites but not predicted by the model. The fly{\textquoteright}s behavioral and neural responses to the reverse-phi illusion reveal unexpected interactions between motion and flicker signals in the fly visual system and suggest that a similar correlation-based mechanism underlies visual motion detection across the animal kingdom.

}, keywords = {Algorithms, Animals, Dendrites, Drosophila melanogaster, Female, Humans, Male, Models, Motion, Motion Perception, Neural Pathways, Neurological, Neurons, Time Factors}, issn = {1091-6490}, doi = {10.1073/pnas.1100062108}, author = {Tuthill, John C and Chiappe, M Eugenia and Reiser, Michael B} } @article {6860, title = {Neuronal control of Drosophila courtship song.}, journal = {Neuron}, volume = {69}, year = {2011}, month = {2011 Feb 10}, pages = {509-22}, abstract = {

The courtship song of the Drosophila male serves as a genetically tractable model for the investigation of the neural mechanisms of decision-making, action selection, and motor pattern generation. Singing has been causally linked to the activity of the set of neurons that express the sex-specific fru transcripts, but the specific neurons involved have not been identified. Here we identify five distinct classes of fru neuron that trigger or compose the song. Our data suggest that P1 and pIP10 neurons in the brain mediate the decision to sing, and to act upon this decision, while the thoracic neurons dPR1, vPR6, and vMS11 are components of a central pattern generator that times and shapes the song{\textquoteright}s pulses. These neurons are potentially connected in a functional circuit, with the descending pIP10 neuron linking the brain and thoracic song centers. Sexual dimorphisms in each of these neurons may explain why only males sing.

}, keywords = {Animal, Animals, Courtship, Drosophila, Drosophila Proteins, Female, Genetically Modified, Male, Nerve Net, Nerve Tissue Proteins, Neurons, Sex Characteristics, Sexual Behavior, Transcription Factors, Vocalization}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.01.011}, author = {von Philipsborn, Anne C and Liu, Tianxiao and Yu, Jai Y and Masser, Christopher and Bidaye, Salil S and Dickson, Barry J} } @article {4301, title = {New tools for the analysis of glial cell biology in Drosophila.}, journal = {Glia}, volume = {59}, year = {2011}, month = {2011 Sep}, pages = {1377-86}, abstract = {

Because of its genetic, molecular, and behavioral tractability, Drosophila has emerged as a powerful model system for studying molecular and cellular mechanisms underlying the development and function of nervous systems. The Drosophila nervous system has fewer neurons and exhibits a lower glia:neuron ratio than is seen in vertebrate nervous systems. Despite the simplicity of the Drosophila nervous system, glial organization in flies is as sophisticated as it is in vertebrates. Furthermore, fly glial cells play vital roles in neural development and behavior. In addition, powerful genetic tools are continuously being created to explore cell function in vivo. In taking advantage of these features, the fly nervous system serves as an excellent model system to study general aspects of glial cell development and function in vivo. In this article, we review and discuss advanced genetic tools that are potentially useful for understanding glial cell biology in Drosophila.

}, keywords = {Animals, Cell Biology, Drosophila, Drosophila Proteins, Gene Expression, Genes, Molecular Biology, Mutation, Neuroglia, Reporter, Transcription Factors, Transgenes, Upstream Stimulatory Factors}, issn = {1098-1136}, doi = {10.1002/glia.21133}, author = {Awasaki, Takeshi and Lee, Tzumin} } @article {3629, title = {N-terminal domain of alphaB-crystallin provides a conformational switch for multimerization and structural heterogeneity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Apr 19}, pages = {6409-14}, abstract = {

The small heat shock protein (sHSP) αB-crystallin (αB) plays a key role in the cellular protection system against stress. For decades, high-resolution structural studies on heterogeneous sHSPs have been confounded by the polydisperse nature of αB oligomers. We present an atomic-level model of full-length αB as a symmetric 24-subunit multimer based on solid-state NMR, small-angle X-ray scattering (SAXS), and EM data. The model builds on our recently reported structure of the homodimeric α-crystallin domain (ACD) and C-terminal IXI motif in the context of the multimer. A hierarchy of interactions contributes to build multimers of varying sizes: Interactions between two ACDs define a dimer, three dimers connected by their C-terminal regions define a hexameric unit, and variable interactions involving the N-terminal region define higher-order multimers. Within a multimer, N-terminal regions exist in multiple environments, contributing to the heterogeneity observed by NMR. Analysis of SAXS data allows determination of a heterogeneity parameter for this type of system. A mechanism of multimerization into higher-order asymmetric oligomers via the addition of up to six dimeric units to a 24-mer is proposed. The proposed asymmetric multimers explain the homogeneous appearance of αB in negative-stain EM images and the known dynamic exchange of αB subunits. The model of αB provides a structural basis for understanding known disease-associated missense mutations and makes predictions concerning substrate binding and the reported fibrilogenesis of αB.

}, keywords = {alpha-Crystallin B Chain, Animals, Biomolecular, Humans, Missense, Models, Molecular, Mutation, Nuclear Magnetic Resonance, Protein Multimerization, Protein Structure, Quaternary, Tertiary}, issn = {1091-6490}, doi = {10.1073/pnas.1014656108}, author = {Jehle, Stefan and Vollmar, Breanna S and Bardiaux, Benjamin and Dove, Katja K and Rajagopal, Ponni and Gonen, Tamir and Oschkinat, Hartmut and Klevit, Rachel E} } @article {46741, title = {A nucleoporin, Nup60p, affects the nuclear and cytoplasmic localization of ASH1 mRNA in S. cerevisiae.}, journal = {RNA}, volume = {17}, year = {2011}, month = {2011 Jan}, pages = {134-44}, abstract = {

The biogenesis of a localization-competent mRNP begins in the nucleus. It is thought that the coordinated action of nuclear and cytoplasmic components of the localization machinery is required for the efficient export and subsequent subcellular localization of these mRNAs in the cytoplasm. Using quantitative poly(A)(+) and transcript-specific fluorescent in situ hybridization, we analyzed different nonessential nucleoporins and nuclear pore-associated proteins for their potential role in mRNA export and localization. We found that Nup60p, a nuclear pore protein located on the nucleoplasmic side of the nuclear pore complex, was required for the mRNA localization pathway. In a Δnup60 background, localized mRNAs were preferentially retained within the nucleus compared to nonlocalized transcripts. However, the export block was only partial and some transcripts could still reach the cytoplasm. Importantly, downstream processes were also affected. Localization of ASH1 and IST2 mRNAs to the bud was impaired in the Δnup60 background, suggesting that the assembly of a localization competent mRNP ("locasome") was inhibited when NUP60 was deleted. These results demonstrate transcript specificity of a nuclear mRNA retention defect and identify a specific nucleoporin as a functional component of the localization pathway in budding yeast.

}, keywords = {Cell Nucleus, Cytoplasm, Gene Deletion, In Situ Hybridization, Fluorescence, Nuclear Pore Complex Proteins, Poly A, Repressor Proteins, RNA Transport, RNA, Fungal, RNA, Messenger, RNA-Binding Proteins, Saccharomyces cerevisiae Proteins, Transcription, Genetic}, issn = {1469-9001}, doi = {10.1261/rna.1210411}, author = {Powrie, Erin A and Zenklusen, Daniel and Singer, Robert H} } @article {2908, title = {N-WASp is required for Schwann cell cytoskeletal dynamics, normal myelin gene expression and peripheral nerve myelination.}, journal = {Development}, volume = {138}, year = {2011}, month = {2011 Apr}, pages = {1329-37}, abstract = {

Schwann cells elaborate myelin sheaths around axons by spirally wrapping and compacting their plasma membranes. Although actin remodeling plays a crucial role in this process, the effectors that modulate the Schwann cell cytoskeleton are poorly defined. Here, we show that the actin cytoskeletal regulator, neural Wiskott-Aldrich syndrome protein (N-WASp), is upregulated in myelinating Schwann cells coincident with myelin elaboration. When N-WASp is conditionally deleted in Schwann cells at the onset of myelination, the cells continue to ensheath axons but fail to extend processes circumferentially to elaborate myelin. Myelin-related gene expression is also severely reduced in the N-WASp-deficient cells and in vitro process and lamellipodia formation are disrupted. Although affected mice demonstrate obvious motor deficits these do not appear to progress, the mutant animals achieving normal body weights and living to advanced age. Our observations demonstrate that N-WASp plays an essential role in Schwann cell maturation and myelin formation.

}, keywords = {Animals, Axons, Blotting, Cells, Cultured, Cytoskeleton, Fluorescent Antibody Technique, Gait, Gene Expression, Knockout, Mice, Myelin Sheath, Neuronal, Peripheral Nerves, Reverse Transcriptase Polymerase Chain Reaction, Schwann Cells, Western, Wiskott-Aldrich Syndrome Protein}, issn = {1477-9129}, doi = {10.1242/dev.058677}, author = {Jin, Fuzi and Dong, Baoxia and Georgiou, John and Jiang, Qiuhong and Zhang, Jinyi and Bharioke, Arjun and Qiu, Frank and Lommel, Silvia and Feltri, M Laura and Wrabetz, Lawrence and Roder, John C and Eyer, Joel and Chen, Xiequn and Peterson, Alan C and Siminovitch, Katherine A} } @article {5295, title = {Observations on clustered synaptic plasticity and highly structured input patterns.}, journal = {Neuron}, volume = {72}, year = {2011}, month = {2011 Dec 22}, pages = {887-8}, abstract = {

In this issue of Neuron, Makino and Malinow and Kleindienst et\ al. present evidence of a behaviorally induced form of synaptic plasticity that would encourage the development of fine-scale structured input patterns and\ the binding of features within single neurons.

}, keywords = {Action Potentials, Animals, Cell Compartmentation, Dendrites, Female, Hippocampus, Neuronal Plasticity, Pregnancy, Sensory Deprivation, Synapses, Synaptic Transmission}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.12.009}, author = {Magee, Jeffrey C} } @article {5672, title = {Observers exploit stochastic models of sensory change to help judge the passage of time.}, journal = {Current Biology}, volume = {21}, year = {2011}, month = {2011 Feb 8}, pages = {200-6}, abstract = {

Sensory stimulation can systematically bias the perceived passage of time, but why and how this happens is mysterious. In this report, we provide evidence that such biases may ultimately derive from an innate and adaptive use of stochastically evolving dynamic stimuli to help refine estimates derived from internal timekeeping mechanisms. A simplified statistical model based on probabilistic expectations of stimulus change derived from the second-order temporal statistics of the natural environment makes three predictions. First, random noise-like stimuli whose statistics violate natural expectations should induce timing bias. Second, a previously unexplored obverse of this effect is that similar noise stimuli with natural statistics should reduce the variability of timing estimates. Finally, this reduction in variability should scale with the interval being timed, so as to preserve the overall Weber law of interval timing. All three predictions are borne out experimentally. Thus, in the context of our novel theoretical framework, these results suggest that observers routinely rely on sensory input to augment their sense of the passage of time, through a process of Bayesian inference based on expectations of change in the natural environment.

}, keywords = {Biological, Humans, Models, Photic Stimulation, Stochastic Processes, Time Perception}, issn = {1879-0445}, doi = {10.1016/j.cub.2010.12.043}, author = {Ahrens, Misha B and Sahani, Maneesh} } @article {6488, title = {Optogenetics: potentials for addiction research.}, journal = {Addiction Biology}, volume = {16}, year = {2011}, month = {2011 Oct}, pages = {519-31}, abstract = {

Research on the biology of addiction has advanced significantly over the last 50 years expanding our understanding of the brain mechanisms underlying reward, reinforcement and craving. Novel experimental approaches and techniques have provided an ever increasing armory of tools to dissect behavioral processes, neural networks and molecular mechanisms. The ultimate goal is to reintegrate this knowledge into a coherent, mechanistic framework of addiction to help identify new treatment. This can be greatly facilitated by using tools that allow, with great spatial and temporal specificity, to link molecular changes with altered activation of neural circuits and behavior. Such specificity can now be achieved by using optogenetic tools. Our review describes the general principles of optogenetics and its use to understand the links between neural activity and behavior. We also provide an overview of recent studies using optogenetic tools in addiction and consider some outstanding questions of addiction research that are particularly amenable for optogenetic approaches.

}, keywords = {Animals, Brain, Dopamine, Gene Expression, Genetic Techniques, Humans, Light, Nerve Net, Nerve Tissue Proteins, Neurons, Neurosciences, Optical Tweezers, Rhodopsin, Substance-Related Disorders, Translational Medical Research, Voltage-Sensitive Dye Imaging}, issn = {1369-1600}, doi = {10.1111/j.1369-1600.2011.00386.x}, author = {Cao, Zhen Fang Huang and Burdakov, Denis and Sarnyai, Zolt{\'a}n} } @article {65019, title = {Orphan nuclear receptors control neuronal remodeling during fly metamorphosis.}, journal = {Nature Neuroscience}, volume = {14}, year = {2011}, month = {2010 Dec 27}, pages = {6-7}, abstract = {

News \& Views\ |\ Published:\ 27 December 2010

Orphan nuclear receptors control neuronal remodeling during fly metamorphosis

Nature Neuroscience\ volume\ 14,\ pages\ 6{\textendash}7\ (2011)\ |\ Download Citation

Pruning of excess branches is essential for the maturation of developing neuronal circuits. Cross-talk between TGF-β signaling and two antagonistic orphan nuclear receptors governs the pruning of larval γ neurons in the\ Drosophila\ pupa.

Neural circuits are remodeled as the brain matures or acquires new functions. Such developmental remodeling involves complex cellular changes that are tightly regulated in space and time. During metamorphosis of holometabolous insect brains, most larval functional neurons are rewired into the adult circuitry, and study of these processes has been particularly fruitful for the elucidation of the mechanisms that underlie neuron remodeling1. In metamorphosing\ Drosophila, nuclear signaling of the steroid hormone receptor ecdysone receptor B1 isoform (EcR-B1) cell-autonomously orchestrates neuron remodeling. Only neurons destined to remodel upregulate EcR-B1 expression before a crucial pre-pupal ecdysone pulse2. It is therefore necessary to determine the mechanisms that pattern EcR-B1 expression to understand how developmental neuronal remodeling is programmed in\ Drosophila.

}, doi = {10.1038/nn0111-6}, author = {Tzumin Lee and Takeshi Awasaki} } @article {6489, title = {PALM and STORM: unlocking live-cell super-resolution.}, journal = {Biopolymers}, volume = {95}, year = {2011}, month = {2011 May}, pages = {322-31}, abstract = {

Live-cell fluorescence light microscopy has emerged as an important tool in the study of cellular biology. The development of fluorescent markers in parallel with super-resolution imaging systems has pushed light microscopy into the realm of molecular visualization at the nanometer scale. Resolutions previously only attained with electron microscopes are now within the grasp of light microscopes. However, until recently, live-cell imaging approaches have eluded super-resolution microscopy, hampering it from reaching its full potential for revealing the dynamic interactions in biology occurring at the single molecule level. Here we examine recent advances in the super-resolution imaging of living cells by reviewing recent breakthroughs in single molecule localization microscopy methods such as PALM and STORM to achieve this important goal.

}, keywords = {Buffers, Fluorescence, Fluorescent Dyes, Luminescent Proteins, Microscopy, Nanotechnology, Photochemical Processes, Single-Cell Analysis}, issn = {0006-3525}, doi = {10.1002/bip.21586}, author = {Henriques, Ricardo and Griffiths, Caron and Hesper Rego, E and Mhlanga, Musa M} } @article {2475, title = {Parallel wavefront optimization method for focusing light through random scattering media.}, journal = {Optics Letters}, volume = {36}, year = {2011}, month = {2011 Mar 15}, pages = {870-2}, abstract = {

A parallel wavefront optimization method is demonstrated experimentally to focus light through random scattering media. The simultaneous modulation of multiple phase elements, each at a unique frequency, enables a parallel determination of the optimal wavefront. Compared to a pixel-by-pixel measurement, the reported parallel method uses the target signal in a highly efficient way. With 441 phase elements, a high-quality focus was formed through a glass diffuser with a peak-to-background ratio of \~{}270. The accuracy and repeatability of the system were tested through experiments.

}, issn = {1539-4794}, doi = {10.1364/OL.36.000870}, author = {Cui, Meng} } @article {4308, title = {The past, present, and future of single neuron reconstruction.}, journal = {Neuroinformatics}, volume = {9}, year = {2011}, month = {2011 Sep}, pages = {97-8}, issn = {1559-0089}, doi = {10.1007/s12021-011-9097-y}, author = {Svoboda, Karel} } @article {4148, title = {Perception of sniff phase in mouse olfaction.}, journal = {Nature}, volume = {14}, year = {2011}, month = {2011 Oct 12}, pages = {1039-44}, abstract = {

Olfactory systems encode odours by which neurons respond and by when they respond. In mammals, every sniff evokes a precise, odour-specific sequence of activity across olfactory neurons. Likewise, in a variety of neural systems, ranging from sensory periphery to cognitive centres, neuronal activity is timed relative to sampling behaviour and/or internally generated oscillations. As in these neural systems, relative timing of activity may represent information in the olfactory system. However, there is no evidence that mammalian olfactory systems read such cues. To test whether mice perceive the timing of olfactory activation relative to the sniff cycle ({\textquoteright}sniff phase{\textquoteright}), we used optogenetics in gene-targeted mice to generate spatially constant, temporally controllable olfactory input. Here we show that mice can behaviourally report the sniff phase of optogenetically driven activation of olfactory sensory neurons. Furthermore, mice can discriminate between light-evoked inputs that are shifted in the sniff cycle by as little as 10 milliseconds, which is similar to the temporal precision of olfactory bulb odour responses. Electrophysiological recordings in the olfactory bulb of awake mice show that individual cells encode the timing of photoactivation in relation to the sniff in both the timing and the amplitude of their responses. Our work provides evidence that the mammalian olfactory system can read temporal patterns, and suggests that timing of activity relative to sampling behaviour is a potent cue that may enable accurate olfactory percepts to form quickly.

}, issn = {1476-4687}, doi = {10.1038/nature10521}, author = {Smear, Matthew and Shusterman, Roman and O{\textquoteright}Connor, Rodney and Bozza, Thomas and Rinberg, Dmitry} } @article {3602, title = {Phase resolved interferometric spectral modulation (PRISM) for ultrafast pulse measurement and compression.}, journal = {Optics Express}, volume = {19}, year = {2011}, month = {2011 Jul 4}, pages = {12961-8}, abstract = {

We show through experiments and simulations that parallel phase modulation, a technique developed in the field of adaptive optics, can be employed to quickly determine the spectral phase profile of ultrafast laser pulses and to perform phase compensation as well as pulse shaping. Different from many existing ultrafast pulse measurement methods, the technique reported here requires no spectrum measurements of nonlinear signals. Instead, the power of nonlinear signals is used directly to quickly measure the spectral phase, a convenient feature for applications such as two-photon fluorescence microscopy. The method is found to work with both smooth and even completely random distortions. The experimental results are verified with MIIPS measurements.

}, issn = {1094-4087}, doi = {10.1364/OE.19.012961}, author = {Wu, Tsai-Wei and Tang, Jianyong and Hajj, Bassam and Cui, Meng} } @article {6495, title = {Phosphorylation at the interface.}, journal = {Structure }, volume = {19}, year = {2011}, month = {2011 Dec 7}, pages = {1726-7}, abstract = {

Proteomic studies have identified thousands of eukaryotic phosphorylation sites (phosphosites), but few are functionally characterized. Nishi et\ al., in this issue of Structure, characterize phosphosites at protein-protein interfaces and estimate the effect of their phosphorylation on interaction affinity, by combining proteomics data with protein structures.

}, issn = {1878-4186}, doi = {10.1016/j.str.2011.11.006}, author = {Davis, Fred P} } @article {3421, title = {Precise olfactory responses tile the sniff cycle.}, journal = {Nature Neuroscience}, volume = {14}, year = {2011}, month = {2011 Jul 17}, pages = {1039-44}, abstract = {

In terrestrial vertebrates, sniffing controls odorant access to receptors, and therefore sets the timescale of olfactory stimuli. We found that odorants evoked precisely sniff-locked activity in mitral/tufted cells in the olfactory bulb of awake mouse. The trial-to-trial response jitter averaged 12 ms, a precision comparable to other sensory systems. Individual cells expressed odor-specific temporal patterns of activity and, across the population, onset times tiled the duration of the sniff cycle. Responses were more tightly time-locked to the sniff phase than to the time after inhalation onset. The spikes of single neurons carried sufficient information to discriminate odors. In addition, precise locking to sniff phase may facilitate ensemble coding by making synchrony relationships across neurons robust to variation in sniff rate. The temporal specificity of mitral/tufted cell output provides a potentially rich source of information for downstream olfactory areas.

}, issn = {1546-1726}, doi = {10.1038/nn.2877}, author = {Shusterman, Roman and Smear, Matthew C and Koulakov, Alexei A and Rinberg, Dmitry} } @article {45732, title = {Preparation of cuticles from feeding Drosophila larvae.}, journal = {Cold Spring Harb Protoc}, volume = {2011}, year = {2011}, month = {2011 Nov}, pages = {1394-8}, abstract = {

The Drosophila cuticle carries a rich array of morphological details. Thus, cuticle examination has had a central role in the history of genetics. Studies of the Drosophila cuticle have focused mainly on first-instar larvae and adult cuticular morphology. Although the cuticles of second- and third-instar larvae are strikingly different from those of the first instar, these differences have been poorly studied. This protocol describes three methods for preparing cuticles from fed larvae. One commonly used procedure involves manually pricking the larvae. A simpler method for preparing larval cuticles is to burst the larvae once they have been mounted. This method is used for first- and second-instar larvae and does not require pricking; it removes the gut contents by "popping" the rear of the embryo using pressure from the coverslip. If just the right amount of medium is used, the coverslip will be pulled toward the slide, applying pressure on the samples. The larvae usually burst from their posterior ends. Also presented is an alternative procedure designed specifically for the use with third-instar larvae, although the "pricking" method can be used at this stage.

}, keywords = {Animals, Dissection, Drosophila, Entomology, Female, Integumentary System, Larva}, issn = {1559-6095}, doi = {10.1101/pdb.prot066498}, author = {Stern, David L and Sucena, Elio} } @article {45733, title = {Preparation of cuticles from unhatched first-instar Drosophila larvae.}, journal = {Cold Spring Harb Protoc}, volume = {2011}, year = {2011}, month = {2011 Sep}, abstract = {

The finely sculpted cuticle of Drosophila carries a rich array of morphological details. Thus, cuticle examination has had a central role in the history of genetics. Studies of the Drosophila cuticle have focused mainly on first-instar larvae and adult cuticular morphology. This protocol describes the preparation of cuticles from larvae that have not yet hatched from the egg. It is designed for sampling all eggs laid by one or more females. This can be particularly useful, for example, when a mutation produces embryos that are unable to hatch from the egg.

}, keywords = {Animals, Drosophila, Entomology, Female, Integumentary System, Larva}, issn = {1559-6095}, doi = {10.1101/pdb.prot065532}, author = {Stern, David L and Sucena, Elio} } @article {47673, title = {Principles and current strategies for targeting autophagy for cancer treatment.}, journal = {Clinical cancer research : an official journal of the American Association for Cancer Research}, volume = {17}, year = {2011}, month = {2011 Feb 15}, pages = {654-66}, abstract = {

Autophagy is an evolutionarily conserved, intracellular self-defense mechanism in which organelles and proteins are sequestered into autophagic vesicles that are subsequently degraded through fusion with lysosomes. Cells, thereby, prevent the toxic accumulation of damaged or unnecessary components, but also recycle these components to sustain metabolic homoeostasis. Heightened autophagy is a mechanism of resistance for cancer cells faced with metabolic and therapeutic stress, revealing opportunities for exploitation as a therapeutic target in cancer. We summarize recent developments in the field of autophagy and cancer and build upon the results presented at the Cancer Therapy Evaluation Program (CTEP) Early Drug Development meeting in March 2010. Herein, we describe our current understanding of the core components of the autophagy machinery and the functional relevance of autophagy within the tumor microenvironment, and we outline how this knowledge has informed preclinical investigations combining the autophagy inhibitor hydroxychloroquine (HCQ) with chemotherapy, targeted therapy, and immunotherapy. Finally, we describe ongoing clinical trials involving HCQ as a first generation autophagy inhibitor, as well as strategies for the development of novel, more potent, and specific inhibitors of autophagy.

}, keywords = {Animals, Antineoplastic Agents, Autophagy, Clinical Trials, Phase III as Topic, Combined Modality Therapy, Cytoplasmic Vesicles, Humans, Hydroxychloroquine, Immune Tolerance, Immunotherapy, Inflammation, Metabolic Networks and Pathways, Molecular Targeted Therapy, Neoplasms, Proteasome Endopeptidase Complex, Signal Transduction}, issn = {1078-0432}, doi = {10.1158/1078-0432.CCR-10-2634}, author = {Amaravadi, Ravi K and Lippincott-Schwartz, Jennifer and Yin, Xiao-Ming and Weiss, William A and Takebe, Naoko and Timmer, William and DiPaola, Robert S and Lotze, Michael T and White, Eileen} } @article {47667, title = {Probing protein heterogeneity in the plasma membrane using PALM and pair correlation analysis.}, journal = {Nature methods}, volume = {8}, year = {2011}, month = {2011 Nov}, pages = {969-75}, abstract = {

Photoactivated localization microscopy (PALM) is a powerful approach for investigating protein organization, yet tools for quantitative, spatial analysis of PALM datasets are largely missing. Combining pair-correlation analysis with PALM (PC-PALM), we provide a method to analyze complex patterns of protein organization across the plasma membrane without determination of absolute protein numbers. The approach uses an algorithm to distinguish a single protein with multiple appearances from clusters of proteins. This enables quantification of different parameters of spatial organization, including the presence of protein clusters, their size, density and abundance in the plasma membrane. Using this method, we demonstrate distinct nanoscale organization of plasma-membrane proteins with different membrane anchoring and lipid partitioning characteristics in COS-7 cells, and show dramatic changes in glycosylphosphatidylinositol (GPI)-anchored protein arrangement under varying perturbations. PC-PALM is thus an effective tool with broad applicability for analysis of protein heterogeneity and function, adaptable to other single-molecule strategies.

}, keywords = {Algorithms, Membrane Proteins}, issn = {1548-7105}, doi = {10.1038/nmeth.1704}, author = {Sengupta, Prabuddha and Jovanovic-Talisman, Tijana and Skoko, Dunja and Renz, Malte and Veatch, Sarah L and Lippincott-Schwartz, Jennifer} } @article {5383, title = {Probing tension and dynamics in actomyosin mediated cell shape change.}, journal = {Molecular Biology of the Cell}, volume = {22}, year = {2011}, month = {2011}, author = {Higgins, C. D. and Tulu, U. S. and Gao, L. and Betzig, E and Kiehart, D. P. and Goldstein, B.} } @article {5297, title = {Proof-editing is the bottleneck of 3D neuron reconstruction: the problem and solutions.}, journal = {Neuroinformatics}, volume = {9}, year = {2011}, month = {2011 Sep}, pages = {103-5}, keywords = {Algorithms, Animals, Computer-Assisted, Data Mining, Humans, Image Cytometry, Image Processing, Imaging, Neuroanatomical Tract-Tracing Techniques, Neurons, Software, Software Design, Three-Dimensional}, issn = {1559-0089}, doi = {10.1007/s12021-010-9090-x}, author = {Peng, Hanchuan and Long, Fuhui and Zhao, Ting and Myers, Eugene} } @article {5299, title = {Proteome-wide prediction of overlapping small molecule and protein binding sites using structure.}, journal = {Molecular BioSystems}, volume = {7}, year = {2011}, month = {2011 Feb}, pages = {545-57}, abstract = {

Small molecules that modulate protein-protein interactions are of great interest for chemical biology and therapeutics. Here I present a structure-based approach to predict {\textquoteright}bi-functional{\textquoteright} sites able to bind both small molecule ligands and proteins, in proteins of unknown structure. First, I develop a homology-based annotation method that transfers binding sites of known three-dimensional structure onto protein sequences, predicting residues in ligand and protein binding sites with estimated true positive rates of 98\% and 88\%, respectively, at 1\% false positive rates. Applying this method to the human proteome predicts 8463 proteins with bi-functional residues and correctly recovers the targets of known interaction modulators. Proteins with significantly (p \< 0.01) more bi-functional residues than expected were found to be enriched in regulatory and depleted in metabolism functions. Finally, I demonstrate the utility of the method by describing examples of predicted overlap and evidence of their biological and therapeutic relevance. The results suggest that combining the structures of known binding sites with established fold detection algorithms can predict regions of protein-protein interfaces that are amenable to small molecule modulation. Open-source software and the results for several complete proteomes are available at http://pibase.janelia.org/homolobind.

}, keywords = {Algorithms, Binding Sites, Humans, Ligands, Protein Binding, Protein Conformation, Proteome}, issn = {1742-2051}, doi = {10.1039/c0mb00200c}, author = {Davis, Fred P} } @article {4392, title = {Pupil-segmentation-based adaptive optical microscopy with full-pupil illumination.}, journal = {Optics Letters}, volume = {36}, year = {2011}, month = {2011 Nov 1}, pages = {4206-8}, abstract = {

Optical aberrations deteriorate the performance of microscopes. Adaptive optics can be used to improve imaging performance via wavefront shaping. Here, we demonstrate a pupil-segmentation based adaptive optical approach with full-pupil illumination. When implemented in a two-photon fluorescence microscope, it recovers diffraction-limited performance and improves imaging signal and resolution.

}, issn = {1539-4794}, doi = {10.1364/OL.36.004206}, author = {Milkie, Daniel E and Betzig, Eric and Ji, Na} } @article {6309, title = {Pupil-segmentation-based adaptive optics for microscopy.}, journal = {Proceedings of SPIE}, volume = {7931}, year = {2011}, month = {2011}, pages = {79310I}, abstract = {

Inhomogeneous optical properties of biological samples make it difficult to obtain diffraction-limited resolution in depth. Correcting the sample-induced optical aberrations needs adaptive optics (AO). However, the direct wavefront-sensing approach commonly used in astronomy is not suitable for most biological samples due to their strong scattering of light. We developed an image-based AO approach that is insensitive to sample scattering. By comparing images of the sample taken with different segments of the pupil illuminated, local tilt in the wavefront is measured from image shift. The aberrated wavefront is then obtained either by measuring the local phase directly using interference or with phase reconstruction algorithms similar to those used in astronomical AO. We implemented this pupil-segmentation-based approach in a two-photon fluorescence microscope and demonstrated that diffraction-limited resolution can be recovered from nonbiological and biological samples.

}, doi = {10.1117/12.876398}, author = {Ji, Na and Milkie, Daniel E and Betzig, Eric} } @article {46739, title = {Qualification of a new and precise automatic tool for the assessment of hair diameters in phototrichograms.}, journal = {Skin Research \& Technology}, volume = {17}, year = {2011}, month = {2011 May}, pages = {186-95}, abstract = {

BACKGROUND/PURPOSE: To automatically assess hair growth during cosmetic trials, incorporating parameters such as anagen-to-telogen rate, growth rate, and especially hair diameter.

METHODS: We designed and qualified a new and automatic phototrichogram system based on a high-resolution DSLR camera system (theoretical resolution of 2.557 μm/pixel) and modular macrolens system with fixed focus, combined with a trainable pattern recognition software for automated analysis.

RESULTS: We improved the standard routine for dermatological phototrichogram technique to overcome inaccuracy in thickness measurements due to hair swelling by using an alternative immersion fluid, and increased the effective resolution for hair size and thickness measurement to \<4 μm. After having qualified manual measurements as gold standard for the determination of hair diameters, we established a new trainable automatic picture analysis software able to locate and measure individual hairs in length and thickness even in picture series taken from the same skin area at different time points. Comparisons between manual and automatic measurements of the same hairs showed a \>90\% correlation, and by comparing the automatic results with manual measurements of the same images without individual hair annotation, we could find a correlation of at least 80\%.

CONCLUSION: According to the results and findings generated in this qualification study, we have a reliable tool now that enables us to test cosmetic products for hair treatment in a highly automated way with a sufficient degree of precision and accuracy to detect even small changes in hair diameter during cosmetic trials.

}, keywords = {Alopecia, Dermatology, Equipment Design, Female, Hair, Hair Preparations, Humans, Image Processing, Computer-Assisted, Male, Photography, Software}, issn = {1600-0846}, doi = {10.1111/j.1600-0846.2010.00482.x}, author = {Scheede, Stefan and Herpens, Andreas and Burmeister, Frank and Oltrogge, Bernhard and Saenger, K and Schmidt-Rose, Thomas and Schreiner, Volker and Wenck, Horst and Knieps, Torsten and Berlage, Thomas} } @article {2760, title = {Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination.}, journal = {Nature Methods}, volume = {8}, year = {2011}, month = {2011 May}, pages = {417-23}, abstract = {

A key challenge when imaging living cells is how to noninvasively extract the most spatiotemporal information possible. Unlike popular wide-field and confocal methods, plane-illumination microscopy limits excitation to the information-rich vicinity of the focal plane, providing effective optical sectioning and high speed while minimizing out-of-focus background and premature photobleaching. Here we used scanned Bessel beams in conjunction with structured illumination and/or two-photon excitation to create thinner light sheets (\<0.5 μm) better suited to three-dimensional (3D) subcellular imaging. As demonstrated by imaging the dynamics of mitochondria, filopodia, membrane ruffles, intracellular vesicles and mitotic chromosomes in live cells, the microscope currently offers 3D isotropic resolution down to \~{}0.3 μm, speeds up to nearly 200 image planes per second and the ability to noninvasively acquire hundreds of 3D data volumes from single living cells encompassing tens of thousands of image frames.

}, issn = {1548-7105}, doi = {10.1038/nmeth.1586}, author = {Planchon, Thomas A and Gao, Liang and Milkie, Daniel E and Davidson, Michael W and Galbraith, James A and Galbraith, Catherine G and Betzig, Eric} } @article {3370, title = {Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination. (With commentary)}, journal = {Nature Methods}, volume = {8}, year = {2011}, month = {2011 May}, pages = {417-23}, abstract = {

A key challenge when imaging living cells is how to noninvasively extract the most spatiotemporal information possible. Unlike popular wide-field and confocal methods, plane-illumination microscopy limits excitation to the information-rich vicinity of the focal plane, providing effective optical sectioning and high speed while minimizing out-of-focus background and premature photobleaching. Here we used scanned Bessel beams in conjunction with structured illumination and/or two-photon excitation to create thinner light sheets (\<0.5 μm) better suited to three-dimensional (3D) subcellular imaging. As demonstrated by imaging the dynamics of mitochondria, filopodia, membrane ruffles, intracellular vesicles and mitotic chromosomes in live cells, the microscope currently offers 3D isotropic resolution down to \~{}0.3 μm, speeds up to nearly 200 image planes per second and the ability to noninvasively acquire hundreds of 3D data volumes from single living cells encompassing tens of thousands of image frames.

Commentary: Plane illumination microscopy has proven to be a powerful tool for studying multicellular organisms and their development at single cell resolution. However, the light sheets employed are usually too thick to provide much benefit for imaging organelles within single cultured cells. Here we introduce the use of scanned Bessel beams to create much thinner light sheets better suited to long-term dynamic live cell imaging. Such light sheets not only minimize photobleaching and phototoxicity at the sub-cellular level, but also provide axial resolution enhancement, yielding isotropic three dimensional spatial resolution. Numerous movies are provided to demonstrate the wealth of 4D information (x,y,x,t) that can be obtained from single living cells by the method. Besides providing an attractive alternative to spinning disk, AOD-driven, or line scan confocal microscopes for high speed live cell imaging, the Bessel microscope might serve as a valuable platform for superresolution microscopy (PALM, structured Illumination, or RESOLFT), since confinement of the excitation to the focal plane makes far better use of the limited fluorescence photon budget than does the traditional epi-illumination configuration.

}, keywords = {Animals, Chromosomes, Confocal, Hela Cells, Humans, Imaging, LLC-PK1 Cells, Luminescent Proteins, Microscopy, Mitosis, Optical Phenomena, Swine, Three-Dimensional}, issn = {1548-7105}, doi = {10.1038/nmeth.1586}, author = {Planchon, Thomas A and Gao, Liang and Milkie, Daniel E and Davidson, Michael W and Galbraith, James A and Galbraith, Catherine G and Betzig, Eric} } @article {6596, title = {Real-time observation of transcription initiation and elongation on an endogenous yeast gene.}, journal = {Science}, volume = {332}, year = {2011}, month = {2011 Apr 22}, pages = {475-8}, abstract = {

Cellular messenger RNA levels are achieved by the combinatorial complexity of factors controlling transcription, yet the small number of molecules involved in these pathways fluctuates stochastically. It has not yet been experimentally possible to observe the activity of single polymerases on an endogenous gene to elucidate how these events occur in vivo. Here, we describe a method of fluctuation analysis of fluorescently labeled RNA to measure dynamics of nascent RNA{\textendash}including initiation, elongation, and termination{\textendash}at an active yeast locus. We find no transcriptional memory between initiation events, and elongation speed can vary by threefold throughout the cell cycle. By measuring the abundance and intranuclear mobility of an upstream transcription factor, we observe that the gene firing rate is directly determined by trans-activating factor search times.

}, keywords = {Adenosine Triphosphatases, Cell Cycle, Cell Nucleus, DNA Polymerase I, Facilitated Diffusion, Fluorescence, Fungal, Genes, Genetic, Glutamate Synthase, Green Fluorescent Proteins, Kinetics, Messenger, Microscopy, Models, Promoter Regions, RNA, RNA Polymerase II, RNA Precursors, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Spectrometry, Transcription, Transcription Factors, Transcriptional Activation}, issn = {1095-9203}, doi = {10.1126/science.1202142}, author = {Larson, Daniel R and Zenklusen, Daniel and Wu, Bin and Chao, Jeffrey A and Singer, Robert H} } @article {6333, title = {Recent progress in understanding Alzheimer{\textquoteright}s β-amyloid structures.}, journal = {Trends in Biochemical Sciences}, volume = {36}, year = {2011}, month = {2011 Jun}, pages = {338-45}, abstract = {

The formation of amyloid fibrils, protofibrils and oligomers from the β-amyloid (Aβ) peptide represents a hallmark of Alzheimer{\textquoteright}s disease. Aβ-peptide-derived assemblies might be crucial for disease onset, but determining their atomic structures has proven to be a major challenge. Progress over the past 5 years has yielded substantial new data obtained with improved methodologies including electron cryo-microscopy and NMR. It is now possible to resolve the global fibril topology and the cross-β sheet organization within protofilaments, and to identify residues that are crucial for stabilizing secondary structural elements and peptide conformations within specific assemblies. These data have significantly enhanced our understanding of the mechanism of Aβ aggregation and have illuminated the possible relevance of specific conformers for neurodegenerative pathologies.

}, keywords = {Alzheimer Disease, Amyloid, Amyloid beta-Peptides, Animals, Humans, Protein Conformation}, issn = {0968-0004}, doi = {10.1016/j.tibs.2011.02.002}, author = {F{\"a}ndrich, Marcus and Schmidt, Matthias and Grigorieff, Nikolaus} } @article {1680, title = {Reconstructing embryonic development.}, journal = {Genesis}, volume = {49}, year = {2011}, month = {2010 Dec 7}, pages = {488-513}, abstract = {

Novel approaches to bio-imaging and automated computational image processing allow the design of truly quantitative studies in developmental biology. Cell behavior, cell fate decisions, cell interactions during tissue morphogenesis, and gene expression dynamics can be analyzed in vivo for entire complex organisms and throughout embryonic development. We review state-of-the-art technology for live imaging, focusing on fluorescence light microscopy techniques for system-level investigations of animal development and discuss computational approaches to image segmentation, cell tracking, automated data annotation, and biophysical modeling. We argue that the substantial increase in data complexity and size requires sophisticated new strategies to data analysis to exploit the enormous potential of these new resources.

}, issn = {1526-968X}, doi = {10.1002/dvg.20698}, author = {Khairy, Khaled and Keller, Philipp J} } @article {1927, title = {Rfam: Wikipedia, clans and the "decimal" release.}, journal = {Nucleic Acids Research}, volume = {39}, year = {2011}, month = {2011 Jan}, pages = {D141-5}, abstract = {

The Rfam database aims to catalogue non-coding RNAs through the use of sequence alignments and statistical profile models known as covariance models. In this contribution, we discuss the pros and cons of using the online encyclopedia, Wikipedia, as a source of community-derived annotation. We discuss the addition of groupings of related RNA families into clans and new developments to the website. Rfam is available on the Web at http://rfam.sanger.ac.uk.

}, issn = {1362-4962}, doi = {10.1093/nar/gkq1129}, author = {Gardner, Paul P and Daub, Jennifer and Tate, John and Moore, Benjamin L and Osuch, Isabelle H and Griffiths-Jones, Sam and Finn, Robert D and Nawrocki, Eric P and Kolbe, Diana L and Eddy, Sean R. and Bateman, Alex} } @article {4485, title = {RNIE: genome-wide prediction of bacterial intrinsic terminators.}, journal = {Nucleic Acids Research}, volume = {39}, year = {2011}, month = {2011 Aug}, pages = {5845-52}, abstract = {

Bacterial Rho-independent terminators (RITs) are important genomic landmarks involved in gene regulation and terminating gene expression. In this investigation we present RNIE, a probabilistic approach for predicting RITs. The method is based upon covariance models which have been known for many years to be the most accurate computational tools for predicting homology in structural non-coding RNAs. We show that RNIE has superior performance in model species from a spectrum of bacterial phyla. Further analysis of species where a low number of RITs were predicted revealed a highly conserved structural sequence motif enriched near the genic termini of the pathogenic Actinobacteria, Mycobacterium tuberculosis. This motif, together with classical RITs, account for up to 90\% of all the significantly structured regions from the termini of M. tuberculosis genic elements. The software, predictions and alignments described below are available from http://github.com/ppgardne/RNIE.

}, keywords = {Bacterial, Base Sequence, Conserved Sequence, Genetic, Genome, Genomics, Models, Molecular Sequence Annotation, Mycobacterium tuberculosis, Software, Statistical, Terminator Regions}, issn = {1362-4962}, doi = {10.1093/nar/gkr168}, author = {Gardner, Paul P and Barquist, Lars and Bateman, Alex and Nawrocki, Eric P and Weinberg, Zasha} } @article {65032, title = {Robo-3--mediated repulsive interactions guide R8 axons during Drosophila visual system development.}, journal = {Proc Natl Acad Sci U S A}, volume = {108}, year = {2011}, month = {2011 May 03}, pages = {7571-6}, abstract = {

The formation of neuronal connections requires the precise guidance of developing axons toward their targets. In the Drosophila visual system, photoreceptor neurons (R cells) project from the eye into the brain. These cells are grouped into some 750 clusters comprised of eight photoreceptors or R cells each. R cells fall into three classes: R1 to R6, R7, and R8. Posterior R8 cells are the first to project axons into the brain. How these axons select a specific pathway is not known. Here, we used a microarray-based approach to identify genes expressed in R8 neurons as they extend into the brain. We found that Roundabout-3 (Robo3), an axon-guidance receptor, is expressed specifically and transiently in R8 growth cones. In wild-type animals, posterior-most R8 axons extend along a border of glial cells demarcated by the expression of Slit, the secreted ligand of Robo3. In contrast, robo3 mutant R8 axons extend across this border and fasciculate inappropriately with other axon tracts. We demonstrate that either Robo1 or Robo2 rescues the robo3 mutant phenotype when each is knocked into the endogenous robo3 locus separately, indicating that R8 does not require a function unique to the Robo3 paralog. However, persistent expression of Robo3 in R8 disrupts the layer-specific targeting of R8 growth cones. Thus, the transient cell-specific expression of Robo3 plays a crucial role in establishing neural circuits in the Drosophila visual system by selectively regulating pathway choice for posterior-most R8 growth cones.

}, keywords = {Animals, Axons, Drosophila, Drosophila Proteins, Growth Cones, Image Processing, Computer-Assisted, Immunohistochemistry, Microarray Analysis, Nerve Tissue Proteins, Photoreceptor Cells, Invertebrate, Receptors, Immunologic, Visual Pathways}, issn = {1091-6490}, doi = {10.1073/pnas.1103419108}, author = {Pappu, Kartik S and Morey, Marta and Nern, Aljoscha and Spitzweck, Bettina and Dickson, Barry J and Zipursky, S L} } @article {47671, title = {A role for actin arcs in the leading-edge advance of migrating cells.}, journal = {Nature cell biology}, volume = {13}, year = {2011}, month = {2011 Apr}, pages = {371-81}, abstract = {

Epithelial cell migration requires coordination of two actin modules at the leading edge: one in the lamellipodium and one in the lamella. How the two modules connect mechanistically to regulate directed edge motion is not understood. Using live-cell imaging and photoactivation approaches, we demonstrate that the actin network of the lamellipodium evolves spatio-temporally into the lamella. This occurs during the retraction phase of edge motion, when myosin II redistributes to the lamellipodial actin and condenses it into an actin arc parallel to the edge. The new actin arc moves rearward, slowing down at focal adhesions in the lamella. We propose that net edge extension occurs by nascent focal adhesions advancing the site at which new actin arcs slow down and form the base of the next protrusion event. The actin arc thereby serves as a structural element underlying the temporal and spatial connection between the lamellipodium and the lamella during directed cell motion.

}, keywords = {Actins, Cell Movement, Cytoskeleton, Epithelial Cells, Focal Adhesions, Myosin Type II, Pseudopodia, Recombinant Fusion Proteins}, issn = {1476-4679}, doi = {10.1038/ncb2205}, author = {Burnette, Dylan T and Manley, Suliana and Sengupta, Prabuddha and Sougrat, Rachid and Davidson, Michael W and Kachar, Bechara and Lippincott-Schwartz, Jennifer} } @article {4926, title = {Secretins: dynamic channels for protein transport across membranes.}, journal = {Trends in Biochemical Sciences}, volume = {36}, year = {2011}, month = {2011 Aug}, pages = {433-43}, abstract = {

Secretins form megadalton bacterial-membrane channels in at least four sophisticated multiprotein systems that are crucial for translocation of proteins and assembled fibers across the outer membrane of many species of bacteria. Secretin subunits contain multiple domains, which interact with numerous other proteins, including pilotins, secretion-system partner proteins, and exoproteins. Our understanding of the structure of secretins is rapidly progressing, and it is now recognized that features common to all secretins include a cylindrical arrangement of 12-15 subunits, a large periplasmic vestibule with a wide opening at one end and a periplasmic gate at the other. Secretins might also play a key role in the biogenesis of their cognate secretion systems.

}, keywords = {Bacterial Outer Membrane Proteins, Bacterial Proteins, Carrier Proteins, Gram-Negative Bacteria, Membrane Transport Proteins, Models, Molecular, Protein Binding, Protein Conformation, Protein Structure, Protein Transport, Secondary, Secretin, Tertiary}, issn = {0968-0004}, doi = {10.1016/j.tibs.2011.04.002}, author = {Korotkov, Konstantin V and Gonen, Tamir and Hol, Wim G J} } @article {4304, title = {Serotonin-mushroom body circuit modulating the formation of anesthesia-resistant memory in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Aug 16}, pages = {13794-9}, abstract = {

Pavlovian olfactory learning in Drosophila produces two genetically distinct forms of intermediate-term memories: anesthesia-sensitive memory, which requires the amnesiac gene, and anesthesia-resistant memory (ARM), which requires the radish gene. Here, we report that ARM is specifically enhanced or inhibited in flies with elevated or reduced serotonin (5HT) levels, respectively. The requirement for 5HT was additive with the memory defect of the amnesiac mutation but was occluded by the radish mutation. This result suggests that 5HT and Radish protein act on the same pathway for ARM formation. Three supporting lines of evidence indicate that ARM formation requires 5HT released from only two dorsal paired medial (DPM) neurons onto the mushroom bodies (MBs), the olfactory learning and memory center in Drosophila: (i) DPM neurons were 5HT-antibody immunopositive; (ii) temporal inhibition of 5HT synthesis or release from DPM neurons, but not from other serotonergic neurons, impaired ARM formation; (iii) knocking down the expression of d5HT1A serotonin receptors in α/β MB neurons, which are innervated by DPM neurons, inhibited ARM formation. Thus, in addition to the Amnesiac peptide required for anesthesia-sensitive memory formation, the two DPM neurons also release 5HT acting on MB neurons for ARM formation.

}, issn = {1091-6490}, doi = {10.1073/pnas.1019483108}, author = {Lee, Pei-Tseng and Lin, Hsuan-Wen and Chang, Yu-Hsuan and Fu, Tsai-Feng and Dubnau, Josh and Hirsh, Jay and Lee, Tzumin and Chiang, Ann-Shyn} } @article {3684, title = {Shedding light on the system: studying embryonic development with light sheet microscopy.}, journal = {Current Opinion in Genetics and Development}, volume = {21}, year = {2011}, month = {2011 Aug}, pages = {558-65}, abstract = {

Light sheet-based fluorescence microscopy (LSFM) is emerging as a powerful imaging technique for the life sciences. LSFM provides an exceptionally high imaging speed, high signal-to-noise ratio, low level of photo-bleaching and good optical penetration depth. This unique combination of capabilities makes light sheet-based microscopes highly suitable for live imaging applications. There is an outstanding potential in applying this technology to the quantitative study of embryonic development. Here, we provide an overview of the different basic implementations of LSFM, review recent technical advances in the field and highlight applications in the context of embryonic development. We conclude with a discussion of promising future directions.

}, issn = {1879-0380}, doi = {10.1016/j.gde.2011.07.003}, author = {Tomer, Raju and Khairy, Khaled and Keller, Philipp J} } @article {3839, title = {Simultaneous recognition and segmentation of cells: application in C. elegans.}, journal = {Bioinformatics}, volume = {27}, year = {2011}, month = {2011 Aug 17}, pages = {2895-902}, abstract = {

MOTIVATION: Automatic recognition of cell identities is critical for quantitative measurement, targeting, and manipulation of cells of model animals at single-cell resolution. It has been shown to be a powerful tool for studying gene expression and regulation, cell lineages, and cell fates. Existing methods first segment cells, before applying a recognition algorithm in the second step. As a result, the segmentation errors in the first step directly affect and complicate the subsequent cell recognition step. Moreover, in new experimental settings, some of the image features that have been previously relied upon to recognize cells may not be easy to reproduce, due to limitations on the number of color channels available for fluorescent imaging or to the cost of building transgenic animals. An approach that is more accurate and relies on only a single signal channel is clearly desirable. RESULTS: We have developed a new method, called SRS (for Simultaneous Recognition and Segmentation of cells), and applied it to 3D image stacks of the model organism C. elegans. Given a 3D image stack of the animal and a 3D atlas of target cells, SRS is effectively an atlas-guided voxel classification process: cell recognition is realized by smoothly deforming the atlas to best fit the image, where the segmentation is obtained naturally via classification of all image voxels. The method achieved a 97.7\% overall recognition accuracy in recognizing a key class of marker cells, the body wall muscle (BWM) cells, on a data set of 175 C. elegans image stacks containing 14,118 manually curated BWM cells providing the "ground-truth" for accuracy. This result was achieved without any additional fiducial image features. SRS also automatically identified 14 of the image stacks as involving {\textpm}90-degree rotations. With these stacks excluded from the data set, the recognition accuracy rose to 99.1\%. We also show SRS is generally applicable to other cell-types, e.g. intestinal cells. AVAILABILITY: The supplementary movies can be downloaded from our website http://penglab.janelia.org/proj/celegans_seganno. The method has been implemented as a plug-in program within the V3D system (http://penglab.janelia.org/proj/v3d) and will be released in the V3D plugin source code repository.

}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btr480}, author = {Qu, Lei and Long, Fuhui and Liu, Xiao and Kim, Stuart and Myers, Eugene and Peng, Hanchuan} } @article {46734, title = {Single-molecule mRNA decay measurements reveal promoter- regulated mRNA stability in yeast.}, journal = {Cell}, volume = {147}, year = {2011}, month = {2011 Dec 23}, pages = {1484-97}, abstract = {

Messenger RNA decay measurements are typically performed on a population of cells. However, this approach cannot reveal sufficient complexity to provide information on mechanisms that may regulate mRNA degradation, possibly on short timescales. To address this deficiency, we measured cell cycle-regulated decay in single yeast cells using single-molecule FISH. We found that two genes responsible for mitotic progression, SWI5 and CLB2, exhibit a mitosis-dependent mRNA stability switch. Their transcripts are stable until mitosis, when a precipitous decay eliminates the mRNA complement, preventing carryover into the next cycle. Remarkably, the specificity and timing of decay is entirely regulated by their promoter, independent of specific cis mRNA sequences. The mitotic exit network protein Dbf2p binds to SWI5 and CLB2 mRNAs cotranscriptionally and regulates their decay. This work reveals the promoter-dependent control of mRNA stability, a regulatory mechanism that could be employed by a variety of mRNAs and organisms.

}, keywords = {Cell Cycle, Cell Cycle Proteins, Cyclin B, Gene Expression Regulation, Fungal, In Situ Hybridization, Fluorescence, Kinetics, Promoter Regions, Genetic, Protein-Serine-Threonine Kinases, RNA Stability, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription Factors, Transcription, Genetic}, issn = {1097-4172}, doi = {10.1016/j.cell.2011.11.051}, author = {Trcek, Tatjana and Larson, Daniel R and Mold{\'o}n, Alberto and Query, Charles C and Singer, Robert H} } @article {6779, title = {Slow integration leads to persistent action potential firing in distal axons of coupled interneurons.}, journal = {Nature Neuroscience}, volume = {14}, year = {2011}, month = {2011 Feb}, pages = {200-7}, abstract = {

The conventional view of neurons is that synaptic inputs are integrated on a timescale of milliseconds to seconds in the dendrites, with action potential initiation occurring in the axon initial segment. We found a much slower form of integration that leads to action potential initiation in the distal axon, well beyond the initial segment. In a subset of rodent hippocampal and neocortical interneurons, hundreds of spikes, evoked over minutes, resulted in persistent firing that lasted for a similar duration. Although axonal action potential firing was required to trigger persistent firing, somatic depolarization was not. In paired recordings, persistent firing was not restricted to the stimulated neuron; it could also be produced in the unstimulated cell. Thus, these interneurons can slowly integrate spiking, share the output across a coupled network of axons and respond with persistent firing even in the absence of input to the soma or dendrites.

}, keywords = {Action Potentials, Animals, Axons, Cerebral Cortex, Dendrites, Hippocampus, Interneurons, Mice, Nerve Net, Patch-Clamp Techniques, Synapses, Transgenic}, issn = {1546-1726}, doi = {10.1038/nn.2728}, author = {Sheffield, Mark E J and Best, Tyler K and Mensh, Brett D and Kath, William L and Spruston, Nelson} } @article {4147, title = {Sparse incomplete representations: a potential role of olfactory granule cells.}, journal = {Neuron}, volume = {72}, year = {2011}, month = {2011 Oct 6}, pages = {124-36}, abstract = {

Mitral/tufted cells of the olfactory bulb receive odorant information from receptor neurons and transmit this information to the cortex. Studies in awake behaving animals have found that sustained responses of mitral cells to odorants are rare, suggesting sparse combinatorial representation of the odorants. Careful alignment of mitral cell firing with the phase of the respiration cycle revealed brief transient activity in the larger population of mitral cells, which respond to odorants during a small fraction of the respiration cycle. Responses of these cells are therefore temporally sparse. Here, we propose a mathematical model for the olfactory bulb network that can reproduce both combinatorially and temporally sparse mitral cell codes. We argue that sparse codes emerge as a result of the balance between mitral cells{\textquoteright} excitatory inputs and inhibition provided by the granule cells. Our model suggests functional significance for the dendrodendritic synapses mediating interactions between mitral and granule cells.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.07.031}, author = {Koulakov, Alexei A and Rinberg, Dmitry} } @article {6444, title = {A structural and functional ground plan for neurons in the hindbrain of zebrafish.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Jan 18}, pages = {1164-9}, abstract = {

The vertebrate hindbrain contains various sensory-motor networks controlling movements of the eyes, jaw, head, and body. Here we show that stripes of neurons with shared neurotransmitter phenotype that extend throughout the hindbrain of young zebrafish reflect a broad underlying structural and functional patterning. The neurotransmitter stripes contain cell types with shared gross morphologies and transcription factor markers. Neurons within a stripe are stacked systematically by extent and location of axonal projections, input resistance, and age, and are recruited along the axis of the stripe during behavior. The implication of this pattern is that the many networks in hindbrain are constructed from a series of neuronal components organized into stripes that are ordered from top to bottom according to a neuron{\textquoteright}s age, structural and functional properties, and behavioral roles. This simple organization probably forms a foundation for the construction of the networks underlying the many behaviors produced by the hindbrain.

}, keywords = {Age Factors, Animals, Body Patterning, Calcium, Confocal, Electrophysiology, Genetically Modified, Interneurons, Microscopy, Models, Nerve Net, Neurological, Neurotransmitter Agents, Rhombencephalon, Zebrafish}, issn = {1091-6490}, doi = {10.1073/pnas.1012185108}, author = {Kinkhabwala, Amina and Riley, Michael and Koyama, Minoru and Monen, Joost and Satou, Chie and Kimura, Yukiko and Higashijima, Shin-Ichi and Fetcho, Joseph} } @article {68822, title = {A structural and functional ground plan for neurons in the hindbrain of zebrafish}, journal = {Proceedings of the National Academy of Sciences}, volume = {108}, year = {2011}, month = {01/2011}, pages = {1164-1169}, abstract = {

The vertebrate hindbrain contains various sensory-motor networks controlling movements of the eyes, jaw, head, and body. Here we show that stripes of neurons with shared neurotransmitter phenotype that extend throughout the hindbrain of young zebrafish reflect a broad underlying structural and functional patterning. The neurotransmitter stripes contain cell types with shared gross morphologies and transcription factor markers. Neurons within a stripe are stacked systematically by extent and location of axonal projections, input resistance, and age, and are recruited along the axis of the stripe during behavior. The implication of this pattern is that the many networks in hindbrain are constructed from a series of neuronal components organized into stripes that are ordered from top to bottom according to a neuron{\textquoteright}s age, structural and functional properties, and behavioral roles. This simple organization probably forms a foundation for the construction of the networks underlying the many behaviors produced by the hindbrain.

}, doi = {10.1073/pnas.1012185108}, url = {https://www.pnas.org/doi/abs/10.1073/pnas.1012185108}, author = {Amina Kinkhabwala and Michael Riley and Minoru Koyama and Joost Monen and Chie Satou and Yukiko Kimura and Shin-ichi Higashijima and Joseph Fetcho} } @article {6334, title = {Structural complexity of a composite amyloid fibril.}, journal = {Journal of the American Chemical Society}, volume = {133}, year = {2011}, month = {2011 Sep 21}, pages = {14686-98}, abstract = {

The molecular structure of amyloid fibrils and the mechanism of their formation are of substantial medical and biological importance, but present an ongoing experimental and computational challenge. An early high-resolution view of amyloid-like structure was obtained on amyloid-like crystals of a small fragment of the yeast prion protein Sup35p: the peptide GNNQQNY. As GNNQQNY also forms amyloid-like fibrils under similar conditions, it has been theorized that the crystal{\textquoteright}s structural features are shared by the fibrils. Here we apply magic-angle-spinning (MAS) NMR to examine the structure and dynamics of these fibrils. Previously multiple NMR signals were observed for such samples, seemingly consistent with the presence of polymorphic fibrils. Here we demonstrate that peptides with these three distinct conformations instead assemble together into composite protofilaments. Electron microscopy (EM) of the ribbon-like fibrils indicates that these protofilaments combine in differing ways to form striations of variable widths, presenting another level of structural complexity. Structural and dynamic NMR data reveal the presence of highly restricted side-chain conformations involved in interfaces between differently structured peptides, likely comprising interdigitated steric zippers. We outline molecular interfaces that are consistent with the observed EM and NMR data. The rigid and uniform structure of the GNNQQNY crystals is found to contrast distinctly with the more complex structural and dynamic nature of these "composite" amyloid fibrils. These results provide insight into the fibril-crystal distinction and also indicate a necessary caution with respect to the extrapolation of crystal structures to the study of fibril structure and formation.

}, keywords = {Amino Acid Sequence, Amyloid, Biomolecular, Fungal Proteins, Models, Molecular, Nuclear Magnetic Resonance, Prions, Yeasts}, issn = {1520-5126}, doi = {10.1021/ja203736z}, author = {Lewandowski, J{\'o}zef R and van der Wel, Patrick C A and Rigney, Mike and Grigorieff, Nikolaus and Griffin, Robert G} } @article {1233, title = {Structural properties of the Caenorhabditis elegans neuronal network.}, journal = {PLoS Computational Biology}, volume = {7}, year = {2011}, month = {2011 Feb 3}, pages = {e1001066}, abstract = {

Despite recent interest in reconstructing neuronal networks, complete wiring diagrams on the level of individual synapses remain scarce and the insights into function they can provide remain unclear. Even for Caenorhabditis elegans, whose neuronal network is relatively small and stereotypical from animal to animal, published wiring diagrams are neither accurate nor complete and self-consistent. Using materials from White et al. and new electron micrographs we assemble whole, self-consistent gap junction and chemical synapse networks of hermaphrodite C. elegans. We propose a method to visualize the wiring diagram, which reflects network signal flow. We calculate statistical and topological properties of the network, such as degree distributions, synaptic multiplicities, and small-world properties, that help in understanding network signal propagation. We identify neurons that may play central roles in information processing, and network motifs that could serve as functional modules of the network. We explore propagation of neuronal activity in response to sensory or artificial stimulation using linear systems theory and find several activity patterns that could serve as substrates of previously described behaviors. Finally, we analyze the interaction between the gap junction and the chemical synapse networks. Since several statistical properties of the C. elegans network, such as multiplicity and motif distributions are similar to those found in mammalian neocortex, they likely point to general principles of neuronal networks. The wiring diagram reported here can help in understanding the mechanistic basis of behavior by generating predictions about future experiments involving genetic perturbations, laser ablations, or monitoring propagation of neuronal activity in response to stimulation.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1001066}, author = {Varshney, Lav R and Chen, Beth L and Paniagua, Eric and Hall, David H and Chklovskii, Dmitri B} } @article {46412, title = {The structure, molecular dynamics, and energetics of centrin-melittin complex.}, journal = {Proteins}, volume = {79}, year = {2011}, month = {2011 Nov}, pages = {3132-43}, abstract = {

Centrin is a calcium binding protein (CaBP) belonging to the EF-hand superfamily. As with other proteins within this family, centrin is a calcium sensor with multiple biological target proteins. We chose to study Chlamydomonas reinhardtii centrin (Crcen) and its interaction with melittin (MLT) as a model for CaBP complexes due to its amphipathic properties. Our goal was to determine the molecular interactions that lead to centrin-MLT complex formation, their relative stability, and the conformational changes associated with the interaction, when compared to the single components. For this, we determined the thermodynamic parameters that define Crcen-MLT complex formation. Two-dimensional infrared (2D IR) correlation spectroscopy were used to study the amide I{\textquoteright}, I{\textquoteright}*, and side chain bands for (13)C-Crcen, MLT, and the (13)C-Crcen-MLT complex. This approach resulted in the determination of MLT{\textquoteright}s increased helicity, while centrin was stabilized within the complex. Herein we provide the first complete molecular description of centrin-MLT complex formation and the dissociation process. Also, discussed is the first structure of a CaBP-MLT complex by X-ray crystallography, which shows that MLT has a different binding orientation than previously characterized centrin-bound peptides. Finally, all of the experimental results presented herein are consistent with centrin maintaining an extended conformation while interacting with MLT. The molecular implications of these results are: (1) the recognition of hydrophobic contacts as requirements for initial binding, (2) minimum electrostatic interactions within the C-terminal end of the peptide, and (3) van der Waals interactions within MLTs N-terminal end are required for complex formation.

}, keywords = {Calcium-Binding Proteins, Crystallography, X-Ray, Melitten, Molecular Dynamics Simulation, Protein Binding, Protein Conformation, Spectroscopy, Fourier Transform Infrared, Thermodynamics}, issn = {1097-0134}, doi = {10.1002/prot.23142}, author = {Sosa, Liliana Del Valle and Alfaro, Elisa and Santiago, Jorge and Narv{\'a}ez, Daniel and Rosado, Marie Cely and Rodr{\'\i}guez, Aslin and G{\'o}mez, Ana Mar{\'\i}a and Schreiter, Eric R and Pastrana-R{\'\i}os, Belinda} } @article {4373, title = {Structure of the escherichia coli phosphonate binding protein PhnD and rationally optimized phosphonate biosensors.}, journal = {Journal of Molecular Biology}, volume = {414}, year = {2011}, month = {2011 Dec 2}, pages = {356-69}, abstract = {

The phnD gene of Escherichia coli encodes the periplasmic binding protein of the phosphonate (Pn) uptake and utilization pathway. We have crystallized and determined structures of E. coli PhnD (EcPhnD) in the absence of ligand and in complex with the environmentally abundant 2-aminoethylphosphonate (2AEP). Similar to other bacterial periplasmic binding proteins, 2AEP binds near the center of mass of EcPhnD in a cleft formed between two lobes. Comparison of the open, unliganded structure with the closed 2AEP-bound structure shows that the two lobes pivot around a hinge by \~{}70{\textdegree} between the two states. Extensive hydrogen bonding and electrostatic interactions stabilize 2AEP, which binds to EcPhnD with low nanomolar affinity. These structures provide insight into Pn uptake by bacteria and facilitated the rational design of high signal-to-noise Pn biosensors based on both coupled small-molecule dyes and autocatalytic fluorescent proteins.

}, issn = {1089-8638}, doi = {10.1016/j.jmb.2011.09.047}, author = {Alicea, Ismael and Marvin, Jonathan S and Miklos, Aleksandr E and Ellington, Andrew D and Looger, Loren L and Schreiter, Eric R} } @article {3328, title = {Studying sensorimotor integration in insects.}, journal = {Current Opinion in Neurobiology}, volume = {21}, year = {2011}, month = {2011 Jun 24}, pages = {527-34}, abstract = {

Sensorimotor integration is a field rich in theory backed by a large body of psychophysical evidence. Relating the underlying neural circuitry to these theories has, however, been more challenging. With a wide array of complex behaviors coordinated by their small brains, insects provide powerful model systems to study key features of sensorimotor integration at a mechanistic level. Insect neural circuits perform both hard-wired and learned sensorimotor transformations. They modulate their neural processing based on both internal variables, such as the animal{\textquoteright}s behavioral state, and external ones, such as the time of day. Here we present some studies using insect model systems that have produced insights, at the level of individual neurons, about sensorimotor integration and the various ways in which it can be modified by context.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2011.05.030}, author = {Huston*, Stephen J and Jayaraman, Vivek} } @article {5305, title = {Studying sensorimotor processing with physiology in behaving Drosophila.}, journal = {International Review of Neurobiology}, volume = {99}, year = {2011}, month = {2011}, pages = {169-89}, abstract = {

The neural underpinnings of sensorimotor integration are best studied in the context of well-characterized behavior. A rich trove of Drosophila behavioral genetics research offers a variety of well-studied behaviors and candidate brain regions that can form the bases of such studies. The development of tools to perform in vivo physiology from the Drosophila brain has made it possible to monitor activity in defined neurons in response to sensory stimuli. More recently still, it has become possible to perform recordings from identified neurons in the brain of head-fixed flies during walking or flight behaviors. In this chapter, we discuss how experiments that simultaneously monitor behavior and physiology in Drosophila can be combined with other techniques to produce testable models of sensorimotor circuit function.

}, keywords = {Animal, Animals, Behavior, Brain, Drosophila, Electrophysiology, Motivation, Neurons, Psychomotor Performance}, issn = {0074-7742}, doi = {10.1016/B978-0-12-387003-2.00007-0}, author = {Seelig, Johannes D and Jayaraman, Vivek} } @article {5307, title = {Sub-nuclear compartmentalization of core promoter factors and target genes.}, journal = {Cell Cycle}, volume = {10}, year = {2011}, month = {2011 Aug 1}, pages = {2405-6}, issn = {1551-4005}, author = {Yao, Jie and Tjian, Robert} } @article {2385, title = {Subnuclear segregation of genes and core promoter factors in myogenesis. (With commentary)}, journal = {Genes \& Development}, volume = {25}, year = {2011}, month = {2011 Mar 15}, pages = {569-80}, abstract = {

Recent findings implicate alternate core promoter recognition complexes in regulating cellular differentiation. Here we report a spatial segregation of the alternative core factor TAF3, but not canonical TFIID subunits, away from the nuclear periphery, where the key myogenic gene MyoD is preferentially localized in myoblasts. This segregation is correlated with the differential occupancy of TAF3 versus TFIID at the MyoD promoter. Loss of this segregation by modulating either the intranuclear location of the MyoD gene or TAF3 protein leads to altered TAF3 occupancy at the MyoD promoter. Intriguingly, in differentiated myotubes, the MyoD gene is repositioned to the nuclear interior, where TAF3 resides. The specific high-affinity recognition of H3K4Me3 by the TAF3 PHD (plant homeodomain) finger appears to be required for the sequestration of TAF3 to the nuclear interior. We suggest that intranuclear sequestration of core transcription components and their target genes provides an additional mechanism for promoter selectivity during differentiation.

Commentary: Jie Yao in Bob Tijan{\textquoteright}s lab used a combination of confocal microscopy and dual label PALM in thin sections cut from resin-embedded cells to show that certain core transcription components and their target genes are spatially segregated in myoblasts, but not in differentiated myotubes, suggesting that such spatial segregation may play a role in guiding cellular differentiation.

}, issn = {1549-5477}, doi = {10.1073/pnas.1100640108}, author = {Yao, Jie and Fetter, Richard D and Hu, Ping and Betzig, Eric and Tjian, Robert} } @article {5309, title = {Super-resolution 3D microscopy of live whole cells using structured illumination.}, journal = {Nature Methods}, volume = {8}, year = {2011}, month = {2011 Dec}, pages = {1044-6}, abstract = {

Three-dimensional (3D) structured-illumination microscopy (SIM) can double the lateral and axial resolution of a wide-field fluorescence microscope but has been too slow for live imaging. Here we apply 3D SIM to living samples and record whole cells at up to 5 s per volume for \>50 time points with 120-nm lateral and 360-nm axial resolution. We demonstrate the technique by imaging microtubules in S2 cells and mitochondria in HeLa cells.

}, keywords = {Animals, Cell Line, Cell Survival, Drosophila melanogaster, Fluorescence, Hela Cells, Humans, Imaging, Microscopy, Microtubules, Mitochondria, Three-Dimensional}, issn = {1548-7105}, doi = {10.1038/nmeth.1734}, author = {Shao, Lin and Kner, Peter and Rego, E Hesper and Gustafsson, Mats G L} } @article {4469, title = {Superresolution fluorescence imaging of mitochondrial nucleoids reveals their spatial range, limits, and membrane interaction.}, journal = {Molecular and Cellular Biology}, volume = {31}, year = {2011}, month = {2011 Dec}, pages = {4994-5010}, abstract = {

A fundamental objective in molecular biology is to understand how DNA is organized in concert with various proteins, RNA, and biological membranes. Mitochondria maintain and express their own DNA (mtDNA), which is arranged within structures called nucleoids. Their functions, dimensions, composition, and precise locations relative to other mitochondrial structures are poorly defined. Superresolution fluorescence microscopy techniques that exceed the previous limits of imaging within the small and highly compartmentalized mitochondria have been recently developed. We have improved and employed both two- and three-dimensional applications of photoactivated localization microscopy (PALM and iPALM, respectively) to visualize the core dimensions and relative locations of mitochondrial nucleoids at an unprecedented resolution. PALM reveals that nucleoids differ greatly in size and shape. Three-dimensional volumetric analysis indicates that, on average, the mtDNA within ellipsoidal nucleoids is extraordinarily condensed. Two-color PALM shows that the freely diffusible mitochondrial matrix protein is largely excluded from the nucleoid. In contrast, nucleoids are closely associated with the inner membrane and often appear to be wrapped around cristae or crista-like inner membrane invaginations. Determinations revealing high packing density, separation from the matrix, and tight association with the inner membrane underscore the role of mechanisms that regulate access to mtDNA and that remain largely unknown.

}, keywords = {3T3 Cells, Animals, Confocal, DNA, Fluorescence, Mice, Microscopy, Mitochondria, Mitochondrial, Mitochondrial Proteins, Plasmids, Sequence Alignment, Sequence Analysis}, issn = {1098-5549}, doi = {10.1128/MCB.05694-11}, url = {http://mcb.asm.org/content/31/24/4994.short}, author = {Brown, Timothy A and Tkachuk, Ariana N and Shtengel, Gleb and Kopek, Benjamin G and Bogenhagen, Daniel F and Hess, Harald F and Clayton, David A} } @conference {2844, title = {Supervised hypergraph labeling.}, booktitle = {IEEE Conference on Computer Vision Pattern Recognition}, year = {2011}, month = {2011}, abstract = {

We address the problem of labeling individual datapoints given some knowledge about (small) subsets or groups of them. The knowledge we have for a group is the likelihood value for each group member to satisfy a certain model. This problem is equivalent to hypergraph labeling problem where each datapoint corresponds to a node and the each subset correspond to a hyperedge with likelihood value as its weight. We propose a novel method to model the label dependence using an Undirected Graphical Model and reduce the problem of hypergraph labeling into an inference problem. This paper describes the structure and necessary components of such model and proposes useful cost functions. We discuss the behavior of proposed algorithm with different forms of the cost functions, identify suitable algorithms for inference and analyze required properties when it is theoretically guaranteed to have exact solution. Examples of several real world problems are shown as applications of the proposed method.

}, author = {Parag, Toufiq and Elgammal, Ahmed} } @article {46738, title = {The survival of motor neuron (SMN) protein interacts with the mRNA-binding protein HuD and regulates localization of poly(A) mRNA in primary motor neuron axons.}, journal = {The Journal of Neuroscience}, volume = {31}, year = {2011}, month = {2011 Mar 9}, pages = {3914-25}, abstract = {

Spinal muscular atrophy (SMA) results from reduced levels of the survival of motor neuron (SMN) protein, which has a well characterized function in spliceosomal small nuclear ribonucleoprotein assembly. Currently, it is not understood how deficiency of a housekeeping protein leads to the selective degeneration of spinal cord motor neurons. Numerous studies have shown that SMN is present in neuronal processes and has many interaction partners, including mRNA-binding proteins, suggesting a potential noncanonical role in axonal mRNA metabolism. In this study, we have established a novel technological approach using bimolecular fluorescence complementation (BiFC) and quantitative image analysis to characterize SMN-protein interactions in primary motor neurons. Consistent with biochemical studies on the SMN complex, BiFC analysis revealed that SMN dimerizes and interacts with Gemin2 in nuclear gems and axonal granules. In addition, using pull down assays, immunofluorescence, cell transfection, and BiFC, we characterized a novel interaction between SMN and the neuronal mRNA-binding protein HuD, which was dependent on the Tudor domain of SMN. A missense mutation in the SMN Tudor domain, which is known to cause SMA, impaired the interaction with HuD, but did not affect SMN axonal localization or self-association. Furthermore, time-lapse microscopy revealed SMN cotransport with HuD in live motor neurons. Importantly, SMN knockdown in primary motor neurons resulted in a specific reduction of both HuD protein and poly(A) mRNA levels in the axonal compartment. These findings reveal a noncanonical role for SMN whereby its interaction with mRNA-binding proteins may facilitate the localization of associated poly(A) mRNAs into axons.

}, keywords = {Animals, Axons, Blotting, Western, Chick Embryo, Fluorescent Antibody Technique, HEK293 Cells, Hippocampus, Hu Paraneoplastic Encephalomyelitis Antigens, Humans, Immunoprecipitation, In Situ Hybridization, Fluorescence, Mice, Motor Neurons, Poly A, Poly(A)-Binding Proteins, Prosencephalon, Rats, SMN Complex Proteins}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3631-10.2011}, author = {Fallini, Claudia and Zhang, Honglai and Su, Yuehang and Silani, Vincenzo and Singer, Robert H and Rossoll, Wilfried and Bassell, Gary J} } @article {48393, title = {Symmetries in stimulus statistics shape the form of visual motion estimators.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Aug 02}, pages = {12909-14}, abstract = {

The estimation of visual motion has long been studied as a paradigmatic neural computation, and multiple models have been advanced to explain behavioral and neural responses to motion signals. A broad class of models, originating with the Reichardt correlator model, proposes that animals estimate motion by computing a temporal cross-correlation of light intensities from two neighboring points in visual space. These models provide a good description of experimental data in specific contexts but cannot explain motion percepts in stimuli lacking pairwise correlations. Here, we develop a theoretical formalism that can accommodate diverse stimuli and behavioral goals. To achieve this, we treat motion estimation as a problem of Bayesian inference. Pairwise models emerge as one component of the generalized strategy for motion estimation. However, correlation functions beyond second order enable more accurate motion estimation. Prior expectations that are asymmetric with respect to bright and dark contrast use correlations of both even and odd orders, and we show that psychophysical experiments using visual stimuli with symmetric probability distributions for contrast cannot reveal whether the subject uses odd-order correlators for motion estimation. This result highlights a gap in previous experiments, which have largely relied on symmetric contrast distributions. Our theoretical treatment provides a natural interpretation of many visual motion percepts, indicates that motion estimation should be revisited using a broader class of stimuli, demonstrates how correlation-based motion estimation is related to stimulus statistics, and provides multiple experimentally testable predictions.

}, keywords = {Algorithms, Animals, Computer Simulation, Models, Neurological, Motion, Motion Perception, Photic Stimulation, Time Factors}, issn = {1091-6490}, doi = {10.1073/pnas.1015680108}, author = {Fitzgerald, James E and Katsov, Alexander Y and Clandinin, Thomas R and Schnitzer, Mark J} } @article {46047, title = {A synaptic mechanism for retinal adaptation to luminance and contrast.}, journal = {Journal of Neuroscience}, volume = {31}, year = {2011}, month = {2011 Jul 27}, pages = {11003-15}, abstract = {

The gain of signaling in primary sensory circuits is matched to the stimulus intensity by the process of adaptation. Retinal neural circuits adapt to visual scene statistics, including the mean (background adaptation) and the temporal variance (contrast adaptation) of the light stimulus. The intrinsic properties of retinal bipolar cells and synapses contribute to background and contrast adaptation, but it is unclear whether both forms of adaptation depend on the same cellular mechanisms. Studies of bipolar cell synapses identified synaptic mechanisms of gain control, but the relevance of these mechanisms to visual processing is uncertain because of the historical focus on fast, phasic transmission rather than the tonic transmission evoked by ambient light. Here, we studied use-dependent regulation of bipolar cell synaptic transmission evoked by small, ongoing modulations of membrane potential (V(M)) in the physiological range. We made paired whole-cell recordings from rod bipolar (RB) and AII amacrine cells in a mouse retinal slice preparation. Quasi-white noise voltage commands modulated RB V(M) and evoked EPSCs in the AII. We mimicked changes in background luminance or contrast, respectively, by depolarizing the V(M) or increasing its variance. A linear systems analysis of synaptic transmission showed that increasing either the mean or the variance of the presynaptic V(M) reduced gain. Further electrophysiological and computational analyses demonstrated that adaptation to mean potential resulted from both Ca channel inactivation and vesicle depletion, whereas adaptation to variance resulted from vesicle depletion alone. Thus, background and contrast adaptation apparently depend in part on a common synaptic mechanism.

}, keywords = {Adaptation, Physiological, Amacrine Cells, Animals, Biophysical Phenomena, Biophysics, Calcium, Contrast Sensitivity, Electric Stimulation, Excitatory Postsynaptic Potentials, Female, In Vitro Techniques, Lighting, Male, Mice, Mice, Inbred C57BL, Models, Neurological, Numerical Analysis, Computer-Assisted, Patch-Clamp Techniques, Photic Stimulation, Presynaptic Terminals, Retina, Retinal Bipolar Cells, Synaptic Transmission}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2631-11.2011}, author = {Jarsky, Tim and Cembrowski, Mark and Logan, Stephen M and Kath, William L and Riecke, Hermann and Demb, Jonathan B and Singer, Joshua H} } @article {4927, title = {Synaptosomes as a platform for loading nanoparticles into synaptic vesicles.}, journal = {ACS Chemical Neuroscience}, volume = {2}, year = {2011}, month = {2011 May 18}, pages = {236-241}, abstract = {

Synaptosomes are intact, isolated nerve terminals that contain the necessary machinery to recycle synaptic vesicles via endocytosis and exocytosis upon stimulation. Here we use this property of synaptosomes to load quantum dots into synaptic vesicles. Vesicles are then isolated from the synaptosomes, providing a method to probe isolated, individual synaptic vesicles where each vesicle contains a single, encapsulated nanoparticle. This technique provided an encapsulation efficiency of \ 16\%, that is, \ 16\% of the vesicles contained a single quantum dot while the remaining vesicles were empty. The ability to load single nanoparticles into synaptic vesicles opens new opportunity for employing various nanoparticle-based sensors to study the dynamics of vesicular transporters.

}, issn = {1948-7193}, doi = {10.1021/cn200009n}, author = {Budzinski, Kristi L and Sgro, Allyson E and Fujimoto, Bryant S and Gadd, Jennifer C and Shuart, Noah G and Gonen, Tamir and Bajjaleih, Sandra M and Chiu, Daniel T} } @article {4185, title = {Synthesis and utility of fluorogenic acetoxymethyl ethers.}, journal = {Chemical Science}, volume = {2}, year = {2011}, month = {2011 Jan 1}, pages = {521-30}, abstract = {

Phenolic fluorophores such as fluorescein, Tokyo Green, resorufin, and their derivatives are workhorses of biological science. Acylating the phenolic hydroxyl group(s) in these fluorophores masks their fluorescence. The ensuing ester is a substrate for cellular esterases, which can restore fluorescence. These esters are, however, notoriously unstable to hydrolysis, severely compromising their utility. The acetoxymethyl (AM) group is an esterase-sensitive motif that can mask polar functionalities in small molecules. Here, we report on the use of AM ether groups to mask phenolic fluorophores. The resulting profluorophores have a desirable combination of low background fluorescence, high chemical stability, and high enzymatic reactivity, both in vitro and in cellulo. These simple phenyl ether-based profluorophores could supplement or supplant the use of phenyl esters for imaging biochemical and biological systems.

}, issn = {2041-6539}, doi = {10.1039/C0SC00466A}, author = {Lavis, Luke D and Chao, Tzu-Yuan and Raines, Ronald T} } @article {4496, title = {Synthesis of rhodamines from fluoresceins using Pd-catalyzed C-N cross-coupling.}, journal = {Organic Letters}, volume = {13}, year = {2011}, month = {2011 Dec 16}, pages = {6354-7}, abstract = {

A unified, convenient, and efficient strategy for the preparation of rhodamines and N,N{\textquoteright}-diacylated rhodamines has been developed. Fluorescein ditriflates were found to undergo palladium-catalyzed C-N cross-coupling with amines, amides, carbamates, and other nitrogen nucleophiles to provide direct access to known and novel rhodamine derivatives, including fluorescent dyes, quenchers, and latent fluorophores.

}, issn = {1523-7052}, doi = {10.1021/ol202618t}, author = {Grimm, Jonathan B and Lavis, Luke D} } @article {46609, title = {Tao kinases as coordinators of actin and microtubule dynamics in developing neurons.}, journal = {Communicative \& Integrative Biology}, volume = {4}, year = {2011}, month = {2011 Sep}, pages = {554-6}, abstract = {

Drosophila tao, encoding a Ste20 family kinase, was identified as a gene involved in ethanol, cocaine and nicotine sensitivity. The behavioral phenotypes appear to be caused by defects in the development of the adult brain. Specifically, Drosophila tao functions to promote axon guidance of mushroom body (MB) neurons. The MB is a large structure in the central brain of the fly whose development and function have been well characterized. tao interacts genetically with mutations in the par-1 gene, also encoding a serine-threonine kinase. Since Par-1 has been implicated in the regulation of microtubule dynamics, this suggests that tao regulates the microtubule cytoskeleton in developing MB neurons. Here we discuss these results in light of previous studies that have proposed that Drosophila tao and its mammalian homologs function as a link between the actin and microtubule cytoskeletons, regulating microtubule stability in response to actin signals.

}, issn = {1942-0889}, doi = {10.4161/cib.4.5.16051}, author = {King, Ian and Heberlein, Ulrike} } @article {6332, title = {Tilt-pair analysis of images from a range of different specimens in single-particle electron cryomicroscopy.}, journal = {Journal of Molecular Biology}, volume = {413}, year = {2011}, month = {2011 Nov 11}, pages = {1028-46}, abstract = {

The comparison of a pair of electron microscope images recorded at different specimen tilt angles provides a powerful approach for evaluating the quality of images, image-processing procedures, or three-dimensional structures. Here, we analyze tilt-pair images recorded from a range of specimens with different symmetries and molecular masses and show how the analysis can produce valuable information not easily obtained otherwise. We show that the accuracy of orientation determination of individual single particles depends on molecular mass, as expected theoretically since the information in each particle image increases with molecular mass. The angular uncertainty is less than 1{\textdegree} for particles of high molecular mass (\ 50 MDa), several degrees for particles in the range 1-5 MDa, and tens of degrees for particles below 1 MDa. Orientational uncertainty may be the major contributor to the effective temperature factor (B-factor) describing contrast loss and therefore the maximum resolution of a structure determination. We also made two unexpected observations. Single particles that are known to be flexible showed a wider spread in orientation accuracy, and the orientations of the largest particles examined changed by several degrees during typical low-dose exposures. Smaller particles presumably also reorient during the exposure; hence, specimen movement is a second major factor that limits resolution. Tilt pairs thus enable assessment of orientation accuracy, map quality, specimen motion, and conformational heterogeneity. A convincing tilt-pair parameter plot, where 60\% of the particles show a single cluster around the expected tilt axis and tilt angle, provides confidence in a structure determined using electron cryomicroscopy.

}, keywords = {Adenosine Triphosphatases, Animals, beta-Galactosidase, Cattle, Computer-Assisted, Cryoelectron Microscopy, Image Processing, Rotavirus, Virion, Yeasts}, issn = {1089-8638}, doi = {10.1016/j.jmb.2011.09.008}, author = {Henderson, Richard and Chen, Shaoxia and Chen, James Z and Grigorieff, Nikolaus and Passmore, Lori A and Ciccarelli, Luciano and Rubinstein, John L and Crowther, R Anthony and Stewart, Phoebe L and Rosenthal, Peter B} } @article {47665, title = {Together we are stronger: fusion protects mitochondria from autophagosomal degradation.}, journal = {Autophagy}, volume = {7}, year = {2011}, month = {2011 Dec}, pages = {1568-9}, abstract = {

Starvation induces a protective process of self-cannibalization called autophagy that is thought to mediate nonselective degradation of cytoplasmic material. We recently reported that mitochondria escape autophagosomal degradation through extensive fusion into mitochondrial networks upon certain starvation conditions. The extent of mitochondrial elongation is dependent on the type of nutrient deprivation, with amino acid depletion having a particularly strong effect. Downregulation of the mitochondrial fission protein Drp1 was determined to be important in bringing about starvation-induced mitochondrial fusion. The formation of mitochondrial networks during nutrient depletion selectively blocked their autophagic degradation, presumably allowing cells to sustain efficient ATP production and thereby survive starvation.

}, keywords = {Animals, Autophagy, Cyclic AMP-Dependent Protein Kinases, Membrane Fusion, Mice, Mitochondria, Phagosomes, Signal Transduction, TOR Serine-Threonine Kinases}, issn = {1554-8635}, author = {Rambold, Angelika S and Kostelecky, Brenda and Lippincott-Schwartz, Jennifer} } @article {46740, title = {Transcription of functionally related constitutive genes is not coordinated.}, journal = {Nature Structural \& Molecular Biology}, volume = {18}, year = {2011}, month = {2011 Jan}, pages = {27-34}, abstract = {

Expression of an individual gene can vary considerably among genetically identical cells because of stochastic fluctuations in transcription. However, proteins comprising essential complexes or pathways have similar abundances and lower variability. It is not known whether coordination in the expression of subunits of essential complexes occurs at the level of transcription, mRNA abundance or protein expression. To directly measure the level of coordination in the expression of genes, we used highly sensitive fluorescence in situ hybridization (FISH) to count individual mRNAs of functionally related and unrelated genes within single Saccharomyces cerevisiae cells. Our results revealed that transcript levels of temporally induced genes are highly correlated in individual cells. In contrast, transcription of constitutive genes encoding essential subunits of complexes is not coordinated because of stochastic fluctuations. The coordination of these functional complexes therefore must occur post-transcriptionally, and likely post-translationally.

}, keywords = {Gene Expression Regulation, In Situ Hybridization, Fluorescence, Models, Genetic, RNA, Messenger, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription, Genetic}, issn = {1545-9985}, doi = {10.1038/nsmb.1934}, author = {Gandhi, Saumil J and Zenklusen, Daniel and Lionnet, Timoth{\'e}e and Singer, Robert H} } @article {6601, title = {A transgenic mouse for in vivo detection of endogenous labeled mRNA.}, journal = {Nature Methods}, volume = {8}, year = {2011}, month = {2011 Feb}, pages = {165-70}, abstract = {

Live-cell single mRNA imaging is a powerful tool but has been restricted in higher eukaryotes to artificial cell lines and reporter genes. We describe an approach that enables live-cell imaging of single endogenous labeled mRNA molecules transcribed in primary mammalian cells and tissue. We generated a knock-in mouse line with an MS2 binding site (MBS) cassette targeted to the 3{\textquoteright} untranslated region of the essential β-actin gene. As β-actin-MBS was ubiquitously expressed, we could uniquely address endogenous mRNA regulation in any tissue or cell type. We simultaneously followed transcription from the β-actin alleles in real time and observed transcriptional bursting in response to serum stimulation with precise temporal resolution. We tracked single endogenous labeled mRNA particles being transported in primary hippocampal neurons. The MBS cassette also enabled high-sensitivity fluorescence in situ hybridization (FISH), allowing detection and localization of single β-actin mRNA molecules in various mouse tissues.

}, keywords = {Animals, Cell Survival, Cells, Cultured, Fluorescence, Genetic, In Situ Hybridization, Messenger, Mice, RNA, Transcription, Transgenic}, issn = {1548-7105}, doi = {10.1038/nmeth.1551}, author = {Lionnet, Timoth{\'e}e and Czaplinski, Kevin and Darzacq, Xavier and Shav-Tal, Yaron and Wells, Amber L and Chao, Jeffrey A and Park, Hye Yoon and de Turris, Valeria and Lopez-Jones, Melissa and Singer, Robert H} } @article {47669, title = {Tubular network formation protects mitochondria from autophagosomal degradation during nutrient starvation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Jun 21}, pages = {10190-5}, abstract = {

Mitochondria are highly dynamic organelles that mediate essential cell functions such as apoptosis and cell-cycle control in addition to their role as efficient ATP generators. Mitochondrial morphology changes are tightly regulated, and their shape can shift between small, fragmented units and larger networks of elongated mitochondria. We demonstrate that mitochondrial elements become significantly elongated and interconnected shortly after nutrient depletion. This mitochondrial morphological shift depends on the type of starvation, with an additive effect observed when multiple nutrients are depleted simultaneously. We further show that starvation-induced mitochondrial elongation is mediated by down-regulation of dynamin-related protein 1 (Drp1) through modulation of two Drp1 phosphorylation sites, leading to unopposed mitochondrial fusion. Finally, we establish that mitochondrial tubulation upon nutrient deprivation protects mitochondria from autophagosomal degradation, which could permit mitochondria to maximize energy production and supply autophagosomal membranes during starvation.

}, keywords = {Animals, Autophagy, Cells, Cultured, Dynamins, Fibroblasts, GTP Phosphohydrolases, Mice, Microtubule-Associated Proteins, Mitochondria, Mitochondrial Proteins, Phagosomes, Protein Processing, Post-Translational, Starvation}, issn = {1091-6490}, doi = {10.1073/pnas.1107402108}, author = {Rambold, Angelika S and Kostelecky, Brenda and Elia, Natalie and Lippincott-Schwartz, Jennifer} } @article {3357, title = {Turning males on: activation of male courtship behavior in Drosophila melanogaster.}, journal = {PLoS One}, volume = {6}, year = {2011}, month = {2011}, pages = {e21144}, abstract = {

The innate sexual behaviors of Drosophila melanogaster males are an attractive system for elucidating how complex behavior patterns are generated. The potential for male sexual behavior in D. melanogaster is specified by the fruitless (fru) and doublesex (dsx) sex regulatory genes. We used the temperature-sensitive activator dTRPA1 to probe the roles of fru(M)- and dsx-expressing neurons in male courtship behaviors. Almost all steps of courtship, from courtship song to ejaculation, can be induced at very high levels through activation of either all fru(M) or all dsx neurons in solitary males. Detailed characterizations reveal different roles for fru(M) and dsx in male courtship. Surprisingly, the system for mate discrimination still works well when all dsx neurons are activated, but is impaired when all fru(M) neurons are activated. Most strikingly, we provide evidence for a fru(M)-independent courtship pathway that is primarily vision dependent.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0021144}, author = {Pan, Yufeng and Robinett, Carmen C and Baker, Bruce S} } @article {4305, title = {Two-photon calcium imaging of evoked activity from L5 somatosensory neurons in vivo.}, journal = {Nature Neuroscience}, volume = {14}, year = {2011}, month = {2011 Aug}, pages = {1089-93}, abstract = {

Multiphoton imaging (MPI) is widely used for recording activity simultaneously from many neurons in superficial cortical layers in vivo. We combined regenerative amplification multiphoton microscopy (RAMM) with genetically encoded calcium indicators to extend MPI of neuronal population activity into layer 5 (L5) of adult mouse somatosensory cortex. We found that this approach could be used to record and quantify spontaneous and sensory-evoked activity in populations of L5 neuronal somata located as much as 800 μm below the pia. In addition, we found that RAMM could be used to simultaneously image activity from large (80) populations of apical dendrites and follow these dendrites down to their somata of origin.

}, keywords = {Animals, Axons, Calcium, Dendrites, Evoked Potentials, Green Fluorescent Proteins, Inbred C57BL, Mice, Nerve Net, Neurons, Newborn, Photons, Physical Stimulation, Probability, Reaction Time, Somatosensory, Somatosensory Cortex, Statistics as Topic, Transgenic}, issn = {1546-1726}, doi = {10.1038/nn.2879}, author = {Mittmann, Wolfgang and Wallace, Damian J and Czubayko, Uwe and Herb, Jan T and Schaefer, Andreas T and Looger, Loren L and Denk, Winfried and Kerr, Jason N D} } @article {46737, title = {Variegated gene expression caused by cell-specific long-range DNA interactions.}, journal = {Nature Cell Biology}, volume = {13}, year = {2011}, month = {2011 Aug}, pages = {944-51}, abstract = {

Mammalian genomes contain numerous regulatory DNA sites with unknown target genes. We used mice with an extra β-globin locus control region (LCR) to investigate how a regulator searches the genome for target genes. We find that the LCR samples a restricted nuclear subvolume, wherein it preferentially contacts genes controlled by shared transcription factors. No contacted gene is detectably upregulated except for endogenous β-globin genes located on another chromosome. This demonstrates genetically that mammalian trans activation is possible, but suggests that it will be rare. Trans activation occurs not pan-cellularly, but in {\textquoteright}jackpot{\textquoteright} cells enriched for the interchromosomal interaction. Therefore, cell-specific long-range DNA contacts can cause variegated expression.

}, keywords = {Animals, beta-Globins, DNA, GATA1 Transcription Factor, Gene Expression, In Situ Hybridization, Fluorescence, Kruppel-Like Transcription Factors, Locus Control Region, Mice, Mice, Transgenic, RNA, Messenger, Transcriptional Activation}, issn = {1476-4679}, doi = {10.1038/ncb2278}, author = {Noordermeer, Daan and de Wit, Elzo and Klous, Petra and van de Werken, Harmen and Simonis, Marieke and Lopez-Jones, Melissa and Eussen, Bert and de Klein, Annelies and Singer, Robert H and de Laat, Wouter} } @article {6357, title = {A versatile strategy for gene trapping and trap conversion in emerging model organisms.}, journal = {Development }, volume = {138}, year = {2011}, month = {2011 Jun}, pages = {2625-30}, abstract = {

Genetic model organisms such as Drosophila, C. elegans and the mouse provide formidable tools for studying mechanisms of development, physiology and behaviour. Established models alone, however, allow us to survey only a tiny fraction of the morphological and functional diversity present in the animal kingdom. Here, we present iTRAC, a versatile gene-trapping approach that combines the implementation of unbiased genetic screens with the generation of sophisticated genetic tools both in established and emerging model organisms. The approach utilises an exon-trapping transposon vector that carries an integrase docking site, allowing the targeted integration of new constructs into trapped loci. We provide proof of principle for iTRAC in the emerging model crustacean Parhyale hawaiensis: we generate traps that allow specific developmental and physiological processes to be visualised in unparalleled detail, we show that trapped genes can be easily cloned from an unsequenced genome, and we demonstrate targeting of new constructs into a trapped locus. Using this approach, gene traps can serve as platforms for generating diverse reporters, drivers for tissue-specific expression, gene knockdown and other genetic tools not yet imagined.

}, keywords = {Animal, Animals, Cloning, Crustacea, DNA Transposable Elements, Genetic Techniques, Genetic Vectors, Integrases, Models, Molecular}, issn = {1477-9129}, doi = {10.1242/dev.066324}, author = {Kontarakis, Zacharias and Pavlopoulos, Anastasios and Kiupakis, Alexandros and Konstantinides, Nikolaos and Douris, Vassilis and Averof, Michalis} } @article {3837, title = {Visual place learning in Drosophila melanogaster.}, journal = {Nature}, volume = {474}, year = {2011}, month = {2011 Jun 9}, pages = {204-7}, abstract = {

The ability of insects to learn and navigate to specific locations in the environment has fascinated naturalists for decades. The impressive navigational abilities of ants, bees, wasps and other insects demonstrate that insects are capable of visual place learning, but little is known about the underlying neural circuits that mediate these behaviours. Drosophila melanogaster (common fruit fly) is a powerful model organism for dissecting the neural circuitry underlying complex behaviours, from sensory perception to learning and memory. Drosophila can identify and remember visual features such as size, colour and contour orientation. However, the extent to which they use vision to recall specific locations remains unclear. Here we describe a visual place learning platform and demonstrate that Drosophila are capable of forming and retaining visual place memories to guide selective navigation. By targeted genetic silencing of small subsets of cells in the Drosophila brain, we show that neurons in the ellipsoid body, but not in the mushroom bodies, are necessary for visual place learning. Together, these studies reveal distinct neuroanatomical substrates for spatial versus non-spatial learning, and establish Drosophila as a powerful model for the study of spatial memories.

}, keywords = {Animal, Animals, Brain, Conditioning (Psychology), Cues, Drosophila melanogaster, Female, Glass, Learning, Locomotion, Memory, Models, Mushroom Bodies, Neurological, Odors, Orientation, Silicon Dioxide, Temperature, Time Factors, Visual Perception}, issn = {1476-4687}, doi = {10.1038/nature10131}, author = {Ofstad, Tyler A and Zuker, Charles S and Reiser, Michael B} } @article {3919, title = {When is weight critical?}, journal = {The Journal of Experimental Biology}, volume = {214}, year = {2011}, month = {2011 May 15}, pages = {1613-5}, keywords = {20th Century, Animals, Biological, Body Size, Ecdysone, History, Juvenile Hormones, Manduca, Metamorphosis, Pupa}, issn = {1477-9145}, doi = {10.1242/jeb.049098}, author = {Riddiford, Lynn M} } @article {5385, title = {Wireless neural/EMG telemetry systems for small freely moving animals.}, journal = {IEEE Transactions on Biomedical Circuits and Systems}, volume = {5}, year = {2011}, month = {2011 Apr}, pages = {103-11}, abstract = {

We have developed miniature telemetry systems that capture neural, EMG, and acceleration signals from a freely moving insect or other small animal and transmit the data wirelessly to a remote digital receiver. The systems are based on custom low-power integrated circuits (ICs) that amplify, filter, and digitize four biopotential signals using low-noise circuits. One of the chips also digitizes three acceleration signals from an off-chip microelectromechanical-system accelerometer. All information is transmitted over a wireless ~ 900-MHz telemetry link. The first unit, using a custom chip fabricated in a 0.6- μm BiCMOS process, weighs 0.79 g and runs for two hours on two small batteries. We have used this system to monitor neural and EMG signals in jumping and flying locusts as well as transdermal potentials in weakly swimming electric fish. The second unit, using a custom chip fabricated in a 0.35-μ m complementary metal-oxide semiconductor CMOS process, weighs 0.17 g and runs for five hours on a single 1.5-V battery. This system has been used to monitor neural potentials in untethered perching dragonflies.

}, issn = {1932-4545}, doi = {10.1109/TBCAS.2011.2131140}, author = {Harrison, Reid R. and Fotowat, Haleh and Chan, Raymond and Kier, Ryan J and Olberg, Robert and Leonardo, Anthony and Gabbiani, Fabrizio} } @article {4327, title = {Wiring economy and volume exclusion determine neuronal placement in the Drosophila brain.}, journal = {Current Biology}, volume = {21}, year = {2011}, month = {2011 Dec}, pages = {2000-5}, abstract = {

Wiring economy has successfully explained the individual placement of neurons in simple nervous systems like that of Caenorhabditis elegans [1-3] and the locations of coarser structures like cortical areas in complex vertebrate brains [4]. However, it remains unclear whether wiring economy can explain the placement of individual neurons in brains larger than that of C.\ elegans. Indeed, given the greater number of neuronal interconnections in larger brains, simply minimizing the length of connections results in unrealistic configurations, with multiple neurons occupying the same position in space. Avoiding such configurations, or volume exclusion, repels neurons from each other, thus counteracting wiring economy. Here we test whether wiring economy together with volume exclusion can explain the placement of neurons in a module of the Drosophila melanogaster brain known as lamina cartridge [5-13]. We used newly developed techniques for semiautomated reconstruction from serial electron microscopy (EM) [14] to obtain the shapes of neurons, the location of synapses, and the resultant synaptic connectivity. We show that wiring length minimization and volume exclusion together can explain the structure of the lamina microcircuit. Therefore, even in brains larger than that of C.\ elegans, at least for some circuits, optimization can play an important role in individual neuron placement.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2011.10.022}, author = {Rivera-Alba, Marta and Vitaladevuni, Shiv N. and Mischenko, Yuriy and Lu, Zhiyuan and Takemura, Shin-ya and Scheffer, Lou and Meinertzhagen, Ian and Chklovskii, Dmitri and Polavieja, Gonzalo} } @article {48172, title = {3D reconstruction of the human rib cage from 2D projection images using a statistical shape model.}, journal = {International journal of computer assisted radiology and surgery}, volume = {5}, year = {2010}, month = {2010 Mar}, pages = {111-24}, abstract = {

PURPOSE: This paper describes an approach for the three-dimensional (3D) shape and pose reconstruction of the human rib cage from few segmented two-dimensional (2D) projection images. Our work is aimed at supporting temporal subtraction techniques of subsequently acquired radiographs by establishing a method for the assessment of pose differences in sequences of chest radiographs of the same patient.

METHODS: The reconstruction method is based on a 3D statistical shape model (SSM) of the rib cage, which is adapted to binary 2D projection images of an individual rib cage. To drive the adaptation we minimize a distance measure that quantifies the dissimilarities between 2D projections of the 3D SSM and the projection images of the individual rib cage. We propose different silhouette-based distance measures and evaluate their suitability for the adaptation of the SSM to the projection images.

RESULTS: An evaluation was performed on 29 sets of biplanar binary images (posterior-anterior and lateral). Depending on the chosen distance measure, our experiments on the combined reconstruction of shape and pose of the rib cages yield reconstruction errors from 2.2 to 4.7 mm average mean 3D surface distance. Given a geometry of an individual rib cage, the rotational errors for the pose reconstruction range from 0.1 degrees to 0.9 degrees.

CONCLUSIONS: The results show that our method is suitable for the estimation of pose differences of the human rib cage in binary projection images. Thus, it is able to provide crucial 3D information for registration during the generation of 2D subtraction images.

}, keywords = {Humans, Image Interpretation, Computer-Assisted, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Models, Anatomic, Radiographic Image Enhancement, Ribs, Subtraction Technique}, issn = {1861-6429}, doi = {10.1007/s11548-009-0390-2}, author = {Dworzak, Jalda and Lamecker, Hans and von Berg, Jens and Klinder, Tobias and Lorenz, Cristian and Kainm{\"u}ller, Dagmar and Seim, Heiko and Hege, Hans-Christian and Zachow, Stefan} } @article {1454, title = {3D segmentation of cell boundaries from whole cell cryogenic electron tomography volumes.}, journal = {Journal of Structural Biology}, volume = {170}, year = {2010}, month = {2010 Apr}, pages = {134-45}, abstract = {

Cryogenic electron tomography (cryo-ET) has gained increasing interest in recent years due to its ability to image whole cells and subcellular structures in 3D at nanometer resolution in their native environment. However, due to dose restrictions and the inability to acquire high tilt angle images, the reconstructed volumes are noisy and have missing information. Thus, features are unreliable, and precision extraction of the cell boundary is difficult, manual and time intensive. This paper presents an efficient recursive algorithm called BLASTED (Boundary Localization using Adaptive Shape and Texture Discovery) to automatically extract the cell boundary using a conditional random field (CRF) framework in which boundary points and shape are jointly inferred. The algorithm learns the texture of the boundary region progressively, and uses a global shape model and shape-dependent features to propose candidate boundary points on a slice of the membrane. It then updates the shape of that slice by accepting the appropriate candidate points using local spatial clustering, the global shape model, and trained boosted texture classifiers. The BLASTED algorithm segmented the cell membrane over an average of 93\% of the length of the cell in 19 difficult cryo-ET datasets.

}, keywords = {Algorithms, Cell Membrane, Cryoelectron Microscopy, Electron Microscope Tomography}, issn = {1095-8657}, doi = {10.1016/j.jsb.2009.12.015}, author = {Moussavi, Farshid and Heitz, Geremy and Amat, Fernando and Comolli, Luis R and Koller, Daphne and Horowitz, Mark} } @article {6385, title = {Acousto-optic laser scanning for multi-site photo-stimulation of single neurons in vitro.}, journal = {Journal of Neural Engineering}, volume = {7}, year = {2010}, month = {2010 Aug}, pages = {045002}, abstract = {

To study the complex synaptic interactions underpinning dendritic information processing in single neurons, experimenters require methods to mimic presynaptic neurotransmitter release at multiple sites with no physiological damage. We show that laser scanning systems built around large-aperture acousto-optic deflectors and high numerical aperture objective lenses provide the sub-millisecond, sub-micron precision necessary to achieve physiological, exogenous synaptic stimulation. Our laser scanning systems can produce the sophisticated spatio-temporal patterns of synaptic input that are necessary to investigate single-neuron dendritic physiology.

}, keywords = {Acoustic Stimulation, Acoustics, Action Potentials, Animals, Cells, Confocal, Cultured, Equipment Design, Equipment Failure Analysis, Hippocampus, Light, Microscopy, Neurons, Photic Stimulation, Rats, Reproducibility of Results, Sensitivity and Specificity, Sprague-Dawley}, issn = {1741-2552}, doi = {10.1088/1741-2560/7/4/045002}, author = {Losavio, Bradley E and Iyer, Vijay and Patel, Saumil and Saggau, Peter} } @article {2075, title = {Adaptive optics via pupil segmentation for high-resolution imaging in biological tissues. (With commentary)}, journal = {Nature Methods}, volume = {7}, year = {2010}, month = {2010 Feb}, pages = {141-7}, abstract = {

Biological specimens are rife with optical inhomogeneities that seriously degrade imaging performance under all but the most ideal conditions. Measuring and then correcting for these inhomogeneities is the province of adaptive optics. Here we introduce an approach to adaptive optics in microscopy wherein the rear pupil of an objective lens is segmented into subregions, and light is directed individually to each subregion to measure, by image shift, the deflection faced by each group of rays as they emerge from the objective and travel through the specimen toward the focus. Applying our method to two-photon microscopy, we could recover near-diffraction-limited performance from a variety of biological and nonbiological samples exhibiting aberrations large or small and smoothly varying or abruptly changing. In particular, results from fixed mouse cortical slices illustrate our ability to improve signal and resolution to depths of 400 microm.

Commentary: Introduces a new, zonal approach to adaptive optics (AO) in microscopy suitable for highly inhomogeneous and/or scattering samples such as living tissue. The method is unique in its ability to handle large amplitude aberrations (\>20 wavelengths), including spatially complex aberrations involving high order modes beyond the ability of most AO actuators to correct. As befitting a technique designed for in vivo fluorescence imaging, it is also photon efficient.
Although used here in conjunction with two photon microscopy to demonstrate correction deep into scattering tissue, the same principle of pupil segmentation might be profitably adapted to other point-scanning or widefield methods. For example, plane illumination microscopy of multicellular specimens is often beset by substantial aberrations, and all far-field superresolution methods are exquisitely sensitive to aberrations.

}, keywords = {Artifacts, Computer-Aided Design, Equipment Design, Equipment Failure Analysis, Fluorescence, Image Enhancement, Lenses, Lighting, Microscopy, Multiphoton, Reproducibility of Results, Sensitivity and Specificity}, issn = {1548-7105}, doi = {10.1038/nmeth.1411}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20037592}, author = {Ji, Na and Milkie, Daniel E and Betzig, Eric} } @article {4019, title = {Adaptive optics via pupil segmentation for high-resolution imaging in biological tissues.}, journal = {Nature Methods}, volume = {7}, year = {2010}, month = {2010 Feb}, pages = {141-7}, abstract = {

Biological specimens are rife with optical inhomogeneities that seriously degrade imaging performance under all but the most ideal conditions. Measuring and then correcting for these inhomogeneities is the province of adaptive optics. Here we introduce an approach to adaptive optics in microscopy wherein the rear pupil of an objective lens is segmented into subregions, and light is directed individually to each subregion to measure, by image shift, the deflection faced by each group of rays as they emerge from the objective and travel through the specimen toward the focus. Applying our method to two-photon microscopy, we could recover near-diffraction-limited performance from a variety of biological and nonbiological samples exhibiting aberrations large or small and smoothly varying or abruptly changing. In particular, results from fixed mouse cortical slices illustrate our ability to improve signal and resolution to depths of 400 microm.

}, keywords = {Artifacts, Computer-Aided Design, Equipment Design, Equipment Failure Analysis, Fluorescence, Image Enhancement, Lenses, Lighting, Microscopy, Multiphoton, Reproducibility of Results, Sensitivity and Specificity}, issn = {1548-7105}, doi = {10.1038/nmeth.1411}, author = {Ji, Na and Milkie, Daniel E and Betzig, Eric} } @article {46615, title = {Addiction-like behavior in Drosophila.}, journal = {Communicative \& Integrative Biology}, volume = {3}, year = {2010}, month = {2010 Jul}, pages = {357-9}, abstract = {

Alcohol abuse is a pervasive problem known to be influenced by genetic factors, yet our understanding of the mechanisms underlying alcohol addiction is far from complete. Drosophila melanogaster has been established as a model for studying the molecular mechanisms that mediate the acute and chronic effects of alcohol. However, the Drosophila model has not yet been extended to include more complex alcohol-related behaviors such as self-administration. We recently established a paradigm to characterize ethanol consumption and preference in flies. We demonstrated that flies prefer to consume ethanol-containing food over regular food, and this preference exhibits several features of alcohol addiction: flies increase ethanol consumption over time, they consume ethanol to pharmacologically relevant concentrations, they will overcome an aversive stimulus in order to consume ethanol, and they exhibit relapse after a period of ethanol deprivation. Thus, ethanol preference in flies provides a new model for studying important aspects of addiction and their underlying mechanisms. One mutant that displayed decreased ethanol preference, krasavietz, may represent a first step toward uncovering those mechanisms.

}, issn = {1942-0889}, author = {Devineni, Anita V and Heberlein, Ulrike} } @article {6337, title = {Adenomatous polyposis coli protein nucleates actin assembly and synergizes with the formin mDia1.}, journal = {The Journal of Cell Biology}, volume = {189}, year = {2010}, month = {2010 Jun 28}, pages = {1087-96}, abstract = {

The tumor suppressor protein adenomatous polyposis coli (APC) regulates cell protrusion and cell migration, processes that require the coordinated regulation of actin and microtubule dynamics. APC localizes in vivo to microtubule plus ends and actin-rich cortical protrusions, and has well-documented direct effects on microtubule dynamics. However, its potential effects on actin dynamics have remained elusive. Here, we show that the C-terminal "basic" domain of APC (APC-B) potently nucleates the formation of actin filaments in vitro and stimulates actin assembly in cells. Nucleation is achieved by a mechanism involving APC-B dimerization and recruitment of multiple actin monomers. Further, APC-B nucleation activity is synergistic with its in vivo binding partner, the formin mDia1. Together, APC-B and mDia1 overcome a dual cellular barrier to actin assembly imposed by profilin and capping protein. These observations define a new function for APC and support an emerging view of collaboration between distinct actin assembly-promoting factors with complementary activities.

}, keywords = {Actin Capping Proteins, Actins, Adenomatous Polyposis Coli Protein, Animals, Carrier Proteins, Fetal Proteins, Mice, Microfilament Proteins, NIH 3T3 Cells, Nuclear Proteins, Profilins, Protein Multimerization, Protein Transport}, issn = {1540-8140}, doi = {10.1083/jcb.201001016}, author = {Okada, Kyoko and Bartolini, Francesca and Deaconescu, Alexandra M and Moseley, James B and Dogic, Zvonimir and Grigorieff, Nikolaus and Gundersen, Gregg G and Goode, Bruce L} } @article {1450, title = {Alignment of cryo-electron tomography datasets.}, journal = {Methods in Enzymology}, volume = {482}, year = {2010}, month = {2010}, pages = {343-67}, abstract = {

Data acquisition of cryo-electron tomography (CET) samples described in previous chapters involves relatively imprecise mechanical motions: the tilt series has shifts, rotations, and several other distortions between projections. Alignment is the procedure of correcting for these effects in each image and requires the estimation of a projection model that describes how points from the sample in three-dimensions are projected to generate two-dimensional images. This estimation is enabled by finding corresponding common features between images. This chapter reviews several software packages that perform alignment and reconstruction tasks completely automatically (or with minimal user intervention) in two main scenarios: using gold fiducial markers as high contrast features or using relevant biological structures present in the image (marker-free). In particular, we emphasize the key decision points in the process that users should focus on in order to obtain high-resolution reconstructions.

}, keywords = {Computer-Assisted, Cryoelectron Microscopy, Electron Microscope Tomography, Image Processing}, issn = {1557-7988}, doi = {10.1016/S0076-6879(10)82014-2}, author = {Amat, Fernando and Casta{\~n}o-Diez, Daniel and Lawrence, Albert and Moussavi, Farshid and Winkler, Hanspeter and Horowitz, Mark} } @article {47682, title = {Analysis of mitochondrial dynamics and functions using imaging approaches.}, journal = {Current protocols in cell biology / editorial board, Juan S. Bonifacino ... [et al.]}, volume = {Chapter 4}, year = {2010}, month = {2010 Mar}, pages = {Unit 4.25.1-21}, abstract = {

Mitochondria are organelles that have been primarily known as the powerhouse of the cell. However, recent advances in the field have revealed that mitochondria are also involved in many other cellular activities like lipid modifications, redox balance, calcium balance, and even controlled cell death. These multifunctional organelles are motile and highly dynamic in shapes and forms; the dynamism is brought about by the mitochondria{\textquoteright}s ability to undergo fission and fusion with each other. Therefore, it is very important to be able to image mitochondrial shape changes to relate to the variety of cellular functions these organelles have to accomplish. The protocols described here will enable researchers to perform steady-state and time-lapse imaging of mitochondria in live cells by using confocal microscopy. High-resolution three-dimensional imaging of mitochondria will not only be helpful in understanding mitochondrial structure in detail but it also could be used to analyze their structural relationships with other organelles in the cell. FRAP (fluorescence recovery after photobleaching) studies can be performed to understand mitochondrial dynamics or dynamics of any mitochondrial molecule within the organelle. The microirradiation assay can be performed to study functional continuity between mitochondria. A protocol for measuring mitochondrial potential has also been included in this unit. In conclusion, the protocols described here will aid the understanding of mitochondrial structure-function relationship.

}, keywords = {Cell Survival, Electricity, Fluorescence Recovery After Photobleaching, Humans, Imaging, Three-Dimensional, Membrane Potential, Mitochondrial, Microtubules, Mitochondria, Nocodazole, Staining and Labeling, Time Factors}, issn = {1934-2616}, doi = {10.1002/0471143030.cb0425s46}, author = {Mitra, Kasturi and Lippincott-Schwartz, Jennifer} } @article {1452, title = {Analysis of the intact surface layer of Caulobacter crescentus by cryo-electron tomography.}, journal = {Journal of Bacteriology}, volume = {192}, year = {2010}, month = {2010 Nov}, pages = {5855-65}, abstract = {

The surface layers (S layers) of those bacteria and archaea that elaborate these crystalline structures have been studied for 40 years. However, most structural analysis has been based on electron microscopy of negatively stained S-layer fragments separated from cells, which can introduce staining artifacts and allow rearrangement of structures prone to self-assemble. We present a quantitative analysis of the structure and organization of the S layer on intact growing cells of the Gram-negative bacterium Caulobacter crescentus using cryo-electron tomography (CET) and statistical image processing. Instead of the expected long-range order, we observed different regions with hexagonally organized subunits exhibiting short-range order and a broad distribution of periodicities. Also, areas of stacked double layers were found, and these increased in extent when the S-layer protein (RsaA) expression level was elevated by addition of multiple rsaA copies. Finally, we combined high-resolution amino acid residue-specific Nanogold labeling and subtomogram averaging of CET volumes to improve our understanding of the correlation between the linear protein sequence and the structure at the 2-nm level of resolution that is presently available. The results support the view that the U-shaped RsaA monomer predicted from negative-stain tomography proceeds from the N terminus at one vertex, corresponding to the axis of 3-fold symmetry, to the C terminus at the opposite vertex, which forms the prominent 6-fold symmetry axis. Such information will help future efforts to analyze subunit interactions and guide selection of internal sites for display of heterologous protein segments.

}, keywords = {Amino Acids, Bacterial Proteins, Caulobacter crescentus, Computer-Assisted, Cryoelectron Microscopy, Electron Microscope Tomography, Image Processing, Membrane Glycoproteins, Metal Nanoparticles, Staining and Labeling}, issn = {1098-5530}, doi = {10.1128/JB.00747-10}, author = {Amat, Fernando and Comolli, Luis R and Nomellini, John F and Moussavi, Farshid and Downing, Kenneth H and Smit, John and Horowitz, Mark} } @article {5369, title = {Anatomic analysis of Gal4 expression patterns of the Rubin line collection: the central complex.}, journal = {Journal of Neurogenetics}, volume = {24}, year = {2010}, month = {2010}, pages = {71-2}, chapter = {71}, author = {Jenett, A and Wolff, T and Nern, A. and Pfeiffer, B D and Ngo, T. and Murphy, C. and Long, F. and Peng, H. and Rubin, G M} } @article {1415, title = {Anatomy of a songbird basal ganglia circuit essential for vocal learning and plasticity.}, journal = {Journal of Chemical Neuroanatomy}, volume = {39}, year = {2010}, month = {2010 Mar}, pages = {124-31}, abstract = {

Vocal learning in songbirds requires an anatomically discrete and functionally dedicated circuit called the anterior forebrain pathway (AFP). The AFP is homologous to cortico-basal ganglia-thalamo-cortical loops in mammals. The basal ganglia portion of this pathway, Area X, shares many features characteristic of the mammalian striatum and pallidum, including cell types and connectivity. The AFP also deviates from mammalian basal ganglia circuits in fundamental ways. In addition, the microcircuitry, role of neuromodulators, and function of Area X are still unclear. Elucidating the mechanisms by which both mammalian-like and unique features of the AFP contribute to vocal learning may help lead to a broad understanding of the sensorimotor functions of basal ganglia circuits.

}, keywords = {Animal, Animals, Basal Ganglia, Birds, Brain, Catecholamines, Globus Pallidus, Learning, Neural Pathways, Neuronal Plasticity, Neurons, Thalamus, Vocalization}, issn = {1873-6300}, doi = {10.1016/j.jchemneu.2009.07.003}, author = {Gale, Samuel D and Perkel, David J} } @article {2686, title = {Appetitive and aversive visual learning in freely moving Drosophila.}, journal = {Frontiers in Behavioral Neuroscience}, volume = {4}, year = {2010}, month = {2010 Mar 9}, pages = {10}, abstract = {

To compare appetitive and aversive visual memories of the fruit fly Drosophila melanogaster, we developed a new paradigm for classical conditioning. Adult flies are trained en masse to differentially associate one of two visual conditioned stimuli (CS) (blue and green light as CS) with an appetitive or aversive chemical substance (unconditioned stimulus or US). In a test phase, flies are given a choice between the paired and the unpaired visual stimuli. Associative memory is measured based on altered visual preference in the test. If a group of flies has, for example, received a sugar reward with green light in the training, they show a significantly higher preference for the green stimulus during the test than another group of flies having received the same reward with blue light. We demonstrate critical parameters for the formation of visual appetitive memory, such as training repetition, order of reinforcement, starvation, and individual conditioning. Furthermore, we show that formic acid can act as an aversive chemical reinforcer, yielding weak, yet significant, aversive memory. These results provide a basis for future investigations into the cellular and molecular mechanisms underlying visual memory and perception in Drosophila.

}, issn = {1662-5153}, doi = {10.3389/fnbeh.2010.00010}, author = {Schnaitmann, Christopher and Vogt, Katrin and Triphan, Tilman and Tanimoto, Hiromu} } @article {1160, title = {Approaches toward super-resolution fluorescence imaging of mitochondrial proteins using PALM.}, journal = {Methods}, volume = {51}, year = {2010}, month = {2010 Aug}, pages = {458-63}, abstract = {

Mitochondria are difficult targets for microscopy because of their small size and highly compartmentalized, membranous interior. Super-resolution fluorescence microscopy methods have recently been developed that exceed the historical limits of optical imaging. Here we outline considerations and techniques in preparing to image the relative location of mitochondrial proteins using photoactivated localization microscopy (PALM). PALM and similar methods have the capacity to dramatically increase our ability to image proteins within mitochondria, and to expand our knowledge of the location of macromolecules beyond the current limits of immunoEM.

}, keywords = {Animals, Cryoultramicrotomy, Fluorescence, Freeze Substitution, Genetic, Luminescent Proteins, Mice, Microscopy, Mitochondria, Mitochondrial Proteins, NIH 3T3 Cells, Plastic Embedding, Promoter Regions, Recombinant Fusion Proteins, Transfection}, issn = {1095-9130}, doi = {10.1016/j.ymeth.2010.01.001}, author = {Brown, Timothy A and Fetter, Richard D and Tkachuk, Ariana N and Clayton, David A} } @article {5690, title = {As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets.}, journal = {Bioinformatics}, volume = {26}, year = {2010}, month = {2010 Jun 15}, pages = {i57-63}, abstract = {

Tiled serial section Transmission Electron Microscopy (ssTEM) is increasingly used to describe high-resolution anatomy of large biological specimens. In particular in neurobiology, TEM is indispensable for analysis of synaptic connectivity in the brain. Registration of ssTEM image mosaics has to recover the 3D continuity and geometrical properties of the specimen in presence of various distortions that are applied to the tissue during sectioning, staining and imaging. These include staining artifacts, mechanical deformation, missing sections and the fact that structures may appear dissimilar in consecutive sections.

}, keywords = {Animals, Databases, Drosophila, Electron, Factual, Imaging, Microscopy, Three-Dimensional, Transmission}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btq219}, author = {Saalfeld, Stephan and Cardona, Albert and Hartenstein, Volker and Tomancak, Pavel.} } @article {2327, title = {Automated tracking and analysis of centrosomes in early Caenorhabditis elegans embryos.}, journal = {Bioinformatics}, volume = {26}, year = {2010}, month = {2010 Jun 15}, pages = {i13-20}, abstract = {

The centrosome is a dynamic structure in animal cells that serves as a microtubule organizing center during mitosis and also regulates cell-cycle progression and sets polarity cues. Automated and reliable tracking of centrosomes is essential for genetic screens that study the process of centrosome assembly and maturation in the nematode Caenorhabditis elegans.

}, keywords = {Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Cell Division, Cell Lineage, Centrosome, Embryo, Fluorescence, Microscopy, Mitotic Spindle Apparatus, Nonmammalian}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btq190}, author = {Jaensch, Steffen and Decker, Markus and Hyman, Anthony A and Myers, Eugene W} } @article {2698, title = {Automatic neuron tracing in volumetric microscopy images with anisotropic path searching.}, journal = {Medical Image Computing and Computer-Assisted Intervention: MICCAI International Conference on Medical Image Computing and Computer-Assisted Intervention}, volume = {13}, year = {2010}, month = {2010}, pages = {472-9}, abstract = {

Full reconstruction of neuron morphology is of fundamental interest for the analysis and understanding of neuron function. We have developed a novel method capable of tracing neurons in three-dimensional microscopy data automatically. In contrast to template-based methods, the proposed approach makes no assumptions on the shape or appearance of neuron{\textquoteright}s body. Instead, an efficient seeding approach is applied to find significant pixels almost certainly within complex neuronal structures and the tracing problem is solved by computing an graph tree structure connecting these seeds. In addition, an automated neuron comparison method is introduced for performance evaluation and structure analysis. The proposed algorithm is computationally efficient. Experiments on different types of data show promising results.

}, keywords = {Algorithms, Animals, Anisotropy, Artificial Intelligence, Automated, Cells, Computer-Assisted, Cultured, Humans, Image Enhancement, Image Interpretation, Imaging, Microscopy, Neurons, Pattern Recognition, Reproducibility of Results, Sensitivity and Specificity, Three-Dimensional}, author = {Xie, Jun and Zhao, Ting and Lee, Tzumin and Myers, Eugene and Peng, Hanchuan} } @article {2183, title = {Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model.}, journal = {Bioinformatics}, volume = {26}, year = {2010}, month = {2010 Jun 15}, pages = {i38-46}, abstract = {

Digital reconstruction of 3D neuron structures is an important step toward reverse engineering the wiring and functions of a brain. However, despite a number of existing studies, this task is still challenging, especially when a 3D microscopic image has low single-to-noise ratio and discontinued segments of neurite patterns.

}, keywords = {Animals, Caenorhabditis elegans, Computer-Assisted, Drosophila, Image Processing, Imaging, Mice, Neurons, Three-Dimensional}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btq212}, author = {Peng, Hanchuan and Ruan, Zongcai and Atasoy, Deniz and Sternson, Scott} } @article {2783, title = {Axial CID and high pressure resonance CID in a miniature ion trap mass spectrometer using a discontinuous atmospheric pressure interface.}, journal = {Journal of the American Society for Mass Spectrometry}, volume = {21}, year = {2010}, month = {2010 Feb}, pages = {209-14}, abstract = {

Axial collision induced dissociation (CID) and high-pressure resonance CID were implemented and compared with normal low-pressure resonance CID in a miniature ion trap mass spectrometer to obtain more complete fragmentation spectra. Axial CID was realized simply by applying a potential to the discontinuous atmospheric pressure interface (DAPI) capillary without performing parent ion isolation before dissociation. High-pressure resonance CID employed a double-introduction pulse scan function, by means of which precursor ions isolated at low-pressure (\<10(-3) torr) were dissociated at high-pressure (0.1 torr-1 torr) with higher excitation energy, so that tandem MS of isolated precursor ions was achieved and extensive fragmentation was obtained. A simple peptide (Leu-enkephalin) and dye molecule (rhodamine B) ionized by ESI were used to investigate both methods and compare them with normal low-pressure resonance CID.

}, issn = {1879-1123}, doi = {10.1364/AO.50.001792}, author = {Gao, Liang and Li, Guangtao and Cooks, R Graham} } @article {1416, title = {A basal ganglia pathway drives selective auditory responses in songbird dopaminergic neurons via disinhibition.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {30}, year = {2010}, month = {2010 Jan 20}, pages = {1027-37}, abstract = {

Dopaminergic neurons in mammals respond to rewards and reward-predicting cues, and are thought to play an important role in learning actions or sensory cues that lead to reward. The anatomical sources of input that drive or modulate such responses are not well understood; these ultimately define the range of behavior to which dopaminergic neurons contribute. Primary rewards are not the immediate objective of all goal-directed behavior. For example, a goal of vocal learning is to imitate vocal-communication signals. Here, we demonstrate activation of dopaminergic neurons in songbirds driven by a basal ganglia region required for vocal learning, area X. Dopaminergic neurons in anesthetized zebra finches respond more strongly to the bird{\textquoteright}s own song (BOS) than to other sounds, and area X is critical for these responses. Direct pharmacological modulation of area X output, in the absence of auditory stimulation, is sufficient to bidirectionally modulate the firing rate of dopaminergic neurons. The only known pathway from song control regions to dopaminergic neurons involves a projection from area X to the ventral pallidum (VP), which in turn projects to dopaminergic regions. We show that VP neurons are spontaneously active and inhibited preferentially by BOS, suggesting that area X disinhibits dopaminergic neurons by inhibiting VP. Supporting this model, auditory-response latencies are shorter in area X than VP, and shorter in VP than dopaminergic neurons. Thus, dopaminergic neurons can be disinhibited selectively by complex sensory stimuli via input from the basal ganglia. The functional pathway we identify may allow dopaminergic neurons to contribute to vocal learning.

}, keywords = {Acoustic Stimulation, Action Potentials, Animal, Animals, Auditory Pathways, Basal Ganglia, Discrimination (Psychology), Dopamine, Electric Stimulation, Excitatory Amino Acid Antagonists, Finches, gamma-Aminobutyric Acid, Male, Neural Inhibition, Neurons, Reaction Time, Tyrosine 3-Monooxygenase, Ventral Tegmental Area, Vocalization}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3585-09.2010}, author = {Gale, Samuel D and Perkel, David J} } @article {4287, title = {Birth time/order-dependent neuron type specification.}, journal = {Current Opinion in Neurobiology}, volume = {20}, year = {2010}, month = {2010 Feb}, pages = {14-21}, abstract = {

Neurons derived from the same progenitor may acquire different fates according to their birth timing/order. To reveal temporally guided cell fates, we must determine neuron types as well as their lineage relationships and times of birth. Recent advances in genetic lineage analysis and fate mapping are facilitating such studies. For example, high-resolution lineage analysis can identify each sequentially derived neuron of a lineage and has revealed abrupt temporal identity changes in diverse Drosophila neuronal lineages. In addition, fate mapping of mouse neurons made from the same pool of precursors shows production of specific neuron types in specific temporal patterns. The tools used in these analyses are helping to further our understanding of the genetics of neuronal temporal identity.

}, keywords = {Animals, Cell Lineage, Drosophila, Mice, Neurogenesis, Neurons, Time Factors}, issn = {1873-6882}, doi = {10.1016/j.conb.2009.10.017}, author = {Kao, Chih-Fei and Lee, Tzumin} } @conference {3858, title = {Boundary learning by optimization with topological constraints.}, booktitle = {IEEE Conference on Computer Vision and Pattern Recognition}, year = {2010}, month = {2010}, abstract = {

Recent studies have shown that machine learning can improve the accuracy of detecting object boundaries in images. In the standard approach, a boundary detector is trained by minimizing its pixel-level disagreement with human boundary tracings. This naive metric is problematic because it is overly sensitive to boundary locations. This problem is solved by metrics provided with the Berkeley Segmentation Dataset, but these can be insensitive to topological differences, such as gaps in boundaries. Furthermore, the Berkeley metrics have not been useful as cost functions for supervised learning. Using concepts from digital topology, we propose a new metric called the warping error that tolerates disagreements over boundary location, penalizes topological disagreements, and can be used directly as a cost function for learning boundary detection, in a method that we call Boundary Learning by Optimization with Topological Constraints (BLOTC). We trained boundary detectors on electron microscopic images of neurons, using both BLOTC and standard training. BLOTC produced substantially better performance on a 1.2 million pixel test set, as measured by both the warping error and the Rand index evaluated on segmentations generated from the boundary labelings. We also find our approach yields significantly better segmentation performance than either gPb-OWT-UCM or multiscale normalized cut, as well as Boosted Edge Learning trained directly on our data.

}, author = {Jain, Viren and Bollmann, Benjamin and Richardson, Mark and Berger, Daniel R. and Helmstaedter, Moritz N. and Briggman, Kevin L and Denk, Winfried and Bowden, Jared B. and Mendenhall, John M. and Abraham, Wickliffe C. and Harris, Kristen M and Kasthuri, Narayanan and Hayworth, Ken J. and Schalek, Richard and Tapia, Juan Carlos and Lichtman, Jeff W. and Seung, Hyunjune Sebastian} } @article {47685, title = {Bright monomeric photoactivatable red fluorescent protein for two-color super-resolution sptPALM of live cells.}, journal = {Journal of the American Chemical Society}, volume = {132}, year = {2010}, month = {2010 May 12}, pages = {6481-91}, abstract = {

Rapidly emerging techniques of super-resolution single-molecule microscopy of living cells rely on the continued development of genetically encoded photoactivatable fluorescent proteins. On the basis of monomeric TagRFP, we have developed a photoactivatable TagRFP protein that is initially dark but becomes red fluorescent after violet light irradiation. Compared to other monomeric dark-to-red photoactivatable proteins including PAmCherry, PATagRFP has substantially higher molecular brightness, better pH stability, substantially less sensitivity to blue light, and better photostability in both ensemble and single-molecule modes. Spectroscopic analysis suggests that PATagRFP photoactivation is a two-step photochemical process involving sequential one-photon absorbance by two distinct chromophore forms. True monomeric behavior, absence of green fluorescence, and single-molecule performance in live cells make PATagRFP an excellent protein tag for two-color imaging techniques, including conventional diffraction-limited photoactivation microscopy, super-resolution photoactivated localization microscopy (PALM), and single particle tracking PALM (sptPALM) of living cells. Two-color sptPALM imaging was demonstrated using several PATagRFP tagged transmembrane proteins together with PAGFP-tagged clathrin light chain. Analysis of the resulting sptPALM images revealed that single-molecule transmembrane proteins, which are internalized into a cell via endocytosis, colocalize in space and time with plasma membrane domains enriched in clathrin light-chain molecules.

}, keywords = {Amino Acid Sequence, Animals, Cell Survival, Cercopithecus aethiops, Color, COS Cells, Hela Cells, Humans, Light, Luminescent Proteins, Membrane Proteins, Microscopy, Molecular Imaging, Molecular Sequence Data, Mutagenesis, Photochemical Processes, Temperature}, issn = {1520-5126}, doi = {10.1021/ja100906g}, author = {Subach, Fedor V and Patterson, George H and Renz, Malte and Lippincott-Schwartz, Jennifer and Verkhusha, Vladislav V} } @article {2550, title = {Capture of particles by direct interception by cilia during feeding of a gastropod veliger.}, journal = {The Biological Bulletin}, volume = {218}, year = {2010}, month = {2010 Apr}, pages = {145-59}, abstract = {

Ciliary feeders vary in the arrangement of ciliary bands and mechanisms of capture of food. Some larvae use opposed parallel bands of preoral (prototroch) and postoral (metatroch) cilia. Hypotheses for the mechanism of particle capture include filtration by adhesion to a cilium that overtakes a particle (direct interception), but until now unequivocal evidence for this mechanism has been lacking. Here, high-speed video recordings of veliger larvae of the gastropod Lacuna vincta demonstrated direct interception of particles by prototrochal cilia. Adhesion between cilium and particle was seen when a prototrochal cilium tugged a diatom chain into the food groove while in contact with one part of the chain. In several recorded events, a prototochal cilium overtook a particle during its effective stroke and subsequently pulled the particle inward with its recovery stroke; thereupon, the particle was deposited onto the food groove and transported to the mouth. Captures varied, however. In some cases the particle was intercepted multiple times in one capture event; in others, several cilia passed a particle without interception. Particles occasionally remained in the area of recovery strokes, indicating retention without continuing adhesion to a cilium. In three events, a particle lost from prototrochal cilia was intercepted and moved into the food groove by metatrochal cilia. Particles as wide as or wider than the food groove were also captured and transported but were not ingested.

}, keywords = {Animals, Biological, Cilia, Feeding Behavior, Gastropoda, Microscopy, Models, Particulate Matter, Video}, issn = {1939-8697}, author = {Romero, Melissa R and Kelstrup, Hans C P and Strathmann, Richard R} } @article {1767, title = {The cells and peripheral representation of sodium taste in mice.}, journal = {Nature}, volume = {464}, year = {2010}, month = {2010 Mar 11}, pages = {297-301}, abstract = {

Salt taste in mammals can trigger two divergent behavioural responses. In general, concentrated saline solutions elicit robust behavioural aversion, whereas low concentrations of NaCl are typically attractive, particularly after sodium depletion. Notably, the attractive salt pathway is selectively responsive to sodium and inhibited by amiloride, whereas the aversive one functions as a non-selective detector for a wide range of salts. Because amiloride is a potent inhibitor of the epithelial sodium channel (ENaC), ENaC has been proposed to function as a component of the salt-taste-receptor system. Previously, we showed that four of the five basic taste qualities-sweet, sour, bitter and umami-are mediated by separate taste-receptor cells (TRCs) each tuned to a single taste modality, and wired to elicit stereotypical behavioural responses. Here we show that sodium sensing is also mediated by a dedicated population of TRCs. These taste cells express the epithelial sodium channel ENaC, and mediate behavioural attraction to NaCl. We genetically engineered mice lacking ENaCalpha in TRCs, and produced animals exhibiting a complete loss of salt attraction and sodium taste responses. Together, these studies substantiate independent cellular substrates for all five basic taste qualities, and validate the essential role of ENaC for sodium taste in mice.

}, keywords = {Animals, Behavior, Epithelial Sodium Channel, Mice, Sodium, Taste, Taste Buds, Transgenic}, issn = {1476-4687}, doi = {10.1038/nature08783}, author = {Chandrashekar, Jayaram and Kuhn, Christina and Oka, Yuki and Yarmolinsky, David A and Hummler, Edith and Ryba, Nicholas J P and Zuker, Charles S} } @article {6862, title = {Cellular organization of the neural circuit that drives Drosophila courtship behavior.}, journal = {Current Biology}, volume = {20}, year = {2010}, month = {2010 Sep 28}, pages = {1602-14}, abstract = {

BACKGROUND: Courtship behavior in Drosophila has been causally linked to the activity of the heterogeneous set of \~{}1500 neurons that express the sex-specific transcripts of the fruitless (fru) gene, but we currently lack an appreciation of the cellular diversity within this population, the extent to which these cells are sexually dimorphic, and how they might be organized into functional circuits. RESULTS: We used genetic methods to define 100 distinct classes of fru neuron, which we compiled into a digital 3D atlas at cellular resolution. We determined the polarity of many of these neurons and computed their likely patterns of connectivity, thereby assembling them into a neural circuit that extends from sensory input to motor output. The cellular organization of this circuit reveals neuronal pathways in the brain that are likely to integrate multiple sensory cues from other flies and to issue descending control signals to motor circuits in the thoracic ganglia. We identified 11 anatomical dimorphisms within this circuit: neurons that are male specific, are more numerous in males than females, or have distinct arborization patterns in males and females. CONCLUSIONS: The cellular organization of the fru circuit suggests how multiple distinct sensory cues are integrated in the fly{\textquoteright}s brain to drive sex-specific courtship behavior. We propose that sensory processing and motor control are mediated through circuits that are largely similar in males and females. Sex-specific behavior may instead arise through dimorphic circuits in the brain and nerve cord that differentially couple sensory input to motor output.

}, keywords = {Animal, Animals, Brain, Drosophila melanogaster, Female, Male, Nerve Net, Neurons, Sexual Behavior}, issn = {1879-0445}, doi = {10.1016/j.cub.2010.08.025}, author = {Yu, Jai Y and Kanai, Makoto I and Demir, Ebru and Jefferis, Gregory S X E and Dickson, Barry J} } @article {1094, title = {Cellular uptake of ribonuclease A relies on anionic glycans.}, journal = {Biochemistry}, volume = {49}, year = {2010}, month = {2010 Dec 21}, pages = {10666-73}, abstract = {

Bovine pancreatic ribonuclease (RNase A) can enter human cells, even though it lacks a cognate cell-surface receptor protein. Here, we report on the biochemical basis for its cellular uptake. Analyses in vitro and in cellulo revealed that RNase A interacts tightly with abundant cell-surface proteoglycans containing glycosaminoglycans, such as heparan sulfate and chondroitin sulfate, as well as with sialic acid-containing glycoproteins. The uptake of RNase A correlates with cell anionicity, as quantified by measuring electrophoretic mobility. The cellular binding and uptake of RNase A contrast with those of Onconase, an amphibian homologue that does not interact tightly with anionic cell-surface glycans. As anionic glycans are especially abundant on human tumor cells, our data predicate utility for mammalian ribonucleases as cancer chemotherapeutic agents.

}, keywords = {Affinity, Animals, Anions, Cattle, Cell Line, Cell Proliferation, CHO Cells, Chondroitin Sulfates, Chromatography, Cricetinae, Cricetulus, Flow Cytometry, Fluorescence, Glycoproteins, Glycosaminoglycans, Heparitin Sulfate, Humans, Mass, Matrix-Assisted Laser Desorption-Ionization, Microscopy, Molecular Weight, N-Acetylneuraminic Acid, Pancreatic, Polysaccharides, Protein Binding, Ribonuclease, Spectrometry}, issn = {1520-4995}, doi = {10.1021/bi1013485}, author = {Chao, Tzu-Yuan and Lavis, Luke D and Raines, Ronald T} } @article {5896, title = {Clarke{\textquoteright}s column neurons as the focus of a corticospinal corollary circuit.}, journal = {Nature Neuroscience}, volume = {13}, year = {2010}, month = {2010 Oct}, pages = {1233-9}, abstract = {

Proprioceptive sensory signals inform the CNS of the consequences of motor acts, but effective motor planning involves internal neural systems capable of anticipating actual sensory feedback. Just where and how predictive systems exert their influence remains poorly understood. We explored the possibility that spinocerebellar neurons that convey proprioceptive sensory information also integrate information from cortical command systems. Analysis of the circuitry and physiology of identified dorsal spinocerebellar tract neurons in mouse spinal cord revealed distinct populations of Clarke{\textquoteright}s column neurons that received direct excitatory and/or indirect inhibitory inputs from descending corticospinal axons. The convergence of these descending inhibitory and excitatory inputs to Clarke{\textquoteright}s column neurons established local spinal circuits with the capacity to mark or modulate incoming proprioceptive input. Together, our genetic, anatomical and physiological results indicate that Clarke{\textquoteright}s column spinocerebellar neurons nucleate local spinal corollary circuits that are relevant to motor planning and evaluation.

}, keywords = {3-dione, 6-Cyano-7-nitroquinoxaline-2, Animals, beta-Galactosidase, Bicuculline, Cerebellum, Cholera Toxin, Electric Stimulation, Estrogen Antagonists, Excitatory Amino Acid Antagonists, Feedback, GABA Antagonists, Gene Expression Regulation, Glial Cell Line-Derived Neurotrophic Factor, Glycine Agents, Glycine Plasma Membrane Transport Proteins, Green Fluorescent Proteins, Homeodomain Proteins, Lysine, Membrane Potentials, Messenger, Mice, Models, Nerve Net, Neural Inhibition, Neural Pathways, Neurological, Newborn, Parvalbumins, Patch-Clamp Techniques, Protein Kinase C, RNA, Sensory, Sensory Receptor Cells, Spinal Cord, Stilbamidines, Strychnine, Tamoxifen, tau Proteins, Transcription Factors, Transgenic, Vesicular Glutamate Transport Protein 1}, issn = {1546-1726}, doi = {10.1038/nn.2637}, author = {Hantman, Adam W and Jessell, Thomas M} } @article {783, title = {A complete developmental sequence of a Drosophila neuronal lineage as revealed by twin-spot MARCM.}, journal = {PLoS Biology}, volume = {8}, year = {2010}, month = {2010 Aug 24}, abstract = {

Drosophila brains contain numerous neurons that form complex circuits. These neurons are derived in stereotyped patterns from a fixed number of progenitors, called neuroblasts, and identifying individual neurons made by a neuroblast facilitates the reconstruction of neural circuits. An improved MARCM (mosaic analysis with a repressible cell marker) technique, called twin-spot MARCM, allows one to label the sister clones derived from a common progenitor simultaneously in different colors. It enables identification of every single neuron in an extended neuronal lineage based on the order of neuron birth. Here we report the first example, to our knowledge, of complete lineage analysis among neurons derived from a common neuroblast that relay olfactory information from the antennal lobe (AL) to higher brain centers. By identifying the sequentially derived neurons, we found that the neuroblast serially makes 40 types of AL projection neurons (PNs). During embryogenesis, one PN with multi-glomerular innervation and 18 uniglomerular PNs targeting 17 glomeruli of the adult AL are born. Many more PNs of 22 additional types, including four types of polyglomerular PNs, derive after the neuroblast resumes dividing in early larvae. Although different offspring are generated in a rather arbitrary sequence, the birth order strictly dictates the fate of each post-mitotic neuron, including the fate of programmed cell death. Notably, the embryonic progenitor has an altered temporal identity following each self-renewing asymmetric cell division. After larval hatching, the same progenitor produces multiple neurons for each cell type, but the number of neurons for each type is tightly regulated. These observations substantiate the origin-dependent specification of neuron types. Sequencing neuronal lineages will not only unravel how a complex brain develops but also permit systematic identification of neuron types for detailed structure and function analysis of the brain.

}, keywords = {Animals, Brain, Cell Lineage, Clone Cells, Drosophila, Genetic Techniques, Mosaicism, Neurogenesis, Neurons, Olfactory Pathways}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1000461}, author = {Yu, Hung-Hsiang and Kao, Chih-Fei and He, Yisheng and Ding, Peng and Kao, Jui-Chun and Lee, Tzumin} } @article {4404, title = {Comprehensive survey of developmental genes in the pea aphid, Acyrthosiphon pisum: frequent lineage-specific duplications and losses of developmental genes.}, journal = {Insect Molecular Biology}, volume = {19 Suppl 2}, year = {2010}, month = {2010 Mar}, pages = {47-62}, abstract = {

Aphids exhibit unique attributes, such as polyphenisms and specialized cells to house endosymbionts, that make them an interesting system for studies at the interface of ecology, evolution and development. Here we present a comprehensive characterization of the developmental genes in the pea aphid, Acyrthosiphon pisum, and compare our results to other sequenced insects. We investigated genes involved in fundamental developmental processes such as establishment of the body plan and organogenesis, focusing on transcription factors and components of signalling pathways. We found that most developmental genes were well conserved in the pea aphid, although many lineage-specific gene duplications and gene losses have occurred in several gene families. In particular, genetic components of transforming growth factor beta (TGFbeta) Wnt, JAK/STAT (Janus kinase/signal transducer and activator of transcription) and EGF (Epidermal Growth Factor) pathways appear to have been significantly modified in the pea aphid.

}, keywords = {Amino Acid, Amino Acid Sequence, Animals, Aphids, Body Patterning, Cytoplasmic and Nuclear, Female, Gene Deletion, Gene Duplication, Genes, Genome, Homeobox, Insect, Insect Proteins, Male, Molecular Sequence Data, Peas, Phylogeny, Receptors, Sequence Homology, Signal Transduction, Transcription Factors}, issn = {1365-2583}, doi = {10.1111/j.1365-2583.2009.00944.x}, author = {Shigenobu, S and Bickel, R D and Brisson, J A and Butts, T and Chang, C-C and Christiaens, O and Davis, G K and Duncan, E J and Ferrier, D E K and Iga, M and Janssen, R and Lin, G-W and Lu, H-L and McGregor, A P and Miura, T and Smagghe, G and Smith, J M and van der Zee, M and Velarde, R A and Wilson, M J and Dearden, P K and Stern, D L} } @article {46301, title = {Continuous attractors with morphed/correlated maps.}, journal = {PLoS Computational Biology}, volume = {6}, year = {2010}, month = {2010 Aug 5}, pages = {e1000869}, abstract = {

Continuous attractor networks are used to model the storage and representation of analog quantities, such as position of a visual stimulus. The storage of multiple continuous attractors in the same network has previously been studied in the context of self-position coding. Several uncorrelated maps of environments are stored in the synaptic connections, and a position in a given environment is represented by a localized pattern of neural activity in the corresponding map, driven by a spatially tuned input. Here we analyze networks storing a pair of correlated maps, or a morph sequence between two uncorrelated maps. We find a novel state in which the network activity is simultaneously localized in both maps. In this state, a fixed cue presented to the network does not determine uniquely the location of the bump, i.e. the response is unreliable, with neurons not always responding when their preferred input is present. When the tuned input varies smoothly in time, the neuronal responses become reliable and selective for the environment: the subset of neurons responsive to a moving input in one map changes almost completely in the other map. This form of remapping is a non-trivial transformation between the tuned input to the network and the resulting tuning curves of the neurons. The new state of the network could be related to the formation of direction selectivity in one-dimensional environments and hippocampal remapping. The applicability of the model is not confined to self-position representations; we show an instance of the network solving a simple delayed discrimination task.

}, keywords = {Animals, Computer Simulation, Discrimination (Psychology), Hippocampus, Models, Biological, Neural Networks (Computer), Numerical Analysis, Computer-Assisted}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1000869}, author = {Romani, Sandro and Tsodyks, Misha} } @article {3844, title = {Convolutional networks can learn to generate affinity graphs for image segmentation.}, journal = {Neural Computation}, volume = {22}, year = {2010}, month = {2010 Feb}, pages = {511-38}, abstract = {

Many image segmentation algorithms first generate an affinity graph and then partition it. We present a machine learning approach to computing an affinity graph using a convolutional network (CN) trained using ground truth provided by human experts. The CN affinity graph can be paired with any standard partitioning algorithm and improves segmentation accuracy significantly compared to standard hand-designed affinity functions. We apply our algorithm to the challenging 3D segmentation problem of reconstructing neuronal processes from volumetric electron microscopy (EM) and show that we are able to learn a good affinity graph directly from the raw EM images. Further, we show that our affinity graph improves the segmentation accuracy of both simple and sophisticated graph partitioning algorithms. In contrast to previous work, we do not rely on prior knowledge in the form of hand-designed image features or image preprocessing. Thus, we expect our algorithm to generalize effectively to arbitrary image types.

}, keywords = {Algorithms, Artificial Intelligence, Automated, Computer-Assisted, Electron, Image Processing, Mathematical Computing, Mathematical Concepts, Mathematics, Microscopy, Neural Networks (Computer), Pattern Recognition}, issn = {1530-888X}, doi = {10.1162/neco.2009.10-08-881}, author = {Turaga, Srinivas C and Murray, Joseph F and Jain, Viren and Roth, Fabian and Helmstaedter, Moritz and Briggman, Kevin and Denk, Winfried and Seung, Hyunjune Sebastian} } @article {3636, title = {Cooperation of the Dam1 and Ndc80 kinetochore complexes enhances microtubule coupling and is regulated by aurora B.}, journal = {The Journal of Cell Biology}, volume = {189}, year = {2010}, month = {2010 May 17}, pages = {713-23}, abstract = {

The coupling of kinetochores to dynamic spindle microtubules is crucial for chromosome positioning and segregation, error correction, and cell cycle progression. How these fundamental attachments are made and persist under tensile forces from the spindle remain important questions. As microtubule-binding elements, the budding yeast Ndc80 and Dam1 kinetochore complexes are essential and not redundant, but their distinct contributions are unknown. In this study, we show that the Dam1 complex is a processivity factor for the Ndc80 complex, enhancing the ability of the Ndc80 complex to form load-bearing attachments to and track with dynamic microtubule tips in vitro. Moreover, the interaction between the Ndc80 and Dam1 complexes is abolished when the Dam1 complex is phosphorylated by the yeast aurora B kinase Ipl1. This provides evidence for a mechanism by which aurora B resets aberrant kinetochore-microtubule attachments. We propose that the action of the Dam1 complex as a processivity factor in kinetochore-microtubule attachment is regulated by conserved signals for error correction.

}, keywords = {Cell Cycle Proteins, Green Fluorescent Proteins, Kinetochores, Microtubule-Associated Proteins, Microtubules, Mitotic Spindle Apparatus, Nuclear Proteins, Protein-Serine-Threonine Kinases, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins}, issn = {1540-8140}, doi = {10.1083/jcb.200910142}, author = {Tien, Jerry F and Umbreit, Neil T and Gestaut, Daniel R and Franck, Andrew D and Cooper, Jeremy and Wordeman, Linda and Gonen, Tamir and Asbury, Charles L and Davis, Trisha N} } @article {1449, title = {Cortical representations of olfactory input by trans-synaptic tracing.}, journal = {Nature}, volume = {472}, year = {2010}, month = {2010 Dec 22}, pages = {191-6}, abstract = {

In the mouse, each class of olfactory receptor neurons expressing a given odorant receptor has convergent axonal projections to two specific glomeruli in the olfactory bulb, thereby creating an odour map. However, it is unclear how this map is represented in the olfactory cortex. Here we combine rabies-virus-dependent retrograde mono-trans-synaptic labelling with genetics to control the location, number and type of {\textquoteright}starter{\textquoteright} cortical neurons, from which we trace their presynaptic neurons. We find that individual cortical neurons receive input from multiple mitral cells representing broadly distributed glomeruli. Different cortical areas represent the olfactory bulb input differently. For example, the cortical amygdala preferentially receives dorsal olfactory bulb input, whereas the piriform cortex samples the whole olfactory bulb without obvious bias. These differences probably reflect different functions of these cortical areas in mediating innate odour preference or associative memory. The trans-synaptic labelling method described here should be widely applicable to mapping connections throughout the mouse nervous system.

}, issn = {1476-4687}, doi = {10.1038/nature09714}, author = {Miyamichi, Kazunari and Amat, Fernando and Moussavi, Farshid and Wang, Chen and Wickersham, Ian and Wall, Nicholas R and Taniguchi, Hiroki and Tasic, Bosiljka and Huang, Z Josh and He, Zhigang and Callaway, Edward M and Horowitz, Mark A and Luo, Liqun} } @article {2769, title = {Delivery of picosecond lasers in multimode fibers for coherent anti-Stokes Raman scattering imaging.}, journal = {Optics Express}, volume = {18}, year = {2010}, month = {2010 Jun 7}, pages = {13017-28}, abstract = {

We investigated the possibility of using standard commercial multimode fibers (MMF), Corning SMF28 fibers, to deliver picosecond excitation lasers for coherent anti-Stokes Raman scattering (CARS) imaging. We theoretically and/or experimentally analyzed issues associated with the fiber delivery, such as dispersion length, walk-off length, nonlinear length, average threshold power for self-phase modulations, and four-wave mixing (FWM). These analyses can also be applied to other types of fibers. We found that FWM signals are generated in MMF, but they can be filtered out using a long-pass filter for CARS imaging. Finally, we demonstrated that MMF can be used for delivery of picosecond excitation lasers in the CARS imaging system without any degradation of image quality.

}, keywords = {Animals, Computer Simulation, Ear, Kidney, Lasers, Mice, Optical Fibers, Raman, Spectrum Analysis, Time Factors}, issn = {1094-4087}, doi = {10.1364/AO.50.001792}, author = {Wang, Zhiyong and Yang, Yaliang and Luo, Pengfei and Gao, Liang and Wong, Kelvin K and Wong, Stephen T C} } @article {68825, title = {Dermal morphogenesis controls lateral line patterning during postembryonic development of teleost fish}, journal = {Developmental Biology}, volume = {340}, year = {2010}, month = {04/2010}, pages = {583-594}, abstract = {

The lateral line system displays highly divergent patterns in adult teleost fish. The mechanisms underlying this variability are poorly understood. Here, we demonstrate that the lateral line mechanoreceptor, the neuromast, gives rise to a series of accessory neuromasts by a serial budding process during postembryonic development in zebrafish. We also show that accessory neuromast formation is highly correlated to the development of underlying dermal structures such as bones and scales. Abnormalities in opercular bone morphogenesis, in endothelin 1-knockdown embryos, are accompanied by stereotypic errors in neuromast budding and positioning, further demonstrating the tight correlation between the patterning of neuromasts and of the underlying dermal bones. In medaka, where scales form between peridermis and opercular bones, the lateral line displays a scale-specific pattern which is never observed in zebrafish. These results strongly suggest a control of postembryonic neuromast patterns by underlying dermal structures. This dermal control may explain some aspects of the evolution of lateral line patterns.

}, keywords = {Dermal bone, Lateral line, Medaka, Neuromast, Opercle, Postembryonic development, Scale, Zebrafish}, issn = {0012-1606}, doi = {https://doi.org/10.1016/j.ydbio.2010.02.017}, url = {https://www.sciencedirect.com/science/article/pii/S0012160610001028}, author = {Hironori Wada and Alain Ghysen and Chie Satou and Shin-ichi Higashijima and Koichi Kawakami and Satoshi Hamaguchi and Mitsuru Sakaizumi} } @article {47675, title = {Determining membrane protein topologies in single cells and high-throughput screening applications.}, journal = {Current protocols in cell biology / editorial board, Juan S. Bonifacino ... [et al.]}, volume = {Chapter 5}, year = {2010}, month = {2010 Dec}, pages = {Unit 5.7}, abstract = {

Correct localization and topology are crucial for a protein{\textquoteright}s cellular function. To determine topologies of membrane proteins, a new technique, called fluorescence protease protection (FPP) assay, has recently been established. The sole requirements for FPP are the expression of fluorescent-protein fusion proteins and the selective permeabilization of the plasma membrane, permitting a wide range of cell types and organelles to be investigated. Proteins topologies in organelles like endoplasmic reticulum, Golgi apparatus, mitochondria, peroxisomes, and autophagosomes have already been determined by FPP. Here, two different step-by-step protocols of the FPP assay are provided. First, we describe the FPP assay using fluorescence microscopy for single adherent cells, and second, we outline the FPP assay for high-throughput screening applications.

}, keywords = {Animals, Cell Line, Cytological Techniques, High-Throughput Screening Assays, Humans, Luminescent Proteins, Membrane Proteins, Microscopy, Fluorescence, Peptide Hydrolases, Protein Transport, Recombinant Fusion Proteins, Single-Cell Analysis}, issn = {1934-2616}, doi = {10.1002/0471143030.cb0507s49}, author = {Wunder, Christian and Lippincott-Schwartz, Jennifer and Lorenz, Holger} } @article {2493, title = {Developmental expression of mRNAs for epidermal and fat body proteins and hormonally regulated transcription factors in the tobacco hornworm, Manduca sexta.}, journal = {Journal of Insect Physiology}, volume = {56}, year = {2010}, month = {2010 Oct}, pages = {1390-5}, abstract = {

This paper provides a compilation of diagrammatic representations of the expression profiles of epidermal and fat body mRNAs during the last two larval instars and metamorphosis of the tobacco hornworm, Manduca sexta. Included are those encoding insecticyanin, three larval cuticular proteins, dopa decarboxylase, moling, and the juvenile hormone-binding protein JP29 produced by the dorsal abdominal epidermis, and arylphorin and the methionine-rich storage proteins made by the fat body. The mRNA profiles of the ecdysteroid-regulated cascade of transcription factors in the epidermis during the larval molt and the onset of metamorphosis and in the pupal wing during the onset of adult development are also shown. These profiles are accompanied by a brief summary of the current knowledge about the regulation of these mRNAs by ecdysteroids and juvenile hormone based on experimental manipulations, both in vivo and in vitro.

}, keywords = {Animals, Developmental, Epidermis, Fat Body, Gene Expression Regulation, Insect Hormones, Insect Proteins, Manduca, Messenger, RNA, Transcription Factors}, issn = {1879-1611}, doi = {10.1016/j.jinsphys.2010.03.029}, author = {Hiruma, Kiyoshi and Riddiford, Lynn M} } @article {65010, title = {Development-based compartmentalization of the Drosophila central brain.}, journal = {J Comp Neurol}, volume = {518}, year = {2010}, month = {2010 Aug 01}, pages = {2996-3023}, abstract = {

The neuropile of the Drosophila brain is subdivided into anatomically discrete compartments. Compartments are rich in terminal neurite branching and synapses; they are the neuropile domains in which signal processing takes place. Compartment boundaries are defined by more or less dense layers of glial cells as well as long neurite fascicles. These fascicles are formed during the larval period, when the approximately 100 neuronal lineages that constitute the Drosophila central brain differentiate. Each lineage forms an axon tract with a characteristic trajectory in the neuropile; groups of spatially related tracts congregate into the brain fascicles that can be followed from the larva throughout metamorphosis into the adult stage. Here we provide a map of the adult brain compartments and the relevant fascicles defining compartmental boundaries. We have identified the neuronal lineages contributing to each fascicle, which allowed us to compare compartments of the larval and adult brain directly. Most adult compartments can be recognized already in the early larval brain, where they form a "protomap" of the later adult compartments. Our analysis highlights the morphogenetic changes shaping the Drosophila brain; the data will be important for studies that link early-acting genetic mechanisms to the adult neuronal structures and circuits controlled by these mechanisms.

}, keywords = {Animals, Antibodies, Monoclonal, Axons, Brain, Brain Mapping, Cadherins, Chemokine CX3CL1, Drosophila, Image Processing, Computer-Assisted, Immunohistochemistry, Larva, Neural Pathways, Neuroglia, Synapses}, issn = {1096-9861}, doi = {10.1002/cne.22376}, author = {Pereanu, Wayne and Kumar, Abilasha and Jennett, Arnim and Reichert, Heinrich and Hartenstein, Volker} } @article {1683, title = {Digital scanned laser light sheet fluorescence microscopy.}, journal = {Cold Spring Harbor Protocols}, volume = {2010}, year = {2010}, month = {2011 Oct}, pages = {pdb.top78}, abstract = {

Modern applications in the life sciences are frequently based on in vivo imaging of biological specimens, a domain for which light microscopy approaches are typically best suited. Often, quantitative information must be obtained from large multicellular organisms at the cellular or even subcellular level and with a good temporal resolution. However, this usually requires a combination of conflicting features: high imaging speed, low photobleaching and low phototoxicity in the specimen, good three-dimensional (3D) resolution, an excellent signal-to-noise ratio, and multiple-view imaging capability. The latter feature refers to the capability of recording a specimen along multiple directions, which is crucial for the imaging of large specimens with strong light-scattering or light-absorbing tissue properties. An imaging technique that fulfills these requirements is essential for many key applications: For example, studying fast cellular processes over long periods of time, imaging entire embryos throughout development, or reconstructing the formation of morphological defects in mutants. Here, we discuss digital scanned laser light sheet fluorescence microscopy (DSLM) as a novel tool for quantitative in vivo imaging in the post-genomic era and show how this emerging technique relates to the currently most widely applied 3D microscopy techniques in biology: confocal fluorescence microscopy and two-photon microscopy.

}, keywords = {Computer-Assisted, Confocal, Fluorescence, Image Processing, Microscopy}, issn = {1559-6095}, doi = {10.1101/pdb.top78}, author = {Keller, Philipp J and Stelzer, Ernst H K} } @article {4295, title = {A dimorphic pheromone circuit in Drosophila from sensory input to descending output.}, journal = {Nature}, volume = {468}, year = {2010}, month = {2010 Dec 2}, pages = {686-90}, abstract = {

Drosophila show innate olfactory-driven behaviours that are observed in naive animals without previous learning or experience, suggesting that the neural circuits that mediate these behaviours are genetically programmed. Despite the numerical simplicity of the fly nervous system, features of the anatomical organization of the fly brain often confound the delineation of these circuits. Here we identify a neural circuit responsive to cVA, a pheromone that elicits sexually dimorphic behaviours. We have combined neural tracing using an improved photoactivatable green fluorescent protein (PA-GFP) with electrophysiology, optical imaging and laser-mediated microlesioning to map this circuit from the activation of sensory neurons in the antennae to the excitation of descending neurons in the ventral nerve cord. This circuit is concise and minimally comprises four neurons, connected by three synapses. Three of these neurons are overtly dimorphic and identify a male-specific neuropil that integrates inputs from multiple sensory systems and sends outputs to the ventral nerve cord. This neural pathway suggests a means by which a single pheromone can elicit different behaviours in the two sexes.

}, keywords = {Acetates, Animal, Animals, Arthropod Antennae, Drosophila melanogaster, Drosophila Proteins, Female, Male, Nerve Tissue Proteins, Neuroanatomical Tract-Tracing Techniques, Odors, Oleic Acids, Olfactory Pathways, Olfactory Perception, Pheromones, Physical Stimulation, Sensory Receptor Cells, Sex Characteristics, Sexual Behavior, Transcription Factors}, issn = {1476-4687}, doi = {10.1038/nature09554}, author = {Ruta, Vanessa and Datta, Sandeep Robert and Vasconcelos, Maria Lu{\'\i}sa and Freeland, Jessica and Looger, Loren L and Axel, Richard} } @article {2784, title = {Direct detection of benzene, toluene, and ethylbenzene at trace levels in ambient air by atmospheric pressure chemical ionization using a handheld mass spectrometer.}, journal = {Journal of the American Society for Mass Spectrometry}, volume = {21}, year = {2010}, month = {2010 Jan}, pages = {132-5}, abstract = {

The capabilities of a portable mass spectrometer for real-time monitoring of trace levels of benzene, toluene, and ethylbenzene in air are illustrated. An atmospheric pressure interface was built to implement atmospheric pressure chemical ionization for direct analysis of gas-phase samples on a previously described miniature mass spectrometer (Gao et al. Anal. Chem.2006, 78, 5994-6002). Linear dynamic ranges, limits of detection and other analytical figures of merit were evaluated: for benzene, a limit of detection of 0.2 parts-per-billion was achieved for air samples without any sample preconcentration. The corresponding limits of detection for toluene and ethylbenzene were 0.5 parts-per-billion and 0.7 parts-per-billion, respectively. These detection limits are well below the compounds{\textquoteright} permissible exposure levels, even in the presence of added complex mixtures of organics at levels exceeding the parts-per-million level. The linear dynamic ranges of benzene, toluene, and ethylbenzene are limited to approximately two orders of magnitude by saturation of the detection electronics.

}, keywords = {Air, Atmospheric Pressure, Benzene, Benzene Derivatives, Equipment Design, Ions, Limit of Detection, Mass Spectrometry, Toluene}, issn = {1879-1123}, doi = {10.1364/AO.50.001792}, author = {Huang, Guangming and Gao, Liang and Duncan, Jason and Harper, Jason D and Sanders, Nathaniel L and Ouyang, Zheng and Cooks, R Graham} } @article {6861, title = {Distinct protein domains and expression patterns confer divergent axon guidance functions for Drosophila Robo receptors.}, journal = {Cell}, volume = {140}, year = {2010}, month = {2010 Feb 5}, pages = {409-20}, abstract = {

The orthogonal array of axon pathways in the Drosophila CNS is constructed in part under the control of three Robo family axon guidance receptors: Robo1, Robo2 and Robo3. Each of these receptors is responsible for a distinct set of guidance decisions. To determine the molecular basis for these functional specializations, we used homologous recombination to create a series of 9 "robo swap" alleles: expressing each of the three Robo receptors from each of the three robo loci. We demonstrate that the lateral positioning of longitudinal axon pathways relies primarily on differences in gene regulation, not distinct combinations of Robo proteins as previously thought. In contrast, specific features of the Robo1 and Robo2 proteins contribute to their distinct functions in commissure formation. These specializations allow Robo1 to prevent crossing and Robo2 to promote crossing. These data demonstrate how diversification of expression and structure within a single family of guidance receptors can shape complex patterns of neuronal wiring.

}, keywords = {Animals, Axons, Central Nervous System, Developmental, Drosophila melanogaster, Drosophila Proteins, Embryo, Gene Expression Regulation, Immunologic, Nerve Tissue Proteins, Nonmammalian, Receptors}, issn = {1097-4172}, doi = {10.1016/j.cell.2010.01.002}, author = {Spitzweck, Bettina and Brankatschk, Marko and Dickson, Barry J} } @article {4294, title = {Distinct representations and theta dynamics in dorsal and ventral hippocampus.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {30}, year = {2010}, month = {2010 Feb 3}, pages = {1777-87}, abstract = {

Although anatomical, lesion, and imaging studies of the hippocampus indicate qualitatively different information processing along its septo-temporal axis, physiological mechanisms supporting such distinction are missing. We found fundamental differences between the dorsal (dCA3) and the ventral-most parts (vCA3) of the hippocampus in both environmental representation and temporal dynamics. Discrete place fields of dCA3 neurons evenly covered all parts of the testing environments. In contrast, vCA3 neurons (1) rarely showed continuous two-dimensional place fields, (2) differentiated open and closed arms of a radial maze, and (3) discharged similar firing patterns with respect to the goals, both on multiple arms of a radial maze and during opposite journeys in a zigzag maze. In addition, theta power and the fraction of theta-rhythmic neurons were substantially reduced in the ventral compared with dorsal hippocampus. We hypothesize that the spatial representation in the septo-temporal axis of the hippocampus is progressively decreased. This change is paralleled with a reduction of theta rhythm and an increased representation of nonspatial information.

}, keywords = {Animals, Hippocampus, Long-Evans, Male, Maze Learning, Neurons, Rats, Space Perception, Theta Rhythm}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4681-09.2010}, author = {Royer, S{\'e}bastien and Sirota, Anton and Patel, Jagdish and Buzs{\'a}ki, Gy{\"o}rgy} } @article {6386, title = {Droplet confinement and fluorescence measurement of single molecules.}, journal = {Methods in Enzymology}, volume = {472}, year = {2010}, month = {2010}, pages = {61-88}, abstract = {

We describe a method for molecular confinement and single-fluorophore sensitive measurement in aqueous nanodroplets in oil. The sequestration of individual molecules in droplets has become a useful tool in genomics and molecular evolution. Similarly, the use of single fluorophores, or pairs of fluorophores, to study biomolecular interactions and structural dynamics is now common. Most often these single-fluorophore sensitive measurements are performed on molecules that are surface attached. Confinement via surface attachment permits molecules to be located and studied for a prolonged period of time. For molecules that denature on surfaces, for interactions that are transient or out-of-equilibrium, or to observe the dynamic equilibrium of freely diffusing reagents, surface attachment may not be an option. In these cases, droplet confinement presents an alternative method for molecular confinement. Here, we describe this method as used in single-fluorophore sensitive measurement and discuss its advantages, limitations, and future prospects.

}, keywords = {Diffusion, Electrochemical Techniques, Emulsions, Fluorescence, Fluorescent Dyes, Microfluidics, Nanostructures, Oils, Optical Tweezers, Spectrometry, Water}, issn = {1557-7988}, doi = {10.1016/S0076-6879(10)72015-2}, author = {Goldner, Lori S and Jofre, Ana M and Tang, Jianyong} } @article {68487, title = {Droplet freezing, docking, and the exchange of immiscible phase and surfactant around frozen droplets.}, journal = {Lab Chip}, volume = {10}, year = {2010}, month = {07/2010}, pages = {1873-7}, abstract = {

This paper describes a platform for cooling microfluidic chips so as to freeze aqueous droplets flowing in oil. Using a whole-chip cooling chamber, we can control the ambient temperature surrounding a microfluidic chip and induce cooling and freezing inside the channels. When combined with a droplet generation and droplet docking chip, this platform allows for the facile freezing of droplets immobilized in resistance-based docks. Depending on the design and shape of the docks, the frozen droplets can either be trapped stably in the docks or be released because deformed non-frozen aqueous droplets turn spherical when frozen, and thus can become dislodged from the docks. Additionally, using this chamber and chip combination we are able to exchange immiscible phases and surfactants surrounding the frozen droplets. The materials and methods are inexpensive and easily accessible to microfluidics researchers, making this a simple addition to an existing microfluidic platform.

}, keywords = {Equipment Design, Equipment Failure Analysis, Freezing, Ice, Microfluidic Analytical Techniques, Phase Transition, Surface-Active Agents}, issn = {1473-0197}, doi = {10.1039/c001108h}, author = {Sgro, Allyson E and Chiu, Daniel T} } @article {2353, title = {Drosophila fly straight by fixating objects in the face of expanding optic flow.}, journal = {The Journal of Experimental Biology}, volume = {213}, year = {2010}, month = {2010 May}, pages = {1771-81}, abstract = {

Flies, like all animals that depend on vision to navigate through the world, must integrate the optic flow created by self-motion with the images generated by prominent features in their environment. Although much is known about the responses of Drosophila melanogaster to rotating flow fields, their reactions to the more complex patterns of motion that occur as they translate through the world are not well understood. In the present study we explore the interactions between two visual reflexes in Drosophila: object fixation and expansion avoidance. As a fly flies forward, it encounters an expanding visual flow field. However, recent results have demonstrated that Drosophila strongly turn away from patterns of expansion. Given the strength of this reflex, it is difficult to explain how flies make forward progress through a visual landscape. This paradox is partially resolved by the finding reported here that when undergoing flight directed towards a conspicuous object, Drosophila will tolerate a level of expansion that would otherwise induce avoidance. This navigation strategy allows flies to fly straight when orienting towards prominent visual features.

}, keywords = {Animal, Animals, Drosophila melanogaster, Fixation, Flight, Ocular, Photic Stimulation, Visual Pathways}, issn = {1477-9145}, doi = {10.1016/j.cub.2010.06.072}, author = {Reiser, Michael B and Dickinson, Michael H} } @article {4408, title = {Dynamics of genome evolution in facultative symbionts of aphids.}, journal = {Environmental Microbiology}, volume = {12}, year = {2010}, month = {2010 Aug}, pages = {2060-9}, abstract = {

Aphids are sap-feeding insects that host a range of bacterial endosymbionts including the obligate, nutritional mutualist Buchnera plus several bacteria that are not required for host survival. Among the latter, {\textquoteright}Candidatus Regiella insecticola{\textquoteright} and {\textquoteright}Candidatus Hamiltonella defensa{\textquoteright} are found in pea aphids and other hosts and have been shown to protect aphids from natural enemies. We have sequenced almost the entire genome of R. insecticola (2.07 Mbp) and compared it with the recently published genome of H. defensa (2.11 Mbp). Despite being sister species the two genomes are highly rearranged and the genomes only have \~{}55\% of genes in common. The functions encoded by the shared genes imply that the bacteria have similar metabolic capabilities, including only two essential amino acid biosynthetic pathways and active uptake mechanisms for the remaining eight, and similar capacities for host cell toxicity and invasion (type 3 secretion systems and RTX toxins). These observations, combined with high sequence divergence of orthologues, strongly suggest an ancient divergence after establishment of a symbiotic lifestyle. The divergence in gene sets and in genome architecture implies a history of rampant recombination and gene inactivation and the ongoing integration of mobile DNA (insertion sequence elements, prophage and plasmids).

}, keywords = {Animals, Aphids, Bacterial, Comparative Genomic Hybridization, DNA, Enterobacteriaceae, Evolution, Genome, Genomic Islands, Molecular, Molecular Sequence Data, Phylogeny, Sequence Analysis, Symbiosis}, issn = {1462-2920}, doi = {10.1111/j.1462-2920.2009.02085.x}, author = {Degnan, Patrick H and Leonardo, Teresa E and Cass, Bodil N and Hurwitz, Bonnie and Stern, David and Gibbs, Richard A and Richards, Stephen and Moran, Nancy A} } @article {3634, title = {An engineered DNA-binding protein self-assembles metallic nanostructures.}, journal = {Chembiochem: A European Journal of Chemical Biology}, volume = {11}, year = {2010}, month = {2010 Oct 18}, pages = {2108-12}, abstract = {

The golden age of DNA: We describe a strategy for engineering bifunctional proteins that simultaneously associate with metals and DNA to create self-assembled nanostructures. A DNA binding protein engineered with a gold binding peptide arranges colloidal gold particles along a DNA guide by virtue of its introduced peptide motif. These self-assembled complexes represent a step toward constructing nanoarchitectures with potential in nanoelectronic and photonic devices.

}, keywords = {Amino Acid Sequence, DNA, DNA Helicases, Escherichia coli Proteins, Gold, Nanostructures, Nucleic Acid Conformation, Peptide Library, Peptides, Protein Binding, Protein Engineering, Single-Stranded}, issn = {1439-7633}, doi = {10.1002/cbic.201000407}, author = {Hall Sedlak, Ruth and Hnilova, Marketa and Gachelet, Eliora and Przybyla, Laralynne and Dranow, David and Gonen, Tamir and Sarikaya, Mehmet and Tamerler, Candan and Traxler, Beth} } @article {65007, title = {Ephus: multipurpose data acquisition software for neuroscience experiments.}, journal = {Front Neural Circuits}, volume = {4}, year = {2010}, month = {2010}, pages = {100}, abstract = {

Physiological measurements in neuroscience experiments often involve complex stimulus paradigms and multiple data channels. Ephus (http://www.ephus.org) is an open-source software package designed for general-purpose data acquisition and instrument control. Ephus operates as a collection of modular programs, including an ephys program for standard whole-cell recording with single or multiple electrodes in typical electrophysiological experiments, and a mapper program for synaptic circuit mapping experiments involving laser scanning photostimulation based on glutamate uncaging or channelrhodopsin-2 excitation. Custom user functions allow user-extensibility at multiple levels, including on-line analysis and closed-loop experiments, where experimental parameters can be changed based on recently acquired data, such as during in vivo behavioral experiments. Ephus is compatible with a variety of data acquisition and imaging hardware. This paper describes the main features and modules of Ephus and their use in representative experimental applications.

}, issn = {1662-5110}, doi = {10.3389/fncir.2010.00100}, author = {Suter, Benjamin A and O{\textquoteright}Connor, Timothy and Iyer, Vijay and Petreanu, Leopoldo T and Hooks, Bryan M and Kiritani, Taro and Svoboda, Karel and Shepherd, Gordon M G} } @article {2326, title = {Error tolerant indexing and alignment of short reads with covering template families.}, journal = {Journal of Computational Biology: A Journal of Computational Molecular Cell Biology}, volume = {17}, year = {2010}, month = {2010 Oct}, pages = {1397-1411}, abstract = {

The rapid adoption of high-throughput next generation sequence data in biological research is presenting a major challenge for sequence alignment tools{\textemdash}specifically, the efficient alignment of vast amounts of short reads to large references in the presence of differences arising from sequencing errors and biological sequence variations. To address this challenge, we developed a short read aligner for high-throughput sequencer data that is tolerant of errors or mutations of all types{\textemdash}namely, substitutions, deletions, and insertions. The aligner utilizes a multi-stage approach in which template-based indexing is used to identify candidate regions for alignment with dynamic programming. A template is a pair of gapped seeds, with one used with the read and one used with the reference. In this article, we focus on the development of template families that yield error-tolerant indexing up to a given error-budget. A general algorithm for finding those families is presented, and a recursive construction that creates families with higher error tolerance from ones with a lower error tolerance is developed.

}, keywords = {Algorithms, Base Sequence, DNA, Genetic, Molecular Sequence Data, Sequence Alignment, Sequence Analysis, Software, Templates}, issn = {1557-8666}, doi = {10.1089/cmb.2010.0005}, author = {Giladi, Eldar and Healy, John and Myers, Gene and Hart, Chris and Kapranov, Philipp and Lipson, Doron and Roels, Steve and Thayer, Edward and Letovsky, Stan} } @article {46619, title = {Ethanol-regulated genes that contribute to ethanol sensitivity and rapid tolerance in Drosophila.}, journal = {Alcoholism, Clinical and Experimental Research}, volume = {34}, year = {2010}, month = {2010 Feb}, pages = {302-16}, abstract = {

BACKGROUND: Increased ethanol intake, a major predictor for the development of alcohol use disorders, is facilitated by the development of tolerance to both the aversive and pleasurable effects of the drug. The molecular mechanisms underlying ethanol tolerance development are complex and are not yet well understood.

METHODS: To identify genetic mechanisms that contribute to ethanol tolerance, we examined the time course of gene expression changes elicited by a single sedating dose of ethanol in Drosophila, and completed a behavioral survey of strains harboring mutations in ethanol-regulated genes.

RESULTS: Enrichment for genes in metabolism, nucleic acid binding, olfaction, regulation of signal transduction, and stress suggests that these biological processes are coordinately affected by ethanol exposure. We also detected a coordinate up-regulation of genes in the Toll and Imd innate immunity signal transduction pathways. A multi-study comparison revealed a small set of genes showing similar regulation, including increased expression of 3 genes for serine biosynthesis. A survey of Drosophila strains harboring mutations in ethanol-regulated genes for ethanol sensitivity and tolerance phenotypes revealed roles for serine biosynthesis, olfaction, transcriptional regulation, immunity, and metabolism. Flies harboring deletions of the genes encoding the olfactory co-receptor Or83b or the sirtuin Sir2 showed marked changes in the development of ethanol tolerance.

CONCLUSIONS: Our findings implicate novel roles for these genes in regulating ethanol behavioral responses.

}, keywords = {Animals, Behavior, Animal, Central Nervous System Depressants, Coenzyme A Ligases, Drosophila, Drosophila Proteins, Drug Tolerance, Ethanol, Female, Gene Expression Regulation, Histone Deacetylases, Male, Motor Activity, Mutation, Oligonucleotide Array Sequence Analysis, Receptors, Odorant, Reverse Transcriptase Polymerase Chain Reaction, Serpins, Sirtuins, Species Specificity}, issn = {1530-0277}, doi = {10.1111/j.1530-0277.2009.01093.x}, author = {Kong, Eric C and Allouche, Lorien and Chapot, Paul A and Vranizan, Karen and Moore, Monica S and Heberlein, Ulrike and Wolf, Fred W} } @book {45796, title = {Evolution, Development, and the Predictable Genome}, year = {2010}, publisher = {Roberts and Company Publishers}, organization = {Roberts and Company Publishers}, address = {Austin, TX}, abstract = {

For too long, efforts to synthesize evolution and development have failed to build a united view of the origins and evolution of biological diversity. In this groundbreaking book, David Stern sets out to draw evolutionary biology and developmental biology together by cutting through the differences that divide the disciplines and by revealing their deeper similarities. He draws upon the insights of generations of evolutionary biologists and scores of developmental biologists to build a solid foundation for future investigation of the genetic and developmental causes of diversity. Along the way, and in plain English, he explicates many of the guiding principles of evolution, population genetics, and developmental biology. Each chapter offers a clear review of fundamental principles, together with thoughtprovoking ideas that will be tested only with data emerging from current and future studies. With the basic principles established, he then offers a new way of thinking about development{\textemdash}backwards{\textemdash}to clarify precisely how the mechanisms of development influence evolution. In the same spirit, he takes a fresh look at evolution in populations, arguing that population history influences precisely how developmental mechanisms evolve. Both Stern{\textquoteright}s new perspective on development and his reassessment of the role of populations leads to the surprising conclusion that the evolution of genomes appears to be predictable. Stern argues that developmental biology and evolutionary biology are intertwined: it is impossible to understand one of them fully without understanding the other. This book provides a clear and wide-ranging introduction to evolution and development for the basic reader; graduate students will be introduced to the cutting-edge of research in evolutionary developmental biology; and experts in evolution or development will receive both an uncomplicated introduction to the other discipline and an abundance of new, provocative ideas.

Stern, David L. Evolution, Development, and the Predictable Genome. Austin, TX: Roberts and Company Publishers, 2010.

}, isbn = {9781936221011}, url = {http://www.roberts-publishers.com/evolution-development-and-the-predictable-genome-physical.html}, author = {Stern, David L} } @article {6391, title = {Evolutionary divergence of the paralogs Methoprene tolerant (Met) and germ cell expressed (gce) within the genus Drosophila.}, journal = {Journal of Insect Physiology}, volume = {56}, year = {2010}, month = {2010 Oct}, pages = {1445-55}, abstract = {

Juvenile hormone (JH) signaling underpins both regulatory and developmental pathways in insects. However, the JH receptor is poorly understood. Methoprene tolerant (Met) and germ cell expressed (gce) have been implicated in JH signaling in Drosophila. We investigated the evolution of Met and gce across 12 Drosophila species and found that these paralogs are conserved across at least 63 million years of dipteran evolution. Distinct patterns of selection found using estimates of dN/dS ratios across Drosophila Met and gce coding sequences, along with their incongruent temporal expression profiles in embryonic Drosophila melanogaster, illustrate avenues through which these genes have diverged within the Diptera. Additionally, we demonstrate that the annotated gene CG15032 is the 5{\textquoteright} terminus of gce. In mosquitoes and beetles, a single Met-like homolog displays structural similarity to both Met and gce, and the intron locations are conserved with those of gce. We found that Tribolium and mosquito Met orthologs are assembled from Met- and gce-specific domains in a modular fashion. Our results suggest that Drosophila Met and gce experienced divergent evolutionary pressures following the duplication of an ancestral gce-like gene found in less derived holometabolous insects.

}, keywords = {Amino Acid Sequence, Animals, Drosophila, Drosophila Proteins, Evolution, Gene Duplication, Methoprene, Molecular, Molecular Sequence Data, Phylogeny, Protein Structure, Sequence Alignment, Tertiary}, issn = {1879-1611}, doi = {10.1016/j.jinsphys.2010.05.001}, author = {Baumann, Aaron and Fujiwara, Yoshihiro and Wilson, Thomas G} } @article {2752, title = {Examining the combinatorial model of motor neuron survival by expression profiling of trophic factors and their receptors in the embryonic Gallus gallus.}, journal = {Developmental Dynamics: An Official Publication of the American Association of Anatomists}, volume = {239}, year = {2010}, month = {2010 Mar}, pages = {965-79}, abstract = {

During embryogenesis, limb-innervating lateral motor column (LMC) spinal motor neurons (MN) are generated in excess and subsequently nearly half of them die. Many motor neuron survival factors (MnSFs) have been shown to suppress this default programmed cell death (PCD) program through their receptors (MnSFRs), raising the possibility that they are involved in matching specific MNs with their target muscles. Published observations suggest a combinatorial model of MnSF/Rs function, which assumes that during the PCD phase, MNs are expressing combinations of MnSFRs, whereas the limb muscles innervated by these MNs express cognate combinations of MnSFs. We tested this model by expression profiling of MnSFs and their receptors in the avian lumbosacral spinal cord and limb muscles during the peak PCD period. Our findings highlight the complexity of MnSF/Rs function in the control of LMC motor neuron survival.

}, keywords = {Animals, Biological, Cell Death, Chick Embryo, Chickens, Computer-Assisted, Developmental, Developmental Biology, DNA Primers, Gene Expression Profiling, Gene Expression Regulation, Image Processing, Ligands, Lumbosacral Region, Models, Motor Neurons, Reverse Transcriptase Polymerase Chain Reaction, Spinal Cord}, issn = {1097-0177}, doi = {10.1002/dvdy.22215}, author = {Gu, Wendy X W and Kania, Artur} } @article {2027, title = {Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy.}, journal = {Nature Methods}, volume = {7}, year = {2010}, month = {08/2010}, pages = {637-42}, abstract = {

Recording light-microscopy images of large, nontransparent specimens, such as developing multicellular organisms, is complicated by decreased contrast resulting from light scattering. Early zebrafish development can be captured by standard light-sheet microscopy, but new imaging strategies are required to obtain high-quality data of late development or of less transparent organisms. We combined digital scanned laser light-sheet fluorescence microscopy with incoherent structured-illumination microscopy (DSLM-SI) and created structured-illumination patterns with continuously adjustable frequencies. Our method discriminates the specimen-related scattered background from signal fluorescence, thereby removing out-of-focus light and optimizing the contrast of in-focus structures. DSLM-SI provides rapid control of the illumination pattern, exceptional imaging quality, and high imaging speeds. We performed long-term imaging of zebrafish development for 58 h and fast multiple-view imaging of early Drosophila melanogaster development. We reconstructed cell positions over time from the Drosophila DSLM-SI data and created a fly digital embryo.

}, keywords = {Animals, Drosophila melanogaster, Embryo, Microscopy, Nonmammalian, Zebrafish}, issn = {1548-7105}, doi = {10.1038/nmeth.1476}, author = {Keller, Philipp J and Schmidt, Annette D and Santella, Anthony and Khairy, Khaled and Zhirong Bao and Wittbrodt, Joachim and Stelzer, Ernst H K} } @article {2955, title = {Fast live simultaneous multiwavelength four-dimensional optical microscopy.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, year = {2010}, month = {2010 Sep 14}, pages = {16016-22}, abstract = {

Live fluorescence microscopy has the unique capability to probe dynamic processes, linking molecular components and their localization with function. A key goal of microscopy is to increase spatial and temporal resolution while simultaneously permitting identification of multiple specific components. We demonstrate a new microscope platform, OMX, that enables subsecond, multicolor four-dimensional data acquisition and also provides access to subdiffraction structured illumination imaging. Using this platform to image chromosome movement during a complete yeast cell cycle at one 3D image stack per second reveals an unexpected degree of photosensitivity of fluorophore-containing cells. To avoid perturbation of cell division, excitation levels had to be attenuated between 100 and 10,000{\texttimes} below the level normally used for imaging. We show that an image denoising algorithm that exploits redundancy in the image sequence over space and time allows recovery of biological information from the low light level noisy images while maintaining full cell viability with no fading.

}, keywords = {Algorithms, Animals, Cell Survival, Drosophila melanogaster, Fluorescence, Microscopy, Saccharomyces cerevisiae, Software}, issn = {1091-6490}, doi = {10.1073/pnas.1004037107}, author = {Carlton, Peter M and Boulanger, J{\'e}r{\^o}me and Kervrann, Charles and Sibarita, Jean-Baptiste and Salamero, Jean and Gordon-Messer, Susannah and Bressan, Debra and Haber, James E and Haase, Sebastian and Shao, Lin and Winoto, Lukman and Matsuda, Atsushi and Kner, Peter and Uzawa, Satoru and Gustafsson, Mats and Kam, Zvi and Agard, David A and Sedat, John W} } @article {4369, title = {Filtering of visual information in the tectum by an identified neural circuit.}, journal = {Science}, volume = {330}, year = {2010}, month = {2010 Oct 29}, pages = {669-73}, abstract = {

The optic tectum of zebrafish is involved in behavioral responses that require the detection of small objects. The superficial layers of the tectal neuropil receive input from retinal axons, while its deeper layers convey the processed information to premotor areas. Imaging with a genetically encoded calcium indicator revealed that the deep layers, as well as the dendrites of single tectal neurons, are preferentially activated by small visual stimuli. This spatial filtering relies on GABAergic interneurons (using the neurotransmitter γ-aminobutyric acid) that are located in the superficial input layer and respond only to large visual stimuli. Photo-ablation of these cells with KillerRed, or silencing of their synaptic transmission, eliminates the size tuning of deeper layers and impairs the capture of prey.

}, keywords = {Animals, Axons, Bicuculline, Dendrites, GABA Antagonists, gamma-Aminobutyric Acid, Genetically Modified, Interneurons, Neural Inhibition, Neurons, Neuropil, Nonmammalian, Optic Lobe, Photic Stimulation, Retina, Retinal Neurons, Synaptic Transmission, Visual Pathways, Visual Perception, Zebrafish}, issn = {1095-9203}, doi = {10.1126/science.1192949}, author = {Del Bene, Filippo and Wyart, Claire and Robles, Estuardo and Tran, Amanda and Looger, Loren and Scott, Ethan K and Isacoff, Ehud Y and Baier, Herwig} } @article {4403, title = {A full-length cDNA resource for the pea aphid, acyrthosiphon pisum.}, journal = {Insect Molecular Biology}, volume = {19 Suppl 2}, year = {2010}, month = {2010 Mar}, pages = {23-31}, abstract = {

Large collections of full-length cDNAs are important resources for genome annotation and functional genomics. We report the creation of a collection of 50 599 full-length cDNA clones from the pea aphid, Acyrthosiphon pisum. Sequencing from 5{\textquoteright} and 3{\textquoteright} ends of the clones generated 97 828 high-quality expressed sequence tags, representing approximately 9000 genes. These sequences were imported to AphidBase and are shown to play crucial roles in both automatic gene prediction and manual annotation. Our detailed analyses demonstrated that the full-length cDNAs can further improve gene models and can even identify novel genes that are not included in the current version of the official gene set. This full-length cDNA collection can be utilized for a wide variety of functional studies, serving as a community resource for the study of the functional genomics of the pea aphid.

}, keywords = {3{\textquoteright} Untranslated Regions, 5{\textquoteright} Untranslated Regions, Animals, Aphids, Base Sequence, Complementary, DNA, DNA Primers, Expressed Sequence Tags, Gene Library, Genetic, Genome, Host-Pathogen Interactions, Insect, Models, Peas}, issn = {1365-2583}, doi = {10.1111/j.1365-2583.2009.00946.x}, author = {Shigenobu, S and Richards, S and Cree, A G and Morioka, M and Fukatsu, T and Kudo, T and Miyagishima, S and Gibbs, R A and Stern, D L and Nakabachi, A} } @article {4290, title = {The functional asymmetry of auditory cortex is reflected in the organization of local cortical circuits.}, journal = {Nature Neuroscience}, volume = {13}, year = {2010}, month = {2010 Nov}, pages = {1413-20}, abstract = {

The primary auditory cortex (A1) is organized tonotopically, with neurons sensitive to high and low frequencies arranged in a rostro-caudal gradient. We used laser scanning photostimulation in acute slices to study the organization of local excitatory connections onto layers 2 and 3 (L2/3) of the mouse A1. Consistent with the organization of other cortical regions, synaptic inputs along the isofrequency axis (orthogonal to the tonotopic axis) arose predominantly within a column. By contrast, we found that local connections along the tonotopic axis differed from those along the isofrequency axis: some input pathways to L3 (but not L2) arose predominantly out-of-column. In vivo cell-attached recordings revealed differences between the sound-responsiveness of neurons in L2 and L3. Our results are consistent with the hypothesis that auditory cortical microcircuitry is specialized to the one-dimensional representation of frequency in the auditory cortex.

}, keywords = {Acoustic Stimulation, Adjuvants, Amino Acids, Animals, Anisotropy, Auditory Cortex, Brain Mapping, Cholera Toxin, Confocal, Excitatory Postsynaptic Potentials, Functional Laterality, Glutamic Acid, Immunologic, Inbred C57BL, Inbred CBA, Long-Evans, Mice, Microscopy, Nerve Net, Neural Pathways, Neurons, Newborn, Nonparametric, Photic Stimulation, Psychoacoustics, Rats, Statistics, Time Factors}, issn = {1546-1726}, doi = {10.1038/nn.2659}, author = {Oviedo, Hysell V and Bureau, Ingrid and Svoboda, Karel and Zador, Anthony M} } @article {3931, title = {Functional imaging of hippocampal place cells at cellular resolution during virtual navigation.}, journal = {Nature Neuroscience}, volume = {13}, year = {2010}, month = {2010 Nov}, pages = {1433-40}, abstract = {

Spatial navigation is often used as a behavioral task in studies of the neuronal circuits that underlie cognition, learning and memory in rodents. The combination of in vivo microscopy with genetically encoded indicators has provided an important new tool for studying neuronal circuits, but has been technically difficult to apply during navigation. Here we describe methods for imaging the activity of neurons in the CA1 region of the hippocampus with subcellular resolution in behaving mice. Neurons that expressed the genetically encoded calcium indicator GCaMP3 were imaged through a chronic hippocampal window. Head-restrained mice performed spatial behaviors in a setup combining a virtual reality system and a custom-built two-photon microscope. We optically identified populations of place cells and determined the correlation between the location of their place fields in the virtual environment and their anatomical location in the local circuit. The combination of virtual reality and high-resolution functional imaging should allow a new generation of studies to investigate neuronal circuit dynamics during behavior.

}, keywords = {Action Potentials, Animals, Calcium, Cerebral Cortex, Computer-Assisted, Dendrites, Genetic, Hippocampus, Image Processing, Inbred C57BL, Male, Membrane Potentials, Mice, Neurons, Nonlinear Dynamics, Patch-Clamp Techniques, Space Perception, Spatial Behavior, Synapsins, Transduction, User-Computer Interface}, issn = {1546-1726}, doi = {10.1038/nn.2648}, author = {Dombeck, Daniel A and Harvey, Christopher D and Tian, Lin and Looger, Loren L and Tank, David W} } @article {4296, title = {The functional properties of barrel cortex neurons projecting to the primary motor cortex.}, journal = {The Journal of Neuroscience}, volume = {30}, year = {2010}, month = {2010 Mar 24}, pages = {4256-60}, abstract = {

Nearby neurons, sharing the same locations within the mouse whisker map, can have dramatically distinct response properties. To understand the significance of this diversity, we studied the relationship between the responses of individual neurons and their projection targets in the mouse barrel cortex. Neurons projecting to primary motor cortex (MI) or secondary somatosensory area (SII) were labeled with red fluorescent protein (RFP) using retrograde viral infection. We used in vivo two-photon Ca(2+) imaging to map the responses of RFP-positive and neighboring L2/3 neurons to whisker deflections. Neurons projecting to MI displayed larger receptive fields compared with other neurons, including those projecting to SII. Our findings support the view that intermingled neurons in primary sensory areas send specific stimulus features to different parts of the brain.

}, keywords = {Afferent Pathways, Aniline Compounds, Animals, Brain Mapping, Calcium, Evoked Potentials, Functional Laterality, Genetic, Luminescent Proteins, Mice, Motor Cortex, Neurons, Newborn, Physical Stimulation, Somatosensory, Somatosensory Cortex, Transduction, Vibrissae, Xanthenes}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3774-09.2010}, author = {Sato, Takashi R and Svoboda, Karel} } @article {4402, title = {Genome sequence of the pea aphid Acyrthosiphon pisum.}, journal = {PLoS Biology}, volume = {8}, year = {2010}, month = {2010 Feb}, pages = {e1000313}, abstract = {

Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.

}, keywords = {Animals, Aphids, Buchnera, Gene Transfer, Genome, Horizontal, Insect, Symbiosis}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1000313} } @article {6338, title = {GPU-enabled FREALIGN: accelerating single particle 3D reconstruction and refinement in Fourier space on graphics processors.}, journal = {Journal of Structural Biology}, volume = {172}, year = {2010}, month = {2010 Dec}, pages = {407-12}, abstract = {

Among all the factors that determine the resolution of a 3D reconstruction by single particle electron cryo-microscopy (cryoEM), the number of particle images used in the dataset plays a major role. More images generally yield better resolution, assuming the imaged protein complex is conformationally and compositionally homogeneous. To facilitate processing of very large datasets, we modified the computer program, FREALIGN, to execute the computationally most intensive procedures on Graphics Processing Units (GPUs). Using the modified program, the execution speed increased between 10 and 240-fold depending on the task performed by FREALIGN. Here we report the steps necessary to parallelize critical FREALIGN subroutines and evaluate its performance on computers with multiple GPUs.

}, keywords = {Computer-Assisted, Cryoelectron Microscopy, Image Processing, Imaging, Three-Dimensional}, issn = {1095-8657}, doi = {10.1016/j.jsb.2010.06.010}, author = {Li, Xueming and Grigorieff, Nikolaus and Cheng, Yifan} } @article {46410, title = {The heparin-binding domain of HB-EGF mediates localization to sites of cell-cell contact and prevents HB-EGF proteolytic release.}, journal = {Journal of Cell Science}, volume = {123}, year = {2010}, month = {2010 Jul 1}, pages = {2308-18}, abstract = {

Heparin-binding EGF-like growth factor (HB-EGF) is a ligand for EGF receptor (EGFR) and possesses the ability to signal in juxtacrine, autocrine and/or paracrine mode, with these alternatives being governed by the degree of proteolytic release of the ligand. Although the spatial range of diffusion of released HB-EGF is restricted by binding heparan-sulfate proteoglycans (HSPGs) in the extracellular matrix and/or cellular glycocalyx, ascertaining mechanisms governing non-released HB-EGF localization is also important for understanding its effects. We have employed a new method for independently tracking the localization of the extracellular EGF-like domain of HB-EGF and the cytoplasmic C-terminus. A striking observation was the absence of the HB-EGF transmembrane pro-form from the leading edge of COS-7 cells in a wound-closure assay; instead, this protein localized in regions of cell-cell contact. A battery of detailed experiments found that this localization derives from a trans interaction between extracellular HSPGs and the HB-EGF heparin-binding domain, and that disruption of this interaction leads to increased release of soluble ligand and a switch in cell phenotype from juxtacrine-induced growth inhibition to autocrine-induced proliferation. Our results indicate that extracellular HSPGs serve to sequester the transmembrane pro-form of HB-EGF at the point of cell-cell contact, and that this plays a role in governing the balance between juxtacrine versus autocrine and paracrine signaling.

}, keywords = {Amino Acid Sequence, Amphiregulin, Animals, Cell Communication, Cell Proliferation, Cercopithecus aethiops, COS Cells, EGF Family of Proteins, Glycoproteins, Heparan Sulfate Proteoglycans, Heparin, Heparin-binding EGF-like Growth Factor, Intercellular Junctions, Intercellular Signaling Peptides and Proteins, Mice, Molecular Sequence Data, Mutation, Peptides, Protein Precursors, Protein Structure, Tertiary}, issn = {1477-9137}, doi = {10.1242/jcs.058321}, author = {Prince, Robin N and Schreiter, Eric R and Zou, Peng and Wiley, H Steven and Ting, Alice Y and Lee, Richard T and Lauffenburger, Douglas A} } @article {4286, title = {Hidden Markov model speed heuristic and iterative HMM search procedure.}, journal = {BMC Bioinformatics}, volume = {11}, year = {2010}, month = {2010}, pages = {431}, abstract = {

Profile hidden Markov models (profile-HMMs) are sensitive tools for remote protein homology detection, but the main scoring algorithms, Viterbi or Forward, require considerable time to search large sequence databases.

}, keywords = {Algorithms, Artificial Intelligence, Base Sequence, Databases, Markov Chains, Protein, Proteins, Sequence Alignment, Software}, issn = {1471-2105}, doi = {10.1186/1471-2105-11-431}, author = {Johnson, L Steven and Eddy, Sean R. and Portugaly, Elon} } @article {5691, title = {A high-level 3D visualization API for Java and ImageJ.}, journal = {BMC Bioinformatics}, volume = {11}, year = {2010}, month = {2010}, pages = {274}, abstract = {

Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set.

}, keywords = {Automated, Computer Graphics, Computer-Assisted, Confocal, Image Interpretation, Imaging, Microscopy, Pattern Recognition, Programming Languages, Software, Three-Dimensional}, issn = {1471-2105}, doi = {10.1186/1471-2105-11-274}, author = {Schmid, Benjamin and Schindelin, Johannes and Cardona, Albert and Longair, Mark and Heisenberg, Martin.} } @article {2751, title = {Identification of genes controlled by LMX1B in E13.5 mouse limbs.}, journal = {Developmental Dynamics: An Official Publication of the American Association of Anatomists}, volume = {239}, year = {2010}, month = {2010 Aug}, pages = {2246-55}, abstract = {

During limb development, the dorsal limb mesenchyme expression of the transcription factor LMX1B is required for dorsoventral limb patterning. In mice, Lmx1b mutations result in the mirror-image duplication of ventral limb structures and loss of dorsal limb structures. Heterozygous LMX1B mutations in humans cause the Nail-Patella Syndrome characterized by limb, kidney, and eye developmental defects. We used DNA microarrays to compare the mRNAs in E13.5 mouse Lmx1b mutant and wild-type limbs. We report 14 genes that require Lmx1b for their normal expression in the dorsal limb or the restriction of their expression to the ventral limb.

}, keywords = {Animals, Body Patterning, Extremities, Gene Expression, Genes, Homeodomain Proteins, Humans, Messenger, Mice, Oligonucleotide Array Sequence Analysis, RNA, Transcription Factors}, issn = {1097-0177}, doi = {10.1002/dvdy.22357}, author = {Gu, Wendy X W and Kania, Artur} } @article {5689, title = {Identifying neuronal lineages of Drosophila by sequence analysis of axon tracts.}, journal = {The Journal of Neuroscience}, volume = {30}, year = {2010}, month = {2010 Jun 2}, pages = {7538-53}, abstract = {

The Drosophila brain is formed by an invariant set of lineages, each of which is derived from a unique neural stem cell (neuroblast) and forms a genetic and structural unit of the brain. The task of reconstructing brain circuitry at the level of individual neurons can be made significantly easier by assigning neurons to their respective lineages. In this article we address the automation of neuron and lineage identification. We focused on the Drosophila brain lineages at the larval stage when they form easily recognizable secondary axon tracts (SATs) that were previously partially characterized. We now generated an annotated digital database containing all lineage tracts reconstructed from five registered wild-type brains, at higher resolution and including some that were previously not characterized. We developed a method for SAT structural comparisons based on a dynamic programming approach akin to nucleotide sequence alignment and a machine learning classifier trained on the annotated database of reference SATs. We quantified the stereotypy of SATs by measuring the residual variability of aligned wild-type SATs. Next, we used our method for the identification of SATs within wild-type larval brains, and found it highly accurate (93-99\%). The method proved highly robust for the identification of lineages in mutant brains and in brains that differed in developmental time or labeling. We describe for the first time an algorithm that quantifies neuronal projection stereotypy in the Drosophila brain and use the algorithm for automatic neuron and lineage recognition.

}, keywords = {Algorithms, Animals, Automatic Data Processing, Axons, Brain, Brain Mapping, Caspase 3, Cell Lineage, Computer-Assisted, Confocal, Dendrites, Drosophila, Drosophila Proteins, Embryo, Genetically Modified, Green Fluorescent Proteins, Image Processing, Microscopy, Models, Neurological, Neurons, Nonmammalian, Reproducibility of Results, Software}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0186-10.2010}, author = {Cardona, Albert and Saalfeld, Stephan and Arganda, Ignacio and Pereanu, Wayne and Schindelin, Johannes and Hartenstein, Volker.} } @article {47676, title = {Imaging: visualizing the possibilities.}, journal = {Journal of cell science}, volume = {123}, year = {2010}, month = {2010 Nov 1}, pages = {3619-20}, keywords = {Diagnostic Imaging, Fluorescence Recovery After Photobleaching, Fluorescence Resonance Energy Transfer, Green Fluorescent Proteins, Humans, Image Enhancement, Molecular Probes, Photoaffinity Labels}, issn = {1477-9137}, doi = {10.1242/jcs081539}, author = {Lippincott-Schwartz, Jennifer} } @article {1344, title = {Impact of spikelets on hippocampal CA1 pyramidal cell activity during spatial exploration.}, journal = {Science}, volume = {327}, year = {2010}, month = {2010 Jan 22}, pages = {474-7}, abstract = {

In vivo intracellular recordings of hippocampal neurons reveal the occurrence of fast events of small amplitude called spikelets or fast prepotentials. Because intracellular recordings have been restricted to anesthetized or head-fixed animals, it is not known how spikelet activity contributes to hippocampal spatial representations. We addressed this question in CA1 pyramidal cells by using in vivo whole-cell recording in freely moving rats. We observed a high incidence of spikelets that occurred either in isolation or in bursts and could drive spiking as fast prepotentials of action potentials. Spikelets strongly contributed to spiking activity, driving approximately 30\% of all action potentials. CA1 pyramidal cell firing and spikelet activity were comodulated as a function of the animal{\textquoteright}s location in the environment. We conclude that spikelets have a major impact on hippocampal activity during spatial exploration.

}, keywords = {Action Potentials, Animals, CA1 Region, Exploratory Behavior, Hippocampal, Male, Maze Learning, Patch-Clamp Techniques, Pyramidal Cells, Rats, Space Perception, Wistar}, issn = {1095-9203}, doi = {10.1126/science.1182773}, author = {Epsztein, J{\'e}r{\^o}me and Lee, Albert K and Chorev, Edith and Brecht, Michael} } @article {48167, title = {Improving deformable surface meshes through omni-directional displacements and MRFs.}, journal = {Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention}, volume = {13}, year = {2010}, month = {2010}, pages = {227-34}, abstract = {

Deformable surface models are often represented as triangular meshes in image segmentation applications. For a fast and easily regularized deformation onto the target object boundary, the vertices of the mesh are commonly moved along line segments (typically surface normals). However, in case of high mesh curvature, these lines may intersect with the target boundary at "non-corresponding" positions, or even not at all. Consequently, certain deformations cannot be achieved. We propose an approach that allows each vertex to move not only along a line segment, but within a surrounding sphere. We achieve globally regularized deformations via Markov Random Field optimization. We demonstrate the potential of our approach with experiments on synthetic data, as well as an evaluation on 2 x 106 coronoid processes of the mandible in Cone-Beam CTs, and 56 coccyxes (tailbones) in low-resolution CTs.

}, keywords = {Algorithms, Computer Simulation, Cone-Beam Computed Tomography, Finite Element Analysis, Humans, Imaging, Three-Dimensional, Models, Biological, Radiographic Image Enhancement, Radiographic Image Interpretation, Computer-Assisted, Reproducibility of Results, Sensitivity and Specificity}, author = {Kainmueller, D and Lamecker, H and Seim, H and Zachow, S and Hege, H C} } @article {1245, title = {Increasing depth resolution of electron microscopy of neural circuits using sparse tomographic reconstruction.}, journal = {Computer Vision and Pattern Recognition (CVPR)}, year = {2010}, month = {2010}, pages = {1767-74}, issn = {1063-6919}, doi = {10.1109/CVPR.2010.5539846}, author = {Veeraraghavan, Ashok and Genkin, Alex V and Vitaladevuni, Shiv and Scheffer, Lou and Xu, CShan and Hess, Harald and Fetter, Richard and Cantoni, Marco and Knott, Graham and Chklovskii, Dmitri B} } @article {5687, title = {An integrated micro- and macroarchitectural analysis of the Drosophila brain by computer-assisted serial section electron microscopy.}, journal = {PLoS Biology}, volume = {8}, year = {2010}, month = {2010}, abstract = {

The analysis of microcircuitry (the connectivity at the level of individual neuronal processes and synapses), which is indispensable for our understanding of brain function, is based on serial transmission electron microscopy (TEM) or one of its modern variants. Due to technical limitations, most previous studies that used serial TEM recorded relatively small stacks of individual neurons. As a result, our knowledge of microcircuitry in any nervous system is very limited. We applied the software package TrakEM2 to reconstruct neuronal microcircuitry from TEM sections of a small brain, the early larval brain of Drosophila melanogaster. TrakEM2 enables us to embed the analysis of the TEM image volumes at the microcircuit level into a light microscopically derived neuro-anatomical framework, by registering confocal stacks containing sparsely labeled neural structures with the TEM image volume. We imaged two sets of serial TEM sections of the Drosophila first instar larval brain neuropile and one ventral nerve cord segment, and here report our first results pertaining to Drosophila brain microcircuitry. Terminal neurites fall into a small number of generic classes termed globular, varicose, axiform, and dendritiform. Globular and varicose neurites have large diameter segments that carry almost exclusively presynaptic sites. Dendritiform neurites are thin, highly branched processes that are almost exclusively postsynaptic. Due to the high branching density of dendritiform fibers and the fact that synapses are polyadic, neurites are highly interconnected even within small neuropile volumes. We describe the network motifs most frequently encountered in the Drosophila neuropile. Our study introduces an approach towards a comprehensive anatomical reconstruction of neuronal microcircuitry and delivers microcircuitry comparisons between vertebrate and insect neuropile.

}, keywords = {Animals, Brain, Computer-Assisted, Drosophila melanogaster, Electron, Humans, Image Processing, Imaging, Microscopy, Neurons, Neuropil, Software, Synapses, Three-Dimensional, Transmission}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1000502}, author = {Cardona, Albert and Saalfeld, Stephan and Preibisch, Stephan and Schmid, Benjamin and Cheng, Anchi and Pulokas, Jim and Tomancak, Pavel and Hartenstein, Volker.} } @article {3635, title = {Interactions of the transmembrane polymeric rings of the Salmonella enterica serovar Typhimurium type III secretion system.}, journal = {mBio}, volume = {1}, year = {2010}, month = {2010}, abstract = {

The type III secretion system (T3SS) is an interspecies protein transport machine that plays a major role in interactions of Gram-negative bacteria with animals and plants by delivering bacterial effector proteins into host cells. T3SSs span both membranes of Gram-negative bacteria by forming a structure of connected oligomeric rings termed the needle complex (NC). Here, the localization of subunits in the Salmonella enterica serovar Typhimurium T3SS NC were probed via mass spectrometry-assisted identification of chemical cross-links in intact NC preparations. Cross-links between amino acids near the amino terminus of the outer membrane ring component InvG and the carboxyl terminus of the inner membrane ring component PrgH and between the two inner membrane components PrgH and PrgK allowed for spatial localization of the three ring components within the electron density map structures of NCs. Mutational and biochemical analysis demonstrated that the amino terminus of InvG and the carboxyl terminus of PrgH play a critical role in the assembly and function of the T3SS apparatus. Analysis of an InvG mutant indicates that the structure of the InvG oligomer can affect the switching of the T3SS substrate to translocon and effector components. This study provides insights into how structural organization of needle complex base components promotes T3SS assembly and function.

}, keywords = {Bacterial Proteins, Membrane Transport Proteins, Models, Molecular, Protein Binding, Protein Multimerization, Salmonella typhimurium}, issn = {2150-7511}, doi = {10.1128/mBio.00158-10}, author = {Sanowar, Sarah and Singh, Pragya and Pfuetzner, Richard A and Andr{\'e}, Ingemar and Zheng, Hongjin and Spreter, Thomas and Strynadka, Natalie C J and Gonen, Tamir and Baker, David and Goodlett, David R and Miller, Samuel I} } @proceedings {46792, title = {Into ImgLib{\textemdash}Generic image processing in Java}, year = {2010}, month = {2012 Oct 27}, address = {Mondorf-les-Bains, Luxembourg}, abstract = {

The purpose of ImgLib, a Generic Java Image Processing Library, is to provide an abstract framework enabling Java developers to design and implement data processing algorithms without having to consider dimensionality, type of data (e. g. byte, float, complex float), or strategies for data access (e. g. linear arrays, cells, paged cells). This kind of programming has significant advantages over the classical way. An algorithm written once for a certain class of Type will potentially run on any compatible Type, even if it does not exist yet. Same applies for data access strategies and the number of dimensions.
We achieve this abstraction by accessing data through Iterators and Type interfaces. Iterators guarantee efficient traversal through pixels depending on whether random coordinate access is required or just all pixels have to be visited once, whether real or integer coordinates are accessed, whether coordinates outside of image boundaries are accessed or not. Type interfaces define the supported operators on pixel values (like basic algebra) and hide the underlying basic type from algorithm implementation.

}, author = {Preibisch, Stephan and Tomancak, Pavel and Saalfeld, Stephan} } @article {2785, title = {Ion trap mass analysis at high pressure: an experimental characterization.}, journal = {Journal of Mass Spectrometry}, volume = {45}, year = {2010}, month = {2010 Jan}, pages = {26-34}, abstract = {

In recent years, it has become increasingly interesting to understand the performance of mass spectrometers at pressures much higher than those employed with conventional operating conditions. This interest has been driven by several influences, including demand for the development of reduced-power miniature mass spectrometers, desire for improved ion transfer into and through mass spectrometers, enhanced-yield preparative mass separations, and mass filtering at the atmospheric pressure interface. In this study, an instrument was configured to allow for the performance characterization of a rectilinear ion trap (RIT) at pressures up to 50 mtorr with air used as the buffer gas. The mass analysis efficiency, mass resolution, isolation efficiency, and collision-induced dissociation (CID) efficiency were evaluated at pressures ranging from 1 to 50 mtorr. The extent of degradation of mass resolution, isolation efficiency and ion stability as functions of pressure were characterized. Also, the optimal resonance ejection conditions were obtained at various pressures. Operations at 50 mtorr demonstrated improved CID efficiency in addition to peak widths of 2 and 5 m/z units (full width at half-maximum, FWHM) for protonated caffeine (m/z 195) and Ultramark (m/z 1521) respectively.

}, keywords = {Equipment Design, Ions, Mass Spectrometry, Pressure, Proteins}, issn = {1096-9888}, doi = {10.1364/AO.50.001792}, author = {Song, Qingyu and Xu, Wei and Smith, Scott A and Gao, Liang and Chappell, William J and Cooks, R Graham and Ouyang, Zheng} } @article {6346, title = {IP3 receptor sensitization during in vivo amphetamine experience enhances NMDA receptor plasticity in dopamine neurons of the ventral tegmental area.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {30}, year = {2010}, month = {2010 May 12}, pages = {6689-99}, abstract = {

Synaptic plasticity in the mesolimbic dopamine (DA) system is critically involved in reward-based conditioning and the development of drug addiction. Ca2+ signals triggered by postsynaptic action potentials (APs) drive the induction of synaptic plasticity in the CNS. However, it is not clear how AP-evoked Ca2+ signals and the resulting synaptic plasticity are altered during in vivo exposure to drugs of abuse. We have recently described long-term potentiation (LTP) of NMDA receptor (NMDAR)-mediated transmission onto DA neurons that is induced in a manner dependent on bursts of APs. LTP induction requires amplification of burst-evoked Ca2+ signals by preceding activation of metabotropic glutamate receptors (mGluRs) generating inositol 1,4,5-trisphosphate (IP3). In this study, using brain slices prepared from male rats, we show that repeated in vivo exposure to the psychostimulant amphetamine (5 mg/kg, i.p., 3-7 d) upregulates mGluR-dependent facilitation of burst-evoked Ca2+ signals in DA neurons of the ventral tegmental area (VTA). Protein kinase A (PKA)-induced sensitization of IP3 receptors mediates this upregulation of mGluR action. As a consequence, NMDAR-mediated transmission becomes more susceptible to LTP induction after repeated amphetamine exposure. We have also found that the magnitude of amphetamine-conditioned place preference (CPP) in behaving rats correlates with the magnitude of mGluR-dependent Ca2+ signal facilitation measured in VTA slices prepared from these rats. Furthermore, the development of amphetamine CPP is significantly attenuated by intra-VTA infusion of the PKA inhibitor H89. We propose that enhancement of mGluR-dependent NMDAR plasticity in the VTA may promote the learning of environmental stimuli repeatedly associated with amphetamine experience.

}, keywords = {4, 5-Trisphosphate Receptors, Amphetamine, Animals, Calcium, Central Nervous System Stimulants, Classical, Conditioning, Cyclic AMP-Dependent Protein Kinases, Dopamine, Inositol 1, Isoquinolines, Long-Term Potentiation, Male, N-Methyl-D-Aspartate, Neurons, Protein Kinase Inhibitors, Rats, Receptors, Space Perception, Sprague-Dawley, Sulfonamides, Synaptic Transmission, Ventral Tegmental Area}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4453-09.2010}, author = {Ahn, Kee-Chan and Bernier, Brian E and Harnett, Mark T and Morikawa, Hitoshi} } @article {6394, title = {Juvenile hormone action requires paralogous genes in Drosophila melanogaster.}, journal = {Genetics}, volume = {185}, year = {2010}, month = {2010}, pages = {1327-36}, author = {Baumann, Aaron and Barry, J and Wang, S and WIlson, TG} } @article {4288, title = {Learning-related fine-scale specificity imaged in motor cortex circuits of behaving mice.}, journal = {Nature}, volume = {464}, year = {2010}, month = {2010 Apr 22}, pages = {1182-6}, abstract = {

Cortical neurons form specific circuits, but the functional structure of this microarchitecture and its relation to behaviour are poorly understood. Two-photon calcium imaging can monitor activity of spatially defined neuronal ensembles in the mammalian cortex. Here we applied this technique to the motor cortex of mice performing a choice behaviour. Head-fixed mice were trained to lick in response to one of two odours, and to withhold licking for the other odour. Mice routinely showed significant learning within the first behavioural session and across sessions. Microstimulation and trans-synaptic tracing identified two non-overlapping candidate tongue motor cortical areas. Inactivating either area impaired voluntary licking. Imaging in layer 2/3 showed neurons with diverse response types in both areas. Activity in approximately half of the imaged neurons distinguished trial types associated with different actions. Many neurons showed modulation coinciding with or preceding the action, consistent with their involvement in motor control. Neurons with different response types were spatially intermingled. Nearby neurons (within approximately 150 mum) showed pronounced coincident activity. These temporal correlations increased with learning within and across behavioural sessions, specifically for neuron pairs with similar response types. We propose that correlated activity in specific ensembles of functionally related neurons is a signature of learning-related circuit plasticity. Our findings reveal a fine-scale and dynamic organization of the frontal cortex that probably underlies flexible behaviour.

}, keywords = {Animal, Animals, Axonal Transport, Behavior, Chemical, Choice Behavior, Inbred C57BL, Learning, Male, Mice, Motor Cortex, Motor Neurons, Neural Pathways, Odors, Pyramidal Cells, Reward, Stimulation, Time Factors, Tongue}, issn = {1476-4687}, doi = {10.1038/nature08897}, author = {Komiyama, Takaki and Sato, Takashi R and O{\textquoteright}Connor, Daniel H and Zhang, Ying-Xin and Huber, Daniel and Hooks, Bryan M and Gabitto, Mariano and Svoboda, Karel} } @article {4299, title = {Light-avoidance-mediating photoreceptors tile the Drosophila larval body wall.}, journal = {Nature}, volume = {468}, year = {2010}, month = {2010 Dec 16}, pages = {921-6}, abstract = {

Photoreceptors for visual perception, phototaxis or light avoidance are typically clustered in eyes or related structures such as the Bolwig organ of Drosophila larvae. Unexpectedly, we found that the class IV dendritic arborization neurons of Drosophila melanogaster larvae respond to ultraviolet, violet and blue light, and are major mediators of light avoidance, particularly at high intensities. These class IV dendritic arborization neurons, which are present in every body segment, have dendrites tiling the larval body wall nearly completely without redundancy. Dendritic illumination activates class IV dendritic arborization neurons. These novel photoreceptors use phototransduction machinery distinct from other photoreceptors in Drosophila and enable larvae to sense light exposure over their entire bodies and move out of danger.

}, keywords = {Animal Structures, Animals, Avoidance Learning, Cell Surface, Cells, Cultured, Dermis, Drosophila melanogaster, Drosophila Proteins, Invertebrate, Larva, Light, Light Signal Transduction, Neurons, Photoreceptor Cells, Receptors, TRPC Cation Channels}, issn = {1476-4687}, doi = {10.1038/nature09576}, author = {Xiang, Yang and Yuan, Quan and Vogt, Nina and Looger, Loren L and Jan, Lily Yeh and Jan, Yuh Nung} } @article {5367, title = {Lineage-based connectivity map of the Drosophila brain.}, journal = {Journal of Neurogenetics}, volume = {24}, year = {2010}, month = {2010}, pages = {79}, author = {Hartenstein, Volker and Pereanu, Wayne and Truman, Jim and Cardona, Albert} } @article {782, title = {Lineage-specific effects of Notch/Numb signaling in post-embryonic development of the Drosophila brain.}, journal = {Development}, volume = {137}, year = {2010}, month = {2010 Jan}, pages = {43-51}, abstract = {

Numb can antagonize Notch signaling to diversify the fates of sister cells. We report here that paired sister cells acquire different fates in all three Drosophila neuronal lineages that make diverse types of antennal lobe projection neurons (PNs). Only one in each pair of postmitotic neurons survives into the adult stage in both anterodorsal (ad) and ventral (v) PN lineages. Notably, Notch signaling specifies the PN fate in the vPN lineage but promotes programmed cell death in the missing siblings in the adPN lineage. In addition, Notch/Numb-mediated binary sibling fates underlie the production of PNs and local interneurons from common precursors in the lAL lineage. Furthermore, Numb is needed in the lateral but not adPN or vPN lineages to prevent the appearance of ectopic neuroblasts and to ensure proper self-renewal of neural progenitors. These lineage-specific outputs of Notch/Numb signaling show that a universal mechanism of binary fate decision can be utilized to govern diverse neural sibling differentiations.

}, keywords = {Animals, Apoptosis, Biological, Brain, Developmental, Drosophila, Drosophila Proteins, Gene Expression Regulation, Immunohistochemistry, Juvenile Hormones, Models, Nerve Tissue Proteins, Neurons, Notch, POU Domain Factors, Receptors, Signal Transduction}, issn = {1477-9129}, doi = {10.1242/dev.041699}, author = {Lin, Suewei and Lai, Sen-Lin and Yu, Huang-Hsiang and Chihara, Takahiro and Luo, Liqun and Lee, Tzumin} } @article {47684, title = {Lipids and cholesterol as regulators of traffic in the endomembrane system.}, journal = {Annual review of biophysics}, volume = {39}, year = {2010}, month = {2010}, pages = {559-78}, abstract = {

The endomembrane system of eukaryotic cells uses membrane-enclosed carriers to move diverse macromolecules among different membrane-bound compartments, a requirement for cells to secrete and take up molecules from their environment. Two recycling pathways-biosynthetic and endocytic, each with specific lipid components-make up this system, with the Golgi apparatus mediating transport between the two. Here, we integrate lipid-based mechanisms into the description of this system. A partitioning model of the Golgi apparatus is discussed as a working hypothesis to explain how membrane lipids and proteins that are segregated based on lateral lipid partitioning support the unique composition of the biosynthetic and endocytic recycling pathways in the face of constant trafficking of molecular constituents. We further discuss how computational modeling can allow for interpretation of experimental findings and provide mechanistic insight into these important cellular pathways.

}, keywords = {Animals, Bacteria, Cholesterol, Endocytosis, Golgi Apparatus, Humans, Intracellular Membranes, Lipid Metabolism, Protein Transport}, issn = {1936-1238}, doi = {10.1146/annurev.biophys.093008.131357}, author = {Lippincott-Schwartz, Jennifer and Phair, Robert D} } @article {46616, title = {Lmo4 in the nucleus accumbens regulates cocaine sensitivity.}, journal = {Genes, Brain, and Behavior}, volume = {9}, year = {2010}, month = {2010 Oct}, pages = {817-24}, abstract = {

An estimated 2 million Americans use cocaine, resulting in large personal and societal costs. Discovery of the genetic factors that contribute to cocaine abuse is important for understanding this complex disease. Previously, mutations in the Drosophila LIM-only (dLmo) gene were identified because of their increased behavioral sensitivity to cocaine. Here we show that the mammalian homolog Lmo4, which is highly expressed in brain regions implicated in drug addiction, plays a similar role in cocaine-induced behaviors. Mice with a global reduction in Lmo4 levels show increased sensitivity to the locomotor stimulatory effects of cocaine upon chronic cocaine administration. This effect is reproduced with downregulation of Lmo4 in the nucleus accumbens by RNA interference. Thus, Lmo genes play conserved roles in regulating the behavioral effects of cocaine in invertebrate and mammalian models of drug addiction.

}, keywords = {Adaptor Proteins, Signal Transducing, Animals, Behavior, Animal, beta-Galactosidase, Cells, Cultured, Cloning, Molecular, Cocaine, Dendritic Spines, Dopamine Uptake Inhibitors, Gene Expression, Homeodomain Proteins, Immunohistochemistry, Lentivirus, LIM Domain Proteins, Male, Mice, Mice, Inbred C57BL, Microdissection, Motor Activity, Mutagenesis, Insertional, Nucleus Accumbens, Reverse Transcriptase Polymerase Chain Reaction, RNA, RNA Interference, Stereotaxic Techniques, Transcription Factors}, issn = {1601-183X}, doi = {10.1111/j.1601-183X.2010.00620.x}, author = {Lasek, A W and Kapfhamer, D and Kharazia, V and Gesch, J and Giorgetti, F and Heberlein, U} } @article {47677, title = {The long road: peering into live cells.}, journal = {Nature cell biology}, volume = {12}, year = {2010}, month = {2010 Oct}, pages = {918}, keywords = {Cell Biology, Cell Survival, Green Fluorescent Proteins, History, 20th Century, History, 21st Century, Microscopy, Fluorescence, Photobleaching, Protein Transport, Research Personnel}, issn = {1476-4679}, doi = {10.1038/ncb1010-918}, author = {Lippincott-Schwartz, Jennifer} } @article {3843, title = {Machines that learn to segment images: a crucial technology for connectomics.}, journal = {Current Opinion in Neurobiology}, volume = {20}, year = {2010}, month = {2010 Oct}, pages = {653-66}, abstract = {

Connections between neurons can be found by checking whether synapses exist at points of contact, which in turn are determined by neural shapes. Finding these shapes is a special case of image segmentation, which is laborious for humans and would ideally be performed by computers. New metrics properly quantify the performance of a computer algorithm using its disagreement with {\textquoteright}true{\textquoteright} segmentations of example images. New machine learning methods search for segmentation algorithms that minimize such metrics. These advances have reduced computer errors dramatically. It should now be faster for a human to correct the remaining errors than to segment an image manually. Further reductions in human effort are expected, and crucial for finding connectomes more complex than that of Caenorhabditis elegans.

}, keywords = {Algorithms, Animals, Artificial Intelligence, Computer-Assisted, Electron, Humans, Image Processing, Microscopy, Nanotechnology, Neurobiology}, issn = {1873-6882}, doi = {10.1016/j.conb.2010.07.004}, author = {Jain, Viren and Seung, Hyunjune Sebastian and Turaga, Srinivas C} } @article {2290, title = {Malaria severity and human nitric oxide synthase type 2 (NOS2) promoter haplotypes.}, journal = {Human Genetics}, volume = {127}, year = {2010}, month = {2010 Feb}, pages = {163-82}, abstract = {

Nitric oxide (NO) mediates host resistance to severe malaria and other infectious diseases. NO production and mononuclear cell expression of the NO producing enzyme-inducible nitric oxide synthase (NOS2) have been associated with protection from severe falciparum malaria. The purpose of this study was to identify single nucleotide polymorphisms (SNPs) and haplotypes in the NOS2 promoter, to identify associations of these haplotypes with malaria severity and to test the effects of these polymorphisms on promoter activity. We identified 34 SNPs in the proximal 7.3 kb region of the NOS2 promoter and inferred NOS2 promoter haplotypes based on genotyping 24 of these SNPs in a population of Tanzanian children with and without cerebral malaria. We identified 71 haplotypes; 24 of these haplotypes comprised 82\% of the alleles. We determined whether NOS2 promoter haplotypes were associated with malaria severity in two groups of subjects from Dar es Salaam (N = 185 and N = 250) and in an inception cohort of children from Muheza-Tanga, Tanzania (N = 883). We did not find consistent associations of NOS2 promoter haplotypes with malaria severity or malarial anemia, although interpretation of these results was potentially limited by the sample size of each group. Furthermore, cytokine-induced NOS2 promoter activity determined using luciferase reporter constructs containing the proximal 7.3 kb region of the NOS2 promoter and the G-954C or C-1173T SNPs did not differ from NOS2 promoter constructs that lacked these polymorphisms. Taken together, these studies suggest that the relationship between NOS2 promoter polymorphisms and malaria severity is more complex than previously described.

}, keywords = {Alleles, Base Sequence, Cell Line, Child, DNA, Gene Frequency, Genetic, Genetic Heterogeneity, Genotype, Haplotypes, Humans, Infant, Kenya, Linkage Disequilibrium, Malaria, Molecular Sequence Data, Mutation, Nitric Oxide Synthase Type II, Nucleic Acid, Polymorphism, Preschool, Promoter Regions, Sequence Analysis, Sequence Homology, Severity of Illness Index, Single Nucleotide, Tanzania, Tumor}, issn = {1432-1203}, doi = {10.1007/s00439-009-0753-3}, author = {Levesque, Marc C and Hobbs, Maurine R and O{\textquoteright}Loughlin, Charles W and Chancellor, Jennifer A and Chen, Youwei and Tkachuk, Ariana N and Booth, Jennifer and Patch, Kistie B and Allgood, Sallie and Pole, Ann R and Fernandez, Carolyn A and Mwaikambo, Esther D and Mutabingwa, Theonest K and Fried, Michal and Sorensen, Bess and Duffy, Patrick E and Granger, Donald L and Anstey, Nicholas M and Weinberg, J Brice} } @article {4406, title = {Michael Akam and the rise of evolutionary developmental biology.}, journal = {The International Journal of Developmental Biology}, volume = {54}, year = {2010}, month = {2010}, pages = {561-5}, abstract = {

Michael Akam has been awarded the 2007 Kowalevsky medal for his many research accomplishments in the area of evolutionary developmental biology. We highlight three tributaries of Michaels contribution to evolutionary developmental biology. First, he has made major contributions to our understanding of development of the fruit fly, Drosophila melanogaster. Second, he has maintained a consistent focus on several key problems in evolutionary developmental biology, including the evolving role of Hox genes in arthropods and, more recently, the evolution of segmentation mechanisms. Third, Michael has written a series of influential reviews that have integrated progress in developmental biology into an evolutionary perspective. Michael has also made a large impact on the field through his effective mentorship style, his selfless promotion of younger colleagues, and his leadership of the University Museum of Zoology at Cambridge and the European community of evolutionary developmental biologists.

}, keywords = {20th Century, 21st Century, Animals, Arthropods, Awards and Prizes, Biological Evolution, Developmental Biology, Drosophila melanogaster, England, Genes, History, Homeobox, Research}, issn = {1696-3547}, doi = {10.1387/ijdb.092908ds}, author = {Stern, David L and Dawes-Hoang, Rachel E} } @article {2540, title = {Midline crossing by gustatory receptor neuron axons is regulated by fruitless, doublesex and the roundabout receptors.}, journal = {Development}, volume = {137}, year = {2010}, month = {2010 Jan}, pages = {323-32}, abstract = {

Although nervous system sexual dimorphisms are known in many species, relatively little is understood about the molecular mechanisms generating these dimorphisms. Recent findings in Drosophila provide the tools for dissecting how neurogenesis and neuronal differentiation are modulated by the Drosophila sex-determination regulatory genes to produce nervous system sexual dimorphisms. Here we report studies aimed at illuminating the basis of the sexual dimorphic axonal projection patterns of foreleg gustatory receptor neurons (GRNs): only in males do GRN axons project across the midline of the ventral nerve cord. We show that the sex determination genes fruitless (fru) and doublesex (dsx) both contribute to establishing this sexual dimorphism. Male-specific Fru (Fru(M)) acts in foreleg GRNs to promote midline crossing by their axons, whereas midline crossing is repressed in females by female-specific Dsx (Dsx(F)). In addition, midline crossing by these neurons might be promoted in males by male-specific Dsx (Dsx(M)). Finally, we (1) demonstrate that the roundabout (robo) paralogs also regulate midline crossing by these neurons, and (2) provide evidence that Fru(M) exerts its effect on midline crossing by directly or indirectly regulating Robo signaling.

}, keywords = {Animals, Axons, Cell Surface, Confocal, DNA-Binding Proteins, Drosophila melanogaster, Drosophila Proteins, Female, Immunologic, Male, Microscopy, Nerve Tissue Proteins, Neurons, Receptors, Sex Characteristics, Transcription Factors}, issn = {1477-9129}, doi = {10.1242/dev.045047}, author = {Mellert, David J and Knapp, Jon-Michael and Manoli, Devanand S and Meissner, Geoffrey W and Baker, Bruce S} } @article {47681, title = {Mitochondria supply membranes for autophagosome biogenesis during starvation.}, journal = {Cell}, volume = {141}, year = {2010}, month = {2010 May 14}, pages = {656-67}, abstract = {

Starvation-induced autophagosomes engulf cytosol and/or organelles and deliver them to lysosomes for degradation, thereby resupplying depleted nutrients. Despite advances in understanding the molecular basis of this process, the membrane origin of autophagosomes remains unclear. Here, we demonstrate that, in starved cells, the outer membrane of mitochondria participates in autophagosome biogenesis. The early autophagosomal marker, Atg5, transiently localizes to punctae on mitochondria, followed by the late autophagosomal marker, LC3. The tail-anchor of an outer mitochondrial membrane protein also labels autophagosomes and is sufficient to deliver another outer mitochondrial membrane protein, Fis1, to autophagosomes. The fluorescent lipid NBD-PS (converted to NBD-phosphotidylethanolamine in mitochondria) transfers from mitochondria to autophagosomes. Photobleaching reveals membranes of mitochondria and autophagosomes are transiently shared. Disruption of mitochondria/ER connections by mitofusin2 depletion dramatically impairs starvation-induced autophagy. Mitochondria thus play a central role in starvation-induced autophagy, contributing membrane to autophagosomes.

}, keywords = {Animals, Cell Line, Cell Physiological Phenomena, Culture Media, Membrane Proteins, Mitochondria, Mitochondrial Membranes, Mitochondrial Proteins, Phagosomes, Rats}, issn = {1097-4172}, doi = {10.1016/j.cell.2010.04.009}, author = {Hailey, Dale W and Rambold, Angelika S and Satpute-Krishnan, Prasanna and Mitra, Kasturi and Sougrat, Rachid and Kim, Peter K and Lippincott-Schwartz, Jennifer} } @conference {48181, title = {Model-based auto-segmentation of knee bones and cartilage in MRI data.}, booktitle = {Medical Image Analysis for the Clinic - A Grand Challenge, MICCAI 2010, the 13th International Conference on Medical Image Computing and Computer Assisted Intervention}, year = {2010}, month = {2010 Sep 24}, address = {Beijing, China}, abstract = {

We present a method for fully automatic segmentation of the bones and cartilages of the human knee from MRI data. Based on statistical shape models and graph-based optimization, first the femoral and tibial bone surfaces are reconstructed. Starting from the bone sur- faces the cartilages are segmented simultaneously with a multi object technique using prior knowledge on the variation of cartilage thickness. We validate our method on 40 clinical MRI datasets acquired before knee replacement.\ 

}, url = {http://www.ski10.org/data/2010-11-09-1131.pdf}, author = {Seim, Heiko and Kainmueller, Dagmar and Lamecker, Hans and Bindernagel, Matthias and Malinowski, Jana and Zachow, Stefan} } @article {2677, title = {Molecular mechanisms of corticosteroid synergy with thyroid hormone during tadpole metamorphosis.}, journal = {General and Comparative Endocrinology}, volume = {168}, year = {2010}, month = {2010 Sep 1}, pages = {209-19}, abstract = {

Corticosteroids (CS) act synergistically with thyroid hormone (TH) to accelerate amphibian metamorphosis. Earlier studies showed that CS increase nuclear 3,5,3{\textquoteright}-triiodothyronine (T(3)) binding capacity in tadpole tail, and 5{\textquoteright} deiodinase activity in tadpole tissues, increasing the generation of T(3) from thyroxine (T(4)). In the present study we investigated CS synergy with TH by analyzing expression of key genes involved in TH and CS signaling using tadpole tail explant cultures, prometamorphic tadpoles, and frog tissue culture cells (XTC-2 and XLT-15). Treatment of tail explants with T(3) at 100 nM, but not at 10 nM caused tail regression. Corticosterone (CORT) at three doses (100, 500 and 3400 nM) had no effect or increased tail size. T(3) at 10 nM plus CORT caused tails to regress similar to 100 nM T(3). Thyroid hormone receptor beta (TRbeta) mRNA was synergistically upregulated by T(3) plus CORT in tail explants, tail and brain in vivo, and tissue culture cells. The activating 5{\textquoteright} deiodinase type 2 (D2) mRNA was induced by T(3) and CORT in tail explants and tail in vivo. Thyroid hormone increased expression of glucocorticoid (GR) and mineralocorticoid receptor (MR) mRNAs. Our findings support that the synergistic actions of TH and CS in metamorphosis occur at the level of expression of genes for TRbeta and D2, enhancing tissue sensitivity to TH. Concurrently, TH enhances tissue sensitivity to CS by upregulating GR and MR. Environmental stressors can modulate the timing of tadpole metamorphosis in part by CS enhancing the response of tadpole tissues to the actions of TH.

}, keywords = {Adrenal Cortex Hormones, Animals, Biological, Cell Line, Drug Synergism, Larva, Metamorphosis, Reverse Transcriptase Polymerase Chain Reaction, Triiodothyronine, Xenopus}, issn = {1095-6840}, doi = {10.1016/j.ygcen.2010.03.014}, author = {Bonett, Ronald M and Hoopfer, Eric D and Denver, Robert J} } @article {2121, title = {Multi-array silicon probes with integrated optical fibers: light-assisted perturbation and recording of local neural circuits in the behaving animal.}, journal = {The European Journal of Neuroscience}, volume = {31}, year = {2010}, month = {2010 Jun}, pages = {2279-91}, abstract = {

Recordings of large neuronal ensembles and neural stimulation of high spatial and temporal precision are important requisites for studying the real-time dynamics of neural networks. Multiple-shank silicon probes enable large-scale monitoring of individual neurons. Optical stimulation of genetically targeted neurons expressing light-sensitive channels or other fast (milliseconds) actuators offers the means for controlled perturbation of local circuits. Here we describe a method to equip the shanks of silicon probes with micron-scale light guides for allowing the simultaneous use of the two approaches. We then show illustrative examples of how these compact hybrid electrodes can be used in probing local circuits in behaving rats and mice. A key advantage of these devices is the enhanced spatial precision of stimulation that is achieved by delivering light close to the recording sites of the probe. When paired with the expression of light-sensitive actuators within genetically specified neuronal populations, these devices allow the relatively straightforward and interpretable manipulation of network activity.

}, keywords = {Action Potentials, Animal, Animals, Behavior, Electric Stimulation, Electrophysiology, Light, Mice, Neurons, Neuropsychological Tests, Optical Fibers, Photic Stimulation, Rats, Recombinant Fusion Proteins, Silicon}, issn = {1460-9568}, doi = {10.1002/cbic.201000254}, author = {Royer, S{\'e}bastien and Zemelman, Boris V and Barbic, Mladen and Losonczy, Attila and Buzs{\'a}ki, Gy{\"o}rgy and Magee, Jeffrey C} } @article {5676, title = {Multilinear models of single cell responses in the medial nucleus of the trapezoid body.}, journal = {Network}, volume = {21}, year = {2010}, month = {2010}, pages = {91-124}, abstract = {

The representation of acoustic stimuli in the brainstem forms the basis for higher auditory processing. While some characteristics of this representation (e.g. tuning curve) are widely accepted, it remains a challenge to predict the firing rate at high temporal resolution in response to complex stimuli. In this study we explore models for in vivo, single cell responses in the medial nucleus of the trapezoid body (MNTB) under complex sound stimulation. We estimate a family of models, the multilinear models, encompassing the classical spectrotemporal receptive field and allowing arbitrary input-nonlinearities and certain multiplicative interactions between sound energy and its short-term auditory context. We compare these to models of more traditional type, and also evaluate their performance under various stimulus representations. Using the context model, 75\% of the explainable variance could be predicted based on a cochlear-like, gamma-tone stimulus representation. The presence of multiplicative contextual interactions strongly reduces certain inhibitory/suppressive regions of the linear kernels, suggesting an underlying nonlinear mechanism, e.g. cochlear or synaptic suppression, as the source of the suppression in MNTB neuronal responses. In conclusion, the context model provides a rich and still interpretable extension over many previous phenomenological models for modeling responses in the auditory brainstem at submillisecond resolution.

}, keywords = {Action Potentials, Animals, Auditory Pathways, Computer Simulation, Gerbillinae, Linear Models, Models, Neural Inhibition, Neurological, Neurons, Olivary Nucleus, Predictive Value of Tests, Sound Localization, Synaptic Transmission}, issn = {1361-6536}, doi = {10.3109/09548981003801996}, author = {Englitz, B and Ahrens, M and Tolnai, S and R{\"u}bsamen, R and Sahani, M and Jost, J} } @article {47227, title = {The mushroom body (Quick guide.)}, journal = {Current Biology : CB}, volume = {20}, year = {2010}, month = {2010 Jan 12}, pages = {R11-2}, doi = {10.1016/j.cub.2009.10.031}, author = {Campbell, Robert A A and Turner, Glenn C} } @article {4158, title = {Mutation of the Drosophila vesicular GABA transporter disrupts visual figure detection.}, journal = {The Journal of Experimental Biology}, volume = {213}, year = {2010}, month = {2010 May}, pages = {1717-30}, abstract = {

The role of gamma amino butyric acid (GABA) release and inhibitory neurotransmission in regulating most behaviors remains unclear. The vesicular GABA transporter (VGAT) is required for the storage of GABA in synaptic vesicles and provides a potentially useful probe for inhibitory circuits. However, specific pharmacologic agents for VGAT are not available, and VGAT knockout mice are embryonically lethal, thus precluding behavioral studies. We have identified the Drosophila ortholog of the vesicular GABA transporter gene (which we refer to as dVGAT), immunocytologically mapped dVGAT protein expression in the larva and adult and characterized a dVGAT(minos) mutant allele. dVGAT is embryonically lethal and we do not detect residual dVGAT expression, suggesting that it is either a strong hypomorph or a null. To investigate the function of VGAT and GABA signaling in adult visual flight behavior, we have selectively rescued the dVGAT mutant during development. We show that reduced GABA release does not compromise the active optomotor control of wide-field pattern motion. Conversely, reduced dVGAT expression disrupts normal object tracking and figure-ground discrimination. These results demonstrate that visual behaviors are segregated by the level of GABA signaling in flies, and more generally establish dVGAT as a model to study the contribution of GABA release to other complex behaviors.

}, keywords = {Alleles, Amino Acid Sequence, Animal, Animals, Behavior, Brain, Drosophila melanogaster, Drosophila Proteins, Fixation, Ganglia, Gene Knockdown Techniques, Larva, Mice, Molecular Sequence Data, Movement, Mutation, Ocular, Protein Transport, Synaptic Vesicles, Transgenes, Vesicular Inhibitory Amino Acid Transport Proteins, Visual Perception}, issn = {1477-9145}, doi = {10.1242/jeb.036053}, author = {Fei, Hao and Chow, Dawnis M and Chen, Audrey and Romero-Calder{\'o}n, Rafael and Ong, Wei S and Ackerson, Larry C and Maidment, Nigel T and Simpson, Julie H and Frye, Mark A and Krantz, David E} } @article {926, title = {Nanoscale architecture of integrin-based cell adhesions.}, journal = {Nature}, volume = {468}, year = {2010}, month = {2010 Nov 25}, pages = {580-4}, abstract = {

Cell adhesions to the extracellular matrix (ECM) are necessary for morphogenesis, immunity, and wound healing. Focal adhesions are multifunctional organelles that mediate cell-ECM adhesion, force transmission, cytoskeletal regulation and signaling. Focal adhesions consist of a complex network of trans-plasma-membrane integrins and cytoplasmic proteins that form a \<200-nm plaque linking the ECM to the actin cytoskeleton. The complexity of focal adhesion composition and dynamics implicate an intricate molecular machine. However, focal adhesion molecular architecture remains unknown. Here we used three-dimensional super-resolution fluorescence microscopy (interferometric photoactivated localization microscopy) to map nanoscale protein organization in focal adhesions. Our results reveal that integrins and actin are vertically separated by a \~{}40-nm focal adhesion core region consisting of multiple protein-specific strata: a membrane-apposed integrin signaling layer containing integrin cytoplasmic tails, focal adhesion kinase, and paxillin; an intermediate force-transduction layer containing talin and vinculin; and an uppermost actin-regulatory layer containing zyxin, vasodilator-stimulated phosphoprotein and α-actinin. By localizing amino- and carboxy-terminally tagged talins, we reveal talin{\textquoteright}s polarized orientation, indicative of a role in organizing the focal adhesion strata. The composite multilaminar protein architecture provides a molecular blueprint for understanding focal adhesion functions.

}, keywords = {Actins, Animals, Biological, Cell Adhesion, Cell Line, Cell Membrane, Extracellular Matrix, Humans, Integrins, Mice, Models, Tumor}, issn = {1476-4687}, doi = {10.1038/nature09621}, author = {Kanchanawong, Pakorn and Shtengel, Gleb and Pasapera, Ana M and Ramko, Ericka B and Davidson, Michael W and Hess, Harald F and Waterman, Clare M} } @article {6339, title = {Nanoscale flexibility parameters of Alzheimer amyloid fibrils determined by electron cryo-microscopy.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {49}, year = {2010}, month = {2010 Feb 8}, pages = {1321-3}, abstract = {

Versatile nanomaterial: Unusually high nanoscale flexibility was displayed by amyloid fibils in electron microscopy studies (see picture). This finding is relevant for understanding amyloid pathogenicity and for potential biotechnological applications.

}, keywords = {Alzheimer Disease, Amyloid, Cryoelectron Microscopy, Humans, Nanotechnology, Protein Folding}, issn = {1521-3773}, doi = {10.1002/anie.200904781}, author = {Sachse, Carsten and Grigorieff, Nikolaus and F{\"a}ndrich, Marcus} } @article {6322, title = {The Ndc80 kinetochore complex forms oligomeric arrays along microtubules.}, journal = {Nature}, volume = {467}, year = {2010}, month = {2010 Oct 14}, pages = {805-10}, abstract = {

The Ndc80 complex is a key site of regulated kinetochore-microtubule attachment (a process required for cell division), but the molecular mechanism underlying its function remains unknown. Here we present a subnanometre-resolution cryo-electron microscopy reconstruction of the human Ndc80 complex bound to microtubules, sufficient for precise docking of crystal structures of the component proteins. We find that the Ndc80 complex binds the microtubule with a tubulin monomer repeat, recognizing α- and β-tubulin at both intra- and inter-tubulin dimer interfaces in a manner that is sensitive to tubulin conformation. Furthermore, Ndc80 complexes self-associate along protofilaments through interactions mediated by the amino-terminal tail of the NDC80 protein, which is the site of phospho-regulation by Aurora B kinase. The complex{\textquoteright}s mode of interaction with the microtubule and its oligomerization suggest a mechanism by which Aurora B could regulate the stability of load-bearing kinetochore-microtubule attachments.

}, keywords = {Binding Sites, Biological, Cryoelectron Microscopy, Humans, Kinetochores, Microtubules, Mitosis, Models, Molecular, Nuclear Proteins, Protein Conformation, Tubulin}, issn = {1476-4687}, doi = {10.1038/nature09423}, author = {Alushin, Gregory M and Ramey, Vincent H and Pasqualato, Sebastiano and Ball, David A and Grigorieff, Nikolaus and Musacchio, Andrea and Nogales, Eva} } @article {1575, title = {Near-isotropic 3D optical nanoscopy with photon-limited chromophores.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, year = {2010}, month = {2010 Jun 1}, pages = {10068-73}, abstract = {

Imaging approaches based on single molecule localization break the diffraction barrier of conventional fluorescence microscopy, allowing for bioimaging with nanometer resolution. It remains a challenge, however, to precisely localize photon-limited single molecules in 3D. We have developed a new localization-based imaging technique achieving almost isotropic subdiffraction resolution in 3D. A tilted mirror is used to generate a side view in addition to the front view of activated single emitters, allowing their 3D localization to be precisely determined for superresolution imaging. Because both front and side views are in focus, this method is able to efficiently collect emitted photons. The technique is simple to implement on a commercial fluorescence microscope, and especially suitable for biological samples with photon-limited chromophores such as endogenously expressed photoactivatable fluorescent proteins. Moreover, this method is relatively resistant to optical aberration, as it requires only centroid determination for localization analysis. Here we demonstrate the application of this method to 3D imaging of bacterial protein distribution and neuron dendritic morphology with subdiffraction resolution.

}, keywords = {Animals, Base Sequence, Dendrites, DNA Primers, Escherichia coli K12, Escherichia coli Proteins, Fluorescence, Imaging, Luminescent Proteins, Microscopy, Nanotechnology, Optical Devices, Photons, Rats, Recombinant Fusion Proteins, Sprague-Dawley, Three-Dimensional}, issn = {1091-6490}, doi = {10.1073/pnas.1004899107}, author = {Tang, Jianyong and Akerboom, Jasper and Vaziri, Alipasha and Looger, Loren L and Shank, Charles V} } @article {3911, title = {Network mechanisms of theta related neuronal activity in hippocampal CA1 pyramidal neurons.}, journal = {Nature Neuroscience}, volume = {13}, year = {2010}, month = {2010 Aug}, pages = {967-72}, abstract = {

Although hippocampal theta oscillations represent a prime example of temporal coding in the mammalian brain, little is known about the specific biophysical mechanisms. Intracellular recordings support a particular abstract oscillatory interference model of hippocampal theta activity, the soma-dendrite interference model. To gain insight into the cellular and circuit level mechanisms of theta activity, we implemented a similar form of interference using the actual hippocampal network in mice in vitro. We found that pairing increasing levels of phasic dendritic excitation with phasic stimulation of perisomatic projecting inhibitory interneurons induced a somatic polarization and action potential timing profile that reproduced most common features. Alterations in the temporal profile of inhibition were required to fully capture all features. These data suggest that theta-related place cell activity is generated through an interaction between a phasic dendritic excitation and a phasic perisomatic shunting inhibition delivered by interneurons, a subset of which undergo activity-dependent presynaptic modulation.

}, keywords = {Animals, Gene Knock-In Techniques, Hippocampus, Inbred C57BL, Inhibitory Postsynaptic Potentials, Mice, Nerve Net, Organ Culture Techniques, Patch-Clamp Techniques, Pyramidal Cells, Theta Rhythm}, issn = {1546-1726}, doi = {10.1038/nn.2597}, author = {Losonczy, Attila and Zemelman, Boris V and Vaziri, Alipasha and Magee, Jeffrey C} } @article {4289, title = {Neural activity in barrel cortex underlying vibrissa-based object localization in mice.}, journal = {Neuron}, volume = {67}, year = {2010}, month = {2010 Sep 23}, pages = {1048-61}, abstract = {

Classical studies have related the spiking of selected neocortical neurons to behavior, but little is known about activity sampled from the entire neural population. We recorded from neurons selected independent of spiking, using cell-attached recordings and two-photon calcium imaging, in the barrel cortex of mice performing an object localization task. Spike rates varied across neurons, from silence to \>60 Hz. Responses were diverse, with some neurons showing large increases in spike rate when whiskers contacted the object. Nearly half the neurons discriminated object location; a small fraction of neurons discriminated perfectly. More active neurons were more discriminative. Layer (L) 4 and L5 contained the highest fractions of discriminating neurons (\~{}63\% and 79\%, respectively), but a few L2/3 neurons were also highly discriminating. Approximately 13,000 spikes per activated barrel column were available to mice for decision making. Coding of object location in the barrel cortex is therefore highly redundant.

}, keywords = {Action Potentials, Afferent Pathways, Animal, Animals, Behavior, Biological, Brain Mapping, Calcium, Discrimination (Psychology), Inbred C57BL, Male, Mice, Models, Neurons, Physical Stimulation, ROC Curve, Somatosensory Cortex, Vibrissae}, issn = {1097-4199}, doi = {10.1016/j.neuron.2010.08.026}, author = {O{\textquoteright}Connor, Daniel H and Peron, Simon P and Huber, Daniel and Svoboda, Karel} } @article {2386, title = {A new focus on plant sciences.}, journal = {Science}, volume = {330}, year = {2010}, month = {2010 Nov 19}, pages = {1021}, keywords = {Agriculture, Botany, Financing, Government, Plants, Research Support as Topic, United States}, issn = {1095-9203}, doi = {10.1073/pnas.1100640108}, author = {McCormick, Steven J and Tjian, Robert} } @article {1681, title = {Nlcam modulates midline convergence during anterior neural plate morphogenesis.}, journal = {Developmental Biology}, volume = {339}, year = {2010}, month = {2010 Mar 1}, pages = {14-25}, abstract = {

During development, different cell types must undergo distinct morphogenetic programs so that tissues develop the right dimensions in the appropriate place. In early eye morphogenesis, retinal progenitor cells (RPCs) move first towards the midline, before turning around to migrate out into the evaginating optic vesicles. Neighbouring forebrain cells, however, converge rapidly and then remain at the midline. These differential behaviours are regulated by the transcription factor Rx3. Here, we identify a downstream target of Rx3, the Ig-domain protein Nlcam, and characterise its role in regulating cell migration during the initial phase of optic vesicle morphogenesis. Through sophisticated live imaging and comprehensive cell tracking experiments in zebrafish, we show that ectopic expression of Nlcam in RPCs, as is observed in Rx3 mutants, causes enhanced convergence of these cells. Expression levels of Nlcam therefore regulate the migratory properties of RPCs. Our results provide evidence that the two phases of optic vesicle morphogenesis: slowed convergence and outward-directed migration, are under different genetic control. We propose that Nlcam forms part of the guidance machinery directing rapid midline migration of forebrain precursors, where it is normally expressed, and that its ectopic expression upon loss of Rx3 imparts these migratory characteristics upon RPCs.

}, keywords = {Animals, Base Sequence, Body Patterning, Cell Adhesion Molecules, Chick Embryo, DNA Primers, Electrophoretic Mobility Shift Assay, Homeodomain Proteins, Morphogenesis, Neural Plate, Protein Binding, Zebrafish}, issn = {1095-564X}, doi = {10.1016/j.ydbio.2009.12.003}, author = {Brown, Katherine E and Keller, Philipp J and Ramialison, Mirana and Rembold, Martina and Stelzer, Ernst H K and Loosli, Felix and Wittbrodt, Joachim} } @article {1541, title = {Nodavirus-induced membrane rearrangement in replication complex assembly requires replicase protein a, RNA templates, and polymerase activity.}, journal = {Journal of Virology}, volume = {84}, year = {2010}, month = {2010 Dec}, pages = {12492-503}, abstract = {

Positive-strand RNA [(+)RNA] viruses invariably replicate their RNA genomes on modified intracellular membranes. In infected Drosophila cells, Flock House nodavirus (FHV) RNA replication complexes form on outer mitochondrial membranes inside \~{}50-nm, virus-induced spherular invaginations similar to RNA replication-linked spherules induced by many (+)RNA viruses at various membranes. To better understand replication complex assembly, we studied the mechanisms of FHV spherule formation. FHV has two genomic RNAs; RNA1 encodes multifunctional RNA replication protein A and RNA interference suppressor protein B2, while RNA2 encodes the capsid proteins. Expressing genomic RNA1 without RNA2 induced mitochondrial spherules indistinguishable from those in FHV infection. RNA1 mutation showed that protein B2 was dispensable and that protein A was the only FHV protein required for spherule formation. However, expressing protein A alone only "zippered" together the surfaces of adjacent mitochondria, without inducing spherules. Thus, protein A is necessary but not sufficient for spherule formation. Coexpressing protein A plus a replication-competent FHV RNA template induced RNA replication in trans and membrane spherules. Moreover, spherules were not formed when replicatable FHV RNA templates were expressed with protein A bearing a single, polymerase-inactivating amino acid change or when wild-type protein A was expressed with a nonreplicatable FHV RNA template. Thus, unlike many (+)RNA viruses, the membrane-bounded compartments in which FHV RNA replication occurs are not induced solely by viral protein(s) but require viral RNA synthesis. In addition to replication complex assembly, the results have implications for nodavirus interaction with cell RNA silencing pathways and other aspects of virus control.

}, keywords = {Animals, Blotting, Capsid Proteins, DNA-Directed RNA Polymerases, Drosophila melanogaster, Genome, Intracellular Membranes, Mitochondria, Nodaviridae, Northern, Plasmids, RNA, RNA Replicase, RNA Virus Infections, Small Interfering, Viral, Virus Replication, Western}, issn = {1098-5514}, doi = {10.1128/JVI.01495-10}, url = {http://jvi.asm.org/content/84/24/12492.short}, author = {Kopek, Benjamin G and Settles, Erik W and Friesen, Paul D and Ahlquist, Paul} } @article {6597, title = {Nuclear physics: quantitative single-cell approaches to nuclear organization and gene expression.}, journal = {Cold Spring Harbor Symposia on Quantitative Biology}, volume = {75}, year = {2010}, month = {2010}, pages = {113-26}, abstract = {

The internal workings of the nucleus remain a mystery. A list of component parts exists, and in many cases their functional roles are known for events such as transcription, RNA processing, or nuclear export. Some of these components exhibit structural features in the nucleus, regions of concentration or bodies that have given rise to the concept of functional compartmentalization{\textendash}that there are underlying organizational principles to be described. In contrast, a picture is emerging in which transcription appears to drive the assembly of the functional components required for gene expression, drawing from pools of excess factors. Unifying this seemingly dual nature requires a more rigorous approach, one in which components are tracked in time and space and correlated with onset of specific nuclear functions. In this chapter, we anticipate tools that will address these questions and provide the missing kinetics of nuclear function. These tools are based on analyzing the fluctuations inherent in the weak signals of endogenous nuclear processes and determining values for them. In this way, it will be possible eventually to provide a computational model describing the functional relationships of essential components.

}, keywords = {Biological, Biophysical Phenomena, Biophysics, Cell Nucleus, Fluorescence, Fluorescence Recovery After Photobleaching, Gene Dosage, Gene Expression Regulation, Kinetics, Models, Saccharomyces cerevisiae, Spectrometry}, issn = {1943-4456}, doi = {10.1101/sqb.2010.75.057}, author = {Lionnet, T and Wu, B and Gr{\"u}nwald, D and Singer, R H and Larson, D R} } @article {47686, title = {The open reading frame 3a protein of severe acute respiratory syndrome-associated coronavirus promotes membrane rearrangement and cell death.}, journal = {Journal of virology}, volume = {84}, year = {2010}, month = {2010 Jan}, pages = {1097-109}, abstract = {

The genome of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) contains eight open reading frames (ORFs) that encode novel proteins. These accessory proteins are dispensable for in vitro and in vivo replication and thus may be important for other aspects of virus-host interactions. We investigated the functions of the largest of the accessory proteins, the ORF 3a protein, using a 3a-deficient strain of SARS-CoV. Cell death of Vero cells after infection with SARS-CoV was reduced upon deletion of ORF 3a. Electron microscopy of infected cells revealed a role for ORF 3a in SARS-CoV induced vesicle formation, a prominent feature of cells from SARS patients. In addition, we report that ORF 3a is both necessary and sufficient for SARS-CoV-induced Golgi fragmentation and that the 3a protein accumulates and localizes to vesicles containing markers for late endosomes. Finally, overexpression of ADP-ribosylation factor 1 (Arf1), a small GTPase essential for the maintenance of the Golgi apparatus, restored Golgi morphology during infection. These results establish an important role for ORF 3a in SARS-CoV-induced cell death, Golgi fragmentation, and the accumulation of intracellular vesicles.

}, keywords = {ADP-Ribosylation Factor 1, Animals, Cell Death, Cell Membrane, Cercopithecus aethiops, Cytoplasmic Vesicles, Gene Deletion, Golgi Apparatus, Host-Pathogen Interactions, Humans, SARS Virus, Transfection, Vero Cells, Viral Structural Proteins}, issn = {1098-5514}, doi = {10.1128/JVI.01662-09}, author = {Freundt, Eric C and Yu, Li and Goldsmith, Cynthia S and Welsh, Sarah and Cheng, Aaron and Yount, Boyd and Liu, Wei and Frieman, Matthew B and Buchholz, Ursula J and Screaton, Gavin R and Lippincott-Schwartz, Jennifer and Zaki, Sherif R and Xu, Xiao-Ning and Baric, Ralph S and Subbarao, Kanta and Lenardo, Michael J} } @proceedings {5829, title = {Over-complete representations on recurrent neural networks can support persistent percepts.}, volume = {23}, year = {2010}, month = {2010}, pages = {541-9}, publisher = {MIT Press}, abstract = {

A striking aspect of cortical neural networks is the divergence of a relatively small number of input channels from the peripheral sensory apparatus into a large number of cortical neurons, an over-complete representation strategy. Cortical neurons are then connected by a sparse network of lateral synapses. Here we propose that such architecture may increase the persistence of the representation of an incoming stimulus, or a percept. We demonstrate that for a family of networks in which the receptive field of each neuron is re-expressed by its outgoing connections, a represented percept can remain constant despite changing activity. We term this choice of connectivity REceptive FIeld REcombination (REFIRE) networks. The sparse REFIRE network may serve as a high-dimensional integrator and a biologically plausible model of the local cortical circuit.

}, author = {Druckmann, S and Chklovskii, D} } @article {6496, title = {The overlap of small molecule and protein binding sites within families of protein structures.}, journal = {PLoS Computational Biology}, volume = {6}, year = {2010}, month = {2010 Feb}, pages = {e1000668}, abstract = {

Protein-protein interactions are challenging targets for modulation by small molecules. Here, we propose an approach that harnesses the increasing structural coverage of protein complexes to identify small molecules that may target protein interactions. Specifically, we identify ligand and protein binding sites that overlap upon alignment of homologous proteins. Of the 2,619 protein structure families observed to bind proteins, 1,028 also bind small molecules (250-1000 Da), and 197 exhibit a statistically significant (p\<0.01) overlap between ligand and protein binding positions. These "bi-functional positions", which bind both ligands and proteins, are particularly enriched in tyrosine and tryptophan residues, similar to "energetic hotspots" described previously, and are significantly less conserved than mono-functional and solvent exposed positions. Homology transfer identifies ligands whose binding sites overlap at least 20\% of the protein interface for 35\% of domain-domain and 45\% of domain-peptide mediated interactions. The analysis recovered known small-molecule modulators of protein interactions as well as predicted new interaction targets based on the sequence similarity of ligand binding sites. We illustrate the predictive utility of the method by suggesting structural mechanisms for the effects of sanglifehrin A on HIV virion production, bepridil on the cellular entry of anthrax edema factor, and fusicoccin on vertebrate developmental pathways. The results, available at http://pibase.janelia.org, represent a comprehensive collection of structurally characterized modulators of protein interactions, and suggest that homologous structures are a useful resource for the rational design of interaction modulators.

}, keywords = {Binding Sites, Computational Biology, Ligands, Models, Molecular, Nonparametric, Protein Binding, Protein Interaction Domains and Motifs, Proteins, Statistics}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1000668}, author = {Davis, Fred P and Sali, Andrej} } @article {46618, title = {A pair of dopamine neurons target the D1-like dopamine receptor DopR in the central complex to promote ethanol-stimulated locomotion in Drosophila.}, journal = {PLoS One}, volume = {5}, year = {2010}, month = {2010 Apr 1}, pages = {e9954}, abstract = {

Dopamine is a mediator of the stimulant properties of drugs of abuse, including ethanol, in mammals and in the fruit fly Drosophila. The neural substrates for the stimulant actions of ethanol in flies are not known. We show that a subset of dopamine neurons and their targets, through the action of the D1-like dopamine receptor DopR, promote locomotor activation in response to acute ethanol exposure. A bilateral pair of dopaminergic neurons in the fly brain mediates the enhanced locomotor activity induced by ethanol exposure, and promotes locomotion when directly activated. These neurons project to the central complex ellipsoid body, a structure implicated in regulating motor behaviors. Ellipsoid body neurons are required for ethanol-induced locomotor activity and they express DopR. Elimination of DopR blunts the locomotor activating effects of ethanol, and this behavior can be restored by selective expression of DopR in the ellipsoid body. These data tie the activity of defined dopamine neurons to D1-like DopR-expressing neurons to form a neural circuit that governs acute responding to ethanol.

}, keywords = {Animals, Behavior, Animal, Central Nervous System Depressants, Dopamine, Drosophila, Drosophila Proteins, Ethanol, Locomotion, Motor Activity, Neurons, Receptors, Dopamine}, issn = {1932-6203}, doi = {10.1371/journal.pone.0009954}, author = {Kong, Eric C and Woo, Katherine and Li, Haiyan and Lebestky, Tim and Mayer, Nasima and Sniffen, Melissa R and Heberlein, Ulrike and Bainton, Roland J and Hirsh, Jay and Wolf, Fred W} } @proceedings {45797, title = {A patterning difference underlying viviparous and oviparous development in the pea aphid}, volume = {50}, year = {2010}, month = {01/2010}, pages = {E205-E205}, publisher = {OXFORD UNIV PRESS INC}, abstract = {

The pea aphid, Acyrthosiphon pisum, exhibits several environmentally cued, discrete, alternate phenotypes (polyphenisms) during its life cycle. In the case of the reproductive polyphenism, differences in day length determine whether mothers will produce daughters that reproduce either sexually by laying fertilized eggs (oviparous sexual reproduction), or asexually by allowing oocytes to complete embryogenesis within the mother without fertilization (viviparous parthenogenesis). Oocytes and embryos that are produced asexually and develop within the mother develop more rapidly, are yolk-free, and much smaller than oocytes and embryos that are produced sexually. These overt differences suggest that there may be underlying differences in the molecular mechanisms of pattern formation. Indeed, our preliminary comparative gene expression work suggests that there are important differences in the terminal patterning system, involving the Torso pathway, between viviparous and oviparous development. We have so far examined the expression of homologs of torso-like and capicua, members of the Drosophila Torso pathway. We have detected clear differential expression of torso-like and possible differential expression of capicua. Establishing such differences in the expression of patterning genes between these developmental modes is a first step toward understanding how a single genome manages to direct patterning events in such different embryological contexts.

}, author = {R Bickel and N Belletier and H Cleveland and DL Stern and G Davis} } @article {46041, title = {Persistence of coordinated long-term potentiation and dendritic spine enlargement at mature hippocampal CA1 synapses requires N-cadherin.}, journal = {Journal of Neuroscience}, volume = {30}, year = {2010}, month = {2010 Jul 28}, pages = {9984-9}, abstract = {

Persistent changes in spine shape are coupled to long-lasting synaptic plasticity in hippocampus. The molecules that coordinate such persistent structural and functional plasticity are unknown. Here, we generated mice in which the cell adhesion molecule N-cadherin was conditionally ablated from postnatal, excitatory synapses in hippocampus. We applied to adult mice of either sex a combination of whole-cell recording, two-photon microscopy, and spine morphometric analysis to show that postnatal ablation of N-cadherin has profound effects on the stability of coordinated spine enlargement and long-term potentiation (LTP) at mature CA1 synapses, with no effects on baseline spine density or morphology, baseline properties of synaptic neurotransmission, or long-term depression. Thus, N-cadherin couples persistent spine structural modifications with long-lasting synaptic functional modifications associated selectively with LTP, revealing unexpectedly distinct roles at mature synapses in comparison with earlier, broader functions in synapse and spine development.

}, keywords = {Action Potentials, Animals, Biophysics, CA1 Region, Hippocampal, Cadherins, Dendritic Spines, Electric Stimulation, Excitatory Postsynaptic Potentials, In Vitro Techniques, Long-Term Potentiation, Mice, Mice, Inbred C57BL, Mice, Knockout, Microscopy, Immunoelectron, Patch-Clamp Techniques, Pyramidal Cells, Statistics, Nonparametric, Synapses}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.1223-10.2010}, author = {Bozdagi, Ozlem and Wang, Xiao-bin and Nikitczuk, Jessica S and Anderson, Tonya R and Bloss, Erik B and Radice, Glenn L and Zhou, Qiang and Benson, Deanna L and Huntley, George W} } @article {4253, title = {The Pfam protein families database.}, journal = {Nucleic Acids Research}, volume = {38}, year = {2010}, month = {2010 Jan}, pages = {D211-22}, abstract = {

Pfam is a widely used database of protein families and domains. This article describes a set of major updates that we have implemented in the latest release (version 24.0). The most important change is that we now use HMMER3, the latest version of the popular profile hidden Markov model package. This software is approximately 100 times faster than HMMER2 and is more sensitive due to the routine use of the forward algorithm. The move to HMMER3 has necessitated numerous changes to Pfam that are described in detail. Pfam release 24.0 contains 11,912 families, of which a large number have been significantly updated during the past two years. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/).

}, keywords = {Amino Acid, Amino Acid Sequence, Animals, Archaeal, Computational Biology, Databases, Fungal, Genome, Humans, Information Storage and Retrieval, Internet, Molecular Sequence Data, Nucleic Acid, Protein, Protein Structure, Sequence Alignment, Sequence Homology, Software, Tertiary}, issn = {1362-4962}, doi = {10.1093/nar/gkp985}, author = {Finn, Robert D and Mistry, Jaina and Tate, John and Coggill, Penny and Heger, Andreas and Pollington, Joanne E and Gavin, O Luke and Gunasekaran, Prasad and Ceric, Goran and Forslund, Kristoffer and Holm, Liisa and Sonnhammer, Erik L L and Eddy, Sean R. and Bateman, Alex} } @article {4401, title = {Phenotypic robustness conferred by apparently redundant transcriptional enhancers.}, journal = {Nature}, volume = {466}, year = {2010}, month = {2010 Jul 22}, pages = {490-3}, abstract = {

Genes include cis-regulatory regions that contain transcriptional enhancers. Recent reports have shown that developmental genes often possess multiple discrete enhancer modules that drive transcription in similar spatio-temporal patterns: primary enhancers located near the basal promoter and secondary, or {\textquoteright}shadow{\textquoteright}, enhancers located at more remote positions. It has been proposed that the seemingly redundant activity of primary and secondary enhancers contributes to phenotypic robustness. We tested this hypothesis by generating a deficiency that removes two newly discovered enhancers of shavenbaby (svb, a transcript of the ovo locus), a gene encoding a transcription factor that directs development of Drosophila larval trichomes. At optimal temperatures for embryonic development, this deficiency causes minor defects in trichome patterning. In embryos that develop at both low and high extreme temperatures, however, absence of these secondary enhancers leads to extensive loss of trichomes. These temperature-dependent defects can be rescued by a transgene carrying a secondary enhancer driving transcription of the svb cDNA. Finally, removal of one copy of wingless, a gene required for normal trichome patterning, causes a similar loss of trichomes only in flies lacking the secondary enhancers. These results support the hypothesis that secondary enhancers contribute to phenotypic robustness in the face of environmental and genetic variability.

}, keywords = {Animal Structures, Animals, Developmental, DNA-Binding Proteins, Drosophila melanogaster, Drosophila Proteins, Enhancer Elements, Gene Expression Regulation, Genetic, Larva, Models, Phenotype, Temperature, Transcription, Transcription Factors, Transgenes}, issn = {1476-4687}, doi = {10.1038/nature09158}, author = {Frankel, Nicol{\'a}s and Davis, Gregory K and Vargas, Diego and Wang, Shu and Payre, Fran{\c c}ois and Stern, David L} } @article {6780, title = {A post-burst after depolarization is mediated by group i metabotropic glutamate receptor-dependent upregulation of Ca(v)2.3 R-type calcium channels in CA1 pyramidal neurons.}, journal = {PLoS Biology}, volume = {8}, year = {2010}, month = {2010}, pages = {e1000534}, abstract = {

Activation of group I metabotropic glutamate receptors (subtypes mGluR1 and mGluR5) regulates neural activity in a variety of ways. In CA1 pyramidal neurons, activation of group I mGluRs eliminates the post-burst afterhyperpolarization (AHP) and produces an afterdepolarization (ADP) in its place. Here we show that upregulation of Ca(v)2.3 R-type calcium channels is responsible for a component of the ADP lasting several hundred milliseconds. This medium-duration ADP is rapidly and reversibly induced by activation of mGluR5 and requires activation of phospholipase C (PLC) and release of calcium from internal stores. Effects of mGluR activation on subthreshold membrane potential changes are negligible but are large following action potential firing. Furthermore, the medium ADP exhibits a biphasic activity dependence consisting of short-term facilitation and longer-term inhibition. These findings suggest that mGluRs may dramatically alter the firing of CA1 pyramidal neurons via a complex, activity-dependent modulation of Ca(v)2.3 R-type channels that are activated during spiking at physiologically relevant rates and patterns.

}, keywords = {Action Potentials, Animals, Calcium Channels, Cation Transport Proteins, Female, Inbred C57BL, Ion Channel Gating, Male, Metabotropic Glutamate, Methoxyhydroxyphenylglycol, Mice, Neurons, Patch-Clamp Techniques, Pyramidal Cells, R-Type, Rats, Receptors, Up-Regulation, Wistar, Xenopus}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1000534}, author = {Park, Jin-Yong and Remy, Stefan and Varela, Juan and Cooper, Donald C and Chung, Sungkwon and Kang, Ho-Won and Lee, Jung-Ha and Spruston, Nelson} } @article {2146, title = {A principal skeleton algorithm for standardizing confocal images of fruit fly nervous systems.}, journal = {Bioinformatics}, volume = {26}, year = {2010}, month = {2010 Apr 15}, pages = {1091-7}, abstract = {

The fruit fly (Drosophila melanogaster) is a commonly used model organism in biology. We are currently building a 3D digital atlas of the fruit fly larval nervous system (LNS) based on a large collection of fly larva GAL4 lines, each of which targets a subset of neurons. To achieve such a goal, we need to automatically align a number of high-resolution confocal image stacks of these GAL4 lines. One commonly employed strategy in image pattern registration is to first globally align images using an affine transform, followed by local non-linear warping. Unfortunately, the spatially articulated and often twisted LNS makes it difficult to globally align the images directly using the affine method. In a parallel project to build a 3D digital map of the adult fly ventral nerve cord (VNC), we are confronted with a similar problem.

}, keywords = {Algorithms, Animals, Cell Line, Computer-Assisted, Confocal, Drosophila melanogaster, Image Processing, Imaging, Microscopy, Nervous System, Three-Dimensional}, issn = {1367-4811}, doi = {10.1007/s12021-010-9090-x}, author = {Qu, Lei and Peng, Hanchuan} } @article {68824, title = {Proneural gene-linked neurogenesis in zebrafish cerebellum}, journal = {Developmental Biology}, volume = {343}, year = {2010}, month = {07/2010}, pages = {1-17}, abstract = {

In mammals, cerebellar neurons are categorized as glutamatergic or GABAergic, and are derived from progenitors that express the proneural genes atoh1 or ptf1a, respectively. In zebrafish, three atoh1 genes, atoh1a, atoh1b, and atoh1c, are expressed in overlapping but distinct expression domains in the upper rhombic lip (URL): ptf1a is expressed exclusively in the ventricular zone (VZ). Using transgenic lines expressing fluorescent proteins under the control of the regulatory elements of atoh1a and ptf1a, we traced the lineages of the cerebellar neurons. The atoh1+ progenitors gave rise not only to granule cells but also to neurons of the anteroventral rhombencephalon. The ptf1a+ progenitors generated Purkinje cells. The olig2+ eurydendroid cells, which are glutamatergic, were derived mostly from ptf1a+ progenitors in the VZ but some originated from the atoh1+ progenitors in the URL. In the adult cerebellum, atoh1a, atoh1b, and atoh1c are expressed in the molecular layer of the valvula cerebelli and of the medial corpus cerebelli, and ptf1a was detected in the VZ. The proneural gene expression patterns coincided with the sites of proliferating neuronal progenitors in the adult cerebellum. Our data indicate that proneural gene-linked neurogenesis is evolutionarily conserved in the cerebellum among vertebrates, and that the continuously generated neurons help remodel neural circuits in the adult zebrafish cerebellum.

}, keywords = {Adult neurogenesis, Cerebellum, GABAergic neuron, Glutamatergic neuron, Hindbrain, Proneural gene, Zebrafish}, issn = {0012-1606}, doi = {https://doi.org/10.1016/j.ydbio.2010.03.024}, url = {https://www.sciencedirect.com/science/article/pii/S0012160610002071}, author = {Shuichi Kani and Young-Ki Bae and Takashi Shimizu and Koji Tanabe and Chie Satou and Michael J. Parsons and Ethan Scott and Shin-ichi Higashijima and Masahiko Hibi} } @article {46617, title = {Protein Phosphatase 2a and glycogen synthase kinase 3 signaling modulate prepulse inhibition of the acoustic startle response by altering cortical M-Type potassium channel activity.}, journal = {The Journal of Neuroscience}, volume = {30}, year = {2010}, month = {2010 Jun 30}, pages = {8830-40}, abstract = {

There is considerable interest in the regulation of sensorimotor gating, since deficits in this process could play a critical role in the symptoms of schizophrenia and other psychiatric disorders. Sensorimotor gating is often studied in humans and rodents using the prepulse inhibition of the acoustic startle response (PPI) model, in which an acoustic prepulse suppresses behavioral output to a startle-inducing stimulus. However, the molecular and neural mechanisms underlying PPI are poorly understood. Here, we show that a regulatory pathway involving protein phosphatase 2A (PP2A), glycogen synthase kinase 3 beta (GSK3beta), and their downstream target, the M-type potassium channel, regulates PPI. Mice (Mus musculus) carrying a hypomorphic allele of Ppp2r5delta, encoding a regulatory subunit of PP2A, show attenuated PPI. This PPP2R5delta reduction increases the phosphorylation of GSK3beta at serine 9, which inactivates GSK3beta, indicating that PPP2R5delta positively regulates GSK3beta activity in the brain. Consistently, genetic and pharmacological manipulations that reduce GSK3beta function attenuate PPI. The M-type potassium channel subunit, KCNQ2, is a putative GSK3beta substrate. Genetic reduction of Kcnq2 also reduces PPI, as does systemic inhibition of M-channels with linopirdine. Importantly, both the GSK3 inhibitor 3-(2,4-dichlorophenyl)-4-(1-methyl-1H-indol-3-yl)1H-pyrrole-2,5-dione (SB216763) and linopirdine reduce PPI when directly infused into the medial prefrontal cortex (mPFC). Whole-cell electrophysiological recordings of mPFC neurons show that SB216763 and linopirdine have similar effects on firing, and GSK3 inhibition occludes the effects of M-channel inhibition. These data support a previously uncharacterized mechanism by which PP2A/GSK3beta signaling regulates M-type potassium channel activity in the mPFC to modulate sensorimotor gating.

}, keywords = {Amino Acid Sequence, Animals, Auditory Perception, Brain, Glycogen Synthase Kinase 3, Inhibition (Psychology), KCNQ2 Potassium Channel, Mice, Mice, Inbred C57BL, Mice, Transgenic, Models, Neurological, Neurons, Phosphorylation, Potassium Channels, Prefrontal Cortex, Protein Phosphatase 2, Reflex, Startle, Signal Transduction}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.1292-10.2010}, author = {Kapfhamer, David and Berger, Karen H and Hopf, F Woodward and Seif, Taban and Kharazia, Viktor and Bonci, Antonello and Heberlein, Ulrike} } @article {3637, title = {The prototypical H+/galactose symporter GalP assembles into functional trimers.}, journal = {Journal of Molecular Biology}, volume = {396}, year = {2010}, month = {2010 Feb 26}, pages = {593-601}, abstract = {

Glucose is a primary source of energy for human cells. Glucose transporters form specialized membrane channels for the transport of sugars into and out of cells. Galactose permease (GalP) is the closest bacterial homolog of human facilitated glucose transporters. Here, we report the functional reconstitution and 2D crystallization of GalP. Single particle electron microscopy analysis of purified GalP shows that the protein assembles as an oligomer with three distinct densities. Reconstitution assays yield 2D GalP crystals that exhibit a hexagonal array having p3 symmetry. The projection structure of GalP at 18 A resolution shows that the protein is trimeric. Each monomer in the trimer forms its own channel, but an additional cavity (10 approximately 15 A in diameter) is apparent at the 3-fold axis of the oligomer. We show that the crystalline GalP is able to selectively bind substrate, suggesting that the trimeric form is biologically active.

}, keywords = {Calcium-Binding Proteins, Computer-Assisted, Crystallization, Electron, Escherichia coli, Escherichia coli Proteins, Galactose, Image Processing, Microscopy, Monosaccharide Transport Proteins, Periplasmic Binding Proteins, Protein Binding, Protein Multimerization, Protein Structure, Quaternary}, issn = {1089-8638}, doi = {10.1016/j.jmb.2009.12.010}, author = {Zheng, Hongjin and Taraska, Justin and Merz, Alexey J and Gonen, Tamir} } @article {5373, title = {Quantum coherence in ion channels: resonances, transport and verification.}, journal = {New Journal of Physics}, volume = {12}, year = {2010}, month = {2010}, abstract = {

Recently it was demonstrated that long-lived quantum coherence exists during excitation energy transport in photosynthesis. It is a valid question up to which length, time and mass scales quantum coherence may extend, how one may detect this coherence and what, if any, role it plays in the dynamics of the system. Here we suggest that the selectivity filter of ion channels may exhibit quantum coherence, which might be relevant for the process of ion selectivity and conduction. We show that quantum resonances could provide an alternative approach to ultrafast two-dimensional (2D) spectroscopy to probe these quantum coherences. We demonstrate that the emergence of resonances in the conduction of ion channels that are modulated periodically by time-dependent external electric fields can serve as signatures of quantum coherence in such a system. Assessments of experimental feasibility and specific paths towards the experimental realization of such experiments are presented.

}, doi = {10.1088/1367-2630/12/8/085001}, author = {Vaziri, Alipasha and Plenio, Martin B.} } @article {6782, title = {Questions about STDP as a general model of synaptic plasticity.}, journal = {Frontiers in Synaptic Neuroscience}, volume = {2}, year = {2010}, month = {2010}, pages = {140}, abstract = {

According to spike-timing-dependent plasticity (STDP), the timing of the Na(+) spike relative to the EPSP determines whether LTP or LTD will occur. Here, we review our reservations about STDP. Most investigations of this process have been done under conditions in which the spike is evoked by postsynaptic current injection. Under more realistic conditions, in which the spike is evoked by the EPSP, the results do not generally support STDP. For instance, low-frequency stimulation of a group of synapses can cause LTD, not the LTP predicted by the pre-before-post sequence in STDP; this is true regardless of whether or not the EPSP is large enough to produce a Na(+) spike. With stronger or more frequent stimulation, LTP can be induced by the same pre-before-post timing, but in this case block of Na(+) spikes does not necessarily prevent LTP induction. Thus, Na(+) spikes may facilitate LTP and/or LTD under some conditions, but they are not necessary, a finding consistent with their small size relative to the EPSP in many parts of pyramidal cell dendrites. The nature of the dendritic depolarizing events that control bidirectional plasticity is of central importance to understanding neural function. There are several candidates, including backpropagating action potentials, but also dendritic Ca(2+) spikes, the AMPA receptor-mediated EPSP, and NMDA receptor-mediated EPSPs or spikes. These often appear to be more important than the Na(+) spike in providing the depolarization necessary for plasticity. We thus feel that it is premature to accept STDP-like processes as the major determinant of LTP/LTD.

}, issn = {1663-3563}, doi = {10.3389/fnsyn.2010.00140}, author = {Lisman, John and Spruston, Nelson} } @article {46046, title = {Race-specific WBC and neutrophil count reference intervals.}, journal = {International Journal of Laboratory Hematology}, volume = {32}, year = {2010}, month = {2010 Dec}, pages = {590-7}, abstract = {

Healthy African Americans are known to have reduced white blood cell counts (WBC) and absolute neutrophil counts (ANC) compared with European Americans, with little agreement about the levels in reference intervals. The objective is to establish race-specific reference intervals for WBC and ANC using US National Health and Nutrition Examination Survey (NHANES) of 2000-2003. A total of 14,184 civilian noninstitutionalized US citizens participated in NHANES 2000-2003 had complete blood count, red cell distribution width, platelet count and automated WBC differential determined on a Coulter MAXM. The exclusion criteria were used: ferritin \<12 ng/ml, pregnancy, body mass index \>30, diastolic blood pressure \>100 mm Hg, creatinine \>2.5 mg/dl, glucose \>126 mg/dl. Data were separated into six sex/race categories: female non-Hispanic white, non-Hispanic black (NHBF)], Mexican American; male non-Hispanic white, non-Hispanic black (NHBM), Mexican American and two age groupings (12-18 and \>18 years). NHB 2.5-97.5 percentile WBC and (ANC) limits follow (units: {\texttimes} 10$^{9}$ /l): NHBM, ages 12-18: 3.2-9.3 (1.0-6.2); NHBF, ages 12-18: 3.7-10.1 (1.2-6.6); adult NHBM: 3.1-9.9 (1.3-6.6); adult NHBF: 3.4-11 (1.4-7.5). NHB limits are significantly lower than the NHW and MA limits. In most US healthcare organizations, insufficient agreement exists because of large differences in reference intervals for different ethnicities. In areas with peoples of African descent (\>10--20\%), race-specific WBC and ANC reference intervals must be provided for proper diagnosis and clinical research.

}, keywords = {Adult, African Continental Ancestry Group, Blood Cell Count, European Continental Ancestry Group, Female, Hispanic Americans, Humans, Leukocyte Count, Male, Neutrophils, Nutrition Surveys}, issn = {1751-553X}, doi = {10.1111/j.1751-553X.2010.01223.x}, author = {Lim, E-M and Cembrowski, George and Cembrowski, M and Clarke, G} } @article {987, title = {Refinement of tools for targeted gene expression in Drosophila.}, journal = {Genetics}, volume = {186}, year = {2010}, month = {2010 Oct}, pages = {735-55}, abstract = {

A wide variety of biological experiments rely on the ability to express an exogenous gene in a transgenic animal at a defined level and in a spatially and temporally controlled pattern. We describe major improvements of the methods available for achieving this objective in Drosophila melanogaster. We have systematically varied core promoters, UTRs, operator sequences, and transcriptional activating domains used to direct gene expression with the GAL4, LexA, and Split GAL4 transcription factors and the GAL80 transcriptional repressor. The use of site-specific integration allowed us to make quantitative comparisons between different constructs inserted at the same genomic location. We also characterized a set of PhiC31 integration sites for their ability to support transgene expression of both drivers and responders in the nervous system. The increased strength and reliability of these optimized reagents overcome many of the previous limitations of these methods and will facilitate genetic manipulations of greater complexity and sophistication.

}, issn = {1943-2631}, doi = {10.1534/genetics.110.119917}, author = {Pfeiffer, Barret D and Ngo, Teri-T B and Hibbard, Karen L and Murphy, Christine and Jenett, Arnim and Truman, James W and Rubin, Gerald M} } @article {47679, title = {Regulation of bile canalicular network formation and maintenance by AMP-activated protein kinase and LKB1.}, journal = {Journal of cell science}, volume = {123}, year = {2010}, month = {2010 Oct 1}, pages = {3294-302}, abstract = {

AMP-activated protein kinase (AMPK), a cellular metabolic sensor, is essential in energy regulation and metabolism. Hepatocyte polarization during liver development and regeneration parallels increased metabolism. The current study investigates the effects of AMPK and its upstream activator LKB1 on polarity and bile canalicular network formation and maintenance in collagen sandwich cultures of rat hepatocytes. Immunostaining for the apical protein ABCB1 and the tight junction marker occludin demonstrated that canalicular network formation is sequential and is associated with activation of AMPK and LKB1. AMPK and LKB1 activators accelerated canalicular network formation. Inhibition of AMPK or LKB1 by dominant-negative AMPK or kinase-dead LKB1 constructs blocked canalicular network formation. AICAR and 2-deoxyglucose, which activate AMPK, circumvented the inhibitory effect of kinase-dead LKB1 on canalicular formation, indicating that AMPK directly affects canalicular network formation. After the canalicular network was formed, inhibition of AMPK and LKB1 by dominant-negative AMPK or kinase-dead LKB1 constructs resulted in loss of canalicular network, indicating that AMPK and LKB1 also participate in network maintenance. In addition, activation of AMPK and LKB1 prevented low-Ca(2+)-mediated disruption of the canalicular network and tight junctions. These studies reveal that AMPK and its upstream kinase, LKB1, regulate canalicular network formation and maintenance.

}, keywords = {Animals, Bile Canaliculi, Cell Polarity, Cells, Cultured, Cloning, Molecular, Enzyme Activation, Hepatocytes, Male, Mutant Proteins, Organ Culture Techniques, Organogenesis, Protein Kinases, Protein-Serine-Threonine Kinases, Rats, Rats, Sprague-Dawley}, issn = {1477-9137}, doi = {10.1242/jcs.068098}, author = {Fu, Dong and Wakabayashi, Yoshiyuki and Ido, Yasuo and Lippincott-Schwartz, Jennifer and Arias, Irwin M} } @article {2549, title = {Reproductive constraints, direct fitness and indirect fitness benefits explain helping behaviour in the primitively eusocial wasp, Polistes canadensis.}, journal = {Proceedings. Biological Sciences / The Royal Society}, volume = {277}, year = {2010}, month = {2010 Jun 7}, pages = {1721-8}, abstract = {

A key step in the evolution of sociality is the abandonment of independent breeding in favour of helping. In cooperatively breeding vertebrates and primitively eusocial insects, helpers are capable of leaving the group and reproducing independently, and yet many do not. A fundamental question therefore is why do helpers help? Helping behaviour may be explained by constraints on independent reproduction and/or benefits to individuals from helping. Here, we examine simultaneously the reproductive constraints and fitness benefits underlying helping behaviour in a primitively eusocial paper wasp. We gave 31 helpers the opportunity to become egg-layers on their natal nests by removing nestmates. This allowed us to determine whether helpers are reproductively constrained in any way. We found that age strongly influenced whether an ex-helper could become an egg-layer, such that young ex-helpers could become egg-layers while old ex-helpers were less able. These differential reproductive constraints enabled us to make predictions about the behaviours of ex-helpers, depending on the relative importance of direct and indirect fitness benefits. We found little evidence that indirect fitness benefits explain helping behaviour, as 71 per cent of ex-helpers left their nests before the end of the experiment. In the absence of reproductive constraints, however, young helpers value direct fitness opportunities over indirect fitness. We conclude that a combination of reproductive constraints and potential for future direct reproduction explain helping behaviour in this species. Testing several competing explanations for helping behaviour simultaneously promises to advance our understanding of social behaviour in animal groups.

}, keywords = {Animal, Animals, Behavior, Female, Helping Behavior, Population Density, Reproduction, Social Behavior, Wasps}, issn = {1471-2954}, doi = {10.1098/rspb.2009.2289}, author = {Sumner, Seirian and Kelstrup, Hans and Fanelli, Daniele} } @article {2494, title = {A role for juvenile hormone in the prepupal development of Drosophila melanogaster.}, journal = {Development}, volume = {137}, year = {2010}, month = {2010 Apr}, pages = {1117-26}, abstract = {

To elucidate the role of juvenile hormone (JH) in metamorphosis of Drosophila melanogaster, the corpora allata cells, which produce JH, were killed using the cell death gene grim. These allatectomized (CAX) larvae were smaller at pupariation and died at head eversion. They showed premature ecdysone receptor B1 (EcR-B1) in the photoreceptors and in the optic lobe, downregulation of proliferation in the optic lobe, and separation of R7 from R8 in the medulla during the prepupal period. All of these effects of allatectomy were reversed by feeding third instar larvae on a diet containing the JH mimic (JHM) pyriproxifen or by application of JH III or JHM at the onset of wandering. Eye and optic lobe development in the Methoprene-tolerant (Met)-null mutant mimicked that of CAX prepupae, but the mutant formed viable adults, which had marked abnormalities in the organization of their optic lobe neuropils. Feeding Met(27) larvae on the JHM diet did not rescue the premature EcR-B1 expression or the downregulation of proliferation but did partially rescue the premature separation of R7, suggesting that other pathways besides Met might be involved in mediating the response to JH. Selective expression of Met RNAi in the photoreceptors caused their premature expression of EcR-B1 and the separation of R7 and R8, but driving Met RNAi in lamina neurons led only to the precocious appearance of EcR-B1 in the lamina. Thus, the lack of JH and its receptor Met causes a heterochronic shift in the development of the visual system that is likely to result from some cells {\textquoteright}misinterpreting{\textquoteright} the ecdysteroid peaks that drive metamorphosis.

}, keywords = {Animals, Basic Helix-Loop-Helix Transcription Factors, Biological, Corpora Allata, Diet, Drosophila melanogaster, Drosophila Proteins, Invertebrate, Juvenile Hormones, Larva, Metamorphosis, Neurons, Nonmammalian, Optic Lobe, Photoreceptor Cells, Pyridines, Receptors, Recombinant Fusion Proteins, RNA Interference, Steroid}, issn = {1477-9129}, doi = {10.1242/dev.037218}, author = {Riddiford, Lynn M and Truman, James W and Mirth, Christen K and Shen, Yu-Chi} } @article {2439, title = {Role of Notch signaling in establishing the hemilineages of secondary neurons in Drosophila melanogaster.}, journal = {Development}, volume = {137}, year = {2010}, month = {2010 Jan}, pages = {53-61}, abstract = {

The secondary neurons generated in the thoracic central nervous system of Drosophila arise from a hemisegmental set of 25 neuronal stem cells, the neuroblasts (NBs). Each NB undergoes repeated asymmetric divisions to produce a series of smaller ganglion mother cells (GMCs), which typically divide once to form two daughter neurons. We find that the two daughters of the GMC consistently have distinct fates. Using both loss-of-function and gain-of-function approaches, we examined the role of Notch signaling in establishing neuronal fates within all of the thoracic secondary lineages. In all cases, the {\textquoteright}A{\textquoteright} (Notch(ON)) sibling assumes one fate and the {\textquoteright}B{\textquoteright} (Notch(OFF)) sibling assumes another, and this relationship holds throughout the neurogenic period, resulting in two major neuronal classes: the A and B hemilineages. Apparent monotypic lineages typically result from the death of one sibling throughout the lineage, resulting in a single, surviving hemilineage. Projection neurons are predominantly from the B hemilineages, whereas local interneurons are typically from A hemilineages. Although sibling fate is dependent on Notch signaling, it is not necessarily dependent on numb, a gene classically involved in biasing Notch activation. When Numb was removed at the start of larval neurogenesis, both A and B hemilineages were still generated, but by the start of the third larval instar, the removal of Numb resulted in all neurons assuming the A fate. The need for Numb to direct Notch signaling correlated with a decrease in NB cell cycle time and may be a means for coping with multiple sibling pairs simultaneously undergoing fate decisions.

}, keywords = {Animals, Cell Lineage, Central Nervous System, Drosophila melanogaster, Drosophila Proteins, Immunohistochemistry, Neurons, Notch, Receptors, Signal Transduction, Stem Cells, Thorax}, issn = {1477-9129}, doi = {10.1242/dev.041749}, author = {Truman, James W and Moats, Wanda and Altman, Janet and Marin, Elizabeth C and Williams, Darren W} } @article {4378, title = {The role of the TRP channel NompC in Drosophila larval and adult locomotion.}, journal = {Neuron}, volume = {67}, year = {2010}, month = {2010 Aug 12}, pages = {373-80}, abstract = {

The generation of coordinated body movements relies on sensory feedback from mechanosensitive proprioceptors. We have found that the proper function of NompC, a putative mechanosensitive TRP channel, is not only required for fly locomotion, but also crucial for larval crawling. Calcium imaging revealed that NompC is required for the activation of two subtypes of sensory neurons during peristaltic muscle contractions. Having isolated a full-length nompC cDNA with a protein coding sequence larger than previously predicted, we demonstrate its function by rescuing locomotion defects in nompC mutants, and further show that antibodies against the extended C terminus recognize NompC in chordotonal ciliary tips. Moreover, we show that the ankyrin repeats in NompC are required for proper localization and function of NompC in vivo and are required for association of NompC with microtubules. Taken together, our findings suggest that NompC mediates proprioception in locomotion and support its role as a mechanosensitive channel.

}, keywords = {Age Factors, Amino Acid Sequence, Animals, Drosophila, Drosophila Proteins, Genetically Modified, Ion Channels, Larva, Locomotion, Molecular Sequence Data, Predictive Value of Tests, TRPC Cation Channels}, issn = {1097-4199}, doi = {10.1016/j.neuron.2010.07.004}, author = {Cheng, Li E and Ong, Wei S and Looger, Loren L and Jan, Lily Yeh and Jan, Yuh Nung} } @article {6388, title = {Scanning light-sheet microscopy in the whole mouse brain with HiLo background rejection.}, journal = {Journal of Biomedical Optics}, volume = {15}, year = {2010}, month = {2010 Jan-Feb}, pages = {016027}, abstract = {

It is well known that light-sheet illumination can enable optically sectioned wide-field imaging of macroscopic samples. However, the optical sectioning capacity of a light-sheet macroscope is undermined by sample-induced scattering or aberrations that broaden the thickness of the sheet illumination. We present a technique to enhance the optical sectioning capacity of a scanning light-sheet microscope by out-of-focus background rejection. The technique, called HiLo microscopy, makes use of two images sequentially acquired with uniform and structured sheet illumination. An optically sectioned image is then synthesized by fusing high and low spatial frequency information from both images. The benefits of combining light-sheet macroscopy and HiLo background rejection are demonstrated in optically cleared whole mouse brain samples, using both green fluorescent protein (GFP)-fluorescence and dark-field scattered light contrast.

}, keywords = {Animals, Background Radiation, Brain, Computer-Assisted, Fluorescence, Image Processing, Mice, Microscopy}, issn = {1560-2281}, doi = {10.1117/1.3324890}, author = {Mertz, Jerome and Kim, Jinhyun} } @article {2696, title = {Segmentation of center brains and optic lobes in 3D confocal images of adult fruit fly brains.}, journal = {Methods}, volume = {50}, year = {2010}, month = {2010 Feb}, pages = {63-9}, abstract = {

Automatic alignment (registration) of 3D images of adult fruit fly brains is often influenced by the significant displacement of the relative locations of the two optic lobes (OLs) and the center brain (CB). In one of our ongoing efforts to produce a better image alignment pipeline of adult fruit fly brains, we consider separating CB and OLs and align them independently. This paper reports our automatic method to segregate CB and OLs, in particular under conditions where the signal to noise ratio (SNR) is low, the variation of the image intensity is big, and the relative displacement of OLs and CB is substantial. We design an algorithm to find a minimum-cost 3D surface in a 3D image stack to best separate an OL (of one side, either left or right) from CB. This surface is defined as an aggregation of the respective minimum-cost curves detected in each individual 2D image slice. Each curve is defined by a list of control points that best segregate OL and CB. To obtain the locations of these control points, we derive an energy function that includes an image energy term defined by local pixel intensities and two internal energy terms that constrain the curve{\textquoteright}s smoothness and length. Gradient descent method is used to optimize this energy function. To improve both the speed and robustness of the method, for each stack, the locations of optimized control points in a slice are taken as the initialization prior for the next slice. We have tested this approach on simulated and real 3D fly brain image stacks and demonstrated that this method can reasonably segregate OLs from CBs despite the aforementioned difficulties.

}, keywords = {Algorithms, Animals, Automation, Brain, Brain Mapping, Computer Graphics, Computer Simulation, Computer-Assisted, Confocal, Drosophila melanogaster, Image Enhancement, Image Interpretation, Imaging, Microscopy, Models, Nonmammalian, Optic Lobe, Reproducibility of Results, Statistical, Three-Dimensional}, issn = {1095-9130}, doi = {10.1016/j.ymeth.2009.08.004}, author = {Lam, Shing Chun Benny and Ruan, Zongcai and Zhao, Ting and Long, Fuhui and Jenett, Arnim and Simpson, Julie and Myers, Eugene W and Peng, Hanchuan} } @article {1682, title = {Segregation of yeast nuclear pores.}, journal = {Nature}, volume = {466}, year = {2010}, month = {2010 Jul 22}, pages = {E1}, abstract = {

During mitosis in Saccharomyces cerevisiae, senescence factors such as extrachromosomal ribosomal DNA circles (ERCs) are retained in the mother cell and excluded from the bud/daughter cell. Shcheprova et al. proposed a model suggesting segregation of ERCs through their association with nuclear pore complexes (NPCs) and retention of preexisting NPCs in the mother cell during mitosis. However, this model is inconsistent with previous data and we demonstrate here that NPCs do efficiently migrate from the mother into the bud. Therefore, binding to NPCs does not seem to explain the retention of ERCs in the mother cell.

}, keywords = {Chromosome Segregation, DNA, Fungal, Mitosis, Nuclear Pore, Nuclear Pore Complex Proteins, Ribosomal, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins}, issn = {1476-4687}, doi = {10.1038/nature09255}, author = {Khmelinskii, Anton and Keller, Philipp J and Lorenz, Holger and Schiebel, Elmar and Knop, Michael} } @article {1234, title = {Semi-automated reconstruction of neural circuits using electron microscopy.}, journal = {Current Opinion in Neurobiology}, volume = {20}, year = {2010}, month = {2010 Oct}, pages = {667-75}, abstract = {

Reconstructing neuronal circuits at the level of synapses is a central problem in neuroscience, and the focus of the nascent field of connectomics. Previously used to reconstruct the C. elegans wiring diagram, serial-section transmission electron microscopy (ssTEM) is a proven technique for the task. However, to reconstruct more complex circuits, ssTEM will require the automation of image processing. We review progress in the processing of electron microscopy images and, in particular, a semi-automated reconstruction pipeline deployed at Janelia. Drosophila circuits underlying identified behaviors are being reconstructed in the pipeline with the goal of generating a complete Drosophila connectome.

}, issn = {1873-6882}, doi = {10.1371/journal.pcbi.1001066}, author = {Chklovskii, Dmitri B and Vitaladevuni, Shiv and Scheffer, Louis K} } @article {5371, title = {Serial-section EM derived synaptic circuits in the fly{\textquoteright}s visual system: the medulla opens up.}, journal = {Journal of Neurogenetics}, volume = {24}, year = {2010}, month = {2010}, pages = {9}, author = {Meinertzhagen, I. A. and Takemura, S and Vitaladevuni, S. and Lu, Z. and Scheffer, L. and Chklovskii, D.B.} } @article {1032, title = {Sex and the single cell. II. There is a time and place for sex.}, journal = {PLoS Biology}, volume = {8}, year = {2010}, month = {2010 May}, pages = {e1000365}, abstract = {

The Drosophila melanogaster sex hierarchy controls sexual differentiation of somatic cells via the activities of the terminal genes in the hierarchy, doublesex (dsx) and fruitless (fru). We have targeted an insertion of GAL4 into the dsx gene, allowing us to visualize dsx-expressing cells in both sexes. Developmentally and as adults, we find that both XX and XY individuals are fine mosaics of cells and tissues that express dsx and/or fruitless (fru(M)), and hence have the potential to sexually differentiate, and those that don{\textquoteright}t. Evolutionary considerations suggest such a mosaic expression of sexuality is likely to be a property of other animal species having two sexes. These results have also led to a major revision of our view of how sex-specific functions are regulated by the sex hierarchy in flies. Rather than there being a single regulatory event that governs the activities of all downstream sex determination regulatory genes-turning on Sex lethal (Sxl) RNA splicing activity in females while leaving it turned off in males-there are, in addition, elaborate temporal and spatial transcriptional controls on the expression of the terminal regulatory genes, dsx and fru. Thus tissue-specific aspects of sexual development are jointly specified by post-transcriptional control by Sxl and by the transcriptional controls of dsx and fru expression.

}, keywords = {Animals, Developmental, DNA-Binding Proteins, Drosophila melanogaster, Drosophila Proteins, Female, Gene Expression Regulation, Male, Nerve Tissue Proteins, Organ Specificity, RNA-Binding Proteins, Sex Characteristics, Sex Differentiation, Transcription Factors}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1000365}, author = {Robinett, Carmen C and Vaughan, Alexander G and Knapp, Jon-Michael and Baker, Bruce S} } @article {2046, title = {Single-molecule discrimination of discrete perisynaptic and distributed sites of actin filament assembly within dendritic spines. (With commentary)}, journal = {Neuron}, volume = {67}, year = {2010}, month = {2010 Jul 15}, pages = {86-99}, abstract = {

Within dendritic spines, actin is presumed to anchor receptors in the postsynaptic density and play numerous roles regulating synaptic transmission. However, the submicron dimensions of spines have hindered examination of actin dynamics within them and prevented live-cell discrimination of perisynaptic actin filaments. Using photoactivated localization microscopy, we measured movement of individual actin molecules within living spines. Velocity of single actin molecules along filaments, an index of filament polymerization rate, was highly heterogeneous within individual spines. Most strikingly, molecular velocity was elevated in discrete, well-separated foci occurring not principally at the spine tip, but in subdomains throughout the spine, including the neck. Whereas actin velocity on filaments at the synapse was substantially elevated, at the endocytic zone there was no enhanced polymerization activity. We conclude that actin subserves spatially diverse, independently regulated processes throughout spines. Perisynaptic actin forms a uniquely dynamic structure well suited for direct, active regulation of the synapse.

Commentary: A nice application of single particle tracking PALM (sptPALM), showing the flow of actin in the spines of live cultured neurons. Since 2008, the PALM in our lab has largely become a user facility, available to outside users as well as Janelians. Grad student Nick Frost in Tom Blanpied{\textquoteright}s group at the U. of Maryland Med School visited on a number of occasions to use the PALM, with training and assistance from Hari.

}, keywords = {Animals, Biological, Cells, Cultured, Dendritic Spines, Embryo, Green Fluorescent Proteins, Hippocampus, Mammalian, Microfilaments, Models, Nerve Tissue Proteins, Neuronal Plasticity, Neurons, Presynaptic Terminals, Protein Transport, Rats, Sprague-Dawley, Synaptic Transmission, Tissue Distribution, Transfection}, issn = {1097-4199}, doi = {10.1016/j.neuron.2010.05.026}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20624594}, author = {Frost, Nicholas A and Shroff, Hari and Kong, Huihui and Betzig, Eric and Blanpied, Thomas A} } @article {47680, title = {Single-particle tracking photoactivated localization microscopy for mapping single-molecule dynamics.}, journal = {Methods in enzymology}, volume = {475}, year = {2010}, month = {2010}, pages = {109-20}, abstract = {

Recent developments in single-molecule localization techniques using photoactivatable fluorescent proteins have allowed the probing of single-molecule motion in a living cell with high specificity, millisecond time resolution, and nanometer spatial resolution. Analyzing the dynamics of individual molecules at high densities in this manner promises to provide new insights into the mechanisms of many biological processes, including protein heterogeneity in the plasma membrane, the dynamics of cytoskeletal flow, and clustering of receptor complexes in response to signaling cues. Here we describe the method of single-molecule tracking photoactivated localization microscopy (sptPALM) and discuss how its use can contribute to a quantitative understanding of fundamental cellular processes.

}, keywords = {Fluorescent Dyes, Light, Membrane Proteins, Microscopy, Molecular Dynamics Simulation, Molecular Motor Proteins}, issn = {1557-7988}, doi = {10.1016/S0076-6879(10)75005-9}, author = {Manley, Suliana and Gillette, Jennifer M and Lippincott-Schwartz, Jennifer} } @article {2768, title = {Snapshot Image Mapping Spectrometer (IMS) with high sampling density for hyperspectral microscopy.}, journal = {Optics Express}, volume = {18}, year = {2010}, month = {2010 Jul 5}, pages = {14330-44}, abstract = {

A snapshot Image Mapping Spectrometer (IMS) with high sampling density is developed for hyperspectral microscopy, measuring a datacube of dimensions 285 x 285 x 60 (x, y, lambda). The spatial resolution is approximately 0.45 microm with a FOV of 100 x 100 microm(2). The measured spectrum is from 450 nm to 650 nm and is sampled by 60 spectral channels with average sampling interval approximately 3.3 nm. The channel{\textquoteright}s spectral resolution is approximately 8nm. The spectral imaging results demonstrate the potential of the IMS for real-time cellular fluorescence imaging.

}, keywords = {Animals, Cattle, Cell Nucleus, Endothelial Cells, Fluorescence, Imaging, Microscopy, Pulmonary Artery, Spectrum Analysis, Staining and Labeling, Three-Dimensional}, issn = {1094-4087}, doi = {10.1364/AO.50.001792}, author = {Gao, Liang and Kester, Robert T and Hagen, Nathan and Tkaczyk, Tomasz S} } @article {46161, title = {Software for bead-based registration of selective plane illumination microscopy data.}, journal = {Nature Methods}, volume = {7}, year = {2010}, month = {2010 Jun}, pages = {418-9}, keywords = {Animals, Caenorhabditis elegans, Drosophila melanogaster, Imaging, Three-Dimensional, Lighting, Microscopy, Software}, issn = {1548-7105}, doi = {10.1038/nmeth0610-418}, author = {Preibisch, Stephan and Saalfeld, Stephan and Schindelin, Johannes and Tomancak, Pavel} } @article {47678, title = {Starved cells use mitochondria for autophagosome biogenesis.}, journal = {Cell cycle (Georgetown, Tex.)}, volume = {9}, year = {2010}, month = {2010 Sep 15}, pages = {3633-4}, keywords = {Autophagy, Cytochromes b5, Endoplasmic Reticulum, Microtubule-Associated Proteins, Mitochondria, Phosphatidylethanolamines, Phosphatidylserines}, issn = {1551-4005}, doi = {10.4161/cc.9.18.13170}, author = {Rambold, Angelika S and Lippincott-Schwartz, Jennifer} } @article {46411, title = {Structural basis of low-affinity nickel binding to the nickel-responsive transcription factor NikR from Escherichia coli.}, journal = {Biochemistry}, volume = {49}, year = {2010}, month = {2010 Sep 14}, pages = {7830-8}, abstract = {

Escherichia coli NikR regulates cellular nickel uptake by binding to the nik operon in the presence of nickel and blocking transcription of genes encoding the nickel uptake transporter. NikR has two binding affinities for the nik operon: a nanomolar dissociation constant with stoichiometric nickel and a picomolar dissociation constant with excess nickel [Bloom, S. L., and Zamble, D. B. (2004) Biochemistry 43, 10029-10038; Chivers, P. T., and Sauer, R. T. (2002) Chem. Biol. 9, 1141-1148]. While it is known that the stoichiometric nickel ions bind at the NikR tetrameric interface [Schreiter, E. R., et al. (2003) Nat. Struct. Biol. 10, 794-799; Schreiter, E. R., et al. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 13676-13681], the binding sites for excess nickel ions have not been fully described. Here we have determined the crystal structure of NikR in the presence of excess nickel to 2.6 A resolution and have obtained nickel anomalous data (1.4845 A) in the presence of excess nickel for both NikR alone and NikR cocrystallized with a 30-nucleotide piece of double-stranded DNA containing the nik operon. These anomalous data show that excess nickel ions do not bind to a single location on NikR but instead reveal a total of 22 possible low-affinity nickel sites on the NikR tetramer. These sites, for which there are six different types, are all on the surface of NikR, and most are found in both the NikR alone and NikR-DNA structures. Using a combination of crystallographic data and molecular dynamics simulations, the nickel sites can be described as preferring octahedral geometry, utilizing one to three protein ligands (typically histidine) and at least two water molecules.

}, keywords = {Binding Sites, DNA, Escherichia coli, Escherichia coli Proteins, Ligands, Models, Molecular, Nickel, Protein Conformation, Repressor Proteins, Structure-Activity Relationship}, issn = {1520-4995}, doi = {10.1021/bi100923j}, author = {Phillips, Christine M and Schreiter, Eric R and Stultz, Collin M and Drennan, Catherine L} } @article {4298, title = {Structural plasticity underlies experience-dependent functional plasticity of cortical circuits.}, journal = {The Journal of Neuroscience}, volume = {30}, year = {2010}, month = {2010 Apr 7}, pages = {4927-32}, abstract = {

The stabilization of new spines in the barrel cortex is enhanced after whisker trimming, but its relationship to experience-dependent plasticity is unclear. Here we show that in wild-type mice, whisker potentiation and spine stabilization are most pronounced for layer 5 neurons at the border between spared and deprived barrel columns. In homozygote alphaCaMKII-T286A mice, which lack experience-dependent potentiation of responses to spared whiskers, there is no increase in new spine stabilization at the border between barrel columns after whisker trimming. Our data provide a causal link between new spine synapses and plasticity of adult cortical circuits and suggest that alphaCaMKII autophosphorylation plays a role in the stabilization but not formation of new spines.

}, keywords = {Animals, Cerebral Cortex, Dendritic Spines, Inbred C57BL, Learning, Male, Mice, Nerve Net, Neuronal Plasticity, Synapses, Transgenic, Vibrissae}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.6403-09.2010}, author = {Wilbrecht, Linda and Holtmaat, Anthony and Wright, Nick and Fox, Kevin and Svoboda, Karel} } @article {3633, title = {Structural underpinnings of nitrogen regulation by the prototypical nitrogen-responsive transcriptional factor NrpR.}, journal = {Structure}, volume = {18}, year = {2010}, month = {2010 Nov 10}, pages = {1512-21}, abstract = {

Plants and microorganisms reduce environmental inorganic nitrogen to ammonium, which then enters various metabolic pathways solely via conversion of 2-oxoglutarate (2OG) to glutamate and glutamine. Cellular 2OG concentrations increase during nitrogen starvation. We recently identified a family of 2OG-sensing proteins{\textendash}the nitrogen regulatory protein NrpR{\textendash}that bind DNA and repress transcription of nitrogen assimilation genes. We used X-ray crystallography to determine the structure of NrpR regulatory domain. We identified the NrpR 2OG-binding cleft and show that residues predicted to interact directly with 2OG are conserved among diverse classes of 2OG-binding proteins. We show that high levels of 2OG inhibit NrpRs ability to bind DNA. Electron microscopy analyses document that NrpR adopts different quaternary structures in its inhibited 2OG-bound state compared with its active apo state. Our results indicate that upon 2OG release, NrpR repositions its DNA-binding domains correctly for optimal interaction with DNA thereby enabling gene repression.

}, keywords = {Archaeal, Electron, Gene Expression Regulation, Ketoglutaric Acids, Methanococcus, Microscopy, Models, Molecular, Molecular Dynamics Simulation, Nitrogen, PII Nitrogen Regulatory Proteins, Protein Conformation, Quaternary Ammonium Compounds, Transcription Factors}, issn = {1878-4186}, doi = {10.1016/j.str.2010.08.014}, author = {Wisedchaisri, Goragot and Dranow, David M and Lie, Thomas J and Bonanno, Jeffrey B and Patskovsky, Yury and Ozyurt, Sinem A and Sauder, J Michael and Almo, Steven C and Wasserman, Stephen R and Burley, Stephen K and Leigh, John A and Gonen, Tamir} } @article {6340, title = {Structure of clathrin coat with bound Hsc70 and auxilin: mechanism of Hsc70-facilitated disassembly.}, journal = {The EMBO Journal}, volume = {29}, year = {2010}, month = {2010 Feb 3}, pages = {655-65}, abstract = {

The chaperone Hsc70 drives the clathrin assembly-disassembly cycle forward by stimulating dissociation of a clathrin lattice. A J-domain containing co-chaperone, auxilin, associates with a freshly budded clathrin-coated vesicle, or with an in vitro assembled clathrin coat, and recruits Hsc70 to its specific heavy-chain-binding site. We have determined by electron cryomicroscopy (cryoEM), at about 11 A resolution, the structure of a clathrin coat (in the D6-barrel form) with specifically bound Hsc70 and auxilin. The Hsc70 binds a previously analysed site near the C-terminus of the heavy chain, with a stoichiometry of about one per three-fold vertex. Its binding is accompanied by a distortion of the clathrin lattice, detected by a change in the axial ratio of the D6 barrel. We propose that when Hsc70, recruited to a position close to its target by the auxilin J-domain, splits ATP, it clamps firmly onto its heavy-chain site and locks in place a transient fluctuation. Accumulation of the local strain thus imposed at multiple vertices can then lead to disassembly.

}, keywords = {Animals, Auxilins, Biological, Cattle, Clathrin, Clathrin-Coated Vesicles, Cryoelectron Microscopy, HSC70 Heat-Shock Proteins, Models, Molecular, Multiprotein Complexes, Protein Binding, Protein Multimerization, Protein Structure, Quaternary, Secondary}, issn = {1460-2075}, doi = {10.1038/emboj.2009.383}, author = {Xing, Yi and B{\"o}cking, Till and Wolf, Matthias and Grigorieff, Nikolaus and Kirchhausen, Tomas and Harrison, Stephen C} } @article {5688, title = {Structure of the central nervous system of a juvenile acoel, Symsagittifera roscoffensis.}, journal = {Development Genes \& Evolution}, volume = {220}, year = {2010}, month = {2010 Sep}, pages = {61-76}, abstract = {

The neuroarchitecture of Acoela has been at the center of morphological debates. Some authors, using immunochemical tools, suggest that the nervous system in Acoela is organized as a commissural brain that bears little resemblance to the central, ganglionic type brain of other flatworms, and bilaterians in general. Others, who used histological staining on paraffin sections, conclude that it is a compact structure (an endonal brain; e.g., Raikova 2004; von Graff 1891; Delage Arch Zool Exp G{\'e}n 4:109-144, 1886). To address this question with modern tools, we have obtained images from serial transmission electron microscopic sections of the entire hatchling of Symsagittifera roscoffensis. In addition, we obtained data from wholemounts of hatchlings labeled with markers for serotonin and tyrosinated tubulin. Our data show that the central nervous system of a juvenile S. roscoffensis consists of an anterior compact brain, formed by a dense, bilobed mass of neuronal cell bodies surrounding a central neuropile. The neuropile flanks the median statocyst and contains several types of neurites, classified according to their types of synaptic vesicles. The neuropile issues three pairs of nerve cords that run at different dorso-ventral positions along the whole length of the body. Neuronal cell bodies flank the cords, and neuromuscular synapses are abundant. The TEM analysis also reveals different classes of peripheral sensory neurons and provides valuable information about the spatial relationships between neurites and other cell types within the brain and nerve cords. We conclude that the acoel S. roscoffensis has a central brain that is comparable in size and architecture to the brain of other (rhabditophoran) flatworms.

}, keywords = {Anatomic, Animals, Brain, Central Nervous System, Electron, Imaging, Microscopy, Models, Muscles, Nerve Fibers, Nerve Net, Neurites, Neuropil, Platyhelminths, Sensory Receptor Cells, Synapses, Three-Dimensional, Transmission}, issn = {1432-041X}, doi = {10.1007/s00427-010-0328-2}, author = {Bery, Amandine and Cardona, Albert and Martinez, Pedro and Hartenstein, Volker.} } @article {3632, title = {Structure of the cholera toxin secretion channel in its closed state.}, journal = {Nature Structural \& Molecular Biology}, volume = {17}, year = {2010}, month = {2010 Oct}, pages = {1226-32}, abstract = {

The type II secretion system (T2SS) is a macromolecular complex spanning the inner and outer membranes of Gram-negative bacteria. Remarkably, the T2SS secretes folded proteins, including multimeric assemblies such as cholera toxin and heat-labile enterotoxin from Vibrio cholerae and enterotoxigenic Escherichia coli, respectively. The major outer membrane T2SS protein is the {\textquoteright}secretin{\textquoteright} GspD. Cryo-EM reconstruction of the V. cholerae secretin at 19-{\r A} resolution reveals a dodecameric structure reminiscent of a barrel, with a large channel at its center that contains a closed periplasmic gate. The GspD periplasmic domain forms a vestibule with a conserved constriction, and it binds to a pentameric exoprotein and to the trimeric tip of the T2SS pseudopilus. By combining our results with structures of the cholera toxin and T2SS pseudopilus tip, we provide a structural basis for a possible secretion mechanism of the T2SS.

}, keywords = {Amino Acid, Amino Acid Sequence, Bacterial, Bacterial Outer Membrane Proteins, Cholera Toxin, Computer-Assisted, Conserved Sequence, Cryoelectron Microscopy, Fimbriae, Image Processing, Models, Molecular, Molecular Sequence Data, Periplasm, Protein Conformation, Protein Structure, Recombinant Fusion Proteins, Sequence Alignment, Sequence Homology, Surface Plasmon Resonance, Tertiary, Vibrio cholerae}, issn = {1545-9985}, doi = {10.1038/nsmb.1910}, author = {Reichow, Steve L and Korotkov, Konstantin V and Hol, Wim G J and Gonen, Tamir} } @article {1453, title = {Subtomogram alignment by adaptive Fourier coefficient thresholding.}, journal = {Journal of Structural Biology}, volume = {171}, year = {2010}, month = {2010 Sep}, pages = {332-44}, abstract = {

In the past few years, three-dimensional (3D) subtomogram alignment has become an important tool in cryo-electron tomography (CET). This technique allows one to produce higher resolution images of structures which can not be reconstructed using single-particle methods. Building on previous work, we present a new dissimilarity measure between subtomograms that works well for the noisy images that often occur in CET images. A technique that is more robust to noise provides the ability to analyze macromolecules in thicker samples such as whole cells or lower the defocus in thinner samples to push the first zero of the Contrast Transfer Function (CTF). Our method, Threshold Constrained Cross-Correlation (TCCC), uses statistics of the noise to automatically select only a small percentage of the Fourier coefficients to compute the cross-correlation, which has two main advantages: first, it reduces the influence of the noise by looking at only those peaks dominated by signal; and second, it avoids the missing wedge normalization problem since we consider the same number of coefficients for all possible pairs of subtomograms. We present results with synthetic and real data to compare our approach with other existing methods under different SNR and missing wedge conditions, and show that TCCC improves alignment results for datasets with SNR\<0.1. We have made our source code freely available for the community.

}, keywords = {Algorithms, Electron Microscope Tomography}, issn = {1095-8657}, doi = {10.1016/j.jsb.2010.05.013}, author = {Amat, Fernando and Comolli, Luis R and Moussavi, Farshid and Smit, John and Downing, Kenneth H and Horowitz, Mark} } @article {6336, title = {Subunit interactions in bovine papillomavirus.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, year = {2010}, month = {2010 Apr 6}, pages = {6298-303}, abstract = {

Papillomaviruses, members of a group of dsDNA viruses associated with epithelial growths and tumors, have compact capsids assembled from 72 pentamers of the protein L1. We have determined the structure of bovine papillomavirus by electron cryomicrosopy (cryoEM), at approximately 3.6 A resolution. The density map, obtained from single-particle analysis of approximately 4,000 particle images, shows the trace of the L1 polypeptide chain and reveals how the N- and C-terminal "arms" of a subunit (extensions from its beta-jelly-roll core) associate with a neighboring pentamer. Critical contacts come from the C-terminal arm, which loops out from the core of the subunit, forms contacts (including a disulfide) with two subunits in a neighboring pentamer, and reinserts into the pentamer from which it emanates. This trace corrects one feature of an earlier model. We discuss implications of the structure for virion assembly and for pathways of infectious viral entry. We suggest that it should be possible to obtain image reconstructions of comparable resolution from cryoEM images of asymmetric particles. From the work on papillomavirus described here, we estimate that such a reconstruction will require about 1.5 million images to achieve the same number of averaged asymmetric units; structural variability will increase this number substantially.

}, keywords = {Cryoelectron Microscopy, Models, Molecular, Papillomaviridae, Protein Interaction Domains and Motifs, Protein Structure, Protein Subunits, Quaternary, Tertiary, Viral Envelope Proteins, Virion}, issn = {1091-6490}, doi = {10.1073/pnas.0914604107}, author = {Wolf, Matthias and Garcea, Robert L and Grigorieff, Nikolaus and Harrison, Stephen C} } @article {47683, title = {Superresolution imaging using single-molecule localization.}, journal = {Annual review of physical chemistry}, volume = {61}, year = {2010}, month = {2010}, pages = {345-67}, abstract = {

Superresolution imaging is a rapidly emerging new field of microscopy that dramatically improves the spatial resolution of light microscopy by over an order of magnitude (approximately 10-20-nm resolution), allowing biological processes to be described at the molecular scale. Here, we discuss a form of superresolution microscopy based on the controlled activation and sampling of sparse subsets of photoconvertible fluorescent molecules. In this single-molecule-based imaging approach, a wide variety of probes have proved valuable, ranging from genetically encodable photoactivatable fluorescent proteins to photoswitchable cyanine dyes. These have been used in diverse applications of superresolution imaging: from three-dimensional, multicolor molecule localization to tracking of nanometric structures and molecules in living cells. Single-molecule-based superresolution imaging thus offers exciting possibilities for obtaining molecular-scale information on biological events occurring at variable timescales.

}, keywords = {Image Interpretation, Computer-Assisted, Luminescent Proteins, Microscopy, Fluorescence, Microscopy, Polarization}, issn = {1545-1593}, doi = {10.1146/annurev.physchem.012809.103444}, author = {Patterson, George and Davidson, Michael and Manley, Suliana and Lippincott-Schwartz, Jennifer} } @article {6531, title = {Surprisingly simple mechanical behavior of a complex embryonic tissue.}, journal = {PloS one}, volume = {5}, year = {2010}, month = {2010}, pages = {e15359}, abstract = {

BACKGROUND: Previous studies suggest that mechanical feedback could coordinate morphogenetic events in embryos. Furthermore, embryonic tissues have complex structure and composition and undergo large deformations during morphogenesis. Hence we expect highly non-linear and loading-rate dependent tissue mechanical properties in embryos. METHODOLOGY/PRINCIPAL FINDINGS: We used micro-aspiration to test whether a simple linear viscoelastic model was sufficient to describe the mechanical behavior of gastrula stage Xenopus laevis embryonic tissue in vivo. We tested whether these embryonic tissues change their mechanical properties in response to mechanical stimuli but found no evidence of changes in the viscoelastic properties of the tissue in response to stress or stress application rate. We used this model to test hypotheses about the pattern of force generation during electrically induced tissue contractions. The dependence of contractions on suction pressure was most consistent with apical tension, and was inconsistent with isotropic contraction. Finally, stiffer clutches generated stronger contractions, suggesting that force generation and stiffness may be coupled in the embryo. CONCLUSIONS/SIGNIFICANCE: The mechanical behavior of a complex, active embryonic tissue can be surprisingly well described by a simple linear viscoelastic model with power law creep compliance, even at high deformations. We found no evidence of mechanical feedback in this system. Together these results show that very simple mechanical models can be useful in describing embryo mechanics.

}, keywords = {Animals, Developmental Biology, Elasticity, Embryo, Gastrula, Mechanical, Models, Morphogenesis, Muscle Contraction, Nonmammalian, Statistical, Stress, Surface Properties, Viscosity, Xenopus laevis}, issn = {1932-6203}, doi = {10.1371/journal.pone.0015359}, author = {von Dassow, Michelangelo and Strother, James A and Davidson, Lance A} } @article {2342, title = {Temporal delays among place cells determine the frequency of population theta oscillations in the hippocampus.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, year = {2010}, month = {2010 Apr 27}, pages = {7957-62}, abstract = {

Driven either by external landmarks or by internal dynamics, hippocampal neurons form sequences of cell assemblies. The coordinated firing of these active cells is organized by the prominent "theta" oscillations in the local field potential (LFP): place cells discharge at progressively earlier theta phases as the rat crosses the respective place field ("phase precession"). The faster oscillation frequency of active neurons and the slower theta LFP, underlying phase precession, creates a paradox. How can faster oscillating neurons comprise a slower population oscillation, as reflected by the LFP? We built a mathematical model that allowed us to calculate the population activity analytically from experimentally derived parameters of the single neuron oscillation frequency, firing field size (duration), and the relationship between within-theta delays of place cell pairs and their distance representations ("compression"). The appropriate combination of these parameters generated a constant frequency population rhythm along the septo-temporal axis of the hippocampus, while allowing individual neurons to vary their oscillation frequency and field size. Our results suggest that the faster-than-theta oscillations of pyramidal cells are inherent and that phase precession is a result of the coordinated activity of temporally shifted cell assemblies, relative to the population activity, reflected by the LFP.

}, keywords = {Action Potentials, Animals, Hippocampus, Locomotion, Models, Neurological, Pyramidal Cells, Rats, Theta Rhythm}, issn = {1091-6490}, doi = {10.1523/JNEUROSCI.3773-10.2011}, author = {Geisler, Caroline and Diba, Kamran and Pastalkova, Eva and Mizuseki, Kenji and Royer, S{\'e}bastien and Buzs{\'a}ki, Gy{\"o}rgy} } @article {3631, title = {Tension directly stabilizes reconstituted kinetochore-microtubule attachments.}, journal = {Nature}, volume = {468}, year = {2010}, month = {2010 Nov 25}, pages = {576-9}, abstract = {

Kinetochores are macromolecular machines that couple chromosomes to dynamic microtubule tips during cell division, thereby generating force to segregate the chromosomes. Accurate segregation depends on selective stabilization of correct {\textquoteright}bi-oriented{\textquoteright} kinetochore-microtubule attachments, which come under tension as the result of opposing forces exerted by microtubules. Tension is thought to stabilize these bi-oriented attachments indirectly, by suppressing the destabilizing activity of a kinase, Aurora B. However, a complete mechanistic understanding of the role of tension requires reconstitution of kinetochore-microtubule attachments for biochemical and biophysical analyses in vitro. Here we show that native kinetochore particles retaining the majority of kinetochore proteins can be purified from budding yeast and used to reconstitute dynamic microtubule attachments. Individual kinetochore particles maintain load-bearing associations with assembling and disassembling ends of single microtubules for \>30 min, providing a close match to the persistent coupling seen in vivo between budding yeast kinetochores and single microtubules. Moreover, tension increases the lifetimes of the reconstituted attachments directly, through a catch bond-like mechanism that does not require Aurora B. On the basis of these findings, we propose that tension selectively stabilizes proper kinetochore-microtubule attachments in vivo through a combination of direct mechanical stabilization and tension-dependent phosphoregulation.

}, keywords = {Chromosomes, Fungal Proteins, Kinetochores, Microtubules, Saccharomyces cerevisiae}, issn = {1476-4687}, doi = {10.1038/nature09594}, author = {Akiyoshi, Bungo and Sarangapani, Krishna K and Powers, Andrew F and Nelson, Christian R and Reichow, Steve L and Arellano-Santoyo, Hugo and Gonen, Tamir and Ranish, Jeffrey A and Asbury, Charles L and Biggins, Sue} } @article {6487, title = {Tetracycline-controlled transgene activation using the ROSA26-iM2-GFP knock-in mouse strain permits GFP monitoring of DOX-regulated transgene-expression.}, journal = {BMC Developmental Biology}, volume = {10}, year = {2010}, month = {2010}, pages = {95}, abstract = {

BACKGROUND: Conditional gene activation is an efficient strategy for studying gene function in genetically modified animals. Among the presently available gene switches, the tetracycline-regulated system has attracted considerable interest because of its unique potential for reversible and adjustable gene regulation. RESULTS: To investigate whether the ubiquitously expressed Gt(ROSA)26Sor locus enables uniform DOX-controlled gene expression, we inserted the improved tetracycline-regulated transcription activator iM2 together with an iM2 dependent GFP gene into the Gt(ROSA)26Sor locus, using gene targeting to generate ROSA26-iM2-GFP (R26t1Δ) mice. Despite the presence of ROSA26 promoter driven iM2, R26t1Δ mice showed very sparse DOX-activated expression of different iM2-responsive reporter genes in the brain, mosaic expression in peripheral tissues and more prominent expression in erythroid, myeloid and lymphoid lineages, in hematopoietic stem and progenitor cells and in olfactory neurons. CONCLUSIONS: The finding that gene regulation by the DOX-activated transcriptional factor iM2 in the Gt(ROSA)26Sor locus has its limitations is of importance for future experimental strategies involving transgene activation from the endogenous ROSA26 promoter. Furthermore, our ROSA26-iM2 knock-in mouse model (R26t1Δ) represents a useful tool for implementing gene function in vivo especially under circumstances requiring the side-by-side comparison of gene manipulated and wild type cells. Since the ROSA26-iM2 mouse allows mosaic gene activation in peripheral tissues and haematopoietic cells, this model will be very useful for uncovering previously unknown or unsuspected phenotypes.

}, keywords = {Animals, Doxycycline, Gene Knock-In Techniques, Genetic Techniques, Green Fluorescent Proteins, Mice, Tetracycline, Transgenes, Transgenic}, issn = {1471-213X}, doi = {10.1186/1471-213X-10-95}, author = {W{\"o}rtge, Simone and Eshkind, Leonid and Cabezas-Wallscheid, Nina and Lakaye, Bernard and Kim, Jinhyun and Heck, Rosario and Abassi, Yasmin and Diken, Mustafa and Sprengel, Rolf and Bockamp, Ernesto} } @article {6509, title = {Toward the second generation of optogenetic tools.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {30}, year = {2010}, month = {2010 Nov 10}, pages = {14998-5004}, abstract = {

This mini-symposium aims to provide an integrated perspective on recent developments in optogenetics. Research in this emerging field combines optical methods with targeted expression of genetically encoded, protein-based probes to achieve experimental manipulation and measurement of neural systems with superior temporal and spatial resolution. The essential components of the optogenetic toolbox consist of two kinds of molecular devices: actuators and reporters, which respectively enable light-mediated control or monitoring of molecular processes. The first generation of genetically encoded calcium reporters, fluorescent proteins, and neural activators has already had a great impact on neuroscience. Now, a second generation of voltage reporters, neural silencers, and functionally extended fluorescent proteins hold great promise for continuing this revolution. In this review, we will evaluate and highlight the limitations of presently available optogenic tools and discuss where these technologies and their applications are headed in the future.

}, keywords = {Fluorescent Dyes, Genetic Engineering, Neurosciences}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4190-10.2010}, author = {Kn{\"o}pfel, Thomas and Lin, Michael Z and Levskaya, Anselm and Tian, Lin and Lin, John Y and Boyden, Edward S} } @article {4064, title = {Towards automated high-throughput screening of C. elegans on agar.}, journal = {Arxiv}, year = {2010}, abstract = {

High-throughput screening (HTS) using model organisms is a promising method to identify a small number of genes or drugs potentially relevant to human biology or disease. In HTS experiments, robots and computers do a significant portion of the experimental work. However, one remaining major bottleneck is the manual analysis of experimental results, which is commonly in the form of microscopy images. This manual inspection is labor intensive, slow and subjective. Here we report our progress towards applying computer vision and machine learning methods to analyze HTS experiments that use Caenorhabditis elegans (C. elegans) worms grown on agar. Our main contribution is a robust segmentation algorithm for separating the worms from the background using brightfield images. We also show that by combining the output of this segmentation algorithm with an algorithm to detect the fluorescent dye, Nile Red, we can reliably distinguish different fluorescence-based phenotypes even though the visual differences are subtle. The accuracy of our method is similar to that of expert human analysts. This new capability is a significant step towards fully automated HTS experiments using C. elegans.

}, author = {Kabra, Mayank and Conery, Annie L. and O{\textquoteright}Rourke, Eyleen J. and Xie, Xin and Ljosa. Vebjorn and Jones, Thouis R. and Ausubel, Frederick M. and Ruvkun, Gary and Carpenter, Anne E. and Freund, Yoav} } @article {1645, title = {Two-photon calcium imaging from head-fixed Drosophila during optomotor walking behavior.}, journal = {Nature Methods}, volume = {7}, year = {2010}, month = {2010 Jul}, pages = {535-40}, abstract = {

Drosophila melanogaster is a model organism rich in genetic tools to manipulate and identify neural circuits involved in specific behaviors. Here we present a technique for two-photon calcium imaging in the central brain of head-fixed Drosophila walking on an air-supported ball. The ball{\textquoteright}s motion is tracked at high resolution and can be treated as a proxy for the fly{\textquoteright}s own movements. We used the genetically encoded calcium sensor, GCaMP3.0, to record from important elements of the motion-processing pathway, the horizontal-system lobula plate tangential cells (LPTCs) in the fly optic lobe. We presented motion stimuli to the tethered fly and found that calcium transients in horizontal-system neurons correlated with robust optomotor behavior during walking. Our technique allows both behavior and physiology in identified neurons to be monitored in a genetic model organism with an extensive repertoire of walking behaviors.

}, keywords = {Animals, Brain, Calcium, Computer-Assisted, Drosophila melanogaster, Fluorescence, Green Fluorescent Proteins, Image Processing, Motion, Motor Activity, Neurons, Signal Transduction, Walking}, issn = {1548-7105}, doi = {10.1038/nmeth.1468}, author = {Seelig, Johannes D and Chiappe, M Eugenia and Lott, Gus K and Dutta, Anirban and Osborne, Jason E and Reiser, Michael B and Jayaraman, Vivek} } @article {4284, title = {Two-photon single-cell optogenetic control of neuronal activity by sculpted light.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, year = {2010}, month = {2010 Jun 29}, pages = {11981-6}, abstract = {

Recent advances in optogenetic techniques have generated new tools for controlling neuronal activity, with a wide range of neuroscience applications. The most commonly used approach has been the optical activation of the light-gated ion channel channelrhodopsin-2 (ChR2). However, targeted single-cell-level optogenetic activation with temporal precessions comparable to the spike timing remained challenging. Here we report fast (\< or = 1 ms), selective, and targeted control of neuronal activity with single-cell resolution in hippocampal slices. Using temporally focused laser pulses (TEFO) for which the axial beam profile can be controlled independently of its lateral distribution, large numbers of channels on individual neurons can be excited simultaneously, leading to strong (up to 15 mV) and fast (\< or = 1 ms) depolarizations. Furthermore, we demonstrated selective activation of cellular compartments, such as dendrites and large presynaptic terminals, at depths up to 150 microm. The demonstrated spatiotemporal resolution and the selectivity provided by TEFO allow manipulation of neuronal activity, with a large number of applications in studies of neuronal microcircuit function in vitro and in vivo.

}, keywords = {Action Potentials, Animals, Cell Line, Dendrites, Electrophysiological Phenomena, Hippocampus, Humans, Lasers, Mice, Nerve Tissue Proteins, Neurons, Optical Phenomena, Patch-Clamp Techniques, Photic Stimulation, Photons, Presynaptic Terminals, Rats, Recombinant Fusion Proteins, Rhodopsin, Sprague-Dawley, Transgenic}, issn = {1091-6490}, doi = {10.1073/pnas.1006620107}, author = {Andrasfalvy, Bertalan K and Zemelman, Boris V and Tang, Jianyong and Vaziri, Alipasha} } @article {4297, title = {Ultrafast widefield optical sectioning microscopy by multifocal temporal focusing.}, journal = {Optics Express}, volume = {18}, year = {2010}, month = {2010 Sep 13}, pages = {19645-55}, abstract = {

The need for optical sectioning in bio-imaging has amongst others led to the development of the two-photon scanning microscopy. However, this comes with some intrinsic fundamental limitations in the temporal domain as the focused spot has to be scanned mechanically in the sample plane. Hence for a large number of biological applications where imaging speed is a limiting factor, it would be significantly advantageous to generate widefield excitations with an optical sectioning comparable to the two-photon scanning microscopy. Recently by using the technique of temporal focusing it was shown that high axial resolution widefield excitation can be generated in picosecond time scales without any mechanical moving parts. However the achievable axial resolution is still well above that of a two-photon scanning microscope. Here we demonstrate a new ultrafast widefield two-photon imaging technique termed Multifocal Temporal Focusing (MUTEF) which relies on the generation of a set of diffraction limited beams produced by an Echelle grating that scan across a second tilted diffraction grating in picosecond time scale, generating a widefield excitation area with an axial resolution comparable to a two-photon scanning microscope. Using this method we have shown widefield two-photon imaging on fixed biological samples with an axial sectioning with a FWHM of \ 0.85 μm.

}, keywords = {Equipment Design, Equipment Failure Analysis, Fluorescence, Image Enhancement, Lenses, Lighting, Microscopy, Multiphoton, Refractometry, Reproducibility of Results, Sensitivity and Specificity}, issn = {1094-4087}, doi = {10.1364/OE.18.019645}, author = {Vaziri, Alipasha and Shank, Charles V} } @article {1235, title = {Ultrastructural analysis of hippocampal neuropil from the connectomics perspective.}, journal = {Neuron}, volume = {67}, year = {2010}, month = {2010 Sep 23}, pages = {1009-20}, abstract = {

Complete reconstructions of vertebrate neuronal circuits on the synaptic level require new approaches. Here, serial section transmission electron microscopy was automated to densely reconstruct four volumes, totaling 670 μm(3), from the rat hippocampus as proving grounds to determine when axo-dendritic proximities predict synapses. First, in contrast with Peters{\textquoteright} rule, the density of axons within reach of dendritic spines did not predict synaptic density along dendrites because the fraction of axons making synapses was variable. Second, an axo-dendritic touch did not predict a synapse; nevertheless, the density of synapses along a hippocampal dendrite appeared to be a universal fraction, 0.2, of the density of touches. Finally, the largest touch between an axonal bouton and spine indicated the site of actual synapses with about 80\% precision but would miss about half of all synapses. Thus, it will be difficult to predict synaptic connectivity using data sets missing ultrastructural details that distinguish between axo-dendritic touches and bona fide synapses.

}, keywords = {Animals, Automatic Data Processing, Axons, Dendrites, Electron, Hippocampus, Long-Evans, Male, Microscopy, Neuropil, Newborn, Rats, Synapses, Transmission}, issn = {1097-4199}, doi = {10.1371/journal.pcbi.1001066}, author = {Mishchenko, Yuriy and Hu, Tao and Spacek, Josef and Mendenhall, John and Harris, Kristen M and Chklovskii, Dmitri B} } @article {2387, title = {Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation.}, journal = {Nature Reviews. Genetics}, volume = {11}, year = {2010}, month = {2010 Aug}, pages = {549-58}, abstract = {

The eukaryotic core promoter recognition complex was generally thought to play an essential but passive role in the regulation of gene expression. However, recent evidence now indicates that core promoter recognition complexes together with {\textquoteright}non-prototypical{\textquoteright} subunits may have a vital regulatory function in driving cell-specific programmes of transcription during development. Furthermore, new roles for components of these complexes have been identified beyond development; for example, in mediating interactions with chromatin and in maintaining active gene expression across cell divisions.

}, keywords = {Animals, Cell Differentiation, DNA, Embryonic Development, Female, Genetic, Germ Cells, Humans, Male, Promoter Regions, RNA Polymerase II, Transcription, Transcription Factors, Transcriptional Activation}, issn = {1471-0064}, doi = {10.1073/pnas.1100640108}, author = {Goodrich, James A and Tjian, Robert} } @inbook {2558, title = {Using Drosophila to reveal insight into protein misfolding disease.}, booktitle = {Protein Misfolding Diseases: Current and Emerging Principles and Therapies}, year = {2010}, author = {Bilen, Julide and Bonini, Nancy M}, editor = {Ramirez- Alvarado, M and Kelly, J and Dobson, C} } @article {2328, title = {VAA3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets.}, journal = {Nature Biotechnology}, volume = {28}, year = {2010}, month = {2010 Apr}, pages = {348-53}, abstract = {

The V3D system provides three-dimensional (3D) visualization of gigabyte-sized microscopy image stacks in real time on current laptops and desktops. V3D streamlines the online analysis, measurement and proofreading of complicated image patterns by combining ergonomic functions for selecting a location in an image directly in 3D space and for displaying biological measurements, such as from fluorescent probes, using the overlaid surface objects. V3D runs on all major computer platforms and can be enhanced by software plug-ins to address specific biological problems. To demonstrate this extensibility, we built a V3D-based application, V3D-Neuron, to reconstruct complex 3D neuronal structures from high-resolution brain images. V3D-Neuron can precisely digitize the morphology of a single neuron in a fruitfly brain in minutes, with about a 17-fold improvement in reliability and tenfold savings in time compared with other neuron reconstruction tools. Using V3D-Neuron, we demonstrate the feasibility of building a 3D digital atlas of neurite tracts in the fruitfly brain.

}, keywords = {Computer Graphics, Computer-Assisted, Databases, Factual, Image Interpretation, Imaging, Information Storage and Retrieval, Microscopy, Radiology Information Systems, Three-Dimensional, User-Computer Interface}, issn = {1546-1696}, doi = {10.1038/nbt.1612}, author = {Peng, Hanchuan and Ruan, Zongcai and Long, Fuhui and Simpson, Julie H and Myers, Eugene W} } @article {2329, title = {Vibrissa-based object localization in head-fixed mice.}, journal = {The Journal of Neuroscience}, volume = {30}, year = {2010}, month = {2010 Feb 3}, pages = {1947-67}, abstract = {

Linking activity in specific cell types with perception, cognition, and action, requires quantitative behavioral experiments in genetic model systems such as the mouse. In head-fixed primates, the combination of precise stimulus control, monitoring of motor output, and physiological recordings over large numbers of trials are the foundation on which many conceptually rich and quantitative studies have been built. Choice-based, quantitative behavioral paradigms for head-fixed mice have not been described previously. Here, we report a somatosensory absolute object localization task for head-fixed mice. Mice actively used their mystacial vibrissae (whiskers) to sense the location of a vertical pole presented to one side of the head and reported with licking whether the pole was in a target (go) or a distracter (no-go) location. Mice performed hundreds of trials with high performance (\>90\% correct) and localized to \<0.95 mm (\<6 degrees of azimuthal angle). Learning occurred over 1-2 weeks and was observed both within and across sessions. Mice could perform object localization with single whiskers. Silencing barrel cortex abolished performance to chance levels. We measured whisker movement and shape for thousands of trials. Mice moved their whiskers in a highly directed, asymmetric manner, focusing on the target location. Translation of the base of the whiskers along the face contributed substantially to whisker movements. Mice tended to maximize contact with the go (rewarded) stimulus while minimizing contact with the no-go stimulus. We conjecture that this may amplify differences in evoked neural activity between trial types.

}, keywords = {Animals, Exploratory Behavior, Head Movements, Inbred C57BL, Mice, Movement, Physical, Restraint, Somatosensory Cortex, Space Perception, Touch, Vibrissae}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3762-09.2010}, author = {O{\textquoteright}Connor, Daniel H and Clack, Nathan G and Huber, Daniel and Komiyama, Takaki and Myers, Eugene W and Svoboda, Karel} } @article {2685, title = {Visual targeting of motor actions in climbing Drosophila.}, journal = {Current Biology}, volume = {20}, year = {2010}, month = {2010 Apr 13}, pages = {663-8}, abstract = {

Drosophila melanogaster flies cross surmountable gaps in their walkway of widths exceeding their body length with an astounding maneuver but avoid attempts at insurmountable gaps by visual width estimation. Different mutant lines affect specific aspects of this maneuver, indicating a high complexity and modularity of the underlying motor control. Here we report on two mutants, ocelliless(1) and tay bridge(1), that, although making a correct decision to climb, fail dramatically in aiming at the right direction. Both mutants show structural defects in the protocerebral bridge, a central complex neuropil formed like a handlebar spanning the brain hemispheres. The bridge has been implicated in step-length control in walking flies and celestial E-vector orientation in locusts. In rescue experiments using tay bridge(1) flies, the integrity of the bridge was reestablished, concomitantly leading to a significant improvement of their orientation at the gap. Although producing directional scatter, their attempts were clearly aimed at the landing site. However, this partial rescue was lost in these flies at a reduced-visibility landing site. We therefore conclude that the protocerebral bridge is an essential part of a visual targeting network that transmits directional clues to the motor output via a known projection system.

}, keywords = {Animals, Biological, Brain, Drosophila melanogaster, Genes, Genetically Modified, Insect, Models, Motor Activity, Mutation, Visual Perception}, issn = {1879-0445}, doi = {10.1016/j.cub.2010.02.055}, author = {Triphan, Tilman and Poeck, Burkhard and Neuser, Kirsa and Strauss, Roland} } @article {3759, title = {Walking modulates speed sensitivity in Drosophila motion vision.}, journal = {Current Biology}, volume = {20}, year = {2010}, month = {2010 Aug 24}, pages = {1470-5}, abstract = {

Changes in behavioral state modify neural activity in many systems. In some vertebrates such modulation has been observed and interpreted in the context of attention and sensorimotor coordinate transformations. Here we report state-dependent activity modulations during walking in a visual-motor pathway of Drosophila. We used two-photon imaging to monitor intracellular calcium activity in motion-sensitive lobula plate tangential cells (LPTCs) in head-fixed Drosophila walking on an air-supported ball. Cells of the horizontal system (HS){\textendash}a subgroup of LPTCs{\textendash}showed stronger calcium transients in response to visual motion when flies were walking rather than resting. The amplified responses were also correlated with walking speed. Moreover, HS neurons showed a relatively higher gain in response strength at higher temporal frequencies, and their optimum temporal frequency was shifted toward higher motion speeds. Walking-dependent modulation of HS neurons in the Drosophila visual system may constitute a mechanism to facilitate processing of higher image speeds in behavioral contexts where these speeds of visual motion are relevant for course stabilization.

}, keywords = {Animals, Calcium, Calcium Signaling, Drosophila, Motion Perception, Photic Stimulation, Walking}, issn = {1879-0445}, doi = {10.1016/j.cub.2010.06.072}, author = {Chiappe, M Eugenia and Seelig, Johannes D and Reiser, Michael B and Jayaraman, Vivek} } @proceedings {65006, title = {A wireless neural/EMG telemetry system for freely moving insects.}, year = {2010}, month = {2010 May 30}, abstract = {

We have developed a miniature telemetry system that captures neural, EMG, and acceleration signals from a freely moving insect and transmits the data wirelessly to a remote digital receiver. The system is based on a custom low-power integrated circuit that amplifies and digitizes four biopotential signals as well as three acceleration signals from an off-chip MEMS accelerometer, and transmits this information over a wireless 920-MHz telemetry link. The unit weighs 0.79 g and runs for two hours on two small batteries. We have used this system to monitor neural and EMG signals in jumping and flying locusts.

}, doi = {10.1109/ISCAS.2010.5538034}, author = {Reid R. Harrison and Ryan J. Kier and Anthony Leonardo and Haleh Fotowat and Raymond Chan and Fabrizio Gabbiani} } @article {2149, title = {A 3D digital atlas of C. elegans and its application to single-cell analyses.}, journal = {Nature Methods}, volume = {6}, year = {2009}, month = {2009 Sep}, pages = {667-72}, abstract = {

We built a digital nuclear atlas of the newly hatched, first larval stage (L1) of the wild-type hermaphrodite of Caenorhabditis elegans at single-cell resolution from confocal image stacks of 15 individual worms. The atlas quantifies the stereotypy of nuclear locations and provides other statistics on the spatial patterns of the 357 nuclei that could be faithfully segmented and annotated out of the 558 present at this developmental stage. We then developed an automated approach to assign cell names to each nucleus in a three-dimensional image of an L1 worm. We achieved 86\% accuracy in identifying the 357 nuclei automatically. This computational method will allow high-throughput single-cell analyses of the post-embryonic worm, such as gene expression analysis, or ablation or stimulation of cells under computer control in a high-throughput functional screen.

}, keywords = {Animals, Automatic Data Processing, Biological, Caenorhabditis elegans, Cell Lineage, Cell Nucleus, Models}, issn = {1548-7105}, doi = {10.1007/s12021-010-9090-x}, author = {Long, Fuhui and Peng, Hanchuan and Liu, Xiao and Kim, Stuart K and Myers, Eugene} } @article {6343, title = {Abeta(1-40) fibril polymorphism implies diverse interaction patterns in amyloid fibrils.}, journal = {Journal of Molecular Biology}, volume = {386}, year = {2009}, month = {2009 Feb 27}, pages = {869-77}, abstract = {

Amyloid fibrils characterize a diverse group of human diseases that includes Alzheimer{\textquoteright}s disease, Creutzfeldt-Jakob and type II diabetes. Alzheimer{\textquoteright}s amyloid fibrils consist of amyloid-beta (Abeta) peptide and occur in a range of structurally different fibril morphologies. The structural characteristics of 12 single Abeta(1-40) amyloid fibrils, all formed under the same solution conditions, were determined by electron cryo-microscopy and three-dimensional reconstruction. The majority of analyzed fibrils form a range of morphologies that show almost continuously altering structural properties. The observed fibril polymorphism implies that amyloid formation can lead, for the same polypeptide sequence, to many different patterns of inter- or intra-residue interactions. This property differs significantly from native, monomeric protein folding reactions that produce, for one protein sequence, only one ordered conformation and only one set of inter-residue interactions.

}, keywords = {Amyloid beta-Peptides, Cryoelectron Microscopy, Humans, Imaging, Peptide Fragments, Protein Binding, Protein Structure, Quaternary, Three-Dimensional}, issn = {1089-8638}, doi = {10.1016/j.jmb.2008.11.005}, author = {Meinhardt, Jessica and Sachse, Carsten and Hortschansky, Peter and Grigorieff, Nikolaus and F{\"a}ndrich, Marcus} } @article {2165, title = {Accelerating feature based registration using the Johnson-Lindenstrauss Lemma.}, journal = {Medical Image Computing and Computer-Assisted Intervention: MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention}, volume = {12}, year = {2009}, month = {2009}, pages = {632-9}, abstract = {

We introduce an efficient search strategy to substantially accelerate feature based registration. Previous feature based registration algorithms often use truncated search strategies in order to achieve small computation times. Our new accelerated search strategy is based on the realization that the search for corresponding features can be dramatically accelerated by utilizing Johnson-Lindenstrauss dimension reduction. Order of magnitude calculations for the search strategy we propose here indicate that the algorithm proposed is more than a million times faster than previously utilized naive search strategies, and this advantage in speed is directly translated into an advantage in accuracy as the fast speed enables more comparisons to be made in the same amount of time. We describe the accelerated scheme together with a full complexity analysis. The registration algorithm was applied to large transmission electron microscopy (TEM) images of neural ultrastructure. Our experiments demonstrate that our algorithm enables alignment of TEM images with increased accuracy and efficiency compared to previous algorithms.

}, keywords = {Algorithms, Animals, Artificial Intelligence, Automated, Computer-Assisted, Electron, Ferrets, Geniculate Bodies, Image Enhancement, Image Interpretation, Imaging, Microscopy, Pattern Recognition, Reproducibility of Results, Sensitivity and Specificity, Subtraction Technique, Three-Dimensional}, author = {Akselrod-Ballin, Ayelet and Bock, Davi and Reid, R Clay and Warfield, Simon K} } @article {3924, title = {Activity correlation imaging: visualizing function and structure of neuronal populations.}, journal = {Biophysical Journal}, volume = {96}, year = {2009}, month = {2009 May 6}, pages = {3801-9}, abstract = {

For the analysis of neuronal networks it is an important yet unresolved task to relate the neurons{\textquoteright} activities to their morphology. Here we introduce activity correlation imaging to simultaneously visualize the activity and morphology of populations of neurons. To this end we first stain the network{\textquoteright}s neurons using a membrane-permeable [Ca(2+)] indicator (e.g., Fluo-4/AM) and record their activities. We then exploit the recorded temporal activity patterns as a means of intrinsic contrast to visualize individual neurons{\textquoteright} dendritic morphology. The result is a high-contrast, multicolor visualization of the neuronal network. Taking the Xenopus olfactory bulb as an example we show the activities of the mitral/tufted cells of the olfactory bulb as well as their projections into the olfactory glomeruli. This method, yielding both functional and structural information of neuronal populations, will open up unprecedented possibilities for the investigation of neuronal networks.

}, keywords = {Aniline Compounds, Animals, Calcium, Computer Simulation, Confocal, Dendrites, Fura-2, Microscopy, Neurons, Olfactory Bulb, Patch-Clamp Techniques, Time Factors, Video Recording, Xanthenes, Xenopus laevis}, issn = {1542-0086}, doi = {10.1016/j.bpj.2008.12.3962}, author = {Junek, Stephan and Chen, Tsai-Wen and Alevra, Mihai and Schild, Detlev} } @proceedings {3295, title = {Algebraic approach to recovering topological information in distributed camera networks.}, year = {2009}, month = {2009 Apr 13}, abstract = {

Camera networks are widely used for tasks such as surveillance, monitoring and tracking. In order to accomplish these tasks, knowledge of localization information such as camera locations and other geometric constraints about the environment (e.g. walls, rooms, and building layout) are typically considered to be essential. However, this information is not always required for many tasks such as estimating the topology of camera network coverage, or coordinate-free object tracking and navigation. In this paper, we propose a simplicial representation (called CN- complex) that can be constructed from discrete local observations from cameras, and utilize this novel representation to recover the topological information of the network coverage. We prove that our representation captures the correct topological information from network coverage for 2.5-D layouts, and demonstrate their utility in simulations as well as a real-world experimental set-up. Our proposed approach is particularly useful in the context of ad-hoc camera networks in indoor/outdoor urban environments with distributed but limited computational power and energy.

}, author = {Ahammad, Parvez and Lobaton, E and Sastry, S} } @article {2697, title = {Analysis of cell fate from single-cell gene expression profiles in C. elegans.}, journal = {Cell}, volume = {139}, year = {2009}, month = {2009 Oct 30}, pages = {623-33}, abstract = {

The C. elegans cell lineage provides a unique opportunity to look at how cell lineage affects patterns of gene expression. We developed an automatic cell lineage analyzer that converts high-resolution images of worms into a data table showing fluorescence expression with single-cell resolution. We generated expression profiles of 93 genes in 363 specific cells from L1 stage larvae and found that cells with identical fates can be formed by different gene regulatory pathways. Molecular signatures identified repeating cell fate modules within the cell lineage and enabled the generation of a molecular differentiation map that reveals points in the cell lineage when developmental fates of daughter cells begin to diverge. These results demonstrate insights that become possible using computational approaches to analyze quantitative expression from many genes in parallel using a digital gene expression atlas.

}, keywords = {Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Cell Differentiation, Cell Lineage, Gene Expression Profiling}, issn = {1097-4172}, doi = {10.1016/j.cell.2009.08.044}, author = {Liu, Xiao and Long, Fuhui and Peng, Hanchuan and Aerni, Sarah J and Jiang, Min and S{\'a}nchez-Blanco, Adolfo and Murray, John I and Preston, Elicia and Mericle, Barbara and Batzoglou, Serafim and Myers, Eugene W and Kim, Stuart K} } @article {2792, title = {[Analysis on acupuncture literature in Science Citation Index (SCI) periodicals in 2007].}, journal = {Zhongguo Zhen Jiu = Chinese Acupuncture \& Moxibustion}, volume = {29}, year = {2009}, month = {2009 Jun}, pages = {504-7}, abstract = {

To grasp the international developing tendency of acupuncture research and provide some references for promoting acupuncture and moxibustion internationalization process, the articles about acupuncture in Science Citation Index (SCI) periodicals in 2007 were retrieved by adopting the retrieval tactics on line in combination with database searching. Results indicate that 257 articles about acupuncture had been retrived from the SCI Web databases. These articles were published in 125 journals respectively, most of which were Euramerican journals. Among these journals, the impact factor of the Journal of the American Medical Association (JAMA), 25. 547, is the highest one. It is shown that the impact factors of the SCI periodicals, in which acupuncture articles embodied are increased, the quality of these articles are improved obviously and the types of the articles are various in 2007, but there is obvious difference in the results of these studies due to the difference of experimental methods, the subjects of these experiments and acupuncture manipulations. Therefore, standardization of many problems arising from the researches on acupuncture is extremely imminent.

}, keywords = {Acupuncture, Acupuncture Therapy, Journal Impact Factor, Periodicals as Topic, Publications, Reference Standards}, issn = {0255-2930}, doi = {10.1364/AO.50.001792}, author = {Gao, Liang and Tian, Li-xin and Guo, Yi} } @article {48169, title = {An articulated statistical shape model for accurate hip joint segmentation.}, journal = {Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference}, volume = {2009}, year = {2009}, month = {2009}, pages = {6345-51}, abstract = {

In this paper we propose a framework for fully automatic, robust and accurate segmentation of the human pelvis and proximal femur in CT data. We propose a composite statistical shape model of femur and pelvis with a flexible hip joint, for which we extend the common definition of statistical shape models as well as the common strategy for their adaptation. We do not analyze the joint flexibility statistically, but model it explicitly by rotational parameters describing the bent in a ball-and-socket joint. A leave-one-out evaluation on 50 CT volumes shows that image driven adaptation of our composite shape model robustly produces accurate segmentations of both proximal femur and pelvis. As a second contribution, we evaluate a fine grain multi-object segmentation method based on graph optimization. It relies on accurate initializations of femur and pelvis, which our composite shape model can generate. Simultaneous optimization of both femur and pelvis yields more accurate results than separate optimizations of each structure. Shape model adaptation and graph based optimization are embedded in a fully automatic framework.

}, keywords = {Algorithms, Artificial Intelligence, Computer Simulation, Hip Joint, Imaging, Three-Dimensional, Models, Anatomic, Models, Statistical, Pattern Recognition, Automated, Radiographic Image Enhancement, Radiographic Image Interpretation, Computer-Assisted, Reproducibility of Results, Sensitivity and Specificity, Tomography, X-Ray Computed}, issn = {1557-170X}, doi = {10.1109/IEMBS.2009.5333269}, author = {Kainmueller, Dagmar and Lamecker, Hans and Zachow, Stefan and Hege, Hans-Christian} } @article {2678, title = {Automated monitoring and analysis of social behavior in Drosophila.}, journal = {Nature Methods}, volume = {6}, year = {2009}, month = {2009 Apr}, pages = {297-303}, abstract = {

We introduce a method based on machine vision for automatically measuring aggression and courtship in Drosophila melanogaster. The genetic and neural circuit bases of these innate social behaviors are poorly understood. High-throughput behavioral screening in this genetically tractable model organism is a potentially powerful approach, but it is currently very laborious. Our system monitors interacting pairs of flies and computes their location, orientation and wing posture. These features are used for detecting behaviors exhibited during aggression and courtship. Among these, wing threat, lunging and tussling are specific to aggression; circling, wing extension (courtship {\textquoteright}song{\textquoteright}) and copulation are specific to courtship; locomotion and chasing are common to both. Ethograms may be constructed automatically from these measurements, saving considerable time and effort. This technology should enable large-scale screens for genes and neural circuits controlling courtship and aggression.

}, keywords = {Animal, Animals, Artificial Intelligence, Automated, Behavior, Computer-Assisted, Drosophila melanogaster, Humans, Image Interpretation, Monitoring, Movement, Pattern Recognition, Physiologic, Posture, Social Behavior}, issn = {1548-7105}, doi = {10.1038/nmeth.1310}, author = {Dankert, Heiko and Wang, Liming and Hoopfer, Eric D and Anderson, David J and Perona, Pietro} } @article {48176, title = {Automatic Extraction of Anatomical Landmarks From Medical Image Data: An Evaluation of Different Methods}, year = {2009}, abstract = {

This work presents three different methods for automatic detection of anatomical landmarks in CT data, namely for the left and right anterior superior iliac spines and the pubic symphysis. The methods exhibit different degrees of generality in terms of portability to other anatomical landmarks and require a different amount of training data. The srst method is problem-specisc and is based on the convex hull of the pelvis. Method two is a more generic approach based on a statistical shape model including the landmarks of interest for every training shape. With our third method we present the most generic approach, where only a small set of training landmarks is required. Those landmarks are transferred to the patient specisc geometry based on Mean Value Coordinates (MVCs). The methods work on surfaces of the pelvis that need to be extracted beforehand. We perform this geometry reconstruction with our previously introduced fully automatic segmentation framework for the pelvic bones. With a focus on the accuracy of our novel MVC-based approach, we evaluate and compare our methods on 100 clinical CT datasets, for which gold standard landmarks were desned manually by multiple observers.

}, author = {Kainmueller, Dagmar and Hans-Christian Hege and Heiko Seim and Markus Heller and Stefan Zachow} } @article {48174, title = {Automatic extraction of mandibular nerve and bone from cone-beam CT data.}, journal = {Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention}, volume = {12}, year = {2009}, month = {2009}, pages = {76-83}, abstract = {

The exact localization of the mandibular nerve with respect to the bone is important for applications in dental implantology and maxillofacial surgery. Cone beam computed tomography (CBCT), often also called digital volume tomography (DVT), is increasingly utilized in maxillofacial or dental imaging. Compared to conventional CT, however, soft tissue discrimination is worse due to a reduced dose. Thus, small structures like the alveolar nerves are even harder recognizable within the image data. We show that it is nonetheless possible to accurately reconstruct the 3D bone surface and the course of the nerve in a fully automatic fashion, with a method that is based on a combined statistical shape model of the nerve and the bone and a Dijkstra-based optimization procedure. Our method has been validated on 106 clinical datasets: the average reconstruction error for the bone is 0.5 +/- 0.1 mm, and the nerve can be detected with an average error of 1.0 +/- 0.6 mm.

}, keywords = {Algorithms, Artificial Intelligence, Cone-Beam Computed Tomography, Humans, Mandible, Mandibular Nerve, Pattern Recognition, Automated, Radiographic Image Enhancement, Radiographic Image Interpretation, Computer-Assisted, Reproducibility of Results, Sensitivity and Specificity, Subtraction Technique}, author = {Kainmueller, Dagmar and Lamecker, Hans and Seim, Heiko and Zinser, Max and Zachow, Stefan} } @article {1495, title = {Automatic tracking of Escherichia coli in phase-contrast microscopy video.}, journal = {IEEE Transactions on Bio-Medical Engineering}, volume = {56}, year = {2009}, month = {2009 Feb}, pages = {390-9}, abstract = {

In this paper, we present an automatic method for estimating the trajectories of Escherichia coli bacteria from in vivo phase-contrast microscopy. To address the low-contrast boundaries in cellular images, an adaptive kernel-based technique is applied to detect cells in each frame. In addition to intensity features, region homogeneity measure and class uncertainty are also applied in this detection technique. To track cells with complex motion, a novel matching gain measure is introduced to cope with the challenges, particularly the presence of low-contrast boundary, the variations of appearance, and the frequent overlapping and occlusion. For multicell tracking over time, an optimal matching strategy is introduced to improve the handling of cell collision and broken trajectories. The results of successful tracking of Escherichia coli from various phase-contrast sequences are reported and compared with manually determined trajectories, as well as those obtained from existing tracking schemes. The stability of the algorithm with different parameter values is also analyzed and discussed.

}, keywords = {Algorithms, Artificial Intelligence, Automated, Chemotaxis, Computer-Assisted, Entropy, Escherichia coli, Image Processing, Microscopy, Pattern Recognition, Phase-Contrast, Video}, issn = {1558-2531}, doi = {10.1109/TBME.2008.2005956}, author = {Xie, Jun and Khan, Shahid and Shah, Mubarak} } @article {4276, title = {Automation of 3D reconstruction of neural tissue from large volume of conventional serial section transmission electron micrographs.}, journal = {Journal of Neuroscience Methods}, volume = {176}, year = {2009}, month = {2009 Jan 30}, pages = {276-89}, abstract = {

We describe an approach for automation of the process of reconstruction of neural tissue from serial section transmission electron micrographs. Such reconstructions require 3D segmentation of individual neuronal processes (axons and dendrites) performed in densely packed neuropil. We first detect neuronal cell profiles in each image in a stack of serial micrographs with multi-scale ridge detector. Short breaks in detected boundaries are interpolated using anisotropic contour completion formulated in fuzzy-logic framework. Detected profiles from adjacent sections are linked together based on cues such as shape similarity and image texture. Thus obtained 3D segmentation is validated by human operators in computer-guided proofreading process. Our approach makes possible reconstructions of neural tissue at final rate of about 5 microm3/manh, as determined primarily by the speed of proofreading. To date we have applied this approach to reconstruct few blocks of neural tissue from different regions of rat brain totaling over 1000microm3, and used these to evaluate reconstruction speed, quality, error rates, and presence of ambiguous locations in neuropil ssTEM imaging data.

}, keywords = {Animals, Automation, Axons, Electron, Imaging, Microscopy, Neurons, Three-Dimensional, Transmission}, issn = {0165-0270}, doi = {10.1016/j.jneumeth.2008.09.006}, author = {Mishchenko, Yuriy} } @proceedings {46793, title = {Bead-based mosaicing of single plane illumination microscopy images using geometric local descriptor matching.}, volume = {7259}, year = {2009}, month = {2009 Mar 27}, pages = {72592S}, publisher = {SPIE}, address = {Lake Buena Vista, FL}, abstract = {

Single Plane Illumination Microscopy (SPIM) is an emerging microscopic technique that enables live imaging of large biological specimens in their entirety. By imaging the biological sample from multiple angles, SPIM has the potential to achieve isotropic resolution throughout relatively large biological specimens. For every angle, however, only a shallow section of the specimen is imaged with high resolution, whereas deeper regions appear increasingly blurred. Existing intensity-based registration techniques still struggle to robustly and accurately align images that are characterized by limited overlap and/or heavy blurring. To be able to register such images, we add sub-resolution fluorescent beads to the rigid agarose medium in which the imaged specimen is embedded. For each segmented bead, we store the relative location of its n nearest neighbors in image space as rotation-invariant geometric local descriptors. Corresponding beads between overlapping images are identified by matching these descriptors. The bead correspondences are used to simultaneously estimate the globally optimal transformation for each individual image. The final output image is created by combining all images in an angle-independent output space, using volume injection and local content-based weighting of contributing images. We demonstrate the performance of our approach on data acquired from living embryos of Drosophila and fixed adult C.elegans worms. Bead-based registration outperformed intensity-based registration in terms of computation speed by two orders of magnitude while producing bead registration errors below 1 μm (about 1 pixel). It, therefore, provides an ideal tool for processing of long term time-lapse recordings of embryonic development consisting of hundreds of time points.

}, doi = {10.1117/12.812612}, author = {Preibisch, Stephan and Saalfeld, Stephan and Rohlfing, Torsten and Tomancak, Pavel} } @article {4275, title = {A bright and photostable photoconvertible fluorescent protein.}, journal = {Nature Methods}, volume = {6}, year = {2009}, month = {2009 Feb}, pages = {131-3}, abstract = {

Photoconvertible fluorescent proteins are potential tools for investigating dynamic processes in living cells and for emerging super-resolution microscopy techniques. Unfortunately, most probes in this class are hampered by oligomerization, small photon budgets or poor photostability. Here we report an EosFP variant that functions well in a broad range of protein fusions for dynamic investigations, exhibits high photostability and preserves the approximately 10-nm localization precision of its parent.

}, keywords = {Animals, Fibroblasts, Fluorescence, Fluorescent Dyes, Hela Cells, Humans, Luminescent Proteins, Microscopy, Mutagenesis, Photochemical Processes, Recombinant Fusion Proteins, Site-Directed}, issn = {1548-7105}, doi = {10.1038/nmeth.1296}, author = {McKinney, Sean A and Murphy, Christopher S and Hazelwood, Kristin L and Davidson, Michael W and Looger, Loren L} } @article {6348, title = {Burst-timing-dependent plasticity of NMDA receptor-mediated transmission in midbrain dopamine neurons.}, journal = {Neuron}, volume = {62}, year = {2009}, month = {2009 Jun 25}, pages = {826-38}, abstract = {

Bursts of spikes triggered by sensory stimuli in midbrain dopamine neurons evoke phasic release of dopamine in target brain areas, driving reward-based reinforcement learning and goal-directed behavior. NMDA-type glutamate receptors (NMDARs) play a critical role in the generation of these bursts. Here we report LTP of NMDAR-mediated excitatory transmission onto dopamine neurons in the substantia nigra. Induction of LTP requires burst-evoked Ca2+ signals amplified by preceding metabotropic neurotransmitter inputs in addition to the activation of NMDARs themselves. PKA activity gates LTP induction by regulating the magnitude of Ca2+ signal amplification. This form of plasticity is associative, input specific, reversible, and depends on the relative timing of synaptic input and postsynaptic bursting in a manner analogous to the timing rule for cue-reward learning paradigms in behaving animals. NMDAR plasticity might thus represent a potential neural substrate for conditioned dopamine neuron burst responses to environmental stimuli acquired during reward-based learning.

}, keywords = {2-Amino-5-phosphonovalerate, 4, 5-Trisphosphate, Action Potentials, Animals, Biophysics, Calcium, Dopamine, Dose-Response Relationship, Drug, Electric Stimulation, Enzyme Inhibitors, Excitatory Amino Acid Antagonists, Gene Expression Regulation, Inositol 1, Intracellular Signaling Peptides and Proteins, Long-Term Potentiation, Male, Mesencephalon, Methoxyhydroxyphenylglycol, N-Methyl-D-Aspartate, Neural Pathways, Neuronal Plasticity, Neurons, Peptide Fragments, Rats, Receptors, Sprague-Dawley, Time Factors}, issn = {1097-4199}, doi = {10.1016/j.neuron.2009.05.011}, author = {Harnett, Mark T and Bernier, Brian E and Ahn, Kee-Chan and Morikawa, Hitoshi} } @article {46421, title = {Caenorhabditis elegans innexins regulate active zone differentiation.}, journal = {The Journal of Neuroscience}, volume = {29}, year = {2009}, month = {2009 Apr 22}, pages = {5207-17}, abstract = {

In a genetic screen for active zone defective mutants in Caenorhabditis elegans, we isolated a loss-of-function allele of unc-7, a gene encoding an innexin/pannexin family gap junction protein. Innexin UNC-7 regulates the size and distribution of active zones at C. elegans neuromuscular junctions. Loss-of-function mutations in another innexin, UNC-9, cause similar active zone defects as unc-7 mutants. In addition to presumptive gap junction localizations, both UNC-7 and UNC-9 are also localized perisynaptically throughout development and required in presynaptic neurons to regulate active zone differentiation. Our mosaic analyses, electron microscopy, as well as expression studies suggest a novel and likely nonjunctional role of specific innexins in active zone differentiation in addition to gap junction formations.

}, keywords = {Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Cell Differentiation, Connexins, Gap Junctions, Gene Expression Regulation, Developmental, Male, Membrane Proteins, Organisms, Genetically Modified, Presynaptic Terminals}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0637-09.2009}, author = {Yeh, Edward and Kawano, Taizo and Ng, Sharon and Fetter, Richard and Hung, Wesley and Wang, Ying and Zhen, Mei} } @article {6347, title = {Calcium-sensing receptor: a high-affinity presynaptic target for aminoglycoside-induced weakness.}, journal = {Neuropharmacology}, volume = {57}, year = {2009}, month = {2009 Oct-Nov}, pages = {502-5}, abstract = {

Administration of aminoglycoside antibiotics can precipitate sudden, profound bouts of weakness that have been attributed to block of presynaptic voltage-activated calcium channels (VACCs) and failure of neuromuscular transmission. This serious adverse drug reaction is more likely in neuromuscular diseases such as myasthenia gravis. The relatively low affinity of VACC for aminoglycosides prompted us to explore alternative mechanisms. We hypothesized that the presynaptic Ca(2+)-sensing receptor (CaSR) may contribute to aminoglycoside-induced weakness due to its role in modulating synaptic transmission and its sensitivity to aminoglycosides in heterologous expression systems. We have previously shown that presynaptic CaSR controls a non-selective cation channel (NSCC) that regulates nerve terminal excitability and transmitter release. Using direct, electrophysiological recording, we report that neuronal VACCs are inhibited by neomycin (IC(50) 830 +/- 110 microM) at a much lower affinity than CaSR-modulated NSCC currents recorded from acutely isolated presynaptic terminals (synaptosomes; IC(50) 20 +/- 1 microM). Thus, at clinically relevant concentrations, aminoglycoside-induced weakness is likely precipitated by enhanced CaSR activation and subsequent decrease in terminal excitability rather than through direct inhibition of VACCs themselves.

}, keywords = {Aminoglycosides, Animals, Anti-Bacterial Agents, Calcium-Sensing, Ion Channels, Kinetics, Membrane Potentials, Muscle Weakness, Neomycin, Neurons, Patch-Clamp Techniques, Presynaptic Terminals, Rats, Receptors, Sprague-Dawley, Superior Cervical Ganglion, Synaptosomes}, issn = {1873-7064}, doi = {10.1016/j.neuropharm.2009.07.031}, author = {Harnett, Mark T and Chen, Wenyan and Smith, Stephen M} } @article {5817, title = {CATMAID: collaborative annotation toolkit for massive amounts of image data.}, journal = {Bioinformatics}, volume = {25}, year = {2009}, month = {2009 Aug 1}, pages = {1984-6}, abstract = {

SUMMARY: High-resolution, three-dimensional (3D) imaging of large biological specimens generates massive image datasets that are difficult to navigate, annotate and share effectively. Inspired by online mapping applications like GoogleMaps, we developed a decentralized web interface that allows seamless navigation of arbitrarily large image stacks. Our interface provides means for online, collaborative annotation of the biological image data and seamless sharing of regions of interest by bookmarking. The CATMAID interface enables synchronized navigation through multiple registered datasets even at vastly different scales such as in comparisons between optical and electron microscopy. AVAILABILITY: http://fly.mpi-cbg.de/catmaid.

}, keywords = {Algorithms, Computational Biology, Computer Graphics, Database Management Systems, Databases, Factual, Imaging, Information Storage and Retrieval, Software, Three-Dimensional}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btp266}, author = {Saalfeld, Stephan and Cardona, Albert and Hartenstein, Volker and Tomancak, Pavel} } @article {2197, title = {The challenges of sequencing by synthesis.}, journal = {Nature Biotechnology}, volume = {27}, year = {2009}, month = {2009 Nov}, pages = {1013-23}, abstract = {

DNA sequencing-by-synthesis (SBS) technology, using a polymerase or ligase enzyme as its core biochemistry, has already been incorporated in several second-generation DNA sequencing systems with significant performance. Notwithstanding the substantial success of these SBS platforms, challenges continue to limit the ability to reduce the cost of sequencing a human genome to $100,000 or less. Achieving dramatically reduced cost with enhanced throughput and quality will require the seamless integration of scientific and technological effort across disciplines within biochemistry, chemistry, physics and engineering. The challenges include sample preparation, surface chemistry, fluorescent labels, optimizing the enzyme-substrate system, optics, instrumentation, understanding tradeoffs of throughput versus accuracy, and read-length/phasing limitations. By framing these challenges in a manner accessible to a broad community of scientists and engineers, we hope to solicit input from the broader research community on means of accelerating the advancement of genome sequencing technology.

}, keywords = {Animals, DNA, Fluorescent Dyes, Humans, Optical Phenomena, Sequence Analysis, Substrate Specificity, Surface Properties}, issn = {1546-1696}, doi = {10.1038/nbt0510-426}, author = {Fuller, Carl W and Middendorf, Lyle R and Benner, Steven A and Church, George M and Harris, Timothy and Huang, Xiaohua and Jovanovich, Stevan B and Nelson, John R and Schloss, Jeffery A and Schwartz, David C and Vezenov, Dmitri V} } @inbook {3326, title = {Circuit dynamics and neural coding in the locust olfactory system.}, booktitle = {The New Encyclopedia of Neuroscience}, year = {2009}, publisher = {Elsevier Science}, organization = {Elsevier Science}, address = {Oxford}, author = {Jayaraman, Vivek and Laurent, Gilles} } @article {65013, title = {Cofactor engineering of lactobacillus brevis alcohol dehydrogenase by computational design.}, journal = {Engineering in Life Sciences}, volume = {9}, year = {2009}, month = {2009 Feb 20}, pages = {38-44}, abstract = {

The R-specific alcohol dehydrogenase from\ Lactobacillus brevis\ (Lb-ADH) catalyzes the enantioselective reduction of prochiral ketones to the corresponding secondary alcohols. It is stable and has broad substrate specificity. These features make this enzyme an attractive candidate for biotechnological applications. A drawback is its preference for NADP(H) as a cofactor, which is more expensive and labile than NAD(H). Structure-based computational protein engineering was used to predict mutations to alter the cofactor specificity of Lb-ADH. Mutations were introduced into Lb-ADH and tested against the substrate acetophenone, with either NAD(H) or NADP(H) as cofactor. The mutant Arg38Pro showed fourfold increased activity with acetophenone and NAD(H) relative to the wild type. Both Arg38Pro and wild type exhibit a pH optimum of 5.5 with NAD(H) as cofactor, significantly more acidic than with NADP(H). These and related Lb-ADH mutants may prove useful for the green synthesis of pharmaceutical precursors.

}, doi = {10.1002/elsc.200800046}, author = {Ronnie Machielsen and Loren L. Looger and John Raedts and Sjoerd Dijkhuizen and Werner Hummel and Hans-Georg Hennemann and Thomas Daussmann and John van der Oost} } @article {4387, title = {Common sense about taste: from mammals to insects.}, journal = {Cell}, volume = {139}, year = {2009}, month = {2009 Oct 16}, pages = {234-44}, abstract = {

The sense of taste is a specialized chemosensory system dedicated to the evaluation of food and drink. Despite the fact that vertebrates and insects have independently evolved distinct anatomic and molecular pathways for taste sensation, there are clear parallels in the organization and coding logic between the two systems. There is now persuasive evidence that tastant quality is mediated by labeled lines, whereby distinct and strictly segregated populations of taste receptor cells encode each of the taste qualities.

}, keywords = {Animals, Chemoreceptor Cells, Insects, Mammals, Taste, Taste Buds, Tongue}, issn = {1097-4172}, doi = {10.1016/j.cell.2009.10.001}, author = {Yarmolinsky, David A and Zuker, Charles S and Ryba, Nicholas J P} } @article {6498, title = {Comparative endocrinology in the 21st century.}, journal = {Integrative and Comparative Biology}, volume = {49}, year = {2009}, month = {2009 Oct}, pages = {339-48}, abstract = {

Hormones coordinate developmental, physiological, and behavioral processes within and between all living organisms. They orchestrate and shape organogenesis from early in development, regulate the acquisition, assimilation, and utilization of nutrients to support growth and metabolism, control gamete production and sexual behavior, mediate organismal responses to environmental change, and allow for communication of information between organisms. Genes that code for hormones; the enzymes that synthesize, metabolize, and transport hormones; and hormone receptors are important targets for natural selection, and variation in their expression and function is a major driving force for the evolution of morphology and life history. Hormones coordinate physiology and behavior of populations of organisms, and thus play key roles in determining the structure of populations, communities, and ecosystems. The field of endocrinology is concerned with the study of hormones and their actions. This field is rooted in the comparative study of hormones in diverse species, which has provided the foundation for the modern fields of evolutionary, environmental, and biomedical endocrinology. Comparative endocrinologists work at the cutting edge of the life sciences. They identify new hormones, hormone receptors and mechanisms of hormone action applicable to diverse species, including humans; study the impact of habitat destruction, pollution, and climatic change on populations of organisms; establish novel model systems for studying hormones and their functions; and develop new genetic strains and husbandry practices for efficient production of animal protein. While the model system approach has dominated biomedical research in recent years, and has provided extraordinary insight into many basic cellular and molecular processes, this approach is limited to investigating a small minority of organisms. Animals exhibit tremendous diversity in form and function, life-history strategies, and responses to the environment. A major challenge for life scientists in the 21st century is to understand how a changing environment impacts all life on earth. A full understanding of the capabilities of organisms to respond to environmental variation, and the resilience of organisms challenged by environmental changes and extremes, is necessary for understanding the impact of pollution and climatic change on the viability of populations. Comparative endocrinologists have a key role to play in these efforts.

}, issn = {1557-7023}, doi = {10.1093/icb/icp082}, author = {Denver, Robert J and Hopkins, Penny M and McCormick, Stephen D and Propper, Catherine R and Riddiford, Lynn and Sower, Stacia A and Wingfield, John C} } @article {48171, title = {Comparison and evaluation of methods for liver segmentation from CT datasets.}, journal = {IEEE transactions on medical imaging}, volume = {28}, year = {2009}, month = {2009 Aug}, pages = {1251-65}, abstract = {

This paper presents a comparison study between 10 automatic and six interactive methods for liver segmentation from contrast-enhanced CT images. It is based on results from the "MICCAI 2007 Grand Challenge" workshop, where 16 teams evaluated their algorithms on a common database. A collection of 20 clinical images with reference segmentations was provided to train and tune algorithms in advance. Participants were also allowed to use additional proprietary training data for that purpose. All teams then had to apply their methods to 10 test datasets and submit the obtained results. Employed algorithms include statistical shape models, atlas registration, level-sets, graph-cuts and rule-based systems. All results were compared to reference segmentations five error measures that highlight different aspects of segmentation accuracy. All measures were combined according to a specific scoring system relating the obtained values to human expert variability. In general, interactive methods reached higher average scores than automatic approaches and featured a better consistency of segmentation quality. However, the best automatic methods (mainly based on statistical shape models with some additional free deformation) could compete well on the majority of test images. The study provides an insight in performance of different segmentation approaches under real-world conditions and highlights achievements and limitations of current image analysis techniques.

}, keywords = {Algorithms, Bayes Theorem, Databases, Factual, Humans, Image Processing, Computer-Assisted, Liver, Tomography, X-Ray Computed}, issn = {1558-254X}, doi = {10.1109/TMI.2009.2013851}, author = {Heimann, Tobias and van Ginneken, Bram and Styner, Martin A and Arzhaeva, Yulia and Aurich, Volker and Bauer, Christian and Beck, Andreas and Becker, Christoph and Beichel, Reinhard and Bekes, Gy{\"o}rgy and Bello, Fernando and Binnig, Gerd and Bischof, Horst and Bornik, Alexander and Cashman, Peter M M and Chi, Ying and Cordova, Andr{\'e}s and Dawant, Benoit M and Fidrich, M{\'a}rta and Furst, Jacob D and Furukawa, Daisuke and Grenacher, Lars and Hornegger, Joachim and Kainm{\"u}ller, Dagmar and Kitney, Richard I and Kobatake, Hidefumi and Lamecker, Hans and Lange, Thomas and Lee, Jeongjin and Lennon, Brian and Li, Rui and Li, Senhu and Meinzer, Hans-Peter and Nemeth, G{\'a}bor and Raicu, Daniela S and Rau, Anne-Mareike and van Rikxoort, Eva M and Rousson, Mika{\"e}l and Rusko, L{\'a}szl{\'o} and Saddi, Kinda A and Schmidt, G{\"u}nter and Seghers, Dieter and Shimizu, Akinobu and Slagmolen, Pieter and Sorantin, Erich and Soza, Grzegorz and Susomboon, Ruchaneewan and Waite, Jonathan M and Wimmer, Andreas and Wolf, Ivo} } @article {46423, title = {A contiguous compartment functions as endoplasmic reticulum and endosome/lysosome in Giardia lamblia.}, journal = {Eukaryotic Cell}, volume = {8}, year = {2009}, month = {2009 Nov}, pages = {1665-76}, abstract = {

The dynamic evolution of organelle compartmentalization in eukaryotes and how strictly compartmentalization is maintained are matters of ongoing debate. While the endoplasmic reticulum (ER) is classically envisioned as the site of protein cotranslational translocation, it has recently been proposed to have pluripotent functions. Using transfected reporter constructs, organelle-specific markers, and functional enzyme assays, we now show that in an early-diverging protozoan, Giardia lamblia, endocytosis and subsequent degradation of exogenous proteins occur in the ER or in an adjacent and communicating compartment. The Giardia endomembrane system is simple compared to those of typical eukaryotes. It lacks peroxisomes, a classical Golgi apparatus, and canonical lysosomes. Giardia orthologues of mammalian lysosomal proteases function within an ER-like tubulovesicular compartment, which itself can dynamically communicate with clathrin-containing vacuoles at the periphery of the cell to receive endocytosed proteins. These primitive characteristics support Giardia{\textquoteright}s proposed early branching and could serve as a model to study the compartmentalization of endocytic and lysosomal functions into organelles distinct from the ER. This system also may have functional similarity to the retrograde transport of toxins and major histocompatibility complex class I function in the ER of mammals.

}, keywords = {Endoplasmic Reticulum, Endosomes, Giardia lamblia, Lysosomes, Protozoan Proteins}, issn = {1535-9786}, doi = {10.1128/EC.00123-09}, author = {Abodeely, Marla and DuBois, Kelly N and Hehl, Adrian and Stefanic, Sasa and Sajid, Mohammed and DeSouza, Wanderley and Attias, Marcia and Engel, Juan C and Hsieh, Ivy and Fetter, Richard D and McKerrow, James H} } @article {1577, title = {Correlated mutation analyses on super-family alignments reveal functionally important residues.}, journal = {Proteins}, volume = {76}, year = {2009}, month = {2009 Aug 15}, pages = {608-16}, abstract = {

Correlated mutation analyses (CMA) on multiple sequence alignments are widely used for the prediction of the function of amino acids. The accuracy of CMA-based predictions is mainly determined by the number of sequences, by their evolutionary distances, and by the quality of the alignments. These criteria are best met in structure-based sequence alignments of large super-families. So far, CMA-techniques have mainly been employed to study the receptor interactions. The present work shows how a novel CMA tool, called Comulator, can be used to determine networks of functionally related residues in enzymes. These analyses provide leads for protein engineering studies that are directed towards modification of enzyme specificity or activity. As proof of concept, Comulator has been applied to four enzyme super-families: the isocitrate lyase/phoshoenol-pyruvate mutase super-family, the hexokinase super-family, the RmlC-like cupin super-family, and the FAD-linked oxidases super-family. In each of those cases networks of functionally related residue positions were discovered that upon mutation influenced enzyme specificity and/or activity as predicted. We conclude that CMA is a powerful tool for redesigning enzyme activity and selectivity.

}, keywords = {Algorithms, Computational Biology, Glucose-6-Phosphate Isomerase, Hexokinase, Isocitrate Lyase, Models, Molecular, Mutagenesis, Oxidoreductases, Oxidoreductases Acting on CH-CH Group Donors, Protein Structure, Secondary, Software}, issn = {1097-0134}, doi = {10.1002/prot.22374}, author = {Kuipers, Remko K P and Joosten, Henk-Jan and Verwiel, Eugene and Paans, Sjoerd and Akerboom, Jasper and van der Oost, John and Leferink, Nicole G H and van Berkel, Willem J H and Vriend, Gert and Schaap, Peter J} } @article {2910, title = {A critical role for N-WASp in cell migration during central nervous system development.}, journal = {International Journal of Developmental Neuroscience}, volume = {26}, year = {2009}, month = {2008}, pages = {413}, author = {Jin, FJ and Bharioke, A and Zhang, JY and Kuhlmann, TK and Georgiou, JG and Lommel, SL and Siminovitch, KS} } @article {1555, title = {Crystal structures of the GCaMP calcium sensor reveal the mechanism of fluorescence signal change and aid rational design.}, journal = {The Journal of Biological Chemistry}, volume = {284}, year = {2009}, month = {2009 Mar 6}, pages = {6455-64}, abstract = {

The genetically encoded calcium indicator GCaMP2 shows promise for neural network activity imaging, but is currently limited by low signal-to-noise ratio. We describe x-ray crystal structures as well as solution biophysical and spectroscopic characterization of GCaMP2 in the calcium-free dark state, and in two calcium-bound bright states: a monomeric form that dominates at intracellular concentrations observed during imaging experiments and an unexpected domain-swapped dimer with decreased fluorescence. This series of structures provides insight into the mechanism of Ca2+-induced fluorescence change. Upon calcium binding, the calmodulin (CaM) domain wraps around the M13 peptide, creating a new domain interface between CaM and the circularly permuted enhanced green fluorescent protein domain. Residues from CaM alter the chemical environment of the circularly permuted enhanced green fluorescent protein chromophore and, together with flexible inter-domain linkers, block solvent access to the chromophore. Guided by the crystal structures, we engineered a series of GCaMP2 point mutants to probe the mechanism of GCaMP2 function and characterized one mutant with significantly improved signal-to-noise. The mutation is located at a domain interface and its effect on sensor function could not have been predicted in the absence of structural data.

}, keywords = {Animals, Calcium, Calcium-Binding Proteins, Crystallography, Fluorescent Dyes, Green Fluorescent Proteins, Models, Molecular, Peptides, Protein Binding, Protein Structure, Recombinant Fusion Proteins, Structure-Activity Relationship, Tertiary, X-Ray}, issn = {0021-9258}, doi = {10.1074/jbc.M807657200}, author = {Akerboom, Jasper and Rivera, Jonathan D V{\'e}lez and Guilbe, Mar{\'\i}a M Rodr{\'\i}guez and Malav{\'e}, Elisa C Alfaro and Hernandez, Hector H and Tian, Lin and Hires, S Andrew and Marvin, Jonathan S and Looger, Loren L and Schreiter, Eric R} } @article {6499, title = {Development of an implanted intramuscular EMG-triggered FES system for ambulation after incomplete spinal cord injury.}, journal = {Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society.}, volume = {2009}, year = {2009}, month = {2009}, pages = {6793-7}, abstract = {

Ambulation after spinal cord injury is possible with the aid of neuroprosthesis employing functional electrical stimulation (FES). Individuals with incomplete spinal cord injury (iSCI) retain partial volitional control of muscles below the level of injury, necessitating careful integration of FES with intact voluntary motor function for efficient walking. In this study, the intramuscular electromyogram (iEMG) was used to detect the intent to step and trigger FES-assisted walking in a volunteer with iSCI via an implanted neuroprosthesis consisting of two channels of bipolar iEMG signal acquisition and 12 independent channels of stimulation. The detection was performed with two types of classifiers- a threshold-based classifier that compared the running mean of the iEMG with a discrimination threshold to generate the trigger and a pattern recognition classifier that compared the time-history of the iEMG with a specified template of activity to generate the trigger whenever the cross-correlation coefficient exceeded a discrimination threshold. The pattern recognition classifier generally outperformed the threshold-based classifier, particularly with respect to minimizing False Positive triggers. The overall True Positive rates for the threshold-based classifier were 61.6\% and 87.2\% for the right and left steps with overall False Positive rates of 38.4\% and 33.3\%. The overall True Positive rates for the left and right step with the pattern recognition classifier were 57.2\% and 93.3\% and the overall False Positive rates were 11.9\% and 24.4\%. The subject showed no preference for either the threshold or pattern recognition-based classifier as determined by the Usability Rating Scale (URS) score collected after each trial and both the classifiers were perceived as moderately easy to use.

}, keywords = {Automated, Electric Stimulation, Electrodes, Electromyography, Humans, Implanted, Male, Muscles, Pattern Recognition, Recovery of Function, Spinal Cord Injuries, Walking}, issn = {1557-170X}, doi = {10.1109/IEMBS.2009.5333980}, author = {Dutta, Anirban and Kobetic, Rudi and Triolo, Ronald} } @article {1225, title = {Differential roles of the fan-shaped body and the ellipsoid body in Drosophila visual pattern memory.}, journal = {Learning \& Memory}, volume = {16}, year = {2009}, month = {2009 Apr 23}, pages = {289-95}, abstract = {

The central complex is a prominent structure in the Drosophila brain. Visual learning experiments in the flight simulator, with flies with genetically altered brains, revealed that two groups of horizontal neurons in one of its substructures, the fan-shaped body, were required for Drosophila visual pattern memory. However, little is known about the role of other components of the central complex for visual pattern memory. Here we show that a small set of neurons in the ellipsoid body, which is another substructure of the central complex and connected to the fan-shaped body, is also required for visual pattern memory. Localized expression of rutabaga adenylyl cyclase in either the fan-shaped body or the ellipsoid body is sufficient to rescue the memory defect of the rut(2080) mutant. We then performed RNA interference of rutabaga in either structure and found that they both were required for visual pattern memory. Additionally, we tested the above rescued flies under several visual pattern parameters, such as size, contour orientation, and vertical compactness, and revealed differential roles of the fan-shaped body and the ellipsoid body for visual pattern memory. Our study defines a complex neural circuit in the central complex for Drosophila visual pattern memory.

}, keywords = {Adenylate Cyclase, Animal, Animals, Behavior, Brain, Classical, Conditioning, Discrimination (Psychology), Drosophila, Drosophila Proteins, Gene Expression, Genetically Modified, Memory, Mutation, Neurons, Orientation, Pattern Recognition, Photic Stimulation, RNA Interference, Visual, Visual Pathways, Visual Perception}, issn = {1549-5485}, doi = {10.1101/lm.1331809}, author = {Pan, Yufeng and Zhou, Yanqiong and Guo, Chao and Gong, Haiyun and Gong, Zhefeng and Liu, Li} } @article {47906, title = {Distinct pose of discodermolide in taxol binding pocket drives a complementary mode of microtubule stabilization.}, journal = {Biochemistry}, volume = {48}, year = {2009}, month = {2009 Dec 15}, pages = {11664-77}, abstract = {

The microtubule cytoskeleton has proven to be an effective target for cancer therapeutics. One class of drugs, known as microtubule stabilizing agents (MSAs), binds to microtubule polymers and stabilizes them against depolymerization. The prototype of this group of drugs, Taxol, is an effective chemotherapeutic agent used extensively in the treatment of human ovarian, breast, and lung carcinomas. Although electron crystallography and photoaffinity labeling experiments determined that the binding site for Taxol is in a hydrophobic pocket in beta-tubulin, little was known about the effects of this drug on the conformation of the entire microtubule. A recent study from our laboratory utilizing hydrogen-deuterium exchange (HDX) in concert with various mass spectrometry (MS) techniques has provided new information on the structure of microtubules upon Taxol binding. In the current study we apply this technique to determine the binding mode and the conformational effects on chicken erythrocyte tubulin (CET) of another MSA, discodermolide, whose synthetic analogues may have potential use in the clinic. We confirmed that, like Taxol, discodermolide binds to the taxane binding pocket in beta-tubulin. However, as opposed to Taxol, which has major interactions with the M-loop, discodermolide orients itself away from this loop and toward the N-terminal H1-S2 loop. Additionally, discodermolide stabilizes microtubules mainly via its effects on interdimer contacts, specifically on the alpha-tubulin side, and to a lesser extent on interprotofilament contacts between adjacent beta-tubulin subunits. Also, our results indicate complementary stabilizing effects of Taxol and discodermolide on the microtubules, which may explain the synergy observed between the two drugs in vivo.

}, keywords = {Alkanes, Animals, Binding Sites, Carbamates, Cattle, Chickens, Deuterium Exchange Measurement, Dimerization, Drug Synergism, Lactones, Microtubules, Paclitaxel, Peptide Fragments, Protein Binding, Protein Isoforms, Protein Stability, Pyrones, Tubulin, Tubulin Modulators}, issn = {1520-4995}, doi = {10.1021/bi901351q}, author = {Khrapunovich-Baine, Marina and Menon, Vilas and Verdier-Pinard, Pascal and Smith, Amos B and Angeletti, Ruth Hogue and Fiser, Andras and Horwitz, Susan Band and Xiao, Hui} } @article {1117, title = {A divergent approach to the synthesis of 3-substituted-2-pyrazolines: Suzuki cross-coupling of 3-sulfonyloxy-2-pyrazolines.}, journal = {The Journal of Organic Chemistry}, volume = {74}, year = {2009}, month = {2009 Aug 21}, pages = {6390-3}, abstract = {

The efficient Suzuki cross-coupling of pyrazoline nonaflates with organoboron reagents was achieved to afford diverse 3-substituted-2-pyrazolines in excellent yield. The nonaflates displayed improved reactivity over the corresponding triflates and smoothly coupled to a variety of aryl- and heteroarylboronic acids. This process and its broad scope constitute a rapid, divergent strategy for the synthesis of elaborated 2-pyrazolines that are not readily obtained via conventional methods.

}, keywords = {Kinetics, Pyrazoles, Sulfonic Acids}, issn = {1520-6904}, doi = {10.1021/jo9011859}, author = {Grimm, Jonathan B and Wilson, Kevin J and Witter, David J} } @article {46623, title = {Drosophila, a genetic model system to study cocaine-related behaviors: a review with focus on LIM-only proteins.}, journal = {Neuropharmacology}, volume = {56 Suppl 1}, year = {2009}, month = {2009}, pages = {97-106}, abstract = {

In the last decade, the fruit fly Drosophila melanogaster, highly accessible to genetic, behavioral and molecular analyses, has been introduced as a novel model organism to help decipher the complex genetic, neurochemical, and neuroanatomical underpinnings of behaviors induced by drugs of abuse. Here we review these data, focusing specifically on cocaine-related behaviors. Several of cocaine{\textquoteright}s most characteristic properties have been recapitulated in Drosophila. First, cocaine induces motor behaviors in flies that are remarkably similar to those observed in mammals. Second, repeated cocaine administration induces behavioral sensitization a form of behavioral plasticity believed to underlie certain aspects of addiction. Third, a key role for dopaminergic systems in mediating cocaine{\textquoteright}s effects has been demonstrated through both pharmacological and genetic methods. Finally, and most importantly, unbiased genetic screens, feasible because of the simplicity and scale with which flies can be manipulated in the laboratory, have identified several novel genes and pathways whose role in cocaine behaviors had not been anticipated. Many of these genes and pathways have been validated in mammalian models of drug addiction. We focus in this review on the role of LIM-only proteins in cocaine-induced behaviors.

}, keywords = {Animals, Animals, Genetically Modified, Behavior, Animal, Cocaine, Cocaine-Related Disorders, Disease Models, Animal, Dopamine Uptake Inhibitors, Drosophila melanogaster, Drosophila Proteins, Homeodomain Proteins, Models, Genetic}, issn = {0028-3908}, doi = {10.1016/j.neuropharm.2008.07.023}, author = {Heberlein, Ulrike and Tsai, Linus T-Y and Kapfhamer, David and Lasek, Amy W} } @article {5692, title = {Drosophila brain development: closing the gap between a macroarchitectural and microarchitectural approach.}, journal = {Cold Spring Harbor Symposia on Quantitative Biology}, volume = {74}, year = {2009}, month = {2009}, pages = {235-48}, abstract = {

Neurobiologists address neural structure, development, and function at the level of "macrocircuits" (how different brain compartments are interconnected; what overall pattern of activity they produce) and at the level of "microcircuits" (how connectivity and physiology of individual neurons and their processes within a compartment determine the functional output of this compartment). Work in our lab aims at reconstructing the developing Drosophila brain at both levels. Macrocircuits can be approached conveniently by reconstructing the pattern of brain lineages, which form groups of neurons whose projections form cohesive fascicles interconnecting the compartments of the larval and adult brain. The reconstruction of microcircuits requires serial section electron microscopy, due to the small size of terminal neuronal processes and their synaptic contacts. Because of the amount of labor that traditionally comes with this approach, very little is known about microcircuitry in brains across the animal kingdom. Many of the problems of serial electron microscopy reconstruction are now solvable with digital image recording and specialized software for both image acquisition and postprocessing. In this chapter, we introduce our efforts to reconstruct the small Drosophila larval brain and discuss our results in light of the published data on neuropile ultrastructure in other animal taxa.

}, keywords = {Animals, Brain, Cell Lineage, Drosophila, Electron, Genetically Modified, Imaging, Larva, Mice, Microscopy, Models, Nerve Net, Neurites, Neurological, Neuropil, Phylogeny, Species Specificity, Synapses, Three-Dimensional, Transmission}, issn = {1943-4456}, doi = {10.1101/sqb.2009.74.037}, author = {Cardona, A and Saalfeld, S and Tomancak, P and Hartenstein, V.} } @article {4278, title = {A Drosophila resource of transgenic RNAi lines for neurogenetics.}, journal = {Genetics}, volume = {182}, year = {2009}, month = {2009 Aug}, pages = {1089-100}, abstract = {

Conditional expression of hairpin constructs in Drosophila is a powerful method to disrupt the activity of single genes with a spatial and temporal resolution that is impossible, or exceedingly difficult, using classical genetic methods. We previously described a method (Ni et al. 2008) whereby RNAi constructs are targeted into the genome by the phiC31-mediated integration approach using Vermilion-AttB-Loxp-Intron-UAS-MCS (VALIUM), a vector that contains vermilion as a selectable marker, an attB sequence to allow for phiC31-targeted integration at genomic attP landing sites, two pentamers of UAS, the hsp70 core promoter, a multiple cloning site, and two introns. As the level of gene activity knockdown associated with transgenic RNAi depends on the level of expression of the hairpin constructs, we generated a number of derivatives of our initial vector, called the "VALIUM" series, to improve the efficiency of the method. Here, we report the results from the systematic analysis of these derivatives and characterize VALIUM10 as the most optimal vector of this series. A critical feature of VALIUM10 is the presence of gypsy insulator sequences that boost dramatically the level of knockdown. We document the efficacy of VALIUM as a vector to analyze the phenotype of genes expressed in the nervous system and have generated a library of 2282 constructs targeting 2043 genes that will be particularly useful for studies of the nervous system as they target, in particular, transcription factors, ion channels, and transporters.

}, keywords = {Animals, Carrier Proteins, Drosophila, Gene Knockdown Techniques, Ion Channels, Methods, Nervous System, RNA, RNA Interference, Small Interfering, Transcription Factors}, issn = {1943-2631}, doi = {10.1534/genetics.109.103630}, author = {Ni, Jian-Quan and Liu, Lu-Ping and Binari, Richard and Hardy, Robert and Shim, Hye-Seok and Cavallaro, Amanda and Booker, Matthew and Pfeiffer, Barret D and Markstein, Michele and Wang, Hui and Villalta, Christians and Laverty, Todd R and Perkins, Lizabeth A and Perrimon, Norbert} } @conference {48656, title = {Dynamics of escaping flight initiations of Drosophila melanogaster.}, booktitle = {2nd IEEE RAS \& EMBS International Conference on Biomedical Robotics and Biomechatronics}, year = {2009}, month = {2008}, abstract = {

We present a reconstruction of the dynamics of flight initiation from kinematic data extracted from high-speed video recordings of the fruit fly Drosophila melanogaster. The dichotomy observed in this insect{\textquoteright}s flight initiation sequences, generated by the presence or absence of visual stimuli, clearly generates two contrasting sets of dynamics once the flies become airborne. By calculating reaction forces and moments using the unconstrained motion formulation for a rigid body, we assess the fly{\textquoteright}s responses amidst these two dynamic patterns as a step towards refining our understanding of insect flight control.

}, doi = {10.1109/BIOROB.2008.4762921}, author = {Zabalax, Francisco A and Card, Gwyneth M and Fontaine, Ebraheem I and Murray, Richard M and Dickinson, Michael H} } @article {2496, title = {The ecdysone receptor controls the post-critical weight switch to nutrition-independent differentiation in Drosophila wing imaginal discs.}, journal = {Development}, volume = {136}, year = {2009}, month = {2009 Jul}, pages = {2345-53}, abstract = {

In holometabolous insects, a species-specific size, known as critical weight, needs to be reached for metamorphosis to be initiated in the absence of further nutritional input. Previously, we found that reaching critical weight depends on the insulin-dependent growth of the prothoracic glands (PGs) in Drosophila larvae. Because the PGs produce the molting hormone ecdysone, we hypothesized that ecdysone signaling switches the larva to a nutrition-independent mode of development post-critical weight. Wing discs from pre-critical weight larvae [5 hours after third instar ecdysis (AL3E)] fed on sucrose alone showed suppressed Wingless (WG), Cut (CT) and Senseless (SENS) expression. Post-critical weight, a sucrose-only diet no longer suppressed the expression of these proteins. Feeding larvae that exhibit enhanced insulin signaling in their PGs at 5 hours AL3E on sucrose alone produced wing discs with precocious WG, CT and SENS expression. In addition, knocking down the Ecdysone receptor (EcR) selectively in the discs also promoted premature WG, CUT and SENS expression in the wing discs of sucrose-fed pre-critical weight larvae. EcR is involved in gene activation when ecdysone is present, and gene repression in its absence. Thus, knocking down EcR derepresses genes that are normally repressed by unliganded EcR, thereby allowing wing patterning to progress. In addition, knocking down EcR in the wing discs caused precocious expression of the ecdysone-responsive gene broad. These results suggest that post-critical weight, EcR signaling switches wing discs to a nutrition-independent mode of development via derepression.

}, keywords = {Animals, Body Patterning, Cell Differentiation, Developmental, Drosophila, Drosophila Proteins, Gene Expression Regulation, Genes, Genetically Modified, Homeodomain Proteins, Insect, Insulin, Nuclear Proteins, Receptors, Signal Transduction, Steroid, Sucrose, Transcription Factors, Wing, Wnt1 Protein}, issn = {0950-1991}, doi = {10.1242/dev.032672}, author = {Mirth, Christen K and Truman, James W and Riddiford, Lynn M} } @article {2905, title = {Electro-optical imaging microscopy of dye-doped artificial lipidic membranes.}, journal = {Biophysical Journal}, volume = {97}, year = {2009}, month = {2009 Dec 2}, pages = {2913-21}, abstract = {

Artificial lipidic bilayers are widely used as a model for the lipid matrix in biological cell membranes. We use the Pockels electro-optical effect to investigate the properties of an artificial lipidic membrane doped with nonlinear molecules in the outer layer. We report here what is believed to be the first electro-optical Pockels signal and image from such a membrane. The electro-optical dephasing distribution within the membrane is imaged and the signal is shown to be linear as a function of the applied voltage. A theoretical analysis taking into account the statistical orientation distribution of the inserted dye molecules allows us to estimate the doped membrane nonlinearity. Ongoing extensions of this work to living cell membranes are discussed.

}, keywords = {Artificial, Cell Membrane, Coloring Agents, Lipid Bilayers, Membrane Potentials, Membranes, Microfluidic Analytical Techniques, Microscopy, Molecular Imaging, Optical Processes, Phosphatidylcholines, Potentiometry, Pyridinium Compounds}, issn = {1542-0086}, doi = {10.1016/j.bpj.2009.08.055}, author = {Hajj, Bassam and De Reguardati, Sophie and Hugonin, Lo\"{\i}c and Le Pioufle, Bruno and Osaki, Toshihisa and Suzuki, Hiroaki and Takeuchi, Shoji and Mojzisova, Halina and Chauvat, Dominique and Zyss, Joseph} } @article {5232, title = {Elucidation of the regulation of an adult cuticle gene Acp65A by the transcription factor Broad.}, journal = {Insect Molecular Biology}, volume = {18}, year = {2009}, month = {2009 Aug}, pages = {421-9}, abstract = {

Broad (BR), an ecdysone-inducible transcription factor, is a major determinant of the pupal stage. The misexpression of BR-Z1 isoform (BR-Z1) during adult development of Drosophila melanogaster prevents the expression of the adult cuticle protein 65A gene (Acp65A). We found that the proximal 237 bp of the 5{\textquoteright} flanking region of Acp65A were sufficient to mediate this suppression. A targeted point mutation of a putative BR-Z1 response element (BRE) within this region showed that it was not involved. Drosophila hormone receptor-like 38 (DHR38) is required for Acp65A expression. We found that BR-Z1 repressed DHR38 expression and that BR{\textquoteright}s inhibition of Acp65A expression was rescued by exogenous expression of DHR38. Thus, BR-Z1 suppresses Acp65A expression by preventing the normal up-regulation of DHR38 at the time of adult cuticle formation.

}, keywords = {Animals, Base Sequence, Binding Sites, Developmental, Drosophila melanogaster, Drosophila Proteins, Gene Expression Regulation, Genetic, Hot Temperature, Insect Proteins, Integumentary System, Molecular Sequence Data, Promoter Regions, Protein Binding, Pupa, Transcription Factors}, issn = {1365-2583}, doi = {10.1111/j.1365-2583.2009.00889.x}, author = {Cui, H-Y and Lestradet, M and Bruey-Sedano, N and Charles, J-P and Riddiford, L M} } @article {796, title = {Endodomain diversity in the Drosophila Dscam and its roles in neuronal morphogenesis.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {29}, year = {2009}, month = {2009 Feb 11}, pages = {1904-14}, abstract = {

Drosophila Down syndrome cell adhesion molecule (Dscam) can be variably spliced to encode 152,064 distinct single-pass transmembrane proteins. In addition to 19,008 possible ectodomains and two alternative transmembrane segments, it may carry endodomains containing or lacking exons 19 and 23. Here, we determine the role of Dscam endodomain diversity in neural development. Dscam with full-length endodomain is largely restricted to embryogenesis. In contrast, most Dscams lack exons 19 and 23 at postembryonic stages. As implicated from the expression patterns, removal of Dscam exon 19-containing variants disrupts wiring of embryonic neurons while silencing of Dscam transcripts lacking exon 19 or exon 23 effectively blocks postembryonic neuronal morphogenesis. Furthermore, compared with exon 19-containing Dscam, transgenic Dscam without exon 19 is more efficiently targeted to neurites and more potently suppresses axon bifurcation in Dscam mutant neurons. In sum, Dscam with or without exon 19 in its endodomain is used to govern different stage-specific neuronal morphogenetic processes, possibly due to differences in protein targeting.

}, keywords = {Amino Acid Motifs, Amino Acid Sequence, Animals, Cell Adhesion Molecules, Drosophila, Drosophila Proteins, Gene Targeting, Genetically Modified, Molecular Sequence Data, Morphogenesis, Neurogenesis, Neurons, Protein Structure, Tertiary}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.5743-08.2009}, author = {Yu, Hung-Hsiang and Yang, Jacob S and Wang, Jian and Huang, Yaling and Lee, Tzumin} } @article {2344, title = {Enemy avoidance task: a novel behavioral paradigm for assessing spatial avoidance of a moving subject.}, journal = {Journal of Neuroscience Methods}, volume = {180}, year = {2009}, month = {2009 May 30}, pages = {29-33}, abstract = {

Navigation with respect to moving goals represents a useful ability in the everyday life of animals. We have developed a novel behavioral paradigm, "enemy avoidance task", in which a laboratory rat (subject) was trained to avoid another rat (enemy), while searching for small pasta pellets dispensed onto an experimental arena. Whenever the distance between the two animals was smaller than 25 cm, the subject was given a mild electric footshock. The results have shown that rats are capable of avoiding another rat while exploring an environment. Therefore, the enemy avoidance task can be used in electrophysiological, lesion or neuropharmacological studies exploring neuronal substrate coding for egocentric and allocentric positions of an observed animal.

}, keywords = {Animal, Animals, Avoidance Learning, Behavior, Behavioral Sciences, Exploratory Behavior, Fear, Long-Evans, Male, Memory, Motor Activity, Movement, Neuropsychological Tests, Neuropsychology, Orientation, Psychomotor Performance, Rats, Space Perception}, issn = {1872-678X}, doi = {10.1523/JNEUROSCI.3773-10.2011}, author = {Telensky, Petr and Svoboda, Jan and Pastalkova, Eva and Blahna, Karel and Bures, Jan and Stuchlik, Ales} } @article {1556, title = {Engineering human IgG1 affinity to human neonatal Fc receptor: impact of affinity improvement on pharmacokinetics in primates.}, journal = {Journal of Immunology}, volume = {182}, year = {2009}, month = {2009 Jun 15}, pages = {7663-71}, abstract = {

The pH-dependent binding of Igs to the neonatal FcR (FcRn) plays a critical role in the in vivo homeostasis of IgGs. Modulating the interaction between Fc and FcRn through protein engineering is one method for improving the pharmacokinetics of therapeutic Abs. Recent studies disputed the direct relationship between increasing FcRn affinity and improved pharmacokinetic properties. In this work, we studied the pharmacokinetics of two human IgG1 Fc variants in cynomolgus monkey to further clarify the affinity-pharmacokinetic relationship. First, we report a number of novel Fc point mutations and combination variants, including some with primate-specific FcRn-binding improvements. By studying these variants along with some previously described variants across a wide range of affinities, we discovered a direct correlation of pH 6 affinity improvements with neutral pH improvements, suggesting that all of the tested variants exhibit similar pH dependency in FcRn binding. We then evaluated the pharmacokinetics of variants N434A and N434W, which, respectively, gave approximately 4- and 80-fold improvements in pH 6-binding affinity to both human and nonhuman primate FcRn. Surprisingly, clearance of N434W was similar to that of wild type. N434W is the first variant studied in primates that exhibits significant binding to FcRn at pH 7.4, and its clearance substantiates the principle that too much affinity improvement, i.e., beyond that of N434W, does not yield improved pharmacokinetics. In contrast, N434A exhibited a approximately 2-fold decrease in clearance in cynomolgus monkey, supporting the notion that modest increases in pH 6 FcRn affinity can result in improved pharmacokinetics in primates.

}, keywords = {Amino Acid Sequence, Animals, Antibody Affinity, Fc, Histocompatibility Antigens Class I, Humans, Hydrogen-Ion Concentration, Immunoglobulin G, Macaca fascicularis, Mice, Models, Molecular, Mutation, Protein Structure, Quaternary, Receptors, Recombinant Proteins}, issn = {1550-6606}, doi = {10.4049/jimmunol.0804182}, author = {Yeung, Yik Andy and Leabman, Maya K and Marvin, Jonathan S and Qiu, Julia and Adams, Camellia W and Lien, Samantha and Starovasnik, Melissa A and Lowman, Henry B} } @article {5239, title = {Enzyme stabilization by domain insertion into a thermophilic protein.}, journal = {Protein Engineering, Design \& Selection : PEDS}, volume = {22}, year = {2009}, month = {2009 Oct}, pages = {615-23}, abstract = {

Insufficient kinetic stability of exoinulinase (EI) restricts its application in many areas including enzymatic transformation of inulin for production of ultra-high fructose syrup and oligofructan, as well as fermentation of inulin into bioethanol. The conventional method for enzyme stabilization involves mutagenesis and therefore risks alteration of an enzyme{\textquoteright}s desired properties, such as activity. Here, we report a novel method for stabilization of EI without any modification of its primary sequence. Our method employs domain insertion of an entire EI domain into a thermophilic scaffold protein. Insertion of EI into a loop of a thermophilic maltodextrin-binding protein from Pyrococcus furiosus (PfMBP) resulted in improvement of kinetic stability (the duration over which an enzyme remains active) at 37 degrees C without any compromise in EI activity. Our analysis suggests that the improved kinetic stability at 37 degrees C might originate from a raised kinetic barrier for irreversible conversion of unfolded intermediates to completely inactivated species, rather than an increased energy difference between the folded and unfolded forms.

}, keywords = {Aspergillus, Bacterial Proteins, Carrier Proteins, Enzyme Stability, Fungal Proteins, Glycoside Hydrolases, Kinetics, Models, Molecular, Protein Engineering, Protein Folding, Protein Structure, Pyrococcus, Recombinant Fusion Proteins, Temperature, Tertiary, Urea}, issn = {1741-0134}, doi = {10.1093/protein/gzp044}, author = {Kim, Chung-Sei and Pierre, Brennal and Ostermeier, Marc and Looger, Loren L and Kim, Jin Ryoun} } @article {2355, title = {The ethomics era?}, journal = {Nature Methods}, volume = {6}, year = {2009}, month = {2009 Jun}, pages = {413-4}, abstract = {

Applying modern machine-vision techniques to the study of animal behavior, two groups developed systems that quantify many aspects of the complex social behaviors of Drosophila melanogaster. These software tools will enable high-throughput screens that seek to uncover the cellular and molecular underpinnings of behavior.

}, keywords = {Animal, Animals, Artificial Intelligence, Automated, Behavior, Computer-Assisted, Drosophila melanogaster, Humans, Image Interpretation, Monitoring, Movement, Pattern Recognition, Physiologic, Posture, Social Behavior}, issn = {1548-7105}, doi = {10.1016/j.cub.2010.06.072}, author = {Reiser, Michael} } @article {1684, title = {Evolution of mutational robustness in the yeast genome: a link to essential genes and meiotic recombination hotspots.}, journal = {PLoS Genetics}, volume = {5}, year = {2009}, month = {2009 Jun}, pages = {e1000533}, abstract = {

Deleterious mutations inevitably emerge in any evolutionary process and are speculated to decisively influence the structure of the genome. Meiosis, which is thought to play a major role in handling mutations on the population level, recombines chromosomes via non-randomly distributed hot spots for meiotic recombination. In many genomes, various types of genetic elements are distributed in patterns that are currently not well understood. In particular, important (essential) genes are arranged in clusters, which often cannot be explained by a functional relationship of the involved genes. Here we show by computer simulation that essential gene (EG) clustering provides a fitness benefit in handling deleterious mutations in sexual populations with variable levels of inbreeding and outbreeding. We find that recessive lethal mutations enforce a selective pressure towards clustered genome architectures. Our simulations correctly predict (i) the evolution of non-random distributions of meiotic crossovers, (ii) the genome-wide anti-correlation of meiotic crossovers and EG clustering, (iii) the evolution of EG enrichment in pericentromeric regions and (iv) the associated absence of meiotic crossovers (cold centromeres). Our results furthermore predict optimal crossover rates for yeast chromosomes, which match the experimentally determined rates. Using a Saccharomyces cerevisiae conditional mutator strain, we show that haploid lethal phenotypes result predominantly from mutation of single loci and generally do not impair mating, which leads to an accumulation of mutational load following meiosis and mating. We hypothesize that purging of deleterious mutations in essential genes constitutes an important factor driving meiotic crossover. Therefore, the increased robustness of populations to deleterious mutations, which arises from clustered genome architectures, may provide a significant selective force shaping crossover distribution. Our analysis reveals a new aspect of the evolution of genome architectures that complements insights about molecular constraints, such as the interference of pericentromeric crossovers with chromosome segregation.

}, keywords = {Chromosomes, Essential, Evolution, Fungal, Genes, Genetic, Genome, Meiosis, Molecular, Mutation, Recombination, Saccharomyces cerevisiae}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1000533}, author = {Keller, Philipp J and Knop, Michael} } @article {4411, title = {Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute et al.}, journal = {Cell}, volume = {139}, year = {2009}, month = {2009 Dec 11}, pages = {1189-96}, abstract = {

We have shown previously that the loss of abdominal pigmentation in D. santomea relative to its sister species D. yakuba resulted, in part, from cis-regulatory mutations at the tan locus. Matute et al. claim, based solely upon extrapolation from genetic crosses of D. santomea and D. melanogaster, a much more divergent species, that at least four X chromosome regions but not tan are responsible for pigmentation differences. Here, we provide additional evidence from introgressions of D. yakuba genes into D. santomea that support a causative role for tan in the loss of pigmentation and present analyses that contradict Matute et al.{\textquoteright}s claims. We discuss how the choice of parental species and other factors affect the ability to identify loci responsible for species divergence, and we affirm that all of our previously reported results and conclusions stand.

}, keywords = {Animals, Chimera, Chromosomal Proteins, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Evolution, Molecular, Non-Histone, Pigmentation, Species Specificity, X Chromosome}, issn = {1097-4172}, doi = {10.1016/j.cell.2009.11.004}, author = {Rebeiz, Mark and Ramos-Womack, Margarita and Jeong, Sangyun and Andolfatto, Peter and Werner, Thomas and True, John and Stern, David L and Carroll, Sean B} } @article {2122, title = {Experience-dependent compartmentalized dendritic plasticity in rat hippocampal CA1 pyramidal neurons.}, journal = {Nature Neuroscience}, volume = {12}, year = {2009}, month = {2009 Dec}, pages = {1485-7}, abstract = {

The excitability of individual dendritic branches is a plastic property of neurons. We found that experience in an enriched environment increased propagation of dendritic Na(+) spikes in a subset of individual dendritic branches in rat hippocampal CA1 pyramidal neurons and that this effect was mainly mediated by localized downregulation of A-type K(+) channel function. Thus, dendritic plasticity might be used to store recent experience in individual branches of the dendritic arbor.

}, keywords = {Action Potentials, Animals, CA1 Region, Dendrites, Down-Regulation, Environment, Hippocampal, Memory, Neuronal Plasticity, Potassium Channels, Pyramidal Cells, Rats}, issn = {1546-1726}, doi = {10.1038/nn.2428}, author = {Makara, Judit K and Losonczy, Attila and Wen, Quan and Magee, Jeffrey C} } @article {4267, title = {Experience-dependent structural synaptic plasticity in the mammalian brain.}, journal = {Nature Reviews Neuroscience}, volume = {10}, year = {2009}, month = {2009 Sep}, pages = {647-58}, abstract = {

Synaptic plasticity in adult neural circuits may involve the strengthening or weakening of existing synapses as well as structural plasticity, including synapse formation and elimination. Indeed, long-term in vivo imaging studies are beginning to reveal the structural dynamics of neocortical neurons in the normal and injured adult brain. Although the overall cell-specific morphology of axons and dendrites, as well as of a subpopulation of small synaptic structures, are remarkably stable, there is increasing evidence that experience-dependent plasticity of specific circuits in the somatosensory and visual cortex involves cell type-specific structural plasticity: some boutons and dendritic spines appear and disappear, accompanied by synapse formation and elimination, respectively. This Review focuses on recent evidence for such structural forms of synaptic plasticity in the mammalian cortex and outlines open questions.

}, keywords = {Animals, Brain, Humans, Nerve Net, Neurogenesis, Neuronal Plasticity, Synapses}, issn = {1471-0048}, doi = {10.1038/nrn2699}, author = {Holtmaat, Anthony and Svoboda, Karel} } @article {1116, title = {Exploring the pharmacokinetic properties of phosphorus-containing selective HDAC 1 and 2 inhibitors (SHI-1:2).}, journal = {Bioorganic \& Medicinal Chemistry Letters}, volume = {19}, year = {2009}, month = {2009 Apr 1}, pages = {2053-8}, abstract = {

We report the preparation and structure-activity relationships of phosphorus-containing histone deacetylase inhibitors. A strong trend between decreasing phosphorus functional group size and superior mouse pharmacokinetic properties was identified. In addition, optimized candidates showed tumor growth inhibition in xenograft studies.

}, keywords = {Administration, Animals, Antineoplastic Agents, Enzyme Inhibitors, Heterologous, Histone Deacetylase 1, Histone Deacetylase 2, Histone Deacetylase Inhibitors, Histone Deacetylases, Mice, Nude, Oral, Phosphonic Acids, Repressor Proteins, Transplantation}, issn = {1464-3405}, doi = {10.1016/j.bmcl.2009.02.009}, author = {Heidebrecht, Richard W and Chenard, Melissa and Close, Joshua and Dahlberg, William K and Fleming, Judith and Grimm, Jonathan B and Hamill, Julie E and Harsch, Andreas and Haines, Brian B and Hughes, Bethany and Kral, Astrid M and Middleton, Richard E and Mushti, Chandrasekhar and Ozerova, Nicole and Szewczak, Alexander A and Wang, Hongmei and Wilson, Kevin and Witter, David J and Secrist, J Paul and Miller, Thomas A} } @article {3913, title = {Fast synaptic subcortical control of hippocampal circuits.}, journal = {Science}, volume = {326}, year = {2009}, month = {2009 Oct 16}, pages = {449-53}, abstract = {

Cortical information processing is under state-dependent control of subcortical neuromodulatory systems. Although this modulatory effect is thought to be mediated mainly by slow nonsynaptic metabotropic receptors, other mechanisms, such as direct synaptic transmission, are possible. Yet, it is currently unknown if any such form of subcortical control exists. Here, we present direct evidence of a strong, spatiotemporally precise excitatory input from an ascending neuromodulatory center. Selective stimulation of serotonergic median raphe neurons produced a rapid activation of hippocampal interneurons. At the network level, this subcortical drive was manifested as a pattern of effective disynaptic GABAergic inhibition that spread throughout the circuit. This form of subcortical network regulation should be incorporated into current concepts of normal and pathological cortical function.

}, keywords = {Afferent, Animals, Electric Stimulation, Excitatory Postsynaptic Potentials, Glutamic Acid, Hippocampus, Inhibitory Postsynaptic Potentials, Interneurons, Mice, Neural Inhibition, Neural Pathways, Neurons, Patch-Clamp Techniques, Photic Stimulation, Raphe Nuclei, Rats, Serotonin, Sprague-Dawley, Synapses, Synaptic Potentials}, issn = {1095-9203}, doi = {10.1126/science.1178307}, author = {Varga, Viktor and Losonczy, Attila and Zemelman, Boris V and Borhegyi, Zsolt and Nyiri, G{\'a}bor and Domonkos, Andor and Hangya, Bal{\'a}zs and Holderith, No{\'e}mi and Magee, Jeffrey C and Freund, Tam{\'a}s F} } @article {5351, title = {Fast throughput low voltage scanning transmission electron microscope imaging of nano-resolution three dimensional tissue.}, journal = {Microscopy and Microanalysis}, volume = {15}, year = {2009}, month = {2009 Jul 26}, pages = {642-3}, doi = {10.1017/S1431927609092435}, author = {Bolorizadeh, Mehdi and Hess, Harald F} } @article {2442, title = {Fine-tuning of secondary arbor development: the effects of the ecdysone receptor on the adult neuronal lineages of the Drosophila thoracic CNS.}, journal = {Development}, volume = {136}, year = {2009}, month = {2009 Oct}, pages = {3247-56}, abstract = {

The adult central nervous system (CNS) of Drosophila is largely composed of relatively homogenous neuronal classes born during larval life. These adult-specific neuron lineages send out initial projections and then arrest development until metamorphosis, when intense sprouting occurs to establish the massive synaptic connections necessary for the behavior and function of the adult fly. In this study, we identified and characterized specific lineages in the adult CNS and described their secondary branch patterns. Because prior studies show that the outgrowth of incumbent remodeling neurons in the CNS is highly dependent on the ecdysone pathway, we investigated the role of ecdysone in the development of the adult-specific neuronal lineages using a dominant-negative construct of the ecdysone receptor (EcR-DN). When EcR-DN was expressed in clones of the adult-specific lineages, neuroblasts persisted longer, but we saw no alteration in the initial projections of the lineages. Defects were observed in secondary arbors of adult neurons, including clumping and cohesion of fine branches, misrouting, smaller arbors and some defasciculation. The defects varied across the multiple neuron lineages in both appearance and severity. These results indicate that the ecdysone receptor complex influences the fine-tuning of connectivity between neuronal circuits, in conjunction with other factors driving outgrowth and synaptic partnering.

}, keywords = {Animals, Central Nervous System, Developmental, Drosophila, Drosophila Proteins, Ecdysone, Gene Expression Regulation, Genes, Genetically Modified, Insect, Interneurons, Motor Neurons, Neurogenesis, Receptors, Signal Transduction, Steroid}, issn = {1477-9129}, doi = {10.1242/dev.039859}, author = {Brown, Heather L D and Truman, James W} } @article {2168, title = {Flight dynamics and control of evasive maneuvers: the fruit fly{\textquoteright}s takeoff.}, journal = {IEEE Transactions on Bio-Medical Engineering}, volume = {56}, year = {2009}, month = {2009 Sep}, pages = {2295-8}, abstract = {

We have approached the problem of reverse-engineering the flight control mechanism of the fruit fly by studying the dynamics of the responses to a visual stimulus during takeoff. Building upon a prior framework [G. Card and M. Dickinson, J. Exp. Biol., vol. 211, pp. 341-353, 2008], we seek to understand the strategies employed by the animal to stabilize attitude and orientation during these evasive, highly dynamical maneuvers. As a first step, we consider the dynamics from a gray-box perspective: examining lumped forces produced by the insect{\textquoteright}s legs and wings. The reconstruction of the flight initiation dynamics, based on the unconstrained motion formulation for a rigid body, allows us to assess the fly{\textquoteright}s responses to a variety of initial conditions induced by its jump. Such assessment permits refinement by using a visual tracking algorithm to extract the kinematic envelope of the wings [E. I. Fontaine, F. Zabala, M. Dickinson, and J. Burdick, "Wing and body motion during flight initiation in Drosophila revealed by automated visual tracking," submitted for publication] in order to estimate lift and drag forces [F. Zabala, M. Dickinson, and R. Murray, "Control and stability of insect flight during highly dynamical maneuvers," submitted for publication], and recording actual leg-joint kinematics and using them to estimate jump forces [F. Zabala, "A bio-inspired model for directionality control of flight initiation," to be published.]. In this paper, we present the details of our approach in a comprehensive manner, including the salient results.

}, keywords = {Algorithms, Animal, Animals, Biomechanics, Computer-Assisted, Drosophila melanogaster, Escape Reaction, Flight, Image Processing, Video Recording}, issn = {1558-2531}, doi = {10.1109/TBME.2009.2027606}, author = {Zabala, Francisco A and Card, Gwyneth M and Fontaine, Ebraheem I and Dickinson, Michael H and Murray, Richard M} } @article {1091, title = {Fluorogenic affinity label for the facile, rapid imaging of proteins in live cells.}, journal = {Organic \& Biomolecular Chemistry}, volume = {7}, year = {2009}, month = {2009 Oct 7}, pages = {3969-75}, abstract = {

Haloalkane dehalogenase (HD) catalyzes the hydrolysis of haloalkanes via a covalent enzyme-substrate intermediate. Fusing a target protein to an HD variant that cannot hydrolyze the intermediate enables labeling of the target protein with a haloalkane in cellulo. The utility of extant probes is hampered, however, by background fluorescence as well as limited membrane permeability. Here, we report on the synthesis and use of a fluorogenic affinity label that, after unmasking by an intracellular esterase, labels an HD variant in cellulo. Labeling is rapid and specific, as expected from the reliance upon enzymic catalysts and the high membrane permeance of the probe both before and after unmasking. Most notably, even high concentrations of the fluorogenic affinity label cause minimal background fluorescence without a need to wash the cells. We envision that such fluorogenic affinity labels, which enlist catalysis by two cellular enzymes, will find utility in pulse-chase experiments, high-content screening, and numerous other protocols.

}, keywords = {Affinity Labels, Animals, Cell Line, Cell Survival, Fluorescent Dyes, Hydrolases, Hydrophobic and Hydrophilic Interactions, Time Factors}, issn = {1477-0539}, doi = {10.1039/b907664f}, author = {Watkins, Rex W and Lavis, Luke D and Kung, Vanessa M and Los, Georgyi V and Raines, Ronald T} } @article {68816, title = {Functional Role of a Specialized Class of Spinal Commissural Inhibitory Neurons during Fast Escapes in Zebrafish}, journal = {Journal of Neuroscience}, volume = {29}, year = {2009}, month = {05/2009}, pages = {6780{\textendash}6793}, abstract = {

In teleost fish, the Mauthner (M) cell, a large reticulospinal neuron in the brainstem, triggers escape behavior. Spinal commissural inhibitory interneurons that are electrotonically excited by the M-axon have been identified, but the behavioral roles of these neurons have not yet been addressed. Here, we studied these neurons, named CoLo (commissural local), in larval zebrafish using an enhancer-trap line in which the entire population of CoLos was visualized by green fluorescent protein. CoLos were present at one cell per hemi-segment. Electrophysiological recordings showed that an M-spike evoked a spike in CoLos via electrotonic transmission and that CoLos made monosynaptic inhibitory connections onto contralateral primary motoneurons, consistent with the results in adult goldfish. We further showed that CoLos were active only during escapes. We examined the behavioral roles of CoLos by investigating escape behaviors in CoLo-ablated larvae. The results showed that the escape behaviors evoked by sound/vibration stimuli were often impaired with a reduced initial bend of the body, indicating that CoLos play important roles in initiating escapes. We obtained several lines of evidence that strongly suggested that the impaired escapes occurred during bilateral activation of the M-cells: in normal larvae, CoLo-mediated inhibitory circuits enable animals to perform escapes even in these occasions by silencing the output of the slightly delayed firing of the second M-cell. This study illustrates (1) a clear example of the behavioral role of a specialized class of interneurons and (2) the capacity of the spinal circuits to filter descending commands and thereby produce the appropriate behavior.

}, issn = {0270-6474}, doi = {10.1523/JNEUROSCI.0801-09.2009}, url = {https://www.jneurosci.org/content/29/21/6780}, author = {Chie Satou and Yukiko Kimura and Tsunehiko Kohashi and Kazuki Horikawa and Hiroyuki Takeda and Yoichi Oda and Shin-ichi Higashijima} } @article {46621, title = {Genetic aspects of behavioral neurotoxicology.}, journal = {Neurotoxicology}, volume = {30}, year = {2009}, month = {2009 Sep}, pages = {741-53}, abstract = {

Considerable progress has been made over the past couple of decades concerning the molecular bases of neurobehavioral function and dysfunction. The field of neurobehavioral genetics is becoming mature. Genetic factors contributing to neurologic diseases such as Alzheimer{\textquoteright}s disease have been found and evidence for genetic factors contributing to other diseases such as schizophrenia and autism are likely. This genetic approach can also benefit the field of behavioral neurotoxicology. It is clear that there is substantial heterogeneity of response with behavioral impairments resulting from neurotoxicants. Many factors contribute to differential sensitivity, but it is likely that genetic variability plays a prominent role. Important discoveries concerning genetics and behavioral neurotoxicity are being made on a broad front from work with invertebrate and piscine mutant models to classic mouse knockout models and human epidemiologic studies of polymorphisms. Discovering genetic factors of susceptibility to neurobehavioral toxicity not only helps identify those at special risk, it also advances our understanding of the mechanisms by which toxicants impair neurobehavioral function in the larger population. This symposium organized by Edward Levin and Annette Kirshner, brought together researchers from the laboratories of Michael Aschner, Douglas Ruden, Ulrike Heberlein, Edward Levin and Kathleen Welsh-Bohmer conducting studies with Caenorhabditis elegans, Drosophila, fish, rodents and humans studies to determine the role of genetic factors in susceptibility to behavioral impairment from neurotoxic exposure.

}, keywords = {Animals, Behavior, Disease Models, Animal, Genetics, Humans, Neurotoxicity Syndromes, Neurotoxins, Phylogeny, Toxicology}, issn = {1872-9711}, doi = {10.1016/j.neuro.2009.07.014}, author = {Levin, Edward D and Aschner, Michael and Heberlein, Ulrike and Ruden, Douglas and Welsh-Bohmer, Kathleen A and Bartlett, Selena and Berger, Karen and Chen, Lang and Corl, Ammon B and Eddins, Donnie and French, Rachael and Hayden, Kathleen M and Helmcke, Kirsten and Hirsch, Helmut V B and Linney, Elwood and Lnenicka, Greg and Page, Grier P and Possidente, Debra and Possidente, Bernard and Kirshner, Annette} } @article {3566, title = {Is genetic evolution predictable?}, journal = {Science}, volume = {323}, year = {2009}, month = {2009 Feb 6}, pages = {746-51}, abstract = {

Ever since the integration of Mendelian genetics into evolutionary biology in the early 20th century, evolutionary geneticists have for the most part treated genes and mutations as generic entities. However, recent observations indicate that all genes are not equal in the eyes of evolution. Evolutionarily relevant mutations tend to accumulate in hotspot genes and at specific positions within genes. Genetic evolution is constrained by gene function, the structure of genetic networks, and population biology. The genetic basis of evolution may be predictable to some extent, and further understanding of this predictability requires incorporation of the specific functions and characteristics of genes into evolutionary theory.

}, keywords = {Animals, Arabidopsis, Biological Evolution, Drosophila, Epistasis, Evolution, Gene Regulatory Networks, Genes, Genetic, Genetic Speciation, Genetic Variation, Molecular, Mutation, Phenotype, Plants, Population Dynamics, Selection}, issn = {1095-9203}, doi = {10.1126/science.1158997}, author = {Stern, David L and Orgogozo, Virginie} } @article {46786, title = {Globally optimal stitching of tiled 3D microscopic image acquisitions.}, journal = {Bioinformatics}, volume = {25}, year = {2009}, month = {2009 Jun 1}, pages = {1463-5}, abstract = {

MOTIVATION: Modern anatomical and developmental studies often require high-resolution imaging of large specimens in three dimensions (3D). Confocal microscopy produces high-resolution 3D images, but is limited by a relatively small field of view compared with the size of large biological specimens. Therefore, motorized stages that move the sample are used to create a tiled scan of the whole specimen. The physical coordinates provided by the microscope stage are not precise enough to allow direct reconstruction (Stitching) of the whole image from individual image stacks.

RESULTS: To optimally stitch a large collection of 3D confocal images, we developed a method that, based on the Fourier Shift Theorem, computes all possible translations between pairs of 3D images, yielding the best overlap in terms of the cross-correlation measure and subsequently finds the globally optimal configuration of the whole group of 3D images. This method avoids the propagation of errors by consecutive registration steps. Additionally, to compensate the brightness differences between tiles, we apply a smooth, non-linear intensity transition between the overlapping images. Our stitching approach is fast, works on 2D and 3D images, and for small image sets does not require prior knowledge about the tile configuration.

AVAILABILITY: The implementation of this method is available as an ImageJ plugin distributed as a part of the Fiji project (Fiji is just ImageJ: http://pacific.mpi-cbg.de/).

}, keywords = {Animals, Drosophila, Imaging, Three-Dimensional, Larva, Microscopy, Confocal}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btp184}, author = {Preibisch, Stephan and Saalfeld, Stephan and Tomancak, Pavel} } @article {5485, title = {Glycogen synthase kinase-3/Shaggy mediates ethanol-induced excitotoxic cell death of Drosophila olfactory neurons.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, month = {2009 Dec 8}, pages = {20924-9}, abstract = {

It has long been known that heavy alcohol consumption leads to neuropathology and neuronal death. While the response of neurons to an ethanol insult is strongly influenced by genetic background, the underlying mechanisms are poorly understood. Here, we show that even a single intoxicating exposure to ethanol causes non-cell-autonomous apoptotic death specifically of Drosophila olfactory neurons, which is accompanied by a loss of a behavioral response to the smell of ethanol and a blackening of the third antennal segment. The Drosophila homolog of glycogen synthase kinase-3 (GSK-3)beta, Shaggy, is required for ethanol-induced apoptosis. Consistent with this requirement, the GSK-3beta inhibitor lithium protects against the neurotoxic effects of ethanol, indicating the possibility for pharmacological intervention in cases of alcohol-induced neurodegeneration. Ethanol-induced death of olfactory neurons requires both their neural activity and functional NMDA receptors. This system will allow the investigation of the genetic and molecular basis of ethanol-induced apoptosis in general and provide an understanding of the molecular role of GSK-3beta in programmed cell death.

}, keywords = {Amino Acid, Animals, Cell Death, Drosophila melanogaster, Drosophila Proteins, Electricity, Ethanol, Gene Silencing, Glycogen Synthase Kinase 3, Lithium, N-Methyl-D-Aspartate, Neurotoxins, Olfactory Receptor Neurons, Receptors, Sequence Homology, Volatilization}, issn = {1091-6490}, doi = {10.1073/pnas.0910813106}, author = {French, Rachael L and Heberlein, Ulrike} } @article {5481, title = {Happyhour, a Ste20 family kinase, implicates EGFR signaling in ethanol-induced behaviors.}, journal = {Cell}, volume = {137}, year = {2009}, month = {2009 May 29}, pages = {949-60}, abstract = {

The consequences of alcohol use disorders (AUDs) are devastating to individuals and society, yet few treatments are currently available. To identify genes regulating the behavioral effects of ethanol, we conducted a genetic screen in Drosophila and identified a mutant, happyhour (hppy), due to its increased resistance to the sedative effects of ethanol. Hppy protein shows strong homology to mammalian Ste20 family kinases of the GCK-1 subfamily. Genetic and biochemical experiments revealed that the epidermal growth factor (EGF)-signaling pathway regulates ethanol sensitivity in Drosophila and that Hppy functions as an inhibitor of the pathway. Acute pharmacological inhibition of the EGF receptor (EGFR) in adult animals altered acute ethanol sensitivity in both flies and mice and reduced ethanol consumption in a preclinical rat model of alcoholism. Inhibitors of the EGFR or components of its signaling pathway are thus potential pharmacotherapies for AUDs.

}, keywords = {Alcohol-Induced Disorders, Animal, Animals, Crosses, Disease Models, Dopamine, Drosophila melanogaster, Drosophila Proteins, Epidermal Growth Factor, Ethanol, Female, Genetic, Insulin, Male, Mice, Mutation, Phosphorylation, Protein-Serine-Threonine Kinases, Receptor, Signal Transduction}, issn = {1097-4172}, doi = {10.1016/j.cell.2009.03.020}, author = {Corl, Ammon B and Berger, Karen H and Ophir-Shohat, Galit and Gesch, Julie and Simms, Jeffrey A and Bartlett, Selena E and Heberlein, Ulrike} } @article {1343, title = {Head-anchored whole-cell recordings in freely moving rats.}, journal = {Nature Protocols}, volume = {4}, year = {2009}, month = {2009}, pages = {385-92}, abstract = {

Intracellular recordings are routinely used to study the synaptic and intrinsic properties of neurons in vitro. A key requirement for these recordings is a mechanically very stable preparation; thus their use in vivo had been limited previously to head-restrained animals. We have recently demonstrated that anchoring the electrode rigidly in place with respect to the skull provides sufficient stabilization for long-lasting, high-quality whole-cell recordings in awake, freely moving rats. This protocol describes our procedure in detail, adds specific instructions for targeting hippocampal CA1 pyramidal neurons and updates it with changes that facilitate patching and improve the success rate. The changes involve combining a standard, nonhead-mounted micromanipulator with a gripper to firmly hold the recording pipette during the anchoring process then gently release it afterwards. The procedure from the beginning of surgery to the end of a recording takes approximately 5 h. This technique allows new studies of the mechanisms underlying neuronal integration and cellular/synaptic plasticity in identified cells during natural behaviors.

}, keywords = {Animals, Brain, Electrodes, Implanted, Neurology, Neurons, Patch-Clamp Techniques, Rats, Wakefulness}, issn = {1750-2799}, doi = {10.1038/nprot.2009.5}, author = {Lee, Albert K and Epsztein, J{\'e}r{\^o}me and Brecht, Michael} } @article {5758, title = {High-throughput ethomics in large groups of Drosophila.}, journal = {Nature Methods}, volume = {6}, year = {2009}, month = {2009 Jun}, pages = {451-7}, abstract = {

We present a camera-based method for automatically quantifying the individual and social behaviors of fruit flies, Drosophila melanogaster, interacting in a planar arena. Our system includes machine-vision algorithms that accurately track many individuals without swapping identities and classification algorithms that detect behaviors. The data may be represented as an ethogram that plots the time course of behaviors exhibited by each fly or as a vector that concisely captures the statistical properties of all behaviors displayed in a given period. We found that behavioral differences between individuals were consistent over time and were sufficient to accurately predict gender and genotype. In addition, we found that the relative positions of flies during social interactions vary according to gender, genotype and social environment. We expect that our software, which permits high-throughput screening, will complement existing molecular methods available in Drosophila, facilitating new investigations into the genetic and cellular basis of behavior.

}, keywords = {Animal, Animals, Artificial Intelligence, Automated, Behavior, Computer-Assisted, Drosophila melanogaster, Humans, Image Interpretation, Monitoring, Movement, Pattern Recognition, Physiologic, Posture, Social Behavior}, issn = {1548-7105}, doi = {10.1038/nmeth.1328}, author = {Branson, Kristin and Robie, Alice A and Bender, John and Perona, Pietro and Dickinson, Michael H} } @article {4409, title = {How different are recently diverged species?: more than 150 phenotypic differences have been reported for the D. melanogaster species subgroup.}, journal = {Fly}, volume = {3}, year = {2009}, month = {2009 Apr-Jun}, pages = {117}, keywords = {Animals, Drosophila melanogaster, Genetic Speciation, Phenotype, Species Specificity}, issn = {1933-6942}, author = {Orgogozo, Virginie and Stern, David L} } @article {5237, title = {Hydrogen peroxide stimulates activity and alters behavior in Drosophila melanogaster.}, journal = {PLoS One}, volume = {4}, year = {2009}, month = {2009 Oct 28}, pages = {e7580}, abstract = {

Circadian rhythms in animals are regulated at the level of individual cells and by systemic signaling to coordinate the activities of multiple tissues. The circadian pacemakers have several physiological outputs, including daily locomotor rhythms. Several redox-active compounds have been found to function in regulation of circadian rhythms in cells, however, how particular compounds might be involved in regulating specific animal behaviors remains largely unknown. Here the effects of hydrogen peroxide on Drosophila movement were analyzed using a recently developed three-dimensional real-time multiple fly tracking assay. Both hydrogen peroxide feeding and direct injection of hydrogen peroxide caused increased adult fly locomotor activity. Continuous treatment with hydrogen peroxide also suppressed daily locomotor rhythms. Conditional over-expression of the hydrogen peroxide-producing enzyme superoxide dismutase (SOD) also increased fly activity and altered the patterns of locomotor activity across days and weeks. The real-time fly tracking system allowed for detailed analysis of the effects of these manipulations on behavior. For example, both hydrogen peroxide feeding and SOD over-expression increased all fly motion parameters, however, hydrogen peroxide feeding caused relatively more erratic movement, whereas SOD over-expression produced relatively faster-moving flies. Taken together, the data demonstrate that hydrogen peroxide has dramatic effects on fly movement and daily locomotor rhythms, and implicate hydrogen peroxide in the normal control of these processes.

}, keywords = {Animal, Animals, Behavior, Biological, Crosses, Drosophila melanogaster, Flight, Fluorescence, Genetic, Genetically Modified, Hydrogen Peroxide, Microscopy, Models, Movement, Oxidants, Oxidation-Reduction, Seasons, Superoxide Dismutase, Time Factors}, issn = {1932-6203}, doi = {10.1371/journal.pone.0007580}, author = {Grover, Dhruv and Ford, Daniel and Brown, Christopher and Hoe, Nicholas and Erdem, Aysen and Tavar{\'e}, Simon and Tower, John} } @article {2148, title = {Imaging informatics for personalised medicine: applications and challenges.}, journal = {International Journal of Functional Informatics and Personalised Medicine}, volume = {2}, year = {2009}, month = {2009}, pages = {125-35}, abstract = {

Imaging informatics has emerged as a major research theme in biomedicine in the last few decades. Currently, personalised, predictive and preventive patient care is believed to be one of the top priorities in biomedical research and practice. Imaging informatics plays a major role in biomedicine studies. This paper reviews main applications and challenges of imaging informatics in biomedicine.

}, issn = {1756-2112}, doi = {10.1007/s12021-010-9090-x}, author = {Liu, Tianming and Peng, Hanchuan and Zhou, Xiaobo} } @article {1646, title = {Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators.}, journal = {Nature Methods}, volume = {6}, year = {2009}, month = {2009 Dec}, pages = {875-81}, abstract = {

Genetically encoded calcium indicators (GECIs) can be used to image activity in defined neuronal populations. However, current GECIs produce inferior signals compared to synthetic indicators and recording electrodes, precluding detection of low firing rates. We developed a single-wavelength GCaMP2-based GECI (GCaMP3), with increased baseline fluorescence (3-fold), increased dynamic range (3-fold) and higher affinity for calcium (1.3-fold). We detected GCaMP3 fluorescence changes triggered by single action potentials in pyramidal cell dendrites, with signal-to-noise ratio and photostability substantially better than those of GCaMP2, D3cpVenus and TN-XXL. In Caenorhabditis elegans chemosensory neurons and the Drosophila melanogaster antennal lobe, sensory stimulation-evoked fluorescence responses were significantly enhanced with GCaMP3 (4-6-fold). In somatosensory and motor cortical neurons in the intact mouse, GCaMP3 detected calcium transients with amplitudes linearly dependent on action potential number. Long-term imaging in the motor cortex of behaving mice revealed large fluorescence changes in imaged neurons over months.

}, keywords = {Animals, Brain, Caenorhabditis elegans, Calcium, Cell Line, Drosophila melanogaster, Fluorescence Resonance Energy Transfer, Humans, Mice, Neurons}, issn = {1548-7105}, doi = {10.1038/nmeth.1398}, author = {Tian, Lin and Hires, S Andrew and Mao, Tianyi and Huber, Daniel and Chiappe, M Eugenia and Chalasani, Sreekanth H and Petreanu, Leopoldo and Akerboom, Jasper and McKinney, Sean A and Schreiter, Eric R and Bargmann, Cornelia I and Jayaraman, Vivek and Svoboda, Karel and Looger, Loren L} } @article {2390, title = {Imaging transcription in living cells.}, journal = {Annual Review of Biophysics}, volume = {38}, year = {2009}, month = {2009 Feb 3}, pages = {173-96}, abstract = {

The advent of new technologies for the imaging of living cells has made it possible to determine the properties of transcription, the kinetics of polymerase movement, the association of transcription factors, and the progression of the polymerase on the gene. We report here the current state of the field and the progress necessary to achieve a more complete understanding of the various steps in transcription. Our Consortium is dedicated to developing and implementing the technology to further this understanding.

}, keywords = {Computer-Assisted, Fluorescence, Gene Expression Profiling, Image Interpretation, Microscopy, Transcription Factors, Transcriptional Activation}, issn = {1936-122X}, doi = {10.1073/pnas.1100640108}, author = {Darzacq, Xavier and Yao, Jie and Larson, Daniel R and Causse, Sebastien Z and Bosanac, Lana and de Turris, Valeria and Ruda, Vera M and Lionnet, Timoth{\'e}e and Zenklusen, Daniel and Guglielmi, Benjamin and Tjian, Robert and Singer, Robert H} } @article {2796, title = {In situ SIMS analysis and reactions of surfaces prepared by soft landing of mass-selected cations and anions using an ion trap mass spectrometer.}, journal = {Journal of the American Society for Mass Spectrometry}, volume = {20}, year = {2009}, month = {2009 Jun}, pages = {949-56}, abstract = {

Mass-selected polyatomic cations and anions, produced by electrosonic spray ionization (ESSI), were deposited onto polycrystalline Au or fluorinated self-assembled monolayer (FSAM) surfaces by soft landing (SL), using a rectilinear ion trap (RIT) mass spectrometer. Protonated and deprotonated molecules, as well as intact cations and anions generated from such molecules as peptides, inorganic catalysts, and fluorescent dyes, were soft-landed onto the surfaces. Analysis of the modified surfaces was performed in situ by Cs(+) secondary ion mass spectrometry (SIMS) using the same RIT mass analyzer to characterize the sputtered ions as that used to mass select the primary ions for SL. Soft-landing times as short as 30 s provided surfaces that yielded good quality SIMS spectra. Chemical reactions of the surfaces modified by SL were generated in an attached reaction chamber into which the surface was transferred under vacuum. For example, a surface on which protonated triethanolamine had been soft landed was silylated using vapor-phase chlorotrimethylsilane before being returned still under vacuum to the preparation chamber where SIMS analysis revealed the silyloxy functionalization. SL and vapor-phase reactions are complementary methods of surface modification and in situ surface analysis by SIMS is a simple way to characterize the products produced by either technique.

}, issn = {1879-1123}, doi = {10.1364/AO.50.001792}, author = {Nie, Zongxiu and Li, Guangtao and Goodwin, Michael P and Gao, Liang and Cyriac, Jobin and Cooks, R Graham} } @article {4277, title = {Infernal 1.0: inference of RNA alignments.}, journal = {Bioinformatics}, volume = {25}, year = {2009}, month = {2009 May 15}, pages = {1335-7}, abstract = {

SUMMARY: INFERNAL builds consensus RNA secondary structure profiles called covariance models (CMs), and uses them to search nucleic acid sequence databases for homologous RNAs, or to create new sequence- and structure-based multiple sequence alignments. AVAILABILITY: Source code, documentation and benchmark downloadable from http://infernal.janelia.org. INFERNAL is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and Mac OS/X.

}, keywords = {Databases, Nucleic Acid, Nucleic Acid Conformation, RNA, Sequence Alignment, Sequence Analysis, Software}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btp157}, author = {Nawrocki, Eric P and Kolbe, Diana L and Eddy, Sean R.} } @article {927, title = {Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, month = {2009 Mar 3}, pages = {3125-30}, abstract = {

Understanding molecular-scale architecture of cells requires determination of 3D locations of specific proteins with accuracy matching their nanometer-length scale. Existing electron and light microscopy techniques are limited either in molecular specificity or resolution. Here, we introduce interferometric photoactivated localization microscopy (iPALM), the combination of photoactivated localization microscopy with single-photon, simultaneous multiphase interferometry that provides sub-20-nm 3D protein localization with optimal molecular specificity. We demonstrate measurement of the 25-nm microtubule diameter, resolve the dorsal and ventral plasma membranes, and visualize the arrangement of integrin receptors within endoplasmic reticulum and adhesion complexes, 3D protein organization previously resolved only by electron microscopy. iPALM thus closes the gap between electron tomography and light microscopy, enabling both molecular specification and resolution of cellular nanoarchitecture.

}, keywords = {Animals, Cell Line, Cercopithecus aethiops, Fluorescence, Humans, Imaging, Interference, Microscopy, Microtubules, Three-Dimensional}, issn = {1091-6490}, doi = {10.1073/pnas.0813131106}, author = {Shtengel, Gleb and Galbraith, James A and Galbraith, Catherine G and Lippincott-Schwartz, Jennifer and Gillette, Jennifer M and Manley, Suliana and Sougrat, Rachid and Waterman, Clare M and Kanchanawong, Pakorn and Davidson, Michael W and Fetter, Richard D and Hess, Harald F} } @article {6360, title = {Knockdown of parhyale ultrabithorax recapitulates evolutionary changes in crustacean appendage morphology.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, month = {2009 Aug 18}, pages = {13892-6}, abstract = {

Crustaceans possess remarkably diverse appendages, both between segments of a single individual as well as between species. Previous studies in a wide range of crustaceans have demonstrated a correlation between the anterior expression boundary of the homeotic (Hox) gene Ultrabithorax (Ubx) and the location and number of specialized thoracic feeding appendages, called maxillipeds. Given that Hox genes regulate regional identity in organisms as diverse as mice and flies, these observations in crustaceans led to the hypothesis that Ubx expression regulates the number of maxillipeds and that evolutionary changes in Ubx expression have generated various aspects of crustacean appendage diversity. Specifically, evolutionary changes in the expression boundary of Ubx have resulted in crustacean species with either 0, 1, 2, or 3 pairs of thoracic maxillipeds. Here we test this hypothesis by altering the expression of Ubx in Parhyale hawaiensis, a crustacean that normally possesses a single pair of maxillipeds. By reducing Ubx expression, we can generate Parhyale with additional maxillipeds in a pattern reminiscent of that seen in other crustacean species, and these morphological alterations are maintained as the animals molt and mature. These results provide critical evidence supporting the proposition that changes in Ubx expression have played a role in generating crustacean appendage diversity and lend general insights into the mechanisms of morphological evolution.

}, keywords = {Animals, Base Sequence, Biological, Biological Evolution, Cloning, Crustacea, Electron, Extremities, Gene Expression Regulation, Genes, Genetic Techniques, Homeobox, Homeodomain Proteins, In Situ Hybridization, Microscopy, Models, Molecular, Molecular Sequence Data, RNA, Scanning, Small Interfering}, issn = {1091-6490}, doi = {10.1073/pnas.0903105106}, author = {Liubicich, Danielle M and Serano, Julia M and Pavlopoulos, Anastasios and Kontarakis, Zacharias and Protas, Meredith E and Kwan, Elaine and Chatterjee, Sandip and Tran, Khoa D and Averof, Michalis and Patel, Nipam H} } @article {2502, title = {Larval leg integrity is maintained by distal-less and is required for proper timing of metamorphosis in the flour beetle, tribolium castaneum.}, journal = {Developmental Biology}, volume = {326}, year = {2009}, month = {2009 Feb 1}, pages = {60-7}, abstract = {

The dramatic transformation from a larva to an adult must be accompanied by a coordinated activity of genes and hormones that enable an orchestrated transformation from larval to pupal/adult tissues. The maintenance of larval appendages and their subsequent transformation to appendages in holometabolous insects remains elusive at the developmental genetic level. Here the role of a key appendage patterning gene Distal-less (Dll) was examined in mid- to late-larval stages of the flour beetle, Tribolium castaneum. During late larval development, Dll was expressed in appendages in a similar manner as previously reported for the tobacco hornworm, Manduca sexta. Removal of this late Dll expression resulted in disruption of adult appendage patterning. Intriguingly, earlier removal resulted in dramatic loss of structural integrity and identity of larval appendages. A large amount of variability in appendage morphology was observed following Dll dsRNA injection, unlike larvae injected with dachshund dsRNA. These Dll dsRNA-injected larvae underwent numerous supernumerary molts, which could be terminated with injection of either JH methyltransferase or Methoprene-tolerant dsRNA. Apparently, the partial dedifferentiation of the appendages in these larvae acts to maintain high JH and, hence, prevents metamorphosis.

}, keywords = {Animals, Biological, Double-Stranded, Extremities, Homeodomain Proteins, Larva, Metamorphosis, Methoprene, RNA, Transcription Factors, Tribolium}, issn = {1095-564X}, doi = {10.1016/j.ydbio.2008.10.022}, author = {Suzuki, Yuichiro and Squires, Diego C and Riddiford, Lynn M} } @article {4605, title = {Leptin targets in the mouse brain.}, journal = {The Journal of Comparative Neurology}, volume = {514}, year = {2009}, month = {2009 Jun 10}, pages = {518-32}, abstract = {

The central actions of leptin are essential for homeostatic control of adipose tissue mass, glucose metabolism, and many autonomic and neuroendocrine systems. In the brain, leptin acts on numerous different cell types via the long-form leptin receptor (LepRb) to elicit its effects. The precise identification of leptin{\textquoteright}s cellular targets is fundamental to understanding the mechanism of its pleiotropic central actions. We have systematically characterized LepRb distribution in the mouse brain using in situ hybridization in wildtype mice as well as by EYFP immunoreactivity in a novel LepRb-IRES-Cre EYFP reporter mouse line showing high levels of LepRb mRNA/EYFP coexpression. We found substantial LepRb mRNA and EYFP expression in hypothalamic and extrahypothalamic sites described before, including the dorsomedial nucleus of the hypothalamus, ventral premammillary nucleus, ventral tegmental area, parabrachial nucleus, and the dorsal vagal complex. Expression in insular cortex, lateral septal nucleus, medial preoptic area, rostral linear nucleus, and in the Edinger-Westphal nucleus was also observed and had been previously unreported. The LepRb-IRES-Cre reporter line was used to chemically characterize a population of leptin receptor-expressing neurons in the midbrain. Tyrosine hydroxylase and Cre reporter were found to be coexpressed in the ventral tegmental area and in other midbrain dopaminergic neurons. Lastly, the LepRb-IRES-Cre reporter line was used to map the extent of peripheral leptin sensing by central nervous system (CNS) LepRb neurons. Thus, we provide data supporting the use of the LepRb-IRES-Cre line for the assessment of the anatomic and functional characteristics of neurons expressing leptin receptor.

}, keywords = {Animals, Brain, Cell Count, Gene Expression, Immunohistochemistry, In Situ Hybridization, Lac Operon, Leptin, Male, Messenger, Mice, Photomicrography, Receptors, RNA, STAT3 Transcription Factor, Transgenic, Tyrosine 3-Monooxygenase}, issn = {1096-9861}, doi = {10.1002/cne.22025}, author = {Scott, Michael M and Lachey, Jennifer L and Sternson, Scott M and Lee, Charlotte E and Elias, Carol F and Friedman, Jeffrey M and Elmquist, Joel K} } @article {4280, title = {Lessons from a compartmental model of a Drosophila neuron.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {29}, year = {2009}, month = {2009 Sep 30}, pages = {12033-4}, abstract = {

Although the vinegar fly, Drosophila melanogaster, has been a biological model organism for over a century, its emergence as a model system for the study of neurophysiology is comparatively recent. The primary reason for this is that the vinegar fly and its neurons are tiny; up until 5 years ago, it was prohibitively difficult to record intracellularly from individual neurons in the intact Drosophila brain (Wilson et al., 2004). Today, fly electrophysiologists can genetically label neurons with GFP and reliably record from many (but not all) neurons in the fruit fly brain. Using genetic tools to drive expression of fluorescent calcium indicators, light-sensitive ion channels, or cell activity suppressors, we are beginning to understand how the external environment is represented with electrical potentials in Drosophila neurons (for review, see Olsen and Wilson, 2008).

}, keywords = {Animals, Drosophila melanogaster, Humans, Models, Neurological, Neurons}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3348-09.2009}, author = {Tuthill, John C} } @article {1439, title = {Like-charge interactions between colloidal particles are asymmetric with respect to sign.}, journal = {Soft Matter}, year = {2009}, month = {2009}, pages = {1931-6}, abstract = {

Two-dimensional dispersions of colloidal particles with a range of surface chemistries and electrostatic potentials are characterized under a series of solution ionic strengths. A combination of optical imaging techniques are employed to monitor both the colloid structure and the electrostatic surface potential of individual particles in situ. We find that like-charge multiparticle interactions can be tuned from exclusively repulsive to long-range attractive by changing the particle surface composition. This behavior is strongly asymmetric with respect to the sign of the surface potential. Collective long-range attractive interactions are only observed among negatively charged particles.

}, author = {Clack, Nathan G and Salaita, Khalid and Wu, HJ and Groves, JT and Gomez, EW} } @article {3638, title = {Lipid-protein interactions probed by electron crystallography.}, journal = {Current Opinion in Structural Biology}, volume = {19}, year = {2009}, month = {2009 Oct}, pages = {560-5}, abstract = {

Electron crystallography is arguably the only electron cryomicroscopy (cryoEM) technique able to deliver an atomic-resolution structure of membrane proteins embedded in the lipid bilayer. In the electron crystallographic structures of the light driven ion pump, bacteriorhodopsin, and the water channel, aquaporin-0, sufficiently high resolution was obtained and both lipid and protein were visualized, modeled, and described in detail. An extensive network of lipid-protein interactions mimicking native membranes is established and maintained in two-dimensional (2D) crystalline vesicles used for structural analysis by electron crystallography. Lipids are tightly integrated into the protein{\textquoteright}s architecture where they can affect the function, structure, quaternary assembly, and the stability of the membrane protein.

}, keywords = {Crystallography, Electron, Lipids, Microscopy, Models, Molecular, Proteins, X-Ray}, issn = {1879-033X}, doi = {10.1016/j.sbi.2009.07.012}, author = {Reichow, Steve L and Gonen, Tamir} } @article {5243, title = {Local RNA structure alignment with incomplete sequence.}, journal = {Bioinformatics}, volume = {25}, year = {2009}, month = {2009 May 15}, pages = {1236-43}, abstract = {

Accuracy of automated structural RNA alignment is improved by using models that consider not only primary sequence but also secondary structure information. However, current RNA structural alignment approaches tend to perform poorly on incomplete sequence fragments, such as single reads from metagenomic environmental surveys, because nucleotides that are expected to be base paired are missing.

}, keywords = {Algorithms, Databases, Genetic, Models, Molecular, Nucleic Acid Conformation, RNA, Sequence Alignment, Sequence Analysis}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btp154}, author = {Kolbe, Diana L and Eddy, Sean R.} } @article {6492, title = {Loss of sensitivity in an analog neural circuit.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {29}, year = {2009}, month = {2009 Mar 11}, pages = {3045-58}, abstract = {

A low-contrast spot that activates just one ganglion cell in the retina is detected in the spike train of the cell with about the same sensitivity as it is detected behaviorally. This is consistent with Barlow{\textquoteright}s proposal that the ganglion cell and later stages of spiking neurons transfer information essentially without loss. Yet, when losses of sensitivity by all preneural factors are accounted for, predicted sensitivity near threshold is considerably greater than behavioral sensitivity, implying that somewhere in the brain information is lost. We hypothesized that the losses occur mainly in the retina, where graded signals are processed by analog circuits that transfer information at high rates and low metabolic cost. To test this, we constructed a model that included all preneural losses for an in vitro mammalian retina, and evaluated the model to predict sensitivity at the cone output. Recording graded responses postsynaptic to the cones (from the type A horizontal cell) and comparing to predicted preneural sensitivity, we found substantial loss of sensitivity (4.2-fold) across the first visual synapse. Recording spike responses from brisk-transient ganglion cells stimulated with the same spot, we found a similar loss (3.5-fold) across the second synapse. The total retinal loss approximated the known overall loss, supporting the hypothesis that from stimulus to perception, most loss near threshold is retinal.

}, keywords = {Action Potentials, Animals, Contrast Sensitivity, Guinea Pigs, Nerve Net, Photic Stimulation, Visual Pathways}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.5071-08.2009}, author = {Borghuis, Bart G and Sterling, Peter and Smith, Robert G} } @mastersthesis {3859, title = {Machine learning of image analysis with convolutional networks and topological constraints.}, year = {2009}, month = {2009}, school = {Massachusetts Institute of Technology}, type = {masters}, abstract = {

We present an approach to solving computer vision problems in which the goal is to produce a high-dimensional, pixel-based interpretation of some aspect of the underlying structure of an image. Such tasks have traditionally been categorized as {\textquotedblleft}low-level vision{\textquotedblright} problems, and examples include image denoising, boundary detection, and motion estimation. Our approach is characterized by two main elements, both of which represent a departure from previous work. The first is a focus on convolutional networks, a machine learning strategy that operates directly on an input image with no use of hand-designed features and employs many thousands of free parameters that are learned from data. Previous work in low-level vision has been largely focused on completely handdesigned algorithms or learning methods with a hand-designed feature space. We demonstrate that a learning approach with high model complexity, but zero prior knowledge about any specific image domain, can outperform existing techniques even in the challenging area of natural image processing. We also present results that establish how convolutional networks are closely related to Markov random fields (MRFs), a popular probabilistic approach to image analysis, but can in practice can achieve significantly greater model complexity. The second aspect of our approach is the use of domain specific cost functions and learning algorithms that reflect the structured nature of certain prediction problems in image analysis. In particular, we show how concepts from digital topology can be used in the context of boundary detection to both evaluate and optimize the high-order property of topological accuracy. We demonstrate that these techniques can significantly improve the machine learning approach and outperform state of the art boundary detection and segmentation methods. Throughout our work we maintain a special interest and focus on application of our methods to connectomics, an emerging scientific discipline that seeks highthroughput methods for recovering neural connectivity data from brains. This application requires solving low-level image analysis problems on a tera-voxel or peta-voxel scale, and therefore represents an extremely challenging and exciting arena for the development of computer vision methods.

}, author = {Jain, Viren} } @article {1205, title = {Manipulation of an innate escape response in Drosophila: photoexcitation of acj6 neurons induces the escape response.}, journal = {PLoS One}, volume = {4}, year = {2009}, month = {2009 Apr 2}, pages = {e5100}, abstract = {

BACKGROUND: The genetic analysis of behavior in Drosophila melanogaster has linked genes controlling neuronal connectivity and physiology to specific neuronal circuits underlying a variety of innate behaviors. We investigated the circuitry underlying the adult startle response, using photoexcitation of neurons that produce the abnormal chemosensory jump 6 (acj6) transcription factor. This transcription factor has previously been shown to play a role in neuronal pathfinding and neurotransmitter modality, but the role of acj6 neurons in the adult startle response was largely unknown. PRINCIPAL FINDINGS: We show that the activity of these neurons is necessary for a wild-type startle response and that excitation is sufficient to generate a synthetic escape response. Further, we show that this synthetic response is still sensitive to the dose of acj6 suggesting that that acj6 mutation alters neuronal activity as well as connectivity and neurotransmitter production. RESULTS/SIGNIFICANCE: These results extend the understanding of the role of acj6 and of the adult startle response in general. They also demonstrate the usefulness of activity-dependent characterization of neuronal circuits underlying innate behaviors in Drosophila, and the utility of integrating genetic analysis into modern circuit analysis techniques.

}, keywords = {Animal, Animals, Base Sequence, Behavior, DNA Primers, Drosophila melanogaster, Genetically Modified, Neurons, Startle Reaction}, issn = {1932-6203}, doi = {10.1371/journal.pone.0005100}, author = {Zimmermann, Gregor and Wang, Li-Ping and Vaughan, Alexander G and Manoli, Devanand S and Zhang, Feng and Deisseroth, Karl and Baker, Bruce S and Scott, Matthew P} } @article {1521, title = {Mapping and manipulating neural circuits in the fly brain.}, journal = {Advances in Genetics}, volume = {65}, year = {2009}, month = {2009}, pages = {79-143}, abstract = {

Drosophila is a marvelous system to study the underlying principles that govern how neural circuits govern behaviors. The scale of the fly brain (approximately 100,000 neurons) and the complexity of the behaviors the fly can perform make it a tractable experimental model organism. In addition, 100 years and hundreds of labs have contributed to an extensive array of tools and techniques that can be used to dissect the function and organization of the fly nervous system. This review discusses both the conceptual challenges and the specific tools for a neurogenetic approach to circuit mapping in Drosophila.

}, keywords = {Animal, Animals, Behavior, Brain, Chromosome Mapping, Drosophila, Nerve Net, Neurons}, issn = {0065-2660}, doi = {10.1016/S0065-2660(09)65003-3}, author = {Simpson, Julie H} } @article {2798, title = {Mass selection of ions from beams using waveform isolation in radiofrequency quadrupoles.}, journal = {Analytical Chemistry}, volume = {81}, year = {2009}, month = {2009 Mar 1}, pages = {1833-40}, abstract = {

A waveform isolation method is described for the mass-selective transmission of ions through quadrupole mass filters, and it is implemented on a new tandem mass analyzer instrument. The method features the application of broad-band waveforms comprising appropriate frequencies to cause mass-selective instability in ions of particular mass-to-charge (m/z) and to transmit all others. The experiment is implemented in a tandem quadrupole system in which the first mass filter is a rectilinear ion trap (RIT) operated in a continuous mass-selective mode to transmit ions of ions of one or more arbitrarily selected m/z value(s). The second analyzer was used to verify the quality of the mass selection achieved using the first analyzer via conventional quadrupole ion trap mass-selective instability scanning. A new subtype of product ion tandem mass spectrometry (MS/MS) scan, termed the summed product ion scan, is demonstrated with a mixture of biological compounds. It is used to characterize product ions arising after simultaneous isolation and collisional activation of multiple precursor species, in this case ions of the same analyte generated in different charge states. The summed product ion scan can be useful for enhancing sensitivity for the analyte of interest or for providing more comprehensive information about an analyte than is available by monitoring a single ionized form of the analyte. The analytical performance of the waveform isolation method is tested using simple drug mixtures, and its potential for increasing overall yields in preparative mass spectrometry is explored briefly. It is shown that efficiencies of ca. 70\% of ion transfer to a surface for ion soft landing surface can be achieved. The upper mass range is limited by axial acceleration arising from the stretched geometry, and one solution to this problem is provided.

}, keywords = {Carmustine, Cytarabine, Electrospray Ionization, Ions, Mass, Mass Spectrometry, Mathematics, Melphalan, Radio Waves, Spectrometry, Tandem Mass Spectrometry}, issn = {1520-6882}, doi = {10.1364/AO.50.001792}, author = {Song, Qingyu and Smith, Scott A and Gao, Liang and Xu, Wei and Voln{\'y}, Michael and Ouyang, Zheng and Cooks, R Graham} } @proceedings {46329, title = {Maximin affinity learning of image segmentation}, volume = {22}, year = {2009}, publisher = {MIT Press}, abstract = {

Images can be segmented by first using a classifier to predict an affinity graph that reflects the degree to which image pixels must be grouped together and then partitioning the graph to yield a segmentation. Machine learning has been applied to the affinity classifier to produce affinity graphs that are good in the sense of minimizing edge misclassification rates. However, this error measure is only indirectly related to the quality of segmentations produced by ultimately partitioning the affinity graph. We present the first machine learning algorithm for training a classifier to produce affinity graphs that are good in the sense of producing segmentations that directly minimize the Rand index, a well known segmentation performance measure. The Rand index measures segmentation performance by quantifying the classification of the connectivity of image pixel pairs after segmentation. By using the simple graph partitioning algorithm of finding the connected components of the thresholded affinity graph, we are able to train an affinity classifier to directly minimize the Rand index of segmentations resulting from the graph partitioning. Our learning algorithm corresponds to the learning of maximin affinities between image pixel pairs, which are predictive of the pixel-pair connectivity.

}, author = {Srinivas C. Turaga and Kevin Briggman and Moritz N. Helmstaedter and Winfried Denk and Sebastian Seung} } @article {1236, title = {Maximization of the connectivity repertoire as a statistical principle governing the shapes of dendritic arbors.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, month = {2009 Jul 28}, pages = {12536-41}, abstract = {

The shapes of dendritic arbors are fascinating and important, yet the principles underlying these complex and diverse structures remain unclear. Here, we analyzed basal dendritic arbors of 2,171 pyramidal neurons sampled from mammalian brains and discovered 3 statistical properties: the dendritic arbor size scales with the total dendritic length, the spatial correlation of dendritic branches within an arbor has a universal functional form, and small parts of an arbor are self-similar. We proposed that these properties result from maximizing the repertoire of possible connectivity patterns between dendrites and surrounding axons while keeping the cost of dendrites low. We solved this optimization problem by drawing an analogy with maximization of the entropy for a given energy in statistical physics. The solution is consistent with the above observations and predicts scaling relations that can be tested experimentally. In addition, our theory explains why dendritic branches of pyramidal cells are distributed more sparsely than those of Purkinje cells. Our results represent a step toward a unifying view of the relationship between neuronal morphology and function.

}, keywords = {Action Potentials, Algorithms, Animals, Axons, Dendrites, Haplorhini, Models, Neural Pathways, Neurological, Purkinje Cells, Pyramidal Cells, Rats, Synapses}, issn = {1091-6490}, doi = {10.1371/journal.pcbi.1001066}, author = {Wen, Quan and Stepanyants, Armen and Elston, Guy N and Grosberg, Alexander Y and Chklovskii, Dmitri B} } @article {48394, title = {Mimicking the folding pathway to improve homology-free protein structure prediction.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, month = {2009 Mar 10}, pages = {3734-9}, abstract = {

Since the demonstration that the sequence of a protein encodes its structure, the prediction of structure from sequence remains an outstanding problem that impacts numerous scientific disciplines, including many genome projects. By iteratively fixing secondary structure assignments of residues during Monte Carlo simulations of folding, our coarse-grained model without information concerning homology or explicit side chains can outperform current homology-based secondary structure prediction methods for many proteins. The computationally rapid algorithm using only single (phi,psi) dihedral angle moves also generates tertiary structures of accuracy comparable with existing all-atom methods for many small proteins, particularly those with low homology. Hence, given appropriate search strategies and scoring functions, reduced representations can be used for accurately predicting secondary structure and providing 3D structures, thereby increasing the size of proteins approachable by homology-free methods and the accuracy of template methods that depend on a high-quality input secondary structure.

}, keywords = {Algorithms, Amino Acid Sequence, Molecular Mimicry, Molecular Sequence Data, Protein Folding, Protein Structure, Secondary, Protein Structure, Tertiary, Proteins, Structural Homology, Protein}, issn = {1091-6490}, doi = {10.1073/pnas.0811363106}, author = {DeBartolo, Joe and Colubri, Andr{\'e}s and Jha, Abhishek K and Fitzgerald, James E and Freed, Karl F and Sosnick, Tobin R} } @article {1564, title = {Modulating protein interactions by rational and computational design.}, journal = {Protein Engineering and Design}, year = {2009}, month = {2009}, pages = {343-66}, author = {Marvin, Jonathan S and Looger, Loren L} } @proceedings {45798, title = {Molecular Basis of Facultative Asexuality in Aphids}, volume = {49}, year = {2009}, month = {01/2009}, pages = {E308-E308}, publisher = {OXFORD UNIV PRESS INC}, abstract = {

Phenotypic plasticity allows organisms to quickly adapt in response to changing environments. Little is known of the genetic, environmental and epigenetic contribution to the expression of alternative adaptive developmental outcomes. We study aphid polyphenisms, which offer a unique, compelling opportunity to study multiple levels of biological organization, especially insect epigenetics. The pea aphid, Acyrthosiphon pisum, exhibits an adaptive reproductive polyphenism whereby genetically identical individuals reproduce either sexually (meiosis) or asexually (parthenogenesis) depending on environmental conditions during maternal development (short or long photoperiod, respectively). To understand how facultative asexuality evolved in aphids, we first determined meiosis gene activity in sexuals and asexuals. I determined that the pea aphid genome encodes single copies of homologs for the majority of the core meiotic machinery, suggesting that meiotic plasticity is not due simply to gene loss or expansion. Next, we determined if these core meiosis genes are expressed using PCR spanning across at least one intron from cDNA isolated from asexual and sexual ovaries. Surprisingly, meiosis specific genes (e.g., Spo11, Msh4, Msh5, Hop2 and Mnd1) are expressed in not only in asexual ovaries but also in somatic tissue and an obligately asexual aphid strain. Interestingly, the Spo11 PCR product contained intronic sequence, thus representing unspliced mRNA. Germline expression of Spo11, Mnd1 and Hop2 was confirmed by in situ analysis. Preliminary results identified candidate methylation sites in the Spo11 locus, indicating an epigenetic basis for this expression difference. Further characterization will help us better understand the molecular and epigenetic mechanisms underlying this adaptive facultative plasticity.

}, url = {http://www.sicb.org/meetings/2009/schedule/abstractdetails.php3?id=1224}, author = {DG Srinivasan and L Ano and GK Davis and DL Stern} } @article {6342, title = {Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, month = {2009 Jun 30}, pages = {10644-8}, abstract = {

Rotaviruses, major causes of childhood gastroenteritis, are nonenveloped, icosahedral particles with double-strand RNA genomes. By the use of electron cryomicroscopy and single-particle reconstruction, we have visualized a rotavirus particle comprising the inner capsid coated with the trimeric outer-layer protein, VP7, at a resolution (4 A) comparable with that of X-ray crystallography. We have traced the VP7 polypeptide chain, including parts not seen in its X-ray crystal structure. The 3 well-ordered, 30-residue, N-terminal "arms" of each VP7 trimer grip the underlying trimer of VP6, an inner-capsid protein. Structural differences between free and particle-bound VP7 and between free and VP7-coated inner capsids may regulate mRNA transcription and release. The Ca(2+)-stabilized VP7 intratrimer contact region, which presents important neutralizing epitopes, is unaltered upon capsid binding.

}, keywords = {Antigens, Biological, Calcium, Capsid Proteins, Cryoelectron Microscopy, Crystallography, Models, Molecular, Protein Multimerization, Protein Structure, Quaternary, Rotavirus, Viral, Viral Core Proteins, Virion, X-Ray}, issn = {1091-6490}, doi = {10.1073/pnas.0904024106}, author = {Chen, James Z and Settembre, Ethan C and Aoki, Scott T and Zhang, Xing and Bellamy, A Richard and Dormitzer, Philip R and Harrison, Stephen C and Grigorieff, Nikolaus} } @article {2497, title = {The molecular mechanisms of cuticular melanization: the ecdysone cascade leading to dopa decarboxylase expression in Manduca sexta.}, journal = {Insect Biochemistry and Molecular Biology}, volume = {39}, year = {2009}, month = {2009 Apr}, pages = {245-53}, abstract = {

Many insect developmental color changes are known to be regulated by both ecdysone and juvenile hormone. Yet the molecular mechanisms underlying this regulation have not been well understood. This review highlights the hormonal mechanisms involved in the regulation of two key enzymes [dopa decarboxylase (DDC) and phenoloxidase] necessary for insect cuticular melanization, and the molecular action of 20-hydroxyecdysone on various transcription factors leading to DDC expression at the end of a larval molt in Manduca sexta. In addition, the ecdysone cascade found in M. sexta is compared with that of other organisms.

}, keywords = {Animals, Developmental, Dopa Decarboxylase, Ecdysone, Gene Expression Regulation, Insect Proteins, Manduca, Melanins}, issn = {1879-0240}, doi = {10.1016/j.ibmb.2009.01.008}, author = {Hiruma, Kiyoshi and Riddiford, Lynn M} } @article {1226, title = {Morphological characterization of single fan-shaped body neurons in Drosophila melanogaster.}, journal = {Cell and Tissue Research}, volume = {336}, year = {2009}, month = {2009 Jun}, pages = {509-19}, abstract = {

The fan-shaped body is the largest substructure of the central complex in Drosophila melanogaster. Two groups of large-field neurons that innervate the fan-shaped body, viz., F1 and F5 neurons, have recently been found to be involved in visual pattern memory for "contour orientation" and "elevation" in a rut-dependent manner. The F5 neurons have been found to be responsible for the parameter "elevation" in a for-dependent manner. We have shown here that the F1 neuron also affects visual memory for "contour orientation" in a for-dependent way. With the help of Gal4/UAS and FLP-out techniques, we have characterized the morphological features of these two groups of neurons at single neuron resolution. We have observed that F1 or F5 neurons are groups of isomorphic individual neurons. Single F1 neurons have three main arborization regions: one in the first layer of the fan-shaped body, one in the ventral body, and another in the inferior medial protocerebrum. Single F5 neurons have two arborization regions: one in the fifth layer of the fan-shaped body and the other in the superior medial protocerebrum. The polarity of the F1 and F5 neurons has been studied with the Syt-GFP marker. Our results indicate the existence of presynaptic sites of both F1 and F5 neurons located in the fan-shaped body and postsynaptic sites outside of the fan-shaped body.

}, keywords = {Animals, Cell Shape, Drosophila melanogaster, Memory, Neurons, Pattern Recognition, Presynaptic Terminals, Visual}, issn = {1432-0878}, doi = {10.1007/s00441-009-0781-2}, author = {Li, Weizhe and Pan, Yufeng and Wang, Zhipeng and Gong, Haiyun and Gong, Zhefeng and Liu, Li} } @article {48183, title = {Multi-object segmentation of head bones.}, journal = {MIDAS Journal}, year = {2009}, month = {2009 Jul 20}, abstract = {

We present a fully automatic method for 3D segmentation of the mandibular bone from CT data. The method includes an adaptation of statistical shape models of the mandible, the skull base and the midfacial bones, followed by a simultaneous graph-based optimization of adjacent deformable models. The adaptation of the models to the image data is performed according to a heuristic model of the typical intensity distribution in the vincinity of the bone boundary, with special focus on an accurate discrimination of adjacent bones in joint regions. An evaluation of our method based on 18 CT scans shows that a manual correction of the automatic segmentations is not necessary in approx. 60\% of the axial slices that contain the mandible.

}, url = {http://hdl.handle.net/10380/3099}, author = {Kainmueller, Dagmar and Lamecker, Hans and Seim, Heiko and Zachow, Stefan} } @article {48182, title = {Multi-object segmentation with coupled deformable models.}, journal = {Annals of the British Machine Vision Association}, volume = {2009}, year = {2009}, month = {2009}, pages = {1-10}, abstract = {

For biomechanical simulations, the segmentation of multiple adjacent anatomical struc- tures from medical image data is often required. If adjacent structures are barely dis- tinguishable in image data, in general automatic segmentation methods for single struc- tures do not yield sufficiently accurate results. To improve segmentation accuracy in these cases, knowledge about adjacent structures must be exploited. Optimal graph searching (graph cuts) based on deformable surface models allows for a simultaneous segmentation of multiple adjacent objects. However, this method requires a correspon- dence relation between vertices of adjacent surface meshes. Line segments, each con- taining two corresponding vertices, may then serve as shared displacement directions in the segmentation process. In this paper we propose a scheme for constructing a corre- spondence relation in adjacent regions of two arbitrary surfaces. This correspondence relation implies shared displacement directions that we apply for segmentation with de- formable surfaces. Here, overlap of the surfaces is guaranteed not to occur. We show correspondence relations for regions on a femoral head and acetabulum and other adja- cent structures, as well as an evaluation of segmentation results on 50 ct images of the hip joint.\ 

}, url = {http://www.bmva.org/annals/2009/2009-0005.pdf}, author = {Kainmueller, Dagmar and Lamecker, Hans and Zachow, Stefan} } @article {4273, title = {Myosin-dependent targeting of transmembrane proteins to neuronal dendrites.}, journal = {Nature Neuroscience}, volume = {12}, year = {2009}, month = {2009 May}, pages = {568-76}, abstract = {

The distinct electrical properties of axonal and dendritic membranes are largely a result of specific transport of vesicle-bound membrane proteins to each compartment. How this specificity arises is unclear because kinesin motors that transport vesicles cannot autonomously distinguish dendritically projecting microtubules from those projecting axonally. We hypothesized that interaction with a second motor might enable vesicles containing dendritic proteins to preferentially associate with dendritically projecting microtubules and avoid those that project to the axon. Here we show that in rat cortical neurons, localization of several distinct transmembrane proteins to dendrites is dependent on specific myosin motors and an intact actin network. Moreover, fusion with a myosin-binding domain from Melanophilin targeted Channelrhodopsin-2 specifically to the somatodendritic compartment of neurons in mice in vivo. Together, our results suggest that dendritic transmembrane proteins direct the vesicles in which they are transported to avoid the axonal compartment through interaction with myosin motors.

}, keywords = {Adaptor Proteins, Animals, Cell Compartmentation, Cell Polarity, Cerebral Cortex, Cytoskeleton, Dendrites, Membrane Proteins, Mice, Microfilaments, Microtubules, Molecular Motor Proteins, Myosins, Protein Transport, Rats, Recombinant Fusion Proteins, Rhodopsin, Signal Transducing, Transport Vesicles}, issn = {1546-1726}, doi = {10.1038/nn.2318}, author = {Lewis, Tommy L and Mao, Tianyi and Svoboda, Karel and Arnold, Don B} } @article {46422, title = {Negative regulation of active zone assembly by a newly identified SR protein kinase.}, journal = {PLoS Biology}, volume = {7}, year = {2009}, month = {2009 Sep}, pages = {e1000193}, abstract = {

Presynaptic, electron-dense, cytoplasmic protrusions such as the T-bar (Drosophila) or ribbon (vertebrates) are believed to facilitate vesicle movement to the active zone (AZ) of synapses throughout the nervous system. The molecular composition of these structures including the T-bar and ribbon are largely unknown, as are the mechanisms that specify their synapse-specific assembly and distribution. In a large-scale, forward genetic screen, we have identified a mutation termed air traffic controller (atc) that causes T-bar-like protein aggregates to form abnormally in motoneuron axons. This mutation disrupts a gene that encodes for a serine-arginine protein kinase (SRPK79D). This mutant phenotype is specific to SRPK79D and is not secondary to impaired kinesin-dependent axonal transport. The srpk79D gene is neuronally expressed, and transgenic rescue experiments are consistent with SRPK79D kinase activity being necessary in neurons. The SRPK79D protein colocalizes with the T-bar-associated protein Bruchpilot (Brp) in both the axon and synapse. We propose that SRPK79D is a novel T-bar-associated protein kinase that represses T-bar assembly in peripheral axons, and that SRPK79D-dependent repression must be relieved to facilitate site-specific AZ assembly. Consistent with this model, overexpression of SRPK79D disrupts AZ-specific Brp organization and significantly impairs presynaptic neurotransmitter release. These data identify a novel AZ-associated protein kinase and reveal a new mechanism of negative regulation involved in AZ assembly. This mechanism could contribute to the speed and specificity with which AZs are assembled throughout the nervous system.

}, keywords = {Animals, Drosophila melanogaster, Drosophila Proteins, Immunohistochemistry, Microscopy, Electron, Transmission, Motor Neurons, Presynaptic Terminals, Protein-Serine-Threonine Kinases, Synaptic Transmission}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1000193}, author = {Johnson, Ervin L and Fetter, Richard D and Davis, Graeme W} } @article {5693, title = {Neuronal fiber tracts connecting the brain and ventral nerve cord of the early Drosophila larva.}, journal = {The Journal of Comparative Neurology}, volume = {515}, year = {2009}, month = {2009 Aug 1}, pages = {427-40}, abstract = {

By using a combination of dye injections, clonal labeling, and molecular markers, we have reconstructed the axonal connections between brain and ventral nerve cord of the first-instar Drosophila larva. Out of the approximately 1,400 neurons that form the early larval brain hemisphere, less than 50 cells have axons descending into the ventral nerve cord. Descending neurons fall into four topologically defined clusters located in the anteromedial, anterolateral, dorsal, and basoposterior brain, respectively. The anterolateral cluster represents a lineage derived from a single neuroblast. Terminations of descending neurons are almost exclusively found in the anterior part of the ventral nerve cord, represented by the gnathal and thoracic neuromeres. This region also contains small numbers of neurons with axons ascending into the brain. Terminals of the ascending axons are found in the same basal brain regions that also contain descending neurons. We have mapped ascending and descending axons to the previously described scaffold of longitudinal fiber tracts that interconnect different neuromeres of the ventral nerve cord and the brain. This work provides a structural framework for functional and genetic studies addressing the control of Drosophila larval behavior by brain circuits.

}, keywords = {Animals, Brain, Cell Count, Drosophila, Drosophila Proteins, Ganglia, Genetically Modified, Green Fluorescent Proteins, Imaging, Invertebrate, Larva, Models, Neural Pathways, Neurological, Neurons, Spinal Cord, Three-Dimensional}, issn = {1096-9861}, doi = {10.1002/cne.22086}, author = {Cardona, Albert and Larsen, Camilla and Hartenstein, Volker.} } @article {2687, title = {Neurotoxic effects induced by the Drosophila amyloid-beta peptide suggest a conserved toxic function.}, journal = {Neurobiology of Disease}, volume = {33}, year = {2009}, month = {2009 Feb}, pages = {274-81}, abstract = {

The accumulation of amyloid-beta (Abeta) into plaques is a hallmark feature of Alzheimer{\textquoteright}s disease (AD). While amyloid precursor protein (APP)-related proteins are found in most organisms, only Abeta fragments from human APP have been shown to induce amyloid deposits and progressive neurodegeneration. Therefore, it was suggested that neurotoxic effects are a specific property of human Abeta. Here we show that Abeta fragments derived from the Drosophila orthologue APPL aggregate into intracellular fibrils, amyloid deposits, and cause age-dependent behavioral deficits and neurodegeneration. We also show that APPL can be cleaved by a novel fly beta-secretase-like enzyme. This suggests that Abeta-induced neurotoxicity is a conserved function of APP proteins whereby the lack of conservation in the primary sequence indicates that secondary structural aspects determine their pathogenesis. In addition, we found that the behavioral phenotypes precede extracellular amyloid deposit formation, supporting results that intracellular Abeta plays a key role in AD.

}, keywords = {Aging, Amino Acid Sequence, Amyloid, Amyloid beta-Protein Precursor, Amyloid Precursor Protein Secretases, Animal, Animals, Apoptosis, Behavior, Blotting, Brain, Cell Surface, Drosophila melanogaster, Drosophila Proteins, Electron, Gene Expression, Immunohistochemistry, Light, Membrane Proteins, Microscopy, Molecular Sequence Data, Nerve Degeneration, Nerve Tissue Proteins, Neurons, Peptide Fragments, Protease Nexins, Receptors, Western}, issn = {1095-953X}, doi = {10.1016/j.nbd.2008.10.014}, author = {Carmine-Simmen, Katia and Proctor, Thomas and Tsch{\"a}pe, Jakob and Poeck, Burkhard and Triphan, Tilman and Strauss, Roland and Kretzschmar, Doris} } @article {4265, title = {A new generation of homology search tools based on probabilistic inference.}, journal = {Genome Informatics. International Conference on Genome Informatics}, volume = {23}, year = {2009}, month = {2009 Oct}, pages = {205-11}, abstract = {

Many theoretical advances have been made in applying probabilistic inference methods to improve the power of sequence homology searches, yet the BLAST suite of programs is still the workhorse for most of the field. The main reason for this is practical: BLAST{\textquoteright}s programs are about 100-fold faster than the fastest competing implementations of probabilistic inference methods. I describe recent work on the HMMER software suite for protein sequence analysis, which implements probabilistic inference using profile hidden Markov models. Our aim in HMMER3 is to achieve BLAST{\textquoteright}s speed while further improving the power of probabilistic inference based methods. HMMER3 implements a new probabilistic model of local sequence alignment and a new heuristic acceleration algorithm. Combined with efficient vector-parallel implementations on modern processors, these improvements synergize. HMMER3 uses more powerful log-odds likelihood scores (scores summed over alignment uncertainty, rather than scoring a single optimal alignment); it calculates accurate expectation values (E-values) for those scores without simulation using a generalization of Karlin/Altschul theory; it computes posterior distributions over the ensemble of possible alignments and returns posterior probabilities (confidences) in each aligned residue; and it does all this at an overall speed comparable to BLAST. The HMMER project aims to usher in a new generation of more powerful homology search tools based on probabilistic inference methods.

}, keywords = {Markov Chains, Probability, Sequence Alignment}, issn = {0919-9454}, author = {Eddy, Sean R.} } @article {4272, title = {New genetic tools for cell lineage analysis in Drosophila.}, journal = {Nature Methods}, volume = {6}, year = {2009}, month = {2009 Aug}, pages = {566-8}, abstract = {

Real-time lineage tracing in flies gets a boost with three techniques to specifically label a progenitor{\textquoteright}s daughter cells.

}, keywords = {Animals, Cell Lineage, Drosophila melanogaster, Genetic Techniques, Recombinant Proteins, Stem Cells, Transgenes}, issn = {1548-7105}, doi = {10.1038/nmeth0809-566}, author = {Lee, Tzumin} } @article {4430, title = {Nonlinear integration of visual and haltere inputs in fly neck motor neurons.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {29}, year = {2009}, month = {2009 Oct 21}, pages = {13097-105}, abstract = {

Animals use information from multiple sensory organs to generate appropriate behavior. Exactly how these different sensory inputs are fused at the motor system is not well understood. Here we study how fly neck motor neurons integrate information from two well characterized sensory systems: visual information from the compound eye and gyroscopic information from the mechanosensory halteres. Extracellular recordings reveal that a subpopulation of neck motor neurons display "gating-like" behavior: they do not fire action potentials in response to visual stimuli alone but will do so if the halteres are coactivated. Intracellular recordings show that these motor neurons receive small, sustained subthreshold visual inputs in addition to larger inputs that are phase locked to haltere movements. Our results suggest that the nonlinear gating-like effect results from summation of these two inputs with the action potential threshold providing the nonlinearity. As a result of this summation, the sustained visual depolarization is transformed into a temporally structured train of action potentials synchronized to the haltere beating movements. This simple mechanism efficiently fuses two different sensory signals and may also explain the context-dependent effects of visual inputs on fly behavior.

}, keywords = {Action Potentials, Age Factors, Animals, Diptera, Female, Functional Laterality, Motor Neurons, Neck, Nonlinear Dynamics, Patch-Clamp Techniques, Photic Stimulation, Sense Organs, Sensory Gating, Touch, Visual Pathways}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2915-09.2009}, author = {Huston, Stephen J and Krapp, Holger G} } @article {2849, title = {A novel mechanism of antagonism between ATP-dependent chromatin remodeling complexes regulates RNR3 expression.}, journal = {Molecular and Cellular Biology}, volume = {29}, year = {2009}, month = {2009 Jun}, pages = {3255-65}, abstract = {

Gene expression depends upon the antagonistic actions of chromatin remodeling complexes. While this has been studied extensively for the enzymes that covalently modify the tails of histones, the mechanism of how ATP-dependent remodeling complexes antagonize each other to maintain the proper level of gene activity is not known. The gene encoding a large subunit of ribonucleotide reductase, RNR3, is regulated by ISW2 and SWI/SNF, complexes that repress and activate transcription, respectively. Here, we studied the functional interactions of these two complexes at RNR3. Deletion of ISW2 causes constitutive recruitment of SWI/SNF, and conditional reexpression of ISW2 causes the repositioning of nucleosomes and reduced SWI/SNF occupancy at RNR3. Thus, ISW2 is required for restriction of access of SWI/SNF to the RNR3 promoter under the uninduced condition. Interestingly, the binding of sequence-specific DNA binding factors and the general transcription machinery are unaffected by the status of ISW2, suggesting that disruption of nucleosome positioning does not cause a nonspecific increase in cross-linking of all factors to RNR3. We provide evidence that ISW2 does not act on SWI/SNF directly but excludes its occupancy by positioning nucleosomes over the promoter. Genetic disruption of nucleosome positioning by other means led to a similar phenotype, linking repressed chromatin structure to SWI/SNF exclusion. Thus, incorporation of promoters into a repressive chromatin structure is essential for prevention of the opportunistic actions of nucleosome-disrupting activities in vivo, providing a novel mechanism for maintaining tight control of gene expression.

}, keywords = {Adenosine Triphosphatases, Adenosine Triphosphate, Base Sequence, Chromatin, Chromatin Assembly and Disassembly, DNA, Fungal, Gene Expression, Genes, Genetic, Multiprotein Complexes, Mutation, Nucleosomes, Promoter Regions, Ribonucleoside Diphosphate Reductase, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription Factors}, issn = {1098-5549}, doi = {10.1128/MCB.01741-08}, author = {Tomar, Raghuvir S and Psathas, James N and Zhang, Hesheng and Zhang, Zhengjian and Reese, Joseph C} } @article {2501, title = {The nuclear receptor E75A has a novel pair-rule-like function in patterning the milkweed bug, Oncopeltus fasciatus.}, journal = {Developmental Biology}, volume = {334}, year = {2009}, month = {2009 Oct 1}, pages = {300-10}, abstract = {

Genetic studies of the fruit fly Drosophila have revealed a hierarchy of segmentation genes (maternal, gap, pair-rule and HOX) that subdivide the syncytial blastoderm into sequentially finer-scale coordinates. Within this hierarchy, the pair-rule genes translate gradients of information into periodic stripes of expression. How pair-rule genes function during the progressive mode of segmentation seen in short and intermediate-germ insects is an ongoing question. Here we report that the nuclear receptor Of{\textquoteright}E75A is expressed with double segment periodicity in the head and thorax. In the abdomen, Of{\textquoteright}E75A is expressed in a unique pattern during posterior elongation, and briefly resembles a sequence that is typical of pair-rule genes. Depletion of Of{\textquoteright}E75A mRNA caused loss of a subset of odd-numbered parasegments, as well as parasegment 6. Because these parasegments straddle segment boundaries, we observe fusions between adjacent segments. Finally, expression of Of{\textquoteright}E75A in the blastoderm requires even-skipped, which is a gap gene in Oncopeltus. These data show that the function of Of{\textquoteright}E75A during embryogenesis shares many properties with canonical pair-rule genes in other insects. They further suggest that parasegment specification may occur through irregular and episodic pair-rule-like activity.

}, keywords = {Animals, Blastoderm, Body Patterning, Cytoplasmic and Nuclear, Embryo, Hemiptera, Insect Proteins, Nonmammalian, Receptors, RNA Interference}, issn = {1095-564X}, doi = {10.1016/j.ydbio.2009.06.038}, author = {Erezyilmaz, Deniz F and Kelstrup, Hans C and Riddiford, Lynn M} } @article {4274, title = {Nuclear receptor unfulfilled regulates axonal guidance and cell identity of Drosophila mushroom body neurons.}, journal = {PLoS One}, volume = {4}, year = {2009}, month = {2009 Dec 22}, pages = {e8392}, abstract = {

Nuclear receptors (NRs) comprise a family of ligand-regulated transcription factors that control diverse critical biological processes including various aspects of brain development. Eighteen NR genes exist in the Drosophila genome. To explore their roles in brain development, we knocked down individual NRs through the development of the mushroom bodies (MBs) by targeted RNAi. Besides recapitulating the known MB phenotypes for three NRs, we found that unfulfilled (unf), an ortholog of human photoreceptor specific nuclear receptor (PNR), regulates axonal morphogenesis and neuronal subtype identity. The adult MBs develop through remodeling of gamma neurons plus de-novo elaboration of both alpha{\textquoteright}/beta{\textquoteright} and alpha/beta neurons. Notably, unf is largely dispensable for the initial elaboration of gamma neurons, but plays an essential role in their re-extension of axons after pruning during early metamorphosis. The subsequently derived MB neuron types also require unf for extension of axons beyond the terminus of the pruned bundle. Tracing single axons revealed misrouting rather than simple truncation. Further, silencing unf in single-cell clones elicited misguidance of axons in otherwise unperturbed MBs. Such axon guidance defects may occur as MB neurons partially lose their subtype identity, as evidenced by suppression of various MB subtype markers in unf knockdown MBs. In sum, unf governs axonal morphogenesis of multiple MB neuron types, possibly through regulating neuronal subtype identity.

}, keywords = {Aging, Animals, Axons, Biological Markers, Cytoplasmic and Nuclear, Drosophila melanogaster, Drosophila Proteins, Gene Knockdown Techniques, Gene Silencing, MicroRNAs, Morphogenesis, Mushroom Bodies, Phenotype, Receptors}, issn = {1932-6203}, doi = {10.1371/journal.pone.0008392}, author = {Lin, Suewei and Huang, Yaling and Lee, Tzumin} } @article {3925, title = {Odor coding by modules of coherent mitral/tufted cells in the vertebrate olfactory bulb.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, month = {2009 Feb 17}, pages = {2401-6}, abstract = {

Odor representation in the olfactory bulb (OB) undergoes a transformation from a combinatorial glomerular map to a distributed mitral/tufted (M/T) cell code. To understand this transformation, we analyzed the odor representation in large populations of individual M/T cells in the Xenopus OB. The spontaneous [Ca(2+)] activities of M/T cells appeared to be irregular, but there were groups of spatially distributed neurons showing synchronized [Ca(2+)] activities. These neurons were always connected to the same glomerulus. Odorants elicited complex spatiotemporal response patterns in M/T cells where nearby neurons generally showed little correlation. But the responses of neurons connected to the same glomerulus were virtually identical, irrespective of whether the responses were excitatory or inhibitory, and independent of the distance between them. Synchronous neurons received correlated EPSCs and were coupled by electrical conductances that could account for the correlated responses. Thus, at the output stage of the OB, odors are represented by modules of distributed and synchronous M/T cells associated with the same glomeruli. This allows for parallel input to higher brain centers.

}, keywords = {Animals, Biological, Brain, Calcium, Electrophysiology, Fluorescent Dyes, Models, Neurons, Odors, Olfactory Bulb, Olfactory Pathways, Patch-Clamp Techniques, Smell, Time Factors, Vertebrates, Xenopus laevis}, issn = {1091-6490}, doi = {10.1073/pnas.0810151106}, author = {Chen, Tsai-Wen and Lin, Bei-Jung and Schild, Detlev} } @article {47226, title = {Olfactory information processing in Drosophila.}, journal = {Current Biology : CB}, volume = {19}, year = {2009}, month = {2009 Aug 25}, pages = {R700-13}, abstract = {

In both insect and vertebrate olfactory systems only two synapses separate the sensory periphery from brain areas required for memory formation and the organisation of behaviour. In the\ Drosophila\ olfactory system, which is anatomically very similar to its vertebrate counterpart, there has been substantial recent progress in understanding the flow of information from experiments using\ molecular genetic, electrophysiological and optical imaging techniques. In this review, we shall focus on how olfactory information is processed and transformed in order to extract behaviourally relevant information. We follow the progress from olfactory receptor neurons, through the first processing area, the antennal lobe, to higher olfactory centres. We address both the underlying anatomy and mechanisms that govern the transformation of neural activity. We emphasise our emerging understanding of how different elementary computations, including signal averaging, gain control, decorrelation and integration, may be mapped onto different circuit elements.

}, doi = {10.1016/j.cub.2009.06.026}, author = {Masse, Nicolas Y and Turner, Glenn C and Jeffers, Gregory SXE} } @article {1097, title = {Onconase cytotoxicity relies on the distribution of its positive charge.}, journal = {The FEBS Journal}, volume = {276}, year = {2009}, month = {2009 Jul}, pages = {3846-57}, abstract = {

Onconase (ONC) is a member of the ribonuclease A superfamily that is toxic to cancer cells in vitro and in vivo. ONC is now in Phase IIIb clinical trials for the treatment of malignant mesothelioma. Internalization of ONC to the cytosol of cancer cells is essential for its cytotoxic activity, despite the apparent absence of a cell-surface receptor protein. Endocytosis and cytotoxicity do, however, appear to correlate with the net positive charge of ribonucleases. To dissect the contribution made by the endogenous arginine and lysine residues of ONC to its cytotoxicity, 22 variants were created in which cationic residues were replaced with alanine. Variants with the same net charge (+2 to +5) as well as equivalent catalytic activity and conformational stability were found to exhibit large (\> 10-fold) differences in toxicity for the cells of a human leukemia line. In addition, a more cationic ONC variant could be either much more or much less cytotoxic than a less cationic variant, again depending on the distribution of its cationic residues. The endocytosis of variants with widely divergent cytotoxic activity was quantified by flow cytometry using a small-molecule fluorogenic label, and was found to vary by twofold or less. This small difference in endocytosis did not account for the large difference in cytotoxicity, implicating the distribution of cationic residues as being critical for lipid-bilayer translocation subsequent to endocytosis. This finding has fundamental implications for understanding the interaction of ribonucleases and other proteins with mammalian cells.

}, keywords = {Amino Acid Sequence, Animals, Antineoplastic Agents, Cations, Cell Line, Cell Proliferation, Endocytosis, Genetic Variation, Humans, Models, Molecular, Molecular Sequence Data, Protein Structure, Rana pipiens, Ribonucleases, Sequence Alignment, Tertiary, Tumor}, issn = {1742-4658}, doi = {10.1111/j.1742-4658.2009.07098.x}, author = {Turcotte, Rebecca F and Lavis, Luke D and Raines, Ronald T} } @article {5486, title = {Oviposition preference for and positional avoidance of acetic acid provide a model for competing behavioral drives in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, month = {2009 Jul 7}, pages = {11352-7}, abstract = {

Selection of appropriate oviposition sites is essential for progeny survival and fitness in generalist insect species, such as Drosophila melanogaster, yet little is known about the mechanisms regulating how environmental conditions and innate adult preferences are evaluated and balanced to yield the final substrate choice for egg-deposition. Female D. melanogaster are attracted to food containing acetic acid (AA) as an oviposition substrate. However, our observations reveal that this egg-laying preference is a complex process, as it directly opposes an otherwise strong, default behavior of positional avoidance for the same food. We show that 2 distinct sensory modalities detect AA. Attraction to AA-containing food for the purpose of egg-laying relies on the gustatory system, while positional repulsion depends primarily on the olfactory system. Similarly, distinct central brain regions are involved in AA attraction and repulsion. Given this unique situation, in which a single environmental stimulus yields 2 opposing behavioral outputs, we propose that the interaction of egg-laying attraction and positional aversion for AA provides a powerful model for studying how organisms balance competing behavioral drives and integrate signals involved in choice-like processes.

}, keywords = {Acetic Acid, Animal, Animal Feed, Animals, Avoidance Learning, Biological, Brain, Drosophila melanogaster, Female, Hydrogen-Ion Concentration, Models, Neurons, Olfactory Pathways, Oviposition, Sexual Behavior, Taste}, issn = {1091-6490}, doi = {10.1073/pnas.0901419106}, author = {Joseph, Ryan M and Devineni, Anita V and King, Ian F G and Heberlein, Ulrike} } @article {3914, title = {Pathway interactions and synaptic plasticity in the dendritic tuft regions of CA1 pyramidal neurons.}, journal = {Neuron}, volume = {62}, year = {2009}, month = {2009 Apr 16}, pages = {102-11}, abstract = {

Input comparison is thought to occur in many neuronal circuits, including the hippocampus, where functionally important interactions between the Schaffer collateral and perforant pathways have been hypothesized. We investigated this idea using multisite, whole-cell recordings and Ca2+ imaging and found that properly timed, repetitive stimulation of both pathways results in the generation of large plateau potentials in distal dendrites of CA1 pyramidal neurons. These dendritic plateau potentials produce widespread Ca2+ influx, large after-depolarizations, burst firing output, and long-term potentiation of perforant path synapses. Plateau duration is directly related to the strength and temporal overlap of pathway activation and involves back-propagating action potentials and both NMDA receptors and voltage-gated Ca2+ channels. Thus, the occurrence of highly correlated SC and PP input to CA1 is signaled by a dramatic change in output mode and an increase in input efficacy, all induced by a large plateau potential in the distal dendrites of CA1 pyramidal neurons.

}, keywords = {Anesthetics, Animals, Biophysics, Calcium, Calcium Channel Blockers, Dendrites, Electric Stimulation, Excitatory Amino Acid Antagonists, Hippocampus, Inhibitory Postsynaptic Potentials, Local, Long-Term Potentiation, Membrane Potentials, Neural Pathways, Neuronal Plasticity, Newborn, Patch-Clamp Techniques, Pyramidal Cells, Rats, Spider Venoms, Sprague-Dawley, Synapses, Tetrodotoxin}, issn = {1097-4199}, doi = {10.1016/j.neuron.2009.03.007}, author = {Takahashi, Hiroto and Magee, Jeffrey C} } @article {6341, title = {Pentameric assembly of potassium channel tetramerization domain-containing protein 5.}, journal = {Journal of Molecular Biology}, volume = {387}, year = {2009}, month = {2009 Mar 20}, pages = {175-91}, abstract = {

We report the X-ray crystal structure of human potassium channel tetramerization domain-containing protein 5 (KCTD5), the first member of the family to be so characterized. Four findings were unexpected. First, the structure reveals assemblies of five subunits while tetramers were anticipated; pentameric stoichiometry is observed also in solution by scanning transmission electron microscopy mass analysis and analytical ultracentrifugation. Second, the same BTB (bric-a-brac, tramtrack, broad complex) domain surface mediates the assembly of five KCTD5 and four voltage-gated K(+) (Kv) channel subunits; four amino acid differences appear crucial. Third, KCTD5 complexes have well-defined N- and C-terminal modules separated by a flexible linker that swivels by approximately 30 degrees; the C-module shows a new fold and is required to bind Golgi reassembly stacking protein 55 with approximately 1 microM affinity, as judged by surface plasmon resonance and ultracentrifugation. Fourth, despite the homology reflected in its name, KCTD5 does not impact the operation of Kv4.2, Kv3.4, Kv2.1, or Kv1.2 channels.

}, keywords = {Amino Acid, Amino Acid Sequence, Biopolymers, Crystallography, Humans, Models, Molecular, Molecular Sequence Data, Potassium Channels, Protein Conformation, Sequence Homology, Static Electricity, Surface Plasmon Resonance, X-Ray}, issn = {1089-8638}, doi = {10.1016/j.jmb.2009.01.030}, author = {Dementieva, Irina S and Tereshko, Valentina and McCrossan, Zoe A and Solomaha, Elena and Araki, Daniel and Xu, Chen and Grigorieff, Nikolaus and Goldstein, Steve A N} } @article {4441, title = {The phase diagram and the pathway of phase transitions for traffic flow in a circular one-lane roadway.}, journal = {Physica A: Statistical Mechanics and its Applications}, volume = {388}, year = {2009}, month = {2009 Apr 15}, pages = {1665-72}, abstract = {

This paper demonstrates that patient driving habits lead to homogenous congested flow while impatient driving habits lead to wide-moving jam flow in the high density region based on the numerical simulation of the intelligent driver model proposed by M.Treiber [M. Treiber, A.Hennecke, D. Helbing, Phys. Rev. E 62 (2) (2000), 1805{\textendash}1824]. In a circular one lane traffic system which includes homogeneous drivers, we obtain the stable condition of homogenous flow and the phase diagram of traffic flow based on the linearization analysis. The phase diagram shows three possible pathways of phase transition along with the increase of global density: from the homogenous free flow to the homogenous congested flow directly, from the homogenous free flow to the synchronized flow then to the homogenous congested flow, or from the homogenous free flow to synchronized flow then to the wide-moving jam flow. The paper also analyzes the traffic flow including heterogenous drivers, and the results indicate that homogenous congested flow will lose its stability when the proportion of impatient drivers reaches a critical value and some new kinds of traffic flow emerge: wide-moving jam flow or a mixture of synchronized flow and wide-moving jam flow.

}, author = {Wei, Ziqiang and Hong, Yiguang and Wang, Dahui} } @article {45911, title = {Plasticity of burst firing induced by synergistic activation of metabotropic glutamate and acetylcholine receptors.}, journal = {Neuron}, volume = {61}, year = {2009}, month = {2009 Jan 29}, pages = {287-300}, abstract = {

Subiculum, the primary efferent pathway of hippocampus, participates in memory for spatial tasks, relapse to drug abuse, and temporal lobe seizures. Subicular pyramidal neurons exhibit low-threshold burst firing driven by a spike afterdepolarization. Here we report that burst firing can be regulated by stimulation of afferent projections to subiculum. Unlike synaptic plasticity, burst plasticity did not require synaptic depolarization, activation of AMPA or NMDA receptors, or action potential firing. Rather, enhancement of burst firing required synergistic activation of group I, subtype 1 metabotropic glutamate receptors (mGluRs) and muscarinic acetylcholine receptors (mAChR). When either of these receptors was blocked, a suppression of bursting was revealed, which in turn was blocked by antagonists of group I, subtype 5 mGluRs. These results indicate that the output of subiculum can be strongly and bidirectionally regulated by activation of glutamatergic inputs within the hippocampus and cholinergic afferents from the medial septum.

}, keywords = {Acetylcholine, Action Potentials, Afferent Pathways, Animals, Cholinergic Fibers, Electric Stimulation, Excitatory Amino Acid Antagonists, Glutamic Acid, Hippocampus, Male, Neuronal Plasticity, Pyramidal Cells, Rats, Rats, Wistar, Receptors, Cholinergic, Receptors, Metabotropic Glutamate, Receptors, Muscarinic, Septal Nuclei, Synaptic Transmission, Theta Rhythm}, issn = {1097-4199}, doi = {10.1016/j.neuron.2008.12.013}, author = {Moore, Shannon J and Cooper, Donald C and Spruston, Nelson} } @article {2377, title = {Positional cues in the Drosophila nerve cord: semaphorins pattern the dorso-ventral axis.}, journal = {PLoS Biology}, volume = {7}, year = {2009}, month = {2009 Jun 16}, pages = {e1000135}, abstract = {

During the development of neural circuitry, neurons of different kinds establish specific synaptic connections by selecting appropriate targets from large numbers of alternatives. The range of alternative targets is reduced by well organised patterns of growth, termination, and branching that deliver the terminals of appropriate pre- and postsynaptic partners to restricted volumes of the developing nervous system. We use the axons of embryonic Drosophila sensory neurons as a model system in which to study the way in which growing neurons are guided to terminate in specific volumes of the developing nervous system. The mediolateral positions of sensory arbors are controlled by the response of Robo receptors to a Slit gradient. Here we make a genetic analysis of factors regulating position in the dorso-ventral axis. We find that dorso-ventral layers of neuropile contain different levels and combinations of Semaphorins. We demonstrate the existence of a central to dorsal and central to ventral gradient of Sema 2a, perpendicular to the Slit gradient. We show that a combination of Plexin A (Plex A) and Plexin B (Plex B) receptors specifies the ventral projection of sensory neurons by responding to high concentrations of Semaphorin 1a (Sema 1a) and Semaphorin 2a (Sema 2a). Together our findings support the idea that axons are delivered to particular regions of the neuropile by their responses to systems of positional cues in each dimension.

}, keywords = {Animals, Axons, Cell Surface, Drosophila, Drosophila Proteins, Nerve Net, Nerve Tissue Proteins, Neurogenesis, Neuropil, Receptors, Semaphorins, Sensory Receptor Cells, Synapses}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1000135}, author = {Zlatic, Marta and Li, Feng and Strigini, Maura and Grueber, Wesley and Bate, Michael} } @article {4526, title = {Preferential ethanol consumption in Drosophila models features of addiction.}, journal = {Current Biology}, volume = {19}, year = {2009}, month = {2009 Dec 29}, pages = {2126-32}, abstract = {

Alcohol addiction is a common affliction with a strong genetic component [1]. Although mammalian studies have provided significant insight into the molecular mechanisms underlying ethanol consumption [2], other organisms such as Drosophila melanogaster are better suited for unbiased, forward genetic approaches to identify novel genes. Behavioral responses to ethanol, such as hyperactivity, sedation, and tolerance, are conserved between flies and mammals [3, 4], as are the underlying molecular pathways [5-9]. However, few studies have investigated ethanol self-administration in flies [10]. Here we characterize ethanol consumption and preference in Drosophila. Flies prefer to consume ethanol-containing food over regular food, and this preference increases over time. Flies are attracted to the smell of ethanol, which partially mediates ethanol preference, but are averse to its taste. Preference for consuming ethanol is not entirely explained by attraction to either its sensory or caloric properties. We demonstrate that flies can exhibit features of alcohol addiction. First, flies self-administer ethanol to pharmacologically relevant concentrations. Second, flies will overcome an aversive stimulus in order to consume ethanol. Third, flies rapidly return to high levels of ethanol consumption after a period of imposed abstinence. Thus, ethanol preference in Drosophila provides a new model for studying aspects of addiction.

}, keywords = {Alcohol Drinking, Alcoholism, Analysis of Variance, Animal, Animals, Disease Models, Drosophila melanogaster, Drosophila Proteins, Ethanol, Eukaryotic Initiation Factor-5, Food Preferences, Smell, Taste}, issn = {1879-0445}, doi = {10.1016/j.cub.2009.10.070}, author = {Devineni, Anita V and Heberlein, Ulrike} } @article {6359, title = {Probing the evolution of appendage specialization by Hox gene misexpression in an emerging model crustacean.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, month = {2009 Aug 18}, pages = {13897-902}, abstract = {

Changes in the expression of Hox genes have been widely linked to the evolution of animal body plans, but functional demonstrations of this relationship have been impeded by the lack of suitable model organisms. A classic case study involves the repeated evolution of specialized feeding appendages, called maxillipeds, from anterior thoracic legs, in many crustacean lineages. These leg-to-maxilliped transformations correlate with the loss of Ultrabithorax (Ubx) expression from corresponding segments, which is proposed to be the underlying genetic cause. To functionally test this hypothesis, we establish tools for conditional misexpression and use these to misexpress Ubx in the crustacean Parhyale hawaiensis. Ectopic Ubx leads to homeotic transformations of anterior appendages toward more posterior thoracic fates, including maxilliped-to-leg transformations, confirming the capacity of Ubx to control thoracic (leg) versus gnathal (feeding) segmental identities. We find that maxillipeds not only are specified in the absence of Ubx, but also can develop in the presence of low/transient Ubx expression. Our findings suggest a path for the gradual evolutionary transition from thoracic legs to maxillipeds, in which stepwise changes in Hox gene expression have brought about this striking morphological and functional transformation.

}, keywords = {Animals, Cloning, Crustacea, Down-Regulation, Electron, Extremities, Gene Expression Regulation, Genes, Genetic, Genetically Modified, Heat-Shock Proteins, Homeobox, Homeodomain Proteins, Immunohistochemistry, Microscopy, Models, Molecular, Phenotype, Scanning, Transgenes}, issn = {1091-6490}, doi = {10.1073/pnas.0902804106}, author = {Pavlopoulos, Anastasios and Kontarakis, Zacharias and Liubicich, Danielle M and Serano, Julia M and Akam, Michael and Patel, Nipam H and Averof, Michalis} } @article {6491, title = {A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale.}, journal = {PLoS Computational Biology}, volume = {5}, year = {2009}, month = {2009 Mar}, pages = {e1000334}, abstract = {

In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly sparse. Such knowledge is critical, however, for both basic and clinical research into brain function. Here we advocate for a concerted effort to fill this gap, through systematic, experimental mapping of neural circuits at a mesoscopic scale of resolution suitable for comprehensive, brainwide coverage, using injections of tracers or viral vectors. We detail the scientific and medical rationale and briefly review existing knowledge and experimental techniques. We define a set of desiderata, including brainwide coverage; validated and extensible experimental techniques suitable for standardization and automation; centralized, open-access data repository; compatibility with existing resources; and tractability with current informatics technology. We discuss a hypothetical but tractable plan for mouse, additional efforts for the macaque, and technique development for human. We estimate that the mouse connectivity project could be completed within five years with a comparatively modest budget.

}, keywords = {Animals, Brain, Databases, Factual, Humans, Macaca, Mice, Models, Nerve Net, Neuroanatomy, Neurological, Research Design}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1000334}, author = {Bohland, Jason W and Wu, Caizhi and Barbas, Helen and Bokil, Hemant and Bota, Mihail and Breiter, Hans C and Cline, Hollis T and Doyle, John C and Freed, Peter J and Greenspan, Ralph J and Haber, Suzanne N and Hawrylycz, Michael and Herrera, Daniel G and Hilgetag, Claus C and Huang, Z Josh and Jones, Allan and Jones, Edward G and Karten, Harvey J and Kleinfeld, David and K{\"o}tter, Rolf and Lester, Henry A and Lin, John M and Mensh, Brett D and Mikula, Shawn and Panksepp, Jaak and Price, Joseph L and Safdieh, Joseph and Saper, Clifford B and Schiff, Nicholas D and Schmahmann, Jeremy D and Stillman, Bruce W and Svoboda, Karel and Swanson, Larry W and Toga, Arthur W and Van Essen, David C and Watson, James D and Mitra, Partha P} } @article {5412, title = {Purification, characterization and crystallization of pyrroline-5-carboxylate reductase from the hyperthermophilic archeon Sulfolobus Solfataricus.}, journal = {Protein Expression and Purification}, volume = {64}, year = {2009}, month = {2009 Apr}, pages = {125-30}, abstract = {

The gene SSO0495 (proC), which encodes pyrroline-5-carboxylate reductase (P5CR) from the thermoacidophilic archeon Sulfolobus solfataricus P2 (Ss-P5CR), was cloned and expressed. The purified recombinant enzyme catalyzes the thioproline dehydrogenase with concomitant oxidation of NAD(P)H to NAD(P)+. This archeal enzyme has an optimal alkaline pH in this reversible reaction and is thermostable with a half-life of approximately 30 min at 80 degrees C. At pH 9.0, the reverse activation rate is nearly 3-fold higher than at pH 7.0. The homopolymer was characterized by cross-linking and size exclusion gel filtration chromatography. Ss-P5CR was crystallized by the hanging-drop vapor-diffusion method at 37 degrees C. Diffraction data were obtained to a resolution of 3.5A and were suitable for X-ray structure determination.

}, keywords = {Archaeal Proteins, Chromatography, Crystallization, Crystallography, Gel, Kinetics, NADP, Pyrroline Carboxylate Reductases, Sulfolobus solfataricus, Temperature, Thiazolidines, X-Ray}, issn = {1096-0279}, doi = {10.1016/j.pep.2008.10.018}, author = {Meng, Zhaohui and Liu, Zhe and Lou, Zhiyong and Gong, Xiaocui and Cao, Yi and Bartlam, Mark and Zhang, Keqin and Rao, Zihe} } @article {2468, title = {Rapid evolution of sex pheromone-producing enzyme expression in Drosophila.}, journal = {PLoS Biology}, volume = {7}, year = {2009}, month = {2009 Aug 4}, pages = {e1000168}, abstract = {

A wide range of organisms use sex pheromones to communicate with each other and to identify appropriate mating partners. While the evolution of chemical communication has been suggested to cause sexual isolation and speciation, the mechanisms that govern evolutionary transitions in sex pheromone production are poorly understood. Here, we decipher the molecular mechanisms underlying the rapid evolution in the expression of a gene involved in sex pheromone production in Drosophilid flies. Long-chain cuticular hydrocarbons (e.g., dienes) are produced female-specifically, notably via the activity of the desaturase DESAT-F, and are potent pheromones for male courtship behavior in Drosophila melanogaster. We show that across the genus Drosophila, the expression of this enzyme is correlated with long-chain diene production and has undergone an extraordinary number of evolutionary transitions, including six independent gene inactivations, three losses of expression without gene loss, and two transitions in sex-specificity. Furthermore, we show that evolutionary transitions from monomorphism to dimorphism (and its reversion) in desatF expression involved the gain (and the inactivation) of a binding-site for the sex-determination transcription factor, DOUBLESEX. In addition, we documented a surprising example of the gain of particular cis-regulatory motifs of the desatF locus via a set of small deletions. Together, our results suggest that frequent changes in the expression of pheromone-producing enzymes underlie evolutionary transitions in chemical communication, and reflect changing regimes of sexual selection, which may have contributed to speciation among Drosophila.

}, keywords = {Animal, Animal Communication, Animals, Binding Sites, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Evolution, Fatty Acid Desaturases, Female, Gene Expression Regulation, In Situ Hybridization, Male, Mating Preference, Molecular, Sex Attractants, Sex Characteristics, Sexual Behavior}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1000168}, author = {Shirangi, Troy R and Dufour, H{\'e}lo\"{\i}se D and Williams, Thomas M and Carroll, Sean B} } @article {5253, title = {Rapid functional maturation of nascent dendritic spines.}, journal = {Neuron}, volume = {61}, year = {2009}, month = {2009 Jan 29}, pages = {247-58}, abstract = {

Spine growth and retraction with synapse formation and elimination plays an important role in shaping brain circuits during development and in the adult brain, yet the temporal relationship between spine morphogenesis and the formation of functional synapses remains poorly defined. We imaged hippocampal pyramidal neurons to identify spines of different ages. We then used two-photon glutamate uncaging, whole-cell recording, and Ca(2+) imaging to analyze the properties of nascent spines and their older neighbors. New spines expressed glutamate-sensitive currents that were indistinguishable from mature spines of comparable volumes. Some spines exhibited negligible AMPA receptor-mediated responses, but the occurrence of these "silent" spines was uncorrelated with spine age. In contrast, NMDA receptor-mediated Ca(2+) accumulations were significantly lower in new spines. New spines reconstructed using electron microscopy made synapses. Our data support a model in which outgrowth and enlargement of nascent spines is tightly coupled to formation and maturation of glutamatergic synapses.

}, keywords = {AMPA, Animals, Calcium, Calcium Signaling, Cell Differentiation, Confocal, Dendritic Spines, Electron, Glutamic Acid, Hippocampus, Microscopy, Neuronal Plasticity, Organ Culture Techniques, Patch-Clamp Techniques, Pyramidal Cells, Rats, Receptors, Synapses, Synaptic Membranes, Synaptic Transmission, Time Factors, Transmission}, issn = {1097-4199}, doi = {10.1016/j.neuron.2008.10.054}, author = {Zito, Karen and Scheuss, Volker and Knott, Graham and Hill, Travis and Svoboda, Karel} } @proceedings {3296, title = {Rate-constrained distributed distance testing and its applications.}, year = {2009}, month = {2009}, abstract = {

We investigate a practical approach to solving one instantiation of a distributed hypothesis testing problem under severe rate constraints that shows up in a wide variety of applications such as camera calibration, biometric authentication and video hashing: given two distributed continuous-valued random sources, determine if they satisfy a certain Euclidean distance criterion. We show a way to convert the problem from continuous-valued to binary-valued using binarized random projections and obtain rate savings by applying a linear syndrome code. In finding visual correspondences, our approach uses just 49\% of the rate of scalar quantization to achieve the same level of retrieval performance. To perform video hashing, our approach requires only a hash rate of 0.0142 bpp to identify corresponding groups of pictures correctly.

}, author = {Yeo, C and Ahammad, Parvez and Zhang, H and Ramchandran, K} } @proceedings {65003, title = {Rate-constrained distributed distance testing and its applications.}, year = {2009}, month = {2009 Apr 24}, abstract = {

We investigate a practical approach to solving one instantiation of a distributed hypothesis testing problem under severe rate constraints that shows up in a wide variety of applications such as camera calibration, biometric authentication and video hashing: given two distributed continuous-valued random sources, determine if they satisfy a certain Euclidean distance criterion. We show a way to convert the problem from continuous-valued to binary-valued using binarized random projections and obtain rate savings by applying a linear syndrome code. In finding visual correspondences, our approach uses just 49\% of the rate of scalar quantization to achieve the same level of retrieval performance. To perform video hashing, our approach requires only a hash rate of 0.0142 bpp to identify corresponding groups of pictures correctly.

}, doi = {10.1109/ICASSP.2009.4959707}, author = {Chuohao Yeo and Parvez Ahammad and Hao Zhang and Kannan Ramchandran} } @article {2780, title = {Reactive astrocytes in glial scar attract olfactory ensheathing cells migration by secreted TNF-alpha in spinal cord lesion of rat.}, journal = {PLoS One}, volume = {4}, year = {2009}, month = {2009 Dec 3}, pages = {e8141}, abstract = {

After spinal cord injury (SCI), the formation of glial scar contributes to the failure of injured adult axons to regenerate past the lesion. Increasing evidence indicates that olfactory ensheathing cells (OECs) implanted into spinal cord are found to migrate into the lesion site and induce axons regeneration beyond glial scar and resumption of functions. However, little is known about the mechanisms of OECs migrating from injection site to glial scar/lesion site.

}, keywords = {Animals, Astrocytes, Cell Movement, Cicatrix, Conditioned, Culture Media, Enzyme Activation, Mitogen-Activated Protein Kinases, Olfactory Pathways, Rats, Receptors, Spinal Cord, Sprague-Dawley, Tumor Necrosis Factor, Tumor Necrosis Factor-alpha, Type I}, issn = {1932-6203}, doi = {10.1364/AO.50.001792}, author = {Su, Zhida and Yuan, Yimin and Chen, Jingjing and Cao, Li and Zhu, Yanling and Gao, Liang and Qiu, Yang and He, Cheng} } @article {1246, title = {Reconstruction of sparse circuits using multi-neuronal excitation (RESCUME).}, journal = {Neural Information Processing Systems}, volume = {22}, year = {2009}, month = {2009}, pages = {790-8}, abstract = {

One of the central problems in neuroscience is reconstructing synaptic connectivity in neural circuits. Synapses onto a neuron can be probed by sequentially stimulating potentially pre-synaptic neurons while monitoring the membrane voltage of the post-synaptic neuron. Reconstructing a large neural circuit using such a "brute force" approach is rather time-consuming and inefficient because the connectivity in neural circuits is sparse. Instead, we propose to measure a post-synaptic neuron{\textquoteright}s voltage while stimulating sequentially random subsets of multiple potentially pre-synaptic neurons. To reconstruct these synaptic connections from the recorded voltage we apply a decoding algorithm recently developed for compressive sensing. Compared to the brute force approach, our method promises significant time savings that grow with the size of the circuit. We use computer simulations to find optimal stimulation parameters and explore the feasibility of our reconstruction method under realistic experimental conditions including noise and non-linear synaptic integration. Multineuronal stimulation allows reconstructing synaptic connectivity just from the spiking activity of post-synaptic neurons, even when sub-threshold voltage is unavailable. By using calcium indicators, voltage-sensitive dyes, or multi-electrode arrays one could monitor activity of multiple postsynaptic neurons simultaneously, thus mapping their synaptic inputs in parallel, potentially reconstructing a complete neural circuit.

}, author = {Hu, Tao and Chklovskii, Dmitri B} } @article {5249, title = {Reverse engineering the mouse brain.}, journal = {Nature}, volume = {461}, year = {2009}, month = {2009 Oct 15}, pages = {923-9}, abstract = {

Behaviour is governed by activity in highly structured neural circuits. Genetically targeted sensors and switches facilitate measurement and manipulation of activity in vivo, linking activity in defined nodes of neural circuits to behaviour. Because of access to specific cell types, these molecular tools will have the largest impact in genetic model systems such as the mouse. Emerging assays of mouse behaviour are beginning to rival those of behaving monkeys in terms of stimulus and behavioural control. We predict that the confluence of new behavioural and molecular tools in the mouse will reveal the logic of complex mammalian circuits.

}, keywords = {Action Potentials, Animal, Animals, Behavior, Brain, Mice, Neural Pathways, Somatosensory Cortex}, issn = {1476-4687}, doi = {10.1038/nature08539}, author = {O{\textquoteright}Connor, Daniel H and Huber, Daniel and Svoboda, Karel} } @article {4266, title = {Rfam: updates to the RNA families database.}, journal = {Nucleic Acids Research}, volume = {37}, year = {2009}, month = {2009 Jan}, pages = {D136-40}, abstract = {

Rfam is a collection of RNA sequence families, represented by multiple sequence alignments and covariance models (CMs). The primary aim of Rfam is to annotate new members of known RNA families on nucleotide sequences, particularly complete genomes, using sensitive BLAST filters in combination with CMs. A minority of families with a very broad taxonomic range (e.g. tRNA and rRNA) provide the majority of the sequence annotations, whilst the majority of Rfam families (e.g. snoRNAs and miRNAs) have a limited taxonomic range and provide a limited number of annotations. Recent improvements to the website, methodologies and data used by Rfam are discussed. Rfam is freely available on the Web at http://rfam.sanger.ac.uk/and http://rfam.janelia.org/.

}, keywords = {Computer Graphics, Databases, Internet, Nucleic Acid, RNA, Sequence Alignment, Sequence Analysis}, issn = {1362-4962}, doi = {10.1093/nar/gkn766}, author = {Gardner, Paul P and Daub, Jennifer and Tate, John G and Nawrocki, Eric P and Kolbe, Diana L and Lindgreen, Stinus and Wilkinson, Adam C and Finn, Robert D and Griffiths-Jones, Sam and Eddy, Sean R. and Bateman, Alex} } @article {2500, title = {The role of the pupal determinant broad during embryonic development of a direct-developing insect.}, journal = {Development Genes \& Evolution}, volume = {219}, year = {2009}, month = {2009 Dec 30}, pages = {535-44}, abstract = {

Metamorphosis is one of the most common, yet dramatic of life history strategies. In insects, complete metamorphosis with morphologically distinct larval stages arose from hemimetabolous ancestors that were more direct developing. Over the past century, several ideas have emerged that suggest the holometabolous pupa is developmentally homologous to the embryonic stages of the hemimetabolous ancestor. Other theories consider the pupal stage to be a modification of a hemimetabolous nymph. To address this question, we have isolated an ortholog of the pupal determinant, broad (br), from the hemimetabolous milkweed bug and examined its role during embryonic development. We show that Oncopeltus fasciatus br (Of{\textquoteright}br) is expressed in two phases. The first occurs during germ band invagination and segmentation when Of{\textquoteright}br is expressed ubiquitously in the embryonic tissues. The second phase of Of{\textquoteright}br expression appears during the pronymphal phase of embryogenesis and persists through nymphal differentiation to decline just before hatching. Knock-down of Of{\textquoteright}br transcripts results in defects that range from posterior truncations in the least-affected phenotypes to completely fragmented embryonic tissues in the most severe cases. Analysis of the patterning genes engrailed and hunchback reveal loss of segments and a failure in neural differentiation after Of{\textquoteright}br depletion. Finally, we show that br is constitutively expressed during embyrogenesis of the ametabolous firebrat, Thermobia domestica. This suggests that br expression is prominent during embryonic development of ametabolous and hemimetabolous insects but was lost with the emergence of the completely metamorphosing insects.

}, keywords = {Animals, Biological, Biological Evolution, Body Patterning, Cloning, Developmental, DNA Primers, Drosophila Proteins, Gene Expression Regulation, Heteroptera, In Situ Hybridization, Insect Proteins, Metamorphosis, Molecular, Reverse Transcriptase Polymerase Chain Reaction, Transcription Factors}, issn = {1432-041X}, doi = {10.1007/s00427-009-0315-7}, author = {Erezyilmaz, Deniz F and Rynerson, Melody R and Truman, James W and Riddiford, Lynn M} } @article {2076, title = {Self-organization of the Escherichia coli chemotaxis network imaged with super-resolution light microscopy. (With commentary)}, journal = {PLoS Biology}, volume = {7}, year = {2009}, month = {2009 Jun 16}, pages = {e1000137}, abstract = {

The Escherichia coli chemotaxis network is a model system for biological signal processing. In E. coli, transmembrane receptors responsible for signal transduction assemble into large clusters containing several thousand proteins. These sensory clusters have been observed at cell poles and future division sites. Despite extensive study, it remains unclear how chemotaxis clusters form, what controls cluster size and density, and how the cellular location of clusters is robustly maintained in growing and dividing cells. Here, we use photoactivated localization microscopy (PALM) to map the cellular locations of three proteins central to bacterial chemotaxis (the Tar receptor, CheY, and CheW) with a precision of 15 nm. We find that cluster sizes are approximately exponentially distributed, with no characteristic cluster size. One-third of Tar receptors are part of smaller lateral clusters and not of the large polar clusters. Analysis of the relative cellular locations of 1.1 million individual proteins (from 326 cells) suggests that clusters form via stochastic self-assembly. The super-resolution PALM maps of E. coli receptors support the notion that stochastic self-assembly can create and maintain approximately periodic structures in biological membranes, without direct cytoskeletal involvement or active transport.

Commentary: Our goal as tool developers is to invent methods capable of uncovering new biological insights unobtainable by pre-existing technologies. A terrific example is given by this paper, where grad students Derek Greenfield and Ann McEvoy in Jan Liphardt{\textquoteright}s group at Berkeley used our PALM to image the size and position distributions of chemotaxis proteins in E. Coli with unprecedented precision and sensitivity. Their analysis revealed that the cluster sizes follow a stretched exponential distribution, and the density of clusters is highest furthest away from the largest (e.g., polar) clusters. Both observations support a model for passive self-assembly rather than active cytoskeletal assembly of the chemotaxis network.

}, keywords = {Bacterial Proteins, Biological, Cell Surface, Chemoreceptor Cells, Chemotaxis, Escherichia coli, Escherichia coli Proteins, Membrane Proteins, Microscopy, Models, Receptors, Recombinant Fusion Proteins, Signal Transduction, Stochastic Processes}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1000137}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19547746}, author = {Greenfield, Derek and McEvoy, Ann L and Shroff, Hari and Crooks, Gavin E and Wingreen, Ned S and Betzig, Eric and Liphardt, Jan} } @article {46622, title = {Sensory neurons in the Drosophila genital tract regulate female reproductive behavior.}, journal = {Neuron}, volume = {61}, year = {2009}, month = {2009 Feb 26}, pages = {511-8}, abstract = {

Females of many animal species behave very differently before and after mating. In Drosophila melanogaster, changes in female behavior upon mating are triggered by the sex peptide (SP), a small peptide present in the male{\textquoteright}s seminal fluid. SP activates a specific receptor, the sex peptide receptor (SPR), which is broadly expressed in the female reproductive tract and nervous system. Here, we pinpoint the action of SPR to a small subset of internal sensory neurons that innervate the female uterus and oviduct. These neurons express both fruitless (fru), a marker for neurons likely to have sex-specific functions, and pickpocket (ppk), a marker for proprioceptive neurons. We show that SPR expression in these fru+ ppk+ neurons is both necessary and sufficient for behavioral changes induced by mating. These neurons project to regions of the central nervous system that have been implicated in the control of reproductive behaviors in Drosophila and other insects.

}, keywords = {Animals, Drosophila, Drosophila Proteins, Female, Ganglia, Invertebrate, Gene Silencing, Genitalia, Female, Immunohistochemistry, Peptides, Sensory Receptor Cells, Sexual Behavior, Animal, Signal Transduction, Uterus}, issn = {1097-4199}, doi = {10.1016/j.neuron.2009.01.009}, author = {H{\"a}semeyer, Martin and Yapici, Nilay and Heberlein, Ulrike and Dickson, Barry J} } @article {2388, title = {Shifting players and paradigms in cell-specific transcription.}, journal = {Molecular Cell}, volume = {36}, year = {2009}, month = {2009 Dec 25}, pages = {924-31}, abstract = {

Historically, developmental-stage- and tissue-specific patterns of gene expression were assumed to be determined primarily by DNA regulatory sequences and their associated activators, while the general transcription machinery including core promoter recognition complexes, coactivators, and chromatin modifiers was held to be invariant. New evidence suggests that significant changes in these general transcription factors including TFIID, BAF, and Mediator may facilitate global changes in cell-type-specific transcription.

}, keywords = {Animals, Developmental, Gene Expression Regulation, Genetic, Mediator Complex, Models, Molecular, Promoter Regions, Protein Isoforms, TATA Box Binding Protein-Like Proteins, Tissue Distribution, Transcription, Transcription Factor TFIID}, issn = {1097-4164}, doi = {10.1073/pnas.1100640108}, author = {D{\textquoteright}Alessio, Joseph A and Wright, Kevin J and Tjian, Robert} } @article {4410, title = {Similar patterns of linkage disequilibrium and nucleotide diversity in native and introduced populations of the pea aphid, Acyrthosiphon pisum.}, journal = {BMC Genetics}, volume = {10}, year = {2009}, month = {2009 May 26}, pages = {22}, abstract = {

The pea aphid, Acyrthosiphon pisum, is an emerging genomic model system for studies of polyphenisms, bacterial symbioses, host-plant specialization, and the vectoring of plant viruses. Here we provide estimates of nucleotide diversity and linkage disequilibrium (LD) in native (European) and introduced (United States) populations of the pea aphid. Because introductions can cause population bottlenecks, we hypothesized that U.S. populations harbor lower levels of nucleotide diversity and higher levels of LD than native populations.

}, keywords = {Animals, Aphids, Europe, Genetic Variation, Genetics, INDEL Mutation, Linkage Disequilibrium, North America, Nucleotides, Population}, issn = {1471-2156}, doi = {10.1186/1471-2156-10-22}, author = {Brisson, Jennifer A and Nuzhdin, Sergey V and Stern, David L} } @article {4634, title = {Simplified approach to diffraction tomography in optical microscopy.}, journal = {Optics Express}, volume = {17}, year = {2009}, month = {2009 Jul 20}, pages = {12407-17}, abstract = {

We present a novel microscopy technique to measure the scattered wavefront emitted from an optically transparent microscopic object. The complex amplitude is decoded via phase stepping in a common-path interferometer, enabling high mechanical stability. We demonstrate theoretically and practically that the incoherent summation of multiple illumination directions into a single image increases the resolving power and facilitates image reconstruction in diffraction tomography. We propose a slice-by-slice object-scatter extraction algorithm entirely based in real space in combination with ordinary z-stepping. Thereby the computational complexity affiliated with tomographic methods is significantly reduced. Using the first order Born approximation for weakly scattering objects it is possible to obtain estimates of the scattering density from the exitwaves.

}, keywords = {Algorithms, Cheek, Computer-Assisted, Equipment Design, Fourier Analysis, Green Fluorescent Proteins, Humans, Image Processing, Imaging, Interferometry, Microscopy, Models, Optics and Photonics, Radiation, Scattering, Statistical, Three-Dimensional, Tomography}, issn = {1094-4087}, author = {Fiolka, Reto and Wicker, Kai and Heintzmann, Rainer and Stemmer, Andreas} } @article {6783, title = {A state-mutating genetic algorithm to design ion-channel models.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, month = {2009 Sep 29}, pages = {16829-34}, abstract = {

Realistic computational models of single neurons require component ion channels that reproduce experimental findings. Here, a topology-mutating genetic algorithm that searches for the best state diagram and transition-rate parameters to model macroscopic ion-channel behavior is described. Important features of the algorithm include a topology-altering strategy, automatic satisfaction of equilibrium constraints (microscopic reversibility), and multiple-protocol fitting using sequential goal programming rather than explicit weighting. Application of this genetic algorithm to design a sodium-channel model exhibiting both fast and prolonged inactivation yields a six-state model that produces realistic activity-dependent attenuation of action-potential backpropagation in current-clamp simulations of a CA1 pyramidal neuron.

}, keywords = {Algorithms, Cell Membrane, Ion Channels, Models, Mutation, Neurons, Sodium Channels, Theoretical}, issn = {1091-6490}, doi = {10.1073/pnas.0903766106}, author = {Menon, Vilas and Spruston, Nelson and Kath, William L} } @article {6500, title = {Stochastic resonance-enhanced laser-based particle detector.}, journal = {Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society.}, volume = {2009}, year = {2009}, month = {2009}, pages = {785-7}, abstract = {

This paper presents a Laser-based particle detector whose response was enhanced by modulating the Laser diode with a white-noise generator. A Laser sheet was generated to cast a shadow of the object on a 200 dots per inch, 512 x 1 pixels linear sensor array. The Laser diode was modulated with a white-noise generator to achieve stochastic resonance. The white-noise generator essentially amplified the wide-bandwidth (several hundred MHz) noise produced by a reverse-biased zener diode operating in junction-breakdown mode. The gain in the amplifier in the white-noise generator was set such that the Receiver Operating Characteristics plot provided the best discriminability. A monofiber 40 AWG (approximately 80 microm) wire was detected with approximately 88\% True Positive rate and approximately 19\% False Positive rate in presence of white-noise modulation and with approximately 71\% True Positive rate and approximately 15\% False Positive rate in absence of white-noise modulation.

}, keywords = {Actigraphy, Animals, Computer-Assisted, Drosophila melanogaster, Equipment Design, Equipment Failure Analysis, Escape Reaction, Lasers, Photometry, Signal Processing, Stochastic Processes}, issn = {1557-170X}, doi = {10.1109/IEMBS.2009.5332748}, author = {Dutta, A and Werner, C} } @article {2312, title = {Stochastically gating ion channels enable patterned spike firing through activity-dependent modulation of spike probability.}, journal = {PLoS Computational Biology}, volume = {5}, year = {2009}, month = {2009 Feb}, pages = {e1000290}, abstract = {

The transformation of synaptic input into patterns of spike output is a fundamental operation that is determined by the particular complement of ion channels that a neuron expresses. Although it is well established that individual ion channel proteins make stochastic transitions between conducting and non-conducting states, most models of synaptic integration are deterministic, and relatively little is known about the functional consequences of interactions between stochastically gating ion channels. Here, we show that a model of stellate neurons from layer II of the medial entorhinal cortex implemented with either stochastic or deterministically gating ion channels can reproduce the resting membrane properties of stellate neurons, but only the stochastic version of the model can fully account for perithreshold membrane potential fluctuations and clustered patterns of spike output that are recorded from stellate neurons during depolarized states. We demonstrate that the stochastic model implements an example of a general mechanism for patterning of neuronal output through activity-dependent changes in the probability of spike firing. Unlike deterministic mechanisms that generate spike patterns through slow changes in the state of model parameters, this general stochastic mechanism does not require retention of information beyond the duration of a single spike and its associated afterhyperpolarization. Instead, clustered patterns of spikes emerge in the stochastic model of stellate neurons as a result of a transient increase in firing probability driven by activation of HCN channels during recovery from the spike afterhyperpolarization. Using this model, we infer conditions in which stochastic ion channel gating may influence firing patterns in vivo and predict consequences of modifications of HCN channel function for in vivo firing patterns.

}, keywords = {Action Potentials, Animals, Cyclic Nucleotide-Gated Cation Channels, Entorhinal Cortex, Humans, Ion Channel Gating, Ion Transport, Models, Neural Conduction, Neurological, Potassium Channels, Stochastic Processes, Synaptic Transmission}, issn = {1553-7358}, doi = {10.3389/fnana.2010.00147}, author = {Dudman, Joshua T and Nolan, Matthew F} } @article {46039, title = {Structural and functional alterations to rat medial prefrontal cortex following chronic restraint stress and recovery.}, journal = {Neuroscience}, volume = {164}, year = {2009}, month = {2009 Dec 1}, pages = {798-808}, abstract = {

Chronic stress has been shown in animal models to result in altered dendritic morphology of pyramidal neurons of the medial prefrontal cortex (mPFC). It has been hypothesized that the stress-induced dendritic retractions and spine loss lead to disrupted connectivity that results in stress-induced functional impairment of mPFC. While these alterations were initially viewed as a neurodegenerative event, it has recently been established that stress induced dendritic alterations are reversible if animals are given time to recover from chronic stress. However, whether spine growth accompanies dendritic extension remains to be demonstrated. It is also not known if recovery-phase dendritic extension allows for re-establishment of functional capacity. The goal of this study, therefore, was to characterize the structural and functional effects of chronic stress and recovery on the infralimbic (IL) region of the rat mPFC. We compared neuronal morphology of IL layer V pyramidal neurons from male Sprague-Dawley rats subjected to 21 days of chronic restraint stress (CRS) to those that experienced CRS followed by a 21 day recovery period. Layer V pyramidal cell functional capacity was assessed by intra-IL long-term potentiation (LTP) both in the absence and presence of SKF38393, a dopamine receptor partial agonist and a known PFC LTP modulator. We found that stress-induced IL apical dendritic retraction and spine loss co-occur with receptor-mediated impairments to catecholaminergic facilitation of synaptic plasticity. We also found that while post-stress recovery did not reverse distal dendritic retraction, it did result in over extension of proximal dendritic arbors and spine growth as well as a full reversal of CRS-induced impairments to catecholaminergic-mediated synaptic plasticity. Our results support the hypothesis that disease-related PFC dysfunction is a consequence of network disruption secondary to altered structural and functional plasticity and that circuitry reestablishment may underlie elements of recovery. Accordingly, we believe that pharmacological treatments targeted at preventing dendritic retraction and spine loss or encouraging circuitry re-establishment and stabilization may be advantageous in the prevention and treatment of mood and anxiety disorders.

}, keywords = {2,3,4,5-Tetrahydro-7,8-dihydroxy-1-phenyl-1H-3-benzazepine, Animals, Chronic Disease, Dendrites, Dendritic Spines, Dopamine, Dopamine Agonists, Long-Term Potentiation, Male, Prefrontal Cortex, Pyramidal Cells, Random Allocation, Rats, Rats, Sprague-Dawley, Receptors, Dopamine D1, Restraint, Physical, Stress, Psychological, Time Factors, Weight Gain}, issn = {1873-7544}, doi = {10.1016/j.neuroscience.2009.08.053}, author = {Goldwater, D S and Pavlides, C and Hunter, R G and Bloss, E B and Hof, P R and McEwen, B S and Morrison, J H} } @article {2389, title = {Structures of three distinct activator-TFIID complexes.}, journal = {Genes \& Development}, volume = {23}, year = {2009}, month = {2009 Jul 1}, pages = {1510-21}, abstract = {

Sequence-specific DNA-binding activators, key regulators of gene expression, stimulate transcription in part by targeting the core promoter recognition TFIID complex and aiding in its recruitment to promoter DNA. Although it has been established that activators can interact with multiple components of TFIID, it is unknown whether common or distinct surfaces within TFIID are targeted by activators and what changes if any in the structure of TFIID may occur upon binding activators. As a first step toward structurally dissecting activator/TFIID interactions, we determined the three-dimensional structures of TFIID bound to three distinct activators (i.e., the tumor suppressor p53 protein, glutamine-rich Sp1 and the oncoprotein c-Jun) and compared their structures as determined by electron microscopy and single-particle reconstruction. By a combination of EM and biochemical mapping analysis, our results uncover distinct contact regions within TFIID bound by each activator. Unlike the coactivator CRSP/Mediator complex that undergoes drastic and global structural changes upon activator binding, instead, a rather confined set of local conserved structural changes were observed when each activator binds holo-TFIID. These results suggest that activator contact may induce unique structural features of TFIID, thus providing nanoscale information on activator-dependent TFIID assembly and transcription initiation.

}, keywords = {Hela Cells, Humans, Imaging, Immunoglobulins, Models, Molecular, Protein Binding, Protein Multimerization, Protein Structure, Proto-Oncogene Proteins c-jun, Quaternary, TATA-Binding Protein Associated Factors, Three-Dimensional, Transcription Factor TFIID, Tumor Suppressor Protein p53}, issn = {1549-5477}, doi = {10.1073/pnas.1100640108}, author = {Liu, Wei-Li and Coleman, Robert A and Ma, Elizabeth and Grob, Patricia and Yang, Joyce L and Zhang, Yixi and Dailey, Gina and Nogales, Eva and Tjian, Robert} } @article {5251, title = {Subcellular dynamics of type II PKA in neurons.}, journal = {Neuron}, volume = {62}, year = {2009}, month = {2009 May 14}, pages = {363-74}, abstract = {

Protein kinase A (PKA) plays multiple roles in neurons. The localization and specificity of PKA are largely controlled by A-kinase anchoring proteins (AKAPs). However, the dynamics of PKA in neurons and the roles of specific AKAPs are poorly understood. We imaged the distribution of type II PKA in hippocampal and cortical layer 2/3 pyramidal neurons in vitro and in vivo. PKA was concentrated in dendritic shafts compared to the soma, axons, and dendritic spines. This spatial distribution was imposed by the microtubule-binding protein MAP2, indicating that MAP2 is the dominant AKAP in neurons. Following cAMP elevation, catalytic subunits dissociated from the MAP2-tethered regulatory subunits and rapidly became enriched in nearby spines. The spatial gradient of type II PKA between dendritic shafts and spines was critical for the regulation of synaptic strength and long-term potentiation. Therefore, the localization and activity-dependent translocation of type II PKA are important determinants of PKA function.

}, keywords = {A Kinase Anchor Proteins, Animals, Cerebral Cortex, Cyclic AMP-Dependent Protein Kinases, Dendritic Spines, Hippocampus, Mice, Microtubule-Associated Proteins, Pyramidal Cells, Rats, Subcellular Fractions, Tissue Distribution, Transgenic}, issn = {1097-4199}, doi = {10.1016/j.neuron.2009.03.013}, author = {Zhong, Haining and Sia, Gek-Ming and Sato, Takashi R and Gray, Noah W and Mao, Tianyi and Khuchua, Zaza and Huganir, Richard L and Svoboda, Karel} } @article {2185, title = {The subcellular organization of neocortical excitatory connections.}, journal = {Nature}, volume = {457}, year = {2009}, month = {2009 Feb 26}, pages = {1142-5}, abstract = {

Understanding cortical circuits will require mapping the connections between specific populations of neurons, as well as determining the dendritic locations where the synapses occur. The dendrites of individual cortical neurons overlap with numerous types of local and long-range excitatory axons, but axodendritic overlap is not always a good predictor of actual connection strength. Here we developed an efficient channelrhodopsin-2 (ChR2)-assisted method to map the spatial distribution of synaptic inputs, defined by presynaptic ChR2 expression, within the dendritic arborizations of recorded neurons. We expressed ChR2 in two thalamic nuclei, the whisker motor cortex and local excitatory neurons and mapped their synapses with pyramidal neurons in layers 3, 5A and 5B (L3, L5A and L5B) in the mouse barrel cortex. Within the dendritic arborizations of L3 cells, individual inputs impinged onto distinct single domains. These domains were arrayed in an orderly, monotonic pattern along the apical axis: axons from more central origins targeted progressively higher regions of the apical dendrites. In L5 arborizations, different inputs targeted separate basal and apical domains. Input to L3 and L5 dendrites in L1 was related to whisker movement and position, suggesting that these signals have a role in controlling the gain of their target neurons. Our experiments reveal high specificity in the subcellular organization of excitatory circuits.

}, keywords = {Animals, Axons, Dendrites, Mice, Neocortex, Neural Pathways, Pyramidal Cells, Rhodopsin, Thalamic Nuclei}, issn = {1476-4687}, doi = {10.1038/nature07709}, author = {Petreanu, Leopoldo and Mao, Tianyi and Sternson, Scott M and Svoboda, Karel} } @article {2956, title = {Super-resolution video microscopy of live cells by structured illumination.}, journal = {Nature Methods}, volume = {6}, year = {2009}, month = {2009 May}, pages = {339-42}, abstract = {

Structured-illumination microscopy can double the resolution of the widefield fluorescence microscope but has previously been too slow for dynamic live imaging. Here we demonstrate a high-speed structured-illumination microscope that is capable of 100-nm resolution at frame rates up to 11 Hz for several hundred time points. We demonstrate the microscope by video imaging of tubulin and kinesin dynamics in living Drosophila melanogaster S2 cells in the total internal reflection mode.

}, keywords = {Algorithms, Animals, Automatic Data Processing, Cell Line, Computer-Assisted, Cytophotometry, Drosophila melanogaster, Fluorescence, Fourier Analysis, Image Processing, Kinesin, Lighting, Microscopy, Microtubules, Mitotic Spindle Apparatus, Tubulin, Video}, issn = {1548-7105}, doi = {10.1038/nmeth.1324}, author = {Kner, Peter and Chhun, Bryant B and Griffis, Eric R and Winoto, Lukman and Gustafsson, Mats G L} } @article {4268, title = {A survey of nematode SmY RNAs.}, journal = {RNA Biology}, volume = {6}, year = {2009}, month = {2009 Jan-Mar}, pages = {5-8}, abstract = {

SmY RNAs are a family of approximately 70-90 nt small nuclear RNAs found in nematodes. In C. elegans, SmY RNAs copurify in a small ribonucleoprotein (snRNP) complex related to the SL1 and SL2 snRNPs that are involved in nematode mRNA trans-splicing. Here we describe a comprehensive computational analysis of SmY RNA homologs found in the currently available genome sequences. We identify homologs in all sequenced nematode genomes in class Chromadorea. We are unable to identify homologs in a more distantly related nematode species, Trichinella spiralis (class: Dorylaimia), and in representatives of non-nematode phyla that use trans-splicing. Using comparative RNA sequence analysis, we infer a conserved consensus SmY RNA secondary structure consisting of two stems flanking a consensus Sm protein binding site. A representative seed alignment of the SmY RNA family, annotated with the inferred consensus secondary structure, has been deposited with the Rfam RNA families database.

}, keywords = {Animals, Base Sequence, Binding Sites, Caenorhabditis elegans, Genome, Molecular Sequence Data, Nematoda, Nucleic Acid Conformation, Phylogeny, RNA, Small Nuclear, snRNP Core Proteins, Trichinella spiralis}, issn = {1555-8584}, author = {Jones, Thomas A and Otto, Wolfgang and Marz, Manja and Eddy, Sean R. and Stadler, Peter F} } @article {6784, title = {Synapse distribution suggests a two-stage model of dendritic integration in CA1 pyramidal neurons.}, journal = {Neuron}, volume = {63}, year = {2009}, month = {2009 Jul 30}, pages = {171-7}, abstract = {

Competing models have been proposed to explain how neurons integrate the thousands of inputs distributed throughout their dendritic trees. In a simple global integration model, inputs from all locations sum in the axon. In a two-stage integration model, inputs contribute directly to dendritic spikes, and outputs from multiple branches sum in the axon. These two models yield opposite predictions of how synapses at different dendritic locations should be scaled if they are to contribute equally to neuronal output. We used serial-section electron microscopy to reconstruct individual apical oblique dendritic branches of CA1 pyramidal neurons and observe a synapse distribution consistent with the two-stage integration model. Computational modeling suggests that the observed synapse distribution enhances the contribution of each dendritic branch to neuronal output.

}, keywords = {Animals, Dendrites, Electron, Hippocampus, Humans, Microscopy, Models, Neural Networks (Computer), Neural Pathways, Neurological, Neurons, Synapses}, issn = {1097-4199}, doi = {10.1016/j.neuron.2009.06.023}, author = {Katz, Yael and Menon, Vilas and Nicholson, Daniel A and Geinisman, Yuri and Kath, William L and Spruston, Nelson} } @article {6132, title = {Synaptic activity-responsive element in the Arc/Arg3.1 promoter essential for synapse-to-nucleus signaling in activated neurons.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, month = {2009 Jan 6}, pages = {316-21}, abstract = {

The neuronal immediate early gene Arc/Arg-3.1 is widely used as one of the most reliable molecular markers for intense synaptic activity in vivo. However, the cis-acting elements responsible for such stringent activity dependence have not been firmly identified. Here we combined luciferase reporter assays in cultured cortical neurons and comparative genome mapping to identify the critical synaptic activity-responsive elements (SARE) of the Arc/Arg-3.1 gene. A major SARE was found as a unique approximately 100-bp element located at \>5 kb upstream of the Arc/Arg-3.1 transcription initiation site in the mouse genome. This single element, when positioned immediately upstream of a minimal promoter, was necessary and sufficient to replicate crucial properties of endogenous Arc/Arg-3.1{\textquoteright}s transcriptional regulation, including rapid onset of transcription triggered by synaptic activity and low basal expression during synaptic inactivity. We identified the major determinants of SARE as a unique cluster of neuronal activity-dependent cis-regulatory elements consisting of closely localized binding sites for CREB, MEF2, and SRF. Consistently, a SARE reporter could readily trace and mark an ensemble of cells that have experienced intense activity in the recent past in vivo. Taken together, our work uncovers a novel transcriptional mechanism by which a critical 100-bp element, SARE, mediates a predominant component of the synapse-to-nucleus signaling in ensembles of Arc/Arg-3.1-positive activated neurons.

}, keywords = {Animals, Binding Sites, Cell Nucleus, Cyclic AMP Response Element-Binding Protein, Cytoskeletal Proteins, Gene Expression Regulation, Genetic, Genomics, Mice, Myogenic Regulatory Factors, Nerve Tissue Proteins, Neurons, Nucleic Acid, Promoter Regions, Regulatory Sequences, Serum Response Factor, Signal Transduction, Synapses}, issn = {1091-6490}, doi = {10.1073/pnas.0806518106}, author = {Kawashima, Takashi and Okuno, Hiroyuki and Nonaka, Mio and Adachi-Morishima, Aki and Kyo, Nan and Okamura, Michiko and Takemoto-Kimura, Sayaka and Worley, Paul F and Bito, Haruhiko} } @article {6785, title = {Synaptic depolarization is more effective than back-propagating action potentials during induction of associative long-term potentiation in hippocampal pyramidal neurons.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {29}, year = {2009}, month = {2009 Mar 11}, pages = {3233-41}, abstract = {

Long-term potentiation (LTP) requires postsynaptic depolarization that can result from EPSPs paired with action potentials or larger EPSPs that trigger dendritic spikes. We explored the relative contribution of these sources of depolarization to LTP induction during synaptically driven action potential firing in hippocampal CA1 pyramidal neurons. Pairing of a weak test input with a strong input resulted in large LTP (approximately 75\% increase) when the weak and strong inputs were both located in the apical dendrites. This form of LTP did not require somatic action potentials. When the strong input was located in the basal dendrites, the resulting LTP was smaller (\< or =25\% increase). Pairing the test input with somatically evoked action potentials mimicked this form of LTP. Thus, back-propagating action potentials may contribute to modest LTP, but local synaptic depolarization and/or dendritic spikes mediate a stronger form of LTP that requires spatial proximity of the associated synaptic inputs.

}, keywords = {Action Potentials, Animals, Ganglia, Hippocampus, Long-Term Potentiation, Neuronal Plasticity, Neurons, Pyramidal Cells, Rats, Spinal, Synapses, Synaptic Transmission, Wistar}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.6000-08.2009}, author = {Hardie, Jason and Spruston, Nelson} } @article {65012, title = {T cells require Foxo1 to populate the peripheral lymphoid organs.}, journal = {Eur J Immunol}, volume = {39}, year = {2009}, month = {2009 Oct 30}, pages = {2991-9}, abstract = {

Forkhead transcription factors play critical roles in leukocyte homeostasis. To study further the immunological functions of Foxo1, we generated mice that selectively lack Foxo1 in T cells (Foxo1(flox/flox) Lck.cre(+)conditional knockout mice (cKO)). Although thymocyte development appeared relatively normal, Foxo1 cKO mice harbored significantly increased percentages of mature single positive T cells in the thymus as compared with WT mice, yet possessed smaller lymph nodes and spleens that contained fewer T cells. Foxo1 cKO T cells were not more prone to apoptosis, but instead were characterized by a CD62L(lo) CCR7(lo) CD44(hi) surface phenotype, a poorly populated lymphoid compartment in the periphery, and were relatively refractory to TCR stimulation, all of which were associated with reduced expression of Sell, Klf2, Ccr7, and S1pr1. Thus, Foxo1 is critical for na{\"\i}ve T cells to populate the peripheral lymphoid organs by coordinating a molecular program that maintains homeostasis and regulates trafficking.

}, keywords = {Animals, Apoptosis, Cell Proliferation, Chemotaxis, Leukocyte, Flow Cytometry, Forkhead Box Protein O1, Forkhead Transcription Factors, Lymphoid Tissue, Mice, Mice, Knockout, Phenotype, Reverse Transcriptase Polymerase Chain Reaction, T-Lymphocyte Subsets, T-Lymphocytes}, issn = {1521-4141}, doi = {10.1002/eji.200939427}, author = {Gubbels Bupp, Melanie R and Edwards, Bonnie and Guo, Caiying and Wei, Datsen and Chen, Gang and Wong, Brian and Masteller, Emma and Peng, Stanford L} } @article {1768, title = {The taste of carbonation.}, journal = {Science}, volume = {326}, year = {2009}, month = {2009 Oct 16}, pages = {443-5}, abstract = {

Carbonated beverages are commonly available and immensely popular, but little is known about the cellular and molecular mechanisms underlying the perception of carbonation in the mouth. In mammals, carbonation elicits both somatosensory and chemosensory responses, including activation of taste neurons. We have identified the cellular and molecular substrates for the taste of carbonation. By targeted genetic ablation and the silencing of synapses in defined populations of taste receptor cells, we demonstrated that the sour-sensing cells act as the taste sensors for carbonation, and showed that carbonic anhydrase 4, a glycosylphosphatidylinositol-anchored enzyme, functions as the principal CO2 taste sensor. Together, these studies reveal the basis of the taste of carbonation as well as the contribution of taste cells in the orosensory response to CO2.

}, keywords = {Action Potentials, Animals, Benzolamide, Bicarbonates, Calcium Channels, Carbon Dioxide, Carbonated Beverages, Carbonic Anhydrase Inhibitors, Carbonic Anhydrase IV, Carbonic Anhydrases, Cell Surface, Chorda Tympani Nerve, Gene Expression Profiling, Mice, Protons, Receptors, Taste, Taste Buds, Taste Perception, Transgenic}, issn = {1095-9203}, doi = {10.1126/science.1174601}, author = {Chandrashekar, Jayaram and Yarmolinsky, David and von Buchholtz, Lars and Oka, Yuki and Sly, William and Ryba, Nicholas J P and Zuker, Charles S} } @article {2495, title = {Temporal patterns of broad isoform expression during the development of neuronal lineages in Drosophila.}, journal = {Neural Development}, volume = {4}, year = {2009}, month = {2009 Nov 2}, pages = {39}, abstract = {

During the development of the central nervous system (CNS) of Drosophila, neuronal stem cells, the neuroblasts (NBs), first generate a set of highly diverse neurons, the primary neurons that mature to control larval behavior, and then more homogeneous sets of neurons that show delayed maturation and are primarily used in the adult. These latter, {\textquoteright}secondary{\textquoteright} neurons show a complex pattern of expression of broad, which encodes a transcription factor usually associated with metamorphosis, where it acts as a key regulator in the transitions from larva and pupa.

}, keywords = {Animals, Biological, Drosophila, Drosophila Proteins, Genetically Modified, Interneurons, Metamorphosis, Motor Neurons, Mushroom Bodies, Neurites, Neurons, Newborn, Nonmammalian, Optic Lobe, Protein Isoforms, Thorax, Time Factors, Transcription Factors}, issn = {1749-8104}, doi = {10.1186/1749-8104-4-39}, author = {Zhou, Baohua and Williams, Darren W and Altman, Janet and Riddiford, Lynn M and Truman, James W} } @article {2343, title = {Theta oscillations provide temporal windows for local circuit computation in the entorhinal-hippocampal loop.}, journal = {Neuron}, volume = {64}, year = {2009}, month = {2009 Oct 29}, pages = {267-80}, abstract = {

Theta oscillations are believed to play an important role in the coordination of neuronal firing in the entorhinal (EC)-hippocampal system but the underlying mechanisms are not known. We simultaneously recorded from neurons in multiple regions of the EC-hippocampal loop and examined their temporal relationships. Theta-coordinated synchronous spiking of EC neuronal populations predicted the timing of current sinks in target layers in the hippocampus. However, the temporal delays between population activities in successive anatomical stages were longer (typically by a half theta cycle) than expected from axon conduction velocities and passive synaptic integration of feed-forward excitatory inputs. We hypothesize that the temporal windows set by the theta cycles allow for local circuit interactions and thus a considerable degree of computational independence in subdivisions of the EC-hippocampal loop.

}, keywords = {Action Potentials, Animals, Electric Stimulation, Entorhinal Cortex, Hippocampus, Long-Evans, Long-Term Potentiation, Male, Models, Movement, Nerve Net, Neural Inhibition, Neural Pathways, Neurological, Neurons, Patch-Clamp Techniques, Rats, Reaction Time, Synaptic Transmission, Theta Rhythm}, issn = {1097-4199}, doi = {10.1523/JNEUROSCI.3773-10.2011}, author = {Mizuseki, Kenji and Sirota, Anton and Pastalkova, Eva and Buzs{\'a}ki, Gy{\"o}rgy} } @article {46409, title = {Thioredoxin-independent regulation of metabolism by the alpha-arrestin proteins.}, journal = {Journal of Biological Chemistry}, volume = {284}, year = {2009}, month = {2009 Sep 11}, pages = {24996-5003}, abstract = {

Thioredoxin-interacting protein (Txnip), originally characterized as an inhibitor of thioredoxin, is now known to be a critical regulator of glucose metabolism in vivo. Txnip is a member of the alpha-arrestin protein family; the alpha-arrestins are related to the classical beta-arrestins and visual arrestins. Txnip is the only alpha-arrestin known to bind thioredoxin, and it is not known whether the metabolic effects of Txnip are related to its ability to bind thioredoxin or related to conserved alpha-arrestin function. Here we show that wild type Txnip and Txnip C247S, a Txnip mutant that does not bind thioredoxin in vitro, both inhibit glucose uptake in mature adipocytes and in primary skin fibroblasts. Furthermore, we show that Txnip C247S does not bind thioredoxin in cells, using thiol alkylation to trap the Txnip-thioredoxin complex. Because Txnip function was independent of thioredoxin binding, we tested whether inhibition of glucose uptake was conserved in the related alpha-arrestins Arrdc4 and Arrdc3. Both Txnip and Arrdc4 inhibited glucose uptake and lactate output, while Arrdc3 had no effect. Structure-function analysis indicated that Txnip and Arrdc4 inhibit glucose uptake independent of the C-terminal WW-domain binding motifs, recently identified as important in yeast alpha-arrestins. Instead, regulation of glucose uptake was intrinsic to the arrestin domains themselves. These data demonstrate that Txnip regulates cellular metabolism independent of its binding to thioredoxin and reveal the arrestin domains as crucial structural elements in metabolic functions of alpha-arrestin proteins.

}, keywords = {Amino Acid Sequence, Animals, Arrestin, Arrestins, Carrier Proteins, Fibroblasts, Gene Expression Regulation, Humans, Mice, Molecular Sequence Data, Mutation, Plasmids, Protein Structure, Tertiary, Sequence Homology, Amino Acid, Thioredoxins}, issn = {1083-351X}, doi = {10.1074/jbc.M109.018093}, author = {Patwari, Parth and Chutkow, William A and Cummings, Kiersten and Verstraeten, Valerie L R M and Lammerding, Jan and Schreiter, Eric R and Lee, Richard T} } @article {5357, title = {Three dimensional super resolution fluorescence imaging of single bacterial cells by stereo photoactivated localization microscopy.}, journal = {Microscopy and Microanalysis}, volume = {15}, year = {2009}, month = {2009 July 26}, pages = {564-5}, doi = {10.1017/S1431927609095737}, author = {Tang, Jianyong and Vaziri, Alipasha and Akerboom, Jasper P. and Looger, Loren and Shank, Charles V} } @article {5363, title = {Three-dimensional nanoscopy of biological samples.}, journal = {2009 Conference on Lasers and Electro-Optics and Quantum Electronics and Laser Science Conference (CLEO/QELS 2009), Vols. 1-5}, volume = {1-5}, year = {2009}, month = {2009 Jun 5}, pages = {147-8}, abstract = {

We have demonstrated super-resolution imaging of protein distributions in cells at depth at multiple layers with a lateral localization precision better than 50 nm. The approach is based on combining photoactivated localization microscopy with temporal focusing.

}, author = {Vaziri, Alipasha and Tang, Jianyong and Shroff, Hari and Shank, Charles V} } @article {5359, title = {Three-dimensional super-resolution imaging of thick biological samples.}, journal = {Microscopy and Microanalysis}, volume = {15}, year = {2009}, month = {2009 Jul 26}, pages = {36-7}, doi = {10.1017/S1431927609092368}, author = {Vaziri, A. and Tang, J. and Shroff, H. and Shank, C.} } @article {46620, title = {Too fat to fly? New brain circuits regulate obesity in Drosophila.}, journal = {Neuron}, volume = {63}, year = {2009}, month = {2009 Aug 13}, pages = {279-81}, abstract = {

In mammals, fat store levels are regulated by brain centers that control food intake and metabolism. A new study by Al-Anzi and colleagues in this issue of Neuron identifies neurons with similar functions in Drosophila, further establishing the fly as a legitimate model to study obesity.

}, keywords = {Animals, Brain, Disease Models, Animal, Drosophila, Drosophila Proteins, Nerve Net, Neurons, Obesity}, issn = {1097-4199}, doi = {10.1016/j.neuron.2009.07.023}, author = {Kaun, Karla R and Heberlein, Ulrike} } @article {4264, title = {A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas.}, journal = {Bioinformatics}, volume = {25}, year = {2009}, month = {2009 Jul 1}, pages = {1647-54}, abstract = {

Gene expression patterns can be useful in understanding the structural organization of the brain and the regulatory logic that governs its myriad cell types. A particularly rich source of spatial expression data is the Allen Brain Atlas (ABA), a comprehensive genome-wide in situ hybridization study of the adult mouse brain. Here, we present an open-source program, ALLENMINER, that searches the ABA for genes that are expressed, enriched, patterned or graded in a user-specified region of interest.

}, keywords = {Animals, Brain, Computer Graphics, Gene Expression, Gene Expression Profiling, Genome, Mice, Oligonucleotide Array Sequence Analysis}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btp288}, author = {Davis, Fred P and Eddy, Sean R.} } @article {1209, title = {TRAPPII is required for cleavage furrow ingression and localization of Rab11 in dividing male meiotic cells of Drosophila.}, journal = {Journal of Cell Science}, volume = {122}, year = {2009}, month = {2009 Dec 15}, pages = {4526-34}, abstract = {

Although membrane addition is crucial for cytokinesis in many animal cell types, the specific mechanisms supporting cleavage furrow ingression are not yet understood. Mutations in the gene brunelleschi (bru), which encodes the Drosophila ortholog of the yeast Trs120p subunit of TRAPPII, cause failure of furrow ingression in male meiotic cells. In non-dividing cells, Brunelleschi protein fused to GFP is dispersed throughout the cytoplasm and enriched at Golgi organelles, similarly to another Drosophila TRAPPII subunit, dBet3. Localization of the membrane-trafficking GTPase Rab11 to the cleavage furrow requires wild-type function of bru, and genetic interactions between bru and Rab11 increase the failure of meiotic cytokinesis and cause synthetic lethality. bru also genetically interacts with four wheel drive (fwd), which encodes a PI4Kbeta, such that double mutants exhibit enhanced failure of male meiotic cytokinesis. These results suggest that Bru cooperates with Rab11 and PI4Kbeta to regulate the efficiency of membrane addition to the cleavage furrow, thus promoting cytokinesis in Drosophila male meiotic cells.

}, keywords = {Amino Acid Sequence, Animals, Cell Division, Cytokinesis, Cytoplasm, Drosophila, Drosophila Proteins, Golgi Apparatus, Male, Meiosis, Molecular Sequence Data, Post-Translational, Protein Processing, Protein Transport, rab GTP-Binding Proteins, Sequence Alignment, Spermatocytes}, issn = {1477-9137}, doi = {10.1242/jcs.054536}, author = {Robinett, Carmen C and Giansanti, Maria Grazia and Gatti, Maurizio and Fuller, Margaret T} } @article {2634, title = {Tweek, an evolutionarily conserved protein, is required for synaptic vesicle recycling.}, journal = {Neuron}, volume = {63}, year = {2009}, month = {2009 Jul 30}, pages = {203-15}, abstract = {

Synaptic vesicle endocytosis is critical for maintaining synaptic communication during intense stimulation. Here we describe Tweek, a conserved protein that is required for synaptic vesicle recycling. tweek mutants show reduced FM1-43 uptake, cannot maintain release during intense stimulation, and harbor larger than normal synaptic vesicles, implicating it in vesicle recycling at the synapse. Interestingly, the levels of a fluorescent PI(4,5)P(2) reporter are reduced at tweek mutant synapses, and the probe is aberrantly localized during stimulation. In addition, various endocytic adaptors known to bind PI(4,5)P(2) are mislocalized and the defects in FM1-43 dye uptake and adaptor localization are partially suppressed by removing one copy of the phosphoinositide phosphatase synaptojanin, suggesting a role for Tweek in maintaining proper phosphoinositide levels at synapses. Our data implicate Tweek in regulating synaptic vesicle recycling via an action mediated at least in part by the regulation of PI(4,5)P(2) levels or availability at the synapse.

}, keywords = {Animals, Blotting, Complementary, Diptera, DNA, Drosophila Proteins, Electron, Endocytosis, Eye Abnormalities, Immunohistochemistry, Microscopy, Molecular Sequence Data, Mutation, Nerve Tissue Proteins, Neurons, Phosphatidylinositol Phosphates, Pyridinium Compounds, Quaternary Ammonium Compounds, Reverse Transcriptase Polymerase Chain Reaction, Synapses, Synaptic Transmission, Synaptic Vesicles, Transmission, Western}, issn = {1097-4199}, doi = {10.1016/j.neuron.2009.06.017}, author = {Verstreken, Patrik and Ohyama, Tomoko and Haueter, Claire and Habets, Ron L P and Lin, Yong Q and Swan, Laura E and Ly, Cindy V and Venken, Koen J T and De Camilli, Pietro and Bellen, Hugo J} } @article {781, title = {Twin-spot MARCM to reveal the developmental origin and identity of neurons.}, journal = {Nature Neuroscience}, volume = {12}, year = {2009}, month = {2009 Jul}, pages = {947-53}, abstract = {

A comprehensive understanding of the brain requires the analysis of individual neurons. We used twin-spot mosaic analysis with repressible cell markers (twin-spot MARCM) to trace cell lineages at high resolution by independently labeling paired sister clones. We determined patterns of neurogenesis and the influences of lineage on neuron-type specification. Notably, neural progenitors were able to yield intermediate precursors that create one, two or more neurons. Furthermore, neurons acquired stereotyped projections according to their temporal position in various brain sublineages. Twin-spot MARCM also permitted birth dating of mutant clones, enabling us to detect a single temporal fate that required chinmo in a sublineage of six Drosophila central complex neurons. In sum, twin-spot MARCM can reveal the developmental origins of neurons and the mechanisms that underlie cell fate.

}, keywords = {Animals, Brain, Cell Lineage, Central Nervous System, Drosophila, Drosophila Proteins, Gene Knockout Techniques, Genetic Techniques, Genetically Modified, Mushroom Bodies, Nerve Tissue Proteins, Neurogenesis, Neurons, RNA Interference, Time Factors}, issn = {1546-1726}, doi = {10.1038/nn.2345}, author = {Yu, Hung-Hsiang and Chen, Chun-Hong and Shi, Lei and Huang, Yaling and Lee, Tzumin} } @article {2331, title = {VANO: a volume-object image annotation system.}, journal = {Bioinformatics}, volume = {25}, year = {2009}, month = {2009 Mar 1}, pages = {695-7}, abstract = {

Volume-object annotation system (VANO) is a cross-platform image annotation system that enables one to conveniently visualize and annotate 3D volume objects including nuclei and cells. An application of VANO typically starts with an initial collection of objects produced by a segmentation computation. The objects can then be labeled, categorized, deleted, added, split, merged and redefined. VANO has been used to build high-resolution digital atlases of the nuclei of Caenorhabditis elegans at the L1 stage and the nuclei of Drosophila melanogaster{\textquoteright}s ventral nerve cord at the late embryonic stage. AVAILABILITY: Platform independent executables of VANO, a sample dataset, and a detailed description of both its design and usage are available at research.janelia.org/peng/proj/vano. VANO is open-source for co-development.

}, keywords = {Animals, Caenorhabditis elegans, Computer-Assisted, Databases, Drosophila, Factual, Image Processing, Software, User-Computer Interface}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btp046}, author = {Peng, Hanchuan and Long, Fuhui and Myers, Eugene W} } @article {4635, title = {Variable phase retarder made of a dielectric elastomer actuator.}, journal = {Optics Letters}, volume = {34}, year = {2009}, month = {2009 Mar 15}, pages = {803-5}, abstract = {

We present a polymeric optical phase retarder that is electrically tunable by a dielectric elastomer actuator. The soft material device affords a large tuning range (14pi at lambda=488 nm) combined with high accuracy in optical path length and low drift rate (8.3 nm/min). Furthermore, the phase retarder is not sensitive to polarization, introduces a wavefront distortion141 kW/cm2). We show the dynamics for periodic phase modulation and demonstrate a simple drive technique for fast phase stepping. The polymer-based device is inexpensive, easy to fabricate, and its design can be adapted to specific applications.

}, issn = {0146-9592}, author = {Beck, Markus and Fiolka, Reto and Stemmer, Andreas} } @conference {6450, title = {Which spatial partition trees are adaptive to intrinsic dimension?}, booktitle = {Conference on Uncertainty in Artificial Intelligence}, year = {2009}, month = {2009 Jun 18}, author = {Verma, N and Kpotufe, S and Dasgupta, S} } @article {2391, title = {Wnt signaling targets ETO coactivation domain of TAF4/TFIID in vivo.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, month = {2009 Jan 6}, pages = {55-60}, abstract = {

Understanding the diverse activities of the multisubunit core promoter recognition complex TFIID in vivo requires knowledge of how individual subunits contribute to overall functions of this TATA box-binding protein (TBP)/TBP-associated factor (TAF) complex. By generating altered holo-TFIID complexes in Drosophila we identify the ETO domain of TAF4 as a coactivator domain likely targeted by Pygopus, a protein that is required for Wingless-induced transcription of naked cuticle. These results establish a coactivator function of TAF4 and provide a strategy to dissect mechanisms of TFIID function in vivo.

}, keywords = {Animals, Binding Sites, Cell Line, Drosophila, Drosophila Proteins, Humans, Intracellular Signaling Peptides and Proteins, Larva, Multiprotein Complexes, Proto-Oncogene Proteins, Signal Transduction, TATA-Binding Protein Associated Factors, Transcription Factor TFIID, Transcription Factors, Tumor, Wnt Proteins}, issn = {1091-6490}, doi = {10.1073/pnas.1100640108}, author = {Wright, Kevin J and Tjian, Robert} } @article {6536, title = {Wnt-Ror signaling to SIA and SIB neurons directs anterior axon guidance and nerve ring placement in C. elegans.}, journal = {Development}, volume = {136}, year = {2009}, month = {2009 Nov}, pages = {3801-10}, abstract = {

Wnt signaling through Frizzled proteins guides posterior cells and axons in C. elegans into different spatial domains. Here we demonstrate an essential role for Wnt signaling through Ror tyrosine kinase homologs in the most prominent anterior neuropil, the nerve ring. A genetic screen uncovered cwn-2, the C. elegans homolog of Wnt5, as a regulator of nerve ring placement. In cwn-2 mutants, all neuronal structures in and around the nerve ring are shifted to an abnormal anterior position. cwn-2 is required at the time of nerve ring formation; it is expressed by cells posterior of the nerve ring, but its precise site of expression is not critical for its function. In nerve ring development, cwn-2 acts primarily through the Wnt receptor CAM-1 (Ror), together with the Frizzled protein MIG-1, with parallel roles for the Frizzled protein CFZ-2. The identification of CAM-1 as a CWN-2 receptor contrasts with CAM-1 action as a non-receptor in other C. elegans Wnt pathways. Cell-specific rescue of cam-1 and cell ablation experiments reveal a crucial role for the SIA and SIB neurons in positioning the nerve ring, linking Wnt signaling to specific cells that organize the anterior nervous system.

}, keywords = {Animals, Axons, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Neurogenesis, Neurons, Receptor Protein-Tyrosine Kinases, Receptor Tyrosine Kinase-like Orphan Receptors, Signal Transduction, Wnt Proteins}, issn = {1477-9129}, doi = {10.1242/dev.038109}, author = {Kennerdell, Jason R and Fetter, Richard D and Bargmann, Cornelia I} } @conference {6530, title = {Action recognition using ballistic dynamics.}, booktitle = {2008 IEEE Conference on Computer Vision and Pattern Recognition}, volume = {2008}, year = {2008}, month = {2008 Jun}, pages = {1-8}, publisher = {IEEE}, organization = {IEEE}, address = {Anchorage, AK}, abstract = {

We present a Bayesian framework for action recognition through ballistic dynamics. Psycho-kinesiological studies indicate that ballistic movements form the natural units for human movement planning. The framework leads to an efficient and robust algorithm for temporally segmenting videos into atomic movements. Individual movements are annotated with person-centric morphological labels called ballistic verbs. This is tested on a dataset of interactive movements, achieving high recognition rates. The approach is also applied on a gesture recognition task, improving a previously reported recognition rate from 84\% to 92\%. Consideration of ballistic dynamics enhances the performance of the popular Motion History Image feature. We also illustrate the approach{\textquoteright}s general utility on real-world videos. Experiments indicate that the method is robust to view, style and appearance variations.

}, isbn = {978-1-4244-2242-5}, issn = {1063-6919}, doi = {10.1109/CVPR.2008.4587806}, author = {Vitadalevuni, Shiv N. and Kellokumpu, Vili and Davis, Larry S.} } @article {4020, title = {Advances in the speed and resolution of light microscopy.}, journal = {Current Opinion in Neurobiology}, volume = {18}, year = {2008}, month = {2008 Dec}, pages = {605-16}, abstract = {

Neurobiological processes occur on spatiotemporal scales spanning many orders of magnitude. Greater understanding of these processes therefore demands improvements in the tools used in their study. Here we review recent efforts to enhance the speed and resolution of one such tool, fluorescence microscopy, with an eye toward its application to neurobiological problems. On the speed front, improvements in beam scanning technology, signal generation rates, and photodamage mediation are bringing us closer to the goal of real-time functional imaging of extended neural networks. With regard to resolution, emerging methods of adaptive optics may lead to diffraction-limited imaging or much deeper imaging in optically inhomogeneous tissues, and super-resolution techniques may prove a powerful adjunct to electron microscopic methods for nanometric neural circuit reconstruction.

}, keywords = {Animals, Electron, Fluorescence, Humans, Microscopy, Nerve Net, Neurology, Photobleaching, Photons}, issn = {1873-6882}, doi = {10.1016/j.conb.2009.03.009}, author = {Ji, Na and Shroff, Hari and Zhong, Haining and Betzig, Eric} } @article {2077, title = {Advances in the speed and resolution of light microscopy. (With commentary)}, journal = {Current Opinion in Neurobiology}, volume = {18}, year = {2008}, month = {2008 Dec}, pages = {605-16}, abstract = {

Neurobiological processes occur on spatiotemporal scales spanning many orders of magnitude. Greater understanding of these processes therefore demands improvements in the tools used in their study. Here we review recent efforts to enhance the speed and resolution of one such tool, fluorescence microscopy, with an eye toward its application to neurobiological problems. On the speed front, improvements in beam scanning technology, signal generation rates, and photodamage mediation are bringing us closer to the goal of real-time functional imaging of extended neural networks. With regard to resolution, emerging methods of adaptive optics may lead to diffraction-limited imaging or much deeper imaging in optically inhomogeneous tissues, and super-resolution techniques may prove a powerful adjunct to electron microscopic methods for nanometric neural circuit reconstruction.

Commentary: A brief review of recent trends in microscopy. The section {\textquotedblleft}Caveats regarding the application of superresolution microscopy{\textquotedblright} was written in an effort to inject a dose of reality and caution into the unquestioning enthusiasm in the academic community for all things superresolution, covering the topics of labeling density and specificity, sample preparation artifacts, speed vs. resolution vs. photodamage, and the implications of signal-to-background for Nyquist vs. Rayleigh definitions of resolution.

}, keywords = {Animals, Electron, Fluorescence, Humans, Microscopy, Nerve Net, Neurology, Photobleaching, Photons}, issn = {1873-6882}, doi = {10.1016/j.conb.2009.03.009}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19375302}, author = {Ji, Na and Shroff, Hari and Zhong, Haining and Betzig, Eric} } @article {3917, title = {Altered synaptic and non-synaptic properties of CA1 pyramidal neurons in Kv4.2 knockout mice.}, journal = {The Journal of Physiology}, volume = {586}, year = {2008}, month = {2008 Aug 15}, pages = {3881-92}, abstract = {

Back-propagating action potentials (bAPs) travelling from the soma to the dendrites of neurons are involved in various aspects of synaptic plasticity. The distance-dependent increase in Kv4.2-mediated A-type K(+) current along the apical dendrites of CA1 pyramidal cells (CA1 PCs) is responsible for the attenuation of bAP amplitude with distance from the soma. Genetic deletion of Kv4.2 reduced dendritic A-type K(+) current and increased the bAP amplitude in distal dendrites. Our previous studies revealed that the amplitude of unitary Schaffer collateral inputs increases with distance from the soma along the apical dendrites of CA1 PCs. We tested the hypothesis that the weight of distal synapses is dependent on dendritic Kv4.2 channels. We compared the amplitude and kinetics of mEPSCs at different locations on the main apical trunk of CA1 PCs from wild-type (WT) and Kv4.2 knockout (KO) mice. While wild-type mice showed normal distance-dependent scaling, it was missing in the Kv4.2 KO mice. We also tested whether there was an increase in inhibition in the Kv4.2 knockout, induced in an attempt to compensate for a non-specific increase in neuronal excitability (after-polarization duration and burst firing probability were increased in KO). Indeed, we found that the magnitude of the tonic GABA current increased in Kv4.2 KO mice by 53\% and the amplitude of mIPSCs increased by 25\%, as recorded at the soma. Our results suggest important roles for the dendritic K(+) channels in distance-dependent adjustment of synaptic strength as well as a primary role for tonic inhibition in the regulation of global synaptic strength and membrane excitability.

}, keywords = {Action Potentials, Animals, Dendrites, Knockout, Mice, Neural Conduction, Neuronal Plasticity, Pyramidal Cells, Shal Potassium Channels, Synapses, Synaptic Transmission}, issn = {1469-7793}, doi = {10.1113/jphysiol.2008.154336}, author = {Andr{\'a}sfalvy, B K and Makara, J K and Johnston, D and J.C. Magee} } @article {2689, title = {Analysis of a spatial orientation memory in Drosophila.}, journal = {Nature}, volume = {453}, year = {2008}, month = {2008 Jun 26}, pages = {1244-7}, abstract = {

Flexible goal-driven orientation requires that the position of a target be stored, especially in case the target moves out of sight. The capability to retain, recall and integrate such positional information into guiding behaviour has been summarized under the term spatial working memory. This kind of memory contains specific details of the presence that are not necessarily part of a long-term memory. Neurophysiological studies in primates indicate that sustained activity of neurons encodes the sensory information even though the object is no longer present. Furthermore they suggest that dopamine transmits the respective input to the prefrontal cortex, and simultaneous suppression by GABA spatially restricts this neuronal activity. Here we show that Drosophila melanogaster possesses a similar spatial memory during locomotion. Using a new detour setup, we show that flies can remember the position of an object for several seconds after it has been removed from their environment. In this setup, flies are temporarily lured away from the direction towards their hidden target, yet they are thereafter able to aim for their former target. Furthermore, we find that the GABAergic (stainable with antibodies against GABA) ring neurons of the ellipsoid body in the central brain are necessary and their plasticity is sufficient for a functional spatial orientation memory in flies. We also find that the protein kinase S6KII (ignorant) is required in a distinct subset of ring neurons to display this memory. Conditional expression of S6KII in these neurons only in adults can restore the loss of the orientation memory of the ignorant mutant. The S6KII signalling pathway therefore seems to be acutely required in the ring neurons for spatial orientation memory in flies.

}, keywords = {90-kDa, Animals, Drosophila melanogaster, gamma-Aminobutyric Acid, Locomotion, Memory, Models, Neurological, Neurons, Orientation, Ribosomal Protein S6 Kinases, Signal Transduction, Space Perception}, issn = {1476-4687}, doi = {10.1038/nature07003}, author = {Neuser, Kirsa and Triphan, Tilman and Mronz, Markus and Poeck, Burkhard and Strauss, Roland} } @article {45737, title = {Aphids.}, journal = {Curr Biol}, volume = {18}, year = {2008}, month = {2008 Jun 24}, pages = {R504-5}, abstract = {

Mammalian herbivores profoundly influence plant-dwelling insects [1]. Most studies have focused on the indirect effect of herbivory on insect populations via damage to the host plant [2,3]. Many insects, however, are in danger of being inadvertently ingested during herbivore feeding. Here, we report that pea aphids (Acyrthosiphon pisum) are able to sense the elevated heat and humidity of the breath of an approaching herbivore and thus salvage most of the colony by simultaneously dropping off the plant in large numbers immediately before the plant is eaten. Dropping entails the risk of losing the host plant and becoming desiccated or preyed upon on the ground [4,5], yet pea aphids may sporadically drop when threatened by insect enemies [6]. The immediate mass dropping, however, is an adaptation to the potential destructive impact of mammalian herbivory on the entire aphid colony. The combination of heat and humidity serves as a reliable cue to impending mammalian herbivory, enabling the aphids to avoid unnecessary dropping. No defensive behavior against incidental predation by herbivores has ever been demonstrated. The pea aphids{\textquoteright} highly adaptive escape behavior uniquely demonstrates the strength of the selective pressure large mammalian herbivores impose on insect herbivores.

}, keywords = {Animals, Aphids, Female, Genome, Insect, Insect Vectors, Male, Peas, Plant Diseases, Plant Tumors, Styrax}, issn = {0960-9822}, doi = {10.1016/j.cub.2008.03.034}, author = {Stern, David L} } @proceedings {46794, title = {Automatic landmark correspondence detection for ImageJ.}, year = {2008}, month = {2008 Nov 7}, address = {Luxembourg}, abstract = {

Landmark correspondences can be used for various tasks in image processing such as image alignment, reconstruction of panoramic photographs, object recognition and simultaneous localization and mapping for mobile robots. The computer vision community knows several techniques for extracting and pairwise associating such landmarks using distinctive invariant local image features. Two very successful methods are the Scale Invariant Feature Transform (SIFT)1 and Multi-Scale Oriented Patches (MOPS).2
We implemented these methods in the Java programming language3 for seamless use in ImageJ.4 We use it for fully automatic registration of gigantic serial section Transmission Electron Microscopy (TEM) mosaics. Using automatically detected landmark correspondences, the registration of large image mosaics simplifies to globally minimizing the displacement of corresponding points.
We present here an introduction to automatic landmark correspondence detection and demonstrate our implementation for ImageJ. We demonstrate the application of the plug-in on diverse image data.

}, author = {Saalfeld, Stephan and Tomancak, Pavel} } @conference {2719, title = {Automatic recognition of cells (ARC) for 3D images of C. elegans.}, booktitle = {Proceedings of the 2008 Conference on Computational Molecular Biology (RECOMB) (Singapore, 2008)}, year = {2008}, month = {2008 Apr 2}, abstract = {

The development of high-resolution microscopy makes possible the high-throughput screening of cellular information, such as gene expression at single cell resolution. One of the critical enabling techniques yet to be developed is the automatic recognition or annotation of specific cells in a 3D image stack. In this paper, we present a novel graph-based algorithm, ARC, that determines cell identities in a 3D confocal image of C. elegans based on their highly stereotyped arrangement. This is an essential step in our work on gene expression analysis of C. elegans at the resolution of single cells. Our ARC method integrates both the absolute and relative spatial locations of cells in a C. elegans body. It uses a marker-guided, spatially-constrained, two-stage bipartite matching to find the optimal match between cells in a subject image and cells in 15 template images that have been manually annotated and vetted. We applied ARC to the recognition of cells in 3D confocal images of the first larval stage (L1) of C. elegans hermaphrodites, and achieved an average accuracy of 94.91\%.

}, author = {Long, Fuhui and Peng, Hanchuan and Liu, X and Kim, Stuart K and Myers, Eugene} } @article {48177, title = {Automatic Segmentation of the Pelvic Bones from CT Data Based on a Statistical Shape Model}, year = {2008}, abstract = {

We present an algorithm for automatic segmentation of the human pelvic bones from CT datasets that is based on the application of a statistical shape model. The proposed method is divided into three steps: 1) The averaged shape of the pelvis model is initially placed within the CT data using the Generalized Hough Transform, 2) the statistical shape model is then adapted to the image data by a transformation and variation of its shape modes, and 3) a final free-form deformation step based on optimal graph searching is applied to overcome the restrictive character of the statistical shape representation. We thoroughly evaluated the method on 50 manually segmented CT datasets by performing a leave-one-out study. The Generalized Hough Transform proved to be a reliable method for an automatic initial placement of the shape model within the CT data. Compared to the manual gold standard segmentations, our automatic segmentation approach produced an average surface distance of 1.2 {\textpm} 0.3mm after the adaptation of the statistical shape model, which could be reduced to 0.7{\textpm}0.3mm using a final free-form deformation step. Together with an average segmentation time of less than 5 minutes, the results of our study indicate that our method meets the requirements of clinical routine.

}, doi = {10.2312/VCBM/VCBM08/093-100}, author = {Kainmueller, Dagmar and Seim, Heiko and Heller, Markus and Lamecker, Hans and Zachow, Stefan and Hege, Hans-Christian} } @article {1496, title = {Automatic tracking of Escherichia coli bacteria.}, journal = {Medical Image Computing and Computer-Assisted Intervention: MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention}, volume = {11}, year = {2008}, month = {2008 Sep 6}, pages = {824-32}, abstract = {

In this paper, we present an automatic method for estimating the trajectories of Escherichia coli bacteria from in vivo phase-contrast microscopy videos. To address the low-contrast boundaries in cellular images, an adaptive kernel-based technique is applied to detect cells in sequence of frames. Then a novel matching gain measure is introduced to cope with the challenges such as dramatic changes of cells{\textquoteright} appearance and serious overlapping and occlusion. For multiple cell tracking, an optimal matching strategy is proposed to improve the handling of cell collision and broken trajectories. The results of successful tracking of Escherichia coli from various phase-contrast sequences are reported and compared with manually-determined trajectories, as well as those obtained from existing tracking methods. The stability of the algorithm with different parameter values is also analyzed and discussed.

}, keywords = {Algorithms, Artificial Intelligence, Automated, Cell Movement, Cluster Analysis, Computer-Assisted, Escherichia coli, Image Enhancement, Image Interpretation, Microscopy, Pattern Recognition, Phase-Contrast, Reproducibility of Results, Sensitivity and Specificity, Subtraction Technique, Video}, author = {Xie, Jun and Khan, Shahid and Shah, Mubarak} } @article {46037, title = {Behavioral and biological effects of chronic S18986, a positive AMPA receptor modulator, during aging.}, journal = {Exp Neurol}, volume = {210}, year = {2008}, month = {2008 Mar}, pages = {109-17}, abstract = {

AMPA receptors are a major subtype of ionotropic receptors that respond to glutamate. Positive allosteric modulators of AMPA receptors selectively enhance fast excitatory neurotransmission in the brain and increase overall neuronal excitability. In addition to enhancing cognitive performance, S18986 (Servier, France) and other AMPA receptor modulators have also been shown to be neuroprotective. A particularly relevant context for AMPAR modulator studies is during aging because of increased neuronal vulnerability. It is currently unknown if chronic AMPAR modulator treatment can alter the course of brain aging, a process characterized by impairment of cognitive function, reduced neuronal excitability, and increased inflammation in the brain. We examined the behavioral and some relevant CNS effects of chronic S18986 in rats from 14 to 18 months of age. Here we show that chronic, oral administration of S18986 increases locomotor activity and performance in a spatial memory task in aged rodents. In addition, chronic S18986 treatment retards the decline of forebrain cholinergic neurons by roughly 37\% and midbrain dopaminergic neurons by as much as 43\% during aging and attenuates the age-related increase in the expression of a microglial marker in the hippocampus. These results provide a framework for further studies of the potentially beneficial effects of AMPAR modulators on brain aging.

}, keywords = {Administration, Oral, Age Factors, Aging, Analysis of Variance, Animals, Antigens, CD11b, Behavior, Animal, Benzothiadiazines, Brain, Brain-Derived Neurotrophic Factor, Choline O-Acetyltransferase, Corticosterone, Dose-Response Relationship, Drug, Glial Fibrillary Acidic Protein, Male, Maze Learning, Motor Activity, Neurons, Radioimmunoassay, Rats, Rats, Sprague-Dawley, Tyrosine 3-Monooxygenase}, issn = {0014-4886}, doi = {10.1016/j.expneurol.2007.10.007}, author = {Bloss, Erik B and Hunter, Richard G and Waters, Elizabeth M and Munoz, Carmen and Bernard, Katie and McEwen, Bruce S} } @article {48395, title = {Benchmarking implicit solvent folding simulations of the amyloid beta(10-35) fragment.}, journal = {The journal of physical chemistry. B}, volume = {112}, year = {2008}, month = {2008 May 15}, pages = {6175-86}, abstract = {

A pathogenetic feature of Alzhemier disease is the aggregation of monomeric beta-amyloid proteins (Abeta) to form oligomers. Usually these oligomers of long peptides aggregate on time scales of microseconds or longer, making computational studies using atomistic molecular dynamics models prohibitively expensive and making it essential to develop computational models that are cheaper and at the same time faithful to physical features of the process. We benchmark the ability of our implicit solvent model to describe equilibrium and dynamic properties of monomeric Abeta(10-35) using all-atom Langevin dynamics (LD) simulations, since Alphabeta(10-35) is the only fragment whose monomeric properties have been measured. The accuracy of the implicit solvent model is tested by comparing its predictions with experiment and with those from a new explicit water MD simulation, (performed using CHARMM and the TIP3P water model) which is approximately 200 times slower than the implicit water simulations. The dependence on force field is investigated by running multiple trajectories for Alphabeta(10-35) using the CHARMM, OPLS-aal, and GS-AMBER94 force fields, whereas the convergence to equilibrium is tested for each force field by beginning separate trajectories from the native NMR structure, a completely stretched structure, and from unfolded initial structures. The NMR order parameter, S2, is computed for each trajectory and is compared with experimental data to assess the best choice for treating aggregates of Alphabeta. The computed order parameters vary significantly with force field. Explicit and implicit solvent simulations using the CHARMM force fields display excellent agreement with each other and once again support the accuracy of the implicit solvent model. Alphabeta(10-35) exhibits great flexibility, consistent with experiment data for the monomer in solution, while maintaining a general strand-loop-strand motif with a solvent-exposed hydrophobic patch that is believed to be important for aggregation. Finally, equilibration of the peptide structure requires an implicit solvent LD simulation as long as 30 ns.

}, keywords = {Amyloid beta-Peptides, Computer Simulation, Diffusion, Magnetic Resonance Spectroscopy, Models, Molecular, Peptide Fragments, Protein Folding, Protein Structure, Tertiary, Solvents, Surface Properties, Water}, issn = {1520-6106}, doi = {10.1021/jp077099h}, author = {Kent, Andrew and Jha, Abhishek K and Fitzgerald, James E and Freed, Karl F} } @article {2151, title = {Bioimage informatics: a new area of engineering biology.}, journal = {Bioinformatics}, volume = {24}, year = {2008}, month = {2008 Sep 1}, pages = {1827-36}, abstract = {

In recent years, the deluge of complicated molecular and cellular microscopic images creates compelling challenges for the image computing community. There has been an increasing focus on developing novel image processing, data mining, database and visualization techniques to extract, compare, search and manage the biological knowledge in these data-intensive problems. This emerging new area of bioinformatics can be called {\textquoteright}bioimage informatics{\textquoteright}. This article reviews the advances of this field from several aspects, including applications, key techniques, available tools and resources. Application examples such as high-throughput/high-content phenotyping and atlas building for model organisms demonstrate the importance of bioimage informatics. The essential techniques to the success of these applications, such as bioimage feature identification, segmentation and tracking, registration, annotation, mining, image data management and visualization, are further summarized, along with a brief overview of the available bioimage databases, analysis tools and other resources.

}, keywords = {Biological, Biomedical Engineering, Computational Biology, Computer Graphics, Computer Simulation, Diagnostic Imaging, Models, User-Computer Interface}, issn = {1367-4811}, doi = {10.1007/s12021-010-9090-x}, author = {Peng, Hanchuan} } @conference {2845, title = {Boosting adaptive linear weak classifiers for online learning and tracking.}, booktitle = {IEEE Conference on Computer Vision and Pattern Recognition}, year = {2008}, month = {2008 Jun 28}, author = {Parag, Toufiq and Porikli, Fatih and Elgammal, Ahmed} } @article {2803, title = {Breaking the pumping speed barrier in mass spectrometry: discontinuous atmospheric pressure interface.}, journal = {Analytical Chemistry}, volume = {80}, year = {2008}, month = {2008 Jun 1}, pages = {4026-32}, abstract = {

The performance of mass spectrometers with limited pumping capacity is shown to be improved through use of a discontinuous atmospheric pressure interface (DAPI). A proof-of-concept DAPI interface was designed and characterized using a miniature rectilinear ion trap mass spectrometer. The interface consists of a simple capillary directly connecting the atmospheric pressure ion source to the vacuum mass analyzer region; it has no ion optical elements and no differential pumping stages. Gases carrying ionized analytes were pulsed into the mass analyzer for short periods at high flow rates rather than being continuously introduced at lower flow rates; this procedure maximized ion transfer. The use of DAPI provides a simple solution to the problem of coupling an atmospheric pressure ionization source to a miniature instrument with limited pumping capacity. Data were recorded using various atmospheric pressure ionization sources, including electrospray ionization (ESI), nano-ESI, atmospheric pressure chemical ionization (APCI), and desorption electrospray ionization (DESI) sources. The interface was opened briefly for ion introduction during each scan. With the use of the 18 W pumping system of the Mini 10, limits of detection in the low part-per-billion levels were achieved and unit resolution mass spectra were recorded.

}, keywords = {Air, Atmospheric Pressure, Electrospray Ionization, Gases, Laboratories, Mass, Mass Spectrometry, Spectrometry, Tandem Mass Spectrometry, Time Factors}, issn = {1520-6882}, doi = {10.1364/AO.50.001792}, author = {Gao, Liang and Cooks, R Graham and Ouyang, Zheng} } @article {1100, title = {Bright ideas for chemical biology.}, journal = {ACS Chemical Biology}, volume = {3}, year = {2008}, month = {2008 Mar 20}, pages = {142-55}, abstract = {

Small-molecule fluorescent probes embody an essential facet of chemical biology. Although numerous compounds are known, the ensemble of fluorescent probes is based on a modest collection of modular "core" dyes. The elaboration of these dyes with diverse chemical moieties is enabling the precise interrogation of biochemical and biological systems. The importance of fluorescence-based technologies in chemical biology elicits a necessity to understand the major classes of small-molecule fluorophores. Here, we examine the chemical and photophysical properties of oft-used fluorophores and highlight classic and contemporary examples in which utility has been built upon these scaffolds.

}, keywords = {Animals, Biology, Fluorescent Dyes, Humans, Photochemistry}, issn = {1554-8937}, doi = {10.1021/cb700248m}, author = {Lavis, Luke D and Raines, Ronald T} } @article {6349, title = {Calcium-sensing receptor activation depresses synaptic transmission.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {28}, year = {2008}, month = {2008 Nov 12}, pages = {12062-70}, abstract = {

At excitatory synapses, decreases in cleft [Ca] arising from activity-dependent transmembrane Ca flux reduce the probability of subsequent transmitter release. Intense neural activity, induced by physiological and pathological stimuli, disturb the external microenvironment reducing extracellular [Ca] ([Ca](o)) and thus may impair neurotransmission. Increases in [Ca](o) activate the extracellular calcium sensing receptor (CaSR) which in turn inhibits nonselective cation channels at the majority of cortical nerve terminals. This pathway may modulate synaptic transmission by attenuating the impact of decreases in [Ca](o) on synaptic transmission. Using patch-clamp recording from isolated cortical terminals, cortical neuronal pairs and isolated neuronal soma we examined the modulation of synaptic transmission by CaSR. EPSCs were increased on average by 88\% in reduced affinity CaSR-mutant (CaSR(-/-)) neurons compared with wild-type. Variance-mean analysis indicates that the enhanced synaptic transmission was due largely to an increase in average probability of release (0.27 vs 0.46 for wild-type vs CaSR(-/-) pairs) with little change in quantal size (23 +/- 4 pA vs 22 +/- 4 pA) or number of release sites (11 vs 13). In addition, the CaSR agonist spermidine reduced synaptic transmission and increased paired-pulse depression at physiological [Ca](o). Spermidine did not affect quantal size, consistent with a presynaptic mechanism of action, nor did it affect voltage-activated Ca channel currents. In summary, reduced CaSR function enhanced synaptic transmission and CaSR stimulation had the opposite effect. Thus CaSR provides a mechanism that may compensate for the fall in release probability that accompanies decreases in [Ca](o).

}, keywords = {Animals, Calcium, Calcium Signaling, Calcium-Sensing, Cells, Cerebral Cortex, Cultured, Down-Regulation, Excitatory Postsynaptic Potentials, Knockout, Mice, Neural Inhibition, Neuronal Plasticity, Neurons, Organ Culture Techniques, Patch-Clamp Techniques, Presynaptic Terminals, Receptors, Spermidine, Synaptic Transmission, Synaptic Vesicles, Synaptosomes}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4134-08.2008}, author = {Phillips, Cecilia G and Harnett, Mark T and Chen, Wenyan and Smith, Stephen M} } @article {4258, title = {Characterization and subcellular targeting of GCaMP-type genetically-encoded calcium indicators.}, journal = {PLoS One}, volume = {3}, year = {2008}, month = {2008 Mar 19}, pages = {e1796}, abstract = {

Genetically-encoded calcium indicators (GECIs) hold the promise of monitoring [Ca(2+)] in selected populations of neurons and in specific cellular compartments. Relating GECI fluorescence to neuronal activity requires quantitative characterization. We have characterized a promising new genetically-encoded calcium indicator-GCaMP2-in mammalian pyramidal neurons. Fluorescence changes in response to single action potentials (17+/-10\% DeltaF/F [mean+/-SD]) could be detected in some, but not all, neurons. Trains of high-frequency action potentials yielded robust responses (302+/-50\% for trains of 40 action potentials at 83 Hz). Responses were similar in acute brain slices from in utero electroporated mice, indicating that long-term expression did not interfere with GCaMP2 function. Membrane-targeted versions of GCaMP2 did not yield larger signals than their non-targeted counterparts. We further targeted GCaMP2 to dendritic spines to monitor Ca(2+) accumulations evoked by activation of synaptic NMDA receptors. We observed robust DeltaF/F responses (range: 37\%-264\%) to single spine uncaging stimuli that were correlated with NMDA receptor currents measured through a somatic patch pipette. One major drawback of GCaMP2 was its low baseline fluorescence. Our results show that GCaMP2 is improved from the previous versions of GCaMP and may be suited to detect bursts of high-frequency action potentials and synaptic currents in vivo.

}, keywords = {Action Potentials, Animals, Calcium, Hippocampus, Humans, Rats, Subcellular Fractions}, issn = {1932-6203}, doi = {10.1371/journal.pone.0001796}, author = {Mao, Tianyi and O{\textquoteright}Connor, Daniel H and Scheuss, Volker and Nakai, Junichi and Svoboda, Karel} } @article {1732, title = {Characterization of vibrational resonances of water-vapor interfaces by phase-sensitive sum-frequency spectroscopy.}, journal = {Physical Review Letters}, volume = {100}, year = {2008}, month = {2008 Mar 7}, pages = {096102}, abstract = {

Phase-sensitive sum-frequency spectroscopy provides correct characterization of vibrational resonances of water-vapor interfaces and allows better identification of interfacial water species contributing to different parts of the spectra. Iodine ions emerging at an interface create a surface field that tends to reorient the more loosely bonded water molecules below the topmost layer.

}, keywords = {Hydrogen Bonding, Models, Molecular, Spectrum Analysis, Surface Properties, Volatilization, Water}, issn = {0031-9007}, author = {Ji, N and Ostroverkhov, V and Tian, C S and Shen, Y R} } @proceedings {3299, title = {CITRIC: A Low-bandwidth wireless camera network platform.}, year = {2008}, pages = {2008}, abstract = {

In this paper, we propose and demonstrate a novel wireless camera network system, called CITRIC. The core component of this system is a new hardware platform that integrates a camera, a frequency-scalable (up to 624 MHz) CPU, 16MB FLASH, and 64MB RAM onto a single device. The device then connects with a standard sensor network mote to form a camera mote. The design enables in-network processing of images to reduce communication requirements, which has traditionally been high in existing camera networks with centralized processing. We also propose a back-end client/server architecture to provide a user interface to the system and support further centralized processing for higher-level applications. Our camera mote enables a wider variety of distributed pattern recognition applications than traditional platforms because it provides more computing power and tighter integration of physical components while still consuming relatively little power. Furthermore, the mote easily integrates with existing low-bandwidth sensor networks because it can communicate over the IEEE 802.15.4 protocol with other sensor network platforms. We demonstrate our system on three applications: image compression, target tracking, and camera localization.

}, author = {Chen, P and Ahammad, Parvez} } @article {46416, title = {Clathrin dependence of synaptic-vesicle formation at the Drosophila neuromuscular junction.}, journal = {Current Biology}, volume = {18}, year = {2008}, month = {2008 Mar 25}, pages = {401-9}, abstract = {

BACKGROUND: Among the most prominent molecular constituents of a recycling synaptic vesicle is the clathrin triskelion, composed of clathrin light chain (Clc) and clathrin heavy chain (Chc). Remarkably, it remains unknown whether clathrin is strictly necessary for the stimulus-dependent re-formation of a synaptic vesicle and, conversely, whether clathrin-independent vesicle endocytosis exists at the neuronal synapse.

RESULTS: We employ FlAsH-FALI-mediated protein photoinactivation to rapidly (3 min) and specifically disrupt Clc function at the Drosophila neuromuscular junction. We first demonstrate that Clc photoinactivation does not impair synaptic-vesicle fusion. We then provide electrophysiological and ultrastructural evidence that synaptic vesicles, once fused with the plasma membrane, cannot be re-formed after Clc photoinactivation. Finally, we demonstrate that stimulus-dependent membrane internalization occurs after Clc photoinactivation. However, newly internalized membrane fails to resolve into synaptic vesicles. Rather, newly internalized membrane forms large and extensive internal-membrane compartments that are never observed at a wild-type synapse.

CONCLUSIONS: We make three major conclusions. (1) FlAsH-FALI-mediated protein photoinactivation rapidly and specifically disrupts Clc function with no effect on synaptic-vesicle fusion. (2) Synaptic-vesicle re-formation does not occur after Clc photoinactivation. By extension, clathrin-independent "kiss-and-run" endocytosis does not sustain synaptic transmission during a stimulus train at this synapse. (3) Stimulus-dependent, clathrin-independent membrane internalization exists at this synapse, but it is unable to generate fusion-competent, small-diameter synaptic vesicles.

}, keywords = {Animals, Clathrin Light Chains, Drosophila, Electrophysiology, Endocytosis, Fluoresceins, Larva, Neuromuscular Junction, Organometallic Compounds, Synaptic Membranes, Synaptic Transmission, Synaptic Vesicles}, issn = {0960-9822}, doi = {10.1016/j.cub.2008.02.055}, author = {Heerssen, Heather and Fetter, Richard D and Davis, Graeme W} } @article {794, title = {Clonal analysis of Drosophila antennal lobe neurons: diverse neuronal architectures in the lateral neuroblast lineage.}, journal = {Development}, volume = {135}, year = {2008}, month = {2008 Sep}, pages = {2883-93}, abstract = {

The antennal lobe (AL) is the primary structure in the Drosophila brain that relays odor information from the antennae to higher brain centers. The characterization of uniglomerular projection neurons (PNs) and some local interneurons has facilitated our understanding of olfaction; however, many other AL neurons remain unidentified. Because neuron types are mostly specified by lineage and temporal origins, we use the MARCM techniques with a set of enhancer-trap GAL4 lines to perform systematical lineage analysis to characterize neuron morphologies, lineage origin and birth timing in the three AL neuron lineages that contain GAL4-GH146-positive PNs: anterodorsal, lateral and ventral lineages. The results show that the anterodorsal lineage is composed of pure uniglomerular PNs that project through the inner antennocerebral tract. The ventral lineage produces uniglomerular and multiglomerular PNs that project through the middle antennocerebral tract. The lateral lineage generates multiple types of neurons, including uniglomeurlar PNs, diverse atypical PNs, various types of AL local interneurons and the neurons that make no connection within the ALs. Specific neuron types in all three lineages are produced in specific time windows, although multiple neuron types in the lateral lineage are made simultaneously. These systematic cell lineage analyses have not only filled gaps in the olfactory map, but have also exemplified additional strategies used in the brain to increase neuronal diversity.

}, keywords = {Animal Structures, Animals, Axons, Cell Lineage, Clone Cells, Drosophila melanogaster, Enhancer Elements, Genetic, Mosaicism, Neurons}, issn = {0950-1991}, doi = {10.1242/dev.024380}, author = {Lai, Sen-Lin and Awasaki, Takeshi and Ito, Kei and Lee, Tzumin} } @article {2392, title = {Codependent activators direct myoblast-specific MyoD transcription.}, journal = {Developmental Cell}, volume = {15}, year = {2008}, month = {2008 Oct}, pages = {534-46}, abstract = {

Although FoxO and Pax proteins represent two important families of transcription factors in determining cell fate, they had not been functionally or physically linked together in mediating regulation of a common target gene during normal cellular transcription programs. Here, we identify MyoD, a key regulator of myogenesis, as a direct target of FoxO3 and Pax3/7 in myoblasts. Our cell-based assays and in vitro studies reveal a tight codependent partnership between FoxO3 and Pax3/7 to coordinately recruit RNA polymerase II and form a preinitiation complex (PIC) to activate MyoD transcription in myoblasts. The role of FoxO3 in regulating muscle differentiation is confirmed in vivo by observed defects in muscle regeneration caused by MyoD downregulation in FoxO3 null mice. These data establish a mutual interdependence and functional link between two families of transcription activators serving as potential signaling sensors and regulators of cell fate commitment in directing tissue specific MyoD transcription.

}, keywords = {Animals, Cell Line, Forkhead Transcription Factors, Genetic, Immunohistochemistry, Knockout, Mice, Myoblasts, MyoD Protein, Paired Box Transcription Factors, RNA, RNA Interference, Small Interfering, Trans-Activators, Transcription, Transfection}, issn = {1878-1551}, doi = {10.1073/pnas.1100640108}, author = {Hu, Ping and Geles, Kenneth G and Paik, Ji-Hye and DePinho, Ronald A and Tjian, Robert} } @article {2291, title = {Coding and non-coding polymorphisms in alcohol dehydrogenase alters protein expression and alcohol-associated erythema.}, journal = {The Journal of Investigative Dermatology}, volume = {128}, year = {2008}, month = {2008 Mar}, pages = {616-27}, abstract = {

Ethanol (EtOH), isopropyl alcohol (IPA), and propylene glycol (PG) increase topical drug delivery, but are sometimes associated with erythema. A potential genetic basis for alcohol-associated erythema was investigated as the function of polymorphisms in coding and non-coding regions of class IB alcohol dehydrogenase (ADHIB) and evaluated for altered gene expression in vitro and metabolic activity in vivo via altered skin blood flow (Doppler velocimeter) and erythema (reflectance colorimeter a*) following topical challenge to 5 M EtOH, IPA, PG, and butanol (ButOH). Promoter polymorphisms G-887A and C-739T and exon G143A form eight ADHIB haplotypes with different frequencies in Caucasians vs Asians and exhibit variable gene expression and metabolic activity. Polymorphisms C-739T and G-887A independently alter gene expression, which is further increased by IPA and PG, but not EtOH or ButOH. EtOH and ButOH increase erythema as a function of skin blood flow. IPA increases skin blood flow without erythema and PG increased erythema with decreased skin blood flow, all as a function of ADHIB haplotype. PG-induced erythema was uniquely associated with tumor necrosis factor-alpha expression. Thus, erythema following alcohol exposure is alcohol type specific, has a pharmacogenetic basis related to ADHIB haplotype and can be functionally evaluated via Doppler velocimetry and reflectance colorimetry in vivo.

}, keywords = {Administration, Adolescent, Adult, Aged, Alcohol Dehydrogenase, Alcohols, Asian Continental Ancestry Group, Enzymologic, Erythema, European Continental Ancestry Group, Female, Gene Expression Regulation, Gene Frequency, Genetic, Haplotypes, Humans, Laser-Doppler Flowmetry, Male, Middle Aged, Patch Tests, Polymorphism, Promoter Regions, Single Nucleotide, Skin, Topical}, issn = {1523-1747}, doi = {10.1038/sj.jid.5701105}, author = {Pershing, Lynn K and Chen, Yuexian and Tkachuk, Ariana N and Rausch, Holly L and Petelenz-Rubin, Kasia and Corlett, Judy L and Hobbs, Maurine R} } @article {45930, title = {Compartmental neural simulations with spatial adaptivity.}, journal = {Journal of Computational Neuroscience}, volume = {25}, year = {2008}, month = {2008 Dec}, pages = {465-80}, abstract = {

Since their inception, computational models have become increasingly complex and useful counterparts to laboratory experiments within the field of neuroscience. Today several software programs exist to solve the underlying mathematical system of equations, but such programs typically solve these equations in all parts of a cell (or network of cells) simultaneously, regardless of whether or not all of the cell is active. This approach can be inefficient if only part of the cell is active and many simulations must be performed. We have previously developed a numerical method that provides a framework for spatial adaptivity by making the computations local to individual branches rather than entire cells (Rempe and Chopp, SIAM Journal on Scientific Computing, 28: 2139-2161, 2006). Once the computation is reduced to the level of branches instead of cells, spatial adaptivity is straightforward: the active regions of the cell are detected and computational effort is focused there, while saving computations in other regions of the cell that are at or near rest. Here we apply the adaptive method to four realistic neuronal simulation scenarios and demonstrate its improved efficiency over non-adaptive methods. We find that the computational cost of the method scales with the amount of activity present in the simulation, rather than the physical size of the system being simulated. For certain problems spatial adaptivity reduces the computation time by up to 80\%.

}, keywords = {Action Potentials, Adaptation, Biological, Algorithms, Animals, Computer Simulation, Dendrites, Gap Junctions, Hippocampus, Ion Channel Gating, Ion Channels, Models, Neurological, Nerve Net, Neural Networks (Computer), Pyramidal Cells, Signal Processing, Computer-Assisted}, issn = {1573-6873}, doi = {10.1007/s10827-008-0089-3}, author = {Rempe, Michael J and Spruston, Nelson and Kath, William L and Chopp, David L} } @article {3915, title = {Compartmentalized dendritic plasticity and input feature storage in neurons.}, journal = {Nature}, volume = {452}, year = {2008}, month = {2008 Mar 27}, pages = {436-41}, abstract = {

Although information storage in the central nervous system is thought to be primarily mediated by various forms of synaptic plasticity, other mechanisms, such as modifications in membrane excitability, are available. Local dendritic spikes are nonlinear voltage events that are initiated within dendritic branches by spatially clustered and temporally synchronous synaptic input. That local spikes selectively respond only to appropriately correlated input allows them to function as input feature detectors and potentially as powerful information storage mechanisms. However, it is currently unknown whether any effective form of local dendritic spike plasticity exists. Here we show that the coupling between local dendritic spikes and the soma of rat hippocampal CA1 pyramidal neurons can be modified in a branch-specific manner through an N-methyl-d-aspartate receptor (NMDAR)-dependent regulation of dendritic Kv4.2 potassium channels. These data suggest that compartmentalized changes in branch excitability could store multiple complex features of synaptic input, such as their spatio-temporal correlation. We propose that this {\textquoteright}branch strength potentiation{\textquoteright} represents a previously unknown form of information storage that is distinct from that produced by changes in synaptic efficacy both at the mechanistic level and in the type of information stored.

}, keywords = {Action Potentials, Animals, Cell Shape, Dendrites, Ion Channel Gating, Male, Mice, Models, N-Methyl-D-Aspartate, Neurological, Neuronal Plasticity, Pyramidal Cells, Rats, Receptors, Shal Potassium Channels, Sprague-Dawley}, issn = {1476-4687}, doi = {10.1038/nature06725}, author = {Losonczy, Attila and Makara, Judit K and Magee, Jeffrey C} } @article {45965, title = {A conformational switch in bacteriophage p22 portal protein primes genome injection.}, journal = {Molecular Cell}, volume = {29}, year = {2008}, month = {2008 Feb 15}, pages = {376-83}, abstract = {

Double-stranded DNA (dsDNA) viruses such as herpesviruses and bacteriophages infect by delivering their genetic material into cells, a task mediated by a DNA channel called "portal protein." We have used electron cryomicroscopy to determine the structure of bacteriophage P22 portal protein in both the procapsid and mature capsid conformations. We find that, just as the viral capsid undergoes major conformational changes during virus maturation, the portal protein switches conformation from a procapsid to a mature phage state upon binding of gp4, the factor that initiates tail assembly. This dramatic conformational change traverses the entire length of the DNA channel, from the outside of the virus to the inner shell, and erects a large dome domain directly above the DNA channel that binds dsDNA inside the capsid. We hypothesize that this conformational change primes dsDNA for injection and directly couples completion of virus morphogenesis to a new cycle of infection.

}, keywords = {Bacteriophage P22, Binding Sites, Capsid Proteins, DNA, Viral, Genome, Models, Molecular, Protein Binding, Protein Conformation, Viral Tail Proteins}, issn = {1097-2765}, doi = {10.1016/j.molcel.2007.11.034}, author = {Zheng, Hongjin and Olia, Adam S and Gonen, Melissa and Andrews, Simeon and Cingolani, Gino and Gonen, Tamir} } @article {1237, title = {A cost-benefit analysis of neuronal morphology.}, journal = {Journal of Neurophysiology}, volume = {99}, year = {2008}, month = {2008 May}, pages = {2320-8}, abstract = {

Over hundreds of millions of years, evolution has optimized brain design to maximize its functionality while minimizing costs associated with building and maintenance. This observation suggests that one can use optimization theory to rationalize various features of brain design. Here, we attempt to explain the dimensions and branching structure of dendritic arbors by minimizing dendritic cost for given potential synaptic connectivity. Assuming only that dendritic cost increases with total dendritic length and path length from synapses to soma, we find that branching, planar, and compact dendritic arbors, such as those belonging to Purkinje cells in the cerebellum, are optimal. The theory predicts that adjacent Purkinje dendritic arbors should spatially segregate. In addition, we propose two explicit cost function expressions, falsifiable by measuring dendritic caliber near bifurcations.

}, keywords = {Algorithms, Axons, Cerebellum, Cost-Benefit Analysis, Dendrites, Models, Neurological, Neurons, Purkinje Cells, Synapses}, issn = {0022-3077}, doi = {10.1371/journal.pcbi.1001066}, author = {Wen, Quan and Chklovskii, Dmitri B} } @article {46433, title = {Crystallization and preliminary X-ray characterization of full-length Chlamydomonas reinhardtii centrin.}, journal = {Acta Crystallographica Section F Structural Biology and Crystallization Communications}, volume = {64}, year = {2008}, month = {2008 May 1}, pages = {402-4}, abstract = {

Chlamydomonas reinhardtii centrin is a member of the EF-hand calcium-binding superfamily. It is found in the basal body complex and is important for flagellar motility. Like other members of the EF-hand family, centrin interacts with and modulates the function of other proteins in a calcium-dependent manner. To understand how C. reinhardtii centrin interacts with its protein targets, it has been crystallized in the presence of the model peptide melittin and X-ray diffraction data have been collected to 2.2 A resolution. The crystals are orthorhombic, with unit-cell parameters a = 52.1, b = 114.4, c = 34.8 A, and are likely to belong to space group P2(1)2(1)2.

}, keywords = {Animals, Calcium, Calcium-Binding Proteins, Chlamydomonas reinhardtii, Crystallization, Crystallography, X-Ray, Escherichia coli, Melitten, Structure-Activity Relationship}, issn = {1744-3091}, doi = {10.1107/S1744309108009123}, author = {Alfaro, Elisa and Sosa, Liliana Del Valle and Sanoguet, Zuleika and Pastrana-R{\'\i}os, Belinda and Schreiter, Eric R} } @article {1580, title = {Crystallization and preliminary x-ray characterization of the genetically encoded fluorescent calcium indicator protein GCaMP2.}, journal = {Acta Crystallographica. Section F, Structural Biology and Crystallization Communications}, volume = {64}, year = {2008}, month = {2008 Jul 1}, pages = {629-31}, abstract = {

Fluorescent proteins and their engineered variants have played an important role in the study of biology. The genetically encoded calcium-indicator protein GCaMP2 comprises a circularly permuted fluorescent protein coupled to the calcium-binding protein calmodulin and a calmodulin target peptide, M13, derived from the intracellular calmodulin target myosin light-chain kinase and has been used to image calcium transients in vivo. To aid rational efforts to engineer improved variants of GCaMP2, this protein was crystallized in the calcium-saturated form. X-ray diffraction data were collected to 2.0 A resolution. The crystals belong to space group C2, with unit-cell parameters a = 126.1.

}, keywords = {Amino Acid Sequence, Calcium-Calmodulin-Dependent Protein Kinase Type 2, Crystallization, Green Fluorescent Proteins, Indicators and Reagents, Molecular Sequence Data, X-Ray Diffraction}, issn = {1744-3091}, doi = {10.1107/S1744309108016059}, author = {Rodr{\'\i}guez Guilbe, Mar{\'\i}a M and Alfaro Malav{\'e}, Elisa C and Akerboom, Jasper and Marvin, Jonathan S and Looger, Loren L and Schreiter, Eric R} } @article {5349, title = {Data-driven decomposition for multi-class classification.}, journal = {Pattern Recognition}, volume = {41}, year = {2008}, month = {2007 Jun 19}, pages = {67-76}, abstract = {

This paper presents a new study on a method of designing a multi-class classifier: Data-driven Error Correcting Output Coding (DECOC). DECOC is based on the principle of Error Correcting Output Coding (ECOC), which uses a code matrix to decompose a multi-class problem into multiple binary problems. ECOC for multi-class classification hinges on the design of the code matrix. We propose to explore the distribution of data classes and optimize both the composition and the number of base learners to design an effective and compact code matrix. Two real world applications are studied: (1) the holistic recognition (i.e., recognition without segmentation) of touching handwritten numeral pairs and (2) the classification of cancer tissue types based on microarray gene expression data. The results show that the proposed DECOC is able to deliver competitive accuracy compared with other ECOC methods, using parsimonious base learners than the pairwise coupling (one-vs-one) decomposition scheme. With a rejection scheme defined by a simple robustness measure, high reliabilities of around 98\% are achieved in both applications.

}, doi = {10.1016/j.patcog.2007.05.020}, author = {Zhou, Jie and Peng, Hanchuan and Suen, Ching Y.} } @article {2802, title = {Design and characterization of a multisource hand-held tandem mass spectrometer.}, journal = {Analytical Chemistry}, volume = {80}, year = {2008}, month = {2008 Oct 1}, pages = {7198-205}, abstract = {

A wireless-controlled miniature rectilinear ion trap mass spectrometer system, total weight with batteries 5.0 kg, consuming less than 35 W of power, and having dimensions of 22 cm in length by 12 cm in width by 18 cm in height, is characterized. The design and construction of the mass spectrometer including mass analyzer, vacuum system, electronics system, and data acquisition and processing systems, is detailed. The mass spectrometer is compatible with various types of ionization sources including a glow discharge electron impact ionization source used in the internal ionization mode, and various atmospheric pressure ionization sources, including electrospray ionization, atmospheric pressure chemical ionization, and desorption electrospray ionization, which are employed for external, atmospheric pressure ionization. These external sources are coupled to the miniature mass spectrometer via a capillary interface that is operated in a discontinuous fashion (discontinuous atmospheric pressure interface) to maximize ion transport. The performance of the mass spectrometer for large and small molecules is characterized. Limits of detection in the parts-per-billion range were obtained for selected compounds examined using both the internal ionization and external ionization modes. Tandem mass spectrometry and fast in situ analysis capabilities are also demonstrated using a variety of compounds and ionization sources. Protein molecules are analyzed as the multiply protonated molecules with mass/charge ratios up to 1500 Da/charge.

}, keywords = {Miniaturization, Sensitivity and Specificity, Tandem Mass Spectrometry}, issn = {1520-6882}, doi = {10.1364/AO.50.001792}, author = {Gao, Liang and Sugiarto, Andy and Harper, Jason D and Cooks, R Graham and Ouyang, Zheng} } @article {6525, title = {Developmental model of static allometry in holometabolous insects.}, journal = {Proceedings of the Royal Society B: Biological Sciences}, volume = {275}, year = {2008}, month = {2008 Aug 22}, pages = {1875-85}, abstract = {

The regulation of static allometry is a fundamental developmental process, yet little is understood of the mechanisms that ensure organs scale correctly across a range of body sizes. Recent studies have revealed the physiological and genetic mechanisms that control nutritional variation in the final body and organ size in holometabolous insects. The implications these mechanisms have for the regulation of static allometry is, however, unknown. Here, we formulate a mathematical description of the nutritional control of body and organ size in Drosophila melanogaster and use it to explore how the developmental regulators of size influence static allometry. The model suggests that the slope of nutritional static allometries, the {\textquoteright}allometric coefficient{\textquoteright}, is controlled by the relative sensitivity of an organ{\textquoteright}s growth rate to changes in nutrition, and the relative duration of development when nutrition affects an organ{\textquoteright}s final size. The model also predicts that, in order to maintain correct scaling, sensitivity to changes in nutrition varies among organs, and within organs through time. We present experimental data that support these predictions. By revealing how specific physiological and genetic regulators of size influence allometry, the model serves to identify developmental processes upon which evolution may act to alter scaling relationships.

}, keywords = {Animal Nutritional Physiological Phenomena, Animals, Biological, Biometry, Body Size, Drosophila, Metamorphosis, Models, Organ Size}, issn = {0962-8452}, doi = {10.1098/rspb.2008.0227}, author = {Shingleton, Alexander W and Mirth, Christen K and Bates, Peter W} } @article {45932, title = {Distribution of bursting neurons in the CA1 region and the subiculum of the rat hippocampus.}, journal = {Journal of Comparative Neurology}, volume = {506}, year = {2008}, month = {2008 Feb 1}, pages = {535-47}, abstract = {

We performed patch-clamp recordings from morphologically identified and anatomically mapped pyramidal neurons of the ventral hippocampus to test the hypothesis that bursting neurons are distributed on a gradient from the CA2/CA1 border (proximal) through the subiculum (distal), with more bursting observed at distal locations. We find that the well-defined morphological boundaries between the hippocampal subregions CA1 and subiculum do not correspond to abrupt changes in electrophysiological properties. Rather, we observed that the percentage of bursting neurons is linearly correlated with position in the proximal-distal axis across the CA1 and the subiculum, the percentages of bursting neurons being 10\% near the CA1-CA2 border, 24\% at the CA1-subiculum border, and higher than 50\% in the distal subiculum. The distribution of bursting neurons was paralleled by a gradient in afterdepolarization (ADP) amplitude. We also tested the hypothesis that there was an association between bursting and two previously described morphologically distinct groups of pyramidal neurons (twin and single apical dendrites) in the CA1 region. We found no difference in output mode between single and twin apical dendrite morphologies, which was consistent with the observation that the two morphologies were equally distributed across the transverse axis of the CA1 region. Taken together with the known organization of connections from CA3 to CA1 and CA1 to subiculum, our results indicate that bursting neurons are most likely to be connected to regular spiking neurons and vice versa.

}, keywords = {Action Potentials, Animals, Axons, Cell Shape, Dendrites, Hippocampus, Lysine, Neural Pathways, Organ Culture Techniques, Patch-Clamp Techniques, Pyramidal Cells, Rats, Rats, Wistar, Staining and Labeling}, issn = {0021-9967}, doi = {10.1002/cne.21564}, author = {Jarsky, Tim and Mady, Rina and Kennedy, Benjamin and Spruston, Nelson} } @article {5818, title = {Dynamics of zebrafish somitogenesis.}, journal = {Developmental Dynamics}, volume = {237}, year = {2008}, month = {2008 Mar}, pages = {545-53}, abstract = {

Vertebrate somitogenesis is a rhythmically repeated morphogenetic process. The dependence of somitogenesis dynamics on axial position and temperature has not been investigated systematically in any species. Here we use multiple embryo time-lapse imaging to precisely estimate somitogenesis period and somite length under various conditions in the zebrafish embryo. Somites form at a constant period along the trunk, but the period gradually increases in the tail. Somite length varies along the axis in a stereotypical manner, with tail somites decreasing in size. Therefore, our measurements prompt important modifications to the steady-state Clock and Wavefront model: somitogenesis period, somite length, and wavefront velocity all change with axial position. Finally, we show that somitogenesis period changes more than threefold across the standard developmental temperature range, whereas the axial somite length distribution is temperature invariant. This finding indicates that the temperature-induced change in somitogenesis period exactly compensates for altered axial growth.

}, keywords = {Animals, Body Patterning, Embryonic Development, Morphogenesis, Somites, Zebrafish}, issn = {1058-8388}, doi = {10.1002/dvdy.21458}, author = {Schr{\"o}ter, Christian and Herrgen, Leah and Cardona, Albert and Brouhard, Gary J and Feldman, Benjamin and Oates, Andrew C} } @article {45966, title = {Electron crystallography of aquaporins.}, journal = {IUBMB Life}, volume = {60}, year = {2008}, month = {2008 Jul}, pages = {430-6}, abstract = {

Aquaporins are a family of ubiquitous membrane proteins that form a pore for the permeation of water. Both electron and X-ray crystallography played major roles in determining the atomic structures of a number of aquaporins. This review focuses on electron crystallography, and its contribution to the field of aquaporin biology. We briefly discuss electron crystallography and the two-dimensional crystallization process. We describe features of aquaporins common to both electron and X-ray crystallographic structures; as well as some structural insights unique to electron crystallography, including aquaporin junction formation and lipid-protein interactions.

}, keywords = {Animals, Aquaporins, Cell Membrane, Crystallization, Crystallography, Crystallography, X-Ray, Electrons, Humans, Lipids, Models, Molecular, Protein Conformation, Protein Folding, Proteins, Water}, issn = {1521-6551}, doi = {10.1002/iub.53}, author = {Andrews, Simeon and Reichow, Steve L and Gonen, Tamir} } @article {1437, title = {Electrostatic readout of DNA microarrays with charged microspheres.}, journal = {Nature Biotechnology}, volume = {26}, year = {2008}, month = {2008 Jul}, pages = {825-30}, abstract = {

DNA microarrays are used for gene-expression profiling, single-nucleotide polymorphism detection and disease diagnosis. A persistent challenge in this area is the lack of microarray screening technology suitable for integration into routine clinical care. Here, we describe a method for sensitive and label-free electrostatic readout of DNA or RNA hybridization on microarrays. The electrostatic properties of the microarray are measured from the position and motion of charged microspheres randomly dispersed over the surface. We demonstrate nondestructive electrostatic imaging with 10-mum lateral resolution over centimeter-length scales, which is four-orders of magnitude larger than that achievable with conventional scanning electrostatic force microscopy. Changes in surface charge density as a result of specific hybridization can be detected and quantified with 50-pM sensitivity, single base-pair mismatch selectivity and in the presence of complex background. Because the naked eye is sufficient to read out hybridization, this approach may facilitate broad application of multiplexed assays.

}, keywords = {Computer-Assisted, Gene Expression Profiling, Image Interpretation, Microspheres, Oligonucleotide Array Sequence Analysis, Static Electricity}, issn = {1546-1696}, doi = {10.1038/nbt1416}, author = {Clack, Nathan G and Salaita, Khalid and Groves, Jay T} } @article {2396, title = {ES cell pluripotency and germ-layer formation require the SWI/SNF chromatin remodeling component BAF250a.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, year = {2008}, month = {2008 May 6}, pages = {6656-61}, abstract = {

ATP-dependent chromatin remodeling complexes are a notable group of epigenetic modifiers that use the energy of ATP hydrolysis to change the structure of chromatin, thereby altering its accessibility to nuclear factors. BAF250a (ARID1a) is a unique and defining subunit of the BAF chromatin remodeling complex with the potential to facilitate chromosome alterations critical during development. Our studies show that ablation of BAF250a in early mouse embryos results in developmental arrest (about embryonic day 6.5) and absence of the mesodermal layer, indicating its critical role in early germ-layer formation. Moreover, BAF250a deficiency compromises ES cell pluripotency, severely inhibits self-renewal, and promotes differentiation into primitive endoderm-like cells under normal feeder-free culture conditions. Interestingly, this phenotype can be partially rescued by the presence of embryonic fibroblast cells. DNA microarray, immunostaining, and RNA analyses revealed that BAF250a-mediated chromatin remodeling contributes to the proper expression of numerous genes involved in ES cell self-renewal, including Sox2, Utf1, and Oct4. Furthermore, the pluripotency defects in BAF250a mutant ES cells appear to be cell lineage-specific. For example, embryoid body-based analyses demonstrated that BAF250a-ablated stem cells are defective in differentiating into fully functional mesoderm-derived cardiomyocytes and adipocytes but are capable of differentiating into ectoderm-derived neurons. Our results suggest that BAF250a is a key component of the gene regulatory machinery in ES cells controlling self-renewal, differentiation, and cell lineage decisions.

}, keywords = {Adipocytes, Animals, Cardiac, Cell Differentiation, Cell Line, Cell Lineage, Cell Proliferation, Chromatin Assembly and Disassembly, Chromosomal Proteins, Developmental, DNA-Binding Proteins, Embryo, Embryonic Development, Embryonic Stem Cells, Female, Genes, Germ Layers, Knockout, Male, Mammalian, Mice, Muscle, Myocytes, Non-Histone, Nuclear Proteins, Pluripotent Stem Cells, Skeletal, Transcription Factors}, issn = {1091-6490}, doi = {10.1073/pnas.1100640108}, author = {Gao, Xiaolin and Tate, Peri and Hu, Ping and Tjian, Robert and Skarnes, William C and Wang, Zhong} } @article {1099, title = {Ester bonds in prodrugs.}, journal = {ACS Chemical Biology}, volume = {3}, year = {2008}, month = {2008 Apr 18}, pages = {203-6}, abstract = {

A recent study challenges the oft-held notion that ester bonds in prodrug molecules are cleaved rapidly and completely inside cells by endogenous, nonspecific esterases. Structure-activity relationship studies on acylated sugars reveal that regioisomeric compounds display disparate biological activity, suggesting that ester bonds can persist in a cellular context.

}, keywords = {Esters, Prodrugs, Structure-Activity Relationship}, issn = {1554-8937}, doi = {10.1021/cb800065s}, author = {Lavis, Luke D} } @article {46624, title = {Ethanol sensitivity and tolerance in long-term memory mutants of Drosophila melanogaster.}, journal = {Alcoholism, Clinical and Experimental Research}, volume = {32}, year = {2008}, month = {2008 May}, pages = {895-908}, abstract = {

BACKGROUND: It has become increasingly clear that molecular and neural mechanisms underlying learning and memory and drug addiction are largely shared. To confirm and extend these findings, we analyzed ethanol-responsive behaviors of a collection of Drosophila long-term memory mutants.

METHODS: For each mutant, sensitivity to the acute uncoordinating effects of ethanol was quantified using the inebriometer. Additionally, 2 distinct forms of ethanol tolerance were measured: rapid tolerance, which develops in response to a single brief exposure to a high concentration of ethanol vapor; and chronic tolerance, which develops following a sustained low-level exposure.

RESULTS: Several mutants were identified with altered sensitivity, rapid or chronic tolerance, while a number of mutants exhibited multiple defects.

CONCLUSIONS: The corresponding genes in these mutants represent areas of potential overlap between learning and memory and behavioral responses to alcohol. These genes also define components shared between different ethanol behavioral responses.

}, keywords = {Animals, Behavior, Animal, Drosophila melanogaster, Drug Tolerance, Ethanol, Learning, Memory}, issn = {1530-0277}, doi = {10.1111/j.1530-0277.2008.00659.x}, author = {Berger, Karen H and Kong, Eric C and Dubnau, Josh and Tully, Tim and Moore, Monica S and Heberlein, Ulrike} } @article {5827, title = {Evaluating automated parameter constraining procedures of neuron models by experimental and surrogate data.}, journal = {Biological Cybernetics}, volume = {99}, year = {2008}, month = {2008 Nov}, pages = {371-9}, abstract = {

Neuron models, in particular conductance-based compartmental models, often have numerous parameters that cannot be directly determined experimentally and must be constrained by an optimization procedure. A common practice in evaluating the utility of such procedures is using a previously developed model to generate surrogate data (e.g., traces of spikes following step current pulses) and then challenging the algorithm to recover the original parameters (e.g., the value of maximal ion channel conductances) that were used to generate the data. In this fashion, the success or failure of the model fitting procedure to find the original parameters can be easily determined. Here we show that some model fitting procedures that provide an excellent fit in the case of such model-to-model comparisons provide ill-balanced results when applied to experimental data. The main reason is that surrogate and experimental data test different aspects of the algorithm{\textquoteright}s function. When considering model-generated surrogate data, the algorithm is required to locate a perfect solution that is known to exist. In contrast, when considering experimental target data, there is no guarantee that a perfect solution is part of the search space. In this case, the optimization procedure must rank all imperfect approximations and ultimately select the best approximation. This aspect is not tested at all when considering surrogate data since at least one perfect solution is known to exist (the original parameters) making all approximations unnecessary. Furthermore, we demonstrate that distance functions based on extracting a set of features from the target data (such as time-to-first-spike, spike width, spike frequency, etc.){\textendash}rather than using the original data (e.g., the whole spike trace) as the target for fitting-are capable of finding imperfect solutions that are good approximations of the experimental data.

}, keywords = {Algorithms, Animals, Models, Neocortex, Neurological, Neurons, Organ Culture Techniques, Patch-Clamp Techniques, Rats, Wistar}, issn = {1432-0770}, doi = {10.1007/s00422-008-0269-2}, author = {Druckmann, Shaul and Berger, Thomas K and Hill, Sean and Sch{\"u}rmann, Felix and Markram, Henry and Segev, Idan} } @article {4638, title = {Even illumination in total internal reflection fluorescence microscopy using laser light.}, journal = {Microscopy Research and Technique}, volume = {71}, year = {2008}, month = {2008 Jan}, pages = {45-50}, abstract = {

In modern fluorescence microscopy, lasers are a widely used source of light, both for imaging in total internal reflection and epi-illumination modes. In wide-field imaging, scattering of highly coherent laser light due to imperfections in the light path typically leads to nonuniform illumination of the specimen, compromising image analysis. We report the design and construction of an objective-launch total internal reflection fluorescence microscopy system with excellent evenness of specimen illumination achieved by azimuthal rotation of the incoming illuminating laser beam. The system allows quick and precise changes of the incidence angle of the laser beam and thus can also be used in an epifluorescence mode.

}, keywords = {Fluorescence, Lasers, Microscopy, Reproducibility of Results}, issn = {1059-910X}, doi = {10.1002/jemt.20527}, author = {Fiolka, R and Belyaev, Y and Ewers, H and Stemmer, A} } @article {2012, title = {Fast monte carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces.}, journal = {SIAM Journal on Scientific Computing: A Publication of the Society for Industrial and Applied Mathematics}, volume = {30}, year = {2008}, month = {2008 Oct 13}, pages = {3126}, abstract = {

Many important physiological processes operate at time and space scales far beyond those accessible to atom-realistic simulations, and yet discrete stochastic rather than continuum methods may best represent finite numbers of molecules interacting in complex cellular spaces. We describe and validate new tools and algorithms developed for a new version of the MCell simulation program (MCell3), which supports generalized Monte Carlo modeling of diffusion and chemical reaction in solution, on surfaces representing membranes, and combinations thereof. A new syntax for describing the spatial directionality of surface reactions is introduced, along with optimizations and algorithms that can substantially reduce computational costs (e.g., event scheduling, variable time and space steps). Examples for simple reactions in simple spaces are validated by comparison to analytic solutions. Thus we show how spatially realistic Monte Carlo simulations of biological systems can be far more cost-effective than often is assumed, and provide a level of accuracy and insight beyond that of continuum methods.

}, issn = {1095-7197}, doi = {10.1137/070692017}, author = {Kerr, Rex A and Bartol, Thomas M and Kaminsky, Boris and Dittrich, Markus and Chang, Jen-Chien Jack and Baden, Scott B and Sejnowski, Terrence J and Stiles, Joel R} } @proceedings {46795, title = {Fast stitching of large 3d biological datasets.}, year = {2008}, month = {2008 Nov 7}, address = {Luxembourg}, abstract = {

In order to study anatomy of organisms with high-resolution there is an increasing demand to image large specimen in three dimensions (3D). Confocal microscopy is able to produce high-resolution 3D images, but these are limited by its relatively small field of view compared to the size of large biological specimens. To overcome this drawback, motorized stages moving the sample are used to create a tiled scan of the whole specimen. The physical coordinates provided by the microscope stage are not precise enough to allow reconstruction ({\textquotedblright}Stitching{\textquotedblright}) of the whole image from individual image stacks.
We developed an algorithm, as well as an ImageJ plug-in, based on the Fourier Shift Theorem that computes all possible translations (x, y, z) between two 3D images at once, yielding the best overlap in terms of the cross correlation measure. Apart from the obvious gain in computation time it has the advantage that it cannot be trapped in local minima as it simply computes all possible solutions. Computing the overlap between two adjacent image stacks is fast (12 seconds for two 512x512x89 images on a Intel {\textregistered} Core2Duo with 2.2GHz) making it suitable for real time use, i.e. computing the output image during acquisition of the individual image stacks.
To compensate the possible shading- and brightness differences we apply a smooth linear intensity transition between the overlapping stacks. Additionally we extended the to generic 3D registration using gradient based rotation detection on top of the phase correlation method. We demonstrate the performance of our 3D stitching plug-in on several tiled confocal images and show an example of its application for 3D registration.

}, author = {Preibisch, Stephan and Saalfeld, Stephan and Tomancak, Pavel} } @article {2186, title = {A FLEX switch targets Channelrhodopsin-2 to multiple cell types for imaging and long-range circuit mapping.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {28}, year = {2008}, month = {2008 Jul 9}, pages = {7025-30}, keywords = {3-dione, 6-Cyano-7-nitroquinoxaline-2, Animals, Arcuate Nucleus, Brain Mapping, Cell Line, Computer-Assisted, Dependovirus, Diagnostic Imaging, Excitatory Amino Acid Antagonists, Gene Expression Regulation, Green Fluorescent Proteins, Humans, Image Processing, Membrane Potentials, Mice, Nerve Net, Patch-Clamp Techniques, Photic Stimulation, Rhodopsin, Transfection, Transformed, Transgenic}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.1954-08.2008}, author = {Atasoy, Deniz and Aponte, Yexica and Su, Helen Hong and Sternson, Scott M} } @article {2394, title = {The future for Howard Hughes. Interview by Erika Check Hayden.}, journal = {Nature}, volume = {455}, year = {2008}, month = {2008 Oct 9}, pages = {718}, keywords = {Academies and Institutes, Creativeness, Disease, Humans, Internationality, Maryland, Molecular Biology, Research, Research Personnel}, issn = {1476-4687}, doi = {10.1073/pnas.1100640108}, author = {Tjian, Robert} } @article {4257, title = {Genetic dissection of neural circuits.}, journal = {Neuron}, volume = {57}, year = {2008}, month = {2008 Mar 13}, pages = {634-60}, abstract = {

Understanding the principles of information processing in neural circuits requires systematic characterization of the participating cell types and their connections, and the ability to measure and perturb their activity. Genetic approaches promise to bring experimental access to complex neural systems, including genetic stalwarts such as the fly and mouse, but also to nongenetic systems such as primates. Together with anatomical and physiological methods, cell-type-specific expression of protein markers and sensors and transducers will be critical to construct circuit diagrams and to measure the activity of genetically defined neurons. Inactivation and activation of genetically defined cell types will establish causal relationships between activity in specific groups of neurons, circuit function, and animal behavior. Genetic analysis thus promises to reveal the logic of the neural circuits in complex brains that guide behaviors. Here we review progress in the genetic analysis of neural circuits and discuss directions for future research and development.

}, keywords = {Animals, Gene Expression Regulation, Humans, Nerve Net, Neural Pathways, Neurons}, issn = {1097-4199}, doi = {10.1016/j.neuron.2008.01.002}, author = {Luo, Liqun and Callaway, Edward M and Svoboda, Karel} } @article {46625, title = {Genetic dissociation of ethanol sensitivity and memory formation in Drosophila melanogaster.}, journal = {Genetics}, volume = {178}, year = {2008}, month = {2008 Apr}, pages = {1895-902}, abstract = {

The ad hoc genetic correlation between ethanol sensitivity and learning mechanisms in Drosophila could overemphasize a common process supporting both behaviors. To challenge directly the hypothesis that these mechanisms are singular, we examined the learning phenotypes of 10 new strains. Five of these have increased ethanol sensitivity, and the other 5 do not. We tested place and olfactory memory in each of these lines and found two new learning mutations. In one case, altering the tribbles gene, flies have a significantly reduced place memory, elevated olfactory memory, and normal ethanol response. In the second case, mutation of a gene we name ethanol sensitive with low memory (elm), place memory was not altered, olfactory memory was sharply reduced, and sensitivity to ethanol was increased. In sum, however, we found no overall correlation between ethanol sensitivity and place memory in the 10 lines tested. Furthermore, there was a weak but nonsignificant correlation between ethanol sensitivity and olfactory learning. Thus, mutations that alter learning and sensitivity to ethanol can occur independently of each other and this implies that the set of genes important for both ethanol sensitivity and learning is likely a subset of the genes important for either process.

}, keywords = {Animals, Behavior, Animal, Cell Cycle Proteins, DNA Transposable Elements, Drosophila melanogaster, Drosophila Proteins, Ethanol, Gene Expression Regulation, Head, Memory, Mutagenesis, Insertional, Phenotype, Protein-Serine-Threonine Kinases, RNA, Messenger}, issn = {0016-6731}, doi = {10.1534/genetics.107.084582}, author = {LaFerriere, Holly and Guarnieri, Douglas J and Sitaraman, Divya and Diegelmann, Soeren and Heberlein, Ulrike and Zars, Troy} } @article {4254, title = {A genetically encoded fluorescent sensor of ERK activity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, year = {2008}, month = {2008 Dec 9}, pages = {19264-9}, abstract = {

The activity of the ERK has complex spatial and temporal dynamics that are important for the specificity of downstream effects. However, current biochemical techniques do not allow for the measurement of ERK signaling with fine spatiotemporal resolution. We developed a genetically encoded, FRET-based sensor of ERK activity (the extracellular signal-regulated kinase activity reporter, EKAR), optimized for signal-to-noise ratio and fluorescence lifetime imaging. EKAR selectively and reversibly reported ERK activation in HEK293 cells after epidermal growth factor stimulation. EKAR signals were correlated with ERK phosphorylation, required ERK activity, and did not report the activities of JNK or p38. EKAR reported ERK activation in the dendrites and nucleus of hippocampal pyramidal neurons in brain slices after theta-burst stimuli or trains of back-propagating action potentials. EKAR therefore permits the measurement of spatiotemporal ERK signaling dynamics in living cells, including in neuronal compartments in intact tissues.

}, keywords = {Action Potentials, Animals, Artifacts, Bacterial Proteins, Cell Line, Dendrites, Endothelial Cells, Enzyme Activation, Extracellular Signal-Regulated MAP Kinases, Fluorescence Resonance Energy Transfer, Fluorescent Dyes, Genes, Green Fluorescent Proteins, Hippocampus, Humans, Kidney, Luminescent Proteins, MAP Kinase Signaling System, Organ Culture Techniques, Patch-Clamp Techniques, Pyramidal Cells, Rats, Reporter}, issn = {1091-6490}, doi = {10.1073/pnas.0804598105}, author = {Harvey, Christopher D and Ehrhardt, Anka G and Cellurale, Cristina and Zhong, Haining and Yasuda, Ryohei and Davis, Roger J and Svoboda, Karel} } @article {3932, title = {Genetically encoded fluorescent sensors for studying healthy and diseased nervous systems.}, journal = {Drug Discovery Today. Disease Models}, volume = {5}, year = {2008}, month = {2008}, pages = {27-35}, abstract = {

Neurons and glia are functionally organized into circuits and higher-order structures via synaptic connectivity, well-orchestrated molecular signaling, and activity-dependent refinement. Such organization allows the precise information processing required for complex behaviors. Disruption of nervous systems by genetic deficiency or events such as trauma or environmental exposure may produce a diseased state in which certain aspects of inter-neuron signaling are impaired. Optical imaging techniques allow the direct visualization of individual neurons in a circuit environment. Imaging probes specific for given biomolecules may help elucidate their contribution to proper circuit function. Genetically encoded sensors can visualize trafficking of particular molecules in defined neuronal populations, non-invasively in intact brain or reduced preparations. Sensor analysis in healthy and diseased brains may reveal important differences and shed light on the development and progression of nervous system disorders. We review the field of genetically encoded sensors for molecules and cellular events, and their potential applicability to the study of nervous system disease.

}, issn = {1740-6757}, doi = {10.1016/j.ddmod.2008.07.003}, author = {Tian, Lin and Looger, Loren L} } @article {2679, title = {Genomic analysis of Drosophila neuronal remodeling: a role for the RNA-binding protein Boule as a negative regulator of axon pruning.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {28}, year = {2008}, month = {2008 Jun 11}, pages = {6092-103}, abstract = {

Drosophila mushroom body (MB) gamma neurons undergo axon pruning during metamorphosis through a process of localized degeneration of specific axon branches. Developmental axon degeneration is initiated by the steroid hormone ecdysone, acting through a nuclear receptor complex composed of USP (ultraspiracle) and EcRB1 (ecdysone receptor B1) to regulate gene expression in MB gamma neurons. To identify ecdysone-dependent gene expression changes in MB gamma neurons at the onset of axon pruning, we use laser capture microdissection to isolate wild-type and mutant MB neurons in which EcR (ecdysone receptor) activity is genetically blocked, and analyze expression changes by microarray. We identify several molecular pathways that are regulated in MB neurons by ecdysone. The most striking observation is the upregulation of genes involved in the UPS (ubiquitin-proteasome system), which is cell autonomously required for gamma neuron pruning. In addition, we characterize the function of Boule, an evolutionarily conserved RNA-binding protein previously implicated in spermatogenesis in flies and vertebrates. boule expression is downregulated by ecdysone in MB neurons at the onset of pruning, and forced expression of Boule in MB gamma neurons is sufficient to inhibit axon pruning. This activity is dependent on the RNA-binding domain of Boule and a conserved DAZ (deleted in azoospermia) domain implicated in interactions with other RNA-binding proteins. However, loss of Boule does not result in obvious defects in axon pruning or morphogenesis of MB neurons, suggesting that it acts redundantly with other ecdyonse-regulated genes. We propose a novel function for Boule in the CNS as a negative regulator of developmental axon pruning.

}, keywords = {Animals, Antigens, Axons, CD8, Developmental, Drosophila, Drosophila Proteins, Ecdysone, Gene Expression Regulation, Genetically Modified, Genomics, Green Fluorescent Proteins, Larva, Microarray Analysis, Mushroom Bodies, Mutation, Neurons, Receptors, RNA-Binding Proteins, Steroid}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0677-08.2008}, author = {Hoopfer, Eric D and Penton, Andrea and Watts, Ryan J and Luo, Liqun} } @article {6502, title = {GFP Reconstitution Across Synaptic Partners (GRASP) defines cell contacts and synapses in living nervous systems.}, journal = {Neuron}, volume = {57}, year = {2008}, month = {2008 Feb 7}, pages = {353-63}, abstract = {

The identification of synaptic partners is challenging in dense nerve bundles, where many processes occupy regions beneath the resolution of conventional light microscopy. To address this difficulty, we have developed GRASP, a system to label membrane contacts and synapses between two cells in living animals. Two complementary fragments of GFP are expressed on different cells, tethered to extracellular domains of transmembrane carrier proteins. When the complementary GFP fragments are fused to ubiquitous transmembrane proteins, GFP fluorescence appears uniformly along membrane contacts between the two cells. When one or both GFP fragments are fused to synaptic transmembrane proteins, GFP fluorescence is tightly localized to synapses. GRASP marks known synaptic contacts in C. elegans, correctly identifies changes in mutants with altered synaptic specificity, and can uncover new information about synaptic locations as confirmed by electron microscopy. GRASP may prove particularly useful for defining connectivity in complex nervous systems.

}, keywords = {Animal, Animals, Behavior, Biological, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Carrier Proteins, Cells, Cultured, Electron, Genetically Modified, Green Fluorescent Proteins, Microscopy, Models, Mutation, Nervous System, Neurons, Synapses}, issn = {0896-6273}, doi = {10.1016/j.neuron.2007.11.030}, author = {Feinberg, Evan H and Vanhoven, Miri K and Bendesky, Andres and Wang, George and Fetter, Richard D and Shen, Kang and Bargmann, Cornelia I} } @conference {3298, title = {High speed action recognition and localization in compressed domain videos.}, booktitle = {IEEE Transactions on Circuits and Systems for Video Technology: Special issue on Video Surveillance}, year = {2008}, month = {2008 Aug}, abstract = {

We present a compressed domain scheme that is able to recognize and localize actions at high speeds. The recognition problem is posed as performing an action video query on a test video sequence. Our method is based on computing motion similarity using compressed domain features which can be extracted with low complexity. We introduce a novel motion correlation measure that takes into account differences in motion directions and magnitudes. Our method is appearance invariant, requires no prior segmentation, alignment or stabilization, and is able to localize actions in both space and time. We evaluated our method on a benchmark action video database consisting of 6 actions performed by 25 people under 3 different scenarios. Our proposed method achieved a classification accuracy of 90\%, comparing favorably with existing methods in action classification accuracy, and is able to localize a template video of 80 x 64 pixels with 23 frames in a test video of 368 x 184 pixels with 835 frames in just 11 seconds, easily outperforming other methods in localization speed. We also perform a systematic investigation of the effects of various encoding options on our proposed approach. In particular, we present results on the compression-classification trade-off, which would provide valuable insight into jointly designing a system that performs video encoding at the camera front-end and action classification at the processing backend.

}, author = {Yeo, C and Ahammad, Parvez and Ramchandran, K and Sastry, S} } @article {2080, title = {High-density mapping of single-molecule trajectories with photoactivated localization microscopy. (With commentary)}, journal = {Nature Methods}, volume = {5}, year = {2008}, month = {2008 Feb}, pages = {155-7}, abstract = {

We combined photoactivated localization microscopy (PALM) with live-cell single-particle tracking to create a new method termed sptPALM. We created spatially resolved maps of single-molecule motions by imaging the membrane proteins Gag and VSVG, and obtained several orders of magnitude more trajectories per cell than traditional single-particle tracking enables. By probing distinct subsets of molecules, sptPALM can provide insight into the origins of spatial and temporal heterogeneities in membranes.

Commentary: As a stepping stone to true live cell PALM (see above), our collaborator Jennifer Lippincott-Schwartz suggested using the sparse photoactivation principle of PALM to track the nanoscale motion of thousands of individual molecules within a single living cell. Termed single particle tracking PALM (sptPALM), Jennifer{\textquoteright}s postdocs Suliana Manley and Jen Gillette used the method in our PALM rig to create spatially resolved maps of diffusion rates in the plasma membrane of live cells. sptPALM is a powerful tool to study the active cytoskeletal or passive diffusional transport of individual molecules with far more measurements per cell than is possible without sparse photoactivation.

}, keywords = {Animals, Cercopithecus aethiops, COS Cells, Fluorescence, Image Enhancement, Membrane Proteins, Microscopy}, issn = {1548-7105}, doi = {10.1038/nmeth.1176}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18193054}, author = {Manley, Suliana and Gillette, Jennifer M and Patterson, George H and Shroff, Hari and Hess, Harald F and Betzig, Eric and Lippincott-Schwartz, Jennifer} } @article {1098, title = {A highly sensitive fluorogenic probe for cytochrome P450 activity in live cells.}, journal = {Bioorganic \& Medicinal Chemistry Letters}, volume = {18}, year = {2008}, month = {2008 Nov 15}, pages = {5864-6}, abstract = {

A derivative of rhodamine 110 has been designed and assessed as a probe for cytochrome P450 activity. This probe is the first to utilize a {\textquoteright}trimethyl lock{\textquoteright} that is triggered by cleavage of an ether bond. In vitro, fluorescence was manifested by the CYP1A1 isozyme with k(cat)/K(M)=8.8x10(3)M(-1)s(-1) and K(M)=0.09microM. In cellulo, the probe revealed the induction of cytochrome P450 activity by the carcinogen 2,3,7,8-tetrachlorodibenzo-p-dioxin, and its repression by the chemoprotectant resveratrol.

}, keywords = {Cytochrome P-450 CYP1A1, Cytochrome P-450 Enzyme System, Fluorescent Dyes, Humans, Isoenzymes, Molecular Structure, Prodrugs, Rhodamines, Stilbenes, Structure-Activity Relationship, Tetrachlorodibenzodioxin}, issn = {1464-3405}, doi = {10.1016/j.bmcl.2008.06.015}, author = {Yatzeck, Melissa M and Lavis, Luke D and Chao, Tzu-Yuan and Chandran, Sunil S and Raines, Ronald T} } @article {2081, title = {High-speed, low-photodamage nonlinear imaging using passive pulse splitters. (With commentary)}, journal = {Nature Methods}, volume = {5}, year = {2008}, month = {2008 Feb}, pages = {197-202}, abstract = {

Pulsed lasers are key elements in nonlinear bioimaging techniques such as two-photon fluorescence excitation (TPE) microscopy. Typically, however, only a percent or less of the laser power available can be delivered to the sample before photoinduced damage becomes excessive. Here we describe a passive pulse splitter that converts each laser pulse into a fixed number of sub-pulses of equal energy. We applied the splitter to TPE imaging of fixed mouse brain slices labeled with GFP and show that, in different power regimes, the splitter can be used either to increase the signal rate more than 100-fold or to reduce the rate of photobleaching by over fourfold. In living specimens, the gains were even greater: a ninefold reduction in photobleaching during in vivo imaging of Caenorhabditis elegans larvae, and a six- to 20-fold decrease in the rate of photodamage during calcium imaging of rat hippocampal brain slices.

Commentary: Na Ji came to me early in her postdoc with an idea to reduce photodamage in nonlinear microscopy by splitting the pulses from an ultrafast laser into multiple subpulses of reduced energy. In six weeks, we constructed a prototype pulse splitter and obtained initial results confirming the validity of her vision. Further experiments with Jeff Magee demonstrated that the splitter could be used to increase imaging speed or reduce photodamage in two photon microscopy by one to two orders of magnitude. This project is a great example of how quickly one can react and exploit new ideas in the Janelia environment.

}, keywords = {Animals, Caenorhabditis elegans, Cell Survival, Cells, Cultured, Equipment Design, Equipment Failure Analysis, Fluorescence, Image Enhancement, Lasers, Light, Lighting, Mice, Microscopy, Nonlinear Dynamics, Rats}, issn = {1548-7105}, doi = {10.1038/nmeth.1175}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18204458}, author = {Ji, Na and Magee, Jeffrey C and Betzig, Eric} } @article {3916, title = {High-speed, low-photodamage nonlinear imaging using passive pulse splitters.}, journal = {Nature Methods}, volume = {5}, year = {2008}, month = {2008 Feb}, pages = {197-202}, abstract = {

Pulsed lasers are key elements in nonlinear bioimaging techniques such as two-photon fluorescence excitation (TPE) microscopy. Typically, however, only a percent or less of the laser power available can be delivered to the sample before photoinduced damage becomes excessive. Here we describe a passive pulse splitter that converts each laser pulse into a fixed number of sub-pulses of equal energy. We applied the splitter to TPE imaging of fixed mouse brain slices labeled with GFP and show that, in different power regimes, the splitter can be used either to increase the signal rate more than 100-fold or to reduce the rate of photobleaching by over fourfold. In living specimens, the gains were even greater: a ninefold reduction in photobleaching during in vivo imaging of Caenorhabditis elegans larvae, and a six- to 20-fold decrease in the rate of photodamage during calcium imaging of rat hippocampal brain slices.

}, keywords = {Animals, Caenorhabditis elegans, Cell Survival, Cells, Cultured, Equipment Design, Equipment Failure Analysis, Fluorescence, Image Enhancement, Lasers, Light, Lighting, Mice, Microscopy, Nonlinear Dynamics, Rats}, issn = {1548-7105}, doi = {10.1038/nmeth.1175}, author = {Ji, Na and Magee, Jeffrey C and Betzig, Eric} } @article {2959, title = {I5S: wide-field light microscopy with 100-nm-scale resolution in three dimensions.}, journal = {Biophysical Journal}, volume = {94}, year = {2008}, month = {2008 Jun}, pages = {4971-83}, abstract = {

A new type of wide-field fluorescence microscopy is described, which produces 100-nm-scale spatial resolution in all three dimensions, by using structured illumination in a microscope that has two opposing objective lenses. Illumination light is split by a grating and a beam splitter into six mutually coherent beams, three of which enter the specimen through each objective lens. The resulting illumination intensity pattern contains high spatial frequency components both axially and laterally. In addition, the emission is collected by both objective lenses coherently, and combined interferometrically on a single camera, resulting in a detection transfer function with axially extended support. These two effects combine to produce near-isotropic resolution. Experimental images of test samples and biological specimens confirm the theoretical predictions.

}, keywords = {Equipment Design, Equipment Failure Analysis, Image Enhancement, Imaging, Lenses, Microscopy, Nanotechnology, Reproducibility of Results, Sensitivity and Specificity, Three-Dimensional}, issn = {1542-0086}, doi = {10.1529/biophysj.107.120352}, author = {Shao, Lin and Isaac, Berith and Uzawa, Satoru and Agard, David A and Sedat, John W and Gustafsson, Mats G L} } @article {2347, title = {Induction of muscle thermogenesis by high-fat diet in mice: association with obesity-resistance.}, journal = {American Journal of Physiology. Endocrinology and Metabolism}, volume = {295}, year = {2008}, month = {2008 Aug}, pages = {E356-67}, abstract = {

The obesogenic effect of a high-fat (HF) diet is counterbalanced by stimulation of energy expenditure and lipid oxidation in response to a meal. The aim of this study was to reveal whether muscle nonshivering thermogenesis could be stimulated by a HF diet, especially in obesity-resistant A/J compared with obesity-prone C57BL/6J (B/6J) mice. Experiments were performed on male mice born and maintained at 30 degrees C. Four-week-old mice were randomly weaned onto a low-fat (LF) or HF diet for 2 wk. In the A/J LF mice, cold exposure (4 degrees C) resulted in hypothermia, whereas the A/J HF, B/6J LF, and B/6J HF mice were cold tolerant. Cold sensitivity of the A/J LF mice was associated with a relatively low whole body energy expenditure under resting conditions, which was normalized by the HF diet. In both strains, the HF diet induced uncoupling protein-1-mediated thermogenesis, with a stronger induction in A/J mice. Only in A/J mice: 1) the HF diet augmented activation of whole body lipid oxidation by cold; and 2) at 30 degrees C, oxygen consumption, total content, and phosphorylation of AMP-activated protein kinase (AMPK), and AICAR-stimulated palmitate oxidation in soleus muscle was increased by the HF diet in parallel with significantly increased leptinemia. Gene expression data in soleus muscle of the A/J HF mice indicated a shift from carbohydrate to fatty acid oxidation. Our results suggest a role for muscle nonshivering thermogenesis and lipid oxidation in the obesity-resistant phenotype of A/J mice and indicate that a HF diet could induce thermogenesis in oxidative muscle, possibly via the leptin-AMPK axis.

}, keywords = {Aminoimidazole Carboxamide, AMP-Activated Protein Kinases, Animals, Basal Metabolism, Body Temperature, Body Weight, Calorimetry, Dietary Fats, Fatty Acids, Inbred C57BL, Indirect, Male, Mice, Multienzyme Complexes, Muscle, Newborn, Nonesterified, Obesity, Oxygen Consumption, Protein-Serine-Threonine Kinases, Random Allocation, Ribonucleotides, Skeletal, Thermogenesis, Triglycerides}, issn = {0193-1849}, doi = {10.1523/JNEUROSCI.3773-10.2011}, author = {Kus, Vladimir and Prazak, Tomas and Brauner, Petr and Hensler, Michal and Kuda, Ondrej and Flachs, Pavel and Janovska, Petra and Medrikova, Dasa and Rossmeisl, Martin and Jilkova, Zuzana and Stefl, Bohumir and Pastalkova, Eva and Drahota, Zdenek and Houstek, Josef and Kopecky, Jan} } @proceedings {5678, title = {Inferring elapsed time from stochastic neural processes.}, volume = {20}, year = {2008}, month = {2008}, publisher = {MIT press}, abstract = {

Many perceptual processes and neural computations, such as speech recognition, motor control and learning, depend on the ability to measure and mark the passage of time. However, the processes that make such temporal judgements possible are unknown. A number of different hypothetical mechanisms have been advanced, all of which depend on the known, temporally predictable evolution of a neural or psychological state, possibly through oscillations or the gradual decay of a memory trace. Alternatively, judgements of elapsed time might be based on observations of temporally structured, but stochastic processes. Such processes need not be specific to the sense of time; typical neural and sensory processes contain at least some statistical structure across a range of time scales. Here, we investigate the statistical properties of an estimator of elapsed time which is based on a simple family of stochastic process.

}, author = {Ahrens MB and Sahani M.} } @article {5673, title = {Inferring input nonlinearities in neural encoding models.}, journal = {Network}, volume = {19}, year = {2008}, month = {2008}, pages = {35-67}, abstract = {

We describe a class of models that predict how the instantaneous firing rate of a neuron depends on a dynamic stimulus. The models utilize a learnt pointwise nonlinear transform of the stimulus, followed by a linear filter that acts on the sequence of transformed inputs. In one case, the nonlinear transform is the same at all filter lag-times. Thus, this "input nonlinearity" converts the initial numerical representation of stimulus value to a new representation that provides optimal input to the subsequent linear model. We describe algorithms that estimate both the input nonlinearity and the linear weights simultaneously; and present techniques to regularise and quantify uncertainty in the estimates. In a second approach, the model is generalized to allow a different nonlinear transform of the stimulus value at each lag-time. Although more general, this model is algorithmically more straightforward to fit. However, it has many more degrees of freedom than the first approach, thus requiring more data for accurate estimation. We test the feasibility of these methods on synthetic data, and on responses from a neuron in rodent barrel cortex. The models are shown to predict responses to novel data accurately, and to recover several important neuronal response properties.

}, keywords = {Models, Neural Networks (Computer), Neurological, Neurons, Nonlinear Dynamics}, issn = {1361-6536}, doi = {10.1080/09548980701813936}, author = {Ahrens, Misha B and Paninski, Liam and Sahani, Maneesh} } @article {2503, title = {Insulin/IGF signaling regulates the change in commitment in imaginal discs and primordia by overriding the effect of juvenile hormone.}, journal = {Developmental Biology}, volume = {324}, year = {2008}, month = {2008 Dec 15}, pages = {258-65}, abstract = {

At the beginning of the final larval (fifth) instar of Manduca sexta, imaginal precursors including wing discs and eye primordia initiate metamorphic changes, such as pupal commitment, patterning and cell proliferation. Juvenile hormone (JH) prevents these changes in earlier instars and in starved final instar larvae, but nutrient intake overcomes this effect of JH in the latter. In this study, we show that a molecular marker of pupal commitment, broad, is up-regulated in the wing discs by feeding on sucrose or by bovine insulin or Manduca bombyxin in starved final instar larvae. This effect of insulin could not be prevented by JH. In vitro insulin had no effect on broad expression but relieved the suppression of broad expression by JH. This effect of insulin was directly on the disc as shown by its reduction in the presence of insulin receptor dsRNA. In starved penultimate fourth instar larvae, broad expression in the wing disc was not up-regulated by insulin. The discs became responsive to this action of insulin during the molt to the fifth instar together with the ability to become pupally committed in response to 20-hydroxyecdysone. Thus, the Manduca bombyxin acts as a metamorphosis-initiating factor in the imaginal precursors.

}, keywords = {Animals, Cells, Cloning, Cultured, Developmental, Ecdysterone, Gene Expression Regulation, Insect Proteins, Insulin, Juvenile Hormones, Larva, Manduca, Messenger, Molecular, Receptor, RNA, RNA Interference, Signal Transduction, Somatomedins, Sucrose, Wing}, issn = {1095-564X}, doi = {10.1016/j.ydbio.2008.09.017}, author = {Koyama, Takashi and Syropyatova, Maria O and Riddiford, Lynn M} } @article {45960, title = {Interactions of lipids with aquaporin-0 and other membrane proteins.}, journal = {Pfl{\"u}gers Archiv - European Journal of Physiology}, volume = {456}, year = {2008}, month = {2008 Jul}, pages = {651-61}, abstract = {

The structure of aquaporin-0 (AQP0) has recently been determined by electron crystallography of two-dimensional (2D) crystals and by X-ray crystallography of three-dimensional (3D) crystals. The electron crystallographic structure revealed nine lipids per AQP0 monomer, which form an almost complete bilayer. The lipids adopt a wide variety of conformations and tightly fill the space between adjacent AQP0 tetramers. The conformations of the lipid acyl chains appear to be determined not only by the protein surface but also by the acyl chains of adjacent lipid molecules. In the X-ray structure, the hydrophobic region of the protein is surrounded by a detergent micelle, with two ordered detergent molecules per AQP0 monomer. Despite the different environments, the electron crystallographic and X-ray structures of AQP0 are virtually identical, but they differ in the temperature factors of the atoms that either contact the lipids in the 2D crystals or are exposed to detergents in the 3D crystals. The temperature factors are higher in the X-ray structure, suggesting that the detergent-exposed AQP0 residues are less ordered than the corresponding ones contacting lipids in the 2D crystals. An examination of ordered detergent molecules in crystal structures of other aquaporins and of lipid molecules in 2D and 3D crystals of bacteriorhodopsin suggests that the increased conformational variability of detergent-exposed residues compared to lipid-contacting residues is a general feature.

}, keywords = {Animals, Aquaporins, Crystallization, Eye Proteins, Humans, Lipid Metabolism, Membrane Proteins, Models, Molecular, X-Ray Diffraction}, issn = {0031-6768}, doi = {10.1007/s00424-007-0353-9}, author = {Hite, Richard K and Gonen, Tamir and Harrison, Stephen C and Walz, Thomas} } @article {1731, title = {Interfacial structures of acidic and basic aqueous solutions.}, journal = {Journal of the American Chemical Society}, volume = {130}, year = {2008}, month = {2008 Oct 1}, pages = {13033-9}, abstract = {

Phase-sensitive sum-frequency vibrational spectroscopy was used to study water/vapor interfaces of HCl, HI, and NaOH solutions. The measured imaginary part of the surface spectral responses provided direct characterization of OH stretch vibrations and information about net polar orientations of water species contributing to different regions of the spectrum. We found clear evidence that hydronium ions prefer to emerge at interfaces. Their OH stretches contribute to the "ice-like" band in the spectrum. Their charges create a positive surface field that tends to reorient water molecules more loosely bonded to the topmost water layer with oxygen toward the interface, and thus enhances significantly the "liquid-like" band in the spectrum. Iodine ions in solution also like to appear at the interface and alter the positive surface field by forming a narrow double-charge layer with hydronium ions. In NaOH solution, the observed weak change of the "liquid-like" band and disappearance of the "ice-like" band in the spectrum indicates that OH(-) ions must also have excess at the interface. How they are incorporated in the interfacial water structure is, however, not clear.

}, issn = {1520-5126}, doi = {10.1021/ja8021297}, author = {Tian, Chuanshan and Ji, Na and Waychunas, Glenn A and Shen, Y Ron} } @article {2345, title = {Internally generated cell assembly sequences in the rat hippocampus.}, journal = {Science}, volume = {321}, year = {2008}, month = {2008 Sep 5}, pages = {1322-7}, abstract = {

A long-standing conjecture in neuroscience is that aspects of cognition depend on the brain{\textquoteright}s ability to self-generate sequential neuronal activity. We found that reliably and continually changing cell assemblies in the rat hippocampus appeared not only during spatial navigation but also in the absence of changing environmental or body-derived inputs. During the delay period of a memory task, each moment in time was characterized by the activity of a particular assembly of neurons. Identical initial conditions triggered a similar assembly sequence, whereas different conditions gave rise to different sequences, thereby predicting behavioral choices, including errors. Such sequences were not formed in control (nonmemory) tasks. We hypothesize that neuronal representations, evolved for encoding distance in spatial navigation, also support episodic recall and the planning of action sequences.

}, keywords = {Action Potentials, Animal, Animals, Behavior, Choice Behavior, Cues, Hippocampus, Interneurons, Long-Evans, Male, Maze Learning, Memory, Mental Recall, Models, Motor Activity, Neurological, Pyramidal Cells, Rats}, issn = {1095-9203}, doi = {10.1523/JNEUROSCI.3773-10.2011}, author = {Pastalkova, Eva and Itskov, Vladimir and Amarasingham, Asohan and Buzs{\'a}ki, Gy{\"o}rgy} } @article {2850, title = {Isolation of highly purified yeast nuclei for nuclease mapping of chromatin structure.}, journal = {Methods in Molecular Biology}, volume = {463}, year = {2008}, month = {2008}, pages = {43-53}, abstract = {

Probing chromatin structure with nucleases is a well-established method for determining the accessibility of DNA to gene regulatory proteins and measuring competency for transcription. A hallmark of many silent genes is the presence of translationally positioned nucleosomes over their promoter regions, which can be inferred by the sensitivity of the underlying DNA to nucleases, particularly micrococcal nuclease. The quality of this data is highly dependent upon the nuclear preparation, especially if the digestion products are analyzed by high-resolution detection methods such as reiterative primer extension. Here we describe a method to isolate highly purified nuclei from the budding yeast Saccharomyces cerevisiae and the use of micrococcal nuclease to map the positions of nucleosomes at the RNR3 gene. Nuclei isolated by this procedure are competent for many of the commonly used chromatin mapping and detection procedures.

}, keywords = {Cell Nucleus, Chromatin, DNA, Fungal, Genetic, Micrococcal Nuclease, Mycology, Promoter Regions, Ribonucleoside Diphosphate Reductase, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins}, issn = {1940-6029}, doi = {10.1007/978-1-59745-406-3_3}, author = {Reese, Joseph C and Zhang, Hesheng and Zhang, Zhengjian} } @article {45964, title = {Junction-forming aquaporins.}, journal = {Current Opinion in Structural Biology}, volume = {18}, year = {2008}, month = {2008 Apr}, pages = {229-35}, abstract = {

Aquaporins (AQPs) are a family of ubiquitous membrane channels that conduct water and solutes across membranes. This review focuses on AQP0 and AQP4, which in addition to forming water channels also appear to play a role in cell adhesion. We discuss the recently determined structures of the membrane junctions mediated by these two AQPs, the mechanisms that regulate junction formation, and evidence that supports a role for AQP0 and AQP4 in cell adhesion.

}, keywords = {Animals, Aquaporin 4, Aquaporins, Eye Proteins, Humans, Intercellular Junctions, Models, Molecular, Protein Structure, Quaternary}, issn = {0959-440X}, doi = {10.1016/j.sbi.2007.11.003}, author = {Engel, Andreas and Fujiyoshi, Yoshinori and Gonen, Tamir and Walz, Thomas} } @article {2499, title = {Juvenile hormone action: a 2007 perspective.}, journal = {Journal of Insect Physiology}, volume = {54}, year = {2008}, month = {2008 Jun}, pages = {895-901}, abstract = {

Juvenile hormone (JH) is a key hormone in regulation of the insect{\textquoteright}s life history, both in maintaining the larval state during molts and in directing reproductive maturation. This short review highlights the recent papers of the past year that lend new insight into the role of this hormone in the larva and the mechanisms whereby it achieves this role.

}, keywords = {Animals, Basic Helix-Loop-Helix Transcription Factors, Biological, DNA-Binding Proteins, Drosophila Proteins, Insects, Juvenile Hormones, Larva, Metamorphosis, Response Elements, Transcription Factors}, issn = {0022-1910}, doi = {10.1016/j.jinsphys.2008.01.014}, author = {Riddiford, Lynn M} } @article {2504, title = {Kr{\"u}ppel homolog 1 (Kr-h1) mediates juvenile hormone action during metamorphosis of Drosophila melanogaster.}, journal = {Mechanisms of Development}, volume = {125}, year = {2008}, month = {2008 Jan-Feb}, pages = {91-105}, abstract = {

Juvenile hormone (JH) given at pupariation inhibits bristle formation and causes pupal cuticle formation in the abdomen of Drosophila melanogaster due to its prolongation of expression of the transcription factor Broad (BR). In a microarray analysis of JH-induced gene expression in abdominal integument, we found that Kr{\"u}ppel homolog 1 (Kr-h1) was up-regulated during most of adult development. Quantitative real-time PCR analyses showed that Kr-h1 up-regulation began at 10h after puparium formation (APF), and Kr-h1 up-regulation occurred in imaginal epidermal cells, persisting larval muscles, and larval oenocytes. Ectopic expression of Kr-h1 in abdominal epidermis using T155-Gal4 to drive UAS-Kr-h1 resulted in missing or short bristles in the dorsal midline. This phenotype was similar to that seen after a low dose of JH or after misexpression of br between 21 and 30 h APF. Ectopic expression of Kr-h1 prolonged the expression of BR protein in the pleura and the dorsal tergite. No Kr-h1 was seen after misexpression of br. Thus, Kr-h1 mediates some of the JH signaling in the adult abdominal epidermis and is upstream of br in this pathway. We also show for the first time that the JH-mediated maintenance of br expression in this epidermis is patterned and that JH delays the fusion of the imaginal cells and the disappearance of Dpp in the dorsal midline.

}, keywords = {Animals, Base Sequence, Biological, DNA Primers, Drosophila melanogaster, Drosophila Proteins, Kruppel-Like Transcription Factors, Larva, Metamorphosis, Oligonucleotide Array Sequence Analysis, Polymerase Chain Reaction, Up-Regulation}, issn = {0925-4773}, doi = {10.1016/j.mod.2007.10.002}, author = {Minakuchi, Chieka and Zhou, Xiaofeng and Riddiford, Lynn M} } @article {2079, title = {Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics.}, journal = {Nature Methods}, volume = {5}, year = {2008}, month = {2008 May}, pages = {417-23}, abstract = {

We demonstrate live-cell super-resolution imaging using photoactivated localization microscopy (PALM). The use of photon-tolerant cell lines in combination with the high resolution and molecular sensitivity of PALM permitted us to investigate the nanoscale dynamics within individual adhesion complexes (ACs) in living cells under physiological conditions for as long as 25 min, with half of the time spent collecting the PALM images at spatial resolutions down to approximately 60 nm and frame rates as short as 25 s. We visualized the formation of ACs and measured the fractional gain and loss of individual paxillin molecules as each AC evolved. By allowing observation of a wide variety of nanoscale dynamics, live-cell PALM provides insights into molecular assembly during the initiation, maturation and dissolution of cellular processes.

Commentary: The first example of true live cell and time lapse imaging by localization microscopy (as opposed to particle tracking), this paper uses the Nyquist criterion to establish a necessary condition for true spatial resolution based on the density of localized molecules {\textendash} a condition often unmet in claims elsewhere in the superresolution literature.
By any method, higher spatiotemporal resolution requires increasing light exposure at the specimen, making noninvasive imaging increasingly difficult. Here, simultaneous differential interference contrast imaging is used to establish that cells behave physiologically before, during, and after PALM imaging. Similar controls are lacking from many supposed {\textquotedblleft}live cell{\textquotedblright} superresolution demonstrations.

}, keywords = {Animals, Cell Adhesion, Cell Survival, CHO Cells, Computer-Assisted, Cricetinae, Cricetulus, Image Processing, Microscopy, Nanotechnology, Paxillin, Protein Transport, Staining and Labeling}, issn = {1548-7105}, doi = {10.1038/nmeth.1202}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18408726}, author = {Shroff, Hari and Galbraith, Catherine G and Galbraith, James A and Betzig, Eric} } @article {1248, title = {Local potential connectivity in cat primary visual cortex.}, journal = {Cerebral Cortex}, volume = {18}, year = {2008}, month = {2008 Jan}, pages = {13-28}, abstract = {

Time invariant description of synaptic connectivity in cortical circuits may be precluded by the ongoing growth and retraction of dendritic spines accompanied by the formation and elimination of synapses. On the other hand, the spatial arrangement of axonal and dendritic branches appears stable. This suggests that an invariant description of connectivity can be cast in terms of potential synapses, which are locations in the neuropil where an axon branch of one neuron is proximal to a dendritic branch of another neuron. In this paper, we attempt to reconstruct the potential connectivity in local cortical circuits of the cat primary visual cortex (V1). Based on multiple single-neuron reconstructions of axonal and dendritic arbors in 3 dimensions, we evaluate the expected number of potential synapses and the probability of potential connectivity among excitatory (pyramidal and spiny stellate) neurons and inhibitory basket cells. The results provide a quantitative description of structural organization of local cortical circuits. For excitatory neurons from different cortical layers, we compute local domains, which contain their potentially pre- and postsynaptic excitatory partners. These domains have columnar shapes with laminar specific radii and are roughly of the size of the ocular dominance column. Therefore, connections between most excitatory neurons in the ocular dominance column can be implemented by local synaptogenesis. Structural connectivity involving inhibitory basket cells is generally weaker than excitatory connectivity. Here, only nearby neurons are capable of establishing more than one potential synapse, implying that within the ocular dominance column these connections have more limited potential for circuit remodeling.

}, keywords = {Animals, Cats, Cells, Cultured, Nerve Net, Neural Pathways, Synapses, Visual Cortex}, issn = {1460-2199}, doi = {10.1093/cercor/bhm027}, author = {Stepanyants, Armen and Hirsch, Judith A and Martinez, Luis M and Kisv{\'a}rday, Zolt{\'a}n F and Ferecsk{\'o}, Alex S and Chklovskii, Dmitri B} } @article {4648, title = {The loci of evolution: how predictable is genetic evolution?}, journal = {Evolution}, volume = {62}, year = {2008}, month = {2008 Sep}, pages = {2155-77}, abstract = {

Is genetic evolution predictable? Evolutionary developmental biologists have argued that, at least for morphological traits, the answer is a resounding yes. Most mutations causing morphological variation are expected to reside in the cis-regulatory, rather than the coding, regions of developmental genes. This "cis-regulatory hypothesis" has recently come under attack. In this review, we first describe and critique the arguments that have been proposed in support of the cis-regulatory hypothesis. We then test the empirical support for the cis-regulatory hypothesis with a comprehensive survey of mutations responsible for phenotypic evolution in multicellular organisms. Cis-regulatory mutations currently represent approximately 22\% of 331 identified genetic changes although the number of cis-regulatory changes published annually is rapidly increasing. Above the species level, cis-regulatory mutations altering morphology are more common than coding changes. Also, above the species level cis-regulatory mutations predominate for genes not involved in terminal differentiation. These patterns imply that the simple question "Do coding or cis-regulatory mutations cause more phenotypic evolution?" hides more interesting phenomena. Evolution in different kinds of populations and over different durations may result in selection of different kinds of mutations. Predicting the genetic basis of evolution requires a comprehensive synthesis of molecular developmental biology and population genetics.

}, keywords = {Animals, Evolution, Humans, Molecular, Phenotype, Regulatory Elements, Transcriptional}, issn = {0014-3820}, doi = {10.1111/j.1558-5646.2008.00450.x}, author = {Stern, David L and Orgogozo, Virginie} } @article {2688, title = {Locomotor control by the central complex in Drosophila-an analysis of the tay bridge mutant.}, journal = {Developmental Neurobiology}, volume = {68}, year = {2008}, month = {2008 Jul}, pages = {1046-58}, abstract = {

Several aspects of locomotor control have been ascribed to the central complex of the insect brain; however, the role of distinct substructures of this complex is not well known. The tay bridge1 (tay1) mutant of Drosophila melanogaster was originally isolated on the basis of reduced walking speed and activity. In addition, tay1 is defective in the compensation of rotatory stimuli during walking and histologically, tay1 causes a mid-sagittal constriction of the protocerebral bridge, a constituent of the central complex. Cloning of the tay gene revealed that it encodes a novel protein with no significant homology to any known protein. To associate the behavioral phenotypes with the anatomical defect in the protocerebral bridge, we used different driver lines to express the tay cDNA in various neuronal subpopulations of the central brain in tay1-mutant flies. These experiments showed an association of the aberrant walking speed and activity with the structural defect in the protocerebral bridge. In contrast, the compensation of rotatory stimuli during walking was rescued without a restoration of the protocerebral bridge. The results of our differential rescue approach are supported by neuronal silencing experiments using conditional tetanus toxin expression in the same subset of neurons. These findings show for the first time that the walking speed and activity is controlled by different substructures of the central brain than the compensatory locomotion for rotatory stimuli.

}, keywords = {Amino Acid Sequence, Animal, Animals, Behavior, Brain, Cell Line, Drosophila melanogaster, Drosophila Proteins, Genetic Vectors, Locomotion, Male, Motor Activity, Mushroom Bodies, Mutation, Neurons, Phenotype, Photic Stimulation, Polymerase Chain Reaction, Transformed}, issn = {1932-8451}, doi = {10.1002/dneu.20643}, author = {Poeck, Burkhard and Triphan, Tilman and Neuser, Kirsa and Strauss, Roland} } @article {46626, title = {Loss of RAB-3/A in Caenorhabditis elegans and the mouse affects behavioral response to ethanol.}, journal = {Genes, Brain, and Behavior}, volume = {7}, year = {2008}, month = {2008 Aug}, pages = {669-76}, abstract = {

The mechanisms by which ethanol induces changes in behavior are not well understood. Here, we show that Caenorhabditis elegans loss-of-function mutations in the synaptic vesicle-associated RAB-3 protein and its guanosine triphosphate exchange factor AEX-3 confer resistance to the acute locomotor effects of ethanol. Similarly, mice lacking one or both copies of Rab3A are resistant to the ataxic and sedative effects of ethanol, and Rab3A haploinsufficiency increases voluntary ethanol consumption. These data suggest a conserved role of RAB-3-/RAB3A-regulated neurotransmitter release in ethanol-related behaviors.

}, keywords = {Alcohol Drinking, Alcohol-Induced Disorders, Nervous System, Animals, Ataxia, Behavior, Animal, Brain, Brain Chemistry, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Central Nervous System Depressants, Consciousness Disorders, Drug Resistance, Ethanol, Haplotypes, Male, Mice, Mice, Inbred C57BL, Mice, Knockout, rab3 GTP-Binding Proteins, rab3A GTP-Binding Protein}, issn = {1601-183X}, doi = {10.1111/j.1601-183X.2008.00404.x}, author = {Kapfhamer, D and Bettinger, J C and Davies, A G and Eastman, C L and Smail, E A and Heberlein, U and McIntire, S L} } @article {1455, title = {Markov random field based automatic image alignment for electron tomography.}, journal = {Journal of Structural Biology}, volume = {161}, year = {2008}, month = {2008 Mar 28}, pages = {260-75}, abstract = {

We present a method for automatic full-precision alignment of the images in a tomographic tilt series. Full-precision automatic alignment of cryo electron microscopy images has remained a difficult challenge to date, due to the limited electron dose and low image contrast. These facts lead to poor signal to noise ratio (SNR) in the images, which causes automatic feature trackers to generate errors, even with high contrast gold particles as fiducial features. To enable fully automatic alignment for full-precision reconstructions, we frame the problem probabilistically as finding the most likely particle tracks given a set of noisy images, using contextual information to make the solution more robust to the noise in each image. To solve this maximum likelihood problem, we use Markov Random Fields (MRF) to establish the correspondence of features in alignment and robust optimization for projection model estimation. The resulting algorithm, called Robust Alignment and Projection Estimation for Tomographic Reconstruction, or RAPTOR, has not needed any manual intervention for the difficult datasets we have tried, and has provided sub-pixel alignment that is as good as the manual approach by an expert user. We are able to automatically map complete and partial marker trajectories and thus obtain highly accurate image alignment. Our method has been applied to challenging cryo electron tomographic datasets with low SNR from intact bacterial cells, as well as several plastic section and X-ray datasets.

}, keywords = {Algorithms, Computer-Assisted, Cryoelectron Microscopy, Image Processing, Markov Chains, Tomography}, issn = {1095-8657}, doi = {10.1016/j.jsb.2007.07.007}, author = {Amat, Fernando and Moussavi, Farshid and Comolli, Luis R and Elidan, Gal and Downing, Kenneth H and Horowitz, Mark} } @conference {48184, title = {Model-based autosegmentation of the central brain of the honeybee, Apis mellifera, using active statistical shape models.}, booktitle = {Neuroinformatics 2008}, year = {2008}, month = {2008 Sep 07}, address = {Stockholm, Sweden}, abstract = {

The Honeybee Brain Atlas serves as 3D database and communicative platform to accumulate structural data, i.e. reconstructed neurons, derived from confocal scans (Brandt et al., 2005) (www.neurobiologie.fu-berlin.de/beebrain/) (1). Transforming neurons into the atlas requires manual segmentation of neuropils within confocal images, a time-consuming task requiring expertise in identifying biological structures which can result in different outcomes from various segmenters.

}, doi = {10.3389/conf.neuro.11.2008.01.064}, author = {Singer, Jochen and Lienhard, Matthias and Seim, Heiko and Kainmueller, Dagmar and Kuss, Anja and Lamecker, Hans and Zachow, Stefan and Menzel, Randolf and Rybak, J{\"u}rgen} } @article {2357, title = {A modular display system for insect behavioral neuroscience.}, journal = {Journal of Neuroscience Methods}, volume = {167}, year = {2008}, month = {2008 Jan 30}, pages = {127-39}, abstract = {

Flying insects exhibit stunning behavioral repertoires that are largely mediated by the visual control of flight. For this reason, presenting a controlled visual environment to tethered insects has been and continues to be a powerful tool for studying the sensory control of complex behaviors. To create an easily controlled, scalable, and customizable visual stimulus, we have designed a modular system, based on panels composed of an 8 x 8 array of individual LEDs, that may be connected together to {\textquoteright}tile{\textquoteright} an experimental environment with controllable displays. The panels have been designed to be extremely bright, with the added flexibility of individual-pixel brightness control, allowing experimentation over a broad range of behaviorally relevant conditions. Patterns to be displayed may be designed using custom software, downloaded to a controller board, and displayed on the individually addressed panels via a rapid communication interface. The panels are controlled by a microprocessor-based display controller which, for most experiments, will not require a computer in the loop, greatly reducing the experimental infrastructure. This technology allows an experimenter to build and program a visual arena with a customized geometry in a matter of hours. To demonstrate the utility of this system, we present results from experiments with tethered Drosophila melanogaster: (1) in a cylindrical arena composed of 44 panels, used to test the contrast dependence of object orientation behavior, and (2) above a 30-panel floor display, used to examine the effects of ground motion on orientation during flight.

}, keywords = {Animal, Animals, Behavior, Computer-Assisted Instruction, Drosophila, Flight, Imaging, Motion, Orientation, Photic Stimulation, Software, Three-Dimensional}, issn = {0165-0270}, doi = {10.1016/j.cub.2010.06.072}, author = {Reiser, Michael B and Dickinson, Michael H} } @article {45800, title = {Molecular characterization of pea aphid facultative parthenogenesis}, journal = {Developmental Biology}, volume = {319}, year = {2008}, month = {07/2008}, pages = {494-495}, abstract = {

Meiosis is a highly conserved process in which a diploid genome is recombined and assorted into haploid gametes. Remarkably, the pea aphid Acyrthosiphon pisum exhibits a reproductive polyphenism whereby environmental signals trigger a switch between apomixis (parthenogenetic reproduction) and meiosis (sexual reproduction). Aphid apomixis results in daughter embryo clones with 2n genome content without male contribution or recombination. This important adaptation allows aphid populations to not only rapidly expand upon abundant resources during summer but also survive winter. How aphids have evolved this ability to switch between parthenogenesis and sexual meiosis is unknown. To arrive at a mechanistic explanation for this developmental plasticity, I determined meiosis gene activity in sexuals and asexuals. I first identified homologs of a core set of meiosis genes from the pea aphid genome. Next, I tested the expression of these core meiosis genes by PCR spanning across at least one intron from cDNA isolated from asexual and sexual ovaries. Surprisingly, meiosis specific genes (e.g., Spo11, Msh4, Msh5, Hop2 and Mnd1) are expressed in asexual ovaries. Additionally, the Spo11 PCR product contained intronic sequence, thus representing unspliced mRNA. Future experiments looking at the quantities and localizations of mRNA and protein will help to distinguish among several possible explanations for these results. Further molecular characterization of this phenotypic plasticity will be helpful in understanding how multiple interacting pathways can evolve to create alternate developmental phenotypes.

}, doi = {10.1016/j.ydbio.2008.05.098}, author = {Dayalan G. Srinivasan and Greg K. Davis and David L. Stern} } @article {2806, title = {Monitoring of toxic compounds in air using a handheld rectilinear ion trap mass spectrometer.}, journal = {Analytical Chemistry}, volume = {80}, year = {2008}, month = {2008 Feb 1}, pages = {734-41}, abstract = {

A miniature, handheld mass spectrometer, based on the rectilinear ion trap mass analyzer, has been applied to air monitoring for traces of toxic compounds. The instrument is battery-operated, hand-portable, and rugged. We anticipate its use in public safety, industrial hygiene, and environmental monitoring. Gaseous samples of nine toxic industrial compounds, phosgene, ethylene oxide, sulfur dioxide, acrylonitrile, cyanogen chloride, hydrogen cyanide, acrolein, formaldehyde, and ethyl parathion, were tested. A sorption trap inlet was constructed to serve as the interface between atmosphere and the vacuum chamber of the mass spectrometer. After selective collection of analytes on the sorbent bed, the sorbent tube was evacuated and then heated to desorb analyte into the instrument. Sampling, detection, identification, and quantitation of all compounds were readily achieved in times of less than 2 min, with detection limits ranging from 800 parts per trillion to 3 parts per million depending on the analyte. For all but one analyte, detection limits were well below (3.5-130 times below) permissible exposure limits. A linear dynamic range of 1-2 orders of magnitude was obtained over the concentration ranges studied (sub-ppbv to ppmv) for all analytes.

}, issn = {0003-2700}, doi = {10.1364/AO.50.001792}, author = {Keil, Adam and Hernandez-Soto, Heriberto and Noll, Robert J and Fico, Miriam and Gao, Liang and Ouyang, Zheng and Cooks, R Graham} } @article {5225, title = {Multilayer three-dimensional super resolution imaging of thick biological samples.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, year = {2008}, month = {2008 Dec 23}, pages = {20221-6}, abstract = {

Recent advances in optical microscopy have enabled biological imaging beyond the diffraction limit at nanometer resolution. A general feature of most of the techniques based on photoactivated localization microscopy (PALM) or stochastic optical reconstruction microscopy (STORM) has been the use of thin biological samples in combination with total internal reflection, thus limiting the imaging depth to a fraction of an optical wavelength. However, to study whole cells or organelles that are typically up to 15 microm deep into the cell, the extension of these methods to a three-dimensional (3D) super resolution technique is required. Here, we report an advance in optical microscopy that enables imaging of protein distributions in cells with a lateral localization precision better than 50 nm at multiple imaging planes deep in biological samples. The approach is based on combining the lateral super resolution provided by PALM with two-photon temporal focusing that provides optical sectioning. We have generated super-resolution images over an axial range of approximately 10 microm in both mitochondrially labeled fixed cells, and in the membranes of living S2 Drosophila cells.

}, keywords = {Animals, Cell Line, Cells, Humans, Imaging, Microscopy, Mitochondria, Organelles, Three-Dimensional}, issn = {1091-6490}, doi = {10.1073/pnas.0810636105}, author = {Vaziri, Alipasha and Tang, Jianyong and Shroff, Hari and Shank, Charles V} } @proceedings {3300, title = {Multi-modal target tracking using heterogeneous sensor networks.}, year = {2008}, month = {2008 Aug 7}, abstract = {

The paper describes a target tracking system running on a Heterogeneous Sensor Network (HSN) and presents results gathered from a realistic deployment. The system fuses audio direction of arrival data from mote class devices and object detection measurements from embedded PCs equipped with cameras. The acoustic sensor nodes perform beamforming and measure the energy as a function of the angle. The camera nodes detect moving objects and estimate their angle. The sensor detections are sent to a centralized sensor fusion node via a combination of two wireless networks. The novelty of our system is the unique combination of target tracking methods customized for the application at hand and their implementation on an actual HSN platform.

}, author = {Kushwaha, M and Amundson, I and Volgyesi, P and Ahammad, Parvez and Simon, G and Koutsoukos, X and Ledeczi, A and Sastry, S} } @article {2393, title = {MyoD targets TAF3/TRF3 to activate myogenin transcription.}, journal = {Molecular Cell}, volume = {32}, year = {2008}, month = {2008 Oct 10}, pages = {96-105}, abstract = {

Skeletal muscle differentiation requires a cascade of transcriptional events to control the spatial and temporal expression of muscle-specific genes. Until recently, muscle-specific transcription was primarily attributed to prototypic enhancer-binding factors, while the role of core promoter recognition complexes in directing myogenesis remained unknown. Here, we report the development of a purified reconstituted system to analyze the properties of a TAF3/TRF3 complex in directing transcription initiation at the Myogenin promoter. Importantly, this new complex is required to replace the canonical TFIID to recapitulate MyoD-dependent activation of Myogenin. In vitro and cell-based assays identify a domain of TAF3 that mediates coactivator functions targeted by MyoD. Our findings also suggest changes to CRSP/Mediator in terminally differentiated myotubes. This switching of the core promoter recognition complex during myogenesis allows a more balanced division of labor between activators and TAF coactivators, thus providing another strategy to accommodate cell-specific regulation during metazoan development.

}, keywords = {Animals, Cell Line, Genetic, Homeodomain Proteins, Mice, Multiprotein Complexes, Muscle Fibers, MyoD Protein, Myogenin, Promoter Regions, Protein Structure, Protein Subunits, Recombinant Proteins, Skeletal, TATA Box Binding Protein-Like Proteins, Tertiary, Trans-Activators, Transcription Factor TFIID, Transcription Initiation Site, Transcriptional Activation}, issn = {1097-4164}, doi = {10.1073/pnas.1100640108}, author = {Deato, Maria Divina E and Marr, Michael T and Sottero, Theo and Inouye, Carla and Hu, Ping and Tjian, Robert} } @article {1161, title = {Native R-loops persist throughout the mouse mitochondrial DNA genome.}, journal = {The Journal of Biological Chemistry}, volume = {283}, year = {2008}, month = {2008 Dec 26}, pages = {36743-51}, abstract = {

Mammalian mtDNA has been found here to harbor RNA-DNA hybrids at a variety of locations throughout the genome. The R-loop, previously characterized in vitro at the leading strand replication origin (OH), is isolated as a native RNA-DNA hybrid copurifying with mtDNA. Surprisingly, other mitochondrial transcripts also form stable partial R-loops. These are abundant and affect mtDNA conformation. Current models regarding the mechanism of mammalian mtDNA replication have been expanded by recent data and discordant hypotheses. The presence of stable, nonreplicative, and partially hybridized RNA on the mtDNA template is significant for the reevaluation of replication models based on two-dimensional agarose gel analyses. In addition, the close association of a subpopulation of mtRNA with the DNA template has further implications regarding the structure, maintenance, and expression of the mitochondrial genome. These results demonstrate that variously processed and targeted mtRNAs within mammalian mitochondria likely have multiple functions in addition to their conventional roles.

}, keywords = {Alleles, Animals, Atomic Force, Blotting, DNA, DNA Primers, Electrophoresis, Gel, Genetic, Genome, Mice, Microscopy, Mitochondrial, Models, Northern, Nucleic Acid Conformation, Protein Conformation, RNA, RNA Probes, Two-Dimensional}, issn = {0021-9258}, doi = {10.1016/j.ymeth.2010.01.001}, author = {Brown, Timothy A and Tkachuk, Ariana N and Clayton, David A} } @proceedings {4527, title = {Natural image denoising with convolutional networks.}, year = {2008}, month = {2008 }, address = {Vancouver, B.C., Canada}, author = {Jain, Viren and Seung, H Sebastian} } @article {45967, title = {Noncanonical binding of calmodulin to aquaporin-0: implications for channel regulation.}, journal = {Structure}, volume = {16}, year = {2008}, month = {2008 Sep 10}, pages = {1389-98}, abstract = {

Aquaporins (AQPs) are a family of ubiquitous membrane channels that conduct water across cell membranes. AQPs form homotetramers containing four functional and independent water pores. Aquaporin-0 (AQP0) is expressed in the eye lens, where its water permeability is regulated by calmodulin (CaM). Here we use a combination of biochemical methods and NMR spectroscopy to probe the interaction between AQP0 and CaM. We show that CaM binds the AQP0 C-terminal domain in a calcium-dependent manner. We demonstrate that only two CaM molecules bind a single AQP0 tetramer in a noncanonical fashion, suggesting a form of cooperativity between AQP0 monomers. Based on these results, we derive a structural model of the AQP0/CaM complex, which suggests CaM may be inhibitory to channel permeability by capping the vestibules of two monomers within the AQP0 tetramer. Finally, phosphorylation within AQP0{\textquoteright}s CaM binding domain inhibits the AQP0/CaM interaction, suggesting a temporal regulatory mechanism for complex formation.

}, keywords = {Amino Acid Sequence, Animals, Aquaporins, Calcium, Calmodulin, Crystallins, Eye Proteins, Ion Channels, Models, Molecular, Molecular Sequence Data, Phosphorylation, Protein Binding, Protein Structure, Quaternary, Protein Structure, Secondary, Protein Structure, Tertiary, Protein-Serine-Threonine Kinases, Sequence Homology, Amino Acid, Sheep}, issn = {0969-2126}, doi = {10.1016/j.str.2008.06.011}, author = {Reichow, Steve L and Gonen, Tamir} } @article {5505, title = {Nonlinearities and contextual influences in auditory cortical responses modeled with multilinear spectrotemporal methods.}, journal = {The Journal of Neuroscience}, volume = {28}, year = {2008}, month = {2008 Feb 20}, pages = {1929-42}, abstract = {

The relationship between a sound and its neural representation in the auditory cortex remains elusive. Simple measures such as the frequency response area or frequency tuning curve provide little insight into the function of the auditory cortex in complex sound environments. Spectrotemporal receptive field (STRF) models, despite their descriptive potential, perform poorly when used to predict auditory cortical responses, showing that nonlinear features of cortical response functions, which are not captured by STRFs, are functionally important. We introduce a new approach to the description of auditory cortical responses, using multilinear modeling methods. These descriptions simultaneously account for several nonlinearities in the stimulus-response functions of auditory cortical neurons, including adaptation, spectral interactions, and nonlinear sensitivity to sound level. The models reveal multiple inseparabilities in cortical processing of time lag, frequency, and sound level, and suggest functional mechanisms by which auditory cortical neurons are sensitive to stimulus context. By explicitly modeling these contextual influences, the models are able to predict auditory cortical responses more accurately than are STRF models. In addition, they can explain some forms of stimulus dependence in STRFs that were previously poorly understood.

}, keywords = {Acoustic Stimulation, Animals, Auditory Cortex, Biological, Mice, Models, Nonlinear Dynamics, Rats, Time Factors}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3377-07.2008}, author = {Ahrens, Misha B and Linden, Jennifer F and Sahani, Maneesh} } @article {1413, title = {A novel basal ganglia pathway forms a loop linking a vocal learning circuit with its dopaminergic input.}, journal = {The Journal of Comparative Neurology}, volume = {508}, year = {2008}, month = {2008 Jun 10}, pages = {824-39}, abstract = {

Dopamine has been implicated in mediating contextual modulation of motor behaviors and learning in many species. In songbirds, dopamine may act on the basal ganglia nucleus Area X to influence the neural activity that contributes to vocal learning and contextual changes in song variability. Neurons in midbrain dopamine centers, the substantia nigra pars compacta (SNc) and ventral tegmental area (VTA), densely innervate Area X and show singing-related changes in firing rate. In addition, dopamine levels in Area X change during singing. It is unknown, however, how song-related information could reach dopaminergic neurons. Here we report an anatomical pathway that could provide song-related information to the SNc and VTA. By using injections of bidirectionally transported fluorescent tracers in adult male zebra finches, we show that Area X and other song control nuclei do not project directly to the SNc or VTA. Instead, we describe an indirect pathway from Area X to midbrain dopaminergic neurons via a connection in the ventral pallidum (VP). Specifically, Area X projects to the VP via axon collaterals of Area X output neurons that also project to the thalamus. Dual injections revealed that the area of VP receiving input from Area X projects to the SNc and VTA. Furthermore, VP terminals in the SNc and VTA overlap with cells that project back to Area X. A portion of the arcopallium also projects to the SNc and VTA and could carry auditory information. These data demonstrate an anatomical loop through which Area X activity could influence its dopaminergic input.

}, keywords = {Animal, Animals, Basal Ganglia, Dopamine, Finches, Learning, Male, Nerve Net, Neural Pathways, Vocalization}, issn = {1096-9861}, doi = {10.1002/cne.21700}, author = {Gale, Samuel D and Person, Abigail L and Perkel, David J} } @article {2397, title = {The nucleosome remodeling factor (NURF) regulates genes involved in Drosophila innate immunity.}, journal = {Developmental Biology}, volume = {316}, year = {2008}, month = {2008 Apr 15}, pages = {538-47}, abstract = {

The Drosophila nucleosome remodeling factor (NURF) is an ISWI-containing chromatin remodeling complex that catalyzes ATP-dependent nucleosome sliding. By sliding nucleosomes, NURF has the ability to alter chromatin structure and regulate transcription. Previous studies have shown that mutation of Drosophila NURF induces melanotic tumors, implicating NURF in innate immune function. Here, we show that NURF mutants exhibit identical innate immune responses to gain-of-function mutants in the Drosophila JAK/STAT pathway. Using microarrays, we identify a common set of target genes that are activated in both mutants. In silico analysis of promoter sequences of these defines a consensus regulatory element comprising a STAT-binding sequence overlapped by a binding-site for the transcriptional repressor Ken. NURF interacts physically and genetically with Ken. Chromatin immunoprecipitation (ChIP) localizes NURF to Ken-binding sites in hemocytes, suggesting that Ken recruits NURF to repress STAT responders. Loss of NURF leads to precocious activation of STAT target genes.

}, keywords = {Animals, Chromosomal Proteins, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Gene Expression Profiling, Gene Expression Regulation, Genetic, Genome, Immunity, Innate, Non-Histone, Oligonucleotide Array Sequence Analysis, Phenotype, Recombinant Proteins, Reverse Transcriptase Polymerase Chain Reaction, RNA, Signal Transduction, Transcription}, issn = {1095-564X}, doi = {10.1073/pnas.1100640108}, author = {Kwon, So Yeon and Xiao, Hua and Glover, Bradley P and Tjian, Robert and Wu, Carl and Badenhorst, Paul} } @article {47223, title = {Olfactory representations by Drosophila mushroom body neurons.}, journal = {Journal of Neurophysiology}, volume = {99}, year = {2008}, month = {2008 Feb}, pages = {734-46}, abstract = {

Learning and memory has been studied extensively in Drosophila using behavioral, molecular, and genetic approaches. These studies have identified the mushroom body as essential for the formation and retrieval of olfactory memories. We investigated odor responses of the principal neurons of the mushroom body, the Kenyon cells (KCs), in Drosophila using whole cell recordings in vivo. KC responses to odors were highly selective and, thus sparse, compared with those of their direct inputs, the antennal lobe projection neurons (PNs). We examined the mechanisms that might underlie this transformation and identified at least three contributing factors: excitatory synaptic potentials (from PNs) decay rapidly, curtailing temporal integration, PN convergence onto individual KCs is low ( approximately 10 PNs per KC on average), and KC firing thresholds are high. Sparse activity is thought to be useful in structures involved in memory in part because sparseness tends to reduce representation overlaps. By comparing activity patterns evoked by the same odors across olfactory receptor neurons and across KCs, we show that representations of different odors do indeed become less correlated as they progress through the olfactory system.

}, keywords = {Anesthetics, Local, Animals, Brain Mapping, Drosophila, Electric Stimulation, Excitatory Postsynaptic Potentials, Membrane Potentials, Mushroom Bodies, Nerve Net, Neurons, Afferent, Odors, Olfactory Pathways, Patch-Clamp Techniques, Spectrum Analysis, Tetrodotoxin}, issn = {0022-3077}, doi = {10.1152/jn.01283.2007}, author = {Turner, Glenn C and Bazhenov, Maxim and Laurent, Gilles} } @article {46302, title = {Optimizing one-shot learning with binary synapses.}, journal = {Neural Computation}, volume = {20}, year = {2008}, month = {2008 Aug}, pages = {1928-50}, abstract = {

A network of excitatory synapses trained with a conservative version of Hebbian learning is used as a model for recognizing the familiarity of thousands of once-seen stimuli from those never seen before. Such networks were initially proposed for modeling memory retrieval (selective delay activity). We show that the same framework allows the incorporation of both familiarity recognition and memory retrieval, and estimate the network{\textquoteright}s capacity. In the case of binary neurons, we extend the analysis of Amit and Fusi (1994) to obtain capacity limits based on computations of signal-to-noise ratio of the field difference between selective and non-selective neurons of learned signals. We show that with fast learning (potentiation probability approximately 1), the most recently learned patterns can be retrieved in working memory (selective delay activity). A much higher number of once-seen learned patterns elicit a realistic familiarity signal in the presence of an external field. With potentiation probability much less than 1 (slow learning), memory retrieval disappears, whereas familiarity recognition capacity is maintained at a similarly high level. This analysis is corroborated in simulations. For analog neurons, where such analysis is more difficult, we simplify the capacity analysis by studying the excess number of potentiated synapses above the steady-state distribution. In this framework, we derive the optimal constraint between potentiation and depression probabilities that maximizes the capacity.

}, keywords = {Algorithms, Brain, Computer Simulation, Learning, Models, Statistical, Neural Networks (Computer), Neurons, Pattern Recognition, Automated, Synapses, Synaptic Transmission}, issn = {0899-7667}, doi = {10.1162/neco.2008.10-07-618}, author = {Romani, Sandro and Amit, Daniel J and Amit, Yali} } @article {795, title = {Organization and postembryonic development of glial cells in the adult central brain of Drosophila.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {28}, year = {2008}, month = {2008 Dec 17}, pages = {13742-53}, abstract = {

Glial cells exist throughout the nervous system, and play essential roles in various aspects of neural development and function. Distinct types of glia may govern diverse glial functions. To determine the roles of glia requires systematic characterization of glia diversity and development. In the adult Drosophila central brain, we identify five different types of glia based on its location, morphology, marker expression, and development. Perineurial and subperineurial glia reside in two separate single-cell layers on the brain surface, cortex glia form a glial mesh in the brain cortex where neuronal cell bodies reside, while ensheathing and astrocyte-like glia enwrap and infiltrate into neuropils, respectively. Clonal analysis reveals that distinct glial types derive from different precursors, and that most adult perineurial, ensheathing, and astrocyte-like glia are produced after embryogenesis. Notably, perineurial glial cells are made locally on the brain surface without the involvement of gcm (glial cell missing). In contrast, the widespread ensheathing and astrocyte-like glia derive from specific brain regions in a gcm-dependent manner. This study documents glia diversity in the adult fly brain and demonstrates involvement of different developmental programs in the derivation of distinct types of glia. It lays an essential foundation for studying glia development and function in the Drosophila brain.

}, keywords = {Animals, Antigens, Brain, Cell Count, Cell Differentiation, Cell Lineage, Clone Cells, Differentiation, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Embryo, Genetically Modified, Homeodomain Proteins, Larva, Neuroglia, Neurons, Neuropil, Nonmammalian, Transcription Factors}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4844-08.2008}, author = {Awasaki, Takeshi and Lai, Sen-Lin and Ito, Kei and Lee, Tzumin} } @article {1414, title = {Organization of the songbird basal ganglia, including area X.}, journal = {The Journal of Comparative Neurology}, volume = {508}, year = {2008}, month = {2008 Jun 10}, pages = {840-66}, abstract = {

Area X is a songbird basal ganglia nucleus that is required for vocal learning. Both Area X and its immediate surround, the medial striatum (MSt), contain cells displaying either striatal or pallidal characteristics. We used pathway-tracing techniques to compare directly the targets of Area X and MSt with those of the lateral striatum (LSt) and globus pallidus (GP). We found that the zebra finch LSt projects to the GP, substantia nigra pars reticulata (SNr) and pars compacta (SNc), but not the thalamus. The GP is reciprocally connected with the subthalamic nucleus (STN) and projects to the SNr and motor thalamus analog, the ventral intermediate area (VIA). In contrast to the LSt, Area X and surrounding MSt project to the ventral pallidum (VP) and dorsal thalamus via pallidal-like neurons. A dorsal strip of the MSt contains spiny neurons that project to the VP. The MSt, but not Area X, projects to the ventral tegmental area (VTA) and SNc, but neither MSt nor Area X projects to the SNr. Largely distinct populations of SNc and VTA dopaminergic neurons innervate Area X and surrounding the MSt. Finally, we provide evidence consistent with an indirect pathway from the cerebellum to the basal ganglia, including Area X. Area X projections thus differ from those of the GP and LSt, but are similar to those of the MSt. These data clarify the relationships among different portions of the oscine basal ganglia as well as among the basal ganglia of birds and mammals.

}, keywords = {Animals, Basal Ganglia, Finches, Male, Neural Pathways, Songbirds}, issn = {1096-9861}, doi = {10.1002/cne.21699}, author = {Person, Abigail L and Gale, Samuel D and Farries, Michael A and Perkel, David J} } @article {46420, title = {A parasite cysteine protease is key to host protein degradation and iron acquisition.}, journal = {Journal of Biological Chemistry}, volume = {283}, year = {2008}, month = {2008 Oct 24}, pages = {28934-43}, abstract = {

Cysteine proteases of the Clan CA (papain) family are the predominant protease group in primitive invertebrates. Cysteine protease inhibitors arrest infection by the protozoan parasite, Trypanosoma brucei. RNA interference studies implicated a cathepsin B-like protease, tbcatB, as a key inhibitor target. Utilizing parasites in which one of the two alleles of tbcatb has been deleted, the key role of this protease in degradation of endocytosed host proteins is delineated. TbcatB deficiency results in a decreased growth rate and dysmorphism of the flagellar pocket and the subjacent endocytic compartment. Western blot and microscopic analysis indicate that deficiency in tbcatB results in accumulation of both host and parasite proteins, including the lysosomal marker p67. A critical function for parasitism is the degradation of host transferrin, which is necessary for iron acquisition. Substrate specificity analysis of recombinant tbcatB revealed the optimal peptide cleavage sequences for the enzyme and these were confirmed experimentally using FRET-based substrates. Degradation of transferrin was validated by SDS-PAGE and the specific cleavage sites identified by N-terminal sequencing. Because even a modest deficiency in tbcatB is lethal for the parasite, tbcatB is a logical target for the development of new anti-trypanosomal chemotherapy.

}, keywords = {Animals, Animals, Genetically Modified, Catalytic Domain, Cysteine, Cysteine Endopeptidases, Endocytosis, Fluorescence Resonance Energy Transfer, Iron, Lysosomes, Microscopy, Electron, Transmission, Models, Biological, Protein Structure, Tertiary, RNA Interference, Transferrin, Trypanosoma brucei brucei}, issn = {0021-9258}, doi = {10.1074/jbc.M805824200}, author = {O{\textquoteright}Brien, Theresa C and Mackey, Zachary B and Fetter, Richard D and Choe, Youngchool and O{\textquoteright}Donoghue, Anthony J and Zhou, Min and Craik, Charles S and Caffrey, Conor R and McKerrow, James H} } @article {2170, title = {Performance trade-offs in the flight initiation of Drosophila.}, journal = {The Journal of Experimental Biology}, volume = {211}, year = {2008}, month = {2008 Feb}, pages = {341-53}, abstract = {

The fruit fly Drosophila melanogaster performs at least two distinct types of flight initiation. One kind is a stereotyped escape response to a visual stimulus that is mediated by the hard-wired giant fiber neural pathway, and the other is a more variable ;voluntary{\textquoteright} response that can be performed without giant fiber activation. Because the simpler escape take-offs are apparently successful, it is unclear why the fly has multiple pathways to coordinate flight initiation. In this study we use high-speed videography to observe flight initiation in unrestrained wild-type flies and assess the flight performance of each of the two types of take-off. Three-dimensional kinematic analysis of take-off sequences indicates that wing use during the jumping phase of flight initiation is essential for stabilizing flight. During voluntary take-offs, early wing elevation leads to a slower and more stable take-off. In contrast, during visually elicited escapes, the wings are pulled down close to the body during take-off, resulting in tumbling flights in which the fly translates faster but also rotates rapidly about all three of its body axes. Additionally, we find evidence that the power delivered by the legs is substantially greater during visually elicited escapes than during voluntary take-offs. Thus, we find that the two types of Drosophila flight initiation result in different flight performances once the fly is airborne, and that these performances are distinguished by a trade-off between speed and stability.

}, keywords = {Animal, Animals, Biological, Biomechanics, Drosophila melanogaster, Escape Reaction, Extremities, Female, Flight, Models, Time Factors, Video Recording, Wing}, issn = {0022-0949}, doi = {10.1242/jeb.012682}, author = {Card, Gwyneth and Dickinson, Michael} } @article {45849, title = {The Pfam protein families database.}, journal = {Nucleic Acids Research}, volume = {36}, year = {2008}, month = {2008 Jan}, pages = {D281-8}, abstract = {

Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318 protein families. Pfam is now based not only on the UniProtKB sequence database, but also on NCBI GenPept and on sequences from selected metagenomics projects. Pfam is available on the web from the consortium members using a new, consistent and improved website design in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/), as well as from mirror sites in France (http://pfam.jouy.inra.fr/) and South Korea (http://pfam.ccbb.re.kr/).

}, keywords = {Animals, Databases, Protein, Genomics, Internet, Protein Structure, Tertiary, Proteins, Sequence Alignment, Sequence Analysis, Protein, User-Computer Interface}, issn = {1362-4962}, doi = {10.1093/nar/gkm960}, author = {Finn, Robert D and Tate, John and Mistry, Jaina and Coggill, Penny C and Sammut, Stephen John and Hotz, Hans-Rudolf and Ceric, Goran and Forslund, Kristoffer and Eddy, Sean R and Sonnhammer, Erik L L and Bateman, Alex} } @article {1115, title = {Phenylglycine and phenylalanine derivatives as potent and selective HDAC1 inhibitors (SHI-1).}, journal = {Bioorganic \& Medicinal Chemistry Letters}, volume = {18}, year = {2008}, month = {2008 Mar 15}, pages = {1859-63}, abstract = {

An HTS screening campaign identified a series of low molecular weight phenols that showed excellent selectivity (\>100-fold) for HDAC1/HDAC2 over other Class I and Class II HDACs. Evolution and optimization of this HTS hit series provided HDAC1-selective (SHI-1) compounds with excellent anti-proliferative activity and improved physical properties. Dose-dependent efficacy in a mouse HCT116 xenograft model was demonstrated with a phenylglycine SHI-1 analog.

}, keywords = {Acetylation, Amides, Animals, Cell Proliferation, Colonic Neoplasms, Cultured, Dogs, Enzyme Inhibitors, Ether-A-Go-Go Potassium Channels, Glycine, Histone Deacetylase 1, Histone Deacetylase Inhibitors, Humans, Macaca mulatta, Mice, Molecular Structure, Phenylalanine, Structure-Activity Relationship, Tumor Cells, Xenograft Model Antitumor Assays}, issn = {1464-3405}, doi = {10.1016/j.bmcl.2008.02.012}, author = {Wilson, Kevin J and Witter, David J and Grimm, Jonathan B and Siliphaivanh, Phieng and Otte, Karin M and Kral, Astrid M and Fleming, Judith C and Harsch, Andreas and Hamill, Julie E and Cruz, Jonathan C and Chenard, Melissa and Szewczak, Alexander A and Middleton, Richard E and Hughes, Bethany L and Dahlberg, William K and Secrist, J Paul and Miller, Thomas A} } @article {2078, title = {Photoactivated localization microscopy (PALM) of adhesion complexes. (With commentary)}, journal = {Current Protocols in Cell Biology}, volume = {Chapter 4}, year = {2008}, month = {2008 Dec}, pages = {21}, abstract = {

Key to understanding a protein{\textquoteright}s biological function is the accurate determination of its spatial distribution inside a cell. Although fluorescent protein markers allow the targeting of specific proteins with molecular precision, much of this information is lost when the resultant fusion proteins are imaged with conventional, diffraction-limited optics. In response, several imaging modalities that are capable of resolution below the diffraction limit (approximately 200 nm) have emerged. Here, both single- and dual-color superresolution imaging of biological structures using photoactivated localization microscopy (PALM) are described. The examples discussed focus on adhesion complexes: dense, protein-filled assemblies that form at the interface between cells and their substrata. A particular emphasis is placed on the instrumentation and photoactivatable fluorescent protein (PA-FP) tags necessary to achieve PALM images at approximately 20 nm resolution in 5 to 30 min in fixed cells.

Commentary: A paper spearheaded by Hari which gives a thorough description of the methods and hardware needed to successfully practice PALM, including cover slip preparation, cell transfection and fixation, drift correction with fiducials, characterization of on/off contrast ratios for different photoactivted fluorescent proteins, identifying PALM-suitable cells, and mechanical and optical components of a PALM system.

}, keywords = {Animals, Cell Line, Cell-Matrix Junctions, Cells, Fluorescence, Humans, Microscopy, Photobleaching, Transfection}, issn = {1934-2616}, doi = {10.1002/0471143030.cb0421s41}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19085989}, author = {Shroff, Hari and White, Helen and Betzig, Eric} } @article {45962, title = {Polymorphic assemblies and crystalline arrays of lens tetraspanin MP20.}, journal = {Journal of Molecular Biology}, volume = {376}, year = {2008}, month = {2008 Feb 15}, pages = {380-92}, abstract = {

Members of the tetraspanin superfamily function as transmembrane scaffold proteins that mediate the assembly of membrane proteins into specific signaling complexes. Tetraspanins also interact with each other and concentrate membrane proteins into tetraspanin-enriched microdomains (TEMs). Here we report that lens-specific tetraspanin MP20 can form multiple types of higher-order assemblies and we present crystalline arrays of MP20. When isolated in the absence of divalent cations, MP20 is solubilized predominantly in tetrameric form, whereas the presence of divalent cations during solubilization promotes the association of MP20 tetramers into higher-order species. This effect only occurs when divalent cations are present during solubilization but not when divalent cations are added to solubilized tetrameric MP20, suggesting that other factors may also be involved. When purified MP20 tetramers are reconstituted with native lens lipids in the presence of magnesium, MP20 forms two-dimensional (2D) crystals. A projection map at 18 A resolution calculated from negatively stained 2D crystals showed that the building block of the crystal is an octamer consisting of two tetramers related to each other by 2-fold symmetry. In addition to 2D crystals, reconstitution of MP20 with native lipids also produced a variety of large protein-lipid complexes, and we present three-dimensional (3D) reconstructions of the four most abundant of these complexes in negative stain. The various complexes formed by MP20 most likely reflect the many ways in which tetraspanins can interact with each other to allow formation of TEMs.

}, keywords = {Animals, Buffers, Cations, Divalent, Cell Membrane, Chelating Agents, Crystallization, Detergents, Edetic Acid, Egtazic Acid, Eye Proteins, Hydrogen-Ion Concentration, Imaging, Three-Dimensional, Lens, Crystalline, Lipid Metabolism, Magnesium, Membrane Microdomains, Membrane Proteins, Protein Structure, Secondary, Protein Structure, Tertiary, Sheep, Silver Staining, Solubility, Tromethamine}, issn = {1089-8638}, doi = {10.1016/j.jmb.2007.09.001}, author = {Gonen, Tamir and Hite, Richard K and Cheng, Yifan and Petre, Benjamin M and Kistler, Joerg and Walz, Thomas} } @article {1770, title = {Preserving cell shape under environmental stress.}, journal = {Nature}, volume = {452}, year = {2008}, month = {2008 Mar 20}, pages = {361-4}, abstract = {

Maintaining cell shape and tone is crucial for the function and survival of cells and tissues. Mechanotransduction relies on the transformation of minuscule mechanical forces into high-fidelity electrical responses. When mechanoreceptors are stimulated, mechanically sensitive cation channels open and produce an inward transduction current that depolarizes the cell. For this process to operate effectively, the transduction machinery has to retain integrity and remain unfailingly independent of environmental changes. This is particularly challenging for poikilothermic organisms, where changes in temperature in the environment may impact the function of mechanoreceptor neurons. Thus, we wondered how insects whose habitat might quickly vary over several tens of degrees of temperature manage to maintain highly effective mechanical senses. We screened for Drosophila mutants with defective mechanical responses at elevated ambient temperatures, and identified a gene, spam, whose role is to protect the mechanosensory organ from massive cellular deformation caused by heat-induced osmotic imbalance. Here we show that Spam protein forms an extracellular shield that guards mechanosensory neurons from environmental insult. Remarkably, heterologously expressed Spam protein also endowed other cells with superb defence against physically and chemically induced deformation. We studied the mechanical impact of Spam coating and show that spam-coated cells are up to ten times stiffer than uncoated controls. Together, these results help explain how poikilothermic organisms preserve the architecture of critical cells during environmental stress, and illustrate an elegant and simple solution to such challenge.

}, keywords = {Animals, Biological, Cell Line, Cell Shape, Cellular, Chemical, Drosophila melanogaster, Drosophila Proteins, Electrophysiology, Environment, Eye Proteins, Hot Temperature, Humidity, Mechanical, Mechanoreceptors, Mechanotransduction, Models, Osmotic Pressure, Stimulation, Stress}, issn = {1476-4687}, doi = {10.1038/nature06603}, author = {Cook, Boaz and Hardy, Robert W and McConnaughey, William B and Zuker, Charles S} } @article {46419, title = {A presynaptic giant ankyrin stabilizes the NMJ through regulation of presynaptic microtubules and transsynaptic cell adhesion.}, journal = {Neuron}, volume = {58}, year = {2008}, month = {2008 Apr 24}, pages = {195-209}, abstract = {

In a forward genetic screen for mutations that destabilize the neuromuscular junction, we identified a novel long isoform of Drosophila ankyrin2 (ank2-L). We demonstrate that loss of presynaptic Ank2-L not only causes synapse disassembly and retraction but also disrupts neuronal excitability and NMJ morphology. We provide genetic evidence that ank2-L is necessary to generate the membrane constrictions that normally separate individual synaptic boutons and is necessary to achieve the normal spacing of subsynaptic protein domains, including the normal organization of synaptic cell adhesion molecules. Mechanistically, synapse organization is correlated with a lattice-like organization of Ank2-L, visualized using extended high-resolution structured-illumination microscopy. The stabilizing functions of Ank2-L can be mapped to the extended C-terminal domain that we demonstrate can directly bind and organize synaptic microtubules. We propose that a presynaptic Ank2-L lattice links synaptic membrane proteins and spectrin to the underlying microtubule cytoskeleton to organize and stabilize the presynaptic terminal.

}, keywords = {Amino Acid Motifs, Animals, Animals, Genetically Modified, Ankyrins, Cell Adhesion Molecules, Neuronal, Drosophila, Drosophila Proteins, Gene Expression Regulation, Horseradish Peroxidase, Larva, Luminescent Proteins, Microscopy, Electron, Transmission, Microtubules, Mutation, Neuromuscular Junction, Presynaptic Terminals, Synapsins, Synaptic Transmission}, issn = {1097-4199}, doi = {10.1016/j.neuron.2008.02.017}, author = {Pielage, Jan and Cheng, Ling and Fetter, Richard D and Carlton, Pete M and Sedat, John W and Davis, Graeme W} } @article {4252, title = {A probabilistic model of local sequence alignment that simplifies statistical significance estimation.}, journal = {PLoS Computational Biology}, volume = {4}, year = {2008}, month = {2008 May 30}, pages = {e1000069}, abstract = {

Sequence database searches require accurate estimation of the statistical significance of scores. Optimal local sequence alignment scores follow Gumbel distributions, but determining an important parameter of the distribution (lambda) requires time-consuming computational simulation. Moreover, optimal alignment scores are less powerful than probabilistic scores that integrate over alignment uncertainty ("Forward" scores), but the expected distribution of Forward scores remains unknown. Here, I conjecture that both expected score distributions have simple, predictable forms when full probabilistic modeling methods are used. For a probabilistic model of local sequence alignment, optimal alignment bit scores ("Viterbi" scores) are Gumbel-distributed with constant lambda = log 2, and the high scoring tail of Forward scores is exponential with the same constant lambda. Simulation studies support these conjectures over a wide range of profile/sequence comparisons, using 9,318 profile-hidden Markov models from the Pfam database. This enables efficient and accurate determination of expectation values (E-values) for both Viterbi and Forward scores for probabilistic local alignments.

}, keywords = {Algorithms, Base Sequence, Chromosome Mapping, Computer Simulation, Data Interpretation, DNA, Genetic, Models, Molecular Sequence Data, Sequence Alignment, Sequence Analysis, Statistical}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1000069}, author = {Sean R. Eddy} } @article {4259, title = {Probabilistic phylogenetic inference with insertions and deletions.}, journal = {PLoS Computational Biology}, volume = {4}, year = {2008}, month = {2008 Sep 19}, pages = {e1000172}, abstract = {

A fundamental task in sequence analysis is to calculate the probability of a multiple alignment given a phylogenetic tree relating the sequences and an evolutionary model describing how sequences change over time. However, the most widely used phylogenetic models only account for residue substitution events. We describe a probabilistic model of a multiple sequence alignment that accounts for insertion and deletion events in addition to substitutions, given a phylogenetic tree, using a rate matrix augmented by the gap character. Starting from a continuous Markov process, we construct a non-reversible generative (birth-death) evolutionary model for insertions and deletions. The model assumes that insertion and deletion events occur one residue at a time. We apply this model to phylogenetic tree inference by extending the program dnaml in phylip. Using standard benchmarking methods on simulated data and a new "concordance test" benchmark on real ribosomal RNA alignments, we show that the extended program dnamlepsilon improves accuracy relative to the usual approach of ignoring gaps, while retaining the computational efficiency of the Felsenstein peeling algorithm.

}, keywords = {Algorithms, Computational Biology, Computer Simulation, DNA, Evolution, Genetic, Insertional, Markov Chains, Models, Molecular, Mutagenesis, Phylogeny, Poisson Distribution, Ribosomal, RNA, Sequence Alignment, Sequence Deletion, Software, Statistical}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1000172}, author = {Rivas, Elena and Sean R. Eddy} } @article {45920, title = {Pyramidal neurons: dendritic structure and synaptic integration.}, journal = {Nature Reviews Neuroscience}, volume = {9}, year = {2008}, month = {2008 Mar}, pages = {206-21}, abstract = {

Pyramidal neurons are characterized by their distinct apical and basal dendritic trees and the pyramidal shape of their soma. They are found in several regions of the CNS and, although the reasons for their abundance remain unclear, functional studies--especially of CA1 hippocampal and layer V neocortical pyramidal neurons--have offered insights into the functions of their unique cellular architecture. Pyramidal neurons are not all identical, but some shared functional principles can be identified. In particular, the existence of dendritic domains with distinct synaptic inputs, excitability, modulation and plasticity appears to be a common feature that allows synapses throughout the dendritic tree to contribute to action-potential generation. These properties support a variety of coincidence-detection mechanisms, which are likely to be crucial for synaptic integration and plasticity.

}, keywords = {Animals, Dendrites, Hippocampus, Models, Neurological, Neocortex, Pyramidal Cells, Synapses}, issn = {1471-0048}, doi = {10.1038/nrn2286}, author = {Spruston, Nelson} } @article {1685, title = {Quantitative in vivo imaging of entire embryos with digital scanned laser light sheet fluorescence microscopy.}, journal = {Current Opinion in Neurobiology}, volume = {18}, year = {2008}, month = {2008 Dec}, pages = {624-32}, abstract = {

The observation of biological processes in their natural in vivo context is a key requirement for quantitative experimental studies in the life sciences. In many instances, it will be crucial to achieve high temporal and spatial resolution over long periods of time without compromising the physiological development of the specimen. Here, we discuss the principles underlying light sheet-based fluorescence microscopes. The most recent implementation DSLM is a tool optimized to deliver quantitative data for entire embryos at high spatio-temporal resolution. We compare DSLM to the two established light microscopy techniques: confocal and two-photon fluorescence microscopy. DSLM provides up to 50 times higher imaging speeds and a 10-100 times higher signal-to-noise ratio, while exposing the specimens to at least three orders of magnitude less light energy than confocal and two-photon fluorescence microscopes. We conclude with a perspective for future development.

}, keywords = {Animals, Computer-Assisted, Confocal, Fetus, Fluorescence, Humans, Image Processing, Lasers, Microscopy, Multiphoton, Photobleaching}, issn = {1873-6882}, doi = {10.1016/j.conb.2009.03.008}, author = {Keller, Philipp J and Stelzer, Ernst H K} } @article {2909, title = {Quantum conditions on dynamics and control in open systems.}, journal = {The Journal of Chemical Physics}, volume = {129}, year = {2008}, month = {2008 Jul 28}, pages = {041105}, abstract = {

Quantum conditions on the control of dynamics of a system coupled to an environment are obtained. Specifically, consider a system initially in a system subspace H(0) of dimensionality M(0), which evolves to populate system subspaces H(1), H(2) of dimensionalities M(1), M(2). Then, there always exists an initial state in H(0) that does not evolve into H(2) if M(0)\>dM(2), where 2

}, issn = {1089-7690}, doi = {10.1063/1.2958220}, author = {Wu, Lian-Ao and Bharioke, Arjun and Brumer, Paul} } @proceedings {3301, title = {A rate-efficient approach for establishing visual correspondences via distributed source coding.}, year = {2008}, month = {2008 Jan 28}, abstract = {

We consider the problem of communicating compact descriptors for the purpose of establishing visual correspondences between two cameras operating under rate constraints. Establishing visual correspondences is a critical step before other tasks such as camera calibration or object recognition can be performed in a network of cameras. We verify that descriptors of regions which are in correspondence are highly correlated, and propose the use of distributed source coding to reduce the bandwidth needed for transmitting descriptors required to establish correspondence. Our experiments demonstrate that the proposed scheme is able to provide compression gains of 57\% with minimal loss in the number of correctly established correspondences compared to a scheme that communicates the entire image of the scene losslessly in compressed form. Over a wide range of rates, the proposed scheme also provides superior performance when compared to simply transmitting all the feature descriptors.

}, author = {Yeo, C and Ahammad, Parvez and Ramchandran, K} } @proceedings {3297, title = {Rate-efficient visual correspondences using random projections.}, year = {2008}, month = {2008}, abstract = {

We consider the problem of establishing visual correspondences in a distributed and rate-efficient fashion by broadcasting compact descriptors. Establishing visual correspondences is a critical task before other vision tasks can be performed in a camera network. We use coarsely quantized random projections of descriptors to build binary hashes, and use the hamming distance between binary hashes as a matching criterion. In this work, we show that the hamming distance between the binary hashes has a binomial distribution, with parameters that are a function of the number of random projections and the euclidean distance between the original descriptors. We present experimental results that verify our result, and show that for the task of finding visual correspondences, sending binary hashes is more rate-efficient than prior approaches.

}, author = {Yeo, C and Ahammad, Parvez and Ramchandran, K} } @article {2363, title = {Receptors, circuits, and behaviors: new directions in chemical senses.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {28}, year = {2008}, month = {2008 Nov 12}, pages = {11802-5}, abstract = {

The chemical senses, smell and taste, are the most poorly understood sensory modalities. In recent years, however, the field of chemosensation has benefited from new methods and technical innovations that have accelerated the rate of scientific progress. For example, enormous advances have been made in identifying olfactory and gustatory receptor genes and mapping their expression patterns. Genetic tools now permit us to monitor and control neural activity in vivo with unprecedented precision. New imaging techniques allow us to watch neural activity patterns unfold in real time. Finally, improved hardware and software enable multineuron electrophysiological recordings on an expanded scale. These innovations have enabled some fresh approaches to classic problems in chemosensation.

}, keywords = {Afferent Pathways, Animals, Brain, Chemoreceptor Cells, Humans, Odorant, Olfactory Pathways, Olfactory Perception, Receptors, Sensory Receptor Cells, Smell, Taste}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3613-08.2008}, author = {Katz, Donald B and Matsunami, Hiroaki and Rinberg, Dmitry and Scott, Kristin and Wachowiak, Matt and Wilson, Rachel I} } @article {1687, title = {Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy.}, journal = {Science}, volume = {322}, year = {2008}, month = {2008 Nov 14}, pages = {1065-9}, abstract = {

A long-standing goal of biology is to map the behavior of all cells during vertebrate embryogenesis. We developed digital scanned laser light sheet fluorescence microscopy and recorded nuclei localization and movement in entire wild-type and mutant zebrafish embryos over the first 24 hours of development. Multiview in vivo imaging at 1.5 billion voxels per minute provides "digital embryos," that is, comprehensive databases of cell positions, divisions, and migratory tracks. Our analysis of global cell division patterns reveals a maternally defined initial morphodynamic symmetry break, which identifies the embryonic body axis. We further derive a model of germ layer formation and show that the mesendoderm forms from one-third of the embryo{\textquoteright}s cells in a single event. Our digital embryos, with 55 million nucleus entries, are provided as a resource.

}, keywords = {Algorithms, Animals, beta Catenin, Biological, Body Patterning, Cell Division, Cell Nucleus, Computer-Assisted, Databases, Embryo, Embryonic Development, Endoderm, Factual, Fluorescence, Germ Layers, Image Processing, Mesoderm, Microscopy, Models, Motion Pictures as Topic, Mutation, Nonmammalian, Software, Zebrafish}, issn = {1095-9203}, doi = {10.1126/science.1162493}, author = {Keller, Philipp J and Schmidt, Annette D and Wittbrodt, Joachim and Stelzer, Ernst H K} } @article {4367, title = {Reporting neural activity with genetically encoded calcium indicators.}, journal = {Brain Cell Biology}, volume = {36}, year = {2008}, month = {2008 Aug 6}, pages = {69-86}, abstract = {

Genetically encoded calcium indicators (GECIs), based on recombinant fluorescent proteins, have been engineered to observe calcium transients in living cells and organisms. Through observation of calcium, these indicators also report neural activity. We review progress in GECI construction and application, particularly toward in vivo monitoring of sparse action potentials (APs). We summarize the extrinsic and intrinsic factors that influence GECI performance. A simple model of GECI response to AP firing demonstrates the relative significance of these factors. We recommend a standardized protocol for evaluating GECIs in a physiologically relevant context. A potential method of simultaneous optical control and recording of neuronal circuits is presented.

}, keywords = {Action Potentials, Animals, Calcium Signaling, Confocal, Electrophysiology, Luminescent Proteins, Microscopy, Neurons, Signal Transduction}, issn = {1559-7113}, doi = {10.1007/s11068-008-9029-4}, author = {Hires, S Andrew and Tian, Lin and Looger, Loren L} } @article {2505, title = {The role of Broad in the development of Tribolium castaneum: implications for the evolution of the holometabolous insect pupa.}, journal = {Development (Cambridge, England)}, volume = {135}, year = {2008}, month = {2008 Feb}, pages = {569-77}, abstract = {

The evolution of complete metamorphosis in insects is a key innovation that has led to the successful diversification of holometabolous insects, yet the origin of the pupa remains an enigma. Here, we analyzed the expression of the pupal specifier gene broad (br), and the effect on br of isoform-specific, double-stranded RNA-mediated silencing, in a basal holometabolous insect, the beetle Tribolium castaneum. All five isoforms are weakly expressed during the penultimate instar and highly expressed during the prepupal period of the final instar. Application of hydroprene, a juvenile hormone analog, during the penultimate instar caused a repeat of the penultimate br expression patterns, and the formation of supernumerary larvae. Use of dsRNA against the br core region, or against a pair of either the br-Z2 or br-Z3 isoform with the br-Z1 or br-Z4 isoform, produced mobile animals with well-differentiated adult-like appendages, but which retained larval-like urogomphi and epidermis. Disruption of either the br-Z2 or the br-Z3 isoform caused the formation of shorter wings. Disruption of both br-Z1 and br-Z4 caused the appearance of pupal traits in the adults, but disruption of br-Z5 had no morphological effect. Our findings show that the br isoform functions are broadly conserved within the Holometabola and suggest that evolution of br isoform expression may have played an important role in the evolution of the pupa in holometabolous insects.

}, keywords = {Animals, Biological Evolution, Developmental, Double-Stranded, Fatty Acids, Gene Expression Profiling, Gene Expression Regulation, Genes, Insect, Insect Proteins, Larva, Phenotype, Protein Isoforms, Pupa, RNA, RNA Interference, Tribolium, Unsaturated}, issn = {0950-1991}, doi = {10.1242/dev.015263}, author = {Suzuki, Yuichiro and Truman, James W and Riddiford, Lynn M} } @article {6510, title = {Serial section scanning electron microscopy of adult brain tissue using focused ion beam milling.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {28}, year = {2008}, month = {2008 Mar 19}, pages = {2959-64}, keywords = {Animals, Brain, Computer-Assisted, Electron, Female, Image Processing, Inbred C57BL, Ions, Mice, Microscopy, Scanning, Specimen Handling, Synapses}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3189-07.2008}, author = {Knott, Graham and Marchman, Herschel and Wall, David and Lich, Ben} } @article {1492, title = {Shape registration by optimally coding shapes.}, journal = {IEEE Transactions on Information Technology in Biomedicine : A Publication of the IEEE Engineering in Medicine and Biology Society}, volume = {12}, year = {2008}, month = {2008 Sep}, pages = {627-35}, abstract = {

This paper formulates shape registration as an optimal coding problem. It employs a set of landmarks to establish the correspondence between shapes, and assumes that the best correspondence can be achieved when the polygons formed by the landmarks optimally code all the shape contours, i.e., obtain their minimum description length (MDL). This is different from previous MDL-based shape registration methods, which code the landmark locations. In this paper, each contour is discretized to be a set of points to make the coding feasible, and a number of strategies are adopted to tackle the difficult optimization problem involved. The resulting algorithm, called CAP, is able to yield statistical shape model with better quality in terms of model generalization error, which is demonstrated on both synthetic and biomedical shapes.

}, keywords = {Algorithms, Artificial Intelligence, Automated, Computer-Assisted, Image Enhancement, Image Interpretation, Pattern Recognition, Reproducibility of Results, Sensitivity and Specificity}, issn = {1558-0032}, doi = {10.1109/TITB.2008.920798}, author = {Jiang, Yifeng and Xie, Jun and Tsui, Hung-Tat} } @article {1976, title = {Signals and noise in an inhibitory interneuron diverge to control activity in nearby retinal ganglion cells.}, journal = {Nature Neuroscience}, volume = {11}, year = {2008}, month = {2008 Mar}, pages = {318-26}, abstract = {

Information about sensory stimuli is represented by spatiotemporal patterns of neural activity. The complexity of the central nervous system, however, frequently obscures the origin and properties of signals and noise that underlie these activity patterns. We minimized this constraint by examining mechanisms governing correlated activity in mouse retinal ganglion cells (RGCs) under conditions in which light-evoked responses traverse a specific circuit, the rod bipolar pathway. Signals and noise in this circuit produced correlated synaptic input to neighboring On and Off RGCs. Temporal modulation of light intensity did not alter the degree to which noise in the input to nearby RGCs was correlated, and action potential generation in individual RGCs was largely insensitive to differences in network noise generated by dynamic and static light stimuli. Together, these features enable noise in shared circuitry to diminish simultaneous action potential generation in neighboring On and Off RGCs under a variety of conditions.

}, keywords = {Action Potentials, Amacrine Cells, Animals, Artifacts, Inbred C57BL, Interneurons, Light, Lighting, Mice, Neural Inhibition, Neural Pathways, Ocular, Organ Culture Techniques, Photic Stimulation, Reaction Time, Retinal Bipolar Cells, Retinal Ganglion Cells, Retinal Rod Photoreceptor Cells, Synaptic Transmission, Vision}, issn = {1097-6256}, doi = {10.1038/nn2045}, author = {Murphy, Gabe J and Rieke, Fred} } @article {2201, title = {Single-molecule DNA sequencing of a viral genome.}, journal = {Science}, volume = {320}, year = {2008}, month = {2008 Apr 4}, pages = {106-9}, abstract = {

The full promise of human genomics will be realized only when the genomes of thousands of individuals can be sequenced for comparative analysis. A reference sequence enables the use of short read length. We report an amplification-free method for determining the nucleotide sequence of more than 280,000 individual DNA molecules simultaneously. A DNA polymerase adds labeled nucleotides to surface-immobilized primer-template duplexes in stepwise fashion, and the asynchronous growth of individual DNA molecules was monitored by fluorescence imaging. Read lengths of \>25 bases and equivalent phred software program quality scores approaching 30 were achieved. We used this method to sequence the M13 virus to an average depth of \>150x and with 100\% coverage; thus, we resequenced the M13 genome with high-sensitivity mutation detection. This demonstrates a strategy for high-throughput low-cost resequencing.

}, keywords = {Algorithms, Bacteriophage M13, Computational Biology, DNA, DNA Primers, Genetic, Genome, Mutation, Sequence Alignment, Sequence Analysis, Software, Templates, Viral}, issn = {1095-9203}, doi = {10.1038/nbt0510-426}, author = {Harris, Timothy D and Buzby, Phillip R and Babcock, Hazen and Beer, Eric and Bowers, Jayson and Braslavsky, Ido and Causey, Marie and Colonell, Jennifer and Dimeo, James and Efcavitch, J William and Giladi, Eldar and Gill, Jaime and Healy, John and Jarosz, Mirna and Lapen, Dan and Moulton, Keith and Quake, Stephen R and Steinmann, Kathleen and Thayer, Edward and Tyurina, Anastasia and Ward, Rebecca and Weiss, Howard and Xie, Zheng} } @article {68488, title = {Single-synapse ablation and long-term imaging in live C. elegans.}, journal = {J Neurosci Methods}, volume = {173}, year = {2008}, month = {09/2008}, pages = {20-6}, abstract = {

Synapses are individually operated, computational units for neural communication. To manipulate physically individual synapses in a living organism, we have developed a laser ablation technique for removing single synapses in live neurons in C. elegans that operates without apparent damage to the axon. As a complementary technique, we applied microfluidic immobilization of C. elegans to facilitate long-term fluorescence imaging and observation of neuronal development. With this technique, we directly demonstrated the existence of competition between developing synapses in the HSNL motor neuron.

}, keywords = {Animals, Axons, Behavior, Animal, Caenorhabditis elegans, Diagnostic Imaging, Laser Therapy, Microfluidic Analytical Techniques, Movement, Neurons, Synapses, Time Factors}, issn = {0165-0270}, doi = {10.1016/j.jneumeth.2008.05.007}, author = {Allen, Peter B and Sgro, Allyson E and Chao, Daniel L and Doepker, Byron E and Scott Edgar, J and Shen, Kang and Chiu, Daniel T} } @article {5215, title = {Sparse optical microstimulation in barrel cortex drives learned behaviour in freely moving mice.}, journal = {Nature}, volume = {451}, year = {2008}, month = {2008 Jan 3}, pages = {61-4}, abstract = {

Electrical microstimulation can establish causal links between the activity of groups of neurons and perceptual and cognitive functions. However, the number and identities of neurons microstimulated, as well as the number of action potentials evoked, are difficult to ascertain. To address these issues we introduced the light-gated algal channel channelrhodopsin-2 (ChR2) specifically into a small fraction of layer 2/3 neurons of the mouse primary somatosensory cortex. ChR2 photostimulation in vivo reliably generated stimulus-locked action potentials at frequencies up to 50 Hz. Here we show that naive mice readily learned to detect brief trains of action potentials (five light pulses, 1 ms, 20 Hz). After training, mice could detect a photostimulus firing a single action potential in approximately 300 neurons. Even fewer neurons (approximately 60) were required for longer stimuli (five action potentials, 250 ms). Our results show that perceptual decisions and learning can be driven by extremely brief epochs of cortical activity in a sparse subset of supragranular cortical pyramidal neurons.

}, keywords = {Action Potentials, Algal Proteins, Animal, Animals, Behavior, Cerebral Cortex, Electric Stimulation, Learning, Mice, Microbial, Movement, Optics and Photonics, Photic Stimulation, Pyramidal Cells, Rhodopsins}, issn = {1476-4687}, doi = {10.1038/nature06445}, author = {Huber, Daniel and Petreanu, Leopoldo and Ghitani, Nima and Ranade, Sachin and Hrom{\'a}dka, Tom{\'a}s and Mainen, Zach and Svoboda, Karel} } @article {5213, title = {The spread of Ras activity triggered by activation of a single dendritic spine.}, journal = {Science}, volume = {321}, year = {2008}, month = {2008 Jul 4}, pages = {136-40}, abstract = {

In neurons, individual dendritic spines isolate N-methyl-d-aspartate (NMDA) receptor-mediated calcium ion (Ca2+) accumulations from the dendrite and other spines. However, the extent to which spines compartmentalize signaling events downstream of Ca2+ influx is not known. We combined two-photon fluorescence lifetime imaging with two-photon glutamate uncaging to image the activity of the small guanosine triphosphatase Ras after NMDA receptor activation at individual spines. Induction of long-term potentiation (LTP) triggered robust Ca2+-dependent Ras activation in single spines that decayed in approximately 5 minutes. Ras activity spread over approximately 10 micrometers of dendrite and invaded neighboring spines by diffusion. The spread of Ras-dependent signaling was necessary for the local regulation of the threshold for LTP induction. Thus, Ca2+-dependent synaptic signals can spread to couple multiple synapses on short stretches of dendrite.

}, keywords = {Animals, Calcium, Cell Membrane, Dendritic Spines, Diffusion, Fluorescence Resonance Energy Transfer, Glutamic Acid, GTPase-Activating Proteins, Guanine Nucleotide Exchange Factors, Hippocampus, Long-Term Potentiation, N-Methyl-D-Aspartate, Pyramidal Cells, ras Proteins, Rats, Receptors, Recombinant Fusion Proteins, Signal Transduction, Synapses, Transfection}, issn = {1095-9203}, doi = {10.1126/science.1159675}, author = {Harvey, Christopher D and Yasuda, Ryohei and Zhong, Haining and Svoboda, Karel} } @article {4980, title = {Standardized atlas of the brain of the desert locust, Schistocerca gregaria.}, journal = {Cell and Tissue Research}, volume = {333}, year = {2008}, month = {2008 Jul 27}, pages = {125-45}, abstract = {

In order to understand the connectivity of neuronal networks, their constituent neurons should ideally be studied in a common framework. Since morphological data from physiologically characterized and stained neurons usually arise from different individual brains, this can only be performed in a virtual standardized brain that compensates for interindividual variability. The desert locust, Schistocerca gregaria, is an insect species used widely for the analysis of olfactory and visual signal processing, endocrine functions, and neural networks controlling motor output. To provide a common multi-user platform for neural circuit analysis in the brain of this species, we have generated a standardized three-dimensional brain of this locust. Serial confocal images from whole-mount locust brains were used to reconstruct 34 neuropil areas in ten brains. For standardization, we compared two different methods: an iterative shape-averaging (ISA) procedure by using affine transformations followed by iterative nonrigid registrations, and the Virtual Insect Brain (VIB) protocol by using global and local rigid transformations followed by local nonrigid transformations. Both methods generated a standard brain, but for different applications. Whereas the VIB technique was designed to visualize anatomical variability between the input brains, the purpose of the ISA method was the opposite, i.e., to remove this variability. A novel individually labeled neuron, connecting the lobula to the midbrain and deutocerebrum, has been registered into the ISA atlas and demonstrates its usefulness and accuracy for future analysis of neural networks. The locust standard brain is accessible at http://www.3d-insectbrain.com .

}, keywords = {Anatomic, Anatomy, Animals, Artistic, Atlases as Topic, Brain, Brain Mapping, Grasshoppers, Imaging, Models, Neuroanatomy, Neurological, Neurons, Three-Dimensional}, issn = {0302-766X}, doi = {10.1007/s00441-008-0620-x}, author = {Kurylas, Angela E and Rohlfing, Torsten and Krofczik, Sabine and Jenett, Arnim and Homberg, Uwe} } @article {2695, title = {Straightening caenorhabditis elegans images.}, journal = {Bioinformatics}, volume = {24}, year = {2008}, month = {2008 Jan 15}, pages = {234-42}, abstract = {

MOTIVATION: Caenorhabditis elegans, a roundworm found in soil, is a widely studied model organism with about 1000 cells in the adult. Producing high-resolution fluorescence images of C.elegans to reveal biological insights is becoming routine, motivating the development of advanced computational tools for analyzing the resulting image stacks. For example, worm bodies usually curve significantly in images. Thus one must {\textquoteright}straighten{\textquoteright} the worms if they are to be compared under a canonical coordinate system. RESULTS: We develop a worm straightening algorithm (WSA) that restacks cutting planes orthogonal to a {\textquoteright}backbone{\textquoteright} that models the anterior-posterior axis of the worm. We formulate the backbone as a parametric cubic spline defined by a series of control points. We develop two methods for automatically determining the locations of the control points. Our experimental methods show that our approaches effectively straighten both 2D and 3D worm images.

}, keywords = {Algorithms, Animals, Caenorhabditis elegans, Computer-Assisted, Fluorescence, Image Enhancement, Image Interpretation, Imaging, Microscopy, Three-Dimensional}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btm569}, author = {Peng, Hanchuan and Long, Fuhui and Liu, Xiao and Kim, Stuart K and Myers, Eugene W} } @article {46408, title = {Structural basis of the metal specificity for nickel regulatory protein NikR.}, journal = {Biochemistry}, volume = {47}, year = {2008}, month = {2008 Feb 19}, pages = {1938-46}, abstract = {

In the presence of excess nickel, Escherichia coli NikR regulates cellular nickel uptake by suppressing the transcription of the nik operon, which encodes the nickel uptake transporter, NikABCDE. Previously published in vitro studies have shown that NikR is capable of binding a range of divalent transition metal ions in addition to Ni2+, including Co2+, Cu2+, Zn2+, and Cd2+. To understand how the high-affinity nickel binding site of NikR is able to accommodate these other metal ions, and to improve our understanding of NikR{\textquoteright}s mechanism of binding to DNA, we have determined structures of the metal-binding domain (MBD) of NikR in the apo form and in complex with Cu2+ and Zn2+ ions and compared them with the previously published structures with Ni2+. We observe that Cu2+ ions bind in a manner very similar to that of Ni2+, with a square planar geometry but with longer bond lengths. Crystals grown in the presence of Zn2+ reveal a protein structure similar to that of apo MBD with a disordered alpha3 helix, but with two electron density peaks near the Ni2+ binding site corresponding to two Zn2+ ions. These structural findings along with biochemical data on NikR support a hypothesis that ordering of the alpha3 helix is important for repressor activation.

}, keywords = {Binding Sites, Circular Dichroism, Escherichia coli Proteins, Metals, Models, Molecular, Protein Conformation, Repressor Proteins}, issn = {0006-2960}, doi = {10.1021/bi702006h}, author = {Phillips, Christine M and Schreiter, Eric R and Guo, Yayi and Wang, Sheila C and Zamble, Deborah B and Drennan, Catherine L} } @article {2399, title = {Structural changes in TAF4b-TFIID correlate with promoter selectivity.}, journal = {Molecular Cell}, volume = {29}, year = {2008}, month = {2008 Jan 18}, pages = {81-91}, abstract = {

Proper ovarian development requires the cell type-specific transcription factor TAF4b, a subunit of the core promoter recognition complex TFIID. We present the 35 A structure of a cell type-specific core promoter recognition complex containing TAF4b and TAF4 (4b/4-IID), which is responsible for directing transcriptional synergy between c-Jun and Sp1 at a TAF4b target promoter. As a first step toward correlating potential structure/function relationships of the prototypic TFIID versus 4b/4-IID, we have compared their 3D structures by electron microscopy and single-particle reconstruction. These studies reveal that TAF4b incorporation into TFIID induces an open conformation at the lobe involved in TFIIA and putative activator interactions. Importantly, this open conformation correlates with differential activator-dependent transcription and promoter recognition by 4b/4-IID. By combining functional and structural analysis, we find that distinct localized structural changes in a megadalton macromolecular assembly can significantly alter its activity and lead to a TAF4b-induced reprogramming of promoter specificity.

}, keywords = {B-Lymphocytes, Cell Line, Computer-Assisted, Electron, Genetic, Hela Cells, Humans, Image Processing, Imaging, Microscopy, Models, Molecular, Organ Specificity, Promoter Regions, Protein Conformation, Protein Interaction Mapping, Proto-Oncogene Proteins c-jun, Sp1 Transcription Factor, Structure-Activity Relationship, TATA-Binding Protein Associated Factors, Three-Dimensional, Transcription Factor TFIIA, Transcription Factor TFIID, Transcriptional Activation, Tumor}, issn = {1097-2765}, doi = {10.1073/pnas.1100640108}, author = {Liu, Wei-Li and Coleman, Robert A and Grob, Patricia and King, David S and Florens, Laurence and Washburn, Michael P and Geles, Kenneth G and Yang, Joyce L and Ramey, Vincent and Nogales, Eva and Tjian, Robert} } @article {1581, title = {Structural insight into substrate binding and catalysis of a novel 2-keto-3-deoxy-D-arabinonate dehydratase illustrates common mechanistic features of the FAH superfamily.}, journal = {Journal of Molecular Biology}, volume = {379}, year = {2008}, month = {2008 May 30}, pages = {357-71}, abstract = {

The archaeon Sulfolobus solfataricus converts d-arabinose to 2-oxoglutarate by an enzyme set consisting of two dehydrogenases and two dehydratases. The third step of the pathway is catalyzed by a novel 2-keto-3-deoxy-D-arabinonate dehydratase (KdaD). In this study, the crystal structure of the enzyme has been solved to 2.1 A resolution. The enzyme forms an oval-shaped ring of four subunits, each consisting of an N-terminal domain with a four-stranded beta-sheet flanked by two alpha-helices, and a C-terminal catalytic domain with a fumarylacetoacetate hydrolase (FAH) fold. Crystal structures of complexes of the enzyme with magnesium or calcium ions and either a substrate analog 2-oxobutyrate, or the aldehyde enzyme product 2,5-dioxopentanoate revealed that the divalent metal ion in the active site is coordinated octahedrally by three conserved carboxylate residues, a water molecule, and both the carboxylate and the oxo groups of the substrate molecule. An enzymatic mechanism for base-catalyzed dehydration is proposed on the basis of the binding mode of the substrate to the metal ion, which suggests that the enzyme enhances the acidity of the protons alpha to the carbonyl group, facilitating their abstraction by glutamate 114. A comprehensive structural comparison of members of the FAH superfamily is presented and their evolution is discussed, providing a basis for functional investigations of this largely unexplored protein superfamily.

}, keywords = {Amino Acid Sequence, Animals, Archaeal Proteins, Binding Sites, Catalysis, Crystallography, Humans, Hydro-Lyases, Hydrolases, Magnesium, Models, Molecular, Molecular Sequence Data, Molecular Structure, Protein Binding, Protein Structure, Protein Subunits, Quaternary, Secondary, Sequence Alignment, Substrate Specificity, Sulfolobus solfataricus, Tertiary, X-Ray}, issn = {1089-8638}, doi = {10.1016/j.jmb.2008.03.064}, author = {Brouns, Stan J J and Barends, Thomas R M and Worm, Petra and Akerboom, Jasper and Turnbull, Andrew P and Salmon, Laurent and van der Oost, John} } @article {4636, title = {Structured illumination in total internal reflection fluorescence microscopy using a spatial light modulator.}, journal = {Optics Letters}, volume = {33}, year = {2008}, month = {2008 Jul 15}, pages = {1629-31}, abstract = {

In wide-field fluorescence microscopy, illuminating the specimen with evanescent standing waves increases lateral resolution more than twofold. We report a versatile setup for standing-wave illumination in total internal reflection fluorescence microscopy. An adjustable diffraction grating written on a phase-only spatial light modulator controls the illumination field. Selecting appropriate diffraction orders and displaying a sheared (tilted) diffraction grating allows one to tune the penetration depth in very fine steps. The setup achieves 91 nm lateral resolution for green emission.

}, issn = {0146-9592}, author = {Fiolka, Reto and Beck, Markus and Stemmer, Andreas} } @article {2957, title = {Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy.}, journal = {Science}, volume = {320}, year = {2008}, month = {2008 Jun 6}, pages = {1332-6}, abstract = {

Fluorescence light microscopy allows multicolor visualization of cellular components with high specificity, but its utility has until recently been constrained by the intrinsic limit of spatial resolution. We applied three-dimensional structured illumination microscopy (3D-SIM) to circumvent this limit and to study the mammalian nucleus. By simultaneously imaging chromatin, nuclear lamina, and the nuclear pore complex (NPC), we observed several features that escape detection by conventional microscopy. We could resolve single NPCs that colocalized with channels in the lamin network and peripheral heterochromatin. We could differentially localize distinct NPC components and detect double-layered invaginations of the nuclear envelope in prophase as previously seen only by electron microscopy. Multicolor 3D-SIM opens new and facile possibilities to analyze subcellular structures beyond the diffraction limit of the emitted light.

}, keywords = {Animals, Cell Line, Cell Nucleus, Chromatin, Confocal, Fluorescence, Fluorescent Dyes, Heterochromatin, Imaging, Indoles, Interphase, Lamins, Mice, Microscopy, Myoblasts, Nuclear Envelope, Nuclear Lamina, Nuclear Pore, Optics and Photonics, Three-Dimensional}, issn = {1095-9203}, doi = {10.1126/science.1156947}, author = {Schermelleh, Lothar and Carlton, Peter M and Haase, Sebastian and Shao, Lin and Winoto, Lukman and Kner, Peter and Burke, Brian and Cardoso, M Cristina and Agard, David A and Gustafsson, Mats G L and Leonhardt, Heinrich and Sedat, John W} } @article {2960, title = {Super-resolution light microscopy goes live.}, journal = {Nature Methods}, volume = {5}, year = {2008}, month = {2008 May}, pages = {385-7}, abstract = {

Microscopic resolution far beyond the diffraction limit is possible by localizing single molecules individually. This approach has now been demonstrated on living cells.

}, keywords = {Computer-Assisted, Image Processing, Microscopy, Staining and Labeling}, issn = {1548-7105}, doi = {10.1038/nmeth0508-385}, author = {Gustafsson, Mats G L} } @article {2395, title = {TBP, Mot1, and NC2 establish a regulatory circuit that controls DPE-dependent versus TATA-dependent transcription.}, journal = {Genes \& Development}, volume = {22}, year = {2008}, month = {2008 Sep 1}, pages = {2353-8}, abstract = {

The RNA polymerase II core promoter is a structurally and functionally diverse transcriptional module. RNAi depletion and overexpression experiments revealed a genetic circuit that controls the balance of transcription from two core promoter motifs, the TATA box and the downstream core promoter element (DPE). In this circuit, TBP activates TATA-dependent transcription and represses DPE-dependent transcription, whereas Mot1 and NC2 block TBP function and thus repress TATA-dependent transcription and activate DPE-dependent transcription. This regulatory circuit is likely to be one means by which biological networks can transmit transcriptional signals, such as those from DPE-specific and TATA-specific enhancers, via distinct pathways.

}, keywords = {Animals, Cells, Cultured, Drosophila, Drosophila Proteins, Enhancer Elements, Gene Expression Regulation, Genetic, Promoter Regions, RNA Polymerase II, TATA Box, TATA-Box Binding Protein, Transcription, Transcription Factors}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Hsu, Jer-Yuan and Juven-Gershon, Tamar and Marr, Michael T and Wright, Kevin J and Tjian, Robert and Kadonaga, James T} } @article {2346, title = {Theta-mediated dynamics of spatial information in hippocampus.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {28}, year = {2008}, month = {2008 Jun 4}, pages = {5959-64}, abstract = {

In rodent hippocampus, neuronal activity is organized by a 6-10 Hz theta oscillation. The spike timing of hippocampal pyramidal cells with respect to the theta rhythm correlates with an animal{\textquoteright}s position in space. This correlation has been suggested to indicate an explicit temporal code for position. Alternatively, it may be interpreted as a byproduct of theta-dependent dynamics of spatial information flow in hippocampus. Here we show that place cell activity on different phases of theta reflects positions shifted into the future or past along the animal{\textquoteright}s trajectory in a two-dimensional environment. The phases encoding future and past positions are consistent across recorded CA1 place cells, indicating a coherent representation at the network level. Consistent theta-dependent time offsets are not simply a consequence of phase-position correlation (phase precession), because they are no longer seen after data randomization that preserves the phase-position relationship. The scale of these time offsets, 100-300 ms, is similar to the latencies of hippocampal activity after sensory input and before motor output, suggesting that offset activity may maintain coherent brain activity in the face of information processing delays.

}, keywords = {Action Potentials, Animals, Hippocampus, Long-Evans, Male, Rats, Spatial Behavior, Theta Rhythm}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3773-10.2011}, author = {Itskov, Vladimir and Pastalkova, Eva and Mizuseki, Kenji and Buzs{\'a}ki, Gy{\"o}rgy and Harris, Kenneth D} } @article {1688, title = {Three-dimensional microtubule behavior in Xenopus egg extracts reveals four dynamic states and state-dependent elastic properties.}, journal = {Biophysical Journal}, volume = {95}, year = {2008}, month = {2008 Aug}, pages = {1474-86}, abstract = {

Although microtubules are key players in many cellular processes, very little is known about their dynamic and mechanical properties in physiological three-dimensional environments. The conventional model of microtubule dynamic instability postulates two dynamic microtubule states, growth and shrinkage. However, several studies have indicated that such a model does not provide a comprehensive quantitative and qualitative description of microtubule behavior. Using three-dimensional laser light-sheet fluorescence microscopy and a three-dimensional sample preparation in spacious Teflon cylinders, we measured microtubule dynamic instability and elasticity in interphase Xenopus laevis egg extracts. Our data are inconsistent with a two-state model of microtubule dynamic instability and favor an extended four-state model with two independent metastable pause states over a three-state model with a single pause state. Moreover, our data on kinetic state transitions rule out a simple GTP cap model as the driving force of microtubule stabilization in egg extracts on timescales of a few seconds or longer. We determined the three-dimensional elastic properties of microtubules as a function of both the contour length and the dynamic state. Our results indicate that pausing microtubules are less flexible than growing microtubules and suggest a growth-speed-dependent persistence length. These data might hint toward mechanisms that enable microtubules to efficiently perform multiple different tasks in the cell and suggest the development of a unified model of microtubule dynamics and microtubule mechanics.

}, keywords = {Animals, Elasticity, Imaging, Mechanical, Microtubules, Ovum, Stress, Three-Dimensional, Xenopus laevis}, issn = {1542-0086}, doi = {10.1529/biophysj.107.128223}, author = {Keller, Philipp J and Pampaloni, Francesco and Lattanzi, Gianluca and Stelzer, Ernst H K} } @article {2958, title = {Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination.}, journal = {Biophysical Journal}, volume = {94}, year = {2008}, month = {2008 Jun}, pages = {4957-70}, abstract = {

Structured illumination microscopy is a method that can increase the spatial resolution of wide-field fluorescence microscopy beyond its classical limit by using spatially structured illumination light. Here we describe how this method can be applied in three dimensions to double the axial as well as the lateral resolution, with true optical sectioning. A grating is used to generate three mutually coherent light beams, which interfere in the specimen to form an illumination pattern that varies both laterally and axially. The spatially structured excitation intensity causes normally unreachable high-resolution information to become encoded into the observed images through spatial frequency mixing. This new information is computationally extracted and used to generate a three-dimensional reconstruction with twice as high resolution, in all three dimensions, as is possible in a conventional wide-field microscope. The method has been demonstrated on both test objects and biological specimens, and has produced the first light microscopy images of the synaptonemal complex in which the lateral elements are clearly resolved.

}, keywords = {Algorithms, Computer-Assisted, Fluorescence, Image Enhancement, Image Interpretation, Imaging, Lighting, Microscopy, Reproducibility of Results, Sensitivity and Specificity, Three-Dimensional}, issn = {1542-0086}, doi = {10.1529/biophysj.107.120345}, author = {Gustafsson, Mats G L and Shao, Lin and Carlton, Peter M and Wang, C J Rachel and Golubovskaya, Inna N and Cande, W Zacheus and Agard, David A and Sedat, John W} } @article {45736, title = {Tinker where the tinkering{\textquoteright}s good.}, journal = {Trends Genet}, volume = {24}, year = {2008}, month = {2008 Jul}, pages = {317-9}, abstract = {

Do general principles govern the genetic causes of phenotypic evolution? One promising idea is that mutations in cis-regulatory regions play a predominant role in phenotypic evolution because they can alter gene activity without causing pleiotropic effects. Recent evidence that revealed the genetic basis of pigmentation pattern evolution in Drosophila santomea supports this notion. Multiple mutations that disrupt an abdominal enhancer of the pleiotropic gene tan partly explain the reduced pigmentation observed in this species.

}, keywords = {Abdomen, Animals, Biological Evolution, Drosophila melanogaster, Genes, Insect, Mutation, Phenotype, Pigmentation}, issn = {0168-9525}, doi = {10.1016/j.tig.2008.04.003}, author = {Rockman, Matthew V and Stern, David L} } @article {988, title = {Tools for neuroanatomy and neurogenetics in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, year = {2008}, month = {2008 Jul 15}, pages = {9715-20}, abstract = {

We demonstrate the feasibility of generating thousands of transgenic Drosophila melanogaster lines in which the expression of an exogenous gene is reproducibly directed to distinct small subsets of cells in the adult brain. We expect the expression patterns produced by the collection of 5,000 lines that we are currently generating to encompass all neurons in the brain in a variety of intersecting patterns. Overlapping 3-kb DNA fragments from the flanking noncoding and intronic regions of genes thought to have patterned expression in the adult brain were inserted into a defined genomic location by site-specific recombination. These fragments were then assayed for their ability to function as transcriptional enhancers in conjunction with a synthetic core promoter designed to work with a wide variety of enhancer types. An analysis of 44 fragments from four genes found that \>80\% drive expression patterns in the brain; the observed patterns were, on average, comprised of \<100 cells. Our results suggest that the D. melanogaster genome contains \>50,000 enhancers and that multiple enhancers drive distinct subsets of expression of a gene in each tissue and developmental stage. We expect that these lines will be valuable tools for neuroanatomy as well as for the elucidation of neuronal circuits and information flow in the fly brain.

}, keywords = {Animals, Biomedical Research, Brain, Developmental, Drosophila melanogaster, Enhancer Elements, Gene Expression Regulation, Genes, Genetic, Genetically Modified, Insect, Neurons, Neurosciences, Recombination}, issn = {1091-6490}, doi = {https://doi.org/10.1073/pnas.0803697105}, author = {Pfeiffer, Barret D and Jenett, Arnim and Hammonds, Ann S and Ngo, Teri-T B and Misra, Sima and Murphy, Christine and Scully, Audra and Carlson, Joseph W and Wan, Kenneth H and Laverty, Todd R and Mungall, Chris and Svirskas, Rob and Kadonaga, James T and Doe, Chris Q and Eisen, Michael B and Celniker, Susan E and Rubin, Gerald M} } @article {1101, title = {Trimethyl lock: a stable chromogenic substrate for esterases.}, journal = {Molecules}, volume = {13}, year = {2008}, month = {2008 Jan 31}, pages = {204-11}, abstract = {

p-Nitrophenyl acetate is the most commonly used substrate for detecting the catalytic activity of esterases, including those that activate prodrugs in human cells. This substrate is unstable in aqueous solution, limiting its utility. Here, a stable chromogenic substrate for esterases is produced by the structural isolation of an acetyl ester and p-nitroaniline group using a trimethyl lock moiety. Upon ester hydrolysis, unfavorable steric interactions between the three methyl groups of this o-hydroxycinnamic acid derivative encourage rapid lactonization to form a hydrocoumarin and release p-nitroaniline. This "prochromophore" could find use in a variety of assays.

}, keywords = {Chromogenic Compounds, Esterases, Humans, Hydrogen-Ion Concentration, Hydrolysis, Kinetics, Spectrum Analysis, Substrate Specificity, Thermodynamics, Time Factors}, issn = {1420-3049}, author = {Levine, Michael N and Lavis, Luke D and Raines, Ronald T} } @conference {6532, title = {Unfolding warping for object recognition.}, booktitle = {19TH International Conference on Pattern Recognition}, year = {2008}, month = {2008 December 11}, publisher = {IEEE}, organization = {IEEE}, address = {Tampa, FL}, abstract = {

In practice, understanding the spatial relationships between the surfaces of an object, can significantly improve the performance of object recognition systems. In this paper we propose a novel framework to recognize objects in pictures taken from arbitrary viewpoints. The idea is to maintain the frontal views of the major faces of objects in a global flat map. Then an unfolding warping technique is used to change the pose of the query object in the test view so that all visible surfaces of the object can be observed from a frontal viewpoint, improving the handling of serious occlusions and large viewpoint changes. We demonstrate the effectiveness of our approach through analysis of recognition trials of complex objects with comparison to popular methods.

}, isbn = {978-1-4244-2174-9}, doi = {10.1109/ICPR.2008.4761188}, author = {Xie, Jun and Hu, Min and Shah, Mubarak} } @article {46303, title = {Universal memory mechanism for familiarity recognition and identification.}, journal = {The Journal of Neuroscience : The Official Journal of the Society for Neuroscience}, volume = {28}, year = {2008}, month = {2008 Jan 2}, pages = {239-48}, abstract = {

Macaque monkeys were tested on a delayed-match-to-multiple-sample task, with either a limited set of well trained images (in randomized sequence) or with never-before-seen images. They performed much better with novel images. False positives were mostly limited to catch-trial image repetitions from the preceding trial. This result implies extremely effective one-shot learning, resembling Standing{\textquoteright}s finding that people detect familiarity for 10,000 once-seen pictures (with 80\% accuracy) (Standing, 1973). Familiarity memory may differ essentially from identification, which embeds and generates contextual information. When encountering another person, we can say immediately whether his or her face is familiar. However, it may be difficult for us to identify the same person. To accompany the psychophysical findings, we present a generic neural network model reproducing these behaviors, based on the same conservative Hebbian synaptic plasticity that generates delay activity identification memory. Familiarity becomes the first step toward establishing identification. Adding an inter-trial reset mechanism limits false positives for previous-trial images. The model, unlike previous proposals, relates repetition-recognition with enhanced neural activity, as recently observed experimentally in 92\% of differential cells in prefrontal cortex, an area directly involved in familiarity recognition. There may be an essential functional difference between enhanced responses to novel versus to familiar images: The maximal signal from temporal cortex is for novel stimuli, facilitating additional sensory processing of newly acquired stimuli. The maximal signal for familiar stimuli arising in prefrontal cortex facilitates the formation of selective delay activity, as well as additional consolidation of the memory of the image in an upstream cortical module.

}, keywords = {Animals, Behavior, Animal, Computer Simulation, Discrimination (Psychology), Haplorhini, Identification (Psychology), Models, Neurological, Neural Networks (Computer), Photic Stimulation, Recognition (Psychology), ROC Curve, Task Performance and Analysis}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4799-07.2008}, author = {Yakovlev, Volodya and Amit, Daniel J and Romani, Sandro and Hochstein, Shaul} } @article {68826, title = {V2a and V2b neurons are generated by the final divisions of pair-producing progenitors in the zebrafish spinal cord}, journal = {Development}, volume = {135}, year = {2008}, month = {09/2008}, pages = {3001-3005}, abstract = {

The p2 progenitor domain in the ventral spinal cord gives rise to two interneuron subtypes: V2a and V2b. Delta-Notch-mediated cell-cell interactions between postmitotic immature neurons have been implicated in the segregation of neuron subtypes. However, lineage relationships between V2a and V2b neurons have not been reported. We address this issue using Tg[vsx1:GFP]zebrafish, a model system in which high GFP expression is initiated near the final stage of p2 progenitors. Cell fates were followed in progeny using time-lapse microscopy. Results indicate that the vast majority, if not all, of GFP-labeled p2 progenitors divide once to produce V2a/V2b neuron pairs,indicating that V2a and V2b neurons are generated by the asymmetric division of pair-producing progenitor cells. Together with evidence that Notch signaling is involved in the cell fate specification process, our results strongly suggest that Delta-Notch interactions between sister cells play a crucial role in the final outcome of these asymmetric divisions. This mechanism for determining cell fate is similar to asymmetric divisions that occur during Drosophila neurogenesis, where ganglion mother cells divide once to produce distinct neurons. However, unlike in Drosophila, the divisional axes of p2 progenitors in zebrafish were not fixed. We report that the terminal division of pair-producing progenitor cells in vertebrate neurogenesis can reproducibly produce two distinct neurons through a mechanism that may not depend on the orientation of the division axis.

}, issn = {0950-1991}, doi = {10.1242/dev.024802}, url = {https://doi.org/10.1242/dev.024802}, author = {Kimura, Yukiko and Satou, Chie and Higashijima, Shin-Ichi} } @article {6516, title = {Vector and parameters for targeted transgenic RNA interference in Drosophila melanogaster.}, journal = {Nature Methods}, volume = {5}, year = {2008}, month = {2008 Jan}, pages = {49-51}, abstract = {

The conditional expression of hairpin constructs in Drosophila melanogaster has emerged in recent years as a method of choice in functional genomic studies. To date, upstream activating site-driven RNA interference constructs have been inserted into the genome randomly using P-element-mediated transformation, which can result in false negatives due to variable expression. To avoid this problem, we have developed a transgenic RNA interference vector based on the phiC31 site-specific integration method.

}, keywords = {Animals, Drosophila melanogaster, Drosophila Proteins, Gene Targeting, Genetic Vectors, RNA Interference}, issn = {1548-7105}, doi = {10.1038/nmeth1146}, author = {Ni, Jian-Quan and Markstein, Michele and Binari, Richard and Pfeiffer, Barret and Liu, Lu-Ping and Villalta, Christians and Booker, Matthew and Perkins, Lizabeth and Perrimon, Norbert} } @article {1227, title = {Visual pattern memory requires foraging function in the central complex of Drosophila.}, journal = {Learning \& Memory}, volume = {15}, year = {2008}, month = {2008 Mar}, pages = {133-42}, abstract = {

The role of the foraging (for) gene, which encodes a cyclic guanosine-3{\textquoteright},5{\textquoteright}-monophosphate (cGMP)-dependent protein kinase (PKG), in food-search behavior in Drosophila has been intensively studied. However, its functions in other complex behaviors have not been well-characterized. Here, we show experimentally in Drosophila that the for gene is required in the operant visual learning paradigm. Visual pattern memory was normal in a natural variant rover (for(R)) but was impaired in another natural variant sitter (for(S)), which has a lower PKG level. Memory defects in for(S) flies could be rescued by either constitutive or adult-limited expression of for in the fan-shaped body. Interestingly, we showed that such rescue also occurred when for was expressed in the ellipsoid body. Additionally, expression of for in the fifth layer of the fan-shaped body restored sufficient memory for the pattern parameter "elevation" but not for "contour orientation," whereas expression of for in the ellipsoid body restored sufficient memory for both parameters. Our study defines a Drosophila model for further understanding the role of cGMP-PKG signaling in associative learning/memory and the neural circuit underlying this for-dependent visual pattern memory.

}, keywords = {Alleles, Animals, Brain, Conditioning, Cyclic GMP-Dependent Protein Kinases, Drosophila melanogaster, Drosophila Proteins, Gene Library, Genetically Modified, Insertional, Isoenzymes, Memory, Mutagenesis, Nerve Tissue Proteins, Operant, Pattern Recognition, Recombinant Fusion Proteins, Short-Term, Visual}, issn = {1549-5485}, doi = {10.1101/lm.873008}, author = {Wang, Zhipeng and Pan, Yufeng and Li, Weizhe and Jiang, Huoqing and Chatzimanolis, Lazaros and Chang, Jianhong and Gong, Zhefeng and Liu, Li} } @article {2169, title = {Visually mediated motor planning in the escape response of Drosophila.}, journal = {Current Biology}, volume = {18}, year = {2008}, month = {2008 Sep 9}, pages = {1300-7}, abstract = {

A key feature of reactive behaviors is the ability to spatially localize a salient stimulus and act accordingly. Such sensory-motor transformations must be particularly fast and well tuned in escape behaviors, in which both the speed and accuracy of the evasive response determine whether an animal successfully avoids predation [1]. We studied the escape behavior of the fruit fly, Drosophila, and found that flies can use visual information to plan a jump directly away from a looming threat. This is surprising, given the architecture of the pathway thought to mediate escape [2, 3]. Using high-speed videography, we found that approximately 200 ms before takeoff, flies begin a series of postural adjustments that determine the direction of their escape. These movements position their center of mass so that leg extension will push them away from the expanding visual stimulus. These preflight movements are not the result of a simple feed-forward motor program because their magnitude and direction depend on the flies{\textquoteright} initial postural state. Furthermore, flies plan a takeoff direction even in instances when they choose not to jump. This sophisticated motor program is evidence for a form of rapid, visually mediated motor planning in a genetically accessible model organism.

}, keywords = {Animal, Animals, Drosophila melanogaster, Escape Reaction, Extremities, Flight, Motor Activity, Motor Cortex, Visual Perception}, issn = {0960-9822}, doi = {10.1016/j.cub.2008.07.094}, author = {Card, Gwyneth and Dickinson, Michael H} } @article {4431, title = {Visuomotor transformation in the fly gaze stabilization system.}, journal = {PLoS Biology}, volume = {6}, year = {2008}, month = {2008 Jul 22}, pages = {e173}, abstract = {

For sensory signals to control an animal{\textquoteright}s behavior, they must first be transformed into a format appropriate for use by its motor systems. This fundamental problem is faced by all animals, including humans. Beyond simple reflexes, little is known about how such sensorimotor transformations take place. Here we describe how the outputs of a well-characterized population of fly visual interneurons, lobula plate tangential cells (LPTCs), are used by the animal{\textquoteright}s gaze-stabilizing neck motor system. The LPTCs respond to visual input arising from both self-rotations and translations of the fly. The neck motor system however is involved in gaze stabilization and thus mainly controls compensatory head rotations. We investigated how the neck motor system is able to selectively extract rotation information from the mixed responses of the LPTCs. We recorded extracellularly from fly neck motor neurons (NMNs) and mapped the directional preferences across their extended visual receptive fields. Our results suggest that-like the tangential cells-NMNs are tuned to panoramic retinal image shifts, or optic flow fields, which occur when the fly rotates about particular body axes. In many cases, tangential cells and motor neurons appear to be tuned to similar axes of rotation, resulting in a correlation between the coordinate systems the two neural populations employ. However, in contrast to the primarily monocular receptive fields of the tangential cells, most NMNs are sensitive to visual motion presented to either eye. This results in the NMNs being more selective for rotation than the LPTCs. Thus, the neck motor system increases its rotation selectivity by a comparatively simple mechanism: the integration of binocular visual motion information.

}, keywords = {Animals, Diptera, Fixation, Motion Perception, Motor Neurons, Neck, Neurons, Ocular, Photic Stimulation, Visual Fields, Visual Pathways}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0060173}, author = {Huston, Stephen J and Krapp, Holger G} } @article {4637, title = {Widefield fluorescence microscopy with extended resolution.}, journal = {Histochemistry and Cell Biology}, volume = {130}, year = {2008}, month = {2008 Nov}, pages = {807-17}, abstract = {

Widefield fluorescence microscopy is seeing dramatic improvements in resolution, reaching today 100 nm in all three dimensions. This gain in resolution is achieved by dispensing with uniform K{\"o}hler illumination. Instead, non-uniform excitation light patterns with sinusoidal intensity variations in one, two, or three dimensions are applied combined with powerful image reconstruction techniques. Taking advantage of non-linear fluorophore response to the excitation field, the resolution can be further improved down to several 10 nm. In this review article, we describe the image formation in the microscope and computational reconstruction of the high-resolution dataset when exciting the specimen with a harmonic light pattern conveniently generated by interfering laser beams forming standing waves. We will also discuss extensions to total internal reflection microscopy, non-linear microscopy, and three-dimensional imaging.

}, keywords = {Animals, Computer-Assisted, Confocal, Equipment Design, Fluorescence, Fluorescent Dyes, Humans, Image Enhancement, Image Processing, Imaging, Microscopy, Reproducibility of Results, Three-Dimensional}, issn = {0948-6143}, doi = {10.1007/s00418-008-0506-8}, author = {Stemmer, Andreas and Beck, Markus and Fiolka, Reto} } @article {1114, title = {Absence of the Thorpe-Ingold Eet by gem-diphenyl groups in ring-closing enyne metathesis.}, journal = {Tetrahedron Letters}, volume = {48}, year = {2007}, month = {2007 Nov 5}, pages = {7961-4}, abstract = {

In tandem ring-closing metathesis of alkynyl silaketals containing two different tethered olefins, the gem-dimethyl group showed the expected Thorpe-Ingold effect, thereby giving good level of group selectivity. Unexpectedly, however, the corresponding gem-diphenyl group did not show any Thorpe-Ingold effect for the ring closure reaction.

}, issn = {0040-4039}, doi = {10.1016/j.tetlet.2007.09.063}, author = {Kim, Yi Jin and Grimm, Jonathan B and Lee, Daesung} } @article {2167, title = {Alignment of large image series using cubic B-splines tessellation: application to transmission electron microscopy data.}, journal = {Medical Image Computing and Computer-Assisted Intervention: MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention}, volume = {10}, year = {2007}, month = {2007}, pages = {710-7}, abstract = {

3D reconstruction from serial 2D microscopy images depends on non-linear alignment of serial sections. For some structures, such as the neuronal circuitry of the brain, very large images at very high resolution are necessary to permit reconstruction. These very large images prevent the direct use of classical registration methods. We propose in this work a method to deal with the non-linear alignment of arbitrarily large 2D images using the finite support properties of cubic B-splines. After initial affine alignment, each large image is split into a grid of smaller overlapping sub-images, which are individually registered using cubic B-splines transformations. Inside the overlapping regions between neighboring sub-images, the coefficients of the knots controlling the B-splines deformations are blended, to create a virtual large grid of knots for the whole image. The sub-images are resampled individually, using the new coefficients, and assembled together into a final large aligned image. We evaluated the method on a series of large transmission electron microscopy images and our results indicate significant improvements compared to both manual and affine alignment.

}, keywords = {Algorithms, Artificial Intelligence, Automated, Computer-Assisted, Electron, Image Enhancement, Image Interpretation, Imaging, Microscopy, Pattern Recognition, Reproducibility of Results, Sensitivity and Specificity, Subtraction Technique, Three-Dimensional, Transmission}, author = {Dauguet, Julien and Bock, Davi and Reid, R Clay and Warfield, Simon K} } @article {2810, title = {Ambient mass spectrometry with a handheld mass spectrometer at high pressure.}, journal = {Analytical Chemistry}, volume = {79}, year = {2007}, month = {2007 Oct 15}, pages = {7734-9}, abstract = {

The first coupling of atmospheric pressure ionization methods, electrospray ionization (ESI) and desorption electrospray ionization (DESI), to a miniature hand-held mass spectrometer is reported. The instrument employs a rectilinear ion trap (RIT) mass analyzer and is battery-operated, hand-portable, and rugged (total system: 10 kg, 0.014 m(3), 75 W power consumption). The mass spectrometer was fitted with an atmospheric inlet, consisting of a 10 cm x 127 microm inner diameter stainless steel capillary tube which was used to introduce gas into the vacuum chamber at 13 mL/min. The operating pressure was 15 mTorr. Ions, generated by the atmospheric pressure ion source, were directed by the inlet along the axis of the ion trap, entering through an aperture in the dc-biased end plate, which was also operated as an ion gate. ESI and DESI sources were used to generate ions; ESI-MS analysis of an aqueous mixture of drugs yielded detection limits in the low parts-per-billion range. Signal response was linear over more than 3 orders of magnitude. Tandem mass spectrometry experiments were used to identify components of this mixture. ESI was also applied to the analysis of peptides and in this case multiply charged species were observed for compounds of molecular weight up to 1200 Da. Cocaine samples deposited or already present on different surfaces, including currency, were rapidly analyzed in situ by DESI. A geometry-independent version of the DESI ion source was also coupled to the miniature mass spectrometer. These results demonstrate that atmospheric pressure ionization can be implemented on simple portable mass spectrometry systems.

}, keywords = {Alkylation, Calibration, Mass Spectrometry, Molecular Structure, Molecular Weight, Pressure, Proteins, Temperature}, issn = {0003-2700}, doi = {10.1364/AO.50.001792}, author = {Keil, Adam and Talaty, Nari and Janfelt, Christian and Noll, Robert J and Gao, Liang and Ouyang, Zheng and Cooks, R Graham} } @article {2126, title = {Associative pairing enhances action potential back-propagation in radial oblique branches of CA1 pyramidal neurons.}, journal = {The Journal of Physiology}, volume = {580}, year = {2007}, month = {2007 May 1}, pages = {787-800}, abstract = {

Back-propagating action potentials (bAPs) are involved in associative synaptic plasticity and the modulation of dendritic excitability. We have used high-speed confocal and two-photon imaging to measure calcium and voltage signals associated with action potential propagation into oblique branches of CA1 pyramidal neurons in adult hippocampal slices. The spatial profile of the bAP-associated Ca(2+) influx was biphasic, with an initial increase in the proximity of the branch point followed by a progressive decrease. Voltage imaging in the branches showed that bAP amplitude was initially constant and then steadily declined with distance from the soma. To determine the role of transient K(+) channels in this profile, we used external Ba(2+) (150 microm) as a channel blocker, after characterizing its effect on A-type K(+) channels in the apical trunk. Bath application of Ba(2+) significantly reduced the A-type K(+) current in outside-out patches and nearly eliminated the distance-dependent decrease in bAP amplitude and its associated Ca(2+) signal. Finally, small amplitude bAPs at more distal oblique branch locations could be boosted by simultaneous branch depolarization, such that the paired Ca(2+) signal became nearly the same for proximal and distal oblique dendrites. These data suggest that dendritic K(+) channels regulate the amplitude of bAPs to create a dendritic Ca(2+) signal whose magnitude is inversely related to the electrotonic distance from the soma when bAPs are not associated with a significant amount of localized synaptic input. This distance-dependent Ca(2+) signal from bAPs, however, can be amplified and a strong associative signal is produced once the proper correlation between synaptic activation and AP output is achieved. We hypothesize that these two signals may be involved in the regulation of the expression and activity of dendritic voltage- and ligand-gated ion channels.

}, keywords = {Action Potentials, Animals, Barium, Calcium, Dendrites, Hippocampus, Knockout, Male, Mice, Neuronal Plasticity, Potassium Channel Blockers, Potassium Channels, Pyramidal Cells, Rats, Sprague-Dawley, Synapses}, issn = {0022-3751}, doi = {10.1002/cbic.201000254}, author = {Gasparini, Sonia and Losonczy, Attila and Chen, Xixi and Johnston, Daniel and Magee, Jeffrey C} } @article {2154, title = {Automatic image analysis for gene expression patterns of fly embryos.}, journal = {BMC Cell Biology}, volume = {8}, year = {2007}, month = {2007 Jul 10}, pages = {S7}, abstract = {

Staining the mRNA of a gene via in situ hybridization (ISH) during the development of a D. melanogaster embryo delivers the detailed spatio-temporal pattern of expression of the gene. Many biological problems such as the detection of co-expressed genes, co-regulated genes, and transcription factor binding motifs rely heavily on the analyses of these image patterns. The increasing availability of ISH image data motivates the development of automated computational approaches to the analysis of gene expression patterns.

}, keywords = {Algorithms, Animals, Computational Biology, Computer-Assisted, Drosophila, Embryo, Gene Expression Profiling, Genes, Image Processing, In Situ Hybridization, Insect, Nonmammalian, Reproducibility of Results, Software Design}, issn = {1471-2121}, doi = {10.1007/s12021-010-9090-x}, author = {Peng, Hanchuan and Long, Fuhui and Zhou, Jie and Leung, Garmay and Eisen, Michael B and Myers, Eugene W} } @article {2156, title = {Automatic recognition and annotation of gene expression patterns of fly embryos.}, journal = {Bioinformatics}, volume = {23}, year = {2007}, month = {2007 Mar 1}, pages = {589-96}, abstract = {

Gene expression patterns obtained by in situ mRNA hybridization provide important information about different genes during Drosophila embryogenesis. So far, annotations of these images are done by manually assigning a subset of anatomy ontology terms to an image. This time-consuming process depends heavily on the consistency of experts.

}, keywords = {Algorithms, Animals, Computational Biology, Drosophila, Embryo, Gene Expression, In Situ Hybridization, Messenger, Nonmammalian, RNA}, issn = {1367-4811}, doi = {10.1007/s12021-010-9090-x}, author = {Zhou, Jie and Peng, Hanchuan} } @article {2718, title = {Automatic segmentation of nuclei in 3D microscopy images of C. elegans.}, journal = {2007 4TH IEEE International Symposium on Biomedical Imaging: Macro to Nano, VOLS 1-3}, year = {2007}, month = {2007 Apr 12-15}, pages = {536-9}, abstract = {

Automatic segmentation of nuclei in 3D microscopy images is essential for many biological studies including high throughput analysis of gene expression level, morphology, and phenotypes in single cell level. The complexity and variability of the microscopy images present many difficulties to the traditional image segmentation methods. In this paper, we present a new method based on 3D watershed algorithm to segment such images. By using both the intensity information of the image and the geometry information of the appropriately detected foreground mask, our method is robust to intensity fluctuation within nuclei and at the same time sensitive to the intensity and geometrical cues between nuclei. Besides, the method can automatically correct potential segmentation errors by using several post-processing steps. We tested this algorithm on the 3D confocal images of C.elegans, an organism that has been widely used in biological studies. Our results show that the algorithm can segment nuclei in high accuracy despite the non-uniform background, tightly clustered nuclei with different sizes and shapes, fluctuated intensities, and hollow-shaped staining patterns in the images.

}, author = {Long, Fuhui and Peng, Hanchuan and Myers, Eugene} } @article {1585, title = {Biochemical and structural exploration of the catalytic capacity of Sulfolobus KDG aldolases.}, journal = {The Biochemical Journal}, volume = {403}, year = {2007}, month = {2007 May 1}, pages = {421-30}, abstract = {

Aldolases are enzymes with potential applications in biosynthesis, depending on their activity, specificity and stability. In the present study, the genomes of Sulfolobus species were screened for aldolases. Two new KDGA [2-keto-3-deoxygluconate (2-oxo-3-deoxygluconate) aldolases] from Sulfolobus acidocaldarius and Sulfolobus tokodaii were identified, overexpressed in Escherichia coli and characterized. Both enzymes were found to have biochemical properties similar to the previously characterized S. solfataricus KDGA, including the condensation of pyruvate and either D,L-glyceraldehyde or D,L-glyceraldehyde 3-phosphate. The crystal structure of S. acidocaldarius KDGA revealed the presence of a novel phosphate-binding motif that allows the formation of multiple hydrogen-bonding interactions with the acceptor substrate, and enables high activity with glyceraldehyde 3-phosphate. Activity analyses with unnatural substrates revealed that these three KDGAs readily accept aldehydes with two to four carbon atoms, and that even aldoses with five carbon atoms are accepted to some extent. Water-mediated interactions permit binding of substrates in multiple conformations in the spacious hydrophilic binding site, and correlate with the observed broad substrate specificity.

}, keywords = {Aldehyde-Lyases, Aldehydes, Binding Sites, Cloning, Crystallization, Crystallography, Escherichia coli, Models, Molecular, Pyruvates, Substrate Specificity, Sulfolobus, X-Ray}, issn = {1470-8728}, doi = {10.1042/BJ20061419}, author = {Wolterink-van Loo, Suzanne and van Eerde, Andr{\'e} and Siemerink, Marco A J and Akerboom, Jasper and Dijkstra, Bauke W and van der Oost, John} } @article {3926, title = {Cell type-specific relationships between spiking and [Ca2+]i in neurons of the Xenopus tadpole olfactory bulb.}, journal = {The Journal of Physiology}, volume = {582}, year = {2007}, month = {2007 Jul 1}, pages = {163-75}, abstract = {

Multi-neuronal recordings with Ca2+ indicator dyes usually relate [Ca2+]i to action potentials (APs) assuming a stereotypical dependency between the two. However, [Ca2+]i affects and is affected by numerous complex mechanisms that differ from cell type to cell type, from cell compartment to cell compartment. Moreover, [Ca2+]i depends on the specific way a cell is activated. Here we investigate, by combining calcium imaging and on-cell patch clamp recordings, the relationship between APs (spiking) and somatic [Ca2+]i in mitral and granule cells of the olfactory bulb in Xenopus laevis tadpoles. Both cell types exhibit ongoing and odour-modulated [Ca2+]i dynamics. In mitral cells, the occurrence of APs in both spontaneous and odour-evoked situations correlates tightly to step-like [Ca2+]i increases. Moreover, odorant-induced suppression of spontaneous firing couples to a decrease in [Ca2+]i. In contrast, granule cells show a substantial number of uncorrelated events such as increases in [Ca2+]i without APs occurring or APs without any effect upon [Ca2+]i. The correlation between spiking and [Ca2+]i is low, possibly due to somatic NMDAR-mediated and subthreshold voltage-activated Ca2+ entries, and thus does not allow a reliable prediction of APs based on calcium imaging. Taken together, our results demonstrate that the relationship between somatic [Ca2+]i and APs can be cell type specific. Taking [Ca2+]i dynamics as an indicator for spiking activity is thus only reliable if the correlation has been established in the system of interest. When [Ca2+]i and APs are precisely correlated, fast calcium imaging is an extremely valuable tool for determining spatiotemporal patterns of APs in neuronal population.

}, keywords = {Action Potentials, Amino Acids, Animals, Calcium, Calcium Signaling, Fluorescence, Intracellular Fluid, Kinetics, Larva, Microscopy, Neurons, Odors, Olfactory Bulb, Olfactory Mucosa, Patch-Clamp Techniques, Reproducibility of Results, Smell, Xenopus laevis}, issn = {0022-3751}, doi = {10.1113/jphysiol.2006.125963}, author = {Lin, Bei-Jung and Chen, Tsai-Wen and Schild, Detlev} } @article {4225, title = {Channelrhodopsin-2-assisted circuit mapping of long-range callosal projections.}, journal = {Nature Neuroscience}, volume = {10}, year = {2007}, month = {2007 May}, pages = {663-8}, abstract = {

The functions of cortical areas depend on their inputs and outputs, but the detailed circuits made by long-range projections are unknown. We show that the light-gated channel channelrhodopsin-2 (ChR2) is delivered to axons in pyramidal neurons in vivo. In brain slices from ChR2-expressing mice, photostimulation of ChR2-positive axons can be transduced reliably into single action potentials. Combining photostimulation with whole-cell recordings of synaptic currents makes it possible to map circuits between presynaptic neurons, defined by ChR2 expression, and postsynaptic neurons, defined by targeted patching. We applied this technique, ChR2-assisted circuit mapping (CRACM), to map long-range callosal projections from layer (L) 2/3 of the somatosensory cortex. L2/3 axons connect with neurons in L5, L2/3 and L6, but not L4, in both ipsilateral and contralateral cortex. In both hemispheres the L2/3-to-L5 projection is stronger than the L2/3-to-L2/3 projection. Our results suggest that laminar specificity may be identical for local and long-range cortical projections.

}, keywords = {Animals, Axons, Brain Mapping, Corpus Callosum, Embryo, Female, Functional Laterality, Inbred C57BL, Mammalian, Membrane Potentials, Mice, Nerve Net, Neural Pathways, Newborn, Patch-Clamp Techniques, Photic Stimulation, Pregnancy, Retinaldehyde, Rhodopsin, Somatosensory Cortex, Transgenic}, issn = {1097-6256}, doi = {10.1038/nn1891}, author = {Petreanu, Leopoldo and Huber, Daniel and Sobczyk, Aleksander and Svoboda, Karel} } @article {45889, title = {Coincidence detection of place and temporal context in a network model of spiking hippocampal neurons.}, journal = {PLoS Computational Biology}, volume = {3}, year = {2007}, month = {2007 Dec}, pages = {e234}, abstract = {

Recent advances in single-neuron biophysics have enhanced our understanding of information processing on the cellular level, but how the detailed properties of individual neurons give rise to large-scale behavior remains unclear. Here, we present a model of the hippocampal network based on observed biophysical properties of hippocampal and entorhinal cortical neurons. We assembled our model to simulate spatial alternation, a task that requires memory of the previous path through the environment for correct selection of the current path to a reward site. The convergence of inputs from entorhinal cortex and hippocampal region CA3 onto CA1 pyramidal cells make them potentially important for integrating information about place and temporal context on the network level. Our model shows how place and temporal context information might be combined in CA1 pyramidal neurons to give rise to splitter cells, which fire selectively based on a combination of place and temporal context. The model leads to a number of experimentally testable predictions that may lead to a better understanding of the biophysical basis of information processing in the hippocampus.

}, keywords = {Action Potentials, Algorithms, Animals, Computer Simulation, Hippocampus, Models, Neurological, Nerve Net, Neurons, Rats, Synaptic Transmission}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.0030234}, author = {Katz, Yael and Kath, William L and Spruston, Nelson and Hasselmo, Michael E} } @article {4140, title = {Combinatorial methods for refined neuronal gene targeting.}, journal = {Current Opinion in Neurobiology}, volume = {17}, year = {2007}, month = {2007 Oct}, pages = {572-80}, abstract = {

Methods for the selective and reproducible expression of genetically encoded tools in targeted subsets of cells are required to facilitate studies of neuronal development, connectivity, and function in living animals. In the absence of techniques for synthesizing promoters that target defined cell groups, current methods exploit the regulatory elements of endogenous genes to achieve specificity of transgene expression. However, single promoters often have expression patterns too broad to pinpoint the functional roles of specific neurons. In this review, we describe emerging combinatorial techniques that make transgene expression contingent not upon a single promoter, but upon two or more promoters. Although only a few such techniques are currently available, recent developments promise rapid growth in this area in the coming years.

}, keywords = {Gene Expression Regulation, Gene Targeting, Gene Transfer Techniques, Humans, Neurons, Transgenes}, issn = {0959-4388}, doi = {10.1016/j.conb.2007.10.001}, author = {Luan, Haojiang and White, Benjamin H} } @article {45739, title = {Common genome-wide patterns of transcript accumulation underlying the wing polyphenism and polymorphism in the pea aphid (Acyrthosiphon pisum).}, journal = {Evol Dev}, volume = {9}, year = {2007}, month = {2007 Jul-Aug}, pages = {338-46}, abstract = {

The pea aphid, Acyrthosiphon pisum, exhibits several environmentally cued polyphenisms, in which discrete, alternative phenotypes are produced. At low-density, parthenogenetic females produce unwinged female progeny, but at high-density females produce progeny that develop with wings. These alternative phenotypes represent a solution to the competing demands of dispersal and reproduction. Males also develop as either winged or unwinged, but these alternatives are determined by a genetic polymorphism. Winged and unwinged males are morphologically less distinct from each other than winged and unwinged females, possibly because males experience fewer trade-offs between dispersal and reproduction. To assess whether shared physiological differences mirror the shared morphological differences that characterize the wing polyphenism and polymorphism, we used a cDNA microarray representing an estimated 10\% of the coding genome (1734 genes) to examine differential transcript accumulation between winged and unwinged females and males. We identified several transcripts that differentially accumulate between winged and unwinged morphs in both sexes, the majority of which are involved in energy production. Unexpectedly, the extent of differential transcript accumulation between winged and unwinged morphs was greater for adult males than for adult females. Together, these results suggest not only that similar physiological differences underlie the polyphenism and polymorphism, but that male morphs, like females, are subject to trade-offs between reproduction and dispersal that are reflected in levels of transcript accumulation and possibly genome-wide patterns of gene regulation. These data also provide a baseline for future studies of the molecular and physiological basis of life-history trade-offs.

}, keywords = {Animals, Aphids, Female, Genome, Male, Phenotype, Polymorphism, Genetic, RNA, Sex Characteristics, Wing}, issn = {1520-541X}, doi = {10.1111/j.1525-142X.2007.00170.x}, author = {Brisson, Jennifer A and Davis, Gregory K and Stern, David L} } @proceedings {3303, title = {Comparative analysis of spatial patterns of gene expression in Drosophila Melanogaster imaginal discs.}, year = {2007}, month = {2007 Apr 21}, abstract = {

Determining the precise spatial extent of expression of genes across different tissues, along with knowledge of the biochemical function of the genes is critical for understanding the roles of various genes in the development of metazoan organisms. To address this problem, we have developed high-throughput methods for generating images of gene expression in Drosophila melanogaster imaginal discs and for the automated analysis of these images. Our method automatically learns tissue shapes from a small number of manually segmented training examples and automatically aligns, extracts and scores new images, which are analyzed to generate gene expression maps for each gene. We have developed a reverse lookup procedure that enables us to identify genes that have spatial expression patterns most similar to a given gene of interest. Our methods enable us to cluster both the genes and the pixels that of the maps, thereby identifying sets of genes that have similar patterns, and regions of the tissues of interest that have similar gene expression profiles across a large number of genes.

}, author = {Harmon, C and Ahammad, Parvez and Hammonds, Ann S and Weiszmann, Richard and Celniker, Susan E and Sastry, S and Rubin, Gerald M} } @article {2506, title = {The coordination of the sequential appearance of MHR4 and dopa decarboxylase during the decline of the ecdysteroid titer at the end of the molt.}, journal = {Molecular and Cellular Endocrinology}, volume = {276}, year = {2007}, month = {2007 Sep 30}, pages = {71-9}, abstract = {

During the last larval molt in Manduca sexta, in response to an increasing, then decreasing ecdysteroid titer, a number of transcription factors such as E75B, MHR3, MHR4, and betaFTZ-F1 appear and disappear in the abdominal epidermis leading to dopa decarboxylase (DDC) expression. Messenger RNAs for both the 20E-induced transcription factors, MHR3 and E75B, are maximal near the peak of the ecdysteroid titer with MHR4 mRNA appearing as the titer declines followed by betaFTZ-F1 and DDC mRNAs. E75B and MHR4 mRNA were not expressed in Manduca GV1 cells, either during exposure to 20E or after its removal. When either MHR3 dsRNA was transfected or E75B was constitutively expressed in these cells, MHR4 mRNA appeared in response to 20E by 6h. E75B was found to form a heterodimer with MHR3 using the BacterioMatch II two-hybrid assay. We conclude that MHR3 apparently suppresses MHR4 expression in the presence of 20E; the appearance of E75B then removes MHR3 by dimerization, allowing MHR4 to be expressed. Because of significant basal activity of the ddc promoter in the GV1 cells, we could perform rescue experiments by adding various factors. Constitutive expression of either E75B or MHR4 in the cells suppressed the significant basal activity of the 3.2kb ddc promoter in the GV1 cells, but 20E had no effect on this activity. Thus, E75B and MHR4 are 20E-induced inhibitory factors that suppress ddc expression and therefore act as ecdysteroid-regulated timers to coordinate the onset of ddc expression at the end of the molt.

}, keywords = {Animals, Biological, Cell Line, Cytoplasmic and Nuclear, Developmental, Dopa Decarboxylase, Ecdysteroids, Gene Expression Regulation, Genetic, Insect Proteins, Manduca, Models, Molting, Promoter Regions, Protein Binding, Receptors}, issn = {0303-7207}, doi = {10.1016/j.mce.2007.07.002}, author = {Hiruma, Kiyoshi and Riddiford, Lynn M} } @article {1583, title = {Crystal structure and biochemical properties of the D-arabinose dehydrogenase from Sulfolobus solfataricus.}, journal = {Journal of Molecular Biology}, volume = {371}, year = {2007}, month = {2007 Aug 31}, pages = {1249-60}, abstract = {

Sulfolobus solfataricus metabolizes the five-carbon sugar d-arabinose to 2-oxoglutarate by an inducible pathway consisting of dehydrogenases and dehydratases. Here we report the crystal structure and biochemical properties of the first enzyme of this pathway: the d-arabinose dehydrogenase. The AraDH structure was solved to a resolution of 1.80 A by single-wavelength anomalous diffraction and phased using the two endogenous zinc ions per subunit. The structure revealed a catalytic and cofactor binding domain, typically present in mesophilic and thermophilic alcohol dehydrogenases. Cofactor modeling showed the presence of a phosphate binding pocket sequence motif (SRS-X2-H), which is likely to be responsible for the enzyme{\textquoteright}s preference for NADP+. The homo-tetrameric enzyme is specific for d-arabinose, l-fucose, l-galactose and d-ribose, which could be explained by the hydrogen bonding patterns of the C3 and C4 hydroxyl groups observed in substrate docking simulations. The enzyme optimally converts sugars at pH 8.2 and 91 degrees C, and displays a half-life of 42 and 26 min at 85 and 90 degrees C, respectively, indicating that the enzyme is thermostable at physiological operating temperatures of 80 degrees C. The structure represents the first crystal structure of an NADP+-dependent member of the medium-chain dehydrogenase/reductase (MDR) superfamily from Archaea.

}, keywords = {Amino Acid, Amino Acid Sequence, Binding Sites, Carbohydrates, Catalytic Domain, Crystallization, Crystallography, Hydrogen-Ion Concentration, Molecular Conformation, Molecular Sequence Data, Protein Binding, Protein Structure, Quaternary, Sequence Homology, Sugar Alcohol Dehydrogenases, Sulfolobus solfataricus, Temperature, X-Ray}, issn = {0022-2836}, doi = {10.1016/j.jmb.2007.05.097}, author = {Brouns, Stan J J and Turnbull, Andrew P and Willemen, Hanneke L D M and Akerboom, Jasper and van der Oost, John} } @article {1103, title = {Cytotoxic ribonucleases: the dichotomy of Coulombic forces.}, journal = {Biochemistry}, volume = {46}, year = {2007}, month = {2007 Sep 11}, pages = {10308-16}, abstract = {

Cells tightly regulate their contents. Still, nonspecific Coulombic interactions between cationic molecules and anionic membrane components can lead to adventitious endocytosis. Here, we characterize this process in a natural system. To do so, we create variants of human pancreatic ribonuclease (RNase 1) that differ in net molecular charge. By conjugating a small-molecule latent fluorophore to these variants and using flow cytometry, we are able to determine the kinetic mechanism for RNase 1 internalization into live human cells. We find that internalization increases with solution concentration and is not saturable. Internalization also increases with time to a steady-state level, which varies linearly with molecular charge. In contrast, the rate constant for internalization (t1/2 = 2 h) is independent of charge. We conclude that internalization involves an extracellular equilibrium complex between the cationic proteins and abundant anionic cell-surface molecules, followed by rate-limiting internalization. The enhanced internalization of more cationic variants of RNase 1 is, however, countered by their increased affinity for the cytosolic ribonuclease inhibitor protein, which is anionic. Thus, Coulombic forces mediate extracellular and intracellular equilibria in a dichotomous manner that both endangers cells and defends them from the potentially lethal enzymatic activity of ribonucleases.

}, keywords = {Biomechanics, Cell Death, Endocytosis, Fluorescent Dyes, Humans, K562 Cells, Kinetics, Mutant Proteins, Pancreatic, Protein Structure, Ribonuclease, Secondary}, issn = {0006-2960}, doi = {10.1021/bi700857u}, author = {Johnson, R Jeremy and Chao, Tzu-Yuan and Lavis, Luke D and Raines, Ronald T} } @article {2401, title = {Daniel E. Koshland, Jr. 1920-2007.}, journal = {Cell}, volume = {130}, year = {2007}, month = {2007 Aug 24}, pages = {579-80}, keywords = {20th Century, 21st Century, Biochemistry, History, United States}, issn = {0092-8674}, doi = {10.1073/pnas.1100640108}, author = {Tjian, Robert} } @article {45900, title = {Dendritic D-type potassium currents inhibit the spike afterdepolarization in rat hippocampal CA1 pyramidal neurons.}, journal = {The Journal of Physiology}, volume = {581}, year = {2007}, month = {2007 May 15}, pages = {175-87}, abstract = {

In CA1 pyramidal neurons, burst firing is correlated with hippocampally dependent behaviours and modulation of synaptic strength. One of the mechanisms underlying burst firing in these cells is the afterdepolarization (ADP) that follows each action potential. Previous work has shown that the ADP results from the interaction of several depolarizing and hyperpolarizing conductances located in the soma and the dendrites. By using patch-clamp recordings from acute rat hippocampal slices we show that D-type potassium current modulates the size of the ADP and the bursting of CA1 pyramidal neurons. Sensitivity to alpha-dendrotoxin suggests that Kv1-containing potassium channels mediate this current. Dual somato-dendritic recording, outside-out dendritic recordings, and focal application of dendrotoxin together indicate that the channels mediating this current are located in the apical dendrites. Thus, our data present evidence for a dendritic segregation of Kv1-like channels in CA1 pyramidal neurons and identify a novel action for these channels, showing that they inhibit action potential bursting by restricting the size of the ADP.

}, keywords = {Action Potentials, Animals, Dendritic Cells, Elapid Venoms, Evoked Potentials, Hippocampus, Male, Patch-Clamp Techniques, Pyramidal Cells, Rats, Rats, Wistar, Shaker Superfamily of Potassium Channels}, issn = {0022-3751}, doi = {10.1113/jphysiol.2006.127068}, author = {Metz, Alexia E and Spruston, Nelson and Martina, Marco} } @article {45917, title = {Dendritic spikes induce single-burst long-term potentiation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, year = {2007}, month = {2007 Oct 23}, pages = {17192-7}, abstract = {

The hippocampus is essential for episodic memory, which requires single-trial learning. Although long-term potentiation (LTP) of synaptic strength is a candidate mechanism for learning, it is typically induced by using repeated synaptic activation to produce precisely timed, high-frequency, or rhythmic firing. Here we show that hippocampal synapses potentiate robustly in response to strong activation by a single burst. The induction mechanism of this single-burst LTP requires activation of NMDA receptors, L-type voltage-gated calcium channels, and dendritic spikes. Thus, dendritic spikes are a critical trigger for a form of LTP that is consistent with the function of the hippocampus in episodic memory.

}, keywords = {Action Potentials, Animals, Dendrites, Excitatory Postsynaptic Potentials, Inhibitory Postsynaptic Potentials, Long-Term Potentiation, Pyramidal Cells, Rats, Rats, Wistar, Synapses}, issn = {0027-8424}, doi = {10.1073/pnas.0707919104}, author = {Remy, Stefan and Spruston, Nelson} } @proceedings {65004, title = {Developing photo activated localization microscopy}, year = {2007}, month = {2007 Apr 15}, abstract = {

In conventional biological imaging, diffraction places a limit on the minimal xy distance at which two marked objects can be discerned. Consequently, resolution of target molecules within cells is typically coarser by two orders of magnitude than the molecular scale at which the proteins are spatially distributed. Photoactivated localization microscopy (PALM) optically resolves selected subsets of protect fluorescent probes within cells at mean separations of \<25 nanometers. It involves serial photoactivation and subsequent photobleaching of numerous sparse subsets of photoactivated fluorescent protein molecules. Individual molecules are localized at near molecular resolution by determining their centers of fluorescent emission via a statistical fit of their point-spread-function. The position information from all subsets is then assembled into a super-resolution image, in which individual fluorescent molecules are isolated at high molecular densities. In this paper, some of the limitations for PALM imaging under current experimental conditions are discussed.

}, doi = {10.1109/isbi.2007.357008}, author = {George H. Patterson and Eric Betzig and Jennifer Lippincott-Schwartz and Harald F. Hess} } @article {45744, title = {The developmental genetics of microevolution.}, journal = {Novartis Found Symp}, volume = {284}, year = {2007}, month = {2007}, pages = {191-200; discussion 200-6}, abstract = {

What is the relationship between variation that segregates within natural populations and the differences that distinguish species? Many studies over the past century have demonstrated that most of the genetic variation within natural populations that contributes to quantitative traits causes relatively small phenotypic effects. In contrast, the genetic causes of quantitative differences between species are at least sometimes caused by few loci of relatively large effect. In addition, most of the results from evolutionary developmental biology are often discussed as though changes at just a few important {\textquoteright}molecular toolbox{\textquoteright} genes provide the key clues to morphological evolution. On the face of it, these divergent results seem incompatible and call into question the neo-Darwinian view that differences between species emerge from precisely the same kinds of variants that segregate much of the time in natural populations. One prediction from the classical model is that many different genes can evolve to generate similar phenotypes. I discuss our studies that demonstrate that similar phenotypes have evolved in multiple lineages of Drosophila by evolution of the same gene, shavenbaby/ovo. This evidence for parallel evolution suggests that svb occupies a privileged position in the developmental network patterning larval trichomes that makes it a favourable target of evolutionary change.

}, keywords = {Animals, Biological Evolution, Developmental Biology, Drosophila, Evolution, Molecular, Gene Expression Regulation, Developmental, Genes, Insect, Genetic Variation, Models, Biological, Models, Genetic, Models, Molecular, Phenotype, Phylogeny}, issn = {1528-2511}, author = {Stern, David L} } @article {6351, title = {Differential regulation of action potential- and metabotropic glutamate receptor-induced Ca2+ signals by inositol 1,4,5-trisphosphate in dopaminergic neurons.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {27}, year = {2007}, month = {2007 Apr 25}, pages = {4776-85}, abstract = {

Ca2+ signals associated with action potentials (APs) and metabotropic glutamate receptor (mGluR) activation exert distinct influences on neuronal activity and synaptic plasticity. However, it is not clear how these two types of Ca2+ signals are differentially regulated by neurotransmitter inputs in a single neuron. We investigated this issue in dopaminergic neurons of the ventral midbrain using brain slices. Intracellular Ca2+ was assessed by measuring Ca2+-sensitive K+ currents or imaging the fluorescence of Ca2+ indicator dyes. Tonic activation of metabotropic neurotransmitter receptors (mGluRs, alpha1 adrenergic receptors, and muscarinic acetylcholine receptors), attained by superfusion of agonists or weak, sustained (approximately 1 s) synaptic stimulation, augmented AP-induced Ca2+ transients. In contrast, Ca2+ signals elicited by strong, transient (50-200 ms) activation of mGluRs with aspartate iontophoresis were suppressed by superfusion of agonists. These opposing effects on Ca2+ signals were both mediated by an increase in intracellular inositol 1,4,5-trisphosphate (IP3) levels, because they were blocked by heparin, an IP3 receptor antagonist, and reproduced by photolytic application of IP3. Evoking APs repetitively at low frequency (2 Hz) caused inactivation of IP3 receptors and abolished IP3 facilitation of single AP-induced Ca2+ signals, whereas facilitation of Ca2+ signals triggered by bursts of APs (five at 20 Hz) was attenuated by less than half. We further obtained evidence suggesting that the psychostimulant amphetamine may augment burst-induced Ca2+ signals via both depression of basal firing and production of IP3. We propose that intracellular IP3 tone provides a mechanism to selectively amplify burst-induced Ca2+ signals in dopaminergic neurons.

}, keywords = {4, 5-Trisphosphate, 5-Trisphosphate Receptors, Action Potentials, Amphetamine, Animals, Aspartic Acid, Calcium Signaling, Central Nervous System Stimulants, Dopamine, Inositol 1, Mesencephalon, Metabotropic Glutamate, Neurons, Organ Culture Techniques, Patch-Clamp Techniques, Rats, Receptors, Ryanodine Receptor Calcium Release Channel, Sprague-Dawley}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0139-07.2007}, author = {Cui, Guohong and Bernier, Brian E and Harnett, Mark T and Morikawa, Hitoshi} } @article {6361, title = {The DNA transposon Minos as a tool for transgenesis and functional genomic analysis in vertebrates and invertebrates.}, journal = {Genome Biology}, volume = {8 Suppl 1}, year = {2007}, month = {2007 Oct 31}, pages = {S2}, abstract = {

Transposons are powerful tools for conducting genetic manipulation and functional studies in organisms that are of scientific, economic, or medical interest. Minos, a member of the Tc1/mariner family of DNA transposons, exhibits a low insertional bias and transposes with high frequency in vertebrates and invertebrates. Its use as a tool for transgenesis and genome analysis of rather different animal species is described.

}, keywords = {Animals, DNA Transposable Elements, Gene Transfer Techniques, Genomics, Invertebrates, Vertebrates}, issn = {1465-6914}, doi = {10.1186/gb-2007-8-s1-s2}, author = {Pavlopoulos, Anastasios and Oehler, Stefan and Kapetanaki, Maria G and Savakis, Charalambos} } @article {46627, title = {Downregulation of mu opioid receptor by RNA interference in the ventral tegmental area reduces ethanol consumption in mice.}, journal = {Genes, Brain, and Behavior}, volume = {6}, year = {2007}, month = {2007 Nov}, pages = {728-35}, abstract = {

Pharmacological and genetic studies have implicated the mu opioid receptor (MOR) in the regulation of ethanol intake in animal models and humans. Non-specific antagonists of opioid receptors have been shown to affect ethanol consumption when infused directly into the ventral tegmental area (VTA) of rats. However, administration of MOR-selective antagonists into the VTA has yielded mixed results. We used RNA interference (RNAi) to specifically decrease levels of MOR messenger RNA in the VTA of mice and examined the effect on ethanol consumption in a two-bottle choice paradigm. Mice were injected in the VTA with lentivirus expressing either a small hairpin RNA (shRNA) targeting MOR or a control shRNA. One week after virus injection, mice were examined for ethanol consumption in a two-bottle choice experiment with increasing concentrations of ethanol over the course of 1 month. Expression of an shRNA targeting MOR in the VTA led to a significant reduction in ethanol consumption. These results strengthen the hypothesis that MOR in the VTA is one of the key brain substrates mediating alcohol consumption. The RNAi combined with lentiviral delivery can be used successfully in brain to effect a sustained reduction in expression of specific genes for behavioral analysis.

}, keywords = {Administration, Oral, Alcohol Drinking, Animals, Choice Behavior, Dose-Response Relationship, Drug, Down-Regulation, Ethanol, Female, Gene Transfer Techniques, Lentivirus, Mice, Mice, Inbred C57BL, Receptors, Opioid, mu, RNA Interference, RNA, Messenger, RNA, Small Interfering, Ventral Tegmental Area}, issn = {1601-1848}, doi = {10.1111/j.1601-183X.2007.00303.x}, author = {Lasek, A W and Janak, P H and He, L and Whistler, J L and Heberlein, U} } @article {6392, title = {Drosophila melanogaster Methoprene-tolerant (Met) gene homologs from three mosquito species: members of PAS transcriptional factor family.}, journal = {Journal of Insect Physiology}, volume = {53}, year = {2007}, month = {2007 Mar}, pages = {246-53}, abstract = {

The Methoprene-tolerant (Met) gene in Drosophila melanogaster has been shown to function in juvenile hormone (JH) action. Met homologs were isolated from three mosquito species, Culex pipiens, Aedes aegypti and Anopheles gambiae. Sequence similarity was found to be high in bHLH and PAS conserved domains, and the majority of the 7-9 introns in AaMet and AgMet are located in either identical or similar positions, indicating evolutionary relatedness. Sequence comparison with Met and the similar germ-cell expressed (gce) gene in D. melanogaster showed that the mosquito genes are more similar to gce than to Met. Moreover, the multiple introns in AgMet and AaMet are more similar in number with the 7 introns in Dmgce than to the single intron in DmMet; in fact, six intron positions in AaMet and AgMet are similar to those in Dmgce. Efforts to identify a second homologous gene in mosquitoes were unsuccessful, suggesting a single gene in lower Diptera, consistent with the single gene uncovered in genomic sequencing of Ae. aegypti and An. gambiae. These results suggest that a gene duplication occurred during the evolution of higher Diptera, resulting in Met and gce.

}, keywords = {Amino Acid Sequence, Animals, Base Sequence, Basic Helix-Loop-Helix Transcription Factors, Culicidae, DNA, DNA Primers, Drosophila melanogaster, Drosophila Proteins, Evolution, Gene Components, Molecular, Molecular Sequence Data, Phylogeny, Reverse Transcriptase Polymerase Chain Reaction, Sequence Alignment, Sequence Analysis, Sequence Homology, Species Specificity}, issn = {0022-1910}, doi = {10.1016/j.jinsphys.2006.07.011}, author = {Wang, Shaoli and Baumann, Aaron and Wilson, Thomas G} } @article {2082, title = {Dual-color superresolution imaging of genetically expressed probes within individual adhesion complexes. (With commentary)}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, year = {2007}, month = {2007 Dec 18}, pages = {20308-13}, abstract = {

Accurate determination of the relative positions of proteins within localized regions of the cell is essential for understanding their biological function. Although fluorescent fusion proteins are targeted with molecular precision, the position of these genetically expressed reporters is usually known only to the resolution of conventional optics ( approximately 200 nm). Here, we report the use of two-color photoactivated localization microscopy (PALM) to determine the ultrastructural relationship between different proteins fused to spectrally distinct photoactivatable fluorescent proteins (PA-FPs). The nonperturbative incorporation of these endogenous tags facilitates an imaging resolution in whole, fixed cells of approximately 20-30 nm at acquisition times of 5-30 min. We apply the technique to image different pairs of proteins assembled in adhesion complexes, the central attachment points between the cytoskeleton and the substrate in migrating cells. For several pairs, we find that proteins that seem colocalized when viewed by conventional optics are resolved as distinct interlocking nano-aggregates when imaged via PALM. The simplicity, minimal invasiveness, resolution, and speed of the technique all suggest its potential to directly visualize molecular interactions within cellular structures at the nanometer scale.

Commentary: Identifies the photoactivatable fluorescent proteins (PA-FPs) Dronpa and PS-CFP2 as green partners to orange-red PA-FPs such as Kaede and Eos for dual color PALM imaging. Very low crosstalk is demonstrated between the two color channels. Furthermore, since the probes are genetically expressed, they are closely bound to their target proteins and exhibit zero non-specific background. All these properties are essential to unambiguously identify regions of co-localization or separate compartmentalization at the nanoscale, as demonstrated in the examples here.

}, keywords = {Cell Adhesion, Cell Line, Fluorescence, Humans, Light, Luminescent Proteins, Microscopy, Molecular Probes, Nanostructures, Photobleaching, Recombinant Fusion Proteins}, issn = {1091-6490}, doi = {10.1073/pnas.0710517105}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18077327}, author = {Shroff, Hari and Galbraith, Catherine G and Galbraith, James A and White, Helen and Gillette, Jennifer and Olenych, Scott and Davidson, Michael W and Betzig, Eric} } @article {2358, title = {Dynamic properties of large-field and small-field optomotor flight responses in Drosophila.}, journal = {Journal of Comparative Physiology. A, Neuroethology, Sensory, Neural, and Behavioral Physiology}, volume = {193}, year = {2007}, month = {2007 Jul}, pages = {787-99}, abstract = {

Optomotor flight control in houseflies shows bandwidth fractionation such that steering responses to an oscillating large-field rotating panorama peak at low frequency, whereas responses to small-field objects peak at high frequency. In fruit flies, steady-state large-field translation generates steering responses that are three times larger than large-field rotation. Here, we examine the optomotor steering reactions to dynamically oscillating visual stimuli consisting of large-field rotation, large-field expansion, and small-field motion. The results show that, like in larger flies, large-field optomotor steering responses peak at low frequency, whereas small-field responses persist under high frequency conditions. However, in fruit flies large-field expansion elicits higher magnitude and tighter phase-locked optomotor responses than rotation throughout the frequency spectrum, which may suggest a further segregation within the large-field pathway. An analysis of wing beat frequency and amplitude reveals that mechanical power output during flight varies according to the spatial organization and motion dynamics of the visual scene. These results suggest that, like in larger flies, the optomotor control system is organized into parallel large-field and small-field pathways, and extends previous analyses to quantify expansion-sensitivity for steering reflexes and flight power output across the frequency spectrum.

}, keywords = {Analysis of Variance, Animal, Animals, Behavior, Biological Clocks, Drosophila, Flight, Nonlinear Dynamics, Photic Stimulation, Visual Pathways}, issn = {0340-7594}, doi = {10.1016/j.cub.2010.06.072}, author = {Duistermars, Brian J and Reiser, Michael B and Zhu, Yan and Frye, Mark A} } @article {1647, title = {Evaluating a genetically encoded optical sensor of neural activity using electrophysiology in intact adult fruit flies.}, journal = {Frontiers in Neural Circuits}, volume = {1}, year = {2007}, month = {2007 Nov 2}, pages = {3}, abstract = {

Genetically encoded optical indicators hold the promise of enabling non-invasive monitoring of activity in identified neurons in behaving organisms. However, the interpretation of images of brain activity produced using such sensors is not straightforward. Several recent studies of sensory coding used G-CaMP 1.3-a calcium sensor-as an indicator of neural activity; some of these studies characterized the imaged neurons as having narrow tuning curves, a conclusion not always supported by parallel electrophysiological studies. To better understand the possible cause of these conflicting results, we performed simultaneous in vivo 2-photon imaging and electrophysiological recording of G-CaMP 1.3 expressing neurons in the antennal lobe (AL) of intact fruitflies. We find that G-CaMP has a relatively high threshold, that its signal often fails to capture spiking response kinetics, and that it can miss even high instantaneous rates of activity if those are not sustained. While G-CaMP can be misleading, it is clearly useful for the identification of promising neural targets: when electrical activity is well above the sensor{\textquoteright}s detection threshold, its signal is fairly well correlated with mean firing rate and G-CaMP does not appear to alter significantly the responses of neurons that express it. The methods we present should enable any genetically encoded sensor, activator, or silencer to be evaluated in an intact neural circuit in vivo in Drosophila.

}, issn = {1662-5110}, doi = {10.3389/neuro.04.003.2007}, author = {Jayaraman, Vivek and Laurent, Gilles} } @article {45741, title = {Evolution. An embarrassment of switches.}, journal = {Science}, volume = {317}, year = {2007}, month = {2007 Aug 10}, pages = {758-9}, keywords = {Animals, Binding Sites, Chromatin Immunoprecipitation, Evolution, Molecular, Gene Expression Regulation, Humans, Mutation, Oligonucleotide Array Sequence Analysis, Phenotype, Regulatory Sequences, Nucleic Acid, Species Specificity, Transcription Factors, Yeasts}, issn = {1095-9203}, doi = {10.1126/science.1146921}, author = {Kruglyak, Leonid and Stern, David L} } @article {6494, title = {Evolution of genes and genomes on the Drosophila phylogeny.}, journal = {Nature}, volume = {450}, year = {2007}, month = {2007 Nov 8}, pages = {203-18}, abstract = {

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

}, keywords = {Animals, Codon, DNA, DNA Transposable Elements, Drosophila, Drosophila Proteins, Evolution, Gene Order, Genes, Genome, Genomics, Immunity, Insect, Mitochondrial, Molecular, Multigene Family, Phylogeny, Reproduction, RNA, Sequence Alignment, Sequence Analysis, Synteny, Untranslated}, issn = {1476-4687}, doi = {10.1038/nature06341}, author = {Clark, Andrew G and Eisen, Michael B and Smith, Douglas R and Bergman, Casey M and Oliver, Brian and Markow, Therese A and Kaufman, Thomas C and Kellis, Manolis and Gelbart, William and Iyer, Venky N and Pollard, Daniel A and Sackton, Timothy B and Larracuente, Amanda M and Singh, Nadia D and Abad, Jose P and Abt, Dawn N and Adryan, Boris and Aguade, Montserrat and Akashi, Hiroshi and Anderson, Wyatt W and Aquadro, Charles F and Ardell, David H and Arguello, Roman and Artieri, Carlo G and Barbash, Daniel A and Barker, Daniel and Barsanti, Paolo and Batterham, Phil and Batzoglou, Serafim and Begun, Dave and Bhutkar, Arjun and Blanco, Enrico and Bosak, Stephanie A and Bradley, Robert K and Brand, Adrianne D and Brent, Michael R and Brooks, Angela N and Brown, Randall H and Butlin, Roger K and Caggese, Corrado and Calvi, Brian R and Bernardo de Carvalho, A and Caspi, Anat and Castrezana, Sergio and Celniker, Susan E and Chang, Jean L and Chapple, Charles and Chatterji, Sourav and Chinwalla, Asif and Civetta, Alberto and Clifton, Sandra W and Comeron, Josep M and Costello, James C and Coyne, Jerry A and Daub, Jennifer and David, Robert G and Delcher, Arthur L and Delehaunty, Kim and Do, Chuong B and Ebling, Heather and Edwards, Kevin and Eickbush, Thomas and Evans, Jay D and Filipski, Alan and Findeiss, Sven and Freyhult, Eva and Fulton, Lucinda and Fulton, Robert and Garcia, Ana C L and Gardiner, Anastasia and Garfield, David A and Garvin, Barry E and Gibson, Greg and Gilbert, Don and Gnerre, Sante and Godfrey, Jennifer and Good, Robert and Gotea, Valer and Gravely, Brenton and Greenberg, Anthony J and Griffiths-Jones, Sam and Gross, Samuel and Guigo, Roderic and Gustafson, Erik A and Haerty, Wilfried and Hahn, Matthew W and Halligan, Daniel L and Halpern, Aaron L and Halter, Gillian M and Han, Mira V and Heger, Andreas and Hillier, LaDeana and Hinrichs, Angie S and Holmes, Ian and Hoskins, Roger A and Hubisz, Melissa J and Hultmark, Dan and Huntley, Melanie A and Jaffe, David B and Jagadeeshan, Santosh and Jeck, William R and Johnson, Justin and Jones, Corbin D and Jordan, William C and Karpen, Gary H and Kataoka, Eiko and Keightley, Peter D and Kheradpour, Pouya and Kirkness, Ewen F and Koerich, Leonardo B and Kristiansen, Karsten and Kudrna, Dave and Kulathinal, Rob J and Kumar, Sudhir and Kwok, Roberta and Lander, Eric and Langley, Charles H and Lapoint, Richard and Lazzaro, Brian P and Lee, So-Jeong and Levesque, Lisa and Li, Ruiqiang and Lin, Chiao-Feng and Lin, Michael F and Lindblad-Toh, Kerstin and Llopart, Ana and Long, Manyuan and Low, Lloyd and Lozovsky, Elena and Lu, Jian and Luo, Meizhong and Machado, Carlos A and Makalowski, Wojciech and Marzo, Mar and Matsuda, Muneo and Matzkin, Luciano and McAllister, Bryant and McBride, Carolyn S and McKernan, Brendan and McKernan, Kevin and Mendez-Lago, Maria and Minx, Patrick and Mollenhauer, Michael U and Montooth, Kristi and Mount, Stephen M and Mu, Xu and Myers, Eugene and Negre, Barbara and Newfeld, Stuart and Nielsen, Rasmus and Noor, Mohamed A F and O{\textquoteright}Grady, Patrick and Pachter, Lior and Papaceit, Montserrat and Parisi, Matthew J and Parisi, Michael and Parts, Leopold and Pedersen, Jakob S and Pesole, Graziano and Phillippy, Adam M and Ponting, Chris P and Pop, Mihai and Porcelli, Damiano and Powell, Jeffrey R and Prohaska, Sonja and Pruitt, Kim and Puig, Marta and Quesneville, Hadi and Ram, Kristipati Ravi and Rand, David and Rasmussen, Matthew D and Reed, Laura K and Reenan, Robert and Reily, Amy and Remington, Karin A and Rieger, Tania T and Ritchie, Michael G and Robin, Charles and Rogers, Yu-Hui and Rohde, Claudia and Rozas, Julio and Rubenfield, Marc J and Ruiz, Alfredo and Russo, Susan and Salzberg, Steven L and Sanchez-Gracia, Alejandro and Saranga, David J and Sato, Hajime and Schaeffer, Stephen W and Schatz, Michael C and Schlenke, Todd and Schwartz, Russell and Segarra, Carmen and Singh, Rama S and Sirot, Laura and Sirota, Marina and Sisneros, Nicholas B and Smith, Chris D and Smith, Temple F and Spieth, John and Stage, Deborah E and Stark, Alexander and Stephan, Wolfgang and Strausberg, Robert L and Strempel, Sebastian and Sturgill, David and Sutton, Granger and Sutton, Granger G and Tao, Wei and Teichmann, Sarah and Tobari, Yoshiko N and Tomimura, Yoshihiko and Tsolas, Jason M and Valente, Vera L S and Venter, Eli and Venter, J Craig and Vicario, Saverio and Vieira, Filipe G and Vilella, Albert J and Villasante, Alfredo and Walenz, Brian and Wang, Jun and Wasserman, Marvin and Watts, Thomas and Wilson, Derek and Wilson, Richard K and Wing, Rod A and Wolfner, Mariana F and Wong, Alex and Wong, Gane Ka-Shu and Wu, Chung-I and Wu, Gabriel and Yamamoto, Daisuke and Yang, Hsiao-Pei and Yang, Shiaw-Pyng and Yorke, James A and Yoshida, Kiyohito and Zdobnov, Evgeny and Zhang, Peili and Zhang, Yu and Zimin, Aleksey V and Baldwin, Jennifer and Abdouelleil, Amr and Abdulkadir, Jamal and Abebe, Adal and Abera, Brikti and Abreu, Justin and Acer, St Christophe and Aftuck, Lynne and Alexander, Allen and An, Peter and Anderson, Erica and Anderson, Scott and Arachi, Harindra and Azer, Marc and Bachantsang, Pasang and Barry, Andrew and Bayul, Tashi and Berlin, Aaron and Bessette, Daniel and Bloom, Toby and Blye, Jason and Boguslavskiy, Leonid and Bonnet, Claude and Boukhgalter, Boris and Bourzgui, Imane and Brown, Adam and Cahill, Patrick and Channer, Sheridon and Cheshatsang, Yama and Chuda, Lisa and Citroen, Mieke and Collymore, Alville and Cooke, Patrick and Costello, Maura and D{\textquoteright}Aco, Katie and Daza, Riza and De Haan, Georgius and DeGray, Stuart and DeMaso, Christina and Dhargay, Norbu and Dooley, Kimberly and Dooley, Erin and Doricent, Missole and Dorje, Passang and Dorjee, Kunsang and Dupes, Alan and Elong, Richard and Falk, Jill and Farina, Abderrahim and Faro, Susan and Ferguson, Diallo and Fisher, Sheila and Foley, Chelsea D and Franke, Alicia and Friedrich, Dennis and Gadbois, Loryn and Gearin, Gary and Gearin, Christina R and Giannoukos, Georgia and Goode, Tina and Graham, Joseph and Grandbois, Edward and Grewal, Sharleen and Gyaltsen, Kunsang and Hafez, Nabil and Hagos, Birhane and Hall, Jennifer and Henson, Charlotte and Hollinger, Andrew and Honan, Tracey and Huard, Monika D and Hughes, Leanne and Hurhula, Brian and Husby, M Erii and Kamat, Asha and Kanga, Ben and Kashin, Seva and Khazanovich, Dmitry and Kisner, Peter and Lance, Krista and Lara, Marcia and Lee, William and Lennon, Niall and Letendre, Frances and LeVine, Rosie and Lipovsky, Alex and Liu, Xiaohong and Liu, Jinlei and Liu, Shangtao and Lokyitsang, Tashi and Lokyitsang, Yeshi and Lubonja, Rakela and Lui, Annie and MacDonald, Pen and Magnisalis, Vasilia and Maru, Kebede and Matthews, Charles and McCusker, William and McDonough, Susan and Mehta, Teena and Meldrim, James and Meneus, Louis and Mihai, Oana and Mihalev, Atanas and Mihova, Tanya and Mittelman, Rachel and Mlenga, Valentine and Montmayeur, Anna and Mulrain, Leonidas and Navidi, Adam and Naylor, Jerome and Negash, Tamrat and Nguyen, Thu and Nguyen, Nga and Nicol, Robert and Norbu, Choe and Norbu, Nyima and Novod, Nathaniel and O{\textquoteright}Neill, Barry and Osman, Sahal and Markiewicz, Eva and Oyono, Otero L and Patti, Christopher and Phunkhang, Pema and Pierre, Fritz and Priest, Margaret and Raghuraman, Sujaa and Rege, Filip and Reyes, Rebecca and Rise, Cecil and Rogov, Peter and Ross, Keenan and Ryan, Elizabeth and Settipalli, Sampath and Shea, Terry and Sherpa, Ngawang and Shi, Lu and Shih, Diana and Sparrow, Todd and Spaulding, Jessica and Stalker, John and Stange-Thomann, Nicole and Stavropoulos, Sharon and Stone, Catherine and Strader, Christopher and Tesfaye, Senait and Thomson, Talene and Thoulutsang, Yama and Thoulutsang, Dawa and Topham, Kerri and Topping, Ira and Tsamla, Tsamla and Vassiliev, Helen and Vo, Andy and Wangchuk, Tsering and Wangdi, Tsering and Weiand, Michael and Wilkinson, Jane and Wilson, Adam and Yadav, Shailendra and Young, Geneva and Yu, Qing and Zembek, Lisa and Zhong, Danni and Zimmer, Andrew and Zwirko, Zac and Jaffe, David B and Alvarez, Pablo and Brockman, Will and Butler, Jonathan and Chin, CheeWhye and Gnerre, Sante and Grabherr, Manfred and Kleber, Michael and Mauceli, Evan and MacCallum, Iain} } @article {8263, title = {Flies at the farm: Drosophila at Janelia.}, journal = {Fly}, volume = {1}, year = {2007}, month = {2007 May-Jun}, pages = {139-41}, abstract = {

On August 1, 2006 the Howard Hughes Medical Institute{\textquoteright}s first stand-alone research campus opened at Janelia Farm, near Washington DC. Our mission at Janelia is to do exceptional fundamental research. Our two scientific foci are to understand the function of neural circuits and to develop synergistic imaging technologies. To achieve this we have changed many of the conventions of academic and/or industrial science. The founding director at Janelia is the well-known Drosophilist Gerry Rubin, who has been a central figure in fly molecular, developmental and genomic biology in recent decades. Not coincidentally, we at Janelia fully appreciate the potential of flies to contribute to an understanding of neuronal circuits. Our objectives are ambitious, and in the first ten months of operations at Janelia we have made some good beginnings.

}, keywords = {Academies and Institutes, Animals, Drosophila, History, 21st Century, Research, Virginia}, issn = {1933-6942}, author = {Moses, Kevin} } @article {45740, title = {The function and regulation of Ultrabithorax in the legs of Drosophila melanogaster.}, journal = {Dev Biol}, volume = {308}, year = {2007}, month = {2007 Aug 15}, pages = {621-31}, abstract = {

Alterations in Hox gene expression patterns have been implicated in both large and small-scale morphological evolution. An improved understanding of these changes requires a detailed understanding of Hox gene cis-regulatory function and evolution. cis-regulatory evolution of the Hox gene Ultrabithorax (Ubx) has been shown to contribute to evolution of trichome patterns on the posterior second femur (T2p) of Drosophila species. As a step toward determining how this function of Ubx has evolved, we performed a series of experiments to clarify the role of Ubx in patterning femurs and to identify the cis-regulatory regions of Ubx that drive expression in T2p. We first performed clonal analysis to further define Ubx function in patterning bristle and trichome patterns in the legs. We found that low levels of Ubx expression are sufficient to repress an eighth bristle row on the posterior second and third femurs, whereas higher levels of expression are required to promote the development and migration of other bristles on the third femur and to repress trichomes. We then tested the hypothesis that the evolutionary difference in T2p trichome patterns due to Ubx was caused by a change in the global cis-regulation of Ubx expression. We found no evidence to support this view, suggesting that the evolved difference in Ubx function reflects evolution of a leg-specific enhancer. We then searched for the regulatory regions of the Ubx locus that drive expression in the second and third femur by assaying all existing regulatory mutations of the Ubx locus and new deficiencies in the large intron of Ubx that we generated by P-element-induced male recombination. We found that two enhancer regions previously known to regulate Ubx expression in the legs, abx and pbx, are required for Ubx expression in the third femur, but that they do not contribute to pupal expression of Ubx in the second femur. This analysis allowed us to rule out at least 100 kb of DNA in and around the Ubx locus as containing a T2p-specific enhancer. We then surveyed an additional approximately 30 kb using enhancer constructs. None of these enhancer constructs produced an expression pattern similar to Ubx expression in T2p. Thus, after surveying over 95\% of the Ubx locus, we have not been able to localize a T2p-specific enhancer. While the enhancer could reside within the small regions we have not surveyed, it is also possible that the enhancer is structurally complex and/or acts only within its native genomic context.

}, keywords = {Animals, Base Sequence, Body Patterning, DNA, Drosophila, Drosophila melanogaster, Drosophila Proteins, Enhancer Elements, Genetic, Evolution, Molecular, Extremities, Female, Gene Expression Regulation, Developmental, Genes, Homeobox, Genes, Insect, Genetic Complementation Test, Homeodomain Proteins, Male, Mutation, Recombination, Genetic, Species Specificity, Transcription Factors}, issn = {0012-1606}, doi = {10.1016/j.ydbio.2007.06.002}, author = {Davis, Gregory K and Srinivasan, Dayalan G and Wittkopp, Patricia J and Stern, David L} } @article {6858, title = {Function of the Drosophila CPEB protein Orb2 in long-term courtship memory.}, journal = {Nature Neuroscience}, volume = {10}, year = {2007}, month = {2007 Dec 28}, pages = {1587-93}, abstract = {

Both long-term behavioral memory and synaptic plasticity require protein synthesis, some of which may occur locally at specific synapses. Cytoplasmic polyadenylation element-binding (CPEB) proteins are thought to contribute to the local protein synthesis that underlies long-term changes in synaptic efficacy, but a role has not been established for them in the formation of long-term behavioral memory. We found that the Drosophila melanogaster CPEB protein Orb2 is acutely required for long-term conditioning of male courtship behavior. Deletion of the N-terminal glutamine-rich region of Orb2 resulted in flies that were impaired in their ability to form long-term, but not short-term, memory. Memory was restored by expressing Orb2 selectively in fruitless (fru)-positive gamma neurons of the mushroom bodies and by providing Orb2 function in mushroom bodies only during and shortly after training. Our data thus demonstrate that a CPEB protein is important in long-term memory and map the molecular, spatial and temporal requirements for its function in memory formation.

}, keywords = {Animal, Animals, Behavior, Computational Biology, Courtship, Drosophila, Drosophila Proteins, Female, Gene Expression, Genetically Modified, Green Fluorescent Proteins, Male, Memory, Memory Disorders, Mushroom Bodies, Neurons, Phylogeny, RNA-Binding Proteins, Sequence Deletion, Time Factors}, issn = {1097-6256}, doi = {10.1038/nn1996}, author = {Keleman, Krystyna and Kr{\"u}ttner, Sebastian and Alenius, Mattias and Dickson, Barry J} } @mastersthesis {1594, title = {Functional analysis of thermostable proteins involved in carbohydrate metabolism.}, year = {2007}, month = {2007}, pages = {174}, school = {Wageningen University}, type = {masters}, isbn = {978-90-8504-712}, author = {Akerboom, Jasper} } @article {4226, title = {The functional microarchitecture of the mouse barrel cortex.}, journal = {PLoS Biology}, volume = {5}, year = {2007}, month = {2007 Jul 10}, pages = {e189}, abstract = {

Cortical maps, consisting of orderly arrangements of functional columns, are a hallmark of the organization of the cerebral cortex. However, the microorganization of cortical maps at the level of single neurons is not known, mainly because of the limitations of available mapping techniques. Here, we used bulk loading of Ca(2+) indicators combined with two-photon microscopy to image the activity of multiple single neurons in layer (L) 2/3 of the mouse barrel cortex in vivo. We developed methods that reliably detect single action potentials in approximately half of the imaged neurons in L2/3. This allowed us to measure the spiking probability following whisker deflection and thus map the whisker selectivity for multiple neurons with known spatial relationships. At the level of neuronal populations, the whisker map varied smoothly across the surface of the cortex, within and between the barrels. However, the whisker selectivity of individual neurons recorded simultaneously differed greatly, even for nearest neighbors. Trial-to-trial correlations between pairs of neurons were high over distances spanning multiple cortical columns. Our data suggest that the response properties of individual neurons are shaped by highly specific subcolumnar circuits and the momentary intrinsic state of the neocortex.

}, keywords = {Algorithms, Aniline Compounds, Animals, Brain Mapping, Evoked Potentials, Fluorescent Dyes, Inbred C57BL, Mice, Models, Neural Pathways, Neurological, Organic Chemicals, Physical Stimulation, Sensory Receptor Cells, Somatosensory, Somatosensory Cortex, Vibrissae, Xanthenes}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0050189}, author = {Sato, Takashi R and Gray, Noah W and Mainen, Zachary F and Svoboda, Karel} } @proceedings {45799, title = {Gene expression patterns underlying wing polyphenism and polymorphism in the pea aphid}, volume = {46}, year = {2007}, month = {01/2007}, pages = {E186-E186}, publisher = {OXFORD UNIV PRESS INC}, abstract = {

The pea aphid, Acyrthosiphon pisum, exhibits several environmentally cued, discrete, alternate phenotypes (polyphenisms) during its life cycle. In the wing polyphenism, female progeny develop as either winged or unwinged depending on the extent of crowding or host plant quality experienced by the mother. Males also have the ability to develop as either winged or unwinged, but this is genetically determined by a single locus on the X chromosome and is thus referred to as a wing polymorphism. In order to gain insight into the patterns of gene expression that underlie the wing polyphenism and polymorphism we have used a pea aphid cDNA microarray to examine gene expression in winged and unwinged females and males. Results suggest that winged and unwinged morphs exhibit systemic differences in gene expression and that many of these differences are shared between the wing polyphenism and polymorphism (i.e., between females and males). In addition, adult winged and unwinged males exhibit pronounced differences when compared to adult females and fourth instar males, as well as to each other.

}, url = {http://www.sicb.org/meetings/2007/schedule/abstractdetails.php3?id=649}, author = {GK Davis and JA Brisson and DL Stern} } @article {1290, title = {Genome-wide screen for modifiers of ataxin-3 neurodegeneration in Drosophila.}, journal = {PLoS Genetics}, volume = {3}, year = {2007}, month = {2007 Oct 19}, pages = {1950-64}, abstract = {

Spinocerebellar ataxia type-3 (SCA3) is among the most common dominantly inherited ataxias, and is one of nine devastating human neurodegenerative diseases caused by the expansion of a CAG repeat encoding glutamine within the gene. The polyglutamine domain confers toxicity on the protein Ataxin-3 leading to neuronal dysfunction and loss. Although modifiers of polyglutamine toxicity have been identified, little is known concerning how the modifiers function mechanistically to affect toxicity. To reveal insight into spinocerebellar ataxia type-3, we performed a genetic screen in Drosophila with pathogenic Ataxin-3-induced neurodegeneration and identified 25 modifiers defining 18 genes. Despite a variety of predicted molecular activities, biological analysis indicated that the modifiers affected protein misfolding. Detailed mechanistic studies revealed that some modifiers affected protein accumulation in a manner dependent on the proteasome, whereas others affected autophagy. Select modifiers of Ataxin-3 also affected tau, revealing common pathways between degeneration due to distinct human neurotoxic proteins. These findings provide new insight into molecular pathways of polyQ toxicity, defining novel targets for promoting neuronal survival in human neurodegenerative disease.

}, keywords = {Animals, Crosses, Drosophila melanogaster, Genetic, Genome, Humans, Models, Nerve Tissue Proteins, Neurodegenerative Diseases, Neurons, Nuclear Proteins, Peptides, Phagocytosis, Proteasome Endopeptidase Complex, Protein Denaturation, Protein Folding, Repressor Proteins, Ubiquitin}, issn = {1553-7404}, doi = {10.1371/journal.pgen.0030177}, author = {Bilen, Julide and Bonini, Nancy M} } @article {6857, title = {A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila.}, journal = {Nature}, volume = {448}, year = {2007}, month = {2007 Jul 12}, pages = {151-6}, abstract = {

Forward genetic screens in model organisms have provided important insights into numerous aspects of development, physiology and pathology. With the availability of complete genome sequences and the introduction of RNA-mediated gene interference (RNAi), systematic reverse genetic screens are now also possible. Until now, such genome-wide RNAi screens have mostly been restricted to cultured cells and ubiquitous gene inactivation in Caenorhabditis elegans. This powerful approach has not yet been applied in a tissue-specific manner. Here we report the generation and validation of a genome-wide library of Drosophila melanogaster RNAi transgenes, enabling the conditional inactivation of gene function in specific tissues of the intact organism. Our RNAi transgenes consist of short gene fragments cloned as inverted repeats and expressed using the binary GAL4/UAS system. We generated 22,270 transgenic lines, covering 88\% of the predicted protein-coding genes in the Drosophila genome. Molecular and phenotypic assays indicate that the majority of these transgenes are functional. Our transgenic RNAi library thus opens up the prospect of systematically analysing gene functions in any tissue and at any stage of the Drosophila lifespan.

}, keywords = {Animals, Drosophila melanogaster, Exons, Female, Genetically Modified, Genomic Library, Male, Messenger, Muscles, Neurons, Organ Specificity, Ribonuclease III, RNA, RNA Interference}, issn = {1476-4687}, doi = {10.1038/nature05954}, author = {Dietzl, Georg and Chen, Doris and Schnorrer, Frank and Su, Kuan-Chung and Barinova, Yulia and Fellner, Michaela and Gasser, Beate and Kinsey, Kaolin and Oppel, Silvia and Scheiblauer, Susanne and Couto, Africa and Marra, Vincent and Keleman, Krystyna and Dickson, Barry J} } @article {6249, title = {Global analyses of mRNA translational control during early Drosophila embryogenesis.}, journal = {Genome Biology}, volume = {8}, year = {2007}, month = {2007}, pages = {R63}, abstract = {

BACKGROUND: In many animals, the first few hours of life proceed with little or no transcription, and developmental regulation at these early stages is dependent on maternal cytoplasm rather than the zygotic nucleus. Translational control is critical for early Drosophila embryogenesis and is exerted mainly at the gene level. To understand post-transcriptional regulation during Drosophila early embryonic development, we used sucrose polysomal gradient analyses and GeneChip analysis to illustrate the translation profile of individual mRNAs. RESULTS: We determined ribosomal density and ribosomal occupancy of over 10,000 transcripts during the first ten hours after egg laying. CONCLUSION: We report the extent and general nature of gene regulation at the translational level during early Drosophila embryogenesis on a genome-wide basis. The diversity of the translation profiles indicates multiple mechanisms modulating transcript-specific translation. Cluster analyses suggest that the genes involved in some biological processes are co-regulated at the translational level at certain developmental stages.

}, keywords = {Animals, Cluster Analysis, Developmental, Drosophila, Embryo, Embryonic Development, Gene Expression Regulation, Messenger, Nonmammalian, Polyribosomes, Protein Biosynthesis, Ribosomes, RNA, RNA 5{\textquoteright} Terminal Oligopyrimidine Sequence}, issn = {1465-6914}, doi = {10.1186/gb-2007-8-4-r63}, author = {Qin, Xiaoli and Ahn, Soyeon and Speed, Terence P and Rubin, Gerald M} } @article {955, title = {Global analysis of patterns of gene expression during Drosophila embryogenesis.}, journal = {Genome Biology}, volume = {8}, year = {2007}, month = {2007 July 23}, pages = {R145}, abstract = {

Cell and tissue specific gene expression is a defining feature of embryonic development in multi-cellular organisms. However, the range of gene expression patterns, the extent of the correlation of expression with function, and the classes of genes whose spatial expression are tightly regulated have been unclear due to the lack of an unbiased, genome-wide survey of gene expression patterns.

}, keywords = {Animals, Drosophila melanogaster, Embryonic Development, Gene Expression Profiling}, issn = {1465-6914}, doi = {10.1186/gb-2007-8-7-r145}, author = {Tomancak, Pavel and Berman, Benjamin P and Beaton, Amy and Weiszmann, Richard and Kwan, Elaine and Hartenstein, Volker and Celniker, Susan E and Rubin, Gerald M} } @article {1582, title = {A global transcriptional regulator in Thermococcus kodakaraensis controls the expression levels of both glycolytic and gluconeogenic enzyme-encoding genes.}, journal = {The Journal of Biological Chemistry}, volume = {282}, year = {2007}, month = {2007 Nov 16}, pages = {33659-70}, abstract = {

We identified a novel regulator, Thermococcales glycolytic regulator (Tgr), functioning as both an activator and a repressor of transcription in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. Tgr (TK1769) displays similarity (28\% identical) to Pyrococcus furiosus TrmB (PF1743), a transcriptional repressor regulating the trehalose/maltose ATP-binding cassette transporter genes, but is more closely related (67\%) to a TrmB paralog in P. furiosus (PF0124). Growth of a tgr disruption strain (Deltatgr) displayed a significant decrease in growth rate under gluconeogenic conditions compared with the wild-type strain, whereas comparable growth rates were observed under glycolytic conditions. A whole genome microarray analysis revealed that transcript levels of almost all genes related to glycolysis and maltodextrin metabolism were at relatively high levels in the Deltatgr mutant even under gluconeogenic conditions. The Deltatgr mutant also displayed defects in the transcriptional activation of gluconeogenic genes under these conditions, indicating that Tgr functions as both an activator and a repressor. Genes regulated by Tgr contain a previously identified sequence motif, the Thermococcales glycolytic motif (TGM). The TGM was positioned upstream of the Transcription factor B-responsive element (BRE)/TATA sequence in gluconeogenic promoters and downstream of it in glycolytic promoters. Electrophoretic mobility shift assay indicated that recombinant Tgr protein specifically binds to promoter regions containing a TGM. Tgr was released from the DNA when maltotriose was added, suggesting that this sugar is most likely the physiological effector. Our results strongly suggest that Tgr is a global transcriptional regulator that simultaneously controls, in response to sugar availability, both glycolytic and gluconeogenic metabolism in T. kodakaraensis via its direct binding to the TGM.

}, keywords = {Amino Acid, Amino Acid Motifs, Amino Acid Sequence, Escherichia coli, Genetic, Genome, Genotype, Gluconeogenesis, Glycolysis, Molecular Sequence Data, Multienzyme Complexes, NADH, NADPH Oxidoreductases, Oligonucleotide Array Sequence Analysis, Promoter Regions, Pyrococcus furiosus, Recombinant Proteins, Sequence Homology, Thermococcus, Transcription}, issn = {0021-9258}, doi = {10.1074/jbc.M703424200}, author = {Kanai, Tamotsu and Akerboom, Jasper and Takedomi, Shogo and van de Werken, Harmen J G and Blombach, Fabian and van der Oost, John and Murakami, Taira and Atomi, Haruyuki and Imanaka, Tadayuki} } @article {46628, title = {GSK-3/Shaggy regulates olfactory habituation in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, year = {2007}, month = {2007 Mar 13}, pages = {4653-7}, abstract = {

Habituation is a universal form of nonassociative learning that results in the devaluation of sensory inputs that have little information content. Although habituation is found throughout nature and has been studied in many organisms, the underlying molecular mechanisms remain poorly understood. We performed a forward genetic screen in Drosophila to search for mutations that modified habituation of an olfactory-mediated locomotor startle response, and we isolated a mutation in the glycogen synthase kinase-3 (GSK-3) homolog Shaggy. Decreases in Shaggy levels blunted habituation, whereas increases promoted habituation. Additionally, habituation acutely regulated Shaggy by an inhibitory phosphorylation mechanism, suggesting that a signal transduction pathway that regulates Shaggy is engaged during habituation. Although shaggy mutations also affected circadian rhythm period, this requirement was genetically separable from its role in habituation. Thus, shaggy functions in different neuronal circuits to regulate behavioral plasticity to an olfactory startle and circadian rhythmicity.

}, keywords = {Alleles, Animals, Behavior, Animal, Circadian Rhythm, Drosophila, Drosophila Proteins, Female, Glycogen Synthase Kinase 3, Habituation, Psychophysiologic, Male, Models, Genetic, Mutation, Phosphorylation, Signal Transduction, Smell}, issn = {0027-8424}, doi = {10.1073/pnas.0700493104}, author = {Wolf, Fred W and Eddison, Mark and Lee, Seonok and Cho, William and Heberlein, Ulrike} } @article {46630, title = {Guidelines on nicotine dose selection for in vivo research.}, journal = {Psychopharmacology (Berl)}, volume = {190}, year = {2007}, month = {2007 Feb}, pages = {269-319}, abstract = {

RATIONALE: This review provides insight for the judicious selection of nicotine dose ranges and routes of administration for in vivo studies. The literature is replete with reports in which a dosaging regimen chosen for a specific nicotine-mediated response was suboptimal for the species used. In many cases, such discrepancies could be attributed to the complex variables comprising species-specific in vivo responses to acute or chronic nicotine exposure.

OBJECTIVES: This review capitalizes on the authors{\textquoteright} collective decades of in vivo nicotine experimentation to clarify the issues and to identify the variables to be considered in choosing a dosaging regimen. Nicotine dose ranges tolerated by humans and their animal models provide guidelines for experiments intended to extrapolate to human tobacco exposure through cigarette smoking or nicotine replacement therapies. Just as important are the nicotine dosaging regimens used to provide a mechanistic framework for acquisition of drug-taking behavior, dependence, tolerance, or withdrawal in animal models.

RESULTS: Seven species are addressed: humans, nonhuman primates, rats, mice, Drosophila, Caenorhabditis elegans, and zebrafish. After an overview on nicotine metabolism, each section focuses on an individual species, addressing issues related to genetic background, age, acute vs chronic exposure, route of administration, and behavioral responses.

CONCLUSIONS: The selected examples of successful dosaging ranges are provided, while emphasizing the necessity of empirically determined dose-response relationships based on the precise parameters and conditions inherent to a specific hypothesis. This review provides a new, experimentally based compilation of species-specific dose selection for studies on the in vivo effects of nicotine.

}, keywords = {Animals, Behavioral Research, Dose-Response Relationship, Drug, Ganglionic Stimulants, Guidelines as Topic, Humans, Models, Biological, Nicotine, Species Specificity}, issn = {0033-3158}, doi = {10.1007/s00213-006-0441-0}, author = {Matta, Shannon G and Balfour, David J and Benowitz, Neal L and Boyd, R Thomas and Buccafusco, Jerry J and Caggiula, Anthony R and Craig, Caroline R and Collins, Allan C and Damaj, M Imad and Donny, Eric C and Gardiner, Phillip S and Grady, Sharon R and Heberlein, Ulrike and Leonard, Sherry S and Levin, Edward D and Lukas, Ronald J and Markou, Athina and Marks, Michael J and McCallum, Sarah E and Parameswaran, Neeraja and Perkins, Kenneth A and Picciotto, Marina R and Quik, Maryka and Rose, Jed E and Rothenfluh, Adrian and Schafer, William R and Stolerman, Ian P and Tyndale, Rachel F and Wehner, Jeanne M and Zirger, Jeffrey M} } @article {4047, title = {HCN1 channels constrain synaptically evoked Ca2+ spikes in distal dendrites of CA1 pyramidal neurons.}, journal = {Neuron}, volume = {56}, year = {2007}, month = {2007 Dec 20}, pages = {1076-89}, abstract = {

HCN1 hyperpolarization-activated cation channels act as an inhibitory constraint of both spatial learning and synaptic integration and long-term plasticity in the distal dendrites of hippocampal CA1 pyramidal neurons. However, as HCN1 channels provide an excitatory current, the mechanism of their inhibitory action remains unclear. Here we report that HCN1 channels also constrain CA1 distal dendritic Ca2+ spikes, which have been implicated in the induction of LTP at distal excitatory synapses. Our experimental and computational results indicate that HCN1 channels provide both an active shunt conductance that decreases the temporal integration of distal EPSPs and a tonic depolarizing current that increases resting inactivation of T-type and N-type voltage-gated Ca2+ channels, which contribute to the Ca2+ spikes. This dual mechanism may provide a general means by which HCN channels regulate dendritic excitability.

}, keywords = {Animals, Calcium, Calcium Channel Blockers, Computer Simulation, Cyclic Nucleotide-Gated Cation Channels, Dendrites, Dose-Response Relationship, Electric Stimulation, Excitatory Amino Acid Antagonists, Excitatory Postsynaptic Potentials, Hippocampus, Knockout, Mice, Newborn, Patch-Clamp Techniques, Potassium Channels, Pyramidal Cells, Pyrimidines, Radiation, Reaction Time, Synapses}, issn = {0896-6273}, doi = {10.1016/j.neuron.2007.11.015}, author = {Tsay, David and Dudman, Joshua T and Siegelbaum, Steven A} } @article {4050, title = {HCN1 channels control resting and active integrative properties of stellate cells from layer II of the entorhinal cortex.}, journal = {The Journal of Neuroscience}, volume = {27}, year = {2007}, month = {2007 Nov 14}, pages = {12440-51}, abstract = {

Whereas recent studies have elucidated principles for representation of information within the entorhinal cortex, less is known about the molecular basis for information processing by entorhinal neurons. The HCN1 gene encodes ion channels that mediate hyperpolarization-activated currents (I(h)) that control synaptic integration and influence several forms of learning and memory. We asked whether hyperpolarization-activated, cation nonselective 1 (HCN1) channels control processing of information by stellate cells found within layer II of the entorhinal cortex. Axonal projections from these neurons form a major component of the synaptic input to the dentate gyrus of the hippocampus. To determine whether HCN1 channels control either the resting or the active properties of stellate neurons, we performed whole-cell recordings in horizontal brain slices prepared from adult wild-type and HCN1 knock-out mice. We found that HCN1 channels are required for rapid and full activation of hyperpolarization-activated currents in stellate neurons. HCN1 channels dominate the membrane conductance at rest, are not required for theta frequency (4-12 Hz) membrane potential fluctuations, but suppress low-frequency (\<4 Hz) components of spontaneous and evoked membrane potential activity. During sustained activation of stellate cells sufficient for firing of repeated action potentials, HCN1 channels control the pattern of spike output by promoting recovery of the spike afterhyperpolarization. These data suggest that HCN1 channels expressed by stellate neurons in layer II of the entorhinal cortex are key molecular components in the processing of inputs to the hippocampal dentate gyrus, with distinct integrative roles during resting and active states.

}, keywords = {Action Potentials, Animals, Cyclic Nucleotide-Gated Cation Channels, Dentate Gyrus, Entorhinal Cortex, Female, Ion Channel Gating, Knockout, Male, Membrane Potentials, Memory, Mice, Neural Inhibition, Neural Pathways, Neurons, Organ Culture Techniques, Patch-Clamp Techniques, Potassium Channels, Synaptic Membranes, Synaptic Transmission, Theta Rhythm}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2358-07.2007}, author = {Nolan, Matthew F and Dudman, Joshua T and Dodson, Paul D and Santoro, Bina} } @article {6362, title = {Hox go omics: insights from Drosophila into Hox gene targets.}, journal = {Genome Biology}, volume = {8}, year = {2007}, month = {2007}, pages = {208}, abstract = {

Genetic studies of the targets of the Hox genes have revealed only the tip of the iceberg. Recent microarray studies that have identified hundreds more transcriptional responses to Hox genes in Drosophila will help elucidate the role of Hox genes in development and evolution.

}, keywords = {Animals, Drosophila, Genes, Genetic, Homeobox, Microarray Analysis, Transcription}, issn = {1465-6914}, doi = {10.1186/gb-2007-8-3-208}, author = {Pavlopoulos, Anastasios and Akam, Michael} } @article {2670, title = {Huntingtin-interacting protein 14, a palmitoyl transferase required for exocytosis and targeting of CSP to synaptic vesicles.}, journal = {The Journal of Cell Biology}, volume = {179}, year = {2007}, month = {2007 Dec 31}, pages = {1481-96}, abstract = {

Posttranslational modification through palmitoylation regulates protein localization and function. In this study, we identify a role for the Drosophila melanogaster palmitoyl transferase Huntingtin-interacting protein 14 (HIP14) in neurotransmitter release. hip14 mutants show exocytic defects at low frequency stimulation and a nearly complete loss of synaptic transmission at higher temperature. Interestingly, two exocytic components known to be palmitoylated, cysteine string protein (CSP) and SNAP25, are severely mislocalized at hip14 mutant synapses. Complementary DNA rescue and localization experiments indicate that HIP14 is required solely in the nervous system and is essential for presynaptic function. Biochemical studies indicate that HIP14 palmitoylates CSP and that CSP is not palmitoylated in hip14 mutants. Furthermore, the hip14 exocytic defects can be suppressed by targeting CSP to synaptic vesicles using a chimeric protein approach. Our data indicate that HIP14 controls neurotransmitter release by regulating the trafficking of CSP to synapses.

}, keywords = {Acyltransferases, Adaptor Proteins, Animals, Drosophila melanogaster, Drosophila Proteins, Exocytosis, Ganglia, Invertebrate, Nerve Tissue Proteins, Nervous System, Neuromuscular Junction, Neurotransmitter Agents, Post-Translational, Protein Processing, Protein Transport, Signal Transducing, Synaptic Transmission, Synaptic Vesicles}, issn = {1540-8140}, doi = {10.1083/jcb.200710061}, author = {Ohyama, Tomoko and Verstreken, Patrik and Ly, Cindy V and Rosenmund, Tanja and Rajan, Akhila and Tien, An-Chi and Haueter, Claire and Schulze, Karen L and Bellen, Hugo J} } @article {4440, title = {Hysteresis phenomena of the intelligent driver model for traffic flow.}, journal = {Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics}, volume = {76}, year = {2007}, month = {2007 Jul}, pages = {016105}, abstract = {

We present hysteresis phenomena of the intelligent driver model for traffic flow in a circular one-lane roadway. We show that the microscopic structure of traffic flow is dependent on its initial state by plotting the fraction of congested vehicles over the density, which shows a typical hysteresis loop, and by investigating the trajectories of vehicles on the velocity-over-headway plane. We find that the trajectories of vehicles on the velocity-over-headway plane, which usually show a hysteresis loop, include multiple loops. We also point out the relations between these hysteresis loops and the congested jams or high-density clusters in traffic flow.

}, issn = {1539-3755}, author = {Dahui, Wang and Ziqiang, Wei and Ying, Fan} } @article {6497, title = {Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics.}, journal = {Molecular Microbiology}, volume = {66}, year = {2007}, month = {2007 Dec}, pages = {1080-91}, abstract = {

Bacterial small non-coding RNAs (sRNAs) are being recognized as novel widespread regulators of gene expression in response to environmental signals. Here, we present the first search for sRNA-encoding genes in the nitrogen-fixing endosymbiont Sinorhizobium meliloti, performed by a genome-wide computational analysis of its intergenic regions. Comparative sequence data from eight related alpha-proteobacteria were obtained, and the interspecies pairwise alignments were scored with the programs eQRNA and RNAz as complementary predictive tools to identify conserved and stable secondary structures corresponding to putative non-coding RNAs. Northern experiments confirmed that eight of the predicted loci, selected among the original 32 candidates as most probable sRNA genes, expressed small transcripts. This result supports the combined use of eQRNA and RNAz as a robust strategy to identify novel sRNAs in bacteria. Furthermore, seven of the transcripts accumulated differentially in free-living and symbiotic conditions. Experimental mapping of the 5{\textquoteright}-ends of the detected transcripts revealed that their encoding genes are organized in autonomous transcription units with recognizable promoter and, in most cases, termination signatures. These findings suggest novel regulatory functions for sRNAs related to the interactions of alpha-proteobacteria with their eukaryotic hosts.

}, keywords = {Bacterial, Blotting, Computational Biology, DNA, Double-Stranded, Fabaceae, Genetic, Genome, Intergenic, Northern, Nucleic Acid Conformation, Promoter Regions, RNA, Sinorhizobium meliloti, Transcription, Untranslated}, issn = {0950-382X}, doi = {10.1111/j.1365-2958.2007.05978.x}, author = {del Val, Coral and Rivas, Elena and Torres-Quesada, Omar and Toro, Nicol{\'a}s and Jim{\'e}nez-Zurdo, Jos{\'e} I} } @article {46405, title = {IL-33 and ST2 comprise a critical biomechanically induced and cardioprotective signaling system.}, journal = {The Journal of Clinical Investigation}, volume = {117}, year = {2007}, month = {2007 Jun}, pages = {1538-49}, abstract = {

ST2 is an IL-1 receptor family member with transmembrane (ST2L) and soluble (sST2) isoforms. sST2 is a mechanically induced cardiomyocyte protein, and serum sST2 levels predict outcome in patients with acute myocardial infarction or chronic heart failure. Recently, IL-33 was identified as a functional ligand of ST2L, allowing exploration of the role of ST2 in myocardium. We found that IL-33 was a biomechanically induced protein predominantly synthesized by cardiac fibroblasts. IL-33 markedly antagonized angiotensin II- and phenylephrine-induced cardiomyocyte hypertrophy. Although IL-33 activated NF-kappaB, it inhibited angiotensin II- and phenylephrine-induced phosphorylation of inhibitor of NF-kappa B alpha (I kappa B alpha) and NF-kappaB nuclear binding activity. sST2 blocked antihypertrophic effects of IL-33, indicating that sST2 functions in myocardium as a soluble decoy receptor. Following pressure overload by transverse aortic constriction (TAC), ST2(-/-) mice had more left ventricular hypertrophy, more chamber dilation, reduced fractional shortening, more fibrosis, and impaired survival compared with WT littermates. Furthermore, recombinant IL-33 treatment reduced hypertrophy and fibrosis and improved survival after TAC in WT mice, but not in ST2(-/-) littermates. Thus, IL-33/ST2 signaling is a mechanically activated, cardioprotective fibroblast-cardiomyocyte paracrine system, which we believe to be novel. IL-33 may have therapeutic potential for beneficially regulating the myocardial response to overload.

}, keywords = {Animals, Biomechanical Phenomena, Cardiotonic Agents, Cells, Cultured, Fibroblasts, Humans, Interleukins, Membrane Proteins, Mice, Mice, Inbred C57BL, Mice, Knockout, Myocytes, Cardiac, NF-kappa B, Rats, Receptors, Cell Surface, Receptors, Interleukin, Recombinant Proteins, Signal Transduction}, issn = {0021-9738}, doi = {10.1172/JCI30634}, author = {Sanada, Shoji and Hakuno, Daihiko and Higgins, Luke J and Schreiter, Eric R and McKenzie, Andrew N J and Lee, Richard T} } @article {46415, title = {An innexin-dependent cell network establishes left-right neuronal asymmetry in C. elegans.}, journal = {Cell}, volume = {129}, year = {2007}, month = {2007 May 18}, pages = {787-99}, abstract = {

Gap junctions are widespread in immature neuronal circuits, but their functional significance is poorly understood. We show here that a transient network formed by the innexin gap-junction protein NSY-5 coordinates left-right asymmetry in the developing nervous system of Caenorhabditis elegans. nsy-5 is required for the left and right AWC olfactory neurons to establish stochastic, asymmetric patterns of gene expression during embryogenesis. nsy-5-dependent gap junctions in the embryo transiently connect the AWC cell bodies with those of numerous other neurons. Both AWCs and several other classes of nsy-5-expressing neurons participate in signaling that coordinates left-right AWC asymmetry. The right AWC can respond to nsy-5 directly, but the left AWC requires nsy-5 function in multiple cells of the network. NSY-5 forms hemichannels and intercellular gap-junction channels in Xenopus oocytes, consistent with a combination of cell-intrinsic and network functions. These results provide insight into gap-junction activity in developing circuits.

}, keywords = {Amino Acid Sequence, Animals, Base Sequence, Body Patterning, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Calcium Signaling, Cell Communication, Cell Differentiation, Connexins, Functional Laterality, Gap Junctions, Membrane Proteins, Molecular Sequence Data, Nerve Net, Nervous System, Neurons, Olfactory Pathways}, issn = {0092-8674}, doi = {10.1016/j.cell.2007.02.052}, author = {Chuang, Chiou-Fen and Vanhoven, Miri K and Fetter, Richard D and Verselis, Vytas K and Bargmann, Cornelia I} } @article {45738, title = {Internal and external constraints in the evolution of morphological allometries in a butterfly.}, journal = {Evolution}, volume = {61}, year = {2007}, month = {2007 Dec}, pages = {2958-70}, abstract = {

Much diversity in animal morphology results from variation in the relative size of morphological traits. The scaling relationships, or allometries, that describe relative trait size can vary greatly in both intercept and slope among species or other animal groups. Yet within such groups, individuals typically exhibit low variation in relative trait size. This pattern of high intra- and low intergroup variation may result from natural selection for particular allometries, from developmental constraints restricting differential growth among traits, or both. Here we explore the relative roles of short-term developmental constraints and natural selection in the evolution of the intercept of the allometry between the forewing and hindwing of a butterfly. First, despite a strong genetic correlation between these two traits, we show that artificial selection perpendicular to the forewing-hindwing scaling relationship results in rapid evolution of the allometry intercept. This demonstrates an absence of developmental constraints limiting intercept evolution for this scaling relationship. Mating experiments in a natural environment revealed strong stabilizing selection favoring males with the wild-type allometry intercept over those with derived intercepts. Our results demonstrate that evolution of this component of the forewing-hindwing allometry is not limited by developmental constraints in the short term and that natural selection on allometry intercepts can be powerful.

}, keywords = {Animals, Biological Evolution, Body Size, Butterflies, Genetic Variation, Phenotype, Selection, Genetic, Wing}, issn = {0014-3820}, doi = {10.1111/j.1558-5646.2007.00249.x}, author = {Frankino, W Anthony and Zwaan, Bas J and Stern, David L and Brakefield, Paul M} } @article {1102, title = {Intraspecies regulation of ribonucleolytic activity.}, journal = {Biochemistry}, volume = {46}, year = {2007}, month = {2007 Nov 13}, pages = {13131-40}, abstract = {

The evolutionary rate of proteins involved in obligate protein-protein interactions is slower and the degree of coevolution higher than that for nonobligate protein-protein interactions. The coevolution of the proteins involved in certain nonobligate interactions is, however, essential to cell survival. To gain insight into the coevolution of one such nonobligate protein pair, the cytosolic ribonuclease inhibitor (RI) proteins and secretory pancreatic-type ribonucleases from cow (Bos taurus) and human (Homo sapiens) were produced in Escherichia coli and purified, and their physicochemical properties were analyzed. The two intraspecies complexes were found to be extremely tight (bovine Kd = 0.69 fM; human Kd = 0.34 fM). Human RI binds to its cognate ribonuclease (RNase 1) with 100-fold greater affinity than to the bovine homologue (RNase A). In contrast, bovine RI binds to RNase 1 and RNase A with nearly equal affinity. This broader specificity is consistent with there being more pancreatic-type ribonucleases in cows (20) than humans (13). Human RI (32 cysteine residues) also has 4-fold less resistance to oxidation by hydrogen peroxide than does bovine RI (29 cysteine residues). This decreased oxidative stability of human RI, which is caused largely by Cys74, implies a larger role for human RI as an antioxidant. The conformational and oxidative stabilities of both RIs increase upon complex formation with ribonucleases. Thus, RI has evolved to maintain its inhibition of invading ribonucleases, even when confronted with extreme environmental stress. That role appears to take precedence over its role in mediating oxidative damage.

}, keywords = {Amino Acid Sequence, Animals, Biological Evolution, Cattle, Enzyme Inhibitors, Humans, Hydrogen Peroxide, Models, Molecular, Molecular Sequence Data, Oxidation-Reduction, Pancreatic, Placental Hormones, Protein Conformation, Protein Interaction Domains and Motifs, Protein Interaction Mapping, Ribonuclease, Sequence Alignment}, issn = {0006-2960}, doi = {10.1021/bi701521q}, author = {Johnson, R Jeremy and Lavis, Luke D and Raines, Ronald T} } @article {2404, title = {IRES-mediated functional coupling of transcription and translation amplifies insulin receptor feedback.}, journal = {Genes \& Development}, volume = {21}, year = {2007}, month = {2007 Jan 15}, pages = {175-83}, abstract = {

It is generally accepted that the growth rate of an organism is modulated by the availability of nutrients. One common mechanism to control cellular growth is through the global down-regulation of cap-dependent translation by eIF4E-binding proteins (4E-BPs). Here, we report evidence for a novel mechanism that allows eukaryotes to coordinate and selectively couple transcription and translation of target genes in response to a nutrient and growth signaling cascade. The Drosophila insulin-like receptor (dINR) pathway incorporates 4E-BP resistant cellular internal ribosome entry site (IRES) containing mRNAs, to functionally couple transcriptional activation with differential translational control in a cell that is otherwise translationally repressed by 4E-BP. Although examples of cellular IRESs have been previously reported, their critical role mediating a key physiological response has not been well documented. Our studies reveal an integrated transcriptional and translational response mechanism specifically dependent on a cellular IRES that coordinates an essential physiological signal responsible for monitoring nutrient and cell growth conditions.

}, keywords = {5{\textquoteright} Untranslated Regions, Animals, Biological, Drosophila melanogaster, Drosophila Proteins, Eukaryotic Initiation Factor-4E, Feedback, Forkhead Transcription Factors, Gene Expression Regulation, Genetic, Insulin, Models, Phosphorylation, Physiological, Protein Biosynthesis, Receptor, Ribosomes, Signal Transduction, Transcription, Transfection}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Marr, Michael T and D{\textquoteright}Alessio, Joseph A and Puig, Oscar and Tjian, Robert} } @article {4222, title = {Locally dynamic synaptic learning rules in pyramidal neuron dendrites.}, journal = {Nature}, volume = {450}, year = {2007}, month = {2007 Dec 20}, pages = {1195-200}, abstract = {

Long-term potentiation (LTP) of synaptic transmission underlies aspects of learning and memory. LTP is input-specific at the level of individual synapses, but neural network models predict interactions between plasticity at nearby synapses. Here we show in mouse hippocampal pyramidal cells that LTP at individual synapses reduces the threshold for potentiation at neighbouring synapses. After input-specific LTP induction by two-photon glutamate uncaging or by synaptic stimulation, subthreshold stimuli, which by themselves were too weak to trigger LTP, caused robust LTP and spine enlargement at neighbouring spines. Furthermore, LTP induction broadened the presynaptic-postsynaptic spike interval for spike-timing-dependent LTP within a dendritic neighbourhood. The reduction in the threshold for LTP induction lasted approximately 10 min and spread over approximately 10 microm of dendrite. These local interactions between neighbouring synapses support clustered plasticity models of memory storage and could allow for the binding of behaviourally linked information on the same dendritic branch.

}, keywords = {Animals, Dendrites, Excitatory Postsynaptic Potentials, Glutamic Acid, Learning, Long-Term Potentiation, Mice, Models, Neurological, Pyramidal Cells, Synapses}, issn = {1476-4687}, doi = {10.1038/nature06416}, author = {Harvey, Christopher D and Svoboda, Karel} } @article {6250, title = {Lola regulates Drosophila olfactory projection neuron identity and targeting specificity.}, journal = {Neural Development}, volume = {2}, year = {2007}, month = {2007 Jul 16}, pages = {14}, abstract = {

BACKGROUND: Precise connections of neural circuits can be specified by genetic programming. In the Drosophila olfactory system, projection neurons (PNs) send dendrites to single glomeruli in the antenna lobe (AL) based upon lineage and birth order and send axons with stereotyped terminations to higher olfactory centers. These decisions are likely specified by a PN-intrinsic transcriptional code that regulates the expression of cell-surface molecules to instruct wiring specificity. RESULTS: We find that the loss of longitudinals lacking (lola), which encodes a BTB-Zn-finger transcription factor with 20 predicted splice isoforms, results in wiring defects in both axons and dendrites of all lineages of PNs. RNA in situ hybridization and quantitative RT-PCR suggest that most if not all lola isoforms are expressed in all PNs, but different isoforms are expressed at widely varying levels. Overexpression of individual lola isoforms fails to rescue the lola null phenotypes and causes additional phenotypes. Loss of lola also results in ectopic expression of Gal4 drivers in multiple cell types and in the loss of transcription factor gene lim1 expression in ventral PNs. CONCLUSION: Our results indicate that lola is required for wiring of axons and dendrites of most PN classes, and suggest a need for its molecular diversity. Expression pattern changes of Gal4 drivers in lola-/- clones imply that lola normally represses the expression of these regulatory elements in a subset of the cells surrounding the AL. We propose that Lola functions as a general transcription factor that regulates the expression of multiple genes ultimately controlling PN identity and wiring specificity.

}, keywords = {Animals, Body Patterning, Brain, Cell Differentiation, Dendrites, Developmental, Drosophila melanogaster, Drosophila Proteins, Gene Expression Regulation, Growth Cones, Larva, Olfactory Pathways, Olfactory Receptor Neurons, Regulatory Elements, Transcription Factors, Transcriptional, Transcriptional Activation}, issn = {1749-8104}, doi = {10.1186/1749-8104-2-14}, author = {Spletter, Maria Lynn and Liu, Jian and Liu, Justin and Su, Helen and Giniger, Edward and Komiyama, Takaki and Quake, Stephen and Luo, Liqun} } @article {6350, title = {Modulation of neuronal voltage-activated calcium and sodium channels by polyamines and pH.}, journal = {Channels }, volume = {1}, year = {2007}, month = {2007 Jul-Aug}, pages = {281-90}, abstract = {

The endogenous polyamines spermine, spermidine and putrescine are present at high concentrations inside neurons and can be released into the extracellular space where they have been shown to modulate ion channels. Here, we have examined polyamine modulation of voltage-activated Ca(2+) channels (VACCs) and voltage-activated Na(+) channels (VANCs) in rat superior cervical ganglion neurons using whole-cell voltage-clamp at physiological divalent concentrations. Polyamines inhibited VACCs in a concentration-dependent manner with IC(50)s for spermine, spermidine, and putrescine of 4.7 +/- 0.7, 11.2 +/- 1.4 and 90 +/- 36 mM, respectively. Polyamines caused inhibition by shifting the VACC half-activation voltage (V(0.5)) to depolarized potentials and by reducing total VACC permeability. The shift was described by Gouy-Chapman-Stern theory with a surface charge density of 0.120 +/- 0.005 e(-) nm(-2) and a surface potential of -19 mV. Attenuation of spermidine and spermine inhibition of VACC at decreased pH was explained by H(+) titration of surface charge. Polyamine-mediated effects also decreased at elevated pH due to the inhibitors having lower valence and being less effective at screening surface charge. Polyamines affected VANC currents indirectly by reducing TTX inhibition of VANCs at high pH. This may reflect surface charge induced decreases in the local TTX concentration or polyamine-TTX interactions. In conclusion, polyamines inhibit neuronal VACCs via complex interactions with extracellular H(+) and Ca. Many of the observed effects can be explained by a model incorporating polyamine binding, H(+) binding and surface charge screening.

}, keywords = {Animals, Calcium, Calcium Channels, Cell Membrane Permeability, Cells, Cultured, Hydrogen-Ion Concentration, Membrane Potentials, Models, Neurological, Neurons, Patch-Clamp Techniques, Polyamines, Putrescine, Rats, Sodium, Sodium Channel Blockers, Sodium Channels, Spermidine, Spermine, Superior Cervical Ganglion, Tetrodotoxin, Time Factors}, issn = {1933-6969}, author = {Chen, Wenyan and Harnett, Mark T and Smith, Stephen M} } @article {2443, title = {Molecular patterning mechanism underlying metamorphosis of the thoracic leg in Manduca sexta.}, journal = {Developmental Biology}, volume = {305}, year = {2007}, month = {2007 May 15}, pages = {539-50}, abstract = {

The tobacco hornworm Manduca sexta, like many holometabolous insects, makes two versions of its thoracic legs. The simple legs of the larva are formed during embryogenesis, but then are transformed into the more complex adult legs at metamorphosis. To elucidate the molecular patterning mechanism underlying this biphasic development, we examined the expression patterns of five genes known to be involved in patterning the proximal-distal axis in insect legs. In the developing larval leg of Manduca, the early patterning genes Distal-less and Extradenticle are already expressed in patterns comparable to the adult legs of other insects. In contrast, Bric-a-brac and dachshund are expressed in patterns similar to transient patterns observed during early stages of leg development in Drosophila. During metamorphosis of the leg, the two genes finally develop mature expression patterns. Our results are consistent with the hypothesis that the larval leg morphology is produced by a transient arrest in the conserved adult leg patterning process in insects. In addition, we find that, during the adult leg development, some cells in the leg express the patterning genes de novo suggesting that the remodeling of the leg involves changes in the patterning gene regulation.

}, keywords = {Animals, Biological, Body Patterning, Extremities, Larva, Manduca, Metamorphosis, Thorax}, issn = {0012-1606}, doi = {10.1016/j.ydbio.2007.02.042}, author = {Tanaka, Kohtaro and Truman, James W} } @article {4649, title = {Morphological evolution through multiple cis-regulatory mutations at a single gene.}, journal = {Nature}, volume = {448}, year = {2007}, month = {2007 Aug 2}, pages = {587-90}, abstract = {

One central, and yet unsolved, question in evolutionary biology is the relationship between the genetic variants segregating within species and the causes of morphological differences between species. The classic neo-darwinian view postulates that species differences result from the accumulation of small-effect changes at multiple loci. However, many examples support the possible role of larger abrupt changes in the expression of developmental genes in morphological evolution. Although this evidence might be considered a challenge to a neo-darwinian micromutationist view of evolution, there are currently few examples of the actual genes causing morphological differences between species. Here we examine the genetic basis of a trichome pattern difference between Drosophila species, previously shown to result from the evolution of a single gene, shavenbaby (svb), probably through cis-regulatory changes. We first identified three distinct svb enhancers from D. melanogaster driving reporter gene expression in partly overlapping patterns that together recapitulate endogenous svb expression. All three homologous enhancers from D. sechellia drive expression in modified patterns, in a direction consistent with the evolved svb expression pattern. To test the influence of these enhancers on the actual phenotypic difference, we conducted interspecific genetic mapping at a resolution sufficient to recover multiple intragenic recombinants. This functional analysis revealed that independent genetic regions upstream of svb that overlap the three identified enhancers are collectively required to generate the D. sechellia trichome pattern. Our results demonstrate that the accumulation of multiple small-effect changes at a single locus underlies the evolution of a morphological difference between species. These data support the view that alleles of large effect that distinguish species may sometimes reflect the accumulation of multiple mutations of small effect at select genes.

}, keywords = {Alleles, Animals, Biological, Biological Evolution, Developmental, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Enhancer Elements, Evolution, Gene Expression Regulation, Genes, Genetic, Genetic Speciation, Models, Molecular, Mutation, Recombination, Reporter, Transcription Factors}, issn = {1476-4687}, doi = {10.1038/nature05988}, author = {McGregor, Alistair P and Orgogozo, Virginie and Delon, Isabelle and Zanet, Jennifer and Srinivasan, Dayalan G and Payre, Fran\c cois and Stern, David L} } @article {6443, title = {MRI-based localization of electrophysiological recording sites within the cerebral cortex at single-voxel accuracy.}, journal = {Nature Methods}, volume = {4}, year = {2007}, month = {2007 Feb}, pages = {161-8}, abstract = {

The localization of microelectrode recording sites in the layers of primate cerebral cortex permits the analysis of relationships between recorded neuronal activities and underlying anatomical connections. We present a magnetic resonance imaging method for precise in vivo localization of cortical recording sites. In this method, the susceptibility-induced effect thickens the appearance of the microelectrode and enhances the detectability of the microelectrode tip, which usually occupies less than a few percent of the volume of an image voxel. In a phantom study, the optimized susceptibility-induced effect allowed tip detection with single-voxel accuracy (in-plane resolution, 50 mum). We applied this method to recording microelectrodes inserted into the brains of macaque monkeys, and localized the microelectrode tip at an in-plane resolution of 150 mum within the cortex of 2-3 mm in thickness. Subsequent histological analyses validated the single-voxel accuracy of the in vivo tip localization. This method opens up a way to investigate information flow during cognitive processes in the brain.

}, keywords = {Animal, Animals, Behavior, Cerebral Cortex, Electrophysiology, Imaging, Macaca, Magnetic Resonance Imaging, Microelectrodes, Phantoms}, issn = {1548-7091}, doi = {10.1038/nmeth987}, author = {Matsui, Teppei and Koyano, Kenji W and Koyama, Minoru and Nakahara, Kiyoshi and Takeda, Masaki and Ohashi, Yohei and Naya, Yuji and Miyashita, Yasushi} } @article {4979, title = {Multiple memory traces for olfactory reward learning in Drosophila.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {27}, year = {2007}, month = {2007 Oct 10}, pages = {11132-8}, abstract = {

Physical traces underlying simple memories can be confined to a single group of cells in the brain. In the fly Drosophila melanogaster, the Kenyon cells of the mushroom bodies house traces for both appetitive and aversive odor memories. The adenylate cyclase protein, Rutabaga, has been shown to mediate both traces. Here, we show that, for appetitive learning, another group of cells can additionally accommodate a Rutabaga-dependent memory trace. Localized expression of rutabaga in either projection neurons, the first-order olfactory interneurons, or in Kenyon cells, the second-order interneurons, is sufficient for rescuing the mutant defect in appetitive short-term memory. Thus, appetitive learning may induce multiple memory traces in the first- and second-order olfactory interneurons using the same plasticity mechanism. In contrast, aversive odor memory of rutabaga is rescued selectively in the Kenyon cells, but not in the projection neurons. This difference in the organization of memory traces is consistent with the internal representation of reward and punishment.

}, keywords = {Animals, Drosophila melanogaster, Female, Learning, Male, Nerve Net, Olfactory Pathways, Reward, Smell}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2712-07.2007}, author = {Thum, Andreas S and Jenett, Arnim and Ito, Kei and Heisenberg, Martin and Tanimoto, Hiromu} } @article {5819, title = {Neurobiology of the basal platyhelminth Macrostomum lignano: map and digital 3D model of the juvenile brain neuropile.}, journal = {Development Genes \& Evolution}, volume = {217}, year = {2007}, month = {2007 Aug}, pages = {569-84}, abstract = {

We have analyzed brain structure in Macrostomum lignano, a representative of the basal platyhelminth taxon Macrostomida. Using confocal microscopy and digital 3D modeling software on specimens labeled with general markers for neurons (tyrTub), muscles (phalloidin), and nuclei (Sytox), an atlas and digital model of the juvenile Macrostomum brain was generated. The brain forms a ganglion with a central neuropile surrounded by a cortex of neuronal cell bodies. The neuropile contains a stereotypical array of compact axon bundles, as well as branched terminal axons and dendrites. Muscle fibers penetrate the flatworm brain horizontally and vertically at invariant positions. Beside the invariant pattern of neurite bundles, these "cerebral muscles" represent a convenient system of landmarks that help define discrete compartments in the juvenile brain. Commissural axon bundles define a dorsal and ventro-medial neuropile compartment, respectively. Longitudinal axons that enter the neuropile through an invariant set of anterior and posterior nerve roots define a ventro-basal and a central medial compartment in the neuropile. Flanking these "fibrous" compartments are neuropile domains that lack thick axon bundles and are composed of short collaterals and terminal arborizations of neurites. Two populations of neurons, visualized by antibodies against FMRFamide and serotonin, respectively, were mapped relative to compartment boundaries. This study will aid in the documentation and interpretation of patterns of gene expression, as well as functional studies, in the developing Macrostomum brain.

}, keywords = {Animals, Brain, Brain Mapping, Cells, Computer Simulation, Cultured, Imaging, Models, Muscle Fibers, Neurological, Neuropil, Platyhelminths, Skeletal, Three-Dimensional}, issn = {0949-944X}, doi = {10.1007/s00427-007-0166-z}, author = {Morris, Joshua and Cardona, Albert and De Miguel-Bonet, Maria Del Mar and Hartenstein, Volker} } @article {1112, title = {A new strategy for the synthesis of benzylic sulfonamides: palladium-catalyzed arylation and sulfonamide metathesis.}, journal = {The Journal of Organic Chemistry}, volume = {72}, year = {2007}, month = {2007 Oct 12}, pages = {8135-8}, abstract = {

An efficient two-step strategy has been developed to access diversely functionalized benzylic sulfonamides. Execution of this strategy required the development of two reaction methods: the palladium-catalyzed cross-coupling of aryl halides with CH-acidic methanesulfonamides and a metathesis reaction between the resulting alpha-arylated sulfonamides and diverse amines. The broad scope of the cross-coupling process combined with a versatile sulfonamide metathesis constitutes an efficient strategy for the synthesis of various benzylic sulfonamides.

}, keywords = {Benzyl Compounds, Catalysis, Molecular Structure, Palladium, Sulfonamides}, issn = {0022-3263}, doi = {10.1021/jo701431j}, author = {Grimm, Jonathan B and Katcher, Matthew H and Witter, David J and Northrup, Alan B} } @article {46427, title = {NF-κB, IκB, and IRAK control glutamate receptor density at the Drosophila NMJ.}, journal = {Neuron}, volume = {55}, year = {2007}, month = {2007 Sep 20}, pages = {859-73}, abstract = {

NF-κB signaling has been implicated in neurodegenerative disease, epilepsy, and neuronal plasticity. However, the cellular and molecular activity of NF-κB signaling within the nervous system remains to be clearly defined. Here,\ we show that the NF-κB and IκB homologs Dorsal and Cactus surround postsynaptic glutamate receptor (GluR) clusters at the Drosophila\ NMJ. We then show that mutations in dorsal, cactus, and IRAK/pelle kinase specifically impair GluR levels, assayed immunohistochemically and electrophysiologically, without affecting NMJ growth, the size of the postsynaptic density, or homeostatic plasticity. Additional genetic experiments support the conclusion that cactus functions in concert with, rather than in opposition to, dorsal and pelle in this process. Finally, we provide evidence that Dorsal and Cactus act\ posttranscriptionally, outside the nucleus, to control GluR density. Based upon our data we speculate that Dorsal, Cactus, and Pelle could function together, locally at the postsynaptic density, to specify GluR levels.

}, keywords = {Developmental Biology, molecular neurology, signaling}, doi = {10.1016/j.neuron.2007.08.005}, author = {Heckscher, Elizabeth S and Fetter, Richard D and Marek, Kurt W and Albin, Stephanie D and Davis, Graeme W} } @article {5828, title = {A novel multiple objective optimization framework for constraining conductance-based neuron models by experimental data.}, journal = {Frontiers in Neuroscience}, volume = {1}, year = {2007}, month = {2007 Nov}, pages = {7-18}, abstract = {

We present a novel framework for automatically constraining parameters of compartmental models of neurons, given a large set of experimentally measured responses of these neurons. In experiments, intrinsic noise gives rise to a large variability (e.g., in firing pattern) in the voltage responses to repetitions of the exact same input. Thus, the common approach of fitting models by attempting to perfectly replicate, point by point, a single chosen trace out of the spectrum of variable responses does not seem to do justice to the data. In addition, finding a single error function that faithfully characterizes the distance between two spiking traces is not a trivial pursuit. To address these issues, one can adopt a multiple objective optimization approach that allows the use of several error functions jointly. When more than one error function is available, the comparison between experimental voltage traces and model response can be performed on the basis of individual features of interest (e.g., spike rate, spike width). Each feature can be compared between model and experimental mean, in units of its experimental variability, thereby incorporating into the fitting this variability. We demonstrate the success of this approach, when used in conjunction with genetic algorithm optimization, in generating an excellent fit between model behavior and the firing pattern of two distinct electrical classes of cortical interneurons, accommodating and fast-spiking. We argue that the multiple, diverse models generated by this method could serve as the building blocks for the realistic simulation of large neuronal networks.

}, issn = {1662-453X}, doi = {10.3389/neuro.01.1.1.001.2007}, author = {Druckmann, Shaul and Banitt, Yoav and Gidon, Albert and Sch{\"u}rmann, Felix and Markram, Henry and Segev, Idan} } @article {2405, title = {Novel TRF1/BRF target genes revealed by genome-wide analysis of Drosophila Pol III transcription.}, journal = {The EMBO Journal}, volume = {26}, year = {2007}, month = {2007 Jan 10}, pages = {79-89}, abstract = {

Metazoans have evolved multiple paralogues of the TATA binding protein (TBP), adding another tunable level of gene control at core promoters. While TBP-related factor 1 (TRF1) shares extensive homology with TBP and can direct both Pol II and Pol III transcription in vitro, TRF1 target sites in vivo have remained elusive. Here, we report the genome-wide identification of TRF1-binding sites using high-resolution genome tiling microarrays. We found 354 TRF1-binding sites genome-wide with approximately 78\% of these sites displaying colocalization with BRF. Strikingly, the majority of TRF1 target genes are Pol III-dependent small noncoding RNAs such as tRNAs and small nonmessenger RNAs. We provide direct evidence that the TRF1/BRF complex is functionally required for the activity of two novel TRF1 targets (7SL RNA and small nucleolar RNAs). Our studies suggest that unlike most other eukaryotic organisms that rely on TBP for Pol III transcription, in Drosophila and possibly other insects the alternative TRF1/BRF complex appears responsible for the initiation of all known classes of Pol III transcription.

}, keywords = {Animals, Base Sequence, Binding Sites, Chromatin Immunoprecipitation, Deoxyribonuclease I, DNA Polymerase III, Drosophila melanogaster, Genetic, Genome, Molecular Sequence Data, Oligonucleotide Probes, Protein Binding, RNA, Small Nucleolar, Telomeric Repeat Binding Protein 1, Transcription, Transcription Factor TFIIIB}, issn = {0261-4189}, doi = {10.1073/pnas.1100640108}, author = {Isogai, Yoh and Takada, Shinako and Tjian, Robert and Kele\c s, S{\"u}nd{\"u}z} } @article {67285, title = {Observability of Higgs produced with top quarks and decaying to bottom quarks}, journal = {Journal of Physics G: Nuclear and Particle Physics}, volume = {34}, year = {2007}, month = {04/20027}, pages = {N221 - N250}, abstract = {

The decay,\ , is dominant for a Standard Model Higgs boson in the mass range just above the exclusion limit of 114.4 GeV/c2\ reported by the LEP experiments. Unfortunately, an overwhelming abundance of\ \ events arising from more mundane sources, together with the lack of precision inherent in the reconstruction of the Higgs mass, renders this decay mode\ a priori\ undetectable in the case of direct Higgs production at the LHC. It is therefore of no small interest to investigate whether\ \ can be observed in those cases where the Higgs is produced in association with other massive particles. In this note, the results of a study of Higgs bosons produced in association with top quarks and decaying via\ \ are presented. The study was performed as realistically as possible by employing a full and detailed Monte Carlo simulation of the CMS detector followed by the application of trigger and reconstruction algorithms that were developed for use with real data. Important systematic effects resulting from such sources as the uncertainties in the jet energy scale and the estimated rates for correctly tagging b jets or mistagging non-b jets have been taken into account. The impact of large theoretical uncertainties in the cross sections for\ \ plus\ N\ jets processes due to an absence of next-to-leading order calculations is also considered.

}, issn = {0954-3899}, doi = {10.1088/0954-3899/34/5/N03}, url = {https://iopscience.iop.org/article/10.1088/0954-3899/34/5/N03}, author = {Benedetti, D and Cucciarelli, S and Hill, C and Incandela, J and Koay, S A and Riccardi, C and Santocchia, A and Schmidt, A and Torre, P and Weiser, C} } @article {2364, title = {Olfactory coding with all-or-nothing glomeruli.}, journal = {Journal of Neurophysiology}, volume = {98}, year = {2007}, month = {2007 Dec}, pages = {3134-42}, abstract = {

We present a model for olfactory coding based on spatial representation of glomerular responses. In this model distinct odorants activate specific subsets of glomeruli, dependent on the odorant{\textquoteright}s chemical identity and concentration. The glomerular response specificities are understood statistically, based on experimentally measured distributions of activation thresholds. A simple version of the model, in which glomerular responses are binary (the all-or-nothing model), allows us to account quantitatively for the following results of human/rodent olfactory psychophysics: 1) just noticeable differences in the perceived concentration of a single odor (Weber ratios) are as low as dC/C approximately 0.04; 2) the number of simultaneously perceived odors can be as high as 12; and 3) extensive lesions of the olfactory bulb do not lead to significant changes in detection or discrimination thresholds. We conclude that a combinatorial code based on a binary glomerular response is sufficient to account for several important features of the discrimination capacity of the mammalian olfactory system.

}, keywords = {Algorithms, Animals, Discrimination (Psychology), Mice, Models, Neurological, Odors, Olfactory Bulb, Olfactory Pathways, Olfactory Receptor Neurons, Psychomotor Performance, Psychophysics, Rats, Smell}, issn = {0022-3077}, doi = {10.1523/JNEUROSCI.3613-08.2008}, author = {Koulakov, Alexei and Gelperin, Alan and Rinberg, Dmitry} } @article {1733, title = {Phase-sensitive sum-frequency vibrational spectroscopy and its application to studies of interfacial alkyl chains.}, journal = {Journal of the American Chemical Society}, volume = {129}, year = {2007}, month = {2007 Aug 22}, pages = {10056-7}, abstract = {

The first general phase-sensitive sum-frequency vibrational spectroscopy (SFVS) was described, which recovers the phase information lost in conventional SFVS measurements. Using a self-assembled monolayer, we demonstrated that this novel technique measures the absolute orientation of surface molecular moieties and is very powerful in resolving spectral features.

}, issn = {0002-7863}, doi = {10.1021/ja071989t}, author = {Ji, Na and Ostroverkhov, Victor and Chen, Chao-Yuan and Shen, Yuen-Ron} } @article {2155, title = {Phenotype clustering of breast epithelial cells in confocal images based on nuclear protein distribution analysis.}, journal = {BMC Cell Biology}, volume = {8 }, year = {2007}, month = {2007 Jul 10}, pages = {S3}, abstract = {

The distribution of chromatin-associated proteins plays a key role in directing nuclear function. Previously, we developed an image-based method to quantify the nuclear distributions of proteins and showed that these distributions depended on the phenotype of human mammary epithelial cells. Here we describe a method that creates a hierarchical tree of the given cell phenotypes and calculates the statistical significance between them, based on the clustering analysis of nuclear protein distributions.

}, keywords = {Breast, Breast Neoplasms, Cell Line, Cluster Analysis, Computer-Assisted, Confocal, Epithelial Cells, Female, Humans, Image Processing, Imaging, Microscopy, Models, Nuclear Proteins, Phenotype, Statistical, Three-Dimensional}, issn = {1471-2121}, doi = {10.1007/s12021-010-9090-x}, author = {Long, Fuhui and Peng, Hanchuan and Sudar, Damir and Leli{\`e}vre, Sophie A and Knowles, David W} } @article {48397, title = {Polypeptide motions are dominated by peptide group oscillations resulting from dihedral angle correlations between nearest neighbors.}, journal = {Biochemistry}, volume = {46}, year = {2007}, month = {2007 Jan 23}, pages = {669-82}, abstract = {

To identify basic local backbone motions in unfolded chains, simulations are performed for a variety of peptide systems using three popular force fields and for implicit and explicit solvent models. A dominant "crankshaft-like" motion is found that involves only a localized oscillation of the plane of the peptide group. This motion results in a strong anticorrelated motion of the phi angle of the ith residue (phi(i)) and the psi angle of the residue i - 1 (psi(i-1)) on the 0.1 ps time scale. Only a slight correlation is found between the motions of the two backbone dihedral angles of the same residue. Aside from the special cases of glycine and proline, no correlations are found between backbone dihedral angles that are separated by more than one torsion angle. These short time, correlated motions are found both in equilibrium fluctuations and during the transit process between Ramachandran basins, e.g., from the beta to the alpha region. A residue{\textquoteright}s complete transit from one Ramachandran basin to another, however, occurs in a manner independent of its neighbors{\textquoteright} conformational transitions. These properties appear to be intrinsic because they are robust across different force fields, solvent models, nonbonded interaction routines, and most amino acids.

}, keywords = {Alanine, Computer Simulation, Glycine, Models, Molecular, Molecular Conformation, Motion, Peptides, Proline, Protein Folding}, issn = {0006-2960}, doi = {10.1021/bi061575x}, author = {Fitzgerald, James E and Jha, Abhishek K and Sosnick, Tobin R and Freed, Karl F} } @article {45959, title = {Projection map of aquaporin-9 at 7 A resolution.}, journal = {Journal of Molecular Biology}, volume = {367}, year = {2007}, month = {2007 Mar 16}, pages = {80-8}, abstract = {

Aquaporin-9, an aquaglyceroporin present in diverse tissues, is unique among aquaporins because it is not only permeable to water, urea and glycerol, but also allows passage of larger uncharged solutes. Single particle analysis of negatively stained recombinant rat aquaporin-9 revealed a particle size characteristic of the tetrameric organization of all members of the aquaporin family. Reconstitution of aquaporin-9 into two-dimensional crystals enabled us to calculate a projection map at 7 A resolution. The projection structure indicates a tetrameric structure, similar to GlpF, with each square-like monomer forming a pore. A comparison of the pore-lining residues between the crystal structure of GlpF and a homology model of aquaporin-9 locates substitutions in these residues predominantly to the hydrophobic edge of the tripathic pore of GlpF, providing first insights into the structural basis for the broader substrate specificity of aquaporin-9.

}, keywords = {Animals, Aquaporins, Crystallography, Escherichia coli, Escherichia coli Proteins, Gene Expression, Models, Molecular, Protein Conformation, Rats, Recombinant Proteins}, issn = {0022-2836}, doi = {10.1016/j.jmb.2006.12.042}, author = {Viadiu, Hector and Gonen, Tamir and Walz, Thomas} } @article {1584, title = {Purification, crystallization and preliminary crystallographic analysis of a GTP-binding protein from the hyperthermophilic archaeon Sulfolobus solfataricus.}, journal = {Acta Crystallographica. Section F, Structural Biology and Crystallization Communications}, volume = {63}, year = {2007}, month = {2007 Mar 1}, pages = {239-41}, abstract = {

A predicted GTP-binding protein from the hyperthermophilic archaeon Sulfolobus solfataricus, termed SsGBP, has been cloned and overexpressed in Escherichia coli. The purified protein was crystallized using the hanging-drop vapour-diffusion technique in the presence of 0.05 M cadmium sulfate and 0.8 M sodium acetate pH 7.5. A single-wavelength anomalous dispersion data set was collected to a maximum resolution of 2.0 A using a single cadmium-incorporated crystal. The crystal form belongs to space group P2(1)2(1)2(1), with approximate unit-cell parameters a = 65.0

}, keywords = {Archaeal Proteins, Crystallization, Crystallography, GTP-Binding Proteins, Hot Temperature, Sulfolobus solfataricus, X-Ray}, issn = {1744-3091}, doi = {10.1107/S1744309107008500}, author = {Wu, Hao and Sun, Lei and Brouns, Stan J J and Fu, Sheng and Akerboom, Jasper and Li, Xuemei and van der Oost, John} } @article {4224, title = {Query-dependent banding (QDB) for faster RNA similarity searches.}, journal = {PLoS Computational Biology}, volume = {3}, year = {2007}, month = {2007 Mar 30}, pages = {e56}, abstract = {

When searching sequence databases for RNAs, it is desirable to score both primary sequence and RNA secondary structure similarity. Covariance models (CMs) are probabilistic models well-suited for RNA similarity search applications. However, the computational complexity of CM dynamic programming alignment algorithms has limited their practical application. Here we describe an acceleration method called query-dependent banding (QDB), which uses the probabilistic query CM to precalculate regions of the dynamic programming lattice that have negligible probability, independently of the target database. We have implemented QDB in the freely available Infernal software package. QDB reduces the average case time complexity of CM alignment from LN(2.4) to LN(1.3) for a query RNA of N residues and a target database of L residues, resulting in a 4-fold speedup for typical RNA queries. Combined with other improvements to Infernal, including informative mixture Dirichlet priors on model parameters, benchmarks also show increased sensitivity and specificity resulting from improved parameterization.

}, keywords = {Base Sequence, Database Management Systems, Databases, Genetic, Information Storage and Retrieval, Molecular Sequence Data, Nucleic Acid, RNA, Sequence Alignment, Sequence Analysis, Sequence Homology}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.0030056}, author = {Nawrocki, Eric P and Eddy, Sean R.} } @article {4251, title = {Rapidly inducible, genetically targeted inactivation of neural and synaptic activity in vivo.}, journal = {Current Opinion in Neurobiology}, volume = {17}, year = {2007}, month = {2007 Oct}, pages = {581-6}, abstract = {

Inducible and reversible perturbation of the activity of selected neurons in vivo is critical to understanding the dynamics of brain circuits. Several genetically encoded systems for rapid inducible neuronal silencing have been developed in the past few years offering an arsenal of tools for in vivo experiments. Some systems are based on ion-channels or pumps, others on G protein coupled receptors, and yet others on modified presynaptic proteins. Inducers range from light to small molecules to peptides. This diversity results in differences in the various parameters that may determine the applicability of each tool to a particular biological question. Although further development would be beneficial, the current silencing tool kit already provides the ability to make specific perturbations of circuit function in behaving animals.

}, keywords = {Animals, Brain, G-Protein-Coupled, Gene Targeting, Neurons, Receptors, Synapses}, issn = {0959-4388}, doi = {10.1016/j.conb.2007.10.002}, author = {Tervo, Dougal and Karpova, Alla Y} } @article {48396, title = {Reduced C(beta) statistical potentials can outperform all-atom potentials in decoy identification.}, journal = {Protein science : a publication of the Protein Society}, volume = {16}, year = {2007}, month = {2007 Oct}, pages = {2123-39}, abstract = {

We developed a series of statistical potentials to recognize the native protein from decoys, particularly when using only a reduced representation in which each side chain is treated as a single C(beta) atom. Beginning with a highly successful all-atom statistical potential, the Discrete Optimized Protein Energy function (DOPE), we considered the implications of including additional information in the all-atom statistical potential and subsequently reducing to the C(beta) representation. One of the potentials includes interaction energies conditional on backbone geometries. A second potential separates sequence local from sequence nonlocal interactions and introduces a novel reference state for the sequence local interactions. The resultant potentials perform better than the original DOPE statistical potential in decoy identification. Moreover, even upon passing to a reduced C(beta) representation, these statistical potentials outscore the original (all-atom) DOPE potential in identifying native states for sets of decoys. Interestingly, the backbone-dependent statistical potential is shown to retain nearly all of the information content of the all-atom representation in the C(beta) representation. In addition, these new statistical potentials are combined with existing potentials to model hydrogen bonding, torsion energies, and solvation energies to produce even better performing potentials. The ability of the C(beta) statistical potentials to accurately represent protein interactions bodes well for computational efficiency in protein folding calculations using reduced backbone representations, while the extensions to DOPE illustrate general principles for improving knowledge-based potentials.

}, keywords = {Carbon, Computational Biology, Models, Statistical, Protein Folding, Protein Structure, Secondary, Proteins}, issn = {0961-8368}, doi = {10.1110/ps.072939707}, author = {Fitzgerald, James E and Jha, Abhishek K and Colubri, Andr{\'e}s and Sosnick, Tobin R and Freed, Karl F} } @article {3927, title = {Response profiles to amino acid odorants of olfactory glomeruli in larval Xenopus laevis.}, journal = {The Journal of Physiology}, volume = {581}, year = {2007}, month = {2007 Jun 1}, pages = {567-79}, abstract = {

Glomeruli in the vertebrate olfactory bulb (OB) appear as anatomically discrete modules receiving direct input from the olfactory epithelium (OE) via axons of olfactory receptor neurons (ORNs). The response profiles with respect to amino acids (AAs) of a large number of ORNs in larval Xenopus laevis have been recently determined and analysed. Here we report on Ca(2+) imaging experiments in a nose-brain preparation of the same species at the same developmental stages. We recorded responses to AAs of glomeruli in the OB and determined the response profiles to AAs of individual glomeruli. We describe the general features of AA-responsive glomeruli and compare their response profiles to AAs with those of ORNs obtained in our previous study. A large number of past studies have focused either on odorant responses in the OE or on odorant-induced responses in the OB. However, a thorough comparison of odorant-induced responses of both stages, ORNs and glomeruli of the same species is as yet lacking. The glomerular response profiles reported herein markedly differ from the previously obtained response profiles of ORNs in that glomeruli clearly have narrower selectivity profiles than ORNs. We discuss possible explanations for the different selectivity profiles of glomeruli and ORNs in the context of the development of the olfactory map.

}, keywords = {3-dione, 6-Cyano-7-nitroquinoxaline-2, Amino Acids, Animals, Calcium, Calcium Signaling, Confocal, Excitatory Amino Acid Antagonists, Larva, Microscopy, Odorant, Olfactory Bulb, Olfactory Mucosa, Olfactory Pathways, Olfactory Receptor Neurons, Receptors, Smell, Time Factors, Valine, Xenopus laevis}, issn = {0022-3751}, doi = {10.1113/jphysiol.2007.130518}, author = {Manzini, Ivan and Brase, Christoph and Chen, Tsai-Wen and Schild, Detlev} } @article {46404, title = {Ribbon-helix-helix transcription factors: variations on a theme.}, journal = {Nature Reviews Microbiology}, volume = {5}, year = {2007}, month = {2007 Sep}, pages = {710-20}, abstract = {

The ribbon-helix-helix (RHH) superfamily of transcription factors uses a conserved three-dimensional structural motif to bind to DNA in a sequence-specific manner. This functionally diverse protein superfamily regulates the transcription of genes that are involved in the uptake of metals, amino-acid biosynthesis, cell division, the control of plasmid copy number, the lytic cycle of bacteriophages and, perhaps, many other cellular processes. In this Analysis, the structures of different RHH transcription factors are compared in order to evaluate the sequence motifs that are required for RHH-domain folding and DNA binding, as well as to identify conserved protein-DNA interactions in this superfamily.

}, keywords = {Amino Acid Sequence, Bacterial Proteins, Dimerization, DNA-Binding Proteins, Helix-Turn-Helix Motifs, Models, Molecular, Protein Binding, Sequence Homology, Amino Acid, Structure-Activity Relationship, Transcription Factors}, issn = {1740-1534}, doi = {10.1038/nrmicro1717}, author = {Schreiter, Eric R and Drennan, Catherine L} } @article {4048, title = {A role for synaptic inputs at distal dendrites: instructive signals for hippocampal long-term plasticity.}, journal = {Neuron}, volume = {56}, year = {2007}, month = {2007 Dec 6}, pages = {866-79}, abstract = {

Synaptic potentials originating at distal dendritic locations are severely attenuated when they reach the soma and, thus, are poor at driving somatic spikes. Nonetheless, distal inputs convey essential information, suggesting that such inputs may be important for compartmentalized dendritic signaling. Here we report a new plasticity rule in which stimulation of distal perforant path inputs to hippocampal CA1 pyramidal neurons induces long-term potentiation at the CA1 proximal Schaffer collateral synapses when the two inputs are paired at a precise interval. This subthreshold form of heterosynaptic plasticity occurs in the absence of somatic spiking but requires activation of both NMDA receptors and IP(3) receptor-dependent release of Ca(2+) from internal stores. Our results suggest that direct sensory information arriving at distal CA1 synapses through the perforant path provide compartmentalized, instructive signals that assess the saliency of mnemonic information propagated through the hippocampal circuit to proximal synapses.

}, keywords = {4, 5-Trisphosphate Receptors, Absorptiometry, AMPA, Animals, Calcium, Computer Simulation, Dendrites, Dendritic Spines, Electrophysiology, Excitatory Postsynaptic Potentials, Hippocampus, Inositol 1, Memory, Mice, Models, N-Methyl-D-Aspartate, Neurological, Neuronal Plasticity, Neurophysiological, Patch-Clamp Techniques, Photon, Pyramidal Cells, Receptors, Recruitment, Signal Transduction, Synapses, Synaptic Transmission}, issn = {0896-6273}, doi = {10.1016/j.neuron.2007.10.020}, author = {Dudman, Joshua T and Tsay, David and Siegelbaum, Steven A} } @article {2807, title = {[Role of Bid protein in the mitochondria and endoplasmic reticulum associated apoptotic pathway].}, journal = {Zhonghua Xue Ye Xue Za Zhi = Zhonghua Xueyexue Zazhi}, volume = {28}, year = {2007}, month = {2007 Jul}, pages = {466-9}, abstract = {

To explore the role of Bid protein in the mitochondria and endoplasmic reticulum (ER) associated apoptotic pathway.

}, keywords = {Apoptosis, BH3 Interacting Domain Death Agonist Protein, Calcium, Caspase 3, Caspases, Cell Line, DNA-Binding Proteins, Endoplasmic Reticulum, Harringtonines, Humans, Initiator, Mitochondria, Transcription Factors}, issn = {0253-2727}, doi = {10.1364/AO.50.001792}, author = {Hu, Jie and He, Dong-Hua and Gao, Liang and Yang, Chun-Hu and Cai, Zhen} } @article {2356, title = {The role of visual and mechanosensory cues in structuring forward flight in Drosophila melanogaster.}, journal = {The Journal of Experimental Biology}, volume = {210}, year = {2007}, month = {2007 Dec}, pages = {4092-103}, abstract = {

It has long been known that many flying insects use visual cues to orient with respect to the wind and to control their groundspeed in the face of varying wind conditions. Much less explored has been the role of mechanosensory cues in orienting insects relative to the ambient air. Here we show that Drosophila melanogaster, magnetically tethered so as to be able to rotate about their yaw axis, are able to detect and orient into a wind, as would be experienced during forward flight. Further, this behavior is velocity dependent and is likely subserved, at least in part, by the Johnston{\textquoteright}s organs, chordotonal organs in the antennae also involved in near-field sound detection. These wind-mediated responses may help to explain how flies are able to fly forward despite visual responses that might otherwise inhibit this behavior. Expanding visual stimuli, such as are encountered during forward flight, are the most potent aversive visual cues known for D. melanogaster flying in a tethered paradigm. Accordingly, tethered flies strongly orient towards a focus of contraction, a problematic situation for any animal attempting to fly forward. We show in this study that wind stimuli, transduced via mechanosensory means, can compensate for the aversion to visual expansion and thus may help to explain how these animals are indeed able to maintain forward flight.

}, keywords = {Animal, Animal Structures, Animals, Cellular, Cues, Drosophila melanogaster, Female, Flight, Magnetics, Mechanotransduction, Orientation, Photic Stimulation, Regression Analysis, Saccades, Visual Fields, Visual Perception, Wind}, issn = {0022-0949}, doi = {10.1016/j.cub.2010.06.072}, author = {Budick, Seth A and Reiser, Michael B and Dickinson, Michael H} } @article {46304, title = {Search for fMRI BOLD signals in networks of spiking neurons.}, journal = {European Journal of Neuroscience}, volume = {25}, year = {2007}, month = {2007 Mar}, pages = {1882-92}, abstract = {

In a recent experiment, functional magnetic resonance imaging blood oxygen level-dependent (fMRI BOLD) signals were compared in different cortical areas (primary-visual and associative), when subjects were required covertly to name images in two protocols: sequences of images, with and without intervening delays. The amplitude of the BOLD signal in protocols with delay was found to be closer to that without delays in associative areas than in primary areas. The present study provides an exploratory proposal for the identification of the neural activity substrate of the BOLD signal in quasi-realistic networks of spiking neurons, in networks sustaining selective delay activity (associative) and in networks responsive to stimuli, but whose unique stationary state is one of spontaneous activity (primary). A variety of observables are {\textquoteright}recorded{\textquoteright} in the network simulations, applying the experimental stimulation protocol. The ratios of the candidate BOLD signals, in the two protocols, are compared in networks with and without delay activity. There are several options for recovering the experimental result in the model networks. One common conclusion is that the distinguishing factor is the presence of delay activity. The effect of NMDAr is marginal. The ultimate quantitative agreement with the experiment results depends on a distinction of the baseline signal level from its value in delay-period spontaneous activity. This may be attributable to the subjects{\textquoteright} attention. Modifying the baseline results in a quantitative agreement for the ratios, and provided a definite choice of the candidate signals. The proposed framework produces predictions for the BOLD signal in fMRI experiments, upon modification of the protocol presentation rate and the form of the response function.

}, keywords = {Action Potentials, Brain, Brain Mapping, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Models, Neurological, Nerve Net, Neurons, Oxygen, Synapses}, issn = {0953-816X}, doi = {10.1111/j.1460-9568.2007.05408.x}, author = {Amit, Daniel J and Romani, Sandro} } @article {45745, title = {Sex and death in the male pea aphid, Acyrthosiphon pisum: The life-history effects of a wing dimorphism.}, journal = {J Insect Sci}, volume = {7}, year = {2007}, month = {2007}, pages = {1-9}, abstract = {

Insect dispersal dimorphisms, in which both flight-capable and flightless individuals occur in the same species, are thought to reflect a balance between the benefits and costs of dispersal. Fitness costs and benefits associated with wing dimorphism were investigated in the male pea aphid, Acyrthosiphon pisum (Harris) (Hemiptera: Aphididae). In one-on-one mating competitions in small arenas between winged and wingless males, the winged aphids obtained most of the matings with virgin females. In contrast, during competition experiments in larger cages with multiple individuals of each morph, the winged males no longer had a clear mating advantage over wingless males. In the absence of competition, wingless males had marginally higher lifetime reproductive success than winged males, probably because mating winged males tended to die faster than wingless males. In the absence of females, winged males survived longer than wingless males and this difference disappeared under starvation conditions. Mating males of both morphs died significantly faster than males without access to females. There does not appear to be a direct tradeoff of dispersal ability with life history characteristics in pea aphid males, suggesting that the advantages of producing winged males may result from outbreeding.

}, keywords = {Animals, Aphids, Female, Fertility, Longevity, Male, Sex Characteristics, Sexual Behavior, Animal, Wing}, issn = {1536-2442}, doi = {10.1673/031.007.4501}, author = {Sack, Coralynn and Stern, David L} } @article {2469, title = {Sex in flies: what {\textquoteright}body{\textendash}mind{\textquoteright} dichotomy?}, journal = {Developmental Biology}, volume = {306}, year = {2007}, month = {2007 Jun 1}, pages = {10-9}, abstract = {

Sexual behavior in Drosophila results from interactions of multiple neural and genetic pathways. Male-specific fruitless (fruM) is a major component inducing male behaviors, but recent work indicates key roles for other sex-specific and sex-non-specific components. Notably, male-like courtship by retained (retn) mutant females reveals an intrinsic pathway for male behavior independent of fruM, while behavioral differences between males and females with equal levels of fruM expression indicate involvement of another sex-specific component. Indeed, sex-specific products of doublesex (dsxF and dsxM), that control sexual differentiation of the body, also contribute to sexual behavior and neural development of both sexes. In addition, the single product of the dissatisfaction (dsf) gene is needed for appropriate behavior in both sexes, implying additional complexities and levels of control. The genetic mechanisms controlling sexual behavior are similar to those controlling body sexual development, suggesting biological advantages of modifying an intermediate intrinsic pathway in generation of two substantially different behavioral or morphological states.

}, keywords = {Animal, Animals, Cytoplasmic and Nuclear, Drosophila, Drosophila Proteins, Female, Genes, Insect, Male, Microtubule-Associated Proteins, Nerve Tissue Proteins, Neurons, Neuropeptides, Receptors, Sex, Sexual Behavior, Transcription Factors}, issn = {0012-1606}, doi = {10.1016/j.ydbio.2007.03.022}, author = {Shirangi, Troy R and McKeown, Michael} } @conference {48185, title = {Shape constrained automatic segmentation of the liver based on a heuristic intensity model.}, booktitle = {MICCAI Workshop 3D Segmentation in the Clinic}, year = {2007}, month = {2007 Oct 29}, address = {Brisbane, Australia}, abstract = {

We present a fully automatic 3D segmentation method for the liver from contrast-enhanced CT data. It is based on a combination of a constrained free-form and statistical deformable model. The adap- tation of the model to the image data is performed according to a simple model of the typical intensity distribution around the liver boundary and neighboring anatomical structures, considering the potential presence of tumors in the liver. All parameters of the deformation as well as the initial positioning of the model in the data are estimated automatically.\ 

}, url = {http://mbi.dkfz-heidelberg.de/grand-challenge2007/web/p109.pdf}, author = {Kainmueller, Dagmar and Lange, Thomas and Lamecker, Hans} } @article {2507, title = {Size assessment and growth control: how adult size is determined in insects.}, journal = {BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology}, volume = {29}, year = {2007}, month = {2007 Apr}, pages = {344-55}, abstract = {

Size control depends on both the regulation of growth rate and the control over when to stop growing. Studies of Drosophila melanogaster have shown that insulin and Target of Rapamycin (TOR) pathways play principal roles in controlling nutrition-dependent growth rates. A TOR-mediated nutrient sensor in the fat body detects nutrient availability, and regulates insulin signaling in peripheral tissues, which in turn controls larval growth rates. After larvae initiate metamorphosis, growth stops. For growth to stop at the correct time, larvae need to surpass a critical weight. Recently, it was found that the insulin-dependent growth of the prothoracic gland is involved in assessing when critical weight has been reached. Furthermore, mutations in DHR4, a repressor of ecdysone signaling, reduce critical weight and adult size. Thus, the mechanisms that control growth rates converge on those assessing size to ensure that the larvae attain the appropriate size at metamorphosis.

}, keywords = {Aging, Animals, Body Size, Hormones, Insects, Signal Transduction}, issn = {0265-9247}, doi = {10.1002/bies.20552}, author = {Mirth, Christen Kerry and Riddiford, Lynn M} } @article {46406, title = {S-nitrosylation-induced conformational change in blackfin tuna myoglobin.}, journal = {Journal of Biological Chemistry}, volume = {282}, year = {2007}, month = {2007 Jul 6}, pages = {19773-80}, abstract = {

S-nitrosylation is a post-translational protein modification that can alter the function of a variety of proteins. Despite the growing wealth of information that this modification may have important functional consequences, little is known about the structure of the moiety or its effect on protein tertiary structure. Here we report high-resolution x-ray crystal structures of S-nitrosylated and unmodified blackfin tuna myoglobin, which demonstrate that in vitro S-nitrosylation of this protein at the surface-exposed Cys-10 directly causes a reversible conformational change by "wedging" apart a helix and loop. Furthermore, we have demonstrated in solution and in a single crystal that reduction of the S-nitrosylated myoglobin with dithionite results in NO cleavage from the sulfur of Cys-10 and rebinding to the reduced heme iron, showing the reversibility of both the modification and the conformational changes. Finally, we report the 0.95-A structure of ferrous nitrosyl myoglobin, which provides an accurate structural view of the NO coordination geometry in the context of a globin heme pocket.

}, keywords = {Animals, Crystallography, X-Ray, Cysteine, Dithionite, Models, Molecular, Myoglobin, Nitric Oxide, Oxidation-Reduction, Protein Processing, Post-Translational, Protein Structure, Tertiary, Tuna}, issn = {0021-9258}, doi = {10.1074/jbc.M701363200}, author = {Schreiter, Eric R and Rodr{\'\i}guez, Mar{\'\i}a M and Weichsel, Andrzej and Montfort, William R and Bonaventura, Joseph} } @article {793, title = {Specific Drosophila Dscam juxtamembrane variants control dendritic elaboration and axonal arborization.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {27}, year = {2007}, month = {2007 Jun 20}, pages = {6723-8}, abstract = {

Drosophila Dscam isoforms are derived from two alternative transmembrane/juxtamembrane domains (TMs) in addition to thousands of ectodomain variants. Using a microRNA-based RNA interference technology, we selectively knocked down different subsets of Dscams containing either the exon 17.1- or exon 17.2-encoding TM. Eliminating Dscam[TM1] reduced Dscam expression but minimally affected postembryonic axonal morphogenesis. In contrast, depleting Dscam[TM2] blocked axon arborization. Further removal of Dscam[TM1] enhanced the loss-of-Dscam[TM2] axonal phenotypes. However, Dscam[TM1] primarily regulates dendritic development, as evidenced by the observations that removing Dscam[TM1] alone impeded elaboration of dendrites and that transgenic Dscam[TM1], but not Dscam[TM2], effectively rescued Dscam mutant dendritic phenotypes in mosaic organisms. These distinct Dscam functions can be attributed to the juxtamembrane regions of TMs that govern dendritic versus axonal targeting of Dscam as well. Together, we suggest that specific Drosophila Dscam juxtamembrane variants control dendritic elaboration and axonal arborization.

}, keywords = {Animals, Axons, Cell Adhesion Molecules, Dendrites, Drosophila, Drosophila Proteins, Genetic Variation, Genetically Modified, Membrane Proteins, Morphogenesis, Neural Cell Adhesion Molecules, Protein Isoforms}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.1517-07.2007}, author = {Shi, Lei and Yu, Hung-Hsiang and Yang, Jacob S and Lee, Tzumin} } @article {45895, title = {Stability and plasticity of intrinsic membrane properties in hippocampal CA1 pyramidal neurons: effects of internal anions.}, journal = {The Journal of Physiology}, volume = {578}, year = {2007}, month = {2007 Feb 1}, pages = {799-818}, abstract = {

CA1 pyramidal neurons from animals that have acquired hippocampal tasks show increased neuronal excitability, as evidenced by a reduction in the postburst afterhyperpolarization (AHP). Studies of AHP plasticity require stable long-term recordings, which are affected by the intracellular solutions potassium methylsulphate (KMeth) or potassium gluconate (KGluc). Here we show immediate and gradual effects of these intracellular solutions on measurement of the AHP and basic membrane properties, and on the induction of AHP plasticity in CA1 pyramidal neurons from rat hippocampal slices. The AHP measured immediately after establishing whole-cell recordings was larger with KMeth than with KGluc. In general, the AHP in KMeth was comparable to the AHP measured in the perforated-patch configuration. However, KMeth induced time-dependent changes in the intrinsic membrane properties of CA1 pyramidal neurons. Specifically, input resistance progressively increased by 70\% after 50 min; correspondingly, the current required to trigger an action potential and the fast afterdepolarization following action potentials gradually decreased by about 50\%. Conversely, these measures were stable in KGluc. We also demonstrate that activity-dependent plasticity of the AHP occurs with physiologically relevant stimuli in KGluc. AHPs triggered with theta-burst firing every 30 s were progressively reduced, whereas AHPs elicited every 150 s were stable. Blockade of the apamin-sensitive AHP current (I(AHP)) was insufficient to block AHP plasticity, suggesting that plasticity is manifested through changes in the apamin-insensitive slow AHP current (sI(AHP)). These changes were observed in the presence of synaptic blockers, and therefore reflect changes in the intrinsic properties of the neurons. However, no AHP plasticity was observed using KMeth. In summary, these data show that KMeth produces time-dependent changes in basic membrane properties and prevents or obscures activity-dependent reduction of the AHP. In whole-cell recordings using KGluc, repetitive theta-burst firing induced AHP plasticity that mimics learning-related reduction in the AHP.

}, keywords = {Animals, Anions, Apamin, Gluconates, Male, Membrane Potentials, Neuronal Plasticity, Norepinephrine, Patch-Clamp Techniques, Pyramidal Cells, Rats, Rats, Wistar, Sulfuric Acid Esters, Time Factors}, issn = {0022-3751}, doi = {10.1113/jphysiol.2006.124586}, author = {Kaczorowski, Catherine Cook and Disterhoft, John and Spruston, Nelson} } @article {5344, title = {Straightening worm images.}, journal = {2007 4TH IEEE International Symposium on Biomedical Imagin : Macro to Nano, VOLS 1-3}, year = {2007}, month = {2007 Apr 12-15}, pages = {292-5}, abstract = {

C. elegans, a roundworm in soil is widely used in studying animal development and aging, cell differentiation, etc. Recentlv, high-resolution fluorescence images of C. elegans have become available, introducing several new image analysis applications. One problem is that worm bodies usually curve greatly in images, thus it is highly desired to straighten worms so that they can be compared easily under the same canonical coordinate system. We develop a worm straightening algorithm (WSA) using a cutting-plane restacking method, which aggregates the linear rotation transforms of a continuous sequence of cutting lines/planes orthogonal to the "backbone" of a worm to best approximate the nonlinearly bended worm body. We formulate the backbone as a parametric form of cubic spline of a series of control points. We develop two minimum-spanning-tree based methods to automatically determine the locations of control points. Our experimental methods show that our approach can effectively straighten both 2D and 3D worm images.

}, doi = {10.1109/ISBI.2007.356846}, author = {Peng, Hanchuan and Long, Fuhui and Myers, Eugene W} } @conference {46328, title = {Supervised Learning of Image Restoration with Convolutional Networks}, booktitle = {IEEE 11th International Conference on Computer Vision, 2007. ICCV 2007}, year = {2007}, month = {2007-10}, publisher = {IEEE}, organization = {IEEE}, address = {Rio de Janeiro}, abstract = {

Convolutional networks have achieved a great deal of success in high-level vision problems such as object recognition. Here we show that they can also be used as a general method for low-level image processing. As an example of our approach, convolutional networks are trained using gradient learning to solve the problem of restoring noisy or degraded images. For our training data, we have used electron microscopic images of neural circuitry with ground truth restorations provided by human experts. On this dataset, Markov random field (MRF), conditional random field (CRF), and anisotropic diffusion algorithms perform about the same as simple thresholding, but superior performance is obtained with a convolutional network containing over 34,000 adjustable parameters. When restored by this convolutional network, the images are clean enough to be used for segmentation, whereas the other approaches fail in this respect. We do not believe that convolutional networks are fundamentally superior to MRFs as a representation for image processing algorithms. On the contrary, the two approaches are closely related. But in practice, it is possible to train complex convolutional networks, while even simple MRF models are hindered by problems with Bayesian learning and inference procedures. Our results suggest that high model complexity is the single most important factor for good performance, and this is possible with convolutional networks.

}, isbn = {978-1-4244-1630-1}, doi = {10.1109/ICCV.2007.4408909}, author = {Jain, V. and Murray, J.F. and Roth, F. and Turaga, S. and Zhigulin, V. and Briggman, K.L. and Helmstaedter, M.N. and Denk, W. and Seung, H.S.} } @proceedings {4528, title = {Supervised learning of image restoration with convolutional networks.}, volume = {2}, year = {2007}, month = {2007 Oct 14}, pages = {1-8}, publisher = {IEEE}, edition = {ICCV}, author = {Jain, Viren and Murray, Joseph F and Roth, Fabian and Turaga, Srinivas and Zhigulin, Valentin and Briggman, Kevin L and Helmstaedter, Moritz N. and Denk, Winfried and Seung, H Sebastian} } @article {2403, title = {Switching of the core transcription machinery during myogenesis.}, journal = {Genes \& Development}, volume = {21}, year = {2007}, month = {2007 Sep 1}, pages = {2137-49}, abstract = {

Transcriptional mechanisms that govern cellular differentiation typically include sequence-specific DNA-binding proteins and chromatin-modifying activities. These regulatory factors are assumed necessary and sufficient to drive both divergent programs of proliferation and terminal differentiation. By contrast, potential contributions of the basal transcriptional apparatus to orchestrate cell-specific gene expression have been poorly explored. In order to probe alternative mechanisms that control differentiation, we have assessed the fate of the core promoter recognition complex, TFIID, during skeletal myogenesis. Here we report that differentiation of myoblast to myotubes involves the disruption of the canonical holo-TFIID and replacement by a novel TRF3/TAF3 (TBP-related factor 3/TATA-binding protein-associated factor 3) complex. This required switching of core promoter complexes provides organisms a simple yet effective means to selectively turn on one transcriptional program while silencing many others. Although this drastic but parsimonious transcriptional switch had previously escaped our attention, it may represent a more general mechanism for regulating cell type-specific terminal differentiation.

}, keywords = {Animals, Cell Differentiation, Cell Line, Developmental, Gene Expression Regulation, Genetic, Humans, Mice, Models, Muscle, Muscle Development, Muscle Fibers, Myofibrils, Nuclear Proteins, RNA Interference, Skeletal, TATA Box Binding Protein-Like Proteins, Transcription, Transcription Factor TFIID}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Deato, Maria Divina E and Tjian, Robert} } @article {45961, title = {Tension applied through the Dam1 complex promotes microtubule elongation providing a direct mechanism for length control in mitosis.}, journal = {Nature Cell Biology}, volume = {9}, year = {2007}, month = {2007 Jul}, pages = {832-7}, abstract = {

In dividing cells, kinetochores couple chromosomes to the tips of growing and shortening microtubule fibres and tension at the kinetochore-microtubule interface promotes fibre elongation. Tension-dependent microtubule fibre elongation is thought to be essential for coordinating chromosome alignment and separation, but the mechanism underlying this effect is unknown. Using optical tweezers, we applied tension to a model of the kinetochore-microtubule interface composed of the yeast Dam1 complex bound to individual dynamic microtubule tips. Higher tension decreased the likelihood that growing tips would begin to shorten, slowed shortening, and increased the likelihood that shortening tips would resume growth. These effects are similar to the effects of tension on kinetochore-attached microtubule fibres in many cell types, suggesting that we have reconstituted a direct mechanism for microtubule-length control in mitosis.

}, keywords = {Biomechanical Phenomena, Cell Cycle Proteins, Fungal Proteins, Kinetochores, Microspheres, Microtubule-Associated Proteins, Microtubules, Mitosis, Optical Tweezers, Saccharomyces cerevisiae Proteins}, issn = {1465-7392}, doi = {10.1038/ncb1609}, author = {Franck, Andrew D and Powers, Andrew F and Gestaut, Daniel R and Gonen, Tamir and Davis, Trisha N and Asbury, Charles L} } @article {68489, title = {Thermoelectric manipulation of aqueous droplets in microfluidic devices.}, journal = {Anal Chem}, volume = {79}, year = {2007}, month = {07/2007}, pages = {4845-51}, abstract = {

This article describes a method for manipulating the temperature inside aqueous droplets, utilizing a thermoelectric cooler to control the temperature of select portions of a microfluidic chip. To illustrate the adaptability of this approach, we have generated an "ice valve" to stop fluid flow in a microchannel. By taking advantage of the vastly different freezing points for aqueous solutions and immiscible oils, we froze a stream of aqueous droplets that were formed on-chip. By integrating this technique with cell encapsulation into aqueous droplets, we were also able to freeze single cells encased in flowing droplets. Using a live-dead stain, we confirmed the viability of cells was not adversely affected by the process of freezing in aqueous droplets provided cryoprotectants were utilized. When combined with current droplet methodologies, this technology has the potential to both selectively heat and cool portions of a chip for a variety of droplet-related applications, such as freezing, temperature cycling, sample archiving, and controlling reaction kinetics.

}, keywords = {Cell Survival, Freezing, Kinetics, Lymphoma, B-Cell, Microfluidic Analytical Techniques, Mineral Oil, Solutions, Water}, issn = {0003-2700}, doi = {10.1021/ac062458a}, author = {Sgro, Allyson E and Allen, Peter B and Chiu, Daniel T} } @article {1542, title = {Three-dimensional analysis of a viral RNA replication complex reveals a virus-induced mini-organelle.}, journal = {PLoS Biology}, volume = {5}, year = {2007}, month = {2007 Sep}, pages = {e220}, abstract = {

Positive-strand RNA viruses are the largest genetic class of viruses and include many serious human pathogens. All positive-strand RNA viruses replicate their genomes in association with intracellular membrane rearrangements such as single- or double-membrane vesicles. However, the exact sites of RNA synthesis and crucial topological relationships between relevant membranes, vesicle interiors, surrounding lumens, and cytoplasm generally are poorly defined. We applied electron microscope tomography and complementary approaches to flock house virus (FHV)-infected Drosophila cells to provide the first 3-D analysis of such replication complexes. The sole FHV RNA replication factor, protein A, and FHV-specific 5-bromouridine 5{\textquoteright}-triphosphate incorporation localized between inner and outer mitochondrial membranes inside approximately 50-nm vesicles (spherules), which thus are FHV-induced compartments for viral RNA synthesis. All such FHV spherules were outer mitochondrial membrane invaginations with interiors connected to the cytoplasm by a necked channel of approximately 10-nm diameter, which is sufficient for ribonucleotide import and product RNA export. Tomographic, biochemical, and other results imply that FHV spherules contain, on average, three RNA replication intermediates and an interior shell of approximately 100 membrane-spanning, self-interacting protein As. The results identify spherules as the site of protein A and nascent RNA accumulation and define spherule topology, dimensions, and stoichiometry to reveal the nature and many details of the organization and function of the FHV RNA replication complex. The resulting insights appear relevant to many other positive-strand RNA viruses and support recently proposed structural and likely evolutionary parallels with retrovirus and double-stranded RNA virus virions.

}, keywords = {Animals, Drosophila, Electron, Imaging, Microscopy, Mitochondrial Membranes, Nodaviridae, Organelles, RNA, Three-Dimensional, Viral, Virus Replication}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0050220}, author = {Kopek, Benjamin G and Perkins, Guy and Miller, David J and Ellisman, Mark H and Ahlquist, Paul} } @article {4479, title = {Three-dimensional analysis of a viral RNA replication complex reveals a virus-induced mini-organelle.}, journal = {PLoS biology}, volume = {5}, year = {2007}, month = {2007 Sep}, pages = {e220}, abstract = {

Positive-strand RNA viruses are the largest genetic class of viruses and include many serious human pathogens. All positive-strand RNA viruses replicate their genomes in association with intracellular membrane rearrangements such as single- or double-membrane vesicles. However, the exact sites of RNA synthesis and crucial topological relationships between relevant membranes, vesicle interiors, surrounding lumens, and cytoplasm generally are poorly defined. We applied electron microscope tomography and complementary approaches to flock house virus (FHV)-infected Drosophila cells to provide the first 3-D analysis of such replication complexes. The sole FHV RNA replication factor, protein A, and FHV-specific 5-bromouridine 5{\textquoteright}-triphosphate incorporation localized between inner and outer mitochondrial membranes inside approximately 50-nm vesicles (spherules), which thus are FHV-induced compartments for viral RNA synthesis. All such FHV spherules were outer mitochondrial membrane invaginations with interiors connected to the cytoplasm by a necked channel of approximately 10-nm diameter, which is sufficient for ribonucleotide import and product RNA export. Tomographic, biochemical, and other results imply that FHV spherules contain, on average, three RNA replication intermediates and an interior shell of approximately 100 membrane-spanning, self-interacting protein As. The results identify spherules as the site of protein A and nascent RNA accumulation and define spherule topology, dimensions, and stoichiometry to reveal the nature and many details of the organization and function of the FHV RNA replication complex. The resulting insights appear relevant to many other positive-strand RNA viruses and support recently proposed structural and likely evolutionary parallels with retrovirus and double-stranded RNA virus virions.

}, keywords = {Animals, Drosophila, Electron, Imaging, Microscopy, Mitochondrial Membranes, Nodaviridae, Organelles, RNA, Three-Dimensional, Viral, Virus Replication}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0050220}, url = {http://www.plosbiology.org/article/info\%3Adoi\%2F10.1371\%2Fjournal.pbio.0050220}, author = {Kopek, Benjamin G and Perkins, Guy and Miller, David J and Ellisman, Mark H and Ahlquist, Paul} } @article {1689, title = {Three-dimensional preparation and imaging reveal intrinsic microtubule properties.}, journal = {Nature Methods}, volume = {4}, year = {2007}, month = {2007 Oct}, pages = {843-6}, abstract = {

We present an experimental investigation of microtubule dynamic instability in three dimensions, based on laser light-sheet fluorescence microscopy. We introduce three-dimensional (3D) preparation of Xenopus laevis egg extracts in Teflon-based cylinders and provide algorithms for 3D image processing. Our approach gives experimental access to the intrinsic dynamic properties of microtubules and to microtubule population statistics in single asters. We obtain evidence for a stochastic nature of microtubule pausing.

}, keywords = {Animals, Computer-Assisted, Fluorescence, Image Processing, Imaging, Microscopy, Microtubules, Ovum, Three-Dimensional, Xenopus laevis}, issn = {1548-7091}, doi = {10.1038/nmeth1087}, author = {Keller, Philipp J and Pampaloni, Francesco and Stelzer, Ernst H K} } @article {4005, title = {Tracking silence: adjusting vocal production to avoid acoustic interference.}, journal = {Journal of Comparative Physiology. A, Neuroethology, Sensory, Neural, and Behavioral Physiology}, volume = {193}, year = {2007}, month = {2007 Apr}, pages = {477-83}, abstract = {

Organisms that use vocal signals to communicate often modulate their vocalizations to avoid being masked by other sounds in the environment. Although some environmental noise is continuous, both biotic and abiotic noise can be intermittent, or even periodic. Interference from intermittent noise can be avoided if calls are timed to coincide with periods of silence, a capacity that is unambiguously present in insects, amphibians, birds, and humans. Surprisingly, we know virtually nothing about this fundamental capacity in nonhuman primates. Here we show that a New World monkey, the cotton-top tamarin (Saguinus oedipus), can restrict calls to periodic silent intervals in loud white noise. In addition, calls produced during these silent intervals were significantly louder than calls recorded in silent baseline sessions. Finally, average call duration dropped across sessions, indicating that experience with temporally patterned noise caused tamarins to compress their calls. Taken together, these results show that in the presence of a predictable, intermittent environmental noise, cotton-top tamarins are able to modify the duration, timing, and amplitude of their calls to avoid acoustic interference.

}, keywords = {Adaptation, Animal, Animals, Auditory Perception, Auditory Threshold, Behavior, Environment, Feedback, Female, Male, Noise, Physiological, Saguinus, Vocalization}, issn = {0340-7594}, doi = {10.1007/s00359-006-0205-7}, author = {Egnor, S E Roian and Wickelgren, Jeanette Graham and Hauser, Marc D} } @article {2400, title = {Transcription of histone gene cluster by differential core-promoter factors.}, journal = {Genes \& Development}, volume = {21}, year = {2007}, month = {2007 Nov 15}, pages = {2936-49}, abstract = {

The 100 copies of tandemly arrayed Drosophila linker (H1) and core (H2A/B and H3/H4) histone gene cluster are coordinately regulated during the cell cycle. However, the molecular mechanisms that must allow differential transcription of linker versus core histones prevalent during development remain elusive. Here, we used fluorescence imaging, biochemistry, and genetics to show that TBP (TATA-box-binding protein)-related factor 2 (TRF2) selectively regulates the TATA-less Histone H1 gene promoter, while TBP/TFIID targets core histone transcription. Importantly, TRF2-depleted polytene chromosomes display severe chromosomal structural defects. This selective usage of TRF2 and TBP provides a novel mechanism to differentially direct transcription within the histone cluster. Moreover, genome-wide chromatin immunoprecipitation (ChIP)-on-chip analyses coupled with RNA interference (RNAi)-mediated functional studies revealed that TRF2 targets several classes of TATA-less promoters of \>1000 genes including those driving transcription of essential chromatin organization and protein synthesis genes. Our studies establish that TRF2 promoter recognition complexes play a significantly more central role in governing metazoan transcription than previously appreciated.

}, keywords = {Animals, Base Sequence, Biological, Cells, Chromatin Immunoprecipitation, Chromosomes, Cluster Analysis, Cultured, Drosophila, Firefly, Fluorescence, Genes, Genetic, Histones, Immunohistochemistry, In Situ Hybridization, Insect, Luciferases, Models, Molecular Sequence Data, Multigene Family, Nucleic Acid, Promoter Regions, Reporter, RNA Interference, Sequence Homology, TATA Box Binding Protein-Like Proteins, TATA-Box Binding Protein, Transcription}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Isogai, Yoh and Keles, S{\"u}nd{\"u}z and Prestel, Matthias and Hochheimer, Andreas and Tjian, Robert} } @article {1104, title = {Tuning the pK(a) of fluorescein to optimize binding assays.}, journal = {Analytical Chemistry}, volume = {79}, year = {2007}, month = {2007 Sep 1}, pages = {6775-82}, abstract = {

The phenolic pKa of fluorescein varies depending on its environment. The fluorescence of the dye varies likewise. Accordingly, a change in fluorescence can report on the association of a fluorescein conjugate to another molecule. Here, we demonstrate how to optimize this process with chemical synthesis. The fluorescence of fluorescein-labeled model protein, bovine pancreatic ribonuclease (RNase A), decreases upon binding to its cognate inhibitor protein (RI). Free and RI-bound fluorescein-RNase A have pKa values of 6.35 and 6.70, respectively, leaving the fluorescein moiety largely unprotonated at physiological pH and thus limiting the sensitivity of the assay. To increase the fluorescein pKa and, hence, the assay sensitivity, we installed an electron-donating alkyl group ortho to each phenol group. 2{\textquoteright},7{\textquoteright}-Diethylfluorescein (DEF) has spectral properties similar to those of fluorescein but a higher phenolic pKa. Most importantly, free and RI-bound DEF-RNase A have pKa values of 6.68 and 7.29, respectively, resulting in a substantial increase in the sensitivity of the assay. Using DEF-RNase A rather than fluorescein-RNase A in a microplate assay at pH 7.12 increased the Z{\textquoteright}-factor from -0.17 to 0.69. We propose that synthetic "tuning" of the pKa of fluorescein and other pH-sensitive fluorophores provides a general means to optimize binding assays.

}, keywords = {Enzyme Inhibitors, Ethylenes, Fluorescein, Humans, Hydrogen-Ion Concentration, Iodoacetamide, Molecular Structure, Pancreatic, Ribonuclease}, issn = {0003-2700}, doi = {10.1021/ac070907g}, author = {Lavis, Luke D and Rutkoski, Thomas J and Raines, Ronald T} } @proceedings {3302, title = {Unsupervised discovery of action hierarchies in large collections of activity videos.}, year = {2007}, month = {2007}, abstract = {

Given a large collection of videos containing activities, we investigate the problem of organizing it in an unsupervised fashion into a hierarchy based on the similarity of actions embedded in the videos. We use spatio-temporal volumes of filtered motion vectors to compute appearance-invariant action similarity measures efficiently - and use these similarity measures in hierarchical agglomerative clustering to organize videos into a hierarchy such that neighboring nodes contain similar actions. This naturally leads to a simple automatic scheme for selecting videos of representative actions (exemplars) from the database and for efficiently indexing the whole database. We compute a performance metric on the hierarchical structure to evaluate goodness of the estimated hierarchy, and show that this metric has potential for predicting the clustering performance of various joining criteria used in building hierarchies. Our results show that perceptually meaningful hierarchies can be constructed based on action similarities with minimal user supervision, while providing favorable clustering performance and retrieval performance.

}, author = {Ahammad, Parvez and Yeo, C and Ramchandran, K and Sastry, S} } @article {45742, title = {Variation in fiber number of a male-specific muscle between Drosophila species: a genetic and developmental analysis.}, journal = {Evol Dev}, volume = {9}, year = {2007}, month = {2007 Jul-Aug}, pages = {368-77}, abstract = {

We characterize a newly discovered morphological difference between species of the Drosophila melanogaster subgroup. The muscle of Lawrence (MOL) contains about four to five fibers in D. melanogaster and Drosophila simulans and six to seven fibers in Drosophila mauritiana and Drosophila sechellia. The same number of nuclei per fiber is present in these species but their total number of MOL nuclei differs. This suggests that the number of muscle precursor cells has changed during evolution. Our comparison of MOL development indicates that the species difference appears during metamorphosis. We mapped the quantitative trait loci responsible for the change in muscle fiber number between D. sechellia and D. simulans to two genomic regions on chromosome 2. Our data eliminate the possibility of evolving mutations in the fruitless gene and suggest that a change in the twist might be partly responsible for this evolutionary change.

}, keywords = {Animals, Drosophila, Genetic Variation, Male, Muscle Fibers, Skeletal, Quantitative Trait Loci}, issn = {1520-541X}, doi = {10.1111/j.1525-142X.2007.00174.x}, author = {Orgogozo, Virginie and Muro, Noelle M and Stern, David L} } @article {4639, title = {Virtual slit scanning microscopy.}, journal = {Histochemistry and Cell Biology}, volume = {128}, year = {2007}, month = {2007 Dec}, pages = {499-505}, abstract = {

We present a novel slit scanning confocal microscope with a CCD camera image sensor and a virtual slit aperture for descanning that can be adjusted during post-processing. A very efficient data structure and mathematical criteria for aligning the virtual aperture guarantee the ease of use. We further introduce a method to reduce the anisotropic lateral resolution of slit scanning microscopes. System performance is evaluated against a spinning disk confocal microscope on identical specimens. The virtual slit scanning microscope works as the spinning disk type and outperforms on thick specimens.

}, keywords = {Confocal, Electron, Equipment Design, Hela Cells, Humans, Microscopy, Scanning, Sensitivity and Specificity, User-Computer Interface}, issn = {0948-6143}, doi = {10.1007/s00418-007-0342-2}, author = {Fiolka, Reto and Stemmer, Andreas and Belyaev, Yury} } @article {2407, title = {An ARC/Mediator subunit required for SREBP control of cholesterol and lipid homeostasis.}, journal = {Nature}, volume = {442}, year = {2006}, month = {2006 Aug 10}, pages = {700-4}, abstract = {

The sterol regulatory element binding protein (SREBP) family of transcription activators are critical regulators of cholesterol and fatty acid homeostasis. We previously demonstrated that human SREBPs bind the CREB-binding protein (CBP)/p300 acetyltransferase KIX domain and recruit activator-recruited co-factor (ARC)/Mediator co-activator complexes through unknown mechanisms. Here we show that SREBPs use the evolutionarily conserved ARC105 (also called MED15) subunit to activate target genes. Structural analysis of the SREBP-binding domain in ARC105 by NMR revealed a three-helix bundle with marked similarity to the CBP/p300 KIX domain. In contrast to SREBPs, the CREB and c-Myb activators do not bind the ARC105 KIX domain, although they interact with the CBP KIX domain, revealing a surprising specificity among structurally related activator-binding domains. The Caenorhabditis elegans SREBP homologue SBP-1 promotes fatty acid homeostasis by regulating the expression of lipogenic enzymes. We found that, like SBP-1, the C. elegans ARC105 homologue MDT-15 is required for fatty acid homeostasis, and show that both SBP-1 and MDT-15 control transcription of genes governing desaturation of stearic acid to oleic acid. Notably, dietary addition of oleic acid significantly rescued various defects of nematodes targeted with RNA interference against sbp-1 and mdt-15, including impaired intestinal fat storage, infertility, decreased size and slow locomotion, suggesting that regulation of oleic acid levels represents a physiologically critical function of SBP-1 and MDT-15. Taken together, our findings demonstrate that ARC105 is a key effector of SREBP-dependent gene regulation and control of lipid homeostasis in metazoans.

}, keywords = {Amino Acid Sequence, Animals, Biomolecular, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Cholesterol, Homeostasis, Humans, Lipid Metabolism, Mediator Complex, Mice, Models, Molecular, Molecular Sequence Data, Nuclear Magnetic Resonance, Protein Binding, Protein Structure, Sterol Regulatory Element Binding Proteins, Tertiary, Transcription Factors, Transcriptional Activation}, issn = {1476-4687}, doi = {10.1073/pnas.1100640108}, author = {Yang, Fajun and Vought, Bryan W and Satterlee, John S and Walker, Amy K and Jim Sun, Z-Y and Watts, Jennifer L and DeBeaumont, Rosalie and Saito, R Mako and Hyberts, Sven G and Yang, Shaosong and Macol, Christine and Iyer, Lakshmanan and Tjian, Robert and van den Heuvel, Sander and Hart, Anne C and Wagner, Gerhard and N{\"a}{\"a}r, Anders M} } @article {1734, title = {Atomic and molecular parity nonconservation and sum frequency generation solutions to the ozma problem.}, journal = {The Journal of Physical Chemistry}, volume = {110}, year = {2006}, month = {2006 Sep 28}, pages = {18744-7}, abstract = {

Two Ozma problems are defined. Parity nonconservation is necessary for their solutions. Both problems may be solved by beta decay or atomic optical activity. Atomic and molecular sum frequency generation is chosen, as it supplies rich methods of effecting "gedanken" solutions to the Ozma problems. A new method of measuring a parameter manifesting molecular parity violations is advanced.

}, issn = {1520-6106}, doi = {10.1021/jp055038i}, author = {Ji, Na and Harris, Robert A} } @article {1557, title = {Bispecific antibodies for dual-modality cancer therapy: killing two signaling cascades with one stone.}, journal = {Current Opinion in Drug Discovery \& Development}, volume = {9}, year = {2006}, month = {2006 Mar}, pages = {184-93}, abstract = {

The additive and synergistic therapeutic effects derived from combinations of chemotherapeutic drugs and radiation have established an indispensable paradigm: cancer must be attacked on multiple fronts. However, the increased antitumor efficacy of such combinational regimens is also associated with severe systemic toxicity, as these drugs cannot selectively target tumor cells. Monoclonal antibodies (mAbs), which have exquisite specificity for their antigens, are becoming an increasingly important class of antitumor agents, as they enhance the efficacy of various therapeutic regimens without significantly increasing systemic toxicity. Furthermore, preclinical and early clinical evidence indicate that combinations of antibody-based drugs provide even greater efficacy with minimal side effects. Unfortunately, the research, manufacturing and regulatory costs of mAb development pose a significant barrier to the use of antibody-based combination therapies. An emerging alternative is the use of dual-targeting bispecific antibodies (BsAbs). BsAbs are derived from the recombination of variable domains of two antibodies with different specificities; BsAbs are thus capable of binding both antigens of their parental antibodies. With the recent progress that has been made in antibody engineering technology, BsAbs that simultaneously target two tumor-associated molecules (eg, growth factor receptors) are being heralded for their potential to deliver two therapeutic moieties in a single molecule.

}, keywords = {Animals, Antibodies, Antibody Specificity, Antineoplastic Agents, Combined Modality Therapy, Humans, Immunotherapy, Neoplasms, Signal Transduction}, issn = {1367-6733}, author = {Marvin, Jonathan S and Zhu, Zhenping} } @article {1490, title = {Boundary enhancement and speckle reduction for ultrasound images via salient structure extraction.}, journal = {IEEE Transactions on Bio-Medical Engineering}, volume = {53}, year = {2006}, month = {2006 Nov}, pages = {2300-9}, abstract = {

In this paper, we present an approach for medical ultrasound (US) image enhancement. It is based on a novel perceptual saliency measure which favors smooth, long curves with constant curvature. The perceptual salient boundaries of tissues in US images are enhanced by computing the saliency of directional vectors in the image space, via a local searching algorithm. Our measure is generally determined by curvature changes, intensity gradient and the interaction of neighboring vectors. To restrain speckle noise during the enhancement process, an adaptive speckle suspension term is also combined into the proposed saliency measure. The results obtained on both simulated images and medical US data reveal superior performance of the novel approach over a number of commonly used speckle filters. Applications of US image segmentation show that although the proposed algorithm cannot remove the speckle noise completely and may discard weak anatomical structures in some case, it still provides a considerable gain to US image processing for computer-aided diagnosis.

}, keywords = {Algorithms, Automated, Computer-Assisted, Humans, Image Enhancement, Image Interpretation, Pattern Recognition, Reproducibility of Results, Sensitivity and Specificity, Ultrasonography}, issn = {0018-9294}, doi = {10.1109/TBME.2006.878088}, author = {Xie, Jun and Jiang, Yifeng and Tsui, Hung-Tat and Heng, Pheng-Ann} } @article {1773, title = {The cells and logic for mammalian sour taste detection.}, journal = {Nature}, volume = {442}, year = {2006}, month = {2006 Aug 24}, pages = {934-8}, abstract = {

Mammals taste many compounds yet use a sensory palette consisting of only five basic taste modalities: sweet, bitter, sour, salty and umami (the taste of monosodium glutamate). Although this repertoire may seem modest, it provides animals with critical information about the nature and quality of food. Sour taste detection functions as an important sensory input to warn against the ingestion of acidic (for example, spoiled or unripe) food sources. We have used a combination of bioinformatics, genetic and functional studies to identify PKD2L1, a polycystic-kidney-disease-like ion channel, as a candidate mammalian sour taste sensor. In the tongue, PKD2L1 is expressed in a subset of taste receptor cells distinct from those responsible for sweet, bitter and umami taste. To examine the role of PKD2L1-expressing taste cells in vivo, we engineered mice with targeted genetic ablations of selected populations of taste receptor cells. Animals lacking PKD2L1-expressing cells are completely devoid of taste responses to sour stimuli. Notably, responses to all other tastants remained unaffected, proving that the segregation of taste qualities even extends to ionic stimuli. Our results now establish independent cellular substrates for four of the five basic taste modalities, and support a comprehensive labelled-line mode of taste coding at the periphery. Notably, PKD2L1 is also expressed in specific neurons surrounding the central canal of the spinal cord. Here we demonstrate that these PKD2L1-expressing neurons send projections to the central canal, and selectively trigger action potentials in response to decreases in extracellular pH. We propose that these cells correspond to the long-sought components of the cerebrospinal fluid chemosensory system. Taken together, our results suggest a common basis for acid sensing in disparate physiological settings.

}, keywords = {Action Potentials, Animals, Calcium Channels, Cell Surface, Computational Biology, Gene Expression Profiling, Hydrogen-Ion Concentration, Membrane Glycoproteins, Mice, Neurons, Phosphoproteins, Receptors, Spinal Cord, Taste, Tongue, Transgenic}, issn = {1476-4687}, doi = {10.1038/nature05084}, author = {Huang, Angela L and Chen, Xiaoke and Hoon, Mark A and Chandrashekar, Jayaram and Guo, Wei and Tr{\"a}nkner, Dimitri and Ryba, Nicholas J P and Zuker, Charles S} } @article {2411, title = {Cell-type-selective induction of c-jun by TAF4b directs ovarian-specific transcription networks.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, year = {2006}, month = {2006 Feb 21}, pages = {2594-9}, abstract = {

Cell-type-selective expression of the TFIID subunit TAF(II)105 (renamed TAF4b) in the ovary is essential for proper follicle development. Although a multitude of signaling pathways required for folliculogenesis have been identified, downstream transcriptional integrators of these signals remain largely unknown. Here, we show that TAF4b controls the granulosa-cell-specific expression of the proto-oncogene c-jun, and together they regulate transcription of ovary-selective promoters. Instead of using cell-type-specific activators, our findings suggest that the coactivator TAF4b regulates the expression of tissue-specific genes, at least in part, through the cell-type-specific induction of c-jun, a ubiquitous activator. Importantly, the loss of TAF4b in ovarian granulosa cells disrupts cellular morphologies and interactions during follicle growth that likely contribute to the infertility observed in TAF4b-null female mice. These data highlight a mechanism for potentiating tissue-selective functions of the basal transcription machinery and reveal intricate networks of gene expression that orchestrate ovarian-specific functions and cell morphology.

}, keywords = {Animals, Developmental, Female, Gene Expression Regulation, Genetic, Gonadotropins, Granulosa Cells, Horses, Messenger, Mice, Mutant Strains, Ovarian Follicle, Ovary, Promoter Regions, Proto-Oncogene Proteins c-jun, Rats, RNA, TATA-Binding Protein Associated Factors, Transcription, Transcription Factor TFIID, Up-Regulation}, issn = {0027-8424}, doi = {10.1073/pnas.1100640108}, author = {Geles, Kenneth G and Freiman, Richard N and Liu, Wei-Li and Zheng, Shuang and Voronina, Ekaterina and Tjian, Robert} } @article {46353, title = {Cluster analysis and robust use of full-field models for sonar beamforming}, journal = {Journal of Acoustical Society of America }, volume = {120}, year = {2006}, month = {11/2006}, pages = { 2635{\textendash}2647}, type = {Journal Article}, chapter = {2635}, abstract = {

Multipath propagation in shallow water can lead to mismatch losses when single-path replicas are\ usedfor horizontal array\ beamforming.Matched field processing(MFP) seeks to remedy this by\ using\ full-fieldacoustic propagationmodels to predict the multipath arrival structure. Ideally MFP can give source localization in range and depth as well as detection gains but\ robustly\ estimating range and depth is difficult in practice. The approach described here seeks to collapse\ full-field\ replica outputs to bearing which is\ robustly\ estimated while retaining any signal gains provided by the\ full-field\ model.Clusteranalysis\ is\ used\ to group together\ full-field\ replicas with similar responses. This yields a less redundant {\textquotedblleft}sampled field{\textquotedblright} describing a set of representative multipath structures for each bearing. A detection algorithm is introduced that\ uses\ clustering\ to collapse\ beamformer\ outputs to bearing such that signal gains are retained while increases in the noise floor are minimized. Horizontal array data from SWELLEX-96 are\ used\ to demonstrate the detection benefits of sampled field as compared to single-pathbeamforming.

}, issn = {0001-4966}, doi = {10.1121/1.2346128}, author = {Brian Tracey and  Nigel Lee and Srinivas Turaga} } @article {2408, title = {Coactivator cross-talk specifies transcriptional output.}, journal = {Genes \& Development}, volume = {20}, year = {2006}, month = {2006 Jun 1}, pages = {1458-69}, abstract = {

Cells often fine-tune gene expression at the level of transcription to generate the appropriate response to a given environmental or developmental stimulus. Both positive and negative influences on gene expression must be balanced to produce the correct level of mRNA synthesis. To this end, the cell uses several classes of regulatory coactivator complexes including two central players, TFIID and Mediator (MED), in potentiating activated transcription. Both of these complexes integrate activator signals and convey them to the basal apparatus. Interestingly, many promoters require both regulatory complexes, although at first glance they may seem to be redundant. Here we have used RNA interference (RNAi) in Drosophila cells to selectively deplete subunits of the MED and TFIID complexes to dissect the contribution of each of these complexes in modulating activated transcription. We exploited the robust response of the metallothionein genes to heavy metal as a model for transcriptional activation by analyzing direct factor recruitment in both heterogeneous cell populations and at the single-cell level. Intriguingly, we find that MED and TFIID interact functionally to modulate transcriptional response to metal. The metal response element-binding transcription factor-1 (MTF-1) recruits TFIID, which then binds promoter DNA, setting up a "checkpoint complex" for the initiation of transcription that is subsequently activated upon recruitment of the MED complex. The appropriate expression level of the endogenous metallothionein genes is achieved only when the activities of these two coactivators are balanced. Surprisingly, we find that the same activator (MTF-1) requires different coactivator subunits depending on the context of the core promoter. Finally, we find that the stability of multi-subunit coactivator complexes can be compromised by loss of a single subunit, underscoring the potential for combinatorial control of transcription activation.

}, keywords = {Animals, Cells, Chromatin Immunoprecipitation, Cultured, Drosophila, Gene Expression, Genetic, Metallothionein, Models, Polymerase Chain Reaction, Promoter Regions, RNA Interference, Transcription}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Marr, Michael T and Isogai, Yoh and Wright, Kevin J and Tjian, Robert} } @proceedings {3304, title = {Compressed domain real-time action recognition.}, year = {2006}, month = {2006 Oct 3}, abstract = {

We present a compressed domain scheme that is able to recognize and localize actions in real-time. The recognition problem is posed as performing a video query on a test video sequence. Our method is based on computing motion similarity using compressed domain features which can be extracted with low complexity. We introduce a novel motion correlation measure that takes into account differences in motion magnitudes. Our method is appearance invariant, requires no prior segmentation, alignment or stabilization, and is able to localize actions in both space and time. We evaluated our method on a large action video database consisting of 6 actions performed by 25 people under 3 different scenarios. Our classification results compare favorably with existing methods at only a fraction of their computational cost.

}, author = {Yeo, C and Ahammad, Parvez and Ramchandran, K and Sastry, S} } @article {1410, title = {Cre recombinase-mediated restoration of nigrostriatal dopamine in dopamine-deficient mice reverses hypophagia and bradykinesia.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, year = {2006}, month = {2006 Jun 6}, pages = {8858-63}, abstract = {

A line of dopamine-deficient (DD) mice was generated to allow selective restoration of normal dopamine signaling to specific brain regions. These DD floxed stop (DDfs) mice have a nonfunctional Tyrosine hydroxylase (Th) gene because of insertion of a NeoR gene flanked by lox P sites targeted to the first intron of the Th gene. DDfs mice have trace brain dopamine content, severe hypoactivity, and aphagia, and they die without intervention. However, they can be maintained by daily treatment with l-3,4-dihydroxyphenylalanine (L-dopa). Injection of a canine adenovirus (CAV-2) engineered to express Cre recombinase into the central caudate putamen restores normal Th gene expression to the midbrain dopamine neurons that project there because CAV-2 efficiently transduces axon terminals and is retrogradely transported to neuronal cell bodies. Bilateral injection of Cre recombinase into the central caudate putamen restores feeding and normalizes locomotion in DDfs mice. Analysis of feeding behavior by using lickometer cages revealed that virally rescued DDfs mice are hyperphagic and have modified meal structures compared with control mice. The virally rescued DDfs mice are also hyperactive at night, have reduced motor coordination, and are thigmotactic compared with controls. These results highlight the critical role for dopamine signaling in the dorsal striatum for most dopamine-dependent behaviors but suggest that dopamine signaling in other brain regions is important to fine-tune these behaviors. This approach offers numerous advantages compared with previous models aimed at examining dopamine signaling in discrete dopaminergic circuits.

}, keywords = {Adenoviridae, Animals, Brain, Dogs, Dopamine, Eating Disorders, Feeding Behavior, Gene Therapy, Hypokinesia, Inbred C57BL, Integrases, Mice, Motor Activity, Tyrosine 3-Monooxygenase, Viral Proteins}, issn = {0027-8424}, doi = {10.1073/pnas.0603081103}, author = {Hnasko, Thomas S and Perez, Francisco A and Scouras, Alex D and Stoll, Elizabeth A and Gale, Samuel D and Luquet, Serge and Phillips, Paul E M and Kremer, Eric J and Palmiter, Richard D} } @article {2410, title = {Cryo-electron microscopy studies of human TFIID: conformational breathing in the integration of gene regulatory cues.}, journal = {Structure}, volume = {14}, year = {2006}, month = {2006 Mar}, pages = {511-20}, abstract = {

The multisubunit transcription factor TFIID is essential for directing eukaryotic promoter recognition and mediating interactions with activators/cofactors during assembly of the preinitiation complex. Despite its central role in transcription initiation and regulation, structural knowledge of the TFIID complex has so far been largely limited to electron microscopy studies of negatively stained samples. Here, we present a cryo-electron microscopy 3D reconstruction of the large endogenous human TFIID complex. The improved cryopreservation has allowed for a more detailed definition of the structural elements in the complex and for the detection, by an extensive statistical analysis of the data, of a conformational opening and closing of the cavity central to the TFIID architecture. We propose that these density rearrangements in the structure are a likely reflection of the plasticity of the interactions between TFIID and its many partner proteins.

}, keywords = {Cryoelectron Microscopy, Gene Expression Regulation, Genetic, Humans, Protein Binding, Protein Structure, Tertiary, Transcription, Transcription Factor TFIID}, issn = {0969-2126}, doi = {10.1073/pnas.1100640108}, author = {Grob, Patricia and Cruse, Michael J and Inouye, Carla and Peris, Marian and Penczek, Pawel A and Tjian, Robert and Nogales, Eva} } @article {5416, title = {Crystal structure of human pyrroline-5-carboxylate reductase.}, journal = {Journal of Molecular Biology}, volume = {359}, year = {2006}, month = {2006 Jun 23}, pages = {1364-77}, abstract = {

Pyrroline-5-carboxylate reductase (P5CR) is a universal housekeeping enzyme that catalyzes the reduction of Delta(1)-pyrroline-5-carboxylate (P5C) to proline using NAD(P)H as the cofactor. The enzymatic cycle between P5C and proline is very important for the regulation of amino acid metabolism, intracellular redox potential, and apoptosis. Here, we present the 2.8 Angstroms resolution structure of the P5CR apo enzyme, its 3.1 Angstroms resolution ternary complex with NAD(P)H and substrate-analog. The refined structures demonstrate a decameric architecture with five homodimer subunits and ten catalytic sites arranged around a peripheral circular groove. Mutagenesis and kinetic studies reveal the pivotal roles of the dinucleotide-binding Rossmann motif and residue Glu221 in the human enzyme. Human P5CR is thermostable and the crystals were grown at 37 degrees C. The enzyme is implicated in oxidation of the anti-tumor drug thioproline.

}, keywords = {Amino Acid Sequence, Binding Sites, Dimerization, Humans, Models, Molecular, Molecular Sequence Data, Mutagenesis, Protein Structure, Pyrroline Carboxylate Reductases, Secondary, Sequence Alignment, Streptococcus pyogenes}, issn = {0022-2836}, doi = {10.1016/j.jmb.2006.04.053}, author = {Meng, Zhaohui and Lou, Zhiyong and Liu, Zhe and Li, Ming and Zhao, Xiaodong and Bartlam, Mark and Rao, Zihe} } @article {45891, title = {Dendritic patch-clamp recording.}, journal = {Nature Protocols}, volume = {1}, year = {2006}, month = {2006}, pages = {1235-47}, abstract = {

The patch-clamp technique allows investigation of the electrical excitability of neurons and the functional properties and densities of ion channels. Most patch-clamp recordings from neurons have been made from the soma, the largest structure of individual neurons, while their dendrites, which form the majority of the surface area and receive most of the synaptic input, have been relatively neglected. This protocol describes techniques for recording from the dendrites of neurons in brain slices under direct visual control. Although the basic technique is similar to that used for somatic patching, we describe refinements and optimizations of slice quality, microscope optics, setup stability and electrode approach that are required for maximizing the success rate for dendritic recordings. Using this approach, all configurations of the patch-clamp technique (cell-attached, inside-out, whole-cell, outside-out and perforated patch) can be achieved, even for relatively distal dendrites, and simultaneous multiple-electrode dendritic recordings are also possible. The protocol--from the beginning of slice preparation to the end of the first successful recording--can be completed in 3 h.

}, keywords = {Dendrites, Patch-Clamp Techniques}, issn = {1750-2799}, doi = {10.1038/nprot.2006.164}, author = {Davie, Jenny T and Kole, Maarten H P and Letzkus, Johannes J and Rancz, Ede A and Spruston, Nelson and Stuart, Greg J and H{\"a}usser, Michael} } @article {45746, title = {Developmental biology. Morphing into shape.}, journal = {Science}, volume = {313}, year = {2006}, month = {2006 Jul 7}, pages = {50-1}, keywords = {Animals, Biological Evolution, Body Size, Cell Proliferation, Drosophila melanogaster, Drosophila Proteins, Gene Expression Regulation, Developmental, Genes, Insect, Homeodomain Proteins, Morphogenesis, Organ Size, Protein-Serine-Threonine Kinases, Receptors, Cell Surface, Signal Transduction, Transcription Factors, Wing}, issn = {1095-9203}, doi = {10.1126/science.1130785}, author = {Stern, David L} } @article {2131, title = {Direct, androgen receptor-mediated regulation of the FKBP5 gene via a distal enhancer element.}, journal = {Endocrinology}, volume = {147}, year = {2006}, month = {2006 Jan 6}, pages = {590-8}, abstract = {

Androgen signaling via the androgen receptor (AR) transcription factor is crucial to normal prostate homeostasis and prostate tumorigenesis. Current models of AR function are predominantly based on studies of prostate-specific antigen regulation in androgen-responsive cell lines. To expand on these in vitro paradigms, we used the mouse prostate to elucidate the mechanisms through which AR regulates another direct target, FKBP5, in vivo. FKBP5 encodes an immunophilin that has been previously implicated in glucocorticoid and progestin signaling pathways and that likely influences prostate physiology in the presence of androgens. In this work, we show that androgens directly regulate FKBP5 via an interaction between the AR and a distal enhancer located 65 kb downstream of the transcription start site in the fifth intron of the FKBP5 gene. We have found that AR selectively recruits cAMP response element-binding protein to this enhancer. These interactions, in turn, result in chromatin remodeling that affects the enhancer proper but not the FKBP5 locus as a whole. Furthermore, in contrast to prostate-specific antigen-regulatory mechanisms, we show that transactivation of the FKBP5 gene does not rely on a single looping complex to mediate communication between the distal enhancer and proximal promoter. Rather, the distal enhancer complex and basal transcription apparatus communicate indirectly with one another, implicating a regulatory mechanism that has not been previously appreciated for AR target genes.

}, keywords = {Androgen, Animals, Base Sequence, Chromosome Mapping, Conserved Sequence, Enhancer Elements, Gene Expression Regulation, Genetic, Humans, Introns, Male, Mice, Molecular Sequence Data, Nucleic Acid, Orchiectomy, Prostate, Receptors, Reverse Transcriptase Polymerase Chain Reaction, Sequence Alignment, Sequence Homology, Tacrolimus Binding Proteins, Transcription}, issn = {0013-7227}, doi = {10.1002/cbic.201000254}, author = {Magee, Jeffrey A and Chang, Li-Wei and Stormo, Gary D and Milbrandt, Jeffrey} } @article {45909, title = {Distance-dependent differences in synapse number and AMPA receptor expression in hippocampal CA1 pyramidal neurons.}, journal = {Neuron}, volume = {50}, year = {2006}, month = {2006 May 4}, pages = {431-42}, abstract = {

The ability of synapses throughout the dendritic tree to influence neuronal output is crucial for information processing in the brain. Synaptic potentials attenuate dramatically, however, as they propagate along dendrites toward the soma. To examine whether excitatory axospinous synapses on CA1 pyramidal neurons compensate for their distance from the soma to counteract such dendritic filtering, we evaluated axospinous synapse number and receptor expression in three progressively distal regions: proximal and distal stratum radiatum (SR), and stratum lacunosum-moleculare (SLM). We found that the proportion of perforated synapses increases as a function of distance from the soma and that their AMPAR, but not NMDAR, expression is highest in distal SR and lowest in SLM. Computational models of pyramidal neurons derived from these results suggest that they arise from the compartment-specific use of conductance scaling in SR and dendritic spikes in SLM to minimize the influence of distance on synaptic efficacy.

}, keywords = {Animals, Cell Polarity, Cell Shape, Crosses, Genetic, Dendritic Spines, Excitatory Postsynaptic Potentials, Glutamic Acid, Hippocampus, Image Cytometry, Immunohistochemistry, Male, Microscopy, Electron, Transmission, Perforant Pathway, Presynaptic Terminals, Pyramidal Cells, Rats, Rats, Inbred BN, Rats, Inbred F344, Receptors, AMPA, Synapses, Synaptic Transmission}, issn = {0896-6273}, doi = {10.1016/j.neuron.2006.03.022}, author = {Nicholson, Daniel A and Trana, Rachel and Katz, Yael and Kath, William L and Spruston, Nelson and Geinisman, Yuri} } @article {5487, title = {Distinct behavioral responses to ethanol are regulated by alternate RhoGAP18B isoforms.}, journal = {Cell}, volume = {127}, year = {2006}, month = {2006 Oct 6}, pages = {199-211}, abstract = {

In most organisms, low ethanol doses induce increased activity, while high doses are sedating. To investigate the underlying mechanisms, we isolated Drosophila mutants with altered ethanol responsiveness. Mutations in white rabbit (whir), disrupting RhoGAP18B, are strongly resistant to the sedating effects of ethanol. This resistance can be suppressed by reducing the levels of Rho1 or Rac, implicating these GTPases in the behavioral response to ethanol. Indeed, expression of constitutively active forms of Rho1 or Rac1 in adult flies results in ethanol resistance similar to that observed in whir mutants. The whir locus produces several transcripts, RA-RD, which are predicted to encode three distinct RhoGAPs that share only the GAP domain. The RC transcript mediates the sedating effects of ethanol, while the RA transcript regulates its stimulant effects. Thus, distinct RhoGAPs, encoded by the same gene, regulate different manifestations of acute ethanol intoxication.

}, keywords = {Animal, Animals, Behavior, Brain, Central Nervous System Depressants, Drosophila melanogaster, Drosophila Proteins, Enzyme Activation, Ethanol, Female, GTPase-Activating Proteins, Humans, Molecular Sequence Data, Motor Activity, Mutation, Protein Isoforms, Rabbits, rho GTP-Binding Proteins, Transgenes}, issn = {0092-8674}, doi = {10.1016/j.cell.2006.09.010}, author = {Rothenfluh, Adrian and Threlkeld, Robert J and Bainton, Roland J and Tsai, Linus T-Y and Lasek, Amy W and Heberlein, Ulrike} } @article {2013, title = {Division accuracy in a stochastic model of Min oscillations in Escherichia coli.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, year = {2006}, month = {2006 Jan 10}, pages = {347-52}, abstract = {

Accurate cell division in Escherichia coli requires the Min proteins MinC, MinD, and MinE as well as the presence of nucleoids. MinD and MinE exhibit spatial oscillations, moving from pole to pole of the bacterium, resulting in an average MinD concentration that is low at the center of the cell and high at the poles. This concentration minimum is thought to signal the site of cell division. Deterministic models of the Min oscillations reproduce many observed features of the system, including the concentration minimum of MinD. However, there are only a few thousand Min proteins in a bacterium, so stochastic effects are likely to play an important role. Here, we show that Monte Carlo simulations with a large number of proteins agree well with the results from a deterministic treatment of the equations. The location of minimum local MinD concentration is too variable to account for cell division accuracy in wild type but is consistent with the accuracy of cell division in cells without nucleoids. This finding confirms the need to include additional mechanisms, such as reciprocal interactions with the cell division ring or positioning of the nucleoids, to explain wild-type accuracy.

}, keywords = {Adenosine Triphosphatases, Biological, Biophysical Phenomena, Biophysics, Cell Cycle Proteins, Cell Division, Escherichia coli, Escherichia coli Proteins, Models, Monte Carlo Method, Stochastic Processes}, issn = {0027-8424}, doi = {10.1073/pnas.0505825102}, author = {Kerr, Rex A and Levine, Herbert and Sejnowski, Terrence J and Rappel, Wouter-Jan} } @article {2470, title = {A double-switch system regulates male courtship behavior in male and female Drosophila melanogaster.}, journal = {Nature Genetics}, volume = {38}, year = {2006}, month = {2006 Dec}, pages = {1435-9}, abstract = {

Current models describe male-specific fruitless (fruM) as a genetic {\textquoteright}switch{\textquoteright} regulating sexual behavior in Drosophila melanogaster, and they postulate that female (F) and male (M) doublesex (dsx) products control body sexual morphology. In contradiction to this simple model, we show that dsx, as well as fruM and non-sex-specific retained (retn), affect both male and female sexual behaviors. In females, both retn and dsxF contribute to female receptivity, and both genes act to repress male-like courtship activity in the presence or absence of fruM. In males, consistent with the opposing functions of dsxM and dsxF, dsxM acts as a positive factor for male courtship. retn also acts counter to fruM in the development of the male-specific muscle of Lawrence. Molecularly, retn seems to regulate sexual behavior via a previously described complex that represses zerknullt. Thus, we show that fru and dsx together act as a {\textquoteright}switch{\textquoteright} system regulating behavior in the context of other developmental genes, such as retn.

}, keywords = {Animal, Animals, DNA-Binding Proteins, Drosophila melanogaster, Drosophila Proteins, Female, Gene Expression Regulation, Genes, Homeodomain Proteins, Insect, Male, Mutation, Nerve Tissue Proteins, Nuclear Proteins, Phenotype, Sexual Behavior, Transcription Factors}, issn = {1061-4036}, doi = {10.1038/ng1908}, author = {Shirangi, Troy R and Taylor, Barbara J and McKeown, Michael} } @article {45750, title = {A dual-genome microarray for the pea aphid, Acyrthosiphon pisum, and its obligate bacterial symbiont, Buchnera aphidicola.}, journal = {BMC Genomics}, volume = {7}, year = {2006}, month = {Mar 2006}, pages = {50}, abstract = {

BACKGROUND: The best studied insect-symbiont system is that of aphids and their primary bacterial endosymbiont Buchnera aphidicola. Buchnera inhabits specialized host cells called bacteriocytes, provides nutrients to the aphid and has co-speciated with its aphid hosts for the past 150 million years. We have used a single microarray to examine gene expression in the pea aphid, Acyrthosiphon pisum, and its resident Buchnera. Very little is known of gene expression in aphids, few studies have examined gene expression in Buchnera, and no study has examined simultaneously the expression profiles of a host and its symbiont. Expression profiling of aphids, in studies such as this, will be critical for assigning newly discovered A. pisum genes to functional roles. In particular, because aphids possess many genes that are absent from Drosophila and other holometabolous insect taxa, aphid genome annotation efforts cannot rely entirely on homology to the best-studied insect systems. Development of this dual-genome array represents a first attempt to characterize gene expression in this emerging model system.

RESULTS: We chose to examine heat shock response because it has been well characterized both in Buchnera and in other insect species. Our results from the Buchnera of A. pisum show responses for the same gene set as an earlier study of heat shock response in Buchnera for the host aphid Schizaphis graminum. Additionally, analyses of aphid transcripts showed the expected response for homologs of known heat shock genes as well as responses for several genes with unknown functional roles.

CONCLUSION: We examined gene expression under heat shock of an insect and its bacterial symbiont in a single assay using a dual-genome microarray. Further, our results indicate that microarrays are a useful tool for inferring functional roles of genes in A. pisum and other insects and suggest that the pea aphid genome may contain many gene paralogs that are differentially regulated.

}, keywords = {Animals, Aphids, Buchnera, Expressed Sequence Tags, Gene Expression Profiling, Gene Expression Regulation, Genome, Insect, Genomics, Heat-Shock Response, Oligonucleotide Array Sequence Analysis, Symbiosis}, issn = {1471-2164}, doi = {10.1186/1471-2164-7-50}, author = {Wilson, Alex C C and Dunbar, Helen E and Davis, Gregory K and Hunter, Wayne B and Stern, David L and Moran, Nancy A} } @article {5820, title = {Early embryogenesis of planaria: a cryptic larva feeding on maternal resources.}, journal = {Development Genes \& Evolution}, volume = {216}, year = {2006}, month = {2006 Nov}, pages = {667-81}, abstract = {

The early planarian embryo presents a complete ciliated epidermis and a pharynx and feeds on maternal yolk cells. In this paper, we report on all the elements involved in the formation of such an autonomous embryo, which we name cryptic larva. First, we provide a description of the spherical and fusiform yolk cells and their relationship with the blastomeres, from the laying of the egg capsule up to their final fate in mid embryonic stages. Then, we describe the early cleavage and the subsequent development of the tissues of the cryptic larva, namely, the primary epidermis, the embryonic pharynx, and a new cell type, the star cells. Finally, we discuss the possibility that the cryptic larva either constitutes a vestigial larva or, more likely, is the evolutionary result of the competition between multiple embryos for the limited and shared maternal resources in the egg capsule.

}, keywords = {Animals, Electron, Feeding Behavior, In Situ Hybridization, Larva, Microscopy, Planarians}, issn = {0949-944X}, doi = {10.1007/s00427-006-0094-3}, author = {Cardona, Albert and Hartenstein, Volker and Romero, Rafael} } @article {5530, title = {Efficient estimation of detailed single-neuron models.}, journal = {Journal of Neurophysiology}, volume = {96}, year = {2006}, month = {2006 Aug}, pages = {872-90}, abstract = {

Biophysically accurate multicompartmental models of individual neurons have significantly advanced our understanding of the input-output function of single cells. These models depend on a large number of parameters that are difficult to estimate. In practice, they are often hand-tuned to match measured physiological behaviors, thus raising questions of identifiability and interpretability. We propose a statistical approach to the automatic estimation of various biologically relevant parameters, including 1) the distribution of channel densities, 2) the spatiotemporal pattern of synaptic input, and 3) axial resistances across extended dendrites. Recent experimental advances, notably in voltage-sensitive imaging, motivate us to assume access to: i) the spatiotemporal voltage signal in the dendrite and ii) an approximate description of the channel kinetics of interest. We show here that, given i and ii, parameters 1-3 can be inferred simultaneously by nonnegative linear regression; that this optimization problem possesses a unique solution and is guaranteed to converge despite the large number of parameters and their complex nonlinear interaction; and that standard optimization algorithms efficiently reach this optimum with modest computational and data requirements. We demonstrate that the method leads to accurate estimations on a wide variety of challenging model data sets that include up to about 10(4) parameters (roughly two orders of magnitude more than previously feasible) and describe how the method gives insights into the functional interaction of groups of channels.

}, keywords = {Algorithms, Biophysical Phenomena, Biophysics, Cell Membrane, Data Interpretation, Dendrites, Electrophysiology, Ion Channel Gating, Ion Channels, Kinetics, Ligands, Likelihood Functions, Models, Monte Carlo Method, N-Methyl-D-Aspartate, Neurological, Neurons, Patch-Clamp Techniques, Receptors, Statistical, Synapses}, issn = {0022-3077}, author = {Huys, Quentin J M and Ahrens, Misha B and Paninski, Liam} } @article {1587, title = {Evidence supporting a cis-enediol-based mechanism for Pyrococcus furiosus phosphoglucose isomerase.}, journal = {Journal of Molecular Biology}, volume = {358}, year = {2006}, month = {2006 May 19}, pages = {1353-66}, abstract = {

The enzymatic aldose ketose isomerisation of glucose and fructose sugars involves the transfer of a hydrogen between their C1 and C2 carbon atoms and, in principle, can proceed through either a direct hydride shift or via a cis-enediol intermediate. Pyrococcus furiosus phosphoglucose isomerase (PfPGI), an archaeal metalloenzyme, which catalyses the interconversion of glucose 6-phosphate and fructose 6-phosphate, has been suggested to operate via a hydride shift mechanism. In contrast, the structurally distinct PGIs of eukaryotic or bacterial origin are thought to catalyse isomerisation via a cis-enediol intermediate. We have shown by NMR that hydrogen exchange between substrate and solvent occurs during the reaction catalysed by PfPGI eliminating the possibility of a hydride-shift-based mechanism. In addition, kinetic measurements on this enzyme have shown that 5-phospho-d-arabinonohydroxamate, a stable analogue of the putative cis-enediol intermediate, is the most potent inhibitor of the enzyme yet discovered. Furthermore, determination and analysis of crystal structures of PfPGI with bound zinc and the substrate F6P, and with a number of competitive inhibitors, and EPR analysis of the coordination of the metal ion within PfPGI, have suggested that a cis-enediol intermediate-based mechanism is used by PfPGI with Glu97 acting as the catalytic base responsible for isomerisation.

}, keywords = {Biomolecular, Catalytic Domain, Chemical, Crystallography, Electron Spin Resonance Spectroscopy, Enzyme Inhibitors, Glucose-6-Phosphate Isomerase, Hydrogen, Hydroxamic Acids, Isomerism, Kinetics, Macromolecular Substances, Metals, Models, Molecular, Nuclear Magnetic Resonance, Pyrococcus furiosus, Stereoisomerism, Substrate Specificity, Sugar Phosphates, X-Ray}, issn = {0022-2836}, doi = {10.1016/j.jmb.2006.03.015}, author = {Berrisford, John M and Hounslow, Andrea M and Akerboom, Jasper and Hagen, Wilfred R and Brouns, Stan J J and van der Oost, John and Murray, Iain A and Michael Blackburn, G and Waltho, Jonathan P and Rice, David W and Baker, Patrick J} } @article {1105, title = {Fluorogenic label for biomolecular imaging.}, journal = {ACS Chemical Biology}, volume = {1}, year = {2006}, month = {2006 May 23}, pages = {252-60}, abstract = {

Traditional small-molecule fluorophores are always fluorescent. This attribute can obscure valuable information in biological experiments. Here, we report on a versatile "latent" fluorophore that overcomes this limitation. At the core of the latent fluorophore is a derivative of rhodamine in which one nitrogen is modified as a urea. That modification enables rhodamine to retain half of its fluorescence while facilitating conjugation to a target molecule. The other nitrogen of rhodamine is modified with a "trimethyl lock", which enables fluorescence to be unmasked fully by a single user-designated chemical reaction. An esterase-reactive latent fluorophore was synthesized in high yield and attached covalently to a cationic protein. The resulting conjugate was not fluorescent in the absence of esterases. The enzymatic activity of esterases in endocytic vesicles and the cytosol educed fluorescence, enabling the time-lapse imaging of endocytosis into live human cells and thus providing unprecedented spatiotemporal resolution of this process. The modular design of this "fluorogenic label" enables the facile synthesis of an ensemble of small-molecule probes for the illumination of numerous biochemical and cell biological processes.

}, keywords = {Fluorescence, Fluorescent Dyes, Hela Cells, Humans, Microscopy, Molecular Probes, Spectrometry}, issn = {1554-8937}, doi = {10.1021/cb600132m}, author = {Lavis, Luke D and Chao, Tzu-Yuan and Raines, Ronald T} } @conference {2846, title = {A framework for feature selection for background subtraction.}, booktitle = {IEEE Conference on Computer Vision and Pattern Recognition}, year = {2006}, month = {2006}, author = {Parag, Toufiq and Elgammal, Ahmed and Mittal, Anurag} } @article {4142, title = {Functional dissection of a neuronal network required for cuticle tanning and wing expansion in Drosophila.}, journal = {The Journal of Neuroscience The Official Journal of the Society for Neuroscience}, volume = {26}, year = {2006}, month = {2006 Jan 11}, pages = {573-84}, abstract = {

A subset of Drosophila neurons that expresses crustacean cardioactive peptide (CCAP) has been shown previously to make the hormone bursicon, which is required for cuticle tanning and wing expansion after eclosion. Here we present evidence that CCAP-expressing neurons (NCCAP) consist of two functionally distinct groups, one of which releases bursicon into the hemolymph and the other of which regulates its release. The first group, which we call NCCAP-c929, includes 14 bursicon-expressing neurons of the abdominal ganglion that lie within the expression pattern of the enhancer-trap line c929-Gal4. We show that suppression of activity within this group blocks bursicon release into the hemolymph together with tanning and wing expansion. The second group, which we call NCCAP-R, consists of NCCAP neurons outside the c929-Gal4 pattern. Because suppression of synaptic transmission and protein kinase A (PKA) activity throughout NCCAP, but not in NCCAP-c929, also blocks tanning and wing expansion, we conclude that neurotransmission and PKA are required in NCCAP-R to regulate bursicon secretion from NCCAP-c929. Enhancement of electrical activity in NCCAP-R by expression of the bacterial sodium channel NaChBac also blocks tanning and wing expansion and leads to depletion of bursicon from central processes. NaChBac expression in NCCAP-c929 is without effect, suggesting that the abdominal bursicon-secreting neurons are likely to be silent until stimulated to release the hormone. Our results suggest that NCCAP form an interacting neuronal network responsible for the regulation and release of bursicon and suggest a model in which PKA-mediated stimulation of inputs to normally quiescent bursicon-expressing neurons activates release of the hormone.

}, keywords = {Animals, Bacterial Proteins, Cyclic AMP-Dependent Protein Kinases, Drosophila melanogaster, Drosophila Proteins, Electroretinography, Ganglia, Gene Targeting, Genetically Modified, Invertebrate, Invertebrate Hormones, Nerve Net, Neurons, Neuropeptides, Phenotype, Pigmentation, Recombinant Fusion Proteins, Shaker Superfamily of Potassium Channels, Sodium Channels, Synaptic Transmission, Wing}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3916-05.2006}, author = {Luan, Haojiang and Lemon, William C and Peabody, Nathan C and Pohl, Jascha B and Zelensky, Paul K and Wang, Ding and Nitabach, Michael N and Holmes, Todd C and White, Benjamin H} } @article {1188, title = {Genesis and wanderings: origins and migrations in asymmetrically replicating mitochondrial DNA.}, journal = {Cell Cycle}, volume = {5}, year = {2006}, month = {2006 May}, pages = {917-21}, abstract = {

Mammalian mitochondria maintain a small circular genome that encodes RNA and polypeptides that are essential for the generation of ATP through oxidative phosphorylation. The mechanism of replication of mammalian mitochondrial DNA (mtDNA) has recently been a topic of controversy. New evidence has led to a modified strand-displacement model that reconciles much of the current data. This revision stems from a new appreciation for alternative light-strand origins. We consider here some of the potential mechanisms for light-strand origin initiation. We also consider further the susceptibility of branch migration within replicating mtDNA molecules. The existence of alternative light-strand origins and a propensity for branch migration in replicating mtDNA molecules exposes a new array of possible configurations of mtDNA. The assortment and assignment of these forms is relevant to the interpretation of experimental data and may also yield insight into the molecular basis of replication errors.

}, keywords = {Animals, Atomic Force, DNA, DNA Replication, Electrophoresis, Evolution, Gel, Genetic, Microscopy, Mitochondrial, Models, Molecular, Two-Dimensional}, issn = {1551-4005}, author = {Brown, Timothy A and Clayton, David A} } @article {791, title = {Genetic mosaic with dual binary transcriptional systems in Drosophila.}, journal = {Nature Neuroscience}, volume = {9}, year = {2006}, month = {2006 May}, pages = {703-9}, abstract = {

MARCM (mosaic analysis with a repressible cell marker) involves specific labeling of GAL80-minus and GAL4-positive homozygous cells in otherwise heterozygous tissues. Here we demonstrate how the concurrent use of two independent binary transcriptional systems may facilitate complex MARCM studies in the Drosophila nervous system. By fusing LexA with the VP16 acidic activation domain (VP16) or the GAL4 activation domain (GAD), we obtained both GAL80-insensitive and GAL80-suppressible transcriptional factors. LexA::VP16 can mediate MARCM-independent binary transgene induction in mosaic organisms. The incorporation of LexA::GAD into MARCM, which we call dual-expression-control MARCM, permits the induction of distinct transgenes in different patterns among GAL80-minus cells in mosaic tissues. Lineage analysis with dual-expression-control MARCM suggested the presence of neuroglioblasts in the developing optic lobes but did not indicate the production of glia by postembryonic mushroom body neuronal precursors. In addition, dual-expression-control MARCM with a ubiquitous LexA::GAD driver revealed many unidentified cells in the GAL4-GH146-positive projection neuron lineages.

}, keywords = {Animals, Brain, Developmental, Drosophila, Drosophila Proteins, Gene Expression Regulation, Genetically Modified, Immunohistochemistry, Models, Molecular, Mosaicism, Neurons, Repressor Proteins, Transcription Factors, Transcriptional Activation}, issn = {1097-6256}, doi = {10.1038/nn1681}, author = {Lai, Sen-Lin and Lee, Tzumin} } @article {792, title = {Gradients of the Drosophila Chinmo BTB-zinc finger protein govern neuronal temporal identity.}, journal = {Cell}, volume = {127}, year = {2006}, month = {2006 Oct 20}, pages = {409-22}, abstract = {

Many neural progenitors, including Drosophila mushroom body (MB) and projection neuron (PN) neuroblasts, sequentially give rise to different subtypes of neurons throughout development. We identified a novel BTB-zinc finger protein, named Chinmo (Chronologically inappropriate morphogenesis), that governs neuronal temporal identity during postembryonic development of the Drosophila brain. In both MB and PN lineages, loss of Chinmo autonomously causes early-born neurons to adopt the fates of late-born neurons from the same lineages. Interestingly, primarily due to a posttranscriptional control, MB neurons born at early developmental stages contain more abundant Chinmo than their later-born siblings. Further, the temporal identity of MB progeny can be transformed toward earlier or later fates by reducing or increasing Chinmo levels, respectively. Taken together, we suggest that a temporal gradient of Chinmo (Chinmo(high) {\textendash}\> Chinmo(low)) helps specify distinct birth order-dependent cell fates in an extended neuronal lineage.

}, keywords = {5{\textquoteright} Untranslated Regions, Amino Acid Sequence, Animals, Brain, Cell Differentiation, Cell Lineage, Developmental, Drosophila, Drosophila Proteins, Gene Expression Regulation, Larva, Molecular Sequence Data, Morphogenesis, Mushroom Bodies, Mutation, Nerve Tissue Proteins, Neurons, Post-Translational, Protein Processing, Time Factors, Transgenes, Zinc Fingers}, issn = {0092-8674}, doi = {10.1016/j.cell.2006.08.045}, author = {Zhu, Sijun and Lin, Suewei and Kao, Chih-Fei and Awasaki, Takeshi and Chiang, Ann-Shyn and Lee, Tzumin} } @article {45749, title = {High-resolution quantitative trait locus mapping reveals sign epistasis controlling ovariole number between two Drosophila species.}, journal = {Genetics}, volume = {173}, year = {2006}, month = {2006 May}, pages = {197-205}, abstract = {

Identifying the genes underlying genetically complex traits is of fundamental importance for medicine, agriculture, and evolutionary biology. However, the level of resolution offered by traditional quantitative trait locus (QTL) mapping is usually coarse. We analyze here a trait closely related to fitness, ovariole number. Our initial interspecific mapping between Drosophila sechellia (8 ovarioles/ovary) and D. simulans (15 ovarioles/ovary) identified a major QTL on chromosome 3 and a minor QTL on chromosome 2. To refine the position of the major QTL, we selected 1038 additional recombinants in the region of interest using flanking morphological markers (selective phenotyping). This effort generated approximately one recombination event per gene and increased the mapping resolution by approximately seven times. Our study thus shows that using visible markers to select for recombinants can efficiently increase the resolution of QTL mapping. We resolved the major QTL into two epistatic QTL, QTL3a and QTL3b. QTL3a shows sign epistasis: it has opposite effects in two different genetic backgrounds, the presence vs. the absence of the QTL3b D. sechellia allele. This property of QTL3a allows us to reconstruct the probable order of fixation of the QTL alleles during evolution.

}, keywords = {Animals, Chromosome Mapping, Chromosomes, Crosses, Genetic, Drosophila, Epistasis, Genetic, Evolution, Molecular, Female, Ovary, Quantitative Trait Loci}, issn = {0016-6731}, doi = {10.1534/genetics.105.054098}, author = {Orgogozo, Virginie and Broman, Karl W and Stern, David L} } @article {48655, title = {High-speed pollen release in the white mulberry tree, Morus alba L.}, journal = {Sexual Plant Reproduction}, volume = {19}, year = {2006}, month = {2006 Mar}, pages = {19-24}, abstract = {

Anemophilous plants described as catapulting pollen explosively into the air have rarely attracted detailed examination. We investigated floral anthesis in a male mulberry tree with high-speed video and a force probe. The stamen was inflexed within the floral bud. Exposure to dry air initially resulted in a gradual movement of the stamen. This caused fine threads to tear at the stomium, ensuring dehiscence of the anther, and subsequently enabled the anther to slip off a restraining pistillode. The sudden release of stored elastic energy in the spring-like filament drove the stamen to straighten in less than 25\ μs, and reflex the petals to velocities in excess of half the speed of sound. This is the fastest motion yet observed in biology, and approaches the theoretical physical limits for movements in plants.

}, doi = {10.1007/s00497-005-0018-9}, author = {Taylor, Philip E and Card, Gwyneth M and House, James and Dickinson, Michael H and Flagan, Richard C} } @article {6353, title = {Hyperpolarization-activated cation current (Ih) is an ethanol target in midbrain dopamine neurons of mice.}, journal = {Journal of Neurophysiology}, volume = {95}, year = {2006}, month = {2006 Feb}, pages = {619-26}, abstract = {

Ethanol stimulates the firing activity of midbrain dopamine (DA) neurons, leading to enhanced dopaminergic transmission in the mesolimbic system. This effect is thought to underlie the behavioral reinforcement of alcohol intake. Ethanol has been shown to directly enhance the intrinsic pacemaker activity of DA neurons, yet the cellular mechanism mediating this excitation remains poorly understood. The hyperpolarization-activated cation current, Ih, is known to contribute to the pacemaker firing of DA neurons. To determine the role of Ih in ethanol excitation of DA neurons, we performed patch-clamp recordings in acutely prepared mouse midbrain slices. Superfusion of ethanol increased the spontaneous firing frequency of DA neurons in a reversible fashion. Treatment with ZD7288, a blocker of Ih, irreversibly depressed basal firing frequency and significantly attenuated the stimulatory effect of ethanol on firing. Furthermore, ethanol reversibly augmented Ih amplitude and accelerated its activation kinetics. This effect of ethanol was accompanied by a shift in the voltage dependence of Ih activation to more depolarized potentials and an increase in the maximum Ih conductance. Cyclic AMP mediated the depolarizing shift in Ih activation but not the increase in the maximum conductance. Finally, repeated ethanol treatment in vivo induced downregulation of Ih density in DA neurons and an accompanying reduction in the magnitude of ethanol stimulation of firing. These results suggest an important role of Ih in the reinforcing actions of ethanol and in the neuroadaptations underlying escalation of alcohol consumption associated with alcoholism.

}, keywords = {Action Potentials, Animals, Antiporters, Biological Clocks, Dopamine, Ethanol, Inbred C57BL, Ion Channel Gating, Membrane Potentials, Mesencephalon, Mice, Neurons}, issn = {0022-3077}, doi = {10.1152/jn.00682.2005}, author = {Okamoto, Takashi and Harnett, Mark T and Morikawa, Hitoshi} } @article {1586, title = {Identification of a glycolytic regulon in the archaea Pyrococcus and Thermococcus.}, journal = {FEMS Microbiology Letters}, volume = {260}, year = {2006}, month = {2006 Jul}, pages = {69-76}, abstract = {

The glycolytic pathway of the hyperthermophilic archaea that belong to the order Thermococcales (Pyrococcus, Thermococcus and Palaeococcus) differs significantly from the canonical Embden-Meyerhof pathway in bacteria and eukarya. This archaeal glycolysis variant consists of several novel enzymes, some of which catalyze unique conversions. Moreover, the enzymes appear not to be regulated allosterically, but rather at transcriptional level. To elucidate details of the gene expression control, the transcription initiation sites of the glycolytic genes in Pyrococcus furiosus have been mapped by primer extension analysis and the obtained promoter sequences have been compared with upstream regions of non-glycolytic genes. Apart from consensus sequences for the general transcription factors (TATA-box and BRE) this analysis revealed the presence of a potential transcription factor binding site (TATCAC-N(5)-GTGATA) in glycolytic and starch utilizing promoters of P. furiosus and several thermococcal species. The absence of this inverted repeat in Pyrococcus abyssi and Pyrococcus horikoshii probably reflects that their reduced catabolic capacity does not require this regulatory system. Moreover, this phyletic pattern revealed a TrmB-like regulator (PF0124 and TK1769) which may be involved in recognizing the repeat. This Thermococcales glycolytic regulon, with more than 20 genes, is the largest regulon that has yet been described for Archaea.

}, keywords = {Base Sequence, Binding Sites, Genetic, Glycolysis, Molecular Sequence Data, Promoter Regions, Pyrococcus, Regulon, Thermococcus, Transcription Initiation Site}, issn = {0378-1097}, doi = {10.1111/j.1574-6968.2006.00292.x}, author = {van de Werken, Harmen J G and Verhees, Corn{\'e} H and Akerboom, Jasper and de Vos, Willem M and van der Oost, John} } @article {1489, title = {Image diffusion using saliency bilateral filter.}, journal = {Medical Image Computing and Computer-Assisted Intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention}, volume = {9}, year = {2006}, month = {2006}, pages = {67-75}, abstract = {

Image diffusion can smooth away noise and small-scale structures while retaining important features, thereby enhancing the performances of many image processing algorithms such as image compression, segmentation and recognition. In this paper, we present a novel diffusion algorithm for which the filtering kernels vary according to the perceptual saliency of boundaries in the input images. The boundary saliency is estimated through a saliency measure which is generally determined by curvature changes, intensity gradient and the interaction of neighboring vectors. The connection between filtering kernels and perceptual saliency makes it possible to remove small-scale structures and preserves significant boundaries adaptively. The effectiveness of the proposed approach is validated by experiments on various medical images including the color Chinese Visible Human data set and gray MRI brain images.

}, keywords = {Algorithms, Artificial Intelligence, Automated, Brain, Cluster Analysis, Computer-Assisted, Diffusion Magnetic Resonance Imaging, Humans, Image Enhancement, Image Interpretation, Magnetic Resonance Imaging, Pattern Recognition, Reproducibility of Results, Sensitivity and Specificity}, author = {Xie, Jun and Heng, Pheng-Ann and Ho, Simon S M and Shah, Mubarak} } @article {2083, title = {Imaging intracellular fluorescent proteins at nanometer resolution. (With commentary)}, journal = {Science}, volume = {313}, year = {2006}, month = {2006 Sep 15}, pages = {1642-5}, abstract = {

We introduce a method for optically imaging intracellular proteins at nanometer spatial resolution. Numerous sparse subsets of photoactivatable fluorescent protein molecules were activated, localized (to approximately 2 to 25 nanometers), and then bleached. The aggregate position information from all subsets was then assembled into a superresolution image. We used this method{\textendash}termed photoactivated localization microscopy{\textendash}to image specific target proteins in thin sections of lysosomes and mitochondria; in fixed whole cells, we imaged vinculin at focal adhesions, actin within a lamellipodium, and the distribution of the retroviral protein Gag at the plasma membrane.

Commentary: The original PALM paper by myself and my friend and co-inventor Harald Hess, spanning the before- and after-HHMI eras. Submitted and publicly presented months before other publications in the same year, the lessons of the paper remain widely misunderstood: 1) localization precision is not resolution; 2) the ability to resolve a few molecules by the Rayleigh criterion in a diffraction limited region (DLR) does not imply the ability to resolve structures of arbitrary complexity at the same scale; 3) true resolution well beyond the Abbe limit requires the ability to isolate and localize hundreds or thousands of molecules in one DLR; and 4) certain photoactivatable fluorescent proteins (PA-FPs) and caged dyes can be isolated and precisely localized at such densities; yielding true resolution down to \ 20 nm. The molecular densities we demonstrate (105 molecules/m2) are more than two orders of magnitude greater than in later papers that year (implying ten-fold better true resolution) {\textendash} indeed, these papers demonstrate densities only comparable to earlier spectral or photobleaching based isolation methods. We validate our claims by correlative electron microscopy, and demonstrate the outstanding advantages of PA-FPs for superresolution microscopy: minimally perturbative sample preparation; high labeling densities; close binding to molecular targets; and zero non-specific background.

}, keywords = {Actins, Algorithms, Animals, Cell Line, Cell Membrane, Cercopithecus aethiops, COS Cells, Fluorescence, Focal Adhesions, gag, Gene Products, HIV-1, Light, Luminescent Proteins, Lysosomes, Microscopy, Mitochondria, Nanotechnology, Organelles, Photobleaching, Proteins, Pseudopodia, Recombinant Fusion Proteins, Vinculin}, issn = {1095-9203}, doi = {10.1126/science.1127344}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16902090}, author = {Betzig, Eric and Patterson, George H and Sougrat, Rachid and Lindwasser, O Wolf and Olenych, Scott and Bonifacino, Juan S and Davidson, Michael W and Lippincott-Schwartz, Jennifer and Hess, Harald F} } @article {3928, title = {In situ background estimation in quantitative fluorescence imaging.}, journal = {Biophysical Journal}, volume = {90}, year = {2006}, month = {2006 Apr 1}, pages = {2534-47}, abstract = {

Fluorescence imaging of bulk-stained tissue is a popular technique for monitoring the activities in a large population of cells. However, a precise quantification of such experiments is often compromised by an ambiguity of background estimation. Although, in single-cell-staining experiments, background can be measured from a neighboring nonstained region, such a region often does not exist in bulk-stained tissue. Here we describe a novel method that overcomes this problem. In contrast to previous methods, we determined the background of a given region of interest (ROI) using the information contained in the temporal dynamics of its individual pixels. Since no information outside the ROI is needed, the method can be used regardless of the staining profile in the surrounding tissue. Moreover, we extend the method to deal with background inhomogeneities within a single ROI, a problem not yet solved by any of the currently available tools. We performed computer simulations to demonstrate the accuracy of our method and give example applications in ratiometric calcium imaging of bulk-stained olfactory bulb slices. Converting the fluorescence signals into [Ca2+] gives resting values consistent with earlier single-cell staining results, and odorant-induced [Ca2+] transients can be quantitatively compared in different cells. Using these examples we show that inaccurate background subtraction introduces large errors (easily in the range of 100\%) in the assessment of both resting [Ca2+] and [Ca2+] dynamics. The proposed method allows us to avoid such errors.

}, keywords = {Algorithms, Animals, Biophysics, Brain, Calcium, Computer Simulation, Computer-Assisted, Confocal, Fluorescence, Image Processing, Likelihood Functions, Microscopy, Models, Normal Distribution, Olfactory Bulb, Olfactory Nerve, Regression Analysis, Reproducibility of Results, Software, Statistical, Time Factors, Xenopus laevis}, issn = {0006-3495}, doi = {10.1529/biophysj.105.070854}, author = {Chen, Tsai-Wen and Lin, Bei-Jung and Brunner, Edgar and Schild, Detlev} } @article {1543, title = {An in vitro fluorescence screen to identify antivirals that disrupt hepatitis B virus capsid assembly.}, journal = {Nature Biotechnology}, volume = {24}, year = {2006}, month = {2006 Mar}, pages = {358-62}, abstract = {

Virus assembly has not been routinely targeted in the development of antiviral drugs, in part because of the lack of tractable methods for screening in vitro. We have developed an in vitro assay of hepatitis B virus (HBV) capsid assembly, based on fluorescence quenching of dye-labeled capsid protein, for testing potential inhibitors. This assay is adaptable to high-throughput screening and can identify small-molecule inhibitors of virus assembly that prevent, inappropriately accelerate and/or misdirect capsid formation to yield aberrant particles. An in vitro primary screen has the advantage of identifying promising lead compounds affecting assembly without the requirement that they be taken up by cells in culture and be nontoxic. Our approach may facilitate the identification of antivirals targeting viruses other than HBV, such as avian influenza and HIV.

}, keywords = {Antiviral Agents, Biological Assay, Boron Compounds, Capsid, Capsid Proteins, Dimerization, Fluorescence, Fluorescent Dyes, Hepatitis B virus, Kinetics, Light, Models, Molecular, Radiation, Scattering, Virus Assembly}, issn = {1087-0156}, doi = {10.1038/nbt1187}, author = {Stray, Stephen J and Johnson, Jennifer M and Kopek, Benjamin G and Zlotnick, Adam} } @article {46629, title = {Increased ethanol resistance and consumption in Eps8 knockout mice correlates with altered actin dynamics.}, journal = {Cell}, volume = {127}, year = {2006}, month = {2006 Oct 6}, pages = {213-26}, abstract = {

Dynamic modulation of the actin cytoskeleton is critical for synaptic plasticity, abnormalities of which are thought to contribute to mental illness and addiction. Here we report that mice lacking Eps8, a regulator of actin dynamics, are resistant to some acute intoxicating effects of ethanol and show increased ethanol consumption. In the brain, the N-methyl-D-aspartate (NMDA) receptor is a major target of ethanol. We show that Eps8 is localized to postsynaptic structures and is part of the NMDA receptor complex. Moreover, in Eps8 null mice, NMDA receptor currents and their sensitivity to inhibition by ethanol are abnormal. In addition, Eps8 null neurons are resistant to the actin-remodeling activities of NMDA and ethanol. We propose that proper regulation of the actin cytoskeleton is a key determinant of cellular and behavioral responses to ethanol.

}, keywords = {Actins, Adaptor Proteins, Signal Transducing, Alcohol Drinking, Animals, Behavior, Animal, Cells, Cultured, Central Nervous System Depressants, Cerebellum, Cytoskeletal Proteins, Cytoskeleton, Ethanol, Female, Humans, Male, Mice, Mice, Knockout, Neurons, Receptors, N-Methyl-D-Aspartate, Recombinant Proteins, Signal Transduction}, issn = {0092-8674}, doi = {10.1016/j.cell.2006.09.011}, author = {Offenh{\"a}user, Nina and Castelletti, Daniela and Mapelli, Lisa and Soppo, Blanche Ekalle and Regondi, Maria Cristina and Rossi, Paola and D{\textquoteright}Angelo, Egidio and Frassoni, Carolina and Amadeo, Alida and Tocchetti, Arianna and Pozzi, Benedetta and Disanza, Andrea and Guarnieri, Douglas and Betsholtz, Christer and Scita, Giorgio and Heberlein, Ulrike and Di Fiore, Pier Paolo} } @article {3918, title = {Integrative properties of radial oblique dendrites in hippocampal CA1 pyramidal neurons.}, journal = {Neuron}, volume = {50}, year = {2006}, month = {2006 Apr 20}, pages = {291-307}, abstract = {

Although radial oblique dendrites are a major synaptic input site in CA1 pyramidal neurons, little is known about their integrative properties. We have used multisite two-photon glutamate uncaging to deliver different spatiotemporal input patterns to single branches while simultaneously recording the uncaging-evoked excitatory postsynaptic potentials and local Ca2+ signals. Asynchronous input patterns sum linearly in spite of the spatial clustering and produce Ca2+ signals that are mediated by NMDA receptors (NMDARs). Appropriately timed and sized input patterns ( approximately 20 inputs within approximately 6 ms) produce a supralinear summation due to the initiation of a dendritic spike. The Ca2+ signals associated with synchronous input were larger and mediated by influx through both NMDARs and voltage-gated Ca2+ channels (VGCCs). The oblique spike is a fast Na+ spike whose duration is shaped by the coincident activation of NMDAR, VGCCs, and transient K+ currents. Our results suggest that individual branches can function as single integrative compartments.

}, keywords = {Animals, Calcium Channels, Dendrites, Excitatory Postsynaptic Potentials, Glutamic Acid, N-Methyl-D-Aspartate, Patch-Clamp Techniques, Pyramidal Cells, Rats, Receptors, Sprague-Dawley, Synapses, Synaptic Transmission}, issn = {0896-6273}, doi = {10.1016/j.neuron.2006.03.016}, author = {Losonczy, Attila and Magee, Jeffrey C} } @article {2855, title = {Isolation of yeast nuclei and micrococcal nuclease mapping of nucleosome positioning.}, journal = {Methods in Molecular Biology }, volume = {313}, year = {2006}, month = {2006}, pages = {245-55}, abstract = {

Chromatin structure and nucleosome positioning play a crucial role in gene expression regulation. Nucleosome positioning is often inferred by the protection of underlying DNA to nucleases. Because nucleases are excluded by plasma membranes, chromatin mapping requires isolating nuclei from cells and digesting the chromatin in situ with nucleases. The quality of this data is highly dependent on the nuclei preparation. Here we describe a method to isolate nuclei from the budding yeast Saccharomyces cerevisiae and the use of micrococcal nuclease to map the chromatin structure at the RNR3 gene. Nuclei isolated by this procedure are competent for many of the common chromatin mapping and detection procedures.

}, keywords = {Cell Fractionation, Cell Nucleus, Chromatin, DNA, Fungal, Gene Expression Regulation, Genes, Micrococcal Nuclease, Mycology, Nucleosomes, Saccharomyces cerevisiae}, issn = {1064-3745}, author = {Zhang, Zhengjian and Reese, Joseph C} } @article {6289, title = {Janelia Farm: an experiment in scientific culture.}, journal = {Cell}, volume = {125}, year = {2006}, month = {2006 Apr 21}, pages = {209-12}, abstract = {

Janelia Farm, the new research campus of the Howard Hughes Medical Institute, is an ongoing experiment in the social engineering of research communities.

}, keywords = {Academies and Institutes, Biomedical Research, Culture, Humans, Laboratories, Research Personnel, Research Support as Topic, Residence Characteristics}, issn = {0092-8674}, doi = {10.1016/j.cell.2006.04.005}, author = {Rubin, Gerald M} } @article {2508, title = {Juvenile hormone is required to couple imaginal disc formation with nutrition in insects.}, journal = {Science }, volume = {312}, year = {2006}, month = {2006 Jun 2}, pages = {1385-8}, abstract = {

In starved larvae of the tobacco hornworm moth Manduca sexta, larval and imaginal tissues stop growing, the former because they lack nutrient-dependent signals but the latter because of suppression by juvenile hormone. Without juvenile hormone, imaginal discs form and grow despite severe starvation. This hormone inhibits the intrinsic signaling needed for disc morphogenesis and does so independently of ecdysteroid action. Starvation and juvenile hormone treatments allowed the separation of intrinsic and nutrient-dependent aspects of disc growth and showed that both aspects must occur during the early phases of disc morphogenesis to ensure normal growth leading to typical-sized adults.

}, keywords = {Animal Nutritional Physiological Phenomena, Animals, Ecdysteroids, Juvenile Hormones, Larva, Manduca, Morphogenesis, Pyridines}, issn = {1095-9203}, doi = {10.1126/science.1123652}, author = {Truman, J W and Hiruma, K and Allee, J P and Macwhinnie, S G B and Champlin, D T and Riddiford, L M} } @proceedings {5679, title = {Large-scale biophysical parameter estimation in single neurons via constrained linear regression.}, volume = {18}, year = {2006}, month = {2006}, publisher = {MIT press}, abstract = {

Our understanding of the input-output function of single cells has been substantially advanced by biophysically accurate multi-compartmental models. The large number of parameters needing hand tuning in these models has, however, somewhat hampered their applicability and interpretability. Here we propose a simple and well-founded method for automatic estimation of many of these key parameters: 1) the spatial distribution of channel densities on the cell{\textquoteright}s membrane; 2) the spatiotemporal pattern of synaptic input; 3) the channels{\textquoteright} reversal potentials; 4) the intercompartmental conductances; and 5) the noise level in each compartment. We assume experimental access to: a) the spatiotemporal voltage signal in the dendrite (or some contiguous subpart thereof, e.g. via voltage sensitive imaging techniques), b) an approximate kinetic description of the channels and synapses present in each compartment, and c) the morphology of the part of the neuron under investigation. The key observation is that, given data a)-c), all of the parameters 1)-4) may be simultaneously inferred by a version of constrained linear regression; this regression, in turn, is efficiently solved using standard algorithms, without any {\textquotedblleft}local minima{\textquotedblright} problems despite the large number of parameters and complex dynamics. The noise level 5) may also be estimated by standard techniques. We demonstrate the method{\textquoteright}s accuracy on several model datasets, and describe techniques for quantifying the uncertainty in our estimates.

}, author = {Ahrens, MB and Huys, QJM and Paninski, L} } @article {45751, title = {Large-scale gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera).}, journal = {Genome Biol}, volume = {7}, year = {2006}, month = {2006}, pages = {R21}, abstract = {

Aphids are the leading pests in agricultural crops. A large-scale sequencing of 40,904 ESTs from the pea aphid Acyrthosiphon pisum was carried out to define a catalog of 12,082 unique transcripts. A strong AT bias was found, indicating a compositional shift between Drosophila melanogaster and A. pisum. An in silico profiling analysis characterized 135 transcripts specific to pea-aphid tissues (relating to bacteriocytes and parthenogenetic embryos). This project is the first to address the genetics of the Hemiptera and of a hemimetabolous insect.

}, keywords = {Animals, Aphids, Base Composition, Base Sequence, DNA, DNA, Complementary, Expressed Sequence Tags, Gene Library, Microsatellite Repeats, Peas, Phylogeny, Plant Diseases, Population Density, Transcription, Genetic}, issn = {1465-6914}, doi = {10.1186/gb-2006-7-3-r21}, author = {Sabater-Mu{\~n}oz, Beatriz and Legeai, Fabrice and Rispe, Claude and Bonhomme, Jo{\"e}l and Dearden, Peter and Dossat, Carole and Duclert, Aymeric and Gauthier, Jean-Pierre and Ducray, Dani{\`e}le Giblot and Hunter, Wayne and Dang, Phat and Kambhampati, Srini and Martinez-Torres, David and Cortes, Teresa and Moya, Andr{\`e}s and Nakabachi, Atsushi and Philippe, Cathy and Prunier-Leterme, Nathalie and Rahb{\'e}, Yvan and Simon, Jean-Christophe and Stern, David L and Wincker, Patrick and Tagu, Denis} } @article {1106, title = {Latent blue and red fluorophores based on the trimethyl lock.}, journal = {Chembiochem: A European Journal of Chemical Biology}, volume = {7}, year = {2006}, month = {2006 Aug}, pages = {1151-4}, keywords = {Animals, Cell Line, Color, Fluorescence, Fluorescent Dyes, Humans, Kinetics, Methylation, Molecular Structure, Tumor, Umbelliferones}, issn = {1439-4227}, doi = {10.1002/cbic.200500559}, author = {Lavis, Luke D and Chao, Tzu-Yuan and Raines, Ronald T} } @article {1690, title = {Life sciences require the third dimension.}, journal = {Current Opinion in Cell Biology}, volume = {18}, year = {2006}, month = {2006 Feb}, pages = {117-24}, abstract = {

Novel technologies are required for three-dimensional cell biology and biophysics. By three-dimensional we refer to experimental conditions that essentially try to avoid hard and flat surfaces and favour unconstrained sample dynamics. We believe that light-sheet-based microscopes are particularly well suited to studies of sensitive three-dimensional biological systems. The application of such instruments can be illustrated with examples from the biophysics of microtubule dynamics and three-dimensional cell cultures. Our experience leads us to suggest that three-dimensional approaches reveal new aspects of a system and enable experiments to be performed in a more physiological and hence clinically more relevant context.

}, keywords = {Animals, Biological Science Disciplines, Cell Line, Computer-Assisted, Dogs, Fluorescence, Image Processing, Imaging, Microscopy, Microtubules, Paclitaxel, Three-Dimensional}, issn = {0955-0674}, doi = {10.1016/j.ceb.2005.12.012}, author = {Keller, Philipp J and Pampaloni, Francesco and Stelzer, Ernst H K} } @article {2444, title = {Local caspase activity directs engulfment of dendrites during pruning.}, journal = {Nature Neuroscience}, volume = {9}, year = {2006}, month = {2006 Oct}, pages = {1234-6}, abstract = {

Pruning is important for sculpting neural circuits, as it removes excessive or inaccurate projections. Here we show that the removal of sensory neuron dendrites during pruning in Drosophila melanogaster is directed by local caspase activity. Suppressing caspase activity prevented dendrite removal, whereas a global activation of caspases within a neuron caused cell death. A new genetically encoded caspase probe revealed that caspase activity is confined to the degenerating dendrites of pruning neurons.

}, keywords = {Afferent, Analysis of Variance, Animals, Apoptosis, Caspases, Dendrites, Drosophila melanogaster, Drosophila Proteins, Enzyme Activation, Enzyme Inhibitors, Fluorescent Antibody Technique, Ganglia, Genetically Modified, Neurons, Spinal, Time Factors}, issn = {1097-6256}, doi = {10.1038/nn1774}, author = {Williams, Darren W and Kondo, Shu and Krzyzanowska, Agnieszka and Hiromi, Yasushi and Truman, James W} } @article {2316, title = {Making the grade with models of persistent activity.}, journal = {Neuron}, volume = {49}, year = {2006}, month = {2006 Mar 2}, pages = {649-51}, abstract = {

Persistent neural activity that outlasts an initial stimulus is thought to provide a mechanism for the transient storage of memory. In this issue of Neuron, Frans{\'e}n et al. identify important principles for a cell-autonomous mechanism of graded persistent firing using an elegant combination of experimental and computational approaches.

}, keywords = {Action Potentials, Animals, Calcium, Electric Stimulation, Models, Neurological, Neurons}, issn = {0896-6273}, doi = {10.3389/fnana.2010.00147}, author = {Dudman, Joshua T and Siegelbaum, Steven A} } @article {46305, title = {Mean-field analysis of selective persistent activity in presence of short-term synaptic depression.}, journal = {Journal of Computational Neuroscience}, volume = {20}, year = {2006}, month = {2006 Apr}, pages = {201-17}, abstract = {

Mean-Field theory is extended to recurrent networks of spiking neurons endowed with short-term depression (STD) of synaptic transmission. The extension involves the use of the distribution of interspike intervals of an integrate-and-fire neuron receiving a Gaussian current, with a given mean and variance, in input. This, in turn, is used to obtain an accurate estimate of the resulting postsynaptic current in presence of STD. The stationary states of the network are obtained requiring self-consistency for the currents-those driving the emission processes and those generated by the emitted spikes. The model network stores in the distribution of two-state efficacies of excitatory-to-excitatory synapses, a randomly composed set of external stimuli. The resulting synaptic structure allows the network to exhibit selective persistent activity for each stimulus in the set. Theory predicts the onset of selective persistent, or working memory (WM) activity upon varying the constitutive parameters (e.g. potentiated/depressed long-term efficacy ratio, parameters associated with STD), and provides the average emission rates in the various steady states. Theoretical estimates are in remarkably good agreement with data "recorded" in computer simulations of the microscopic model.

}, keywords = {Action Potentials, Algorithms, Animals, Cerebral Cortex, Excitatory Postsynaptic Potentials, Humans, Memory, Short-Term, Nerve Net, Neural Inhibition, Neural Networks (Computer), Neural Pathways, Neurons, Normal Distribution, Reaction Time, Synaptic Transmission, Time Factors}, issn = {0929-5313}, doi = {10.1007/s10827-006-6308-x}, author = {Romani, Sandro and Amit, Daniel J and Mongillo, Gianluigi} } @article {1291, title = {MicroRNA pathways modulate polyglutamine-induced neurodegeneration.}, journal = {Molecular Cell}, volume = {24}, year = {2006}, month = {2006 Oct 6}, pages = {157-63}, abstract = {

Nine human neurodegenerative diseases are due to expansion of a CAG repeat- encoding glutamine within the open reading frame of the respective genes. Polyglutamine (polyQ) expansion confers dominant toxicity, resulting in neuronal degeneration. MicroRNAs (miRNAs) have been shown to modulate programmed cell death during development. To address whether miRNA pathways play a role in neurodegeneration, we tested whether genes critical for miRNA processing modulated toxicity induced by the spinocerebellar ataxia type 3 (SCA3) protein. These studies revealed a striking enhancement of polyQ toxicity upon reduction of miRNA processing in Drosophila and human cells. In parallel genetic screens, we identified the miRNA bantam (ban) as a potent modulator of both polyQ and tau toxicity in flies. Our studies suggest that ban functions downstream of toxicity of the SCA3 protein, to prevent degeneration. These findings indicate that miRNA pathways dramatically modulate polyQ- and tau-induced neurodegeneration, providing the foundation for new insight into therapeutics.

}, keywords = {Animals, Cyclins, DNA, Drosophila, Drosophila Proteins, Genetically Modified, Hela Cells, Humans, MicroRNAs, Nerve Tissue Proteins, Neurodegenerative Diseases, Neurons, Nuclear Proteins, Open Reading Frames, Peptides, Repressor Proteins, Retina, tau Proteins, Trinucleotide Repeat Expansion}, issn = {1097-2765}, doi = {10.1016/j.molcel.2006.07.030}, author = {Bilen, Julide and Liu, Nan and Burnett, Barrington G and Pittman, Randall N and Bonini, Nancy M} } @article {1980, title = {Network variability limits stimulus-evoked spike timing precision in retinal ganglion cells.}, journal = {Neuron}, volume = {52}, year = {2006}, month = {2006 Nov 9}, pages = {511-24}, abstract = {

Visual, auditory, somatosensory, and olfactory stimuli generate temporally precise patterns of action potentials (spikes). It is unclear, however, how the precision of spike generation relates to the pattern and variability of synaptic input elicited by physiological stimuli. We determined how synaptic conductances evoked by light stimuli that activate the rod bipolar pathway control spike generation in three identified types of mouse retinal ganglion cells (RGCs). The relative amplitude, timing, and impact of excitatory and inhibitory input differed dramatically between On and Off RGCs. Spikes evoked by repeated somatic injection of identical light-evoked synaptic conductances were more temporally precise than those evoked by light. However, the precision of spikes evoked by conductances that varied from trial to trial was similar to that of light-evoked spikes. Thus, the rod bipolar pathway modulates different RGCs via unique combinations of synaptic input, and RGC temporal variability reflects variability in the input this circuit provides.

}, keywords = {Action Potentials, Animals, Dose-Response Relationship, Electric Stimulation, Inbred C57BL, Mice, Models, Neurological, Patch-Clamp Techniques, Photic Stimulation, Radiation, Retinal Ganglion Cells, Synapses, Synaptic Transmission, Visual Pathways}, issn = {0896-6273}, doi = {10.1016/j.neuron.2006.09.014}, author = {Murphy, Gabe J and Rieke, Fred} } @article {1289, title = {A new role for microRNA pathways: modulation of degeneration induced by pathogenic human disease proteins.}, journal = {Cell Cycle }, volume = {5}, year = {2006}, month = {2006 Dec}, pages = {2835-8}, abstract = {

MicroRNAs (miRNAs) are small noncoding RNAs that regulate the expression of target transcript mRNAs. Many miRNAs have been defined, however their roles and the processes influenced by miRNA pathways are still being elucidated. A role for miRNAs in development and cancer has been described. We recently isolated the miRNA bantam (ban) in a genetic screen for modulators of pathogenicity of a human neurodegenerative disease model in Drosophila. These studies showed that upregulation of ban mitigates degeneration induced by the pathogenic polyglutamine (polyQ) protein Ataxin-3, which is mutated in the human polyglutamine disease spinocerebellar ataxia type 3 (SCA3). To address the broader role for miRNAs in neuroprotection, we also showed that loss of all miRNAs, by dicer mutation, dramatically enhances pathogenic polyQ protein toxicity in flies and in human HeLa cells. These studies suggest that miRNAs may be important for neuronal survival in the context of human neurodegenerative disease. These studies provide the foundation to define the miRNAs involved in neurodegenerative disease, and the biological pathways affected.

}, keywords = {Animal, Animals, Cyclins, Disease Models, Drosophila, Drosophila Proteins, Eye, Hela Cells, Humans, MicroRNAs, Nerve Degeneration, Neurodegenerative Diseases, Peptides, Trinucleotide Repeat Expansion}, issn = {1551-4005}, author = {Bilen, Julide and Liu, Nan and Bonini, Nancy M} } @article {46401, title = {NikR-operator complex structure and the mechanism of repressor activation by metal ions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, year = {2006}, month = {2006 Sep 12}, pages = {13676-81}, abstract = {

Metal ion homeostasis is critical to the survival of all cells. Regulation of nickel concentrations in Escherichia coli is mediated by the NikR repressor via nickel-induced transcriptional repression of the nickel ABC-type transporter, NikABCDE. Here, we report two crystal structures of nickel-activated E. coli NikR, the isolated repressor at 2.1 A resolution and in a complex with its operator DNA sequence from the nik promoter at 3.1 A resolution. Along with the previously published structure of apo-NikR, these structures allow us to evaluate functional proposals for how metal ions activate NikR, delineate the drastic conformational changes required for operator recognition, and describe the formation of a second metal-binding site in the presence of DNA. They also provide a rare set of structural views of a ligand-responsive transcription factor in the unbound, ligand-induced, and DNA-bound states, establishing a model system for the study of ligand-mediated effects on transcription factor function.

}, keywords = {Amino Acid Sequence, Base Sequence, Binding Sites, Crystallography, Escherichia coli Proteins, Molecular Sequence Data, Nickel, Operator Regions, Genetic, Protein Conformation, Repressor Proteins}, issn = {0027-8424}, doi = {10.1073/pnas.0606247103}, author = {Schreiter, Eric R and Wang, Sheila C and Zamble, Deborah B and Drennan, Catherine L} } @article {4006, title = {Noise-induced vocal modulation in cotton-top tamarins (Saguinus oedipus).}, journal = {American Journal of Primatology}, volume = {68}, year = {2006}, month = {2006 Dec}, pages = {1183-90}, abstract = {

The Lombard effect-an increase in vocalization amplitude in response to an increase in background noise-is observed in a wide variety of animals. We investigated this basic form of vocal control in the cotton-top tamarin (Saguinus oedipus) by measuring the amplitude of a contact call, the combination long call (CLC), while simultaneously varying the background noise level. All subjects showed a significant increase in call amplitude and syllable duration in response to an increase in background noise amplitude. Together with prior results, this study shows that tamarins have greater vocal control in the context of auditory feedback perturbation than previously suspected.

}, keywords = {Animal, Animals, Female, Head, Male, Noise, Saguinus, Speech Acoustics, Vocalization}, issn = {0275-2565}, doi = {10.1002/ajp.20317}, author = {Egnor, S E Roian and Hauser, Marc D} } @article {1736, title = {A novel spectroscopic probe for molecular chirality.}, journal = {Chirality}, volume = {18}, year = {2006}, month = {2006 Feb}, pages = {146-58}, abstract = {

Recent advances in developing sum frequency generation (SFG) as a novel spectroscopic probe for molecular chirality are reviewed. The basic principle underlying the technique is briefly described, in comparison with circular dichroism (CD). The significantly better sensitivity of the technique than CD is pointed out, and the reason is discussed. Bi-naphthol (BN) and amino acids are used as representatives for two different types of chiral molecules; the measured chirality in their electronic transitions can be understood by two different molecular models, respectively, that are extensions of models developed earlier for CD. Optically active or chiral SFG from vibrational transitions are weaker, but with the help of electronic-vibrational double resonance, the vibrational spectrum of a monolayer of BN has been obtained. Generally, optically active SFG is sufficiently sensitive to be employed to probe in-situ chirality of chiral monolayers and thin films.

}, keywords = {Algorithms, Chemistry, Molecular Conformation, Physical, Physicochemical Phenomena, Stereoisomerism}, issn = {0899-0042}, doi = {10.1002/chir.20238}, author = {Ji, Na and Shen, Yuen-Ron} } @article {1691, title = {Nud1p, the yeast homolog of Centriolin, regulates spindle pole body inheritance in meiosis.}, journal = {The EMBO Journal}, volume = {25}, year = {2006}, month = {2006 Aug 23}, pages = {3856-68}, abstract = {

Nud1p, a protein homologous to the mammalian centrosome and midbody component Centriolin, is a component of the budding yeast spindle pole body (SPB), with roles in anchorage of microtubules and regulation of the mitotic exit network during vegetative growth. Here we analyze the function of Nud1p during yeast meiosis. We find that a nud1-2 temperature-sensitive mutant has two meiosis-related defects that reflect genetically distinct functions of Nud1p. First, the mutation affects spore formation due to its late function during spore maturation. Second, and most important, the mutant loses its ability to distinguish between the ages of the four spindle pole bodies, which normally determine which SPB would be preferentially included in the mature spores. This affects the regulation of genome inheritance in starved meiotic cells and leads to the formation of random dyads instead of non-sister dyads under these conditions. Both functions of Nud1p are connected to the ability of Spc72p to bind to the outer plaque and half-bridge (via Kar1p) of the SPB.

}, keywords = {Cell Cycle Proteins, Deoxyribonucleases, Fungal, Genome, Humans, Meiosis, Microtubule-Associated Proteins, Mitotic Spindle Apparatus, Mutation, Nuclear Proteins, Protein Binding, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Spores, tRNA Methyltransferases}, issn = {0261-4189}, doi = {10.1038/sj.emboj.7601254}, author = {Gordon, Oren and Taxis, Christof and Keller, Philipp J and Benjak, Aleksander and Stelzer, Ernst H K and Simchen, Giora and Knop, Michael} } @article {2409, title = {Nutrient availability and growth: regulation of insulin signaling by dFOXO/FOXO1.}, journal = {Cell Cycle}, volume = {5}, year = {2006}, month = {2006 Mar}, pages = {503-5}, abstract = {

Organisms adjust their rate of growth depending on the availability of nutrients. Thus, when environmental conditions limit nutrients, growth is slowed and is only restored after food again becomes abundant. Many aspects of the molecular mechanisms that govern this complex control system remain unknown. However, it has been shown that the insulin/IGF-1 (insulin-like growth factor 1) receptor pathway, together with the FOXO family of transcription factors, play an important role in this process. Recent studies with the fruit fly Drosophila melanogaster have provided new insights into the regulatory circuitry that controls both growth and gene expression in response to nutrient availability.

}, keywords = {Animal Nutritional Physiological Phenomena, Animals, Drosophila melanogaster, Drosophila Proteins, Forkhead Transcription Factors, Insulin, Receptor, Signal Transduction}, issn = {1551-4005}, doi = {10.1073/pnas.1100640108}, author = {Puig, Oscar and Tjian, Robert} } @article {2368, title = {Olfactory neuronal dynamics in behaving animals.}, journal = {Seminars in Cell \& Developmental Biology}, volume = {17}, year = {2006}, month = {2006 Aug}, pages = {454-61}, abstract = {

More than 50 years have passed since the first recording of neuronal responses to an odor stimulus from the primary olfactory brain area, the main olfactory bulb. During this time very little progress has been achieved in understanding neuronal dynamics in the olfactory bulb in awake behaving animals, which is very different from that in anesthetized preparations. In this paper we formulate a new framework containing the main reasons for studying olfactory neuronal dynamics in awake animals and review advances in the field within this new framework.

}, keywords = {Anesthesia, Animal, Animals, Behavior, Brain, Conditioning (Psychology), Neuronal Plasticity, Olfactory Bulb, Olfactory Receptor Neurons, Rabbits, Rats, Synaptic Transmission}, issn = {1084-9521}, doi = {10.1523/JNEUROSCI.3613-08.2008}, author = {Rinberg, Dmitry and Gelperin, Alan} } @article {1238, title = {Optimal information storage in noisy synapses under resource constraints.}, journal = {Neuron}, volume = {52}, year = {2006}, month = {2006 Nov 9}, pages = {409-23}, abstract = {

Experimental investigations have revealed that synapses possess interesting and, in some cases, unexpected properties. We propose a theoretical framework that accounts for three of these properties: typical central synapses are noisy, the distribution of synaptic weights among central synapses is wide, and synaptic connectivity between neurons is sparse. We also comment on the possibility that synaptic weights may vary in discrete steps. Our approach is based on maximizing information storage capacity of neural tissue under resource constraints. Based on previous experimental and theoretical work, we use volume as a limited resource and utilize the empirical relationship between volume and synaptic weight. Solutions of our constrained optimization problems are not only consistent with existing experimental measurements but also make nontrivial predictions.

}, keywords = {Animals, Excitatory Postsynaptic Potentials, Information Storage and Retrieval, Memory, Models, Neurological, Synapses, Synaptic Transmission}, issn = {0896-6273}, doi = {10.1371/journal.pcbi.1001066}, author = {Varshney, Lav R and Sj{\"o}str{\"o}m, Per Jesper and Chklovskii, Dmitri B} } @article {45748, title = {The pea aphid, Acyrthosiphon pisum: an emerging genomic model system for ecological, developmental and evolutionary studies.}, journal = {Bioessays}, volume = {28}, year = {2006}, month = {2006 Jul}, pages = {747-55}, abstract = {

Aphids display an abundance of adaptations that are not easily studied in existing model systems. Here we review the biology of a new genomic model system, the pea aphid, Acyrthosiphon pisum. We then discuss several phenomena that are particularly accessible to study in the pea aphid: the developmental genetic basis of polyphenisms, aphid-bacterial symbioses, the genetics of adaptation and mechanisms of virus transmission. The pea aphid can be maintained in the laboratory and natural populations can be studied in the field. These properties allow controlled experiments to be performed on problems of direct relevance to natural aphid populations. Combined with new genomic approaches, the pea aphid is poised to become an important model system for understanding the molecular and developmental basis of many ecologically and evolutionarily relevant problems.

}, keywords = {Adaptation, Biological, Animals, Aphids, Biological Evolution, Ecology, Female, Genome, Insect, Life Cycle Stages, Male, Models, Genetic, Peas, Plant Viruses, Polymorphism, Genetic, Symbiosis}, issn = {0265-9247}, doi = {10.1002/bies.20436}, author = {Brisson, Jennifer A and Stern, David L} } @article {4007, title = {Perturbation of auditory feedback causes systematic perturbation in vocal structure in adult cotton-top tamarins.}, journal = {The Journal of Experimental Biology}, volume = {209}, year = {2006}, month = {2006 Sep}, pages = {3652-63}, abstract = {

Auditory feedback is critical for the development and maintenance of speech in humans. In contrast, studies of nonhuman primate vocal production generally report that subjects show little reliance on auditory input. We examined the extent to which cotton-top tamarin (Saguinus oedipus) vocal production is sensitive to perturbation of auditory feedback by manipulating the predictability of presentation of a 1 s burst of white noise during the production of the species-specific contact call, the combination long call (CLC). We used three experimental conditions: the Begin condition, in which white noise was presented only during the first half of a recording session, the End condition, in which white noise was presented only in the last half, and the Random condition, in which each call had a 50\% probability of receiving white noise playback throughout the recording session, making the auditory feedback unpredictable. In addition we recorded calls before and after the experimental series (Baseline condition) to determine whether any changes induced by modification of auditory feedback persisted. Results showed that playback of white noise during the production of the CLC produced changes in the temporal structure of the CLC: calls were shorter and had fewer pulses, indicating that modification of auditory feedback can interrupt vocal production. In addition, calls that received modified feedback were louder and had longer inter-pulse intervals than those that did not, consistent with an adaptive response to the masking effect of white noise playback. The magnitude of this compensatory effect and the interruption rate were both sensitive to whether the feedback modification occurred at the beginning or end of the experimental session: early feedback produced less interruption and more compensation. Finally, when auditory feedback modification was unpredictable, adaptive changes were observed in both calls that received modified feedback and those that received normal feedback, suggesting that tamarins can generate an expectation of noise playback and increase vocal amplitude in anticipation of masking.

}, keywords = {Acoustic Stimulation, Adaptation, Animal, Animals, Female, Male, Perceptual Masking, Psychological, Saguinus, Vocalization}, issn = {0022-0949}, doi = {10.1242/jeb.02420}, author = {Egnor, S E Roian and Iguina, Carmen G and Hauser, Marc D} } @article {1407, title = {Physiological properties of zebra finch ventral tegmental area and substantia nigra pars compacta neurons.}, journal = {Journal of Neurophysiology}, volume = {96}, year = {2006}, month = {2006 Nov}, pages = {2295-306}, abstract = {

The neurotransmitter dopamine plays important roles in motor control, learning, and motivation in mammals and probably other animals as well. The strong dopaminergic projection to striatal regions and more moderate dopaminergic projections to other regions of the telencephalon predominantly arise from midbrain dopaminergic neurons in the substantia nigra pars compacta (SNc) and ventral tegmental area (VTA). Homologous dopaminergic cell groups in songbirds project anatomically in a manner that may allow dopamine to influence song learning or song production. The electrophysiological properties of SNc and VTA neurons have not previously been studied in birds. Here we used whole cell recordings in brain slices in combination with tyrosine-hydroxylase immunolabeling as a marker of dopaminergic neurons to determine electrophysiological and pharmacological properties of dopaminergic and nondopaminergic neurons in the zebra finch SNc and VTA. Our results show that zebra finch dopaminergic neurons possess physiological properties very similar to those of mammalian dopaminergic neurons, including broad action potentials, calcium- and apamin-sensitive membrane-potential oscillations underlying pacemaker firing, powerful spike-frequency adaptation, and autoinhibition via D2 dopamine receptors. Moreover, the zebra finch SNc and VTA also contain nondopaminergic neurons with similarities (fast-firing, inhibition by the mu-opioid receptor agonist [d-Ala(2), N-Me-Phe(4), Gly-ol(5)]-enkephalin (DAMGO)) and differences (strong h-current that contributes to spontaneous firing) compared with GABAergic neurons in the mammalian SNc and VTA. Our results provide insight into the intrinsic membrane properties that regulate the activity of dopaminergic neurons in songbirds and add to strong evidence for anatomical, physiological, and functional similarities between the dopaminergic systems of mammals and birds.

}, keywords = {Action Potentials, Ala(2)-MePhe(4)-Gly(5)-, Animals, Cholera Toxin, Dopamine D2, Electrophysiology, Enkephalin, Finches, Lysine, Male, mu, Neurons, Opioid, Patch-Clamp Techniques, Quinpirole, Receptors, Substantia Nigra, Tetrodotoxin, Tyrosine 3-Monooxygenase, Ventral Tegmental Area}, issn = {0022-3077}, doi = {10.1152/jn.01040.2005}, author = {Gale, Samuel D and Perkel, David J} } @article {2446, title = {The pupal specifier broad directs progressive morphogenesis in a direct-developing insect.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, year = {2006}, month = {2006 May 2}, pages = {6925-30}, abstract = {

A key regulatory gene in metamorphosing (holometabolous) insect life histories is the transcription factor broad (br), which specifies pupal development. To determine the role of br in a direct-developing (hemimetabolous) insect that lacks a pupal stage, we cloned br from the milkweed bug, Oncopeltus fasciatus (Of{\textquoteright}br). We find that, unlike metamorphosing insects, in which br expression is restricted to the larval-pupal transition, Of{\textquoteright}br mRNA is expressed during embryonic development and is maintained at each nymphal molt but then disappears at the molt to the adult. Induction of a supernumerary nymphal stage with a juvenile hormone (JH) mimic prevented the disappearance of br mRNA. In contrast, induction of a precocious adult molt by application of precocene II to third-stage nymphs caused a loss of br mRNA at the precocious adult molt. Thus, JH is necessary to maintain br expression during the nymphal stages. Injection of Of{\textquoteright}br dsRNA into either early third- or fourth-stage nymphs caused a repetition of stage-specific pigmentation patterns and prevented the normal anisometric growth of the wing pads without affecting isometric growth or molting. Therefore, br is necessary for the mutable (heteromorphic) changes that occur during hemimetabolous development. Our results suggest that metamorphosis in insects arose as expression of br, which conveys competence for change, became restricted to one postembryonic instar. After this shift in br expression, the progressive changes that occur within the nymphal series in basal insects became compressed to the one short period of morphogenesis seen in the larva-to-pupa transition of holometabolous insects.

}, keywords = {Animals, Biological, Drosophila Proteins, Heteroptera, Insect Proteins, Juvenile Hormones, Metamorphosis, Molecular Sequence Data, Morphogenesis, Nymph, Pigmentation, RNA, Transcription Factors, Wing}, issn = {0027-8424}, doi = {10.1073/pnas.0509983103}, author = {Erezyilmaz, Deniz F and Riddiford, Lynn M and Truman, James W} } @article {5414, title = {Purification, characterization, and crystallization of human pyrroline-5-carboxylate reductase.}, journal = {Protein Expression and Purification}, volume = {49}, year = {2006}, month = {2006 Sep}, pages = {83-7}, abstract = {

Pyrroline-5-carboxylate reductase (P5CR) catalyzes the reduction of Delta1-pyrroline-5-carboxylate (P5C) to proline with concomitant oxidation of NAD(P)H to NAD(P)(+). The enzymatic cycle between P5C and proline is very important in many physiological and pathological processes. Human P5CR was over-expressed in Escherichia coli and purified to homogeneity by chromatography. Enzymatic assays of the wild-type protein were carried out using 3,4-dehydro-L-proline as substrate and NAD(+) as cofactor. The homopolymer was characterized by cross-linking and size exclusion gel filtration chromatography. Human P5CR was crystallized by the hanging-drop vapor-diffusion method at 37 degrees C. Diffraction data were obtained to a resolution of 2.8A and were suitable for high resolution X-ray structure determination.

}, keywords = {Crystallization, Crystallography, Gene Expression, Humans, Polymers, Proline, Pyrroline Carboxylate Reductases, Solubility, Water, X-Ray}, issn = {1046-5928}, doi = {10.1016/j.pep.2006.02.019}, author = {Meng, Zhaohui and Lou, Zhiyong and Liu, Zhe and Hui, Dong and Bartlam, Mark and Rao, Zihe} } @article {1771, title = {The receptors and cells for mammalian taste.}, journal = {Nature}, volume = {444}, year = {2006}, month = {2006 Nov 16}, pages = {288-94}, abstract = {

The emerging picture of taste coding at the periphery is one of elegant simplicity. Contrary to what was generally believed, it is now clear that distinct cell types expressing unique receptors are tuned to detect each of the five basic tastes: sweet, sour, bitter, salty and umami. Importantly, receptor cells for each taste quality function as dedicated sensors wired to elicit stereotypic responses.

}, keywords = {Animals, G-Protein-Coupled, Humans, Receptors, Signal Transduction, Taste, Taste Buds}, issn = {1476-4687}, doi = {10.1038/nature05401}, author = {Chandrashekar, Jayaram and Hoon, Mark A and Ryba, Nicholas J P and Zuker, Charles S} } @article {2816, title = {Reconstruction of complementary images in second harmonic generation microscopy.}, journal = {Optics Express}, volume = {14}, year = {2006}, month = {2006 May 29}, pages = {4727-35}, abstract = {

Second harmonic generation microscopy(SHGM) has become widely used to image biological samples. Due to the complexity of biological samples, more and more effort has been put on polarization imaging in SHGM technology to uncover their structures. In this work, we put forward a novel stitching method based on careful mathematical calculation, and accomplish it by rotating laser polarization. We first show its validity in imaging a perfectly synthesized bio-origin polymer poly (3-hyroxybutyrate-co-3-hydroxyhexanoate) (PHBHHx). Then, we test its power by getting a true image of fibrillar collagen structure of rat-tail tendon.

}, issn = {1094-4087}, doi = {10.1364/AO.50.001792}, author = {Gao, Liang and Jin, Lei and Xue, Ping and Xu, Jun and Wang, Yi and Ma, Hui and Chen, Dieyan} } @article {5415, title = {Remarkably high activities of testicular cytochrome c in destroying reactive oxygen species and in triggering apoptosis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, year = {2006}, month = {2006 Jun 13}, pages = {8965-70}, abstract = {

Hydrogen peroxide (H(2)O(2)) is the major reactive oxygen species (ROS) produced in sperm. High concentrations of H(2)O(2) in sperm induce nuclear DNA fragmentation and lipid peroxidation and result in cell death. The respiratory chain of the mitochondrion is one of the most productive ROS generating systems in sperm, and thus the destruction of ROS in mitochondria is critical for the cell. It was recently reported that H(2)O(2) generated by the respiratory chain of the mitochondrion can be efficiently destroyed by the cytochrome c-mediated electron-leak pathway where the electron of ferrocytochrome c migrates directly to H(2)O(2) instead of to cytochrome c oxidase. In our studies, we found that mouse testis-specific cytochrome c (T-Cc) can catalyze the reduction of H(2)O(2) three times faster than its counterpart in somatic cells (S-Cc) and that the T-Cc heme has the greater resistance to being degraded by H(2)O(2). Together, these findings strongly imply that T-Cc can protect sperm from the damages caused by H(2)O(2). Moreover, the apoptotic activity of T-Cc is three to five times greater than that of S-Cc in a well established apoptosis measurement system using Xenopus egg extract. The dramatically stronger apoptotic activity of T-Cc might be important for the suicide of male germ cells, considered a physiological mechanism that regulates the number of sperm produced and eliminates those with damaged DNA. Thus, it is very likely that T-Cc has evolved to guarantee the biological integrity of sperm produced in mammalian testis.

}, keywords = {Animals, Apoptosis, Ascorbic Acid, Crystallography, Cytochromes c, DNA Damage, Electron Transport Complex IV, Erythrocytes, Humans, Hydrogen Peroxide, Male, Mice, Models, Molecular, Oocytes, Oxidants, Phylogeny, Protein Conformation, Protein Isoforms, Reactive Oxygen Species, Spermatozoa, Testis, Water, X-Ray, Xenopus laevis}, issn = {0027-8424}, doi = {10.1073/pnas.0603327103}, author = {Liu, Zhe and Lin, Hao and Ye, Sheng and Liu, Qin-Ying and Meng, Zhaohui and Zhang, Chuan-Mao and Xia, Yongjing and Margoliash, Emanuel and Rao, Zihe and Liu, Xiang-Jun} } @article {46403, title = {Role of thioredoxin in cell growth through interactions with signaling molecules.}, journal = {Antioxidants and Redox Signaling}, volume = {8}, year = {2006}, month = {2006 Nov-Dec}, pages = {2143-51}, abstract = {

The thioredoxin system helps maintain a reducing environment in cells, but thioredoxin functions as more than simply an antioxidant. Thioredoxin functions depend on the protein{\textquoteright}s redox state, as determined by two conserved cysteines. Key biologic activities of thioredoxin include antioxidant, growth control, and antiapoptotic properties, resulting from interaction with target molecules including transcription factors. Mechanisms by which thioredoxin regulates cell growth include binding to signaling molecules such as apoptosis signal-regulating kinase-1 (ASK-1) and thioredoxin-interacting protein (Txnip). The molecular interplay between thioredoxin, ASK-1, and Txnip potentially influences cell growth and survival in diverse human diseases such as cancer, diabetes, and heart disease. In this review, we focus on the structure of thioredoxin and its functional regulation of cell growth through the interactions with signaling molecules.

}, keywords = {Carrier Proteins, Cell Growth Processes, Humans, MAP Kinase Kinase Kinase 5, Models, Molecular, Protein Binding, Protein Conformation, Protein Structure, Tertiary, Signal Transduction, Thioredoxins}, issn = {1523-0864}, doi = {10.1089/ars.2006.8.2143}, author = {Yoshioka, Jun and Schreiter, Eric R and Lee, Richard T} } @article {2130, title = {Sleep deprivation-induced alterations in excitatory synaptic transmission in the CA1 region of the rat hippocampus.}, journal = {The Journal of Physiology}, volume = {570}, year = {2006}, month = {2006 Feb 1}, pages = {553-65}, abstract = {

Although the function of sleep remains elusive, there is compelling evidence to suggest that sleep plays an important role in learning and memory. A number of studies have now shown that sleep deprivation (SD) results in significant impairment of long-term potentiation (LTP) in the hippocampus. In this study, we have attempted to determine the mechanisms responsible for this impairment. After 72 h SD using the multiple-platform technique, we observed a reduction in the whole-cell recorded NMDA/AMPA ratio of CA1 pyramidal cells in response to Schaffer collateral stimulation. This impairment was specific to sleep deprivation as rats placed over a single large platform, which allowed sleep, had a normal NMDA/AMPA ratio. mEPSCs evoked by local application of a high osmolarity solution revealed no differences in the AMPA receptor function. NMDA currents recorded from outside-out patches excised from the distal dendrites of CA1 cells displayed a reduction in amplitude after SD. While there were no alterations in the glutamate sensitivity, channel open probability or the single channel conductance of the receptor, a crosslinking assay demonstrated that the NR1 and NR2A subunits of NMDA receptors were preferentially retained in the cytoplasm after SD, indicating that SD alters NMDAR surface expression. In summary, we have identified a potential mechanism underlying SD-induced LTP impairment. This synaptic alteration may underlie the cognitive deficits seen following sleep deprivation and could represent a target for future intervention studies.

}, keywords = {AMPA, Animals, Electric Stimulation, Excitatory Postsynaptic Potentials, Glutamic Acid, Glycine, Hippocampus, Ion Channel Gating, Kinetics, Long-Term Potentiation, Male, N-Methyl-D-Aspartate, Patch-Clamp Techniques, Rats, Receptors, Sleep Deprivation, Sprague-Dawley, Synaptic Transmission}, issn = {0022-3751}, doi = {10.1002/cbic.201000254}, author = {McDermott, Carmel M and Hardy, Mattie N and Bazan, Nicolas G and Magee, Jeffrey C} } @article {2365, title = {Sparse odor coding in awake behaving mice.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {26}, year = {2006}, month = {2006 Aug 23}, pages = {8857-65}, abstract = {

Responses of mitral cells represent the results of the first stage of odor processing in the olfactory bulb. Most of our knowledge about mitral cell activity has been obtained from recordings in anesthetized animals. We compared odor-elicited changes in firing rate of mitral cells in awake behaving mice and in anesthetized mice. We show that odor-elicited changes in mitral cell firing rate were larger and more frequently observed in the anesthetized than in the awake condition. Only 27\% of mitral cells that showed a response to odors in the anesthetized state were also odor responsive in the awake state. The amplitude of their response in the awake state was smaller, and some of the responses changed sign compared with their responses in the anesthetized state. The odor representation in the olfactory bulb is therefore sparser in awake behaving mice than in anesthetized preparations. A qualitative explanation of the mechanism responsible for this phenomenon is proposed.

}, keywords = {Afferent, Anesthesia, Animals, Electrophysiology, Inbred C57BL, Male, Mice, Neurons, Odors, Olfactory Bulb, Smell, Wakefulness}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3613-08.2008}, author = {Rinberg, Dmitry and Koulakov, Alex and Gelperin, Alan} } @article {2366, title = {Speed-accuracy tradeoff in olfaction.}, journal = {Neuron}, volume = {51}, year = {2006}, month = {2006 Aug 3}, pages = {351-8}, abstract = {

The basic psychophysical principle of speed-accuracy tradeoff (SAT) has been used to understand key aspects of neuronal information processing in vision and audition, but the principle of SAT is still debated in olfaction. In this study we present the direct observation of SAT in olfaction. We developed a behavioral paradigm for mice in which both the duration of odorant sampling and the difficulty of the odor discrimination task were controlled by the experimenter. We observed that the accuracy of odor discrimination increases with the duration of imposed odorant sampling, and that the rate of this increase is slower for harder tasks. We also present a unifying picture of two previous, seemingly disparate experiments on timing of odorant sampling in odor discrimination tasks. The presence of SAT in olfaction provides strong evidence for temporal integration in olfaction and puts a constraint on models of olfactory processing.

}, keywords = {Animals, Chemical, Discrimination Learning, Inbred C57BL, Male, Mice, Psychomotor Performance, Reaction Time, Smell, Stimulation}, issn = {0896-6273}, doi = {10.1523/JNEUROSCI.3613-08.2008}, author = {Rinberg, Dmitry and Koulakov, Alexei and Gelperin, Alan} } @article {2128, title = {State-dependent dendritic computation in hippocampal CA1 pyramidal neurons.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {26}, year = {2006}, month = {2006 Feb 15}, pages = {2088-100}, abstract = {

Depending on the behavioral state, hippocampal CA1 pyramidal neurons receive very distinct patterns of synaptic input and likewise produce very different output patterns. We have used simultaneous dendritic and somatic recordings and multisite glutamate uncaging to investigate the relationship between synaptic input pattern, the form of dendritic integration, and action potential output in CA1 neurons. We found that when synaptic input arrives asynchronously or highly distributed in space, the dendritic arbor performs a linear integration that allows the action potential rate and timing to vary as a function of the quantity of the input. In contrast, when synaptic input arrives synchronously and spatially clustered, the dendritic compartment receiving the clustered input produces a highly nonlinear integration that leads to an action potential output that is extraordinarily precise and invariant. We also present evidence that both of these forms of information processing may be independently engaged during the two distinct behavioral states of the hippocampus such that individual CA1 pyramidal neurons could perform two different state-dependent computations: input strength encoding during theta states and feature detection during sharp waves.

}, keywords = {alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid, Animals, Dendrites, Excitatory Postsynaptic Potentials, Glutamic Acid, Hippocampus, Patch-Clamp Techniques, Pyramidal Cells, Rats, Sprague-Dawley, Synapses, Tetrodotoxin}, issn = {1529-2401}, doi = {10.1002/cbic.201000254}, author = {Gasparini, Sonia and Magee, Jeffrey C} } @article {1107, title = {Stereochemically general approach to adjacent bis(tetrahydrofuran) cores of annonaceous acetogenins.}, journal = {Organic Letters}, volume = {8}, year = {2006}, month = {2006 Nov 23}, pages = {5637-40}, abstract = {

A series of six 2,5-disubstituted adjacent bis(tetrahydrofuran) stereoisomers with trans/erythro/cis, trans/threo/trans, or cis/threo/cis relative stereochemistry have been synthesized from known dihydroxycyclooctenes via ring opening/cross metathesis and Pd(0)-mediated asymmetric double cycloetherification. The stereochemistry of four of these isomers has been found in the biologically active annonaceous acetogenin natural products. [reaction: see text].

}, keywords = {Acetogenins, Annonaceae, Cyclization, Dioxanes, Ethers, Fatty Alcohols, Furans, Lactones, Magnetic Resonance Spectroscopy, Palladium, Solvents, Stereoisomerism}, issn = {1523-7060}, doi = {10.1021/ol062390l}, author = {Wysocki, Laura M and Dodge, Matthew W and Voight, Eric A and Burke, Steven D} } @article {2348, title = {Storage of spatial information by the maintenance mechanism of LTP.}, journal = {Science}, volume = {313}, year = {2006}, month = {2006 Aug 25}, pages = {1141-4}, abstract = {

Analogous to learning and memory storage, long-term potentiation (LTP) is divided into induction and maintenance phases. Testing the hypothesis that the mechanism of LTP maintenance stores information requires reversing this mechanism in vivo and finding out whether long-term stored information is lost. This was not previously possible. Recently however, persistent phosphorylation by the atypical protein kinase C isoform, protein kinase Mzeta (PKMz), has been found to maintain late LTP in hippocampal slices. Here we show that a cell-permeable PKMz inhibitor, injected in the rat hippocampus, both reverses LTP maintenance in vivo and produces persistent loss of 1-day-old spatial information. Thus, the mechanism maintaining LTP sustains spatial memory.

}, keywords = {Animals, Avoidance Learning, Conditioning (Psychology), Dentate Gyrus, Electric Stimulation, Excitatory Postsynaptic Potentials, Heat-Shock Proteins, Hippocampus, Long-Evans, Long-Term Potentiation, Male, Memory, Perforant Pathway, Protein Kinase C, Rats, Staurosporine, Time Factors}, issn = {1095-9203}, doi = {10.1523/JNEUROSCI.3773-10.2011}, author = {Pastalkova, Eva and Serrano, Peter and Pinkhasova, Deana and Wallace, Emma and Fenton, Andr{\'e} Antonio and Sacktor, Todd Charlton} } @article {1588, title = {Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family.}, journal = {Nucleic Acids Research}, volume = {34}, year = {2006}, month = {2006 Mar 9}, pages = {1439-49}, abstract = {

The Lrp/AsnC family of transcriptional regulatory proteins is found in both archaea and bacteria. Members of the family influence cellular metabolism in both a global (Lrp) and specific (AsnC) manner, often in response to exogenous amino acid effectors. In the present study we have determined both the first bacterial and the highest resolution structures for members of the family. Escherichia coli AsnC is a specific gene regulator whose activity is triggered by asparagine binding. Bacillus subtilis LrpC is a global regulator involved in chromosome condensation. Our AsnC-asparagine structure is the first for a regulator-effector complex and is revealed as an octameric disc. Key ligand recognition residues are identified together with a route for ligand access. The LrpC structure reveals a stable octamer supportive of a topological role in dynamic DNA packaging. The structures yield significant clues to the functionality of Lrp/AsnC-type regulators with respect to ligand binding and oligomerization states as well as to their role in specific and global DNA regulation.

}, keywords = {Amino Acid Sequence, Asparagine, Bacillus subtilis, Bacterial, Bacterial Proteins, Escherichia coli Proteins, Gene Expression Regulation, Genetic, Ligands, Models, Molecular, Molecular Sequence Data, Sequence Alignment, Trans-Activators, Transcription, Transcription Factors}, issn = {1362-4962}, doi = {10.1093/nar/gkl009}, author = {Thaw, Paul and Sedelnikova, Svetlana E and Muranova, Tatyana and Wiese, Sebastian and Ayora, Sylvia and Alonso, Juan C and Brinkman, Arie B and Akerboom, Jasper and van der Oost, John and Rafferty, John B} } @article {45958, title = {The structure of aquaporins.}, journal = {Quarterly Reviews of Biophysics}, volume = {39}, year = {2006}, month = {2006 Nov}, pages = {361-96}, abstract = {

The ubiquitous members of the aquaporin (AQP) family form transmembrane pores that are either exclusive for water (aquaporins) or are also permeable for other small neutral solutes such as glycerol (aquaglyceroporins). The purpose of this review is to provide an overview of our current knowledge of AQP structures and to describe the structural features that define the function of these membrane pores. The review will discuss the mechanisms governing water conduction, proton exclusion and substrate specificity, and how the pore permeability is regulated in different members of the AQP family.

}, keywords = {Amino Acid Sequence, Animals, Aquaporins, Cell Membrane, Cell Membrane Permeability, Humans, Ion Channel Gating, Molecular Sequence Data, Protein Conformation, Water}, issn = {0033-5835}, doi = {10.1017/S0033583506004458}, author = {Gonen, Tamir and Walz, Thomas} } @article {2129, title = {A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles.}, journal = {Genome Research}, volume = {16}, year = {2006}, month = {2006 Mar}, pages = {405-13}, abstract = {

An important aspect of understanding a biological pathway is to delineate the transcriptional regulatory mechanisms of the genes involved. Two important tasks are often encountered when studying transcription regulation, i.e., (1) the identification of common transcriptional regulators of a set of coexpressed genes; (2) the identification of genes that are regulated by one or several transcription factors. In this study, a systematic and statistical approach was taken to accomplish these tasks by establishing an integrated model considering all of the promoters and characterized transcription factors (TFs) in the genome. A promoter analysis pipeline (PAP) was developed to implement this approach. PAP was tested using coregulated gene clusters collected from the literature. In most test cases, PAP identified the transcription regulators of the input genes accurately. When compared with chromatin immunoprecipitation experiment data, PAP{\textquoteright}s predictions are consistent with the experimental observations. When PAP was used to analyze one published expression-profiling data set and two novel coregulated gene sets, PAP was able to generate biologically meaningful hypotheses. Therefore, by taking a systematic approach of considering all promoters and characterized TFs in our model, we were able to make more reliable predictions about the regulation of gene expression in mammalian organisms.

}, keywords = {Animals, Cell Proliferation, Cholesterol, Chromatin Immunoprecipitation, Computational Biology, Conserved Sequence, Gene Expression Profiling, Gene Expression Regulation, Genetic, Humans, Mice, Models, Promoter Regions, Protein Binding, Transcription Factors}, issn = {1088-9051}, doi = {10.1002/cbic.201000254}, author = {Chang, Li-Wei and Nagarajan, Rakesh and Magee, Jeffrey A and Milbrandt, Jeffrey and Stormo, Gary D} } @article {2406, title = {TAF4 nucleates a core subcomplex of TFIID and mediates activated transcription from a TATA-less promoter.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, year = {2006}, month = {2006 Aug 15}, pages = {12347-52}, abstract = {

Activator-dependent recruitment of TFIID initiates formation of the transcriptional preinitiation complex. TFIID binds core promoter DNA elements and directs the assembly of other general transcription factors, leading to binding of RNA polymerase II and activation of RNA synthesis. How TATA box-binding protein (TBP) and the TBP-associated factors (TAFs) are assembled into a functional TFIID complex with promoter recognition and coactivator activities in vivo remains unknown. Here, we use RNAi to knock down specific TFIID subunits in Drosophila tissue culture cells to determine which subunits are most critical for maintaining stability of TFIID in vivo. Contrary to expectations, we find that TAF4 rather than TBP or TAF1 plays the most critical role in maintaining stability of the complex. Our analysis also indicates that TAF5, TAF6, TAF9, and TAF12 play key roles in stability of the complex, whereas TBP, TAF1, TAF2, and TAF11 contribute very little to complex stability. Based on our results, we propose that holo-TFIID comprises a stable core subcomplex containing TAF4, TAF5, TAF6, TAF9, and TAF12 decorated with peripheral subunits TAF1, TAF2, TAF11, and TBP. Our initial functional studies indicate a specific and significant role for TAF1 and TAF4 in mediating transcription from a TATA-less, downstream core promoter element (DPE)-containing promoter, whereas a TATA-containing, DPE-less promoter was far less dependent on these subunits. In contrast to both TAF1 and TAF4, RNAi knockdown of TAF5 had little effect on transcription from either class of promoter. These studies significantly alter previous models for the assembly, structure, and function of TFIID.

}, keywords = {Animals, Cell Line, Drosophila melanogaster, Drosophila Proteins, Enzyme Stability, Gene Expression Regulation, Genetic, Humans, Macromolecular Substances, Models, Molecular, Protein Subunits, RNA Interference, TATA Box, TATA-Binding Protein Associated Factors, Transcription, Transcription Factor TFIID}, issn = {0027-8424}, doi = {10.1073/pnas.1100640108}, author = {Wright, Kevin J and Marr, Michael T and Tjian, Robert} } @article {1735, title = {Three-dimensional chiral imaging by sum-frequency generation.}, journal = {Journal of the American Chemical Society}, volume = {128}, year = {2006}, month = {2006 Mar 22}, pages = {3482-3}, abstract = {

A sum-frequency generation (SFG) microscope that is sensitive toward molecular chirality was demonstrated for the first time. Optically active images of chiral 1,1{\textquoteright}-bi-2-naphthol solutions were obtained with submicron spatial resolution. Three-dimensional sectioning capability of our microscope was also demonstrated. This optically active SFG microscopy can potentially become a powerful imaging technique for biological samples.

}, keywords = {Computer-Assisted, Fluorescence, Image Processing, Microscopy, Naphthols, Stereoisomerism}, issn = {0002-7863}, doi = {10.1021/ja057775y}, author = {Ji, Na and Zhang, Kai and Yang, Haw and Shen, Yuen-Ron} } @article {2729, title = {Toward chiral sum-frequency spectroscopy.}, journal = {Journal of the American Chemical Society}, volume = {128}, year = {2006}, month = {2006 Jul 12}, pages = {8845-8}, abstract = {

Chiral sum-frequency (SF) spectroscopy that measures both the real and the imaginary components of the SF spectral response was demonstrated for the first time. It was based on interference of the SF signal with a dispersionless SF reference. Solutions of 1,1{\textquoteright}-bi-2-naphthol (BN) were used as model systems, and their chiral SF spectra over the first exciton-split transitions were obtained. Chiral spectra are useful for determination of absolute configuration and conformation of chiral molecules.

}, keywords = {Molecular Conformation, Naphthols, Sensitivity and Specificity, Solutions, Spectrum Analysis}, issn = {0002-7863}, doi = {10.1021/ja060888c}, author = {Ji, Na and Ostroverkhov, Victor and Belkin, Mikhail and Shiu, Ying-Jen and Shen, Yuen-Ron} } @article {6352, title = {Transcriptional signatures of cellular plasticity in mice lacking the alpha1 subunit of GABAA receptors.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {26}, year = {2006}, month = {2006 May 24}, pages = {5673-83}, abstract = {

GABAA receptors mediate the majority of inhibitory neurotransmission in the CNS. Genetic deletion of the alpha1 subunit of GABAA receptors results in a loss of alpha1-mediated fast inhibitory currents and a marked reduction in density of GABAA receptors. A grossly normal phenotype of alpha1-deficient mice suggests the presence of neuronal adaptation to these drastic changes at the GABA synapse. We used cDNA microarrays to identify transcriptional fingerprints of cellular plasticity in response to altered GABAergic inhibition in the cerebral cortex and cerebellum of alpha1 mutants. In silico analysis of 982 mutation-regulated transcripts highlighted genes and functional groups involved in regulation of neuronal excitability and synaptic transmission, suggesting an adaptive response of the brain to an altered inhibitory tone. Public gene expression databases permitted identification of subsets of transcripts enriched in excitatory and inhibitory neurons as well as some glial cells, providing evidence for cellular plasticity in individual cell types. Additional analysis linked some transcriptional changes to cellular phenotypes observed in the knock-out mice and suggested several genes, such as the early growth response 1 (Egr1), small GTP binding protein Rac1 (Rac1), neurogranin (Nrgn), sodium channel beta4 subunit (Scn4b), and potassium voltage-gated Kv4.2 channel (Kcnd2) as cell type-specific markers of neuronal plasticity. Furthermore, transcriptional activation of genes enriched in Bergman glia suggests an active role of these astrocytes in synaptic plasticity. Overall, our results suggest that the loss of alpha1-mediated fast inhibition produces diverse transcriptional responses that act to regulate neuronal excitability of individual neurons and stabilize neuronal networks, which may account for the lack of severe abnormalities in alpha1 null mutants.

}, keywords = {Animals, GABA-A, Gene Expression Profiling, Knockout, Male, Mice, Neural Inhibition, Neuroglia, Neuronal Plasticity, Neurons, Receptors, Synaptic Transmission, Transcription Factors}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0860-06.2006}, author = {Ponomarev, Igor and Maiya, Rajani and Harnett, Mark T and Schafer, Gwen L and Ryabinin, Andrey E and Blednov, Yuri A and Morikawa, Hitoshi and Boehm, Stephen L and Homanics, Gregg E and Berman, Ari E and Berman, Ari and Lodowski, Kerrie H and Bergeson, Susan E and Harris, R Adron} } @article {1772, title = {Transforming the architecture of compound eyes.}, journal = {Nature}, volume = {443}, year = {2006}, month = {2006 Oct 12}, pages = {696-9}, abstract = {

Eyes differ markedly in the animal kingdom, and are an extreme example of the evolution of multiple anatomical solutions to light detection and image formation. A salient feature of all photoreceptor cells is the presence of a specialized compartment (disc outer segments in vertebrates, and microvillar rhabdomeres in insects), whose primary role is to accommodate the millions of light receptor molecules required for efficient photon collection. In insects, compound eyes can have very different inner architectures. Fruitflies and houseflies have an open rhabdom system, in which the seven rhabdomeres of each ommatidium are separated from each other and function as independent light guides. In contrast, bees and various mosquitoes and beetle species have a closed system, in which rhabdomeres within each ommatidium are fused to each other, thus sharing the same visual axis. To understand the transition between open and closed rhabdom systems, we isolated and characterized the role of Drosophila genes involved in rhabdomere assembly. Here we show that Spacemaker, a secreted protein expressed only in the eyes of insects with open rhabdom systems, acts together with Prominin and the cell adhesion molecule Chaoptin to choreograph the partitioning of rhabdomeres into an open system. Furthermore, the complete loss of spacemaker (spam) converts an open rhabdom system to a closed one, whereas its targeted expression to photoreceptors of a closed system markedly reorganizes the architecture of the compound eyes to resemble an open system. Our results provide a molecular atlas for the construction of microvillar assemblies and illustrate the critical effect of differences in a single structural protein in morphogenesis.

}, keywords = {Adhesiveness, Animals, Bees, Drosophila melanogaster, Drosophila Proteins, Eye, Eye Proteins, Membrane Glycoproteins, Molecular Sequence Data, Morphogenesis, Mutation}, issn = {1476-4687}, doi = {10.1038/nature05128}, author = {Zelhof, Andrew C and Hardy, Robert W and Becker, Ann and Zuker, Charles S} } @article {2152, title = {Transitive closure and metric inequality of weighted graphs: detecting protein interaction modules using cliques.}, journal = {International Journal of Data Mining and Bioinformatics}, volume = {1}, year = {2006}, month = {2006 Jun 2}, pages = {162-77}, abstract = {

We study transitivity properties of edge weights in complex networks. We show that enforcing transitivity leads to a transitivity inequality which is equivalent to ultra-metric inequality. This can be used to define transitive closure on weighted undirected graphs, which can be computed using a modified Floyd-Warshall algorithm. These new concepts are extended to dissimilarity graphs and triangle inequalities. From this, we extend the clique concept from unweighted graph to weighted graph. We outline several applications and present results of detecting protein functional modules in a protein interaction network.

}, keywords = {Algorithms, Computational Biology, Fungal Proteins, Models, Protein Binding, Protein Interaction Mapping, Systems Biology, Theoretical}, issn = {1748-5673}, doi = {10.1007/s12021-010-9090-x}, author = {Ding, Chris and He, Xiaofeng and Xiong, Hui and Peng, Hanchuan and Holbrook, Stephen R} } @conference {2847, title = {Unsupervised learning of boosted tree classifier using graph cuts for hand pose recognition.}, booktitle = {British Machine Vision Conference}, year = {2006}, month = {2006 Sep 4}, author = {Parag, Toufiq and Elgammal, Ahmed} } @article {4981, title = {The virtual insect brain protocol: creating and comparing standardized neuroanatomy.}, journal = {BMC Bioinformatics}, volume = {7}, year = {2006}, month = {2006 Dec 29}, pages = {544}, abstract = {

In the fly Drosophila melanogaster, new genetic, physiological, molecular and behavioral techniques for the functional analysis of the brain are rapidly accumulating. These diverse investigations on the function of the insect brain use gene expression patterns that can be visualized and provide the means for manipulating groups of neurons as a common ground. To take advantage of these patterns one needs to know their typical anatomy.

}, keywords = {Anatomic, Animals, Brain, Computer Graphics, Computer Simulation, Drosophila melanogaster, Imaging, Models, Neuroanatomy, Neurological, Software, Subtraction Technique, Three-Dimensional, User-Computer Interface}, issn = {1471-2105}, doi = {10.1186/1471-2105-7-544}, author = {Jenett, Arnim and Schindelin, Johannes E and Heisenberg, Martin} } @article {2367, title = {When good enough is best.}, journal = {Neuron}, volume = {51}, year = {2006}, month = {2006 Aug 3}, pages = {277-8}, abstract = {

In this issue of Neuron, Rinberg et al. show that mice use a speed-accuracy tradeoff in odor discrimination. Shorter sampling results in high performance for easy problems, and enforced longer sampling results in higher accuracy for difficult problems, but mice freely choose intermediate sampling durations and accuracy varies with difficulty. Reward value and task requirements may determine sampling time choice and performance levels.

}, keywords = {Animals, Discrimination Learning, Mice, Reaction Time, Smell}, issn = {0896-6273}, doi = {10.1523/JNEUROSCI.3613-08.2008}, author = {Kay, Leslie M and Beshel, Jennifer and Martin, Claire} } @article {3936, title = {Where to start and when to stop.}, journal = {Nature Structural \& Molecular Biology}, volume = {13}, year = {2006}, month = {2006 Aug}, pages = {668-70}, abstract = {

The activity of a handful of transcription factors, such as mammalian NF-B, Drosophila melanogaster Cubitus interruptus and yeast Spt23 and Mga2, are regulated through partial protein degradation by the proteasome. New data now show that the proteasome activates membrane-bound Spt23 and Mga2 by initiating their proteolysis at an internal site and then degrading the proteins bidirectionally toward both ends of the polypeptide chain, modifying our ideas on how the proteasome degrades targeted substrates.

}, keywords = {Animals, DNA-Binding Proteins, Drosophila Proteins, Membrane Proteins, NF-kappa B, Oncogene Proteins, Proteasome Endopeptidase Complex, Protein Structure, Saccharomyces cerevisiae Proteins, Tertiary, Trans-Activators, Transcription Factors}, issn = {1545-9993}, doi = {10.1038/nsmb0806-668}, author = {Tian, Lin and Matouschek, Andreas} } @article {1342, title = {Whole-cell recordings in freely moving rats.}, journal = {Neuron}, volume = {51}, year = {2006}, month = {2006 Aug 17}, pages = {399-407}, abstract = {

Intracellular recording, which allows direct measurement of the membrane potential and currents of individual neurons, requires a very mechanically stable preparation and has thus been limited to in vitro and head-immobilized in vivo experiments. This restriction constitutes a major obstacle for linking cellular and synaptic physiology with animal behavior. To overcome this limitation we have developed a method for performing whole-cell recordings in freely moving rats. We constructed a miniature head-mountable recording device, with mechanical stabilization achieved by anchoring the recording pipette rigidly in place after the whole-cell configuration is established. We obtain long-duration recordings (mean of approximately 20 min, maximum 60 min) in freely moving animals that are remarkably insensitive to mechanical disturbances, then reconstruct the anatomy of the recorded cells. This head-anchored whole-cell recording technique will enable a wide range of new studies involving detailed measurement and manipulation of the physiological properties of identified cells during natural behaviors.

}, keywords = {Animal, Animals, Behavior, Brain, Electrodes, Implanted, Male, Membrane Potentials, Microelectrodes, Neurons, Newborn, Patch-Clamp Techniques, Rats, Sprague-Dawley, Wakefulness, Wistar}, issn = {0896-6273}, doi = {10.1016/j.neuron.2006.07.004}, author = {Lee, Albert K and Manns, Ian D and Sakmann, Bert and Brecht, Michael} } @article {45747, title = {Wing dimorphism in aphids.}, journal = {Heredity (Edinb)}, volume = {97}, year = {2006}, month = {2006 Sep}, pages = {192-9}, abstract = {

Many species of insects display dispersing and nondispersing morphs. Among these, aphids are one of the best examples of taxa that have evolved specialized morphs for dispersal versus reproduction. The dispersing morphs typically possess a full set of wings as well as a sensory and reproductive physiology that is adapted to flight and reproducing in a new location. In contrast, the nondispersing morphs are wingless and show adaptations to maximize fecundity. In this review, we provide an overview of the major features of the aphid wing dimorphism. We first provide a description of the dimorphism and an overview of its phylogenetic distribution. We then review what is known about the mechanisms underlying the dimorphism and end by discussing its evolutionary aspects.

}, keywords = {Animals, Aphids, Biological Evolution, Female, Hormones, Male, Polymorphism, Genetic, Wing}, issn = {0018-067X}, doi = {10.1038/sj.hdy.6800863}, author = {Braendle, C and Davis, G K and Brisson, J A and Stern, D L} } @article {1239, title = {Wiring optimization can relate neuronal structure and function.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, year = {2006}, month = {2006 Mar 21}, pages = {4723-8}, abstract = {

We pursue the hypothesis that neuronal placement in animals minimizes wiring costs for given functional constraints, as specified by synaptic connectivity. Using a newly compiled version of the Caenorhabditis elegans wiring diagram, we solve for the optimal layout of 279 nonpharyngeal neurons. In the optimal layout, most neurons are located close to their actual positions, suggesting that wiring minimization is an important factor. Yet some neurons exhibit strong deviations from "optimal" position. We propose that biological factors relating to axonal guidance and command neuron functions contribute to these deviations. We capture these factors by proposing a modified wiring cost function.

}, keywords = {Animals, Caenorhabditis elegans, Models, Neurological, Neurons, Synapses}, issn = {0027-8424}, doi = {10.1371/journal.pcbi.1001066}, author = {Chen, Beth L and Hall, David H and Chklovskii, Dmitri B} } @article {2680, title = {Wlds protection distinguishes axon degeneration following injury from naturally occurring developmental pruning.}, journal = {Neuron}, volume = {50}, year = {2006}, month = {2006 Jun 15}, pages = {883-95}, abstract = {

Axon pruning by degeneration remodels exuberant axonal connections and is widely required for the development of proper circuitry in the nervous system from insects to mammals. Developmental axon degeneration morphologically resembles injury-induced Wallerian degeneration, suggesting similar underlying mechanisms. As previously reported for mice, we show that Wlds protein substantially delays Wallerian degeneration in flies. Surprisingly, Wlds has no effect on naturally occurring developmental axon degeneration in flies or mice, although it protects against injury-induced degeneration of the same axons at the same developmental age. By contrast, the ubiquitin-proteasome system is intrinsically required for both developmental and injury-induced axon degeneration. We also show that the glial cell surface receptor Draper is required for efficient clearance of axon fragments during developmental axon degeneration, similar to its function in injury-induced degeneration. Thus, mechanistically, naturally occurring developmental axon pruning by degeneration and injury-induced axon degeneration differ significantly in early steps, but may converge onto a common execution pathway.

}, keywords = {Animals, Axons, Developmental, Drosophila, Drosophila Proteins, Gene Expression Regulation, Genetically Modified, Inbred C57BL, Mice, Nerve Tissue Proteins, Wallerian Degeneration}, issn = {0896-6273}, doi = {10.1016/j.neuron.2006.05.013}, author = {Hoopfer, Eric D and McLaughlin, Todd and Watts, Ryan J and Schuldiner, Oren and O{\textquoteright}Leary, Dennis D M and Luo, Liqun} } @article {1566, title = {Antibody humanization and affinity maturation using phage display.}, journal = {Phage Display in Biotechnology and Drug Discovery}, year = {2005}, month = {2005}, pages = {493-528}, author = {Marvin, Jonathan S and Lowman, Henry B} } @article {2318, title = {Antipsychotic drugs elevate mRNA levels of presynaptic proteins in the frontal cortex of the rat.}, journal = {Biological Psychiatry}, volume = {57}, year = {2005}, month = {2005 May 1}, pages = {1041-51}, abstract = {

Molecular adaptations are believed to contribute to the mechanism of action of antipsychotic drugs (APDs). We attempted to establish common gene regulation patterns induced by chronic treatment with APDs.

}, keywords = {Animals, Antipsychotic Agents, Cluster Analysis, Corpus Striatum, Frontal Lobe, Gene Expression, Male, Messenger, Microtubules, Oligonucleotide Array Sequence Analysis, Presynaptic Terminals, Rats, Reverse Transcriptase Polymerase Chain Reaction, RNA, Sprague-Dawley, Synaptic Vesicles}, issn = {0006-3223}, doi = {10.3389/fnana.2010.00147}, author = {MacDonald, Matthew L and Eaton, Molly E and Dudman, Joshua T and Konradi, Christine} } @article {1292, title = {Ataxin-3 suppresses polyglutamine neurodegeneration in Drosophila by a ubiquitin-associated mechanism.}, journal = {Molecular Cell}, volume = {18}, year = {2005}, month = {2005 Apr 1}, pages = {37-48}, abstract = {

Two central issues in polyglutamine-induced neurodegeneration are the influence of the normal function of the disease protein and modulation by protein quality control pathways. By using Drosophila, we now directly link host protein function and disease pathogenesis to ubiquitin pathways in the polyglutamine disease spinocerebellar ataxia type 3 (SCA3). Normal human ataxin-3{\textendash}a polyubiquitin binding protein with ubiquitin protease activity{\textendash}is a striking suppressor of polyglutamine neurodegeneration in vivo. This suppressor activity requires ubiquitin-associated activities of the protein and is dependent upon proteasome function. Our results highlight the critical importance of host protein function in SCA3 disease and a potential therapeutic role of ataxin-3 activity for polyglutamine disorders.

}, keywords = {Animals, Drosophila melanogaster, Genetic, Genetically Modified, Humans, Machado-Joseph Disease, Mutagenesis, Nerve Degeneration, Nerve Tissue Proteins, Nuclear Proteins, Peptides, Polymorphism, Repressor Proteins, Site-Directed, Ubiquitin}, issn = {1097-2765}, doi = {10.1016/j.molcel.2005.02.030}, author = {Warrick, John M and Morabito, Lance M and Bilen, Julide and Gordesky-Gold, Beth and Faust, Lynn Z and Paulson, Henry L and Bonini, Nancy M} } @article {2448, title = {Cellular mechanisms of dendrite pruning in Drosophila: insights from in vivo time-lapse of remodeling dendritic arborizing sensory neurons.}, journal = {Development}, volume = {132}, year = {2005}, month = {2005 Aug}, pages = {3631-42}, abstract = {

Regressive events that refine exuberant or inaccurate connections are critical in neuronal development. We used multi-photon, time-lapse imaging to examine how dendrites of Drosophila dendritic arborizing (da) sensory neurons are eliminated during early metamorphosis, and how intrinsic and extrinsic cellular mechanisms control this deconstruction. Removal of the larval dendritic arbor involves two mechanisms: local degeneration and branch retraction. In local degeneration, major branch severing events entail focal disruption of the microtubule cytoskeleton, followed by thinning of the disrupted region, severing and fragmentation. Retraction was observed at distal tips of branches and in proximal stumps after severing events. The pruning program of da neuron dendrites is steroid induced; cell-autonomous dominant-negative inhibition of steroid action blocks local degeneration, although retraction events still occur. Our data suggest that steroid-induced changes in the epidermis may contribute to dendritic retraction. Finally, we find that phagocytic blood cells not only engulf neuronal debris but also attack and sever intact branches that show signs of destabilization.

}, keywords = {Abdomen, Afferent, Animals, Biological, Cytoskeleton, Dendrites, Drosophila melanogaster, Fluorescent Dyes, Metamorphosis, Microscopy, Neurons, Phagocytes, Receptors, Steroid, Video}, issn = {0950-1991}, doi = {10.1242/dev.01928}, author = {Williams, Darren W and Truman, James W} } @article {1565, title = {Computation-based engineering of protein and antibody therapeutics.}, journal = {Drug Design Reviews Online}, volume = {2}, year = {2005}, month = {2005}, pages = {419-25}, abstract = {

Recent advances in computation-based protein engineering offer opportunities to introduce or modify the biophysical characteristics of proteins at will. The power of computational design comes from the ability to surpass the combinatorial and physical limitations inherent to laboratory-based high-throughput or trial-and-error methods. As a result, modifications that require significant changes to the amino acid sequence of a protein are now accessible to the protein engineering community. Hydrophobic cores of proteins have been repacked to increase their thermostability. Binding sites in proteins have been modified to increase affinity or alter specificity for proteins, peptides, and small molecules. Enzymes have been designed de novo. Non-natural protein folds have been created. For the most part, these achievements have been applied to proteins that make good model systems in academic settings. How can these computational methods be applied to therapeutically relevant proteins? This review will focus on the ground-breaking achievements of computation-based protein engineering and on recent applications of rational design to improve therapeutic proteins. - See more at: http://www.eurekaselect.com/90585/article/computation-based-design-and-engineering-protein-and-antibody-therapeutics$\#$sthash.kSt3UaNE.dpuf

}, author = {Marvin, Jonathan S and Zhu, Zhenping} } @article {45918, title = {Conditional dendritic spike propagation following distal synaptic activation of hippocampal CA1 pyramidal neurons.}, journal = {Nat Neurosci}, volume = {8}, year = {2005}, month = {2005 Dec}, pages = {1667-76}, abstract = {

The perforant-path projection to the hippocampus forms synapses in the apical tuft of CA1 pyramidal neurons. We used computer modeling to examine the function of these distal synaptic inputs, which led to three predictions that we confirmed in experiments using rat hippocampal slices. First, activation of CA1 neurons by the perforant path is limited, a result of the long distance between these inputs and the soma. Second, activation of CA1 neurons by the perforant path depends on the generation of dendritic spikes. Third, the forward propagation of these spikes is unreliable, but can be facilitated by modest activation of Schaffer-collateral synapses in the upper apical dendrites. This {\textquoteright}gating{\textquoteright} of dendritic spike propagation may be an important activation mode of CA1 pyramidal neurons, and its modulation by neurotransmitters or long-term, activity-dependent plasticity may be an important feature of dendritic integration during mnemonic processing in the hippocampus.

}, keywords = {Action Potentials, Animals, Dendrites, Hippocampus, Long-Term Potentiation, Long-Term Synaptic Depression, Male, Memory, Neural Inhibition, Neural Networks (Computer), Neural Pathways, Neurotransmitter Agents, Organ Culture Techniques, Patch-Clamp Techniques, Perforant Pathway, Pyramidal Cells, Rats, Rats, Wistar, Synaptic Transmission}, issn = {1097-6256}, doi = {10.1038/nn1599}, author = {Jarsky, Tim and Roxin, Alex and Kath, William L and Spruston, Nelson} } @article {3937, title = {A conserved processing mechanism regulates the activity of transcription factors Cubitus interruptus and NF-kappaB.}, journal = {Nature Structural \& Molecular Biology}, volume = {12}, year = {2005}, month = {2005 Dec}, pages = {1045-53}, abstract = {

The proteasome degrades some proteins, such as transcription factors Cubitus interruptus (Ci) and NF-kappaB, to generate biologically active protein fragments. Here we have identified and characterized the signals in the substrate proteins that cause this processing. The minimum signal consists of a simple sequence preceding a tightly folded domain in the direction of proteasome movement. The strength of the processing signal depends primarily on the complexity of the simple sequence rather than on amino acid identity, the resistance of the folded domain to unraveling by the proteasome and the spacing between the simple sequence and folded domain. We show that two unrelated transcription factors, Ci and NF-kappaB, use this mechanism to undergo partial degradation by the proteasome in vivo. These findings suggest that the mechanism is conserved evolutionarily and that processing signals may be widespread in regulatory proteins.

}, keywords = {Amino Acid Sequence, Animals, Cells, Cultured, DNA-Binding Proteins, Drosophila Proteins, Humans, NF-kappa B p50 Subunit, Proteasome Endopeptidase Complex, Protein Folding, Transcription Factors}, issn = {1545-9993}, doi = {10.1038/nsmb1018}, author = {Tian, Lin and Holmgren, Robert A and Matouschek, Andreas} } @article {1741, title = {Degenerate coding in neural systems.}, journal = {Journal of Comparative Physiology. A, Neuroethology, Sensory, Neural, and Behavioral Physiology}, volume = {191}, year = {2005}, month = {2005 Nov}, pages = {995-1010}, abstract = {

When the dimensionality of a neural circuit is substantially larger than the dimensionality of the variable it encodes, many different degenerate network states can produce the same output. In this review I will discuss three different neural systems that are linked by this theme. The pyloric network of the lobster, the song control system of the zebra finch, and the odor encoding system of the locust, while different in design, all contain degeneracies between their internal parameters and the outputs they encode. Indeed, although the dynamics of song generation and odor identification are quite different, computationally, odor recognition can be thought of as running the song generation circuitry backwards. In both of these systems, degeneracy plays a vital role in mapping a sparse neural representation devoid of correlations onto external stimuli (odors or song structure) that are strongly correlated. I argue that degeneracy between input and output states is an inherent feature of many neural systems, which can be exploited as a fault-tolerant method of reliably learning, generating, and discriminating closely related patterns.

}, keywords = {Animal, Animals, Information Storage and Retrieval, Learning, Models, Nerve Net, Neural Pathways, Neurological, Neuronal Plasticity, Smell, Vocalization}, issn = {0340-7594}, doi = {10.1007/s00359-005-0026-0}, author = {Leonardo, Anthony} } @inbook {2556, title = {Drosophila and C. elegans models of human age-associated neurodegeneratiove diseases.}, booktitle = {Protein Misfolding, Aggregation and Conformational Diseases}, year = {2005}, publisher = {Academic / Plenum Publishers}, organization = {Academic / Plenum Publishers}, author = {Bilen, Julide and Bonini, Nancy M}, editor = {Uversky, VN and Fink, AL} } @article {1293, title = {Drosophila as a model for human neurodegenerative disease.}, journal = {Annual Review of Genetics}, volume = {39}, year = {2005}, month = {2005 Jun 28}, pages = {153-71}, abstract = {

Among many achievements in the neurodegeneration field in the past decade, two require special attention due to the huge impact on our understanding of molecular and cellular pathogenesis of human neurodegenerative diseases. First is defining specific mutations in familial neurodegenerative diseases and second is modeling these diseases in easily manipulable model organisms including the fruit fly, nematode, and yeast. The power of these genetic systems has revealed many genetic factors involved in the various pathways affected, as well as provided potential drug targets for therapeutics. This review focuses on fruit fly models of human neurodegenerative diseases, with emphasis on how fly models have provided new insights into various aspects of human diseases.

}, keywords = {Alzheimer Disease, Animal, Animals, Disease Models, Drosophila melanogaster, Humans, Neurodegenerative Diseases, Parkinson Disease, Trinucleotide Repeats}, issn = {0066-4197}, doi = {10.1146/annurev.genet.39.110304.095804}, author = {Bilen, Julide and Bonini, Nancy M} } @article {2471, title = {Drosophila retained/dead ringer is necessary for neuronal pathfinding, female receptivity and repression of fruitless independent male courtship behaviors.}, journal = {Development}, volume = {132}, year = {2005}, month = {2005 Jan}, pages = {155-64}, abstract = {

Mutations in the Drosophila retained/dead ringer (retn) gene lead to female behavioral defects and alter a limited set of neurons in the CNS. retn is implicated as a major repressor of male courtship behavior in the absence of the fruitless (fru) male protein. retn females show fru-independent male-like courtship of males and females, and are highly resistant to courtship by males. Males mutant for retn court with normal parameters, although feminization of retn cells in males induces bisexuality. Alternatively spliced RNAs appear in the larval and pupal CNS, but none shows sex specificity. Post-embryonically, retn RNAs are expressed in a limited set of neurons in the CNS and eyes. Neural defects of retn mutant cells include mushroom body beta-lobe fusion and pathfinding errors by photoreceptor and subesophageal neurons. We posit that some of these retn-expressing cells function to repress a male behavioral pathway activated by fruM.

}, keywords = {Alternative Splicing, Animal, Animals, Behavior, Central Nervous System, Complementary, Crosses, DNA, Drosophila melanogaster, Drosophila Proteins, Female, Genetic, Homeodomain Proteins, Male, Mice, Models, Mutation, Nerve Tissue Proteins, Neurons, Nuclear Proteins, Point Mutation, Reverse Transcriptase Polymerase Chain Reaction, RNA, Sequence Analysis, Sex Factors, Sexual Behavior, Transcription Factors}, issn = {0950-1991}, doi = {10.1242/dev.01568}, author = {Ditch, Lynn M and Shirangi, Troy and Pitman, Jeffrey L and Latham, Kristin L and Finley, Kim D and Edeen, Philip T and Taylor, Barbara J and McKeown, Michael} } @article {1737, title = {A dynamic coupling model for sum frequency chiral response from liquids composed of molecules with a chiral side chain and an achiral chromophore.}, journal = {Journal of the American Chemical Society}, volume = {127}, year = {2005}, month = {2005 Sep 21}, pages = {12933-42}, abstract = {

A theoretical formulation for optically active sum frequency generation (OA-SFG) from isotropic chiral solutions was proposed for molecules with a chiral side chain and an intrinsically achiral chromophore. Adapting an electron correlation model first proposed by H{\"o}hn and Weigang for linear optical activity, we presented a dynamic coupling model for OA-SFG near the electronic resonance of the achiral chromophore. As a demonstration, we used this model to explain the observed OA-SFG spectra of a series of amino acids near the electronic resonance of the intrinsically achiral carboxyl group. Our model shows that the nonlinear chiroptical response comes about by the through-space correlative electronic interactions between the chiral side chain and the achiral chromophore, and its magnitude is determined by the position and orientation of the bonds that make up the chiral side chain. Using the bond polarizability values in the literature and the conformations of amino acids obtained from calculation, we were able to reproduce the relative OA-SFG strength from a series of amino acids.

}, keywords = {Amino Acids, Chemical, Infrared, Models, Spectrophotometry, Thermodynamics}, issn = {0002-7863}, doi = {10.1021/ja052715d}, author = {Ji, Na and Shen, Yuen-Ron} } @article {5822, title = {The embryonic development of the triclad Schmidtea polychroa.}, journal = {Development Genes \& Evolution}, volume = {215}, year = {2005}, month = {2005 Mar}, pages = {109-31}, abstract = {

Triclad flatworms are well studied for their regenerative properties, yet little is known about their embryonic development. We here describe the embryonic development of the triclaty 120d Schmidtea polychroa, using histological and immunocytochemical analysis of whole-mount preparations and sections. During early cleavage (stage 1), yolk cells fuse and enclose the zygote into a syncytium. The zygote divides into blastomeres that dissociate and migrate into the syncytium. During stage 2, a subset of blastomeres differentiate into a transient embryonic epidermis that surrounds the yolk syncytium, and an embryonic pharynx. Other blastomeres divide as a scattered population of cells in the syncytium. During stage 3, the embryonic pharynx imbibes external yolk cells and a gastric cavity is formed in the center of the syncytium. The syncytial yolk and the blastomeres contained within it are compressed into a thin peripheral rind. From a location close to the embryonic pharynx, which defines the posterior pole, bilaterally symmetric ventral nerve cord pioneers extend forward. Stage 4 is characterized by massive proliferation of embryonic cells. Large yolk-filled cells lining the syncytium form the gastrodermis. During stage 5 the external syncytial yolk mantle is resorbed and the embryonic cells contained within differentiate into an irregular scaffold of muscle and nerve cells. Epidermal cells differentiate and replace the transient embryonic epidermis. Through stages 6-8, the embryo adopts its worm-like shape, and loosely scattered populations of differentiating cells consolidate into structurally defined organs. Our analysis reveals a picture of S. polychroa embryogenesis that resembles the morphogenetic events underlying regeneration.

}, keywords = {Animals, Blastomeres, Embryo, Epidermis, Female, Morphogenesis, Nonmammalian, Ovum, Turbellaria}, issn = {0949-944X}, doi = {10.1007/s00427-004-0455-8}, author = {Cardona, Albert and Hartenstein, Volker and Romero, Rafael} } @article {1648, title = {Encoding and decoding of overlapping odor sequences.}, journal = {Neuron}, volume = {51}, year = {2005}, month = {2006 Aug 17}, pages = {467-82}, abstract = {

Odors evoke complex responses in locust antennal lobe projection neurons (PNs)-the mitral cell analogs. These patterns evolve over hundreds of milliseconds and contain information about odor identity and concentration. In nature, animals often encounter many odorants in short temporal succession. We explored the effects of such conditions by presenting two different odors with variable intervening delays. PN ensemble representations tracked stimulus changes and, in some delay conditions, reached states that corresponded neither to the representation of either odor alone nor to the static mixture of the two. We then recorded from Kenyon cells (KCs), the PNs{\textquoteright} targets. Their responses were consistent with the PN population{\textquoteright}s behavior: in some conditions, KCs were recruited that did not fire during single-odor or mixture stimuli. Thus, PN population dynamics are history dependent, and responses of individual KCs are consistent with piecewise temporal decoding of PN output over large sections of the PN population.

}, keywords = {Action Potentials, Afferent, Afferent Pathways, Animals, Chemical, Discrimination (Psychology), Locusta migratoria, Male, Neural Inhibition, Neurons, Odors, Reaction Time, Sense Organs, Stimulation, Time Factors}, issn = {0896-6273}, doi = {10.1016/j.neuron.2006.07.018}, author = {Broome, Bede M and Jayaraman, Vivek and Laurent, Gilles} } @article {1589, title = {Engineering a selectable marker for hyperthermophiles.}, journal = {The Journal of Biological Chemistry}, volume = {280}, year = {2005}, month = {2005 Mar 25}, pages = {11422-31}, abstract = {

Limited thermostability of antibiotic resistance markers has restricted genetic research in the field of extremely thermophilic Archaea and bacteria. In this study, we used directed evolution and selection in the thermophilic bacterium Thermus thermophilus HB27 to find thermostable variants of a bleomycin-binding protein from the mesophilic bacterium Streptoalloteichus hindustanus. In a single selection round, we identified eight clones bearing five types of double mutated genes that provided T. thermophilus transformants with bleomycin resistance at 77 degrees C, while the wild-type gene could only do so up to 65 degrees C. Only six different amino acid positions were altered, three of which were glycine residues. All variant proteins were produced in Escherichia coli and analyzed biochemically for thermal stability and functionality at high temperature. A synthetic mutant resistance gene with low GC content was designed that combined four substitutions. The encoded protein showed up to 17 degrees C increased thermostability and unfolded at 85 degrees C in the absence of bleomycin, whereas in its presence the protein unfolded at 100 degrees C. Despite these highly thermophilic properties, this mutant was still able to function normally at mesophilic temperatures in vivo. The mutant protein was co-crystallized with bleomycin, and the structure of the binary complex was determined to a resolution of 1.5 A. Detailed structural analysis revealed possible molecular mechanisms of thermostabilization and enhanced antibiotic binding, which included the introduction of an intersubunit hydrogen bond network, improved hydrophobic packing of surface indentations, reduction of loop flexibility, and alpha-helix stabilization. The potential applicability of the thermostable selection marker is discussed.

}, keywords = {Amino Acid Sequence, Bacterial, Bacterial Proteins, Biological Markers, Bleomycin, Carrier Proteins, Drug Resistance, Genetic Engineering, Hydrogen Bonding, Hydrophobic and Hydrophilic Interactions, Molecular Sequence Data, Protein Folding, Protein Structure, Secondary, Temperature, Thermus thermophilus}, issn = {0021-9258}, doi = {10.1074/jbc.M413623200}, author = {Brouns, Stan J J and Wu, Hao and Akerboom, Jasper and Turnbull, Andrew P and de Vos, Willem M and van der Oost, John} } @article {1742, title = {Ensemble coding of vocal control in birdsong.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {25}, year = {2005}, month = {2005 Jan 19}, pages = {652-61}, abstract = {

Zebra finch song is represented in the high-level motor control nucleus high vocal center (HVC) (Reiner et al., 2004) as a sparse sequence of spike bursts. In contrast, the vocal organ is driven continuously by smoothly varying muscle control signals. To investigate how the sparse HVC code is transformed into continuous vocal patterns, we recorded in the singing zebra finch from populations of neurons in the robust nucleus of arcopallium (RA), a premotor area intermediate between HVC and the motor neurons. We found that highly similar song elements are typically produced by different RA ensembles. Furthermore, although the song is modulated on a wide range of time scales (10-100 ms), patterns of neural activity in RA change only on a short time scale (5-10 ms). We suggest that song is driven by a dynamic circuit that operates on a single underlying clock, and that the large convergence of RA neurons to vocal control muscles results in a many-to-one mapping of RA activity to song structure. This permits rapidly changing RA ensembles to drive both fast and slow acoustic modulations, thereby transforming the sparse HVC code into a continuous vocal pattern.

}, keywords = {Action Potentials, Animal, Animals, Brain, Finches, Male, Models, Muscles, Neural Pathways, Neurological, Neurons, Sound Spectrography, Time Factors, Vocalization}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3036-04.2005}, author = {Leonardo, Anthony and Fee, Michale S} } @article {6363, title = {Establishing genetic transformation for comparative developmental studies in the crustacean Parhyale hawaiensis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, year = {2005}, month = {2005 May 31}, pages = {7888-93}, abstract = {

The amphipod crustacean Parhyale hawaiensis has been put forward as an attractive organism for evolutionary developmental comparisons, and considerable effort is being invested in isolating developmental genes and studying their expression patterns in this species. The scope of these studies could be significantly expanded by establishing means for genetic manipulation that would enable direct studies of gene functions to be carried out in this species. Here, we report the use of the Minos transposable element for the genetic transformation of P. hawaiensis. Transformed amphipods can be obtained from approximately 30\% of surviving individuals injected with both a Minos element carrying the 3xP3-DsRed fluorescent marker and with mRNA encoding the Minos transposase. Integral copies of the transposon are inserted into the host genome and are stably inherited through successive generations. We have used reporter constructs to identify a muscle-specific regulatory element from Parhyale, demonstrating that this transformation vector can be used to test the activity of cis-regulatory elements in this species. The relatively high efficiency of this transgenic methodology opens new opportunities for the direct study of cis-regulatory elements and gene functions in Parhyale, allowing functional studies to be carried out beyond previously established model systems in insects.

}, keywords = {Amphipoda, Animal, Animals, Cloning, Developmental Biology, DNA Primers, DNA Transposable Elements, Gene Transfer Techniques, Genetic, HSP70 Heat-Shock Proteins, Luminescent Proteins, Microinjections, Models, Molecular, Plasmids, Transformation, Transposases}, issn = {0027-8424}, doi = {10.1073/pnas.0501101102}, author = {Pavlopoulos, Anastasios and Averof, Michalis} } @article {45924, title = {Factors mediating powerful voltage attenuation along CA1 pyramidal neuron dendrites.}, journal = {J Physiol}, volume = {568}, year = {2005}, month = {2005 Oct 1}, pages = {69-82}, abstract = {

We performed simultaneous patch-electrode recordings from the soma and apical dendrite of CA1 pyramidal neurons in hippocampal slices, in order to determine the degree of voltage attenuation along CA1 dendrites. Fifty per cent attenuation of steady-state somatic voltage changes occurred at a distance of 238 microm from the soma in control and 409 microm after blocking the hyperpolarization-activated (H) conductance. The morphology of three neurons was reconstructed and used to generate computer models, which were adjusted to fit the somatic and dendritic voltage responses. These models identify several factors contributing to the voltage attenuation along CA1 dendrites, including high axial cytoplasmic resistivity, low membrane resistivity, and large H conductance. In most cells the resting membrane conductances, including the H conductances, were larger in the dendrites than the soma. Simulations suggest that synaptic potentials attenuate enormously as they propagate from the dendrite to the soma, with greater than 100-fold attenuation for synapses on many small, distal dendrites. A prediction of this powerful EPSP attenuation is that distal synaptic inputs are likely only to be effective in the presence of conductance scaling, dendritic excitability, or both.

}, keywords = {Animals, Dendrites, Excitatory Postsynaptic Potentials, Hippocampus, In Vitro Techniques, Male, Models, Neurological, Neural Conduction, Patch-Clamp Techniques, Pyramidal Cells, Rats, Rats, Wistar, Synaptic Transmission}, issn = {0022-3751}, doi = {10.1113/jphysiol.2005.086793}, author = {Golding, Nace L and Mickus, Timothy J and Katz, Yael and Kath, William L and Spruston, Nelson} } @article {2158, title = {Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy.}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, volume = {27}, year = {2005}, month = {2005 Aug}, pages = {1226-38}, abstract = {

Feature selection is an important problem for pattern classification systems. We study how to select good features according to the maximal statistical dependency criterion based on mutual information. Because of the difficulty in directly implementing the maximal dependency condition, we first derive an equivalent form, called minimal-redundancy-maximal-relevance criterion (mRMR), for first-order incremental feature selection. Then, we present a two-stage feature selection algorithm by combining mRMR and other more sophisticated feature selectors (e.g., wrappers). This allows us to select a compact set of superior features at very low cost. We perform extensive experimental comparison of our algorithm and other methods using three different classifiers (naive Bayes, support vector machine, and linear discriminate analysis) and four different data sets (handwritten digits, arrhythmia, NCI cancer cell lines, and lymphoma tissues). The results confirm that mRMR leads to promising improvement on feature selection and classification accuracy.

}, keywords = {Algorithms, Artificial Intelligence, Automated, Cluster Analysis, Computer Simulation, Computer-Assisted, Diagnosis, Humans, Information Storage and Retrieval, Models, Neoplasms, Numerical Analysis, Pattern Recognition, Statistical}, issn = {0162-8828}, doi = {10.1007/s12021-010-9090-x}, author = {Peng, Hanchuan and Long, Fuhui and Ding, Chris} } @article {45759, title = {Genetic mapping of aphicarus -- a sex-linked locus controlling a wing polymorphism in the pea aphid (Acyrthosiphon pisum).}, journal = {Heredity (Edinb)}, volume = {94}, year = {2005}, month = {2005 Apr}, pages = {435-42}, abstract = {

We have initiated research to determine the genetic basis of a male wing polymorphism in the pea aphid Acyrthosiphon pisum (Hemiptera: Aphididae). Previous studies showed that this polymorphism is controlled by a single biallelic locus, which we name aphicarus (api), on the X chromosome. Our objectives were to confirm that api segregates as a polymorphism of a single gene on the X chromosome, and to obtain molecular markers flanking api that can be used as a starting point for high-resolution genetic and physical mapping of the target region, which will ultimately allow the cloning of api. We have established an F2 population segregating for api and have generated X-linked AFLP markers. The segregation pattern of api in the F2 population shows that the male wing polymorphism segregates as a polymorphism of a single gene, or set of closely linked genes on the X chromosome. Using a subset of 78 F2 males, we have constructed a linkage map of the chromosomal region encompassing api using seven AFLP markers. The map spans 74.1 cM and we have mapped api to an interval of 10 cM. In addition, we confirmed X linkage of our AFLP markers and api by using one X-linked marker developed in an earlier study. Our study presents the first mapping of a gene with known function in aphids, and the results indicate that target gene mapping in aphids is feasible.

}, keywords = {Animals, Aphids, Chromosome Mapping, Genetic Markers, Linkage Disequilibrium, Male, Polymorphism, Genetic, Quantitative Trait Loci, Random Amplified Polymorphic DNA Technique, Wing, X Chromosome}, issn = {0018-067X}, doi = {10.1038/sj.hdy.6800633}, author = {Braendle, C and Caillaud, M C and Stern, D L} } @article {45756, title = {Genetic variation for an aphid wing polyphenism is genetically linked to a naturally occurring wing polymorphism.}, journal = {Proc Biol Sci}, volume = {272}, year = {2005}, month = {2005 Mar 22}, pages = {657-64}, abstract = {

Many polyphenisms are examples of adaptive phenotypic plasticity where a single genotype produces distinct phenotypes in response to environmental cues. Such alternative phenotypes occur as winged and wingless parthenogenetic females in the pea aphid (Acyrthosiphon pisum). However, the proportion of winged females produced in response to a given environmental cue varies between clonal genotypes. Winged and wingless phenotypes also occur in males of the sexual generation. In contrast to parthenogenetic females, wing production in males is environmentally insensitive and controlled by the sex-linked, biallelic locus, aphicarus (api). Hence, environmental or genetic cues induce development of winged and wingless phenotypes at different stages of the pea aphid life cycle. We have tested whether allelic variation at the api locus explains genetic variation in the propensity to produce winged females. We assayed clones from an F2 cross that were heterozygous or homozygous for alternative api alleles for their propensity to produce winged offspring. We found that clones with different api genotypes differed in their propensity to produce winged offspring. The results indicate genetic linkage of factors controlling the female wing polyphenism and male wing polymorphism. This finding is consistent with the hypothesis that genotype by environment interaction at the api locus explains genetic variation in the environmentally cued wing polyphenism.

}, keywords = {Alleles, Analysis of Variance, Animals, Aphids, Crosses, Genetic, Crowding, Female, Food Deprivation, Genes, Insect, Genetic Linkage, Genetic Variation, Genotype, Male, Phenotype, Wing}, issn = {0962-8452}, doi = {10.1098/rspb.2004.2995}, author = {Braendle, Christian and Friebe, Ilvy and Caillaud, Marina C and Stern, David L} } @article {1250, title = {Geometric and functional organization of cortical circuits.}, journal = {Nature Neuroscience}, volume = {8}, year = {2005}, month = {2005 Jun}, pages = {782-90}, abstract = {

Can neuronal morphology predict functional synaptic circuits? In the rat barrel cortex, {\textquoteright}barrels{\textquoteright} and {\textquoteright}septa{\textquoteright} delineate an orderly matrix of cortical columns. Using quantitative laser scanning photostimulation we measured the strength of excitatory projections from layer 4 (L4) and L5A to L2/3 pyramidal cells in barrel- and septum-related columns. From morphological reconstructions of excitatory neurons we computed the geometric circuit predicted by axodendritic overlap. Within most individual projections, functional inputs were predicted by geometry and a single scale factor, the synaptic strength per potential synapse. This factor, however, varied between projections and, in one case, even within a projection, up to 20-fold. Relationships between geometric overlap and synaptic strength thus depend on the laminar and columnar locations of both the pre- and postsynaptic neurons, even for neurons of the same type. A large plasticity potential appears to be incorporated into these circuits, allowing for functional {\textquoteright}tuning{\textquoteright} with fixed axonal and dendritic arbor geometry.

}, keywords = {Animals, Axons, Brain Mapping, Cell Shape, Dendrites, Electric Stimulation, Excitatory Postsynaptic Potentials, Image Cytometry, Lasers, Lysine, Neural Pathways, Neuronal Plasticity, Organ Culture Techniques, Photic Stimulation, Pyramidal Cells, Rats, Somatosensory Cortex, Sprague-Dawley, Synapses, Synaptic Transmission, Ultraviolet Rays}, issn = {1097-6256}, doi = {10.1016/j.tins.2005.05.006}, author = {Shepherd, Gordon M G and Stepanyants, Armen and Bureau, Ingrid and Chklovskii, Dmitri and Svoboda, Karel} } @article {46631, title = {GPCR signaling is required for blood-brain barrier formation in drosophila.}, journal = {Cell}, volume = {123}, year = {2005}, month = {2005 Oct 7}, pages = {133-44}, abstract = {

The blood-brain barrier of Drosophila is established by surface glia, which ensheath the nerve cord and insulate it against the potassium-rich hemolymph by forming intercellular septate junctions. The mechanisms underlying the formation of this barrier remain obscure. Here, we show that the G protein-coupled receptor (GPCR) Moody, the G protein subunits G alpha i and G alpha o, and the regulator of G protein signaling Loco are required in the surface glia to achieve effective insulation. Our data suggest that the four proteins act in a complex common pathway. At the cellular level, the components function by regulating the cortical actin and thereby stabilizing the extended morphology of the surface glia, which in turn is necessary for the formation of septate junctions of sufficient length to achieve proper sealing of the nerve cord. Our study demonstrates the importance of morphogenetic regulation in blood-brain barrier development and places GPCR signaling at its core.

}, keywords = {Actins, Alternative Splicing, Animals, Blood-Brain Barrier, Brain, Drosophila melanogaster, Drosophila Proteins, Endothelium, Vascular, GTP-Binding Protein alpha Subunits, Gi-Go, Microscopy, Electron, Transmission, Nerve Tissue Proteins, Neuroglia, Receptors, G-Protein-Coupled, Signal Transduction, Tight Junctions}, issn = {0092-8674}, doi = {10.1016/j.cell.2005.08.037}, author = {Schwabe, Tina and Bainton, Roland J and Fetter, Richard D and Heberlein, Ulrike and Gaul, Ulrike} } @article {5489, title = {The hangover gene defines a stress pathway required for ethanol tolerance development.}, journal = {Nature}, volume = {436}, year = {2005}, month = {2005 Aug 11}, pages = {845-7}, abstract = {

Repeated alcohol consumption leads to the development of tolerance, simply defined as an acquired resistance to the physiological and behavioural effects of the drug. This tolerance allows increased alcohol consumption, which over time leads to physical dependence and possibly addiction. Previous studies have shown that Drosophila develop ethanol tolerance, with kinetics of acquisition and dissipation that mimic those seen in mammals. This tolerance requires the catecholamine octopamine, the functional analogue of mammalian noradrenaline. Here we describe a new gene, hangover, which is required for normal development of ethanol tolerance. hangover flies are also defective in responses to environmental stressors, such as heat and the free-radical-generating agent paraquat. Using genetic epistasis tests, we show that ethanol tolerance in Drosophila relies on two distinct molecular pathways: a cellular stress pathway defined by hangover, and a parallel pathway requiring octopamine. hangover encodes a large nuclear zinc-finger protein, suggesting a role in nucleic acid binding. There is growing recognition that stress, at both the cellular and systemic levels, contributes to drug- and addiction-related behaviours in mammals. Our studies suggest that this role may be conserved across evolution.

}, keywords = {Alcoholism, Animals, Drosophila melanogaster, Drosophila Proteins, Drug Tolerance, Ethanol, Heat-Shock Response, Mutation, Physiological, Stress, Zinc Fingers}, issn = {1476-4687}, doi = {10.1038/nature03864}, author = {Scholz, Henrike and Franz, Mirjam and Heberlein, Ulrike} } @article {1251, title = {Highly nonrandom features of synaptic connectivity in local cortical circuits.}, journal = {PLoS Biology}, volume = {3}, year = {2005}, month = {2005 Mar}, pages = {e68}, abstract = {

How different is local cortical circuitry from a random network? To answer this question, we probed synaptic connections with several hundred simultaneous quadruple whole-cell recordings from layer 5 pyramidal neurons in the rat visual cortex. Analysis of this dataset revealed several nonrandom features in synaptic connectivity. We confirmed previous reports that bidirectional connections are more common than expected in a random network. We found that several highly clustered three-neuron connectivity patterns are overrepresented, suggesting that connections tend to cluster together. We also analyzed synaptic connection strength as defined by the peak excitatory postsynaptic potential amplitude. We found that the distribution of synaptic connection strength differs significantly from the Poisson distribution and can be fitted by a lognormal distribution. Such a distribution has a heavier tail and implies that synaptic weight is concentrated among few synaptic connections. In addition, the strengths of synaptic connections sharing pre- or postsynaptic neurons are correlated, implying that strong connections are even more clustered than the weak ones. Therefore, the local cortical network structure can be viewed as a skeleton of stronger connections in a sea of weaker ones. Such a skeleton is likely to play an important role in network dynamics and should be investigated further.

}, keywords = {Animals, Cell Communication, Neural Pathways, Neuronal Plasticity, Neurons, Rats, Signal Transduction, Synapses, Visual Cortex}, issn = {1545-7885}, doi = {10.1016/j.tins.2005.05.006}, author = {Song, Sen and Sj{\"o}str{\"o}m, Per Jesper and Reigl, Markus and Nelson, Sacha and Chklovskii, Dmitri B} } @article {2369, title = {How to find decision makers in neural networks.}, journal = {Biological Cybernetics}, volume = {93}, year = {2005}, month = {2005 Dec}, pages = {447-62}, abstract = {

Nervous systems often face the problem of classifying stimuli and making decisions based on these classifications. The neurons involved in these tasks can be characterized as sensory or motor, according to their correlation with sensory stimulus or motor response. In this study we define a third class of neurons responsible for making perceptual decisions. Our mathematical formalism enables the weighting of neuronal units according to their contribution to decision making, thus narrowing the field for more detailed studies of underlying mechanisms. We develop two definitions of a contribution to decision making. The first definition states that decision making activity can be found at the points of emergence for behavioral correlations in the system. The second definition involves the study of propagation of noise in the network. The latter definition is shown to be equivalent to the first one in the cases when they can be compared. Our results suggest a new approach to analyzing decision making networks.

}, keywords = {Animals, Computer Simulation, Decision Making, Electric Stimulation, Humans, Models, Nerve Net, Neural Networks (Computer), Neurological, Neurons, Nonlinear Dynamics, Stochastic Processes}, issn = {0340-1200}, doi = {10.1523/JNEUROSCI.3613-08.2008}, author = {Koulakov, Alexei A and Rinberg, Dmitry A and Tsigankov, Dmitry N} } @article {5821, title = {An in situ hybridization protocol for planarian embryos: monitoring myosin heavy chain gene expression.}, journal = {Development Genes \& Evolution}, volume = {215}, year = {2005}, month = {2005 Sep}, pages = {482-88}, abstract = {

The monitoring of gene expression is fundamental for understanding developmental biology. Here we report a successful experimental protocol for in situ hybridization in both whole-mount and sectioned planarian embryos. Conventional in situ hybridization techniques in developmental biology are used on whole-mount preparations. However, given that the inherent lack of external morphological markers in planarian embryos hinders the proper interpretation of gene expression data in whole-mount preparations, here we used sectioned material. We discuss the advantages of sectioned versus whole-mount preparations, namely, better probe penetration, improved tissue preservation, and the possibility to interpret gene expression in relation to internal morphological markers such as the epidermis, the embryonic and definitive pharynges, and the gastrodermis. Optimal fixatives and embedding methods for sectioning are also discussed.

}, keywords = {Animals, Developmental, Dose-Response Relationship, Drug, Embryo, Epidermis, Gene Expression Regulation, In Situ Hybridization, Myosin Heavy Chains, Nonmammalian, Planarians, Time Factors, Tissue Preservation}, issn = {0949-944X}, doi = {10.1007/s00427-005-0003-1}, author = {Cardona, Albert and Fern{\'a}ndez, Juani and Solana, Jordi and Romero, Rafael} } @article {2412, title = {In vitro analysis of huntingtin-mediated transcriptional repression reveals multiple transcription factor targets.}, journal = {Cell}, volume = {123}, year = {2005}, month = {2005 Dec 29}, pages = {1241-53}, abstract = {

Transcriptional dysregulation has emerged as a potentially important pathogenic mechanism in Huntington{\textquoteright}s disease, a neurodegenerative disorder associated with polyglutamine expansion in the huntingtin (htt) protein. Here, we report the development of a biochemically defined in vitro transcription assay that is responsive to mutant htt. We demonstrate that both gene-specific activator protein Sp1 and selective components of the core transcription apparatus, including TFIID and TFIIF, are direct targets inhibited by mutant htt in a polyglutamine-dependent manner. The RAP30 subunit of TFIIF specifically interacts with mutant htt both in vitro and in vivo to interfere with formation of the RAP30-RAP74 native complex. Importantly, overexpression of RAP30 in cultured primary striatal cells protects neurons from mutant htt-induced cellular toxicity and alleviates the transcriptional inhibition of the dopamine D2 receptor gene by mutant htt. Our results suggest a mutant htt-directed repression mechanism involving multiple specific components of the basal transcription apparatus.

}, keywords = {Animals, Biological Assay, Cell-Free System, Cells, Cercopithecus aethiops, COS Cells, Cultured, Dopamine D2, Down-Regulation, Genetic, Mice, Mutation, Nerve Tissue Proteins, Neurons, Nuclear Proteins, Protein Binding, Protein Subunits, Rats, Receptors, Sp1 Transcription Factor, TFII, Transcription, Transcription Factor TFIID, Transcription Factors}, issn = {0092-8674}, doi = {10.1073/pnas.1100640108}, author = {Zhai, Weiguo and Jeong, Hyunkyung and Cui, Libin and Krainc, Dimitri and Tjian, Robert} } @article {5490, title = {Insulin signaling in the nervous system regulates ethanol intoxication in Drosophila melanogaster.}, journal = {Nature Neuroscience}, volume = {8}, year = {2005}, month = {2005 Jan}, pages = {18-9}, abstract = {

The insulin signaling pathway regulates multiple physiological processes, including energy metabolism, organismal growth, aging and reproduction. Here we show that genetic manipulations in Drosophila melanogaster that impair the function of insulin-producing cells or of the insulin-receptor signaling pathway in the nervous system lead to increased sensitivity to the intoxicating effects of ethanol. These findings suggest a previously unknown role for this highly conserved pathway in regulating the behavioral responses to an addictive drug.

}, keywords = {Alcoholic Intoxication, Animals, Brain, Drosophila melanogaster, Ethanol, Insulin, Neurons, Receptor, Signal Transduction}, issn = {1097-6256}, doi = {10.1038/nn1363}, author = {Corl, Ammon B and Rodan, Aylin R and Heberlein, Ulrike} } @article {1985, title = {Intraglomerular inhibition: signaling mechanisms of an olfactory microcircuit.}, journal = {Nature Neuroscience}, volume = {8}, year = {2005}, month = {2005 Mar}, pages = {354-64}, abstract = {

Microcircuits composed of principal neuron and interneuron dendrites have an important role in shaping the representation of sensory information in the olfactory bulb. Here we establish the physiological features governing synaptic signaling in dendrodendritic microcircuits of olfactory bulb glomeruli. We show that dendritic gamma-aminobutyric acid (GABA) release from periglomerular neurons mediates inhibition of principal tufted cells, retrograde inhibition of sensory input and lateral signaling onto neighboring periglomerular cells. We find that L-type dendritic Ca(2+) spikes in periglomerular cells underlie dendrodendritic transmission by depolarizing periglomerular dendrites and activating P/Q type channels that trigger GABA release. Ca(2+) spikes in periglomerular cells are evoked by powerful excitatory inputs from a single principal cell, and glutamate release from the dendrites of single principal neurons activates a large ensemble of periglomerular cells.

}, keywords = {1, 3-Pyridinecarboxylic acid, 4-dihydro-2, 6-dimethyl-5-nitro-4-(2-(trifluoromethyl)phenyl)-, Animals, Bicuculline, Cadmium, Calcium, Calcium Channel Agonists, Calcium Channel Blockers, Calcium Signaling, Chelating Agents, Dendrites, Diagnostic Imaging, Dihydropyridines, Dose-Response Relationship, Drug, Drug Interactions, Egtazic Acid, Electric Stimulation, GABA Antagonists, gamma-Aminobutyric Acid, Membrane Potentials, Methyl ester, Neural Conduction, Neural Inhibition, Neural Networks (Computer), Neurons, Newborn, Nickel, Nimodipine, Olfactory Bulb, Patch-Clamp Techniques, Phosphinic Acids, Potassium, Propanolamines, Pyrimidines, Rats, Signal Transduction, Sprague-Dawley, Synapses, Synaptic Transmission, Tetrodotoxin, Time Factors, Valine}, issn = {1097-6256}, doi = {10.1038/nn1403}, author = {Murphy, Gabe J and Darcy, Daniel P and Isaacson, Jeffry S} } @proceedings {3305, title = {Joint nonparametric alignment for analyzing spatial gene expression patterns of Drosophila imaginal discs.}, volume = {2}, year = {2005}, month = {2005 Jun 20}, pages = {755-60}, abstract = {

To compare spatial patterns of gene expression, one must analyze a large number of images as current methods are only able to measure a small number of genes at a time. Bringing images of corresponding tissues into alignment is a critical first step in making a meaningful comparative analysis of these spatial patterns. Significant image noise and variability in the shapes make it hard to pick a canonical shape model. In this paper, we address these problems by combining segmentation and unsupervised shape learning algorithms. We first segment images to acquire structures of interest, then jointly align the shapes of these acquired structures using an unsupervised nonparametric maximum likelihood algorithm along the lines of congealing, while simultaneously learning the underlying shape model and associated transformations. The learned transformations are applied to corresponding images to bring them into alignment in one step. We demonstrate the results for images of various classes of Drosophila imaginal discs and discuss the methodology used for a quantitative analysis of spatial gene expression patterns.

}, author = {Ahammad, Parvez and Harmon, C and Hammonds, Ann S and Sastry, S and Rubin, Gerald M} } @article {46306, title = {Learning in realistic networks of spiking neurons and spike-driven plastic synapses.}, journal = {European Journal of Neuroscience}, volume = {21}, year = {2005}, month = {2005 Jun}, pages = {3143-60}, abstract = {

We have used simulations to study the learning dynamics of an autonomous, biologically realistic recurrent network of spiking neurons connected via plastic synapses, subjected to a stream of stimulus-delay trials, in which one of a set of stimuli is presented followed by a delay. Long-term plasticity, produced by the neural activity experienced during training, structures the network and endows it with active (working) memory, i.e. enhanced, selective delay activity for every stimulus in the training set. Short-term plasticity produces transient synaptic depression. Each stimulus used in training excites a selective subset of neurons in the network, and stimuli can share neurons (overlapping stimuli). Long-term plasticity dynamics are driven by presynaptic spikes and coincident postsynaptic depolarization; stability is ensured by a refresh mechanism. In the absence of stimulation, the acquired synaptic structure persists for a very long time. The dependence of long-term plasticity dynamics on the characteristics of the stimulus response (average emission rates, time course and synchronization), and on the single-cell emission statistics (coefficient of variation) is studied. The study clarifies the specific roles of short-term synaptic depression, NMDA receptors, stimulus representation overlaps, selective stimulation of inhibition, and spike asynchrony during stimulation. Patterns of network spiking activity before, during and after training reproduce most of the in vivo physiological observations in the literature.

}, keywords = {Action Potentials, Animals, Central Nervous System, Electric Stimulation, Humans, Memory, Short-Term, Nerve Net, Neural Inhibition, Neural Networks (Computer), Neural Pathways, Neuronal Plasticity, Neurons, Receptors, N-Methyl-D-Aspartate, Synapses, Synaptic Transmission}, issn = {0953-816X}, doi = {10.1111/j.1460-9568.2005.04087.x}, author = {Mongillo, Gianluigi and Curti, Emanuele and Romani, Sandro and Amit, Daniel J} } @article {45957, title = {Lipid-protein interactions in double-layered two-dimensional AQP0 crystals.}, journal = {Nature}, volume = {438}, year = {2005}, month = {2005 Dec 1}, pages = {633-8}, abstract = {

Lens-specific aquaporin-0 (AQP0) functions as a specific water pore and forms the thin junctions between fibre cells. Here we describe a 1.9 A resolution structure of junctional AQP0, determined by electron crystallography of double-layered two-dimensional crystals. Comparison of junctional and non-junctional AQP0 structures shows that junction formation depends on a conformational switch in an extracellular loop, which may result from cleavage of the cytoplasmic amino and carboxy termini. In the centre of the water pathway, the closed pore in junctional AQP0 retains only three water molecules, which are too widely spaced to form hydrogen bonds with each other. Packing interactions between AQP0 tetramers in the crystalline array are mediated by lipid molecules, which assume preferred conformations. We were therefore able to build an atomic model for the lipid bilayer surrounding the AQP0 tetramers, and we describe lipid-protein interactions.

}, keywords = {Animals, Aquaporins, Crystallization, Crystallography, Hydrogen Bonding, Lens, Crystalline, Lipid Bilayers, Membrane Lipids, Models, Molecular, Protein Binding, Protein Structure, Quaternary, Sheep, Water}, issn = {1476-4687}, doi = {10.1038/nature04321}, author = {Gonen, Tamir and Cheng, Yifan and Sliz, Piotr and Hiroaki, Yoko and Fujiyoshi, Yoshinori and Harrison, Stephen C and Walz, Thomas} } @article {2414, title = {Maintenance of spermatogenesis requires TAF4b, a gonad-specific subunit of TFIID.}, journal = {Genes \& Development}, volume = {19}, year = {2005}, month = {2005 Apr 1}, pages = {794-803}, abstract = {

The establishment and maintenance of spermatogenesis in mammals requires specialized networks of gene expression programs in the testis. The gonad-specific TAF4b component of TFIID (formerly TAF(II)105) is a transcriptional regulator enriched in the mouse testis. Herein we show that TAF4b is required for maintenance of spermatogenesis in the mouse. While young Taf4b-null males are initially fertile, Taf4b-null males become infertile by 3 mo of age and eventually exhibit seminiferous tubules devoid of germ cells. At birth, testes of Taf4b-null males appear histologically normal; however, at post-natal day 3 gonocyte proliferation is impaired and expression of spermatogonial stem cell markers c-Ret, Plzf, and Stra8 is reduced. Together, these data indicate that TAF4b is required for the precise expression of gene products essential for germ cell proliferation and suggest that TAF4b may be required for the regulation of spermatogonial stem cell specification and proliferation that is obligatory for normal spermatogenic maintenance in the adult.

}, keywords = {Aging, Animals, Cell Division, Infertility, Male, Mice, Spermatids, Spermatogenesis, Spermatogonia, TATA-Binding Protein Associated Factors, Testis, Transcription Factor TFIID}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Falender, Allison E and Freiman, Richard N and Geles, Kenneth G and Lo, Kirk C and Hwang, KeumSil and Lamb, Dolores J and Morris, Patricia L and Tjian, Robert and Richards, JoAnne S} } @article {1409, title = {A major role for zygotic hunchback in patterning the Nasonia embryo.}, journal = {Development }, volume = {132}, year = {2005}, month = {2005 Aug}, pages = {3705-15}, abstract = {

Developmental genetic analysis has shown that embryos of the parasitoid wasp Nasonia vitripennis depend more on zygotic gene products to direct axial patterning than do Drosophila embryos. In Drosophila, anterior axial patterning is largely established by bicoid, a rapidly evolving maternal-effect gene, working with hunchback, which is expressed both maternally and zygotically. Here, we focus on a comparative analysis of Nasonia hunchback function and expression. We find that a lesion in Nasonia hunchback is responsible for the severe zygotic headless mutant phenotype, in which most head structures and the thorax are deleted, as are the three most posterior abdominal segments. This defines a major role for zygotic Nasonia hunchback in anterior patterning, more extensive than the functions described for hunchback in Drosophila or Tribolium. Despite the major zygotic role of Nasonia hunchback, we find that it is strongly expressed maternally, as well as zygotically. Nasonia Hunchback embryonic expression appears to be generally conserved; however, the mRNA expression differs from that of Drosophila hunchback in the early blastoderm. We also find that the maternal hunchback message decays at an earlier developmental stage in Nasonia than in Drosophila, which could reduce the relative influence of maternal products in Nasonia embryos. Finally, we extend the comparisons of Nasonia and Drosophila hunchback mutant phenotypes, and propose that the more severe Nasonia hunchback mutant phenotype may be a consequence of differences in functionally overlapping regulatory circuitry.

}, keywords = {Animals, Base Sequence, Body Patterning, Developmental, DNA-Binding Proteins, Drosophila Proteins, Gene Expression Regulation, Genetic Linkage, HMGB Proteins, In Situ Hybridization, Insect Proteins, Messenger, Molecular Sequence Data, RNA, Sequence Alignment, Stored, TCF Transcription Factors, Transcription Factor 7-Like 1 Protein, Transcription Factors, Wasps}, issn = {0950-1991}, doi = {10.1242/dev.01939}, author = {Pultz, Mary Anne and Westendorf, Lori and Gale, Samuel D and Hawkins, Kyle and Lynch, Jeremy and Pitt, Jason N and Reeves, Nick L and Yao, Jennifer C Y and Small, Stephen and Desplan, Claude and Leaf, David S} } @article {1138, title = {Male-specific fruitless specifies the neural substrates of Drosophila courtship behaviour.}, journal = {Nature}, volume = {436}, year = {2005}, month = {2005 Jul 21}, pages = {395-400}, abstract = {

Robust innate behaviours are attractive systems for genetically dissecting how environmental cues are perceived and integrated to generate complex behaviours. During courtship, Drosophila males engage in a series of innate, stereotyped behaviours that are coordinated by specific sensory cues. However, little is known about the specific neural substrates mediating this complex behavioural programme. Genetic, developmental and behavioural studies have shown that the fruitless (fru) gene encodes a set of male-specific transcription factors (FruM) that act to establish the potential for courtship in Drosophila. FruM proteins are expressed in approximately 2\% of central nervous system neurons, at least one subset of which coordinates the component behaviours of courtship. Here we have inserted the yeast GAL4 gene into the fru locus by homologous recombination and show that (1) FruM is expressed in subsets of all peripheral sensory systems previously implicated in courtship, (2) inhibition of FruM function in olfactory system components reduces olfactory-dependent changes in courtship behaviour, (3) transient inactivation of all FruM-expressing neurons abolishes courtship behaviour, with no other gross changes in general behaviour, and (4) {\textquoteright}masculinization{\textquoteright} of FruM-expressing neurons in females is largely sufficient to confer male courtship behaviour. Together, these data demonstrate that FruM proteins specify the neural substrates of male courtship.

}, keywords = {Animal, Animals, Central Nervous System, Courtship, Developmental, Drosophila melanogaster, Drosophila Proteins, Female, Gene Expression Regulation, Male, Nerve Tissue Proteins, Neurons, Sex Characteristics, Sexual Behavior, Transcription Factors}, issn = {1476-4687}, doi = {10.1038/nature03859}, author = {Manoli, Devanand S and Foss, Margit and Villella, Adriana and Taylor, Barbara J and Hall, Jeffrey C and Baker, Bruce S} } @article {1438, title = {Many-particle tracking with nanometer resolution in three dimensions by reflection interference contrast microscopy.}, journal = {Langmuir: The ACS Journal of Surfaces and Colloids}, volume = {21}, year = {2005}, month = {2005 Jul 5}, pages = {6430-5}, abstract = {

We have developed and characterized a method, based on reflection interference contrast microscopy, to simultaneously determine the three-dimensional positions of multiple particles in a colloidal monolayer. To evaluate this method, the interaction of 6.8 microm (+/-5\%) diameter lipid-derivatized silica microspheres with an underlying planar borosilicate substrate is studied. Measured colloidal height distributions are consistent with expectations for an electrostatically levitated colloidal monolayer. The precision of the method is analyzed using experimental techniques in addition to computational bootstrapping algorithms. In its present implementation, this technique achieves 16 nm lateral and 1 nm vertical precision.

}, issn = {0743-7463}, doi = {10.1021/la050372r}, author = {Clack, Nathan G and Groves, Jay T} } @article {2317, title = {Mechanism of positive allosteric modulators acting on AMPA receptors.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {25}, year = {2005}, month = {2005 Sep 28}, pages = {9027-36}, abstract = {

Ligand-gated ion channels involved in the modulation of synaptic strength are the AMPA, kainate, and NMDA glutamate receptors. Small molecules that potentiate AMPA receptor currents relieve cognitive deficits caused by neurodegenerative diseases such as Alzheimer{\textquoteright}s disease and show promise in the treatment of depression. Previously, there has been limited understanding of the molecular mechanism of action for AMPA receptor potentiators. Here we present cocrystal structures of the glutamate receptor GluR2 S1S2 ligand-binding domain in complex with aniracetam [1-(4-methoxybenzoyl)-2-pyrrolidinone] or CX614 (pyrrolidino-1,3-oxazino benzo-1,4-dioxan-10-one), two AMPA receptor potentiators that preferentially slow AMPA receptor deactivation. Both potentiators bind within the dimer interface of the nondesensitized receptor at a common site located on the twofold axis of molecular symmetry. Importantly, the potentiator binding site is adjacent to the "hinge" in the ligand-binding core "clamshell" that undergoes conformational rearrangement after glutamate binding. Using rapid solution exchange, patch-clamp electrophysiology experiments, we show that point mutations of residues that interact with potentiators in the cocrystal disrupt potentiator function. We suggest that the potentiators slow deactivation by stabilizing the clamshell in its closed-cleft, glutamate-bound conformation.

}, keywords = {Allosteric Regulation, AMPA, Benzothiadiazines, Binding Sites, Cell Line, Crystallography, Dimerization, Drug Synergism, Electric Conductivity, Humans, Ligands, Molecular Conformation, Oxazines, Patch-Clamp Techniques, Protein Structure, Pyrrolidinones, Receptors, Tertiary, Time Factors}, issn = {1529-2401}, doi = {10.3389/fnana.2010.00147}, author = {Jin, Rongsheng and Clark, Suzanne and Weeks, Autumn M and Dudman, Joshua T and Gouaux, Eric and Partin, Kathryn M} } @article {2159, title = {Minimum redundancy feature selection from microarray gene expression data.}, journal = {Journal of Bioinformatics and Computational Biology}, volume = {3}, year = {2005}, month = {2005 Apr}, pages = {185-205}, abstract = {

How to selecting a small subset out of the thousands of genes in microarray data is important for accurate classification of phenotypes. Widely used methods typically rank genes according to their differential expressions among phenotypes and pick the top-ranked genes. We observe that feature sets so obtained have certain redundancy and study methods to minimize it. We propose a minimum redundancy - maximum relevance (MRMR) feature selection framework. Genes selected via MRMR provide a more balanced coverage of the space and capture broader characteristics of phenotypes. They lead to significantly improved class predictions in extensive experiments on 6 gene expression data sets: NCI, Lymphoma, Lung, Child Leukemia, Leukemia, and Colon. Improvements are observed consistently among 4 classification methods: Naive Bayes, Linear discriminant analysis, Logistic regression, and Support vector machines. SUPPLIMENTARY: The top 60 MRMR genes for each of the datasets are listed in http://crd.lbl.gov/\ cding/MRMR/. More information related to MRMR methods can be found at http://www.hpeng.net/.

}, keywords = {Algorithms, Automated, Discriminant Analysis, Gene Expression Profiling, Oligonucleotide Array Sequence Analysis, Pattern Recognition}, issn = {0219-7200}, doi = {10.1007/s12021-010-9090-x}, author = {Ding, Chris and Peng, Hanchuan} } @article {5898, title = {Molecular and genetic features of a labeled class of spinal substantia gelatinosa neurons in a transgenic mouse.}, journal = {Journal of Computational Neuroscience}, volume = {492}, year = {2005}, month = {2005 Nov 7}, pages = {90-100}, abstract = {

Genetic incorporation in a mouse of a transgene containing the prion promoter and the green fluorescent protein (GFP) coding sequence labels a set of substantia gelatinosa (SG) neurons (SG-GFP) homogenous in morphology, electrophysiology, and γ-amino-butyric acid expression. In the present analysis the SG-GFP neurons are established to have protein kinase C-βII immunoreactivity and to lack evidence for the presence of calbindin D-28k, parvalbumin, and protein kinase C-γ. These neurons were hyperpolarized by mediators of descending control, norepinephrine and serotonin. Sequential polymerase chain reactions established the insertion of the transgene to be in the receptor protein tyrosine phosphatase kappa (RPTP-κ) and the laminin receptor 1 (ribosomal protein SA) pseudogene 1 locus. RPTP-κ expression in both GFP-labeled dorsal root ganglia and SG neurons raises the possibility that homophilic interactions of RPTP-κ contribute to establishment of connections between specific classes of primary afferent and SG neurons.

}, issn = {0021-9967}, doi = {doi: 10.1002/cne.20709}, author = {Hantman, Adam W. and Perl, Edward R} } @article {2851, title = {Molecular genetic analysis of the yeast repressor Rfx1/Crt1 reveals a novel two-step regulatory mechanism.}, journal = {Molecular and Cellular Biology}, volume = {25}, year = {2005}, month = {2005 Sep}, pages = {7399-411}, abstract = {

In Saccharomyces cerevisiae, the repressor Crt1 and the global corepressor Ssn6-Tup1 repress the DNA damage-inducible ribonucleotide reductase (RNR) genes. Initiation of DNA damage signals causes the release of Crt1 and Ssn6-Tup1 from the promoter, coactivator recruitment, and derepression of transcription, indicating that Crt1 plays a crucial role in the switch between gene repression and activation. Here we have mapped the functional domains of Crt1 and identified two independent repression domains and a region required for gene activation. The N terminus of Crt1 is the major repression domain, it directly binds to the Ssn6-Tup1 complex, and its repression activities are dependent upon Ssn6-Tup1 and histone deacetylases (HDACs). In addition, we identified a C-terminal repression domain, which is independent of Ssn6-Tup1 and HDACs and functions at native genes in vivo. Furthermore, we show that TFIID and SWI/SNF bind to a region within the N terminus of Crt1, overlapping with but distinct from the Ssn6-Tup1 binding and repression domain, suggesting that Crt1 may have activator functions. Crt1 mutants were constructed to dissect its activator and repressor functions. All of the mutants were competent for repression of the DNA damage-inducible genes, but a majority were "derepression-defective" mutants. Further characterization of these mutants indicated that they are capable of receiving DNA damage signals and releasing the Ssn6-Tup1 complex from the promoter but are selectively impaired for TFIID and SWI/SNF recruitment. These results imply a two-step activation model of the DNA damage-inducible genes and that Crt1 functions as a signal-dependent dual-transcription activator and repressor that acts in a transient manner.

}, keywords = {Chromatin, DNA Damage, DNA-Binding Proteins, Epistasis, Fungal, Gene Expression Regulation, Genetic, Histone Deacetylases, Mutation, Nuclear Proteins, Protein Binding, Protein Structure, Repressor Proteins, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Structure-Activity Relationship, Tertiary, Transcriptional Activation}, issn = {0270-7306}, doi = {10.1128/MCB.25.17.7399-7411.2005}, author = {Zhang, Zhengjian and Reese, Joseph C} } @article {5488, title = {Moody encodes two GPCRs that regulate cocaine behaviors and blood-brain barrier permeability in Drosophila.}, journal = {Cell}, volume = {123}, year = {2005}, month = {2005 Oct 7}, pages = {145-56}, abstract = {

We identified moody in a genetic screen for Drosophila mutants with altered cocaine sensitivity. Hypomorphic mutations in moody cause an increased sensitivity to cocaine and nicotine exposure. In contrast, sensitivity to the acute intoxicating effects of ethanol is reduced. The moody locus encodes two novel GPCRs, Moody-alpha and Moody-beta. While identical in their membrane-spanning domains, the two Moody proteins differ in their long carboxy-terminal domains, which are generated by use of alternative reading frames. Both Moody forms are required for normal cocaine sensitivity, suggesting that they carry out distinct but complementary functions. Moody-alpha and Moody-beta are coexpressed in surface glia that surround the nervous system, where they are actively required to maintain the integrity of the blood-brain barrier in the adult fly. We propose that a Moody-mediated signaling pathway functions in glia to regulate nervous system insulation and drug-related behaviors.

}, keywords = {Alternative Splicing, Animal, Animals, Behavior, Blood-Brain Barrier, Brain, Cocaine, Cocaine-Related Disorders, Disease Models, Dopamine Uptake Inhibitors, Drosophila melanogaster, Drosophila Proteins, Drug Tolerance, G-Protein-Coupled, Male, Motor Activity, Neuroglia, Nicotine, Protein Structure, Receptors, Substance-Related Disorders, Tertiary}, issn = {0092-8674}, doi = {10.1016/j.cell.2005.07.029}, author = {Bainton, Roland J and Tsai, Linus T-Y and Schwabe, Tina and DeSalvo, Michael and Gaul, Ulrike and Heberlein, Ulrike} } @article {45757, title = {Natural selection and developmental constraints in the evolution of allometries.}, journal = {Science}, volume = {307}, year = {2005}, month = {2005 Feb 4}, pages = {718-20}, abstract = {

In animals, scaling relationships between appendages and body size exhibit high interspecific variation but low intraspecific variation. This pattern could result from natural selection for specific allometries or from developmental constraints on patterns of differential growth. We performed artificial selection on the allometry between forewing area and body size in a butterfly to test for developmental constraints, and then used the resultant increased range of phenotypic variation to quantify natural selection on the scaling relationship. Our results show that the short-term evolution of allometries is not limited by developmental constraints. Instead, scaling relationships are shaped by strong natural selection.

}, keywords = {Alleles, Animals, Biological Evolution, Body Size, Butterflies, Crosses, Genetic, Female, Flight, Animal, Genetic Variation, Male, Phenotype, Reproduction, Selection, Genetic, Wing}, issn = {1095-9203}, doi = {10.1126/science.1105409}, author = {Frankino, W Anthony and Zwaan, Bas J and Stern, David L and Brakefield, Paul M} } @article {1249, title = {Neurogeometry and potential synaptic connectivity.}, journal = {Trends in Neurosciences}, volume = {28}, year = {2005}, month = {2005 Jul}, pages = {387-94}, abstract = {

The advent of high-quality 3D reconstructions of neuronal arbors has revived the hope of inferring synaptic connectivity from the geometric shapes of axons and dendrites, or {\textquoteright}neurogeometry{\textquoteright}. A quantitative description of connectivity must be built on a sound theoretical framework. Here, we review recent developments in neurogeometry that can provide such a framework. We base the geometric description of connectivity on the concept of a {\textquoteright}potential synapse{\textquoteright}{\textendash}the close apposition between axons and dendrites necessary to form an actual synapse. In addition to describing potential synaptic connectivity in neuronal circuits, neurogeometry provides insight into basic features of functional connectivity, such as specificity and plasticity.

}, keywords = {Animals, Axons, Dendrites, Imaging, Models, Neural Pathways, Neurological, Neuronal Plasticity, Neurons, Synapses, Synaptic Transmission, Three-Dimensional}, issn = {0166-2236}, doi = {10.1016/j.tins.2005.05.006}, author = {Stepanyants, Armen and Chklovskii, Dmitri B} } @article {45755, title = {The origin of a mutualism: a morphological trait promoting the evolution of ant-aphid mutualisms.}, journal = {Evolution}, volume = {59}, year = {2005}, month = {2005 Apr}, pages = {921-6}, abstract = {

Mutualisms are mutually beneficial interactions between species and are fundamentally important at all levels of biological organization. It is not clear, however, why one species participates in a particular mutualism whereas another does not. Here we show that pre-existing traits can dispose particular species to evolve a mutualistic interaction. Combining morphological, ecological, and behavioral data in a comparative analysis, we show that resource use in Chaitophorus aphids (Hemiptera: Aphididae) modulates the origin of their mutualism with ants. We demonstrate that aphid species that feed on deeper phloem elements have longer mouthparts, that this inhibits their ability to withdraw their mouthparts and escape predators and that, consequently, this increases their need for protection by mutualist ants.

}, keywords = {Animals, Ants, Aphids, Biological Evolution, Body Weights and Measures, Feeding Behavior, Great Britain, Mouth, Symbiosis}, issn = {0014-3820}, author = {Shingleton, Alexander W and Stern, David L and Foster, William A} } @article {45901, title = {Output-mode transitions are controlled by prolonged inactivation of sodium channels in pyramidal neurons of subiculum.}, journal = {PLoS Biol}, volume = {3}, year = {2005}, month = {2005 Jun}, pages = {e175}, abstract = {

Transitions between different behavioral states, such as sleep or wakefulness, quiescence or attentiveness, occur in part through transitions from action potential bursting to single spiking. Cortical activity, for example, is determined in large part by the spike output mode from the thalamus, which is controlled by the gating of low-voltage-activated calcium channels. In the subiculum--the major output of the hippocampus--transitions occur from bursting in the delta-frequency band to single spiking in the theta-frequency band. We show here that these transitions are influenced strongly by the inactivation kinetics of voltage-gated sodium channels. Prolonged inactivation of sodium channels is responsible for an activity-dependent switch from bursting to single spiking, constituting a novel mechanism through which network dynamics are controlled by ion channel gating.

}, keywords = {Adenosine Diphosphate, Animals, Cognition, Evoked Potentials, Hippocampus, In Vitro Techniques, Membrane Potentials, Pyramidal Cells, Rats, Sodium Channels}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0030175}, author = {Cooper, Donald C and Chung, Sungkwon and Spruston, Nelson} } @article {2132, title = {Plasticity of dendritic function.}, journal = {Current Opinion in Neurobiology}, volume = {15}, year = {2005}, month = {2005 Jun}, pages = {334-42}, abstract = {

The various properties of neuronal dendrites{\textendash}their morphology, active membrane and synaptic properties{\textendash}all play important roles in determining the functional capabilities of central nervous system neurons. Because of their fundamental involvement in both synaptic integration and synaptic plasticity, the active dendritic properties are important for both neuronal information processing and storage. The active properties of dendrites are determined by the densities of voltage-gated ion channels located within the dendrites in addition to the biophysical characteristics of those channels. The real power of this system resides in the level of plasticity that is provided by the many forms of channel modulation known to exist in neurons. Indeed, voltage gated ion channel modulation shapes the active properties of neuronal dendrites to specific conditions, thus tailoring the functional role of the single neuron within its circuit.

}, keywords = {Action Potentials, Brain, Dendrites, Ion Channel Gating, Ion Channels, Neuronal Plasticity}, issn = {0959-4388}, doi = {10.1002/cbic.201000254}, author = {Magee, Jeffrey C and Johnston, Daniel} } @article {45753, title = {Pleiotropic functions of a conserved insect-specific Hox peptide motif.}, journal = {Development}, volume = {132}, year = {2005}, month = {2005 Dec}, pages = {5261-70}, abstract = {

The proteins that regulate developmental processes in animals have generally been well conserved during evolution. A few cases are known where protein activities have functionally evolved. These rare examples raise the issue of how highly conserved regulatory proteins with many roles evolve new functions while maintaining old functions. We have investigated this by analyzing the function of the ;QA{\textquoteright} peptide motif of the Hox protein Ultrabithorax (Ubx), a motif that has been conserved throughout insect evolution since its establishment early in the lineage. We precisely deleted the QA motif at the endogenous locus via allelic replacement in Drosophila melanogaster. Although the QA motif was originally characterized as involved in the repression of limb formation, we have found that it is highly pleiotropic. Curiously, deleting the QA motif had strong effects in some tissues while barely affecting others, suggesting that QA function is preferentially required for a subset of Ubx target genes. QA deletion homozygotes had a normal complement of limbs, but, at reduced doses of Ubx and the abdominal-A (abd-A) Hox gene, ectopic limb primordia and adult abdominal limbs formed when the QA motif was absent. These results show that redundancy and the additive contributions of activity-regulating peptide motifs play important roles in moderating the phenotypic consequences of Hox protein evolution, and that pleiotropic peptide motifs that contribute quantitatively to several functions are subject to intense purifying selection.

}, keywords = {Amino Acid Motifs, Animals, Conserved Sequence, Drosophila melanogaster, Drosophila Proteins, Extremities, Genes, Homeobox, Homeodomain Proteins, Phenotype, Sequence Deletion, Transcription Factors}, issn = {0950-1991}, doi = {10.1242/dev.02146}, author = {Hittinger, Chris Todd and Stern, David L and Carroll, Sean B} } @article {3432, title = {Pneumatic capillary gun for ballistic delivery of microparticles.}, journal = {Applied Physics Letters}, volume = {87}, year = {2005}, month = {2005 Jun 29}, pages = {014103}, abstract = {

A pneumatic gun for ballistic delivery of microparticles to soft targets is proposed and demonstrated. The particles are accelerated by a high-speed flow of helium in a capillary tube. Vacuum suction applied to a concentric larger diameter tube is used to divert substantially all of the flow of helium from the gun nozzle, thereby preventing the gas from hitting and damaging the target. Speed of ejection of micron-sized gold particles from the gun nozzle, and their depth of penetration into agarose gels are reported.

}, author = {Rinberg, Dmitry and Simonnet, C and Groisman, A} } @article {45921, title = {Postsynaptic depolarization requirements for LTP and LTD: a critique of spike timing-dependent plasticity.}, journal = {Nat Neurosci}, volume = {8}, year = {2005}, month = {2005 Jul}, pages = {839-41}, abstract = {

Long-term potentiation and long-term depression require postsynaptic depolarization, which many current models attribute to backpropagating action potentials. New experimental work suggests, however, that other mechanisms can lead to dendritic depolarization, and that backpropagating action potentials may be neither necessary nor sufficient for synaptic plasticity in vivo.

}, keywords = {Action Potentials, Animals, Dendrites, Electrophysiology, Excitatory Postsynaptic Potentials, Humans, Long-Term Potentiation, Long-Term Synaptic Depression, Neuronal Plasticity, Reaction Time, Synapses}, issn = {1097-6256}, author = {Lisman, John and Spruston, Nelson} } @article {1405, title = {Properties of dopamine release and uptake in the songbird basal ganglia.}, journal = {Journal of Neurophysiology}, volume = {93}, year = {2005}, month = {2005 Apr}, pages = {1871-9}, abstract = {

Vocal learning in songbirds requires a basal ganglia circuit termed the anterior forebrain pathway (AFP). The AFP is not required for song production, and its role in song learning is not well understood. Like the mammalian striatum, the striatal component of the AFP, Area X, receives dense dopaminergic innervation from the midbrain. Since dopamine (DA) clearly plays a crucial role in basal ganglia-mediated motor control and learning in mammals, it seems likely that DA signaling contributes importantly to the functions of Area X as well. In this study, we used voltammetric methods to detect subsecond changes in extracellular DA concentration to gain better understanding of the properties and regulation of DA release and uptake in Area X. We electrically stimulated Ca(2+)- and action potential-dependent release of an electroactive substance in Area X brain slices and identified the substance as DA by the voltammetric waveform, electrode selectivity, and neurochemical and pharmacological evidence. As in the mammalian striatum, DA release in Area X is depressed by autoinhibition, and the lifetime of extracellular DA is strongly constrained by monoamine transporters. These results add to the known physiological similarities of the mammalian and songbird striatum and support further use of voltammetry in songbirds to investigate the role of basal ganglia DA in motor learning.

}, keywords = {Animals, Basal Ganglia, Dopamine, Male, Neural Pathways, Presynaptic, Receptors, Songbirds}, issn = {0022-3077}, doi = {10.1152/jn.01053.2004}, author = {Gale, Samuel D and Perkel, David J} } @article {46399, title = {Rapid and reversible chemical inactivation of synaptic transmission in genetically targeted neurons.}, journal = {Neuron}, volume = {48}, year = {2005}, month = {2005 Dec 8}, pages = {727-35}, abstract = {

Inducible and reversible silencing of selected neurons in vivo is critical to understanding the structure and dynamics of brain circuits. We have developed Molecules for Inactivation of Synaptic Transmission (MISTs) that can be genetically targeted to allow the reversible inactivation of neurotransmitter release. MISTs consist of modified presynaptic proteins that interfere with the synaptic vesicle cycle when crosslinked by small molecule "dimerizers." MISTs based on the vesicle proteins VAMP2/Synaptobrevin and Synaptophysin induced rapid ( approximately 10 min) and reversible block of synaptic transmission in cultured neurons and brain slices. In transgenic mice expressing MISTs selectively in Purkinje neurons, administration of dimerizer reduced learning and performance of the rotarod behavior. MISTs allow for specific, inducible, and reversible lesions in neuronal circuits and may provide treatment of disorders associated with neuronal hyperactivity.

}, keywords = {Animals, Cells, Cultured, Cross-Linking Reagents, Dimerization, Gene Targeting, In Vitro Techniques, Learning, Mice, Mice, Transgenic, Motor Activity, Neural Inhibition, Neurons, Neurotransmitter Agents, Purkinje Cells, Synaptic Transmission, Synaptic Vesicles, Synaptophysin, Time Factors, Vesicle-Associated Membrane Protein 2}, issn = {0896-6273}, doi = {10.1016/j.neuron.2005.11.015}, author = {Karpova, Alla Y and Tervo, Dougal G R and Gray, Noah W and Svoboda, Karel} } @article {1774, title = {The receptors and coding logic for bitter taste.}, journal = {Nature}, volume = {434}, year = {2005}, month = {2005 Mar 10}, pages = {225-9}, abstract = {

The sense of taste provides animals with valuable information about the nature and quality of food. Bitter taste detection functions as an important sensory input to warn against the ingestion of toxic and noxious substances. T2Rs are a family of approximately 30 highly divergent G-protein-coupled receptors (GPCRs) that are selectively expressed in the tongue and palate epithelium and are implicated in bitter taste sensing. Here we demonstrate, using a combination of genetic, behavioural and physiological studies, that T2R receptors are necessary and sufficient for the detection and perception of bitter compounds, and show that differences in T2Rs between species (human and mouse) can determine the selectivity of bitter taste responses. In addition, we show that mice engineered to express a bitter taste receptor in {\textquoteright}sweet cells{\textquoteright} become strongly attracted to its cognate bitter tastants, whereas expression of the same receptor (or even a novel GPCR) in T2R-expressing cells resulted in mice that are averse to the respective compounds. Together these results illustrate the fundamental principle of bitter taste coding at the periphery: dedicated cells act as broadly tuned bitter sensors that are wired to mediate behavioural aversion.

}, keywords = {Animals, Food Preferences, G-Protein-Coupled, Humans, Inbred BALB C, Inbred C57BL, Knockout, Mice, Palate, Physical Stimulation, Receptors, Species Specificity, Substrate Specificity, Taste, Tongue}, issn = {1476-4687}, doi = {10.1038/nature03352}, author = {Mueller, Ken L and Hoon, Mark A and Erlenbach, Isolde and Chandrashekar, Jayaram and Zuker, Charles S and Ryba, Nicholas J P} } @article {1558, title = {Recombinant approaches to IgG-like bispecific antibodies.}, journal = {Acta Pharmacologica Sinica}, volume = {26}, year = {2005}, month = {2005 Jun}, pages = {649-58}, abstract = {

One of the major obstacles in the development of bispecific antibodies (BsAb) has been the difficulty of producing the materials in sufficient quality and quantity by traditional technologies, such as the hybrid hybridoma and chemical conjugation methods. In contrast to the rapid and significant progress in the development of recombinant BsAb fragments (such as diabody and tandem single chain Fv), the successful design and production of full length IgG-like BsAb has been limited. Compared to smaller fragments, IgG-like BsAb have long serum half-life and are capable of supporting secondary immune functions, such as antibody-dependent cellular cytotoxicity and complement-mediated cytotoxicity. The development of IgG-like BsAb as therapeutic agents will depend heavily on our research progress in the design of recombinant BsAb constructs (or formats) and production efficiency. This review will focus on recent advances in various recombinant approaches to the engineering and production of IgG-like BsAb.

}, keywords = {Animals, Antibodies, Bispecific, Cytotoxicity, Humans, Immunoglobulin Fc Fragments, Immunoglobulin Fragments, Immunoglobulin G, Immunoglobulin Variable Region, Immunologic, Recombinant Fusion Proteins}, issn = {1671-4083}, doi = {10.1111/j.1745-7254.2005.00119.x}, author = {Marvin, Jonathan S and Zhu, Zhenping} } @article {1166, title = {Replication of mitochondrial DNA occurs by strand displacement with alternative light-strand origins, not via a strand-coupled mechanism.}, journal = {Genes \& Development}, volume = {19}, year = {2005}, month = {2005 Oct 15}, pages = {2466-76}, abstract = {

The established strand-displacement model for mammalian mitochondrial DNA (mtDNA) replication has recently been questioned in light of new data using two-dimensional (2D) agarose gel electrophoresis. It has been proposed that a synchronous, strand-coupled mode of replication occurs in tissues, thereby casting doubt on the general validity of the "orthodox," or strand-displacement model. We have examined mtDNA replicative intermediates from mouse liver using atomic force microscopy and 2D agarose gel electrophoresis in order to resolve this issue. The data provide evidence for only the orthodox, strand-displacement mode of replication and reveal the presence of additional, alternative origins of lagging light-strand mtDNA synthesis. The conditions used for 2D agarose gel analysis are favorable for branch migration of asymmetrically replicating nascent strands. These data reconcile the original displacement mode of replication with the data obtained from 2D gel analyses.

}, keywords = {Agar Gel, Animals, Atomic Force, DNA, DNA Replication, Electrophoresis, Mice, Microscopy, Mitochondrial, Replication Origin}, issn = {0890-9369}, doi = {10.1101/gad.1352105}, author = {Brown, Timothy A and Cecconi, Ciro and Tkachuk, Ariana N and Bustamante, Carlos and Clayton, David A} } @proceedings {4532, title = {Representing part-whole relationships in recurrent neural networks.}, volume = {18}, year = {2005}, month = {2005}, pages = {563-70}, address = {Whistler, B.C.}, abstract = {

There is little consensus about the computational function of top-down synaptic connections in the visual system. Here we explore the hypothesis that top-down connections, like bottom-up connections, reflect partwhole relationships. We analyze a recurrent network with bidirectional synaptic interactions between a layer of neurons representing parts and a layer of neurons representing wholes. Within each layer, there is lateral inhibition. When the network detects a whole, it can rigorously enforce part-whole relationships by ignoring parts that do not belong. The network can complete the whole by filling in missing parts. The network can refuse to recognize a whole, if the activated parts do not conform to a stored part-whole relationship. Parameter regimes in which these behaviors happen are identified using the theory of permitted and forbidden sets [3, 4]. The network behaviors are illustrated by recreating Rumelhart and McClelland{\textquoteright}s {\textquotedblleft}interactive activation{\textquotedblright} model [7].

}, author = {Jain, Viren and Zhigulin, Valentin and Seung, Hyunjune Sebastian} } @article {2447, title = {The role of the prothoracic gland in determining critical weight for metamorphosis in Drosophila melanogaster.}, journal = {Current Biology}, volume = {15}, year = {2005}, month = {2005 Oct 25}, pages = {1796-807}, abstract = {

The timely onset of metamorphosis in holometabolous insects depends on their reaching the appropriate size known as critical weight. Once critical weight is reached, juvenile hormone (JH) titers decline, resulting in the release of prothoracicotropic hormone (PTTH) at the next photoperiod gate and thereby inducing metamorphosis. How individuals determine when they have reached critical weight is unknown. We present evidence that in Drosophila, a component of the ring gland, the prothoracic gland (PG), assesses growth to determine when critical weight has been achieved.

}, keywords = {Animals, Biological, Body Weight, Developmental, Drosophila, Drosophila Proteins, Ecdysteroids, Endocrine Glands, Gene Expression Regulation, Immunoenzyme Techniques, Insect Hormones, Insulin, Larva, Metamorphosis, PTEN Phosphohydrolase}, issn = {0960-9822}, doi = {10.1016/j.cub.2005.09.017}, author = {Mirth, Christen and Truman, James W and Riddiford, Lynn M} } @article {45926, title = {R-type calcium channels contribute to afterdepolarization and bursting in hippocampal CA1 pyramidal neurons.}, journal = {J Neurosci}, volume = {25}, year = {2005}, month = {2005 Jun 15}, pages = {5763-73}, abstract = {

Action potentials in pyramidal neurons are typically followed by an afterdepolarization (ADP), which in many cells contributes to intrinsic burst firing. Despite the ubiquity of this common excitable property, the responsible ion channels have not been identified. Using current-clamp recordings in hippocampal slices, we find that the ADP in CA1 pyramidal neurons is mediated by an Ni2+-sensitive calcium tail current. Voltage-clamp experiments indicate that the Ni2+-sensitive current has a pharmacological and biophysical profile consistent with R-type calcium channels. These channels are available at the resting potential, are activated by the action potential, and remain open long enough to drive the ADP. Because the ADP correlates directly with burst firing in CA1 neurons, R-type calcium channels are crucial to this important cellular behavior, which is known to encode hippocampal place fields and enhance synaptic plasticity.

}, keywords = {Action Potentials, Adenosine Diphosphate, Animals, Calcium Channels, R-Type, Hippocampus, In Vitro Techniques, Male, Membrane Potentials, Neuronal Plasticity, Patch-Clamp Techniques, Pyramidal Cells, Rats, Rats, Wistar, Synapses}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0624-05.2005}, author = {Metz, Alexia E and Jarsky, Tim and Martina, Marco and Spruston, Nelson} } @article {1240, title = {Segregation of the brain into gray and white matter: a design minimizing conduction delays.}, journal = {PLoS Computational Biology}, volume = {1}, year = {2005}, month = {2005 Dec}, pages = {e78}, abstract = {

A ubiquitous feature of the vertebrate anatomy is the segregation of the brain into white and gray matter. Assuming that evolution maximized brain functionality, what is the reason for such segregation? To answer this question, we posit that brain functionality requires high interconnectivity and short conduction delays. Based on this assumption we searched for the optimal brain architecture by comparing different candidate designs. We found that the optimal design depends on the number of neurons, interneuronal connectivity, and axon diameter. In particular, the requirement to connect neurons with many fast axons drives the segregation of the brain into white and gray matter. These results provide a possible explanation for the structure of various regions of the vertebrate brain, such as the mammalian neocortex and neostriatum, the avian telencephalon, and the spinal cord.

}, keywords = {Animals, Brain, Color, Models, Neural Pathways, Neurological}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1001066}, author = {Wen, Quan and Chklovskii, Dmitri B} } @article {2091, title = {Sparse and composite coherent lattices. (With commentary)}, journal = {Physical Review A}, volume = {71}, year = {2005}, month = {2005 Jun 20}, pages = {063406}, abstract = {

A method is described that yields a series of (D+1)-element wave-vector sets giving rise to (D=2 or 3)-dimensional coherent sparse lattices of any desired Bravais symmetry and primitive cell shape, but of increasing period relative to the excitation wavelength. By applying lattice symmetry operations to any of these sets, composite lattices of N\>D+1 waves are constructed, having increased spatial frequency content but unchanged crystal group symmetry and periodicity. Optical lattices of widely spaced excitation maxima of diffraction-limited confinement and controllable polarization can thereby be created, possibly useful for quan- tum optics, lithography, or multifocal microscopy.

Commentary: Develops a formalism to find a set of wavevectors that create a periodic optical lattice of any desired Bravais symmetry by the mutual interference of the corresponding plane waves. Discovers two new classes of optical lattices, sparse and composite, that together permit the creation of widely spaced, tightly confined excitation maxima in 3D potentially suitable for high speed volumetric live cell imaging. The implementation of this idea was derailed by our exclusive focus on PALM at the time, and many of its goals have since been reached with our Bessel beam plane illumination microscope. Nevertheless, sparse and composite optical lattices may prove useful in atomic physics or for the fabrication of 3D nanostructures.

}, author = {Betzig, E} } @article {1692, title = {Spore number control and breeding in Saccharomyces cerevisiae: a key role for a self-organizing system.}, journal = {The Journal of Cell Biology}, volume = {171}, year = {2005}, month = {2005 Nov 21}, pages = {627-40}, abstract = {

Spindle pole bodies (SPBs) provide a structural basis for genome inheritance and spore formation during meiosis in yeast. Upon carbon source limitation during sporulation, the number of haploid spores formed per cell is reduced. We show that precise spore number control (SNC) fulfills two functions. SNC maximizes the production of spores (1-4) that are formed by a single cell. This is regulated by the concentration of three structural meiotic SPB components, which is dependent on available amounts of carbon source. Using experiments and computer simulation, we show that the molecular mechanism relies on a self-organizing system, which is able to generate particular patterns (different numbers of spores) in dependency on one single stimulus (gradually increasing amounts of SPB constituents). We also show that SNC enhances intratetrad mating, whereby maximal amounts of germinated spores are able to return to a diploid lifestyle without intermediary mitotic division. This is beneficial for the immediate fitness of the population of postmeiotic cells.

}, keywords = {Biological, Carbon, Centromere, Computer Simulation, Cytoplasm, Dominant, Electron, Fungal, Gene Expression Regulation, Genes, Genetic, Genetic Linkage, Genotype, Green Fluorescent Proteins, Haploidy, Meiosis, Microscopy, Mitotic Spindle Apparatus, Models, Mutation, Open Reading Frames, Plasmids, Recombination, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Software, Spores, Time Factors, Video}, issn = {0021-9525}, doi = {10.1083/jcb.200507168}, author = {Taxis, Christof and Keller, Philipp and Kavagiou, Zaharoula and Jensen, Lars Juhl and Colombelli, Julien and Bork, Peer and Stelzer, Ernst H K and Knop, Michael} } @article {2415, title = {Structural studies of the human PBAF chromatin-remodeling complex.}, journal = {Structure}, volume = {13}, year = {2005}, month = {2005 Feb}, pages = {267-75}, abstract = {

ATP-dependent chromatin remodeling is one of the central processes responsible for imparting fluidity to chromatin and thus regulating DNA transactions. Although knowledge on this process is accumulating rapidly, the basic mechanism (or mechanisms) by which the remodeling complexes alter the structure of a nucleosome is not yet understood. Structural information on these macromolecular machines should aid in interpreting the biochemical and genetic data; to this end, we have determined the structure of the human PBAF ATP-dependent chromatin-remodeling complex preserved in negative stain by electron microscopy and have mapped the nucleosome binding site using two-dimensional (2D) image analysis. PBAF has an overall C-shaped architecture{\textendash}with a larger density to which two smaller knobs are attached{\textendash}surrounding a central cavity; one of these knobs appears to be flexible and occupies different positions in each of the structures determined. The 2D analysis of PBAF:nucleosome complexes indicates that the nucleosome binds in the central cavity.

}, keywords = {Binding Sites, Chromosomal Proteins, Humans, Imaging, Molecular Conformation, Non-Histone, Nucleosomes, Three-Dimensional, Transcription Factors}, issn = {0969-2126}, doi = {10.1073/pnas.1100640108}, author = {Leschziner, Andres E and Lemon, Bryan and Tjian, Robert and Nogales, Eva} } @article {1108, title = {Template-dependent morphogenesis of oriented calcite crystals in the presence of magnesium ions.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {44}, year = {2005}, month = {2005 Apr 15}, pages = {2386-90}, issn = {1433-7851}, doi = {10.1002/anie.200462296}, author = {Han, Yong-Jin and Wysocki, Laura M and Thanawala, Monica S and Siegrist, Theo and Aizenberg, Joanna} } @article {45754, title = {The temporal requirements for insulin signaling during development in Drosophila.}, journal = {PLoS Biol}, volume = {3}, year = {2005}, month = {2005 Sep}, pages = {e289}, abstract = {

Recent studies have indicated that the insulin-signaling pathway controls body and organ size in Drosophila, and most metazoans, by signaling nutritional conditions to the growing organs. The temporal requirements for insulin signaling during development are, however, unknown. Using a temperature-sensitive insulin receptor (Inr) mutation in Drosophila, we show that the developmental requirements for Inr activity are organ specific and vary in time. Early in development, before larvae reach the "critical size" (the size at which they commit to metamorphosis and can complete development without further feeding), Inr activity influences total development time but not final body and organ size. After critical size, Inr activity no longer affects total development time but does influence final body and organ size. Final body size is affected by Inr activity from critical size until pupariation, whereas final organ size is sensitive to Inr activity from critical size until early pupal development. In addition, different organs show different sensitivities to changes in Inr activity for different periods of development, implicating the insulin pathway in the control of organ allometry. The reduction in Inr activity is accompanied by a two-fold increase in free-sugar levels, similar to the effect of reduced insulin signaling in mammals. Finally, we find that varying the magnitude of Inr activity has different effects on cell size and cell number in the fly wing, providing a potential linkage between the mode of action of insulin signaling and the distinct downstream controls of cell size and number. We present a model that incorporates the effects of the insulin-signaling pathway into the Drosophila life cycle. We hypothesize that the insulin-signaling pathway controls such diverse effects as total developmental time, total body size and organ size through its effects on the rate of cell growth, and proliferation in different organs.

}, keywords = {Animals, Drosophila, Drosophila Proteins, Insect Hormones, Insulin, Insulin Receptor Substrate Proteins, Intracellular Signaling Peptides and Proteins, Larva, Mutation, Receptor Protein-Tyrosine Kinases, Signal Transduction, Time Factors}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0030289}, author = {Shingleton, Alexander W and Das, Jayatri and Vinicius, Lucio and Stern, David L} } @article {3086, title = {Tetrodotoxin infusions into the dorsal hippocampus block non-locomotor place recognition.}, journal = {Hippocampus}, volume = {15}, year = {2005}, month = {2005 Mar 2}, pages = {460-71}, abstract = {

The hippocampus is critical for navigation in an open field. One component of this navigation requires the subject to recognize the target place using distal cues. The experiments presented in this report tested whether blocking hippocampal function would impair open field place recognition. Hungry rats were trained to press a lever on a feeder for food. In Experiment 1, they were passively transported with the feeder along a circular trajectory. Lever pressing was reinforced only if the feeder was passing through a 60 degrees -wide sector. Thus, rats preferentially lever pressed in the vicinity of the reward sector indicating that they recognized its location. Tetrodotoxin (TTX) infusions aimed at the dorsal hippocampi caused rats to substantially increase lever pressing with no preference for any region. The aim of Experiment 2 was to determine whether the TTX injections caused a loss of place recognition or a general increase of lever pressing. A separate group of rats was conditioned in a stationary apparatus to press the lever in response to a light. The TTX injections did not abolish preferential lever pressing in response to light. Lever pressing increased less than half as much as the TTX-induced increase in Experiment 1. When these animals with functional hippocampi could not determine the rewarded period because the light was always off, lever pressing increased much more and was similar to the TTX-induced increase in Experiment 1. We conclude that the TTX inactivation of the hippocampi impaired the ability to recognize the reward place.

}, keywords = {Anesthetics, Animal, Animals, Behavior, Disease Models, Feeding Behavior, Hippocampus, Local, Long-Evans, Male, Memory, Memory Disorders, Orientation, Rats, Space Perception, Tetrodotoxin}, issn = {1050-9631}, doi = {10.1002/hipo.20072}, author = {Klement, Daniel and Pastalkova, Eva and Fenton, Andr{\'e} A} } @article {2187, title = {Topographic mapping of VMH {\textendash}> arcuate nucleus microcircuits and their reorganization by fasting.}, journal = {Nature Neuroscience}, volume = {8}, year = {2005}, month = {2005 Oct}, pages = {1356-63}, abstract = {

In the hypothalamic arcuate nucleus (ARC), pro-opiomelanocortin (POMC) neurons inhibit feeding and neuropeptide-Y (NPY) neurons stimulate feeding. We tested whether neurons in the ventromedial hypothalamic nucleus (VMH), a known satiety center, activate anorexigenic neuronal pathways in the ARC by projecting either excitatory synaptic inputs to POMC neurons and/or inhibitory inputs to NPY neurons. Using laser scanning photostimulation in brain slices from transgenic mice, we found that POMC and NPY neurons, which are interspersed in the ARC, are nevertheless regulated by anatomically distinct synaptic inputs. POMC neurons received strong excitatory input from the medial VMH (mVMH), whereas NPY neurons did not and, instead, received weak inhibitory input only from within the ARC. The strength of the excitatory input from the mVMH to POMC neurons was diminished by fasting. These data identify a new molecularly defined circuit that is dynamically regulated by nutritional state in a manner consistent with the known role of the VMH as a satiety center.

}, keywords = {Action Potentials, Animals, Arcuate Nucleus, Brain Mapping, Fasting, Glutamic Acid, Immunohistochemistry, Lasers, Leptin, Male, Mice, Nerve Net, Neural Networks (Computer), Neuronal Plasticity, Neurons, Neuropeptide Y, Newborn, Patch-Clamp Techniques, Photic Stimulation, Pro-Opiomelanocortin, Synapses, Transgenic}, issn = {1097-6256}, doi = {10.1038/nn1550}, author = {Sternson, Scott M and Shepherd, Gordon M G and Friedman, Jeffrey M} } @proceedings {5774, title = {Tracking multiple mouse contours (without too many samples).}, year = {2005}, month = {06/2005}, pages = {1039-46}, publisher = {IEEE}, address = {San Diego, CA}, abstract = {

We present a particle filtering algorithm for robustly tracking the contours of multiple deformable objects through severe occlusions. Our algorithm combines a multiple blob tracker with a contour tracker in a manner that keeps the required number of samples small. This is a natural combination because both algorithms have complementary strengths. The multiple blob tracker uses a natural multi-target model and searches a smaller and simpler space. On the other hand, contour tracking gives more fine-tuned results and relies on cues that are available during severe occlusions. Our choice of combination of these two algorithms accentuates the advantages of each. We demonstrate good performance on challenging video of three identical mice that contains multiple instances of severe occlusion.

}, author = {Branson, Kristin and Belongie, Serge} } @article {2413, title = {Transcriptional feedback control of insulin receptor by dFOXO/FOXO1.}, journal = {Genes \& Development}, volume = {19}, year = {2005}, month = {2005 Oct 15}, pages = {2435-46}, abstract = {

The insulin signaling pathway, which is conserved in evolution from flies to humans, evolved to allow a fast response to changes in nutrient availability while keeping glucose concentration constant in serum. Here we show that, both in Drosophila and mammals, insulin receptor (InR) represses its own synthesis by a feedback mechanism directed by the transcription factor dFOXO/FOXO1. In Drosophila, dFOXO is responsible for activating transcription of dInR, and nutritional conditions can modulate this effect. Starvation up-regulates mRNA of dInR in wild-type but not dFOXO-deficient flies. Importantly, FOXO1 acts in mammalian cells like its Drosophila counterpart, up-regulating the InR mRNA level upon fasting. Mammalian cells up-regulate the InR mRNA in the absence of serum, conditions that induce the dephosphorylation and activation of FOXO1. Interestingly, insulin is able to reverse this effect. Therefore, dFOXO/FOXO1 acts as an insulin sensor to activate insulin signaling, allowing a fast response to the hormone after each meal. Our results reveal a key feedback control mechanism for dFOXO/FOXO1 in regulating metabolism and insulin signaling.

}, keywords = {Animals, Cell Line, Drosophila, Drosophila Proteins, Evolution, Food Deprivation, Forkhead Transcription Factors, Genetic, Humans, Insulin, Messenger, Mice, Molecular, Receptor Protein-Tyrosine Kinases, RNA, Signal Transduction, Transcription, Up-Regulation}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Puig, Oscar and Tjian, Robert} } @article {45956, title = {Aquaporin-0 membrane junctions form upon proteolytic cleavage.}, journal = {Journal of Molecular Biology}, volume = {342}, year = {2004}, month = {2004 Sep 24}, pages = {1337-45}, abstract = {

Aquaporin-0 (AQP0), previously known as major intrinsic protein (MIP), is the only water pore protein expressed in lens fiber cells. AQP0 is highly specific to lens fiber cells and constitutes the most abundant intrinsic membrane protein in these cells. The protein is initially expressed as a full-length protein in young fiber cells in the lens cortex, but becomes increasingly cleaved in the lens core region. Reconstitution of AQP0 isolated from the core of sheep lenses containing a proportion of truncated protein, produced double-layered two-dimensional (2D) crystals, which displayed the same dimensions as the thin 11 nm lens fiber cell junctions, which are prominent in the lens core. In contrast reconstitution of full-length AQP0 isolated from the lens cortex reproducibly yielded single-layered 2D crystals. We present electron diffraction patterns and projection maps of both crystal types. We show that cleavage of the intracellular C terminus enhances the adhesive properties of the extracellular surface of AQP0, indicating a conformational change in the molecule. This change of function of AQP0 from a water pore in the cortex to an adhesion molecule in the lens core constitutes another manifestation of the gene sharing concept originally proposed on the basis of the dual function of crystallins.

}, keywords = {Amino Acid Sequence, Animals, Aquaporins, Biopolymers, Eye Proteins, Hydrolysis, Membrane Glycoproteins, Microscopy, Electron, Molecular Sequence Data, Sheep}, issn = {0022-2836}, doi = {10.1016/j.jmb.2004.07.076}, author = {Gonen, Tamir and Cheng, Yifan and Kistler, Joerg and Walz, Thomas} } @article {45955, title = {Aquaporin-0 membrane junctions reveal the structure of a closed water pore.}, journal = {Nature}, volume = {429}, year = {2004}, month = {2004 May 13}, pages = {193-7}, abstract = {

The lens-specific water pore aquaporin-0 (AQP0) is the only aquaporin known to form membrane junctions in vivo. We show here that AQP0 from the lens core, containing some carboxy-terminally cleaved AQP0, forms double-layered crystals that recapitulate in vivo junctions. We present the structure of the AQP0 membrane junction as determined by electron crystallography. The junction is formed by three localized interactions between AQP0 molecules in adjoining membranes, mainly mediated by proline residues conserved in AQP0s from different species but not present in most other aquaporins. Whereas all previously determined aquaporin structures show the pore in an open conformation, the water pore is closed in AQP0 junctions. The water pathway in AQP0 also contains an additional pore constriction, not seen in other known aquaporin structures, which may be responsible for pore gating.

}, keywords = {Animals, Aquaporins, Biological Transport, Cell Membrane, Cell Membrane Permeability, Cryoelectron Microscopy, Crystallization, Electric Conductivity, Eye Proteins, Hydrogen-Ion Concentration, Lens, Crystalline, Membrane Glycoproteins, Models, Molecular, Molecular Sequence Data, Protein Conformation, Sheep, Water}, issn = {1476-4687}, doi = {10.1038/nature02503}, author = {Gonen, Tamir and Sliz, Piotr and Kistler, Joerg and Cheng, Yifan and Walz, Thomas} } @article {2160, title = {A Bayesian morphometry algorithm.}, journal = {IEEE Transactions on Medical Imaging}, volume = {23}, year = {2004}, month = {2004 Jun}, pages = {723-37}, abstract = {

Most methods for structure-function analysis of the brain in medical images are usually based on voxel-wise statistical tests performed on registered magnetic resonance (MR) images across subjects. A major drawback of such methods is the inability to accurately locate regions that manifest nonlinear associations with clinical variables. In this paper, we propose Bayesian morphological analysis methods, based on a Bayesian-network representation, for the analysis of MR brain images. First, we describe how Bayesian networks (BNs) can represent probabilistic associations among voxels and clinical (function) variables. Second, we present a model-selection framework, which generates a BN that captures structure-function relationships from MR brain images and function variables. We demonstrate our methods in the context of determining associations between regional brain atrophy (as demonstrated on MR images of the brain), and functional deficits. We employ two data sets for this evaluation: the first contains MR images of 11 subjects, where associations between regional atrophy and a functional deficit are almost linear; the second data set contains MR images of the ventricles of 84 subjects, where the structure-function association is nonlinear. Our methods successfully identify voxel-wise morphological changes that are associated with functional deficits in both data sets, whereas standard statistical analysis (i.e., t-test and paired t-test) fails in the nonlinear-association case.

}, keywords = {Aged, Algorithms, Atrophy, Automated, Bayes Theorem, Brain, Brain Diseases, Cluster Analysis, Computer-Assisted, Humans, Image Interpretation, Magnetic Resonance Imaging, Pattern Recognition, Reproducibility of Results, Sensitivity and Specificity, Signal Processing, Subtraction Technique}, issn = {0278-0062}, doi = {10.1007/s12021-010-9090-x}, author = {Herskovits, Edward H and Peng, Hanchuan and Davatzikos, Christos} } @article {1262, title = {Biophysical constraints on neuronal branching.}, journal = {Neurocomputing}, volume = {58-60}, year = {2004}, month = {2004 Jun}, pages = {487-95}, abstract = {

We investigate rules that govern neuronal arborization, speci\%cally the local geometry of the

bifurcation of a neurite into its sub-branches. In the present study we set out to determine

the relationship between branch diameter and angle. Existing theories are based on minimizing a

neuronal volume cost function, or, alternatively, on the equilibrium of mechanical tension forces,

whichdepend on branchdiameters. Our experimental results utilizing two-dimensional cultured

neural networks partly corroborate both the volume optimization principles and the tension theory.

Deviation from pure tension forces equilibrium is explained by an additional force exerted by

the anchoring of the junction to the substrate.

}, author = {Shefi, Orit and Harel, Amir and Chklovskii, Dmitri B and Ben-Jacob, Eshel and Ayali, Amir} } @article {2134, title = {Changes in AMPA receptor currents following LTP induction on rat CA1 pyramidal neurones.}, journal = {The Journal of Physiology}, volume = {559}, year = {2004}, month = {2004 Sep 1}, pages = {543-54}, abstract = {

In the CA1 region of the hippocampus, LTP is thought to be initiated by a transient activation of NMDA receptors and is expressed as a persistent increase in synaptic transmission through AMPA receptors. To investigate the postsynaptic modifications of AMPA receptors involved in this enhanced synaptic transmission, the channel density and single-channel properties of extrasynaptic AMPA receptors located in synaptically active dendritic regions were examined following the induction of LTP. Following tetanic stimulation an outside-out patch was excised from the apical dendrite near the point of stimulation and saturating concentrations of glutamate were rapidly applied to the patch. AMPA current amplitude and duration were increased significantly in patches pulled from dendrites that expressed LTP. Non-stationary fluctuation analysis of AMPA currents indicated that AMPA channel number was nearly twofold larger than in controls, while single channel conductance and maximum open-probability were unchanged. Furthermore, while subtle changes in AMPA channel kinetics could also be observed, we did not find any evidence that receptor affinity or rectification properties were altered by LTP induction. Very similar results were found when CaMK-II activity was increased through the intracellular application of Ca/CaM. Together, we interpret our data to indicate that the stimuli used here produce an increased delivery of AMPA receptors to synaptically active regions of the apical dendrite without inducing any significant changes in their basic biophysical properties and that such delivery is a key element in this form of synaptic plasticity.

}, keywords = {AMPA, Animals, Calcium-Calmodulin-Dependent Protein Kinase Type 2, Calcium-Calmodulin-Dependent Protein Kinases, Glutamic Acid, Long-Term Potentiation, Pyramidal Cells, Rats, Receptors, Sprague-Dawley}, issn = {0022-3751}, doi = {10.1002/cbic.201000254}, author = {Andrasfalvy, Bertalan K and Magee, Jeffrey C} } @article {1255, title = {Class-specific features of neuronal wiring.}, journal = {Neuron}, volume = {43}, year = {2004}, month = {2004 Jul 22}, pages = {251-9}, abstract = {

Brain function relies on specificity of synaptic connectivity patterns among different classes of neurons. Yet, the substrates of specificity in complex neuropil remain largely unknown. We search for imprints of specificity in the layout of axonal and dendritic arbors from the rat neocortex. An analysis of 3D reconstructions of pairs consisting of pyramidal cells (PCs) and GABAergic interneurons (GIs) revealed that the layout of GI axons is specific. This specificity is manifested in a relatively high tortuosity, small branch length of these axons, and correlations of their trajectories with the positions of postsynaptic neuron dendrites. Axons of PCs show no such specificity, usually taking a relatively straight course through neuropil. However, wiring patterns among PCs hold a large potential for circuit remodeling and specificity through growth and retraction of dendritic spines. Our results define distinct class-specific rules in establishing synaptic connectivity, which could be crucial in formulating a canonical cortical circuit.

}, keywords = {Animals, Axons, Computer-Assisted, Dendrites, gamma-Aminobutyric Acid, Image Processing, Imaging, Interneurons, Neocortex, Neural Pathways, Neurons, Pyramidal Cells, Rats, Synapses, Three-Dimensional, Wistar}, issn = {0896-6273}, doi = {10.1016/j.tins.2005.05.006}, author = {Stepanyants, Armen and Tam{\'a}s, G{\'a}bor and Chklovskii, Dmitri B} } @article {1341, title = {A combinatorial method for analyzing sequential firing patterns involving an arbitrary number of neurons based on relative time order.}, journal = {Journal of Neurophysiology}, volume = {92}, year = {2004}, month = {2004 Oct}, pages = {2555-73}, abstract = {

Information processing in the brain is believed to require coordinated activity across many neurons. With the recent development of techniques for simultaneously recording the spiking activity of large numbers of individual neurons, the search for complex multicell firing patterns that could help reveal this neural code has become possible. Here we develop a new approach for analyzing sequential firing patterns involving an arbitrary number of neurons based on relative firing order. Specifically, we develop a combinatorial method for quantifying the degree of matching between a "reference sequence" of N distinct "letters" (representing a particular target order of firing by N cells) and an arbitrarily long "word" composed of any subset of those letters including repeats (representing the relative time order of spikes in an arbitrary firing pattern). The method involves computing the probability that a random permutation of the word{\textquoteright}s letters would by chance alone match the reference sequence as well as or better than the actual word does, assuming all permutations were equally likely. Lower probabilities thus indicate better matching. The overall degree and statistical significance of sequence matching across a heterogeneous set of words (such as those produced during the course of an experiment) can be computed from the corresponding set of probabilities. This approach can reduce the sample size problem associated with analyzing complex firing patterns. The approach is general and thus applicable to other types of neural data beyond multiple spike trains, such as EEG events or imaging signals from multiple locations. We have recently applied this method to quantify memory traces of sequential experience in the rodent hippocampus during slow wave sleep.

}, keywords = {Algorithms, Animals, Computer Simulation, Data Interpretation, Electric Stimulation, Electroencephalography, Electrophysiology, Hippocampus, Neural Networks (Computer), Neurons, Probability, Rats, Sample Size, Sleep, Statistical}, issn = {0022-3077}, doi = {10.1152/jn.01030.2003}, author = {Lee, Albert K and Wilson, Matthew A} } @article {45760, title = {Comparison of diverse protein sequences of the nuclear-encoded subunits of cytochrome C oxidase suggests conservation of structure underlies evolving functional sites.}, journal = {Mol Biol Evol}, volume = {21}, year = {2004}, month = {2004 Aug}, pages = {1572-82}, abstract = {

Interspecific comparisons of protein sequences can reveal regions of evolutionary conservation that are under purifying selection because of functional constraints. Interpreting these constraints requires combining evolutionary information with structural, biochemical, and physiological data to understand the biological function of conserved regions. We take this integrative approach to investigate the evolution and function of the nuclear-encoded subunits of cytochrome c oxidase (COX). We find that the nuclear-encoded subunits evolved subsequent to the origin of mitochondria and the subunit composition of the holoenzyme varies across diverse taxa that include animals, yeasts, and plants. By mapping conserved amino acids onto the crystal structure of bovine COX, we show that conserved residues are structurally organized into functional domains. These domains correspond to some known functional sites as well as to other uncharacterized regions. We find that amino acids that are important for structural stability are conserved at frequencies higher than expected within each taxon, and groups of conserved residues cluster together at distances of less than 5 A more frequently than do randomly selected residues. We, therefore, suggest that selection is acting to maintain the structural foundation of COX across taxa, whereas active sites vary or coevolve within lineages.

}, keywords = {Animals, Catalytic Domain, Cattle, Electron Transport Complex IV, Mitochondria, Models, Molecular, Plants, Yeasts}, issn = {0737-4038}, doi = {10.1093/molbev/msh161}, author = {Das, Jayatri and Miller, Stephen T and Stern, David L} } @article {1264, title = {Cortical rewiring and information storage.}, journal = {Nature}, volume = {431}, year = {2004}, month = {2004 Oct 14}, pages = {782-8}, abstract = {

Current thinking about long-term memory in the cortex is focused on changes in the strengths of connections between neurons. But ongoing structural plasticity in the adult brain, including synapse formation/elimination and remodelling of axons and dendrites, suggests that memory could also depend on learning-induced changes in the cortical {\textquoteright}wiring diagram{\textquoteright}. Given that the cortex is sparsely connected, wiring plasticity could provide a substantial boost in storage capacity, although at a cost of more elaborate biological machinery and slower learning.

}, issn = {1476-4687}, author = {Chklovskii, Dmitri B and Mel, B.W. and Svoboda, Karel} } @article {1775, title = {Decoding cilia function: defining specialized genes required for compartmentalized cilia biogenesis.}, journal = {Cell}, volume = {117}, year = {2004}, month = {2004 May 14}, pages = {527-39}, abstract = {

The evolution of the ancestral eukaryotic flagellum is an example of a cellular organelle that became dispensable in some modern eukaryotes while remaining an essential motile and sensory apparatus in others. To help define the repertoire of specialized proteins needed for the formation and function of cilia, we used comparative genomics to analyze the genomes of organisms with prototypical cilia, modified cilia, or no cilia and identified approximately 200 genes that are absent in the genomes of nonciliated eukaryotes but are conserved in ciliated organisms. Importantly, over 80\% of the known ancestral proteins involved in cilia function are included in this small collection. Using Drosophila as a model system, we then characterized a novel family of proteins (OSEGs: outer segment) essential for ciliogenesis. We show that osegs encode components of a specialized transport pathway unique to the cilia compartment and are related to prototypical intracellular transport proteins.

}, keywords = {Afferent, Animals, Carrier Proteins, Cell Compartmentation, Cell Differentiation, Cilia, Developmental, Drosophila melanogaster, Electron, Eukaryotic Cells, Evolution, Gene Expression Regulation, Genome, Humans, Microscopy, Molecular, Neurons, Oligonucleotide Array Sequence Analysis, Phylogeny}, issn = {0092-8674}, author = {Avidor-Reiss, Tomer and Maer, Andreia M and Koundakjian, Edmund and Polyanovsky, Andrey and Keil, Thomas and Subramaniam, Shankar and Zuker, Charles S} } @article {2449, title = {Developmental architecture of adult-specific lineages in the ventral CNS of Drosophila.}, journal = {Development}, volume = {131}, year = {2004}, month = {2004 Oct}, pages = {5167-84}, abstract = {

In Drosophila most thoracic neuroblasts have two neurogenic periods: an initial brief period during embryogenesis and a second prolonged phase during larval growth. This study focuses on the adult-specific neurons that are born primarily during the second phase of neurogenesis. The fasciculated neurites arising from each cluster of adult-specific neurons express the cell-adhesion protein Neurotactin and they make a complex scaffold of neurite bundles within the thoracic neuropils. Using MARCM clones, we identified the 24 lineages that make up the scaffold of a thoracic hemineuromere. Unlike the early-born neurons that are strikingly diverse in both form and function, the adult specific cells in a given lineage are remarkably similar and typically project to only one or two initial targets, which appear to be the bundled neurites from other lineages. Correlated changes in the contacts between the lineages in different segments suggest that these initial contacts have functional significance in terms of future synaptic partners. This paper provides an overall view of the initial connections that eventually lead to the complex connectivity of the bulk of the thoracic neurons.

}, keywords = {Animals, Central Nervous System, Drosophila, Drosophila Proteins, Larva, Membrane Glycoproteins}, issn = {0950-1991}, doi = {10.1242/dev.01371}, author = {Truman, James W and Schuppe, Hansj{\"u}rgen and Shepherd, David and Williams, Darren W} } @article {2512, title = {Differential control of MHR3 promoter activity by isoforms of the ecdysone receptor and inhibitory effects of E75A and MHR3.}, journal = {Developmental Biology}, volume = {272}, year = {2004}, month = {2004 Aug 15}, pages = {510-21}, abstract = {

MHR3 is an ecdysone-inducible transcription factor whose expression in both Manduca sexta epidermis and the Manduca GV1 cell line is induced by 20-hydroxyecdysone (20E) in vitro. There are four putative ecdysone response elements (EcRE) in the 2.6-kb flanking region of the MHR3 promoter. The most proximal, EcRE1, is necessary for activation of the promoter by 20E in the GV1 cells because the mutation of EcRE1 caused the loss of responsiveness to 20E. Previous studies showed that EcR-B1/USP-1 bound only to EcRE1 and high levels of this complex increased the 20E-induced activation, whereas the presence of high USP-2 prevented this increased activation. When we expressed EcR-A alone or in combination with USP-1 under the control of Autographa californica baculovirus promoter (pIE1hr), the activation of the 2.6-kb promoter by 20E was reduced by about 50\%. Moreover, when EcR-A was expressed together with both EcR-B1 and USP-1, it reduced the normal activation caused by EcR-B1 and USP-1 by 50\%. Gel mobility shift assays showed no binding of EcR-A/USP-1 to EcRE1. The presence of EcR-A, however, reduced the binding of EcR-B1/USP-1 by about 50\%. These findings suggest that EcR-A competes with EcR-B1 for binding of USP-1, leading to a decline in activity of the promoter. In addition, E75A, another ecdysone-induced transcription factor, and MHR3 itself suppressed MHR3 promoter activity by binding to the monomeric response element (MRE2). Therefore, MHR3 can be down-regulated both by itself and by E75A.

}, keywords = {Animals, Base Sequence, Binding Sites, Cell Line, DNA-Binding Proteins, Ecdysterone, Epidermis, Gene Expression Regulation, Genetic, Glycoproteins, Insect Proteins, Manduca, Molecular Sequence Data, Mutation, Promoter Regions, Protein Isoforms, Receptors, Response Elements, Serpins, Steroid, Transcription Factors}, issn = {0012-1606}, doi = {10.1016/j.ydbio.2004.04.028}, author = {Hiruma, Kiyoshi and Riddiford, Lynn M} } @article {2417, title = {Distinct conformational states of nuclear receptor-bound CRSP-Med complexes.}, journal = {Nature Structural \& Molecular Biology}, volume = {11}, year = {2004}, month = {2004 Jul}, pages = {664-71}, abstract = {

The human CRSP-Med coactivator complex is targeted by a diverse array of sequence-specific regulatory proteins. Using EM and single-particle reconstruction techniques, we recently completed a structural analysis of CRSP-Med bound to VP16 and SREBP-1a. Notably, these activators induced distinct conformational states upon binding the coactivator. Ostensibly, these different conformational states result from VP16 and SREBP-1a targeting distinct subunits in the CRSP-Med complex. To test this, we conducted a structural analysis of CRSP-Med bound to either thyroid hormone receptor (TR) or vitamin D receptor (VDR), both of which interact with the same subunit (Med220) of CRSP-Med. Structural comparison of TR- and VDR-bound complexes (at a resolution of 29 A) indeed reveals a shared conformational feature that is distinct from other known CRSP- Med structures. Importantly, this nuclear receptor-induced structural shift seems largely dependent on the movement of Med220 within the complex.

}, keywords = {Bacterial Proteins, Binding Sites, Calcitriol, Genetic, Hela Cells, Humans, Protein Binding, Protein Conformation, Receptors, Thyroid Hormone, Trans-Activators, Transcription}, issn = {1545-9993}, doi = {10.1073/pnas.1100640108}, author = {Taatjes, Dylan J and Schneider-Poetsch, Tilman and Tjian, Robert} } @article {48654, title = {Dynamics of leg muscle function in tammar wallabies (M. eugenii) during level versus incline hopping.}, journal = {The Journal of Experimental Biology}, volume = {207}, year = {2004}, month = {2004 Jan}, pages = {211-23}, abstract = {

The goal of our study was to examine whether the in vivo force-length behavior, work and elastic energy savings of distal muscle-tendon units in the legs of tammar wallabies (Macropus eugenii) change during level versus incline hopping. To address this question, we obtained measurements of muscle activation (via electromyography), fascicle strain (via sonomicrometry) and muscle-tendon force (via tendon buckles) from the lateral gastrocnemius (LG) and plantaris (PL) muscles of tammar wallabies trained to hop on a level and an inclined (10 degrees, 17.4\% grade) treadmill at two speeds (3.3 m s(-1) and 4.2 m s(-1)). Similar patterns of muscle activation, force and fascicle strain were observed under both level and incline conditions. This also corresponded to similar patterns of limb timing and movement (duty factor, limb contact time and hopping frequency). During both level and incline hopping, the LG and PL exhibited patterns of fascicle stretch and shortening that yielded low levels of net fascicle strain [LG: level, -1.0+/-4.6\% (mean +/- S.E.M.) vs incline, 0.6+/-4.5\%; PL: level, 0.1+/-1.0\% vs incline, 0.4+/-1.6\%] and muscle work (LG: level, -8.4+/-8.4 J kg(-1) muscle vs incline, -6.8+/-7.5 J kg(-1) muscle; PL: level, -2.0+/-0.6 J kg(-1) muscle vs incline, -1.4+/-0.7 J kg(-1) muscle). Consequently, neither muscle significantly altered its contractile dynamics to do more work during incline hopping. Whereas electromyographic (EMG) phase, duration and intensity did not differ for the LG, the PL exhibited shorter but more intense periods of activation, together with reduced EMG phase (P\<0.01), during incline versus level hopping. Our results indicate that design for spring-like tendon energy savings and economical muscle force generation is key for these two distal muscle-tendon units of the tammar wallaby, and the need to accommodate changes in work associated with level versus incline locomotion is achieved by more proximal muscles of the limb.

}, keywords = {Animals, Biomechanical Phenomena, Electromyography, Hindlimb, Locomotion, Macropodidae, Muscle Contraction, Muscle, Skeletal, Tendons, Time Factors, Transducers}, issn = {0022-0949}, author = {Biewener, A A and McGowan, C and Card, G M and Baudinette, R V} } @article {1111, title = {Efficient synthesis of alkynylsilyl ethers and silaketals via base-induced alkynylsilane alcoholysis.}, journal = {The Journal of Organic Chemistry}, volume = {69}, year = {2004}, month = {2004 Dec 10}, pages = {8967-70}, abstract = {

The efficient silylation of alcohols with di- and trialkynylsilanes was achieved under base-catalyzed conditions to afford alkynyl silyl ethers and symmetrical alkynyl silaketals in good yield. A selective alcoholysis of dialkynyl silyl ethers to mixed silaketals was also demonstrated. These products served as substrates for enyne ring-closing metathesis and, consequently, as precursors to stereochemically defined 1,3-dienes.

}, keywords = {Alcohols, Alkalies, Catalysis, Ethers, Molecular Structure, Organometallic Compounds, Silanes}, issn = {0022-3263}, doi = {10.1021/jo048908l}, author = {Grimm, Jonathan B and Lee, Daesung} } @article {6364, title = {Efficient transformation of the beetle Tribolium castaneum using the Minos transposable element: quantitative and qualitative analysis of genomic integration events.}, journal = {Genetics}, volume = {167}, year = {2004}, month = {2004 Jun}, pages = {737-46}, abstract = {

Genetic transformation in insects holds great promise as a tool for genetic manipulation in species of particular scientific, economic, or medical interest. A number of transposable elements have been tested recently as potential vectors for transformation in a range of insects. Minos is one of the most promising elements because it appears to be active in diverse species and has the capacity to carry large inserts. We report here the use of the Minos element as a transformation vector in the red flour beetle Tribolium castaneum (Coleoptera), an important species for comparative developmental and pest management studies. Transgenic G(1) beetles were recovered from 32.4\% of fertile G(0){\textquoteright}s injected with a plasmid carrying a 3xP3-EGFP-marked transposon and in vitro synthesized mRNA encoding the Minos transposase. This transformation efficiency is 2.8-fold higher than that observed when using a plasmid helper. Molecular and genetic analyses show that several independent insertions can be recovered from a single injected parent, but that the majority of transformed individuals carry single Minos insertions. These results establish Minos as one of the most efficient vectors for genetic transformation in insects. In combination with piggyBac-based transgenesis, our work allows the introduction of sophisticated multicomponent genetic tools in Tribolium.

}, keywords = {Animals, Base Sequence, Crosses, DNA Transposable Elements, Female, Genetic, Genome, Insertional, Male, Mutagenesis, Plasmids, Transformation, Transposases, Tribolium}, issn = {0016-6731}, doi = {10.1534/genetics.103.023085}, author = {Pavlopoulos, Anastasios and Berghammer, Andreas J and Averof, Michalis and Klingler, Martin} } @article {1253, title = {Exact solution for the optimal neuronal layout problem.}, journal = {Neural Computation}, volume = {16}, year = {2004}, month = {2004 Oct}, pages = {2067-78}, abstract = {

Evolution perfected brain design by maximizing its functionality while minimizing costs associated with building and maintaining it. Assumption that brain functionality is specified by neuronal connectivity, implemented by costly biological wiring, leads to the following optimal design problem. For a given neuronal connectivity, find a spatial layout of neurons that minimizes the wiring cost. Unfortunately, this problem is difficult to solve because the number of possible layouts is often astronomically large. We argue that the wiring cost may scale as wire length squared, reducing the optimal layout problem to a constrained minimization of a quadratic form. For biologically plausible constraints, this problem has exact analytical solutions, which give reasonable approximations to actual layouts in the brain. These solutions make the inverse problem of inferring neuronal connectivity from neuronal layout more tractable.

}, keywords = {Animals, Brain, Computer Simulation, Humans, Models, Nerve Net, Neurological, Neurons}, issn = {0899-7667}, doi = {10.1016/j.tins.2005.05.006}, author = {Chklovskii, Dmitri B} } @article {1743, title = {Experimental test of the birdsong error-correction model.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, year = {2004}, month = {2004 Nov 30}, pages = {16935-40}, abstract = {

Adult zebra finches require auditory feedback to maintain their songs. It has been proposed that the lateral magnocellular nucleus of the anterior nidopallium (LMAN) mediates song plasticity based on auditory feedback. In this model, neurons in LMAN, tuned to the spectral and temporal properties of the bird{\textquoteright}s own song (BOS), are thought to compute the difference between the auditory feedback from the bird{\textquoteright}s vocalizations and an internal song template. This error-correction signal is then used to initiate changes in the motor system that make future vocalizations a better match to the song template. This model was tested by recording from single LMAN neurons while manipulating the auditory feedback heard by singing birds. In contrast to the model predictions, LMAN spike patterns are insensitive to manipulations of auditory feedback. These results suggest that BOS tuning in LMAN is not used for error detection and constrain the nature of any error signal from LMAN to the motor system. Finally, LMAN neurons produce spikes locked precisely to the bird{\textquoteright}s song, independent of the auditory feedback heard by the bird. This finding suggests that a large portion of the input to this nucleus is from the motor control signals that generate the song rather than from auditory feedback.

}, keywords = {Action Potentials, Animal Communication, Animals, Feedback, Finches}, issn = {0027-8424}, doi = {10.1073/pnas.0407870101}, author = {Leonardo, Anthony} } @proceedings {4533, title = {Exploratory analysis and visualization of speech and music by locally linear embedding.}, volume = {3}, year = {2004}, month = {2004 May 17}, pages = {iii - 984-7}, address = {Montreal, Quebec, Canada}, abstract = {

Many problems in voice recognition and audio processing involve feature extraction from raw waveforms. The goal of feature extraction is to reduce the dimensionality of the audio signal while preserving the informative signatures that, for example, distinguish different phonemes in speech or identify particular instruments in music. If the acoustic variability of a data set is described by a small number of continuous features, then we can imagine the data as lying on a low dimensional manifold in the high dimensional space of all possible waveforms. Locally linear embedding (LLE) is an unsupervised learning algorithm for feature extraction in this setting. In this paper, we present results from the exploratory analysis and visualization of speech and music by LLE.

}, author = {Jain, Viren and Saul, Lawrence K.} } @article {6442, title = {Functional magnetic resonance imaging of macaque monkeys performing visually guided saccade tasks: comparison of cortical eye fields with humans.}, journal = {Neuron}, volume = {41}, year = {2004}, month = {2004 Mar 4}, pages = {795-807}, abstract = {

The frontal and parietal eye fields serve as functional landmarks of the primate brain, although their correspondences between humans and macaque monkeys remain unclear. We conducted fMRI at 4.7 T in monkeys performing visually-guided saccade tasks and compared brain activations with those in humans using identical paradigms. Among multiple parietal activations, the dorsal lateral intraparietal area in monkeys and an area in the posterior superior parietal lobule in humans exhibited the highest selectivity to saccade directions. In the frontal cortex, the selectivity was highest at the junction of the precentral and superior frontal sulci in humans and in the frontal eye field (FEF) in monkeys. BOLD activation peaks were also found in premotor areas (BA6) in monkeys, which suggests that the apparent discrepancy in location between putative human FEF (BA6, suggested by imaging studies) and monkey FEF (BA8, identified by microstimulation studies) partly arose from methodological differences.

}, keywords = {Analysis of Variance, Animals, Cerebral Cortex, Female, Humans, Macaca, Magnetic Resonance Imaging, Male, Photic Stimulation, Psychomotor Performance, Rats, Saccades, Species Specificity, Visual Fields}, issn = {0896-6273}, author = {Koyama, Minoru and Hasegawa, Isao and Osada, Takahiro and Adachi, Yusuke and Nakahara, Kiyoshi and Miyashita, Yasushi} } @article {45801, title = {Gene Expression in Acyrthosiphon Pisum (Hemiptera: Aphididae)}, journal = {National Center for Biotechnology Information (NCBI)}, year = {2004}, month = {03/2004}, abstract = {

Examination of the genetic differences between aphids that can transmit citrus tristeza virus, CTV, and those which cannot, may lead to a greater understanding of the virus-aphid interactions necessitating virus acquisition and transmission. Since a cDNA library had been completed the previous year for the brown citrus aphid, a vector of CTV, a second aphid cDNA library was made to a non-CTV aphid vector, the pea aphid, Acyrthosiphon pisum. Comparisons between these two genetic datasets will provide a better understanding of the dynamics of aphid feeding, digestion, development, and may elucidate elements related to virus interactions that were previously unknown. Identification of the numerous proteins actively involved in feeding and digestion from aphids will provide specific targets for the development of new methods of control aimed at disrupting aphid feeding and ultimately reducing the acquisition and transmission of plant viruses which cause disease.

}, url = {http://www.ars.usda.gov/research/publications/publications.htm?SEQ_NO_115=168710}, author = {WB Hunter and PM Dang and D Stern} } @article {46634, title = {Habituation of an odorant-induced startle response in Drosophila.}, journal = {Genes, Brain, and Behavior}, volume = {3}, year = {2004}, month = {2004 Jun}, pages = {127-37}, abstract = {

Habituation is a fundamental form of behavioral plasticity that permits organisms to ignore inconsequential stimuli. Here we describe the habituation of a locomotor response to ethanol and other odorants in Drosophila, measured by an automated high-throughput locomotor tracking system. Flies exhibit an immediate and transient startle response upon exposure to a novel odor. Surgical removal of the antennae, the fly{\textquoteright}s major olfactory organs, abolishes this startle response. With repeated discrete exposures to ethanol vapor, the startle response habituates. Habituation is reversible by a mechanical stimulus and is not due to the accumulation of ethanol in the organism, nor to non-specific mechanisms. Ablation or inactivation of the mushroom bodies, central brain structures involved in olfactory and courtship conditioning, results in decreased olfactory habituation. In addition, olfactory habituation to ethanol generalizes to odorants that activate separate olfactory receptors. Finally, habituation is impaired in rutabaga, an adenylyl cyclase mutant isolated based on a defect in olfactory associative learning. These data demonstrate that olfactory habituation operates, at least in part, through central mechanisms. This novel model of olfactory habituation in freely moving Drosophila provides a scalable method for studying the molecular and neural bases of this simple and ubiquitous form of learning.

}, keywords = {Adenylate Cyclase, Animals, Chemoreceptor Cells, Denervation, Drosophila melanogaster, Ethanol, Female, Habituation, Psychophysiologic, Learning, Male, Models, Animal, Motor Activity, Mushroom Bodies, Mutation, Odors, Physical Stimulation, Reflex, Startle, Smell}, issn = {1601-1848}, doi = {10.1111/j.1601-183x.2004.00061.x}, author = {Cho, W and Heberlein, U and Wolf, F W} } @article {2319, title = {Individual differences in trait anxiety predict the response of the basolateral amygdala to unconsciously processed fearful faces.}, journal = {Neuron}, volume = {44}, year = {2004}, month = {2004 Dec 16}, pages = {1043-55}, abstract = {

Responses to threat-related stimuli are influenced by conscious and unconscious processes, but the neural systems underlying these processes and their relationship to anxiety have not been clearly delineated. Using fMRI, we investigated the neural responses associated with the conscious and unconscious (backwardly masked) perception of fearful faces in healthy volunteers who varied in threat sensitivity (Spielberger trait anxiety scale). Unconscious processing modulated activity only in the basolateral subregion of the amygdala, while conscious processing modulated activity only in the dorsal amygdala (containing the central nucleus). Whereas activation of the dorsal amygdala by conscious stimuli was consistent across subjects and independent of trait anxiety, activity in the basolateral amygdala to unconscious stimuli, and subjects{\textquoteright} reaction times, were predicted by individual differences in trait anxiety. These findings provide a biological basis for the unconscious emotional vigilance characteristic of anxiety and a means for investigating the mechanisms and efficacy of treatments for anxiety.

}, keywords = {Adult, Amygdala, Anxiety, Brain Mapping, Emotions, Facial Expression, Fear, Female, Humans, Individuality, Male, Photic Stimulation, Predictive Value of Tests, Reaction Time, Unconscious (Psychology)}, issn = {0896-6273}, doi = {10.3389/fnana.2010.00147}, author = {Etkin, Amit and Klemenhagen, Kristen C and Dudman, Joshua T and Rogan, Michael T and Hen, Ren{\'e} and Kandel, Eric R and Hirsch, Joy} } @article {2133, title = {On the initiation and propagation of dendritic spikes in CA1 pyramidal neurons.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {24}, year = {2004}, month = {2004 Dec 8}, pages = {11046-56}, abstract = {

Under certain conditions, regenerative voltage spikes can be initiated locally in the dendrites of CA1 pyramidal neurons. These are interesting events that could potentially provide neurons with additional computational abilities. Using whole-cell dendritic recordings from the distal apical trunk and proximal tuft regions and realistic computer modeling, we have determined that highly synchronized and moderately clustered inputs are required for dendritic spike initiation: approximately 50 synaptic inputs spread over 100 mum of the apical trunk/tuft need to be activated within 3 msec. Dendritic spikes are characterized by a more depolarized voltage threshold than at the soma [-48 +/- 1 mV (n = 30) vs -56 +/- 1 mV (n = 7), respectively] and are mainly generated and shaped by dendritic Na+ and K+ currents. The relative contribution of AMPA and NMDA currents is also important in determining the actual spatiotemporal requirements for dendritic spike initiation. Once initiated, dendritic spikes can easily reach the soma, but their propagation is only moderately strong, so that it can be modulated by physiologically relevant factors such as changes in the V(m) and the ionic composition of the extracellular solution. With effective spike propagation, an extremely short-latency neuronal output is produced for greatly reduced input levels. Therefore, dendritic spikes function as efficient detectors of specific input patterns, ensuring that the neuronal response to high levels of input synchrony is a precisely timed action potential output.

}, keywords = {Action Potentials, AMPA, Animals, Dendrites, Electrodes, Excitatory Postsynaptic Potentials, Ion Channels, Models, N-Methyl-D-Aspartate, Neurological, Pyramidal Cells, Rats, Receptors, Sprague-Dawley}, issn = {1529-2401}, doi = {10.1002/cbic.201000254}, author = {Gasparini, Sonia and Migliore, Michele and Magee, Jeffrey C} } @conference {3306, title = {Joint MRI bias removal using entropy minimization across images.}, booktitle = {Neural Information Processing Systems Conference}, year = {2004}, month = {2004}, abstract = {

The correction of bias in magnetic resonance images is an important problem in medical image processing. Most previous approaches have used a maximum likelihood method to increase the likelihood of the pixels in a single image by adaptively estimating a correction to the unknown image bias field. The pixel likelihoods are defined either in terms of a pre-existing tissue model, or non-parametrically in terms of the image{\textquoteright}s own pixel values. In both cases, the specific location of a pixel in the image is not used to calculate the likelihoods. We suggest a new approach in which we simultaneously eliminate the bias from a set of images of the same anatomy, but from different patients. We use the statistics from the same location across different images, rather than within an image, to eliminate bias fields from all of the images simultaneously. The method builds a multi-resolution non-parametric tissue model conditioned on image location while eliminating the bias fields associated with the original image set. We present experiments on both synthetic and real MR data sets, and present comparisons with other methods.

}, author = {Learned-Miller, EG and Ahammad, Parvez} } @article {5491, title = {Lmo mutants reveal a novel role for circadian pacemaker neurons in cocaine-induced behaviors.}, journal = {PLoS Biology}, volume = {2}, year = {2004}, month = {2004 Dec}, pages = {e408}, abstract = {

Drosophila has been developed recently as a model system to investigate the molecular and neural mechanisms underlying responses to drugs of abuse. Genetic screens for mutants with altered drug-induced behaviors thus provide an unbiased approach to define novel molecules involved in the process. We identified mutations in the Drosophila LIM-only (LMO) gene, encoding a regulator of LIM-homeodomain proteins, in a genetic screen for mutants with altered cocaine sensitivity. Reduced Lmo function increases behavioral responses to cocaine, while Lmo overexpression causes the opposite effect, reduced cocaine responsiveness. Expression of Lmo in the principal Drosophila circadian pacemaker cells, the PDF-expressing ventral lateral neurons (LN(v)s), is sufficient to confer normal cocaine sensitivity. Consistent with a role for Lmo in LN(v)function,Lmomutants also show defects in circadian rhythms of behavior. However, the role for LN(v)s in modulating cocaine responses is separable from their role as pacemaker neurons: ablation or functional silencing of the LN(v)s reduces cocaine sensitivity, while loss of the principal circadian neurotransmitter PDF has no effect. Together, these results reveal a novel role for Lmo in modulating acute cocaine sensitivity and circadian locomotor rhythmicity, and add to growing evidence that these behaviors are regulated by shared molecular mechanisms. The finding that the degree of cocaine responsiveness is controlled by the Drosophila pacemaker neurons provides a neuroanatomical basis for this overlap. We propose that Lmo controls the responsiveness of LN(v)s to cocaine, which in turn regulate the flies{\textquoteright} behavioral sensitivity to the drug.

}, keywords = {Alleles, Animal, Animals, Behavior, Biological, Biological Clocks, Circadian Rhythm, Cocaine, Drosophila melanogaster, Drosophila Proteins, Gene Expression Regulation, Gene Silencing, Genetic, Homeodomain Proteins, Models, Mutation, Neurons, Neuropeptides, Neurotransmitter Agents, Protein Structure, Reverse Transcriptase Polymerase Chain Reaction, Tertiary}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0020408}, author = {Tsai, Linus T-Y and Bainton, Roland J and Blau, Justin and Heberlein, Ulrike} } @article {2135, title = {LTP is accompanied by an enhanced local excitability of pyramidal neuron dendrites.}, journal = {Nature Neuroscience}, volume = {7}, year = {2004}, month = {2004 Feb}, pages = {126-35}, abstract = {

The propagation and integration of signals in the dendrites of pyramidal neurons is regulated, in part, by the distribution and biophysical properties of voltage-gated ion channels. It is thus possible that any modification of these channels in a specific part of the dendritic tree might locally alter these signaling processes. Using dendritic and somatic whole-cell recordings, combined with calcium imaging in rat hippocampal slices, we found that the induction of long-term potentiation (LTP) was accompanied by a local increase in dendritic excitability that was dependent on the activation of NMDA receptors. These changes favored the back-propagation of action potentials into this dendritic region with a subsequent boost in the Ca(2+) influx. Dendritic cell-attached patch recordings revealed a hyperpolarized shift in the inactivation curve of transient, A-type K(+) currents that can account for the enhanced excitability. These results suggest an important mechanism associated with LTP for shaping signal processing and controlling dendritic function.

}, keywords = {Action Potentials, Animals, Calcium, Dendrites, Excitatory Postsynaptic Potentials, Hippocampus, Ion Channels, Long-Term Potentiation, Memory, N-Methyl-D-Aspartate, Neuronal Plasticity, Organ Culture Techniques, Patch-Clamp Techniques, Rats, Receptors}, issn = {1097-6256}, doi = {10.1002/cbic.201000254}, author = {Frick, Andreas and Magee, Jeffrey and Johnston, Daniel} } @article {2320, title = {L-type Ca2+ channel blockers promote Ca2+ accumulation when dopamine receptors are activated in striatal neurons.}, journal = {Brain Research. Molecular Brain Research}, volume = {131}, year = {2004}, month = {2004 Nov 24}, pages = {65-72}, abstract = {

Dopamine (DA) receptor-mediated signal transduction and gene expression play a central role in many brain disorders from schizophrenia to Parkinson{\textquoteright}s disease to addiction. While trying to evaluate the role of L-type Ca2+ channels in dopamine D1 receptor-mediated phosphorylation of the transcription factor cyclic AMP response element-binding protein (CREB), we found that activation of dopamine D1 receptors alters the properties of L-type Ca2+ channel inhibitors and turns them into facilitators of Ca2+ influx. In D1 receptor-stimulated neurons, L-type Ca2+ channel blockers promote cytosolic Ca2+ accumulation. This leads to the activation of a molecular signal transduction pathway and CREB phosphorylation. In the absence of dopamine receptor stimulation, L-type Ca2+ channel blockers inhibit CREB phosphorylation. The effect of dopamine on L-type Ca2+ channel blockers is dependent on protein kinase A (PKA), suggesting that protein phosphorylation plays a role in this phenomenon. Because of the adverse effect of activated dopamine receptors on L-type Ca2+ channel blocker action, the role of L-type Ca2+ channels in the dopamine D1 receptor signal transduction pathway cannot be assessed with pharmacological tools. However, with antisense technology, we demonstrate that L-type Ca2+ channels contribute to D1 receptor-mediated CREB phosphorylation. We conclude that the D1 receptor signal transduction pathway depends on L-type Ca2+ channels to mediate CREB phosphorylation.

}, keywords = {2, 3, 4, 5-Tetrahydro-7, 8-dihydroxy-1-phenyl-1H-3-benzazepine, Animals, Antisense, Calcium, Calcium Channel Blockers, Calcium Channels, Cells, Corpus Striatum, Cultured, Cyclic AMP Response Element-Binding Protein, Dizocilpine Maleate, Dopamine Antagonists, Dopamine D1, Drug Interactions, Excitatory Amino Acid Antagonists, Female, L-Type, N-Methyl-D-Aspartate, Neurons, Nifedipine, Oligonucleotides, Phosphorylation, Pregnancy, Rats, Receptors, Sprague-Dawley}, issn = {0169-328X}, doi = {10.3389/fnana.2010.00147}, author = {Eaton, Molly E and Mac{\'\i}as, Wendy and Youngs, Rachael M and Rajadhyaksha, Anjali and Dudman, Joshua T and Konradi, Christine} } @article {2157, title = {Mapping of microbial pathways through constrained mapping of orthologous genes.}, journal = {Proceedings / IEEE Computational Systems Bioinformatics Conference, CSB. IEEE Computational Systems Bioinformatics Conference}, year = {2004}, month = {2004}, pages = {363-70}, abstract = {

We present a novel computer algorithm for mapping biological pathways from one prokaryotic genome to another. The algorithm maps genes in a known pathway to their homologous genes (if any) in a target genome that is most consistent with (a) predicted orthologous gene relationship, (b) predicted operon structures, and (c) predicted co-regulation relationship of operons. Mathematically, we have formulated this problem as a constrained minimum spanning tree problem (called a Steiner network problem), and demonstrated that this formulation has the desired property through applications. We have solved this mapping problem using a combinatorial optimization algorithm, with guaranteed global optimality. We have implemented this algorithm as a computer program, called PMAP. Our test results on pathway mapping are highly encouraging {\textendash} we have mapped a number of pathways of H. influenzae, B. subtilis, H. pylori, and M. tuberculosis to E. coli using P-MAP, whose homologous pathways in E coli. are known and hence the mapping accuracy could be checked. We have then mapped known E. coli pathways in the EcoCyc database to the newly sequenced organism Synechococcus sp WH8102, and predicted 158 Synechococcus pathways. Detailed analyses on the predicted pathways indicate that P-MAP{\textquoteright}s mapping results are consistent with our general knowledge about (local) pathways. We believe that P-MAP will be a useful tool for microbial genome annotation projects and inference of individual microbial pathways.

}, keywords = {Algorithms, Amino Acid, Bacterial, Bacterial Physiological Phenomena, Bacterial Proteins, Biological, Chromosome Mapping, Computer Simulation, Conserved Sequence, Genome, Models, Sequence Homology, Signal Transduction}, issn = {1551-7497}, doi = {10.1007/s12021-010-9090-x}, author = {Olman, Victor and Peng, Hanchuan and Su, Zhengchang and Xu, Ying} } @article {1256, title = {Maps in the brain: what can we learn from them?}, journal = {Annual Review of Neuroscience}, volume = {27}, year = {2004}, month = {2004}, pages = {369-92}, abstract = {

In mammalian visual cortex, neurons are organized according to their functional properties into multiple maps such as retinotopic, ocular dominance, orientation preference, direction of motion, and others. What determines the organization of cortical maps? We argue that cortical maps reflect neuronal connectivity in intracortical circuits. Because connecting distant neurons requires costly wiring (i.e., axons and dendrites), there is an evolutionary pressure to place connected neurons as close to each other as possible. Then, cortical maps may be viewed as solutions that minimize wiring cost for given intracortical connectivity. These solutions can help us in inferring intracortical connectivity and, ultimately, in understanding the function of the visual system.

}, keywords = {Animals, Axons, Brain Mapping, Dendrites, Humans, Nerve Net, Neural Pathways, Visual Cortex, Visual Fields, Visual Pathways}, issn = {0147-006X}, doi = {10.1016/j.tins.2005.05.006}, author = {Chklovskii, Dmitri B and Koulakov, Alexei A} } @article {2188, title = {Modular synthesis and preliminary biological evaluation of stereochemically diverse 1,3-dioxanes.}, journal = {Chemistry \& Biology}, volume = {11}, year = {2004}, month = {2004 Sep}, pages = {1279-91}, abstract = {

Modular synthesis and substrate stereocontrol were combined to furnish 18,000 diverse 1,3-dioxanes whose distribution in chemical space rivals that of a reference set of over 2,000 bioactive small molecules. Library quality was assessed at key synthetic stages, culminating in a detailed postsynthesis analysis of purity, yield, and structural characterizability, and the resynthesis of library subsets that did not meet quality standards. The importance of this analysis-resynthesis process is highlighted by the discovery of new biological probes through organismal and protein binding assays, and by determination of the building block and stereochemical basis for their bioactivity. This evaluation of a portion of the 1,3-dioxane library suggests that many additional probes for chemical genetics will be identified as the entire library becomes biologically annotated.

}, keywords = {Amines, Animals, Calmodulin, Combinatorial Chemistry Techniques, Dioxanes, Molecular Structure, Stereoisomerism, Surface Plasmon Resonance, Zebrafish}, issn = {1074-5521}, doi = {10.1016/j.chembiol.2004.07.012}, author = {Wong, Jason C and Sternson, Scott M and Louca, Joseph B and Hong, Roger and Schreiber, Stuart L} } @article {46633, title = {Molecular Genetic Analysis of Ethanol Intoxication in Drosophila melanogaster.}, journal = {Integrative and Comparative Biology}, volume = {44}, year = {2004}, month = {2004 Aug}, pages = {269-74}, abstract = {

Recently, the fruit fly Drosophila melanogaster has been introduced as a model system to study the molecular bases of a variety of ethanol-induced behaviors. It became immediately apparent that the behavioral changes elicited by acute ethanol exposure are remarkably similar in flies and mammals. Flies show signs of acute intoxication, which range from locomotor stimulation at low doses to complete sedation at higher doses and they develop tolerance upon intermittent ethanol exposure. Genetic screens for mutants with altered responsiveness to ethanol have been carried out and a few of the disrupted genes have been identified. This analysis, while still in its early stages, has already revealed some surprising molecular parallels with mammals. The availability of powerful tools for genetic manipulation in Drosophila, together with the high degree of conservation at the genomic level, make Drosophila a promising model organism to study the mechanism by which ethanol regulates behavior and the mechanisms underlying the organism{\textquoteright}s adaptation to long-term ethanol exposure.

}, issn = {1540-7063}, doi = {10.1093/icb/44.4.269}, author = {Heberlein, Ulrike and Wolf, Fred W and Rothenfluh, Adrian and Guarnieri, Douglas J} } @article {5904, title = {Morphological and physiological features of a set of spinal substantia gelatinosa neurons defined by green fluorescent protein expression.}, journal = {The Journal of Neuroscience}, volume = {24}, year = {2004}, month = {2004 Jan 28}, pages = {836-42}, abstract = {

The spinal substantia gelatinosa (SG) is known to be involved in the manipulation of nociceptive and thermal primary afferent input; however, the interrelationships of its neuronal components are poorly understood. As a step toward expanding understanding, we took a relatively unique approach by concentrating on a set of SG neurons selectively labeled by green fluorescent protein (GFP) in a transgenic mouse. These GFP-expressing SG neurons prove to have homogenous morphological and electrophysiological properties, are systematically spaced in the SG, contain GABA, receive C-fiber primary afferent input, and upregulate c-Fos protein in response to noxious stimuli. Together, the properties established for these GFP-labeled neurons are consistent with a modular SG organization in which afferent activity related to nociception or other C-fiber signaling are subject to integration/modulation by repeating, similar circuits of neurons.

}, keywords = {Animals, Biological Markers, Electrophysiology, gamma-Aminobutyric Acid, Ganglia, Green Fluorescent Proteins, Luminescent Proteins, Lysine, Mice, Nerve Fibers, Neurons, Pain Measurement, Patch-Clamp Techniques, Proto-Oncogene Proteins c-fos, Spinal, Substantia Gelatinosa, Transgenic, Unmyelinated}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4221-03.2004}, author = {Hantman, Adam W and van den Pol, Anthony N and Perl, Edward R} } @article {2420, title = {Myc-interacting protein 1 target gene profile: a link to microtubules, extracellular signal-regulated kinase, and cell growth.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, year = {2004}, month = {2004 Jan 13}, pages = {458-63}, abstract = {

To study the role of the transcription factor Myc-interacting protein 1 (MIZ-1) in activating various target genes after induction with the microtubule disrupting agent T113242, we have used small interfering RNA duplexes (siRNAs) to knockdown the expression of MIZ-1. As expected, depletion of MIZ-1 resulted in the inhibition of T113242-dependent activation of the low-density lipoprotein receptor (LDLR) gene in hepatocytes. Cells transfected with MIZ-1 siRNAs also exhibited growth arrest. In addition, inhibition of the extracellular signal-regulated kinase (ERK) pathway inhibited T113242-induced nuclear accumulation of MIZ-1 and activation of LDLR. Gene expression microarray analysis under various induction conditions identified other T113242-activated genes affected by a decrease in MIZ-1 and inhibition of the ERK pathway. We also found that the accumulation of MIZ-1 in the nucleus is influenced by cell-cell contact and/or growth. Taken together, our studies suggest that MIZ-1 regulates a specific set of genes that includes LDLR and that the ERK pathway plays a role in the activation of target promoters by MIZ-1.

}, keywords = {Cell Division, Cell Line, DNA-Binding Proteins, Flow Cytometry, Fluorescent Antibody Technique, Gene Expression Profiling, Humans, Indirect, Kruppel-Like Transcription Factors, Mitogen-Activated Protein Kinases, RNA Interference, Transcription Factors}, issn = {0027-8424}, doi = {10.1073/pnas.1100640108}, author = {Ziegelbauer, Joseph and Wei, Joyce and Tjian, Robert} } @article {2349, title = {Object-location memory impairment in patients with thermal lesions to the right or left hippocampus.}, journal = {Neuropsychologia}, volume = {42}, year = {2004}, month = {2004 Feb 25}, pages = {1017-28}, abstract = {

Memory for object-location was investigated by testing subjects with small unilateral thermolesions to the medial temporal lobe using small-scale 2D (Abstract) or large-scale 3D (Real) recall conditions. Four patients with lesions of the left hippocampus (LH), 10 patients with damage to the right hippocampus (RH) and 9 matched normal controls (NC) were tested. Six task levels were presented in a pseudorandom order. During each level, subjects viewed one to six different objects on the floor of a circular curtained arena 2.90 m in diameter for 10 s. Recall was tested by marking the locations of objects on a map of the arena (Abstract recall) and then by replacing the objects in the arena (Real recall). Two component errors were studied by calculating the Location Error (LE), independent of the object identity and the configuration error by finding the best match to the presented configuration. The RH group was impaired relative to the NC for nearly all combinations of recall and error types. An impairment was observed in this group even for one object and it deepened sharply with an increasing object number. Damage to the right perirhinal or parahippocampal cortices did not add to the impairment. Deficits in the LH group were also observed, but less consistently. The data indicate that spatial memory is strongly but not exclusively lateralised to the right medial temporal lobe.

}, keywords = {Adult, Anterior Temporal Lobectomy, Brain Damage, Brain Mapping, Cerebral, Chronic, Dominance, Electrocoagulation, Epilepsy, Female, Hippocampus, Humans, Male, Memory, Mental Recall, Middle Aged, Orientation, Pattern Recognition, Postoperative Complications, Reference Values, Short-Term, Temporal Lobe, Visual}, issn = {0028-3932}, doi = {10.1016/j.neuropsychologia.2004.01.002}, author = {Stepankova, Katerina and Fenton, Andr{\'e} A and Pastalkova, Eva and Kalina, Miroslav and Bohbot, V{\'e}ronique D} } @article {1738, title = {Optically active sum frequency generation from molecules with a chiral center: amino acids as model systems.}, journal = {Journal of the American Chemical Society}, volume = {126}, year = {2004}, month = {2004 Nov 24}, pages = {15008-9}, abstract = {

With amino acids as model systems, optically active sum frequency generation (OA-SFG) was used to probe the chirality of molecules with a chiral center and an intrinsically achiral chromophore in isotropic solution for the first time. Like that of circular dichroism (CD), the OA-SFG{\textquoteright}s near electronic resonance originates from the extrachromophoric chiral perturbation on the carboxyl chromophore. The difference in the relative strengths of OA-SFG and CD among different amino acids can be explained by the difference in the details of perturbations.

}, keywords = {Amino Acids, Chemical, Circular Dichroism, Models, Optics and Photonics, Stereoisomerism}, issn = {0002-7863}, doi = {10.1021/ja045708i}, author = {Ji, Na and Shen, Yuen-Ron} } @article {2513, title = {Overexpression of broad: a new insight into its role in the Drosophila prothoracic gland cells.}, journal = {The Journal of Experimental Biology}, volume = {207}, year = {2004}, month = {2004 Mar}, pages = {1151-61}, abstract = {

Insect molting is triggered by ecdysteroids, which are produced in the prothoracic glands (PG). The broad (br) gene is one of the {\textquoteright}early genes{\textquoteright} directly regulated by ecdysteroids. Ectopic expression of the BR-Z3 isoform in early second instar Drosophila larvae (L2) before the rise of the ecdysteroid titer prevented molting to the third instar, but the larvae subsequently formed L2 prepupae after prolonged feeding. When these larvae were fed on diet containing 20-hydroxyecdysone (20E), they formed pharate third instar larvae. The critical weight for normal L3 pupariation of w(1118) larvae was found to be 0.8 mg and that for L2 pupariation was 0.45 mg. We also defined a threshold weight for metamorphosis of 0.3 mg, above which L2 larvae will metamorphose when provided with 20E. BR-Z3 apparently works through the PG cells of the ring gland but not the putative neurosecretory cells that drive ecdysone secretion, because ectopic expression of BR-Z3 specifically in the ring gland caused 53\% of the larvae to become permanent first instar larvae. Driving other BR isoforms in the ring gland prevented larval molting or pupariation to varying degrees. These molting defects were rescued by feeding 20E. Overexpression of each of the BR isoforms caused degeneration of the PG cells but on different time courses, indicating that BR is a signal for the degeneration of the PG cells that normally occurs during the pupal-adult transition.

}, keywords = {Animals, Body Weights and Measures, Drosophila, Drosophila Proteins, Ecdysterone, Exocrine Glands, Gene Expression Regulation, Genetically Modified, Immunohistochemistry, Larva, Molting, Protein Isoforms, Transcription Factors}, issn = {0022-0949}, author = {Zhou, Xiaofeng and Zhou, Baohua and Truman, James W and Riddiford, Lynn M} } @article {4008, title = {A paradox in the evolution of primate vocal learning.}, journal = {Trends in Neurosciences}, volume = {27}, year = {2004}, month = {2004 Nov}, pages = {649-54}, abstract = {

The importance of auditory feedback in the development of spoken language in humans is striking. Paradoxically, although auditory-feedback-dependent vocal plasticity has been shown in a variety of taxonomic groups, there is little evidence that our nearest relatives{\textendash}non-human primates{\textendash}require auditory feedback for the development of species-typical vocal signals. Because of the apparent lack of developmental plasticity in the vocal production system, neuroscientists have largely ignored the neural mechanisms of non-human primate vocal production and perception. Recently, the absence of evidence for vocal plasticity from developmental studies has been contrasted with evidence for vocal plasticity in adults. We argue that this new evidence makes non-human primate vocal behavior an attractive model system for neurobiological analysis.

}, keywords = {Acoustic Stimulation, Animal, Animals, Biological Evolution, Humans, Learning, Vocalization}, issn = {0166-2236}, doi = {10.1016/j.tins.2004.08.009}, author = {Egnor, S E Roian and Hauser, Marc D} } @article {2416, title = {Polybromo protein BAF180 functions in mammalian cardiac chamber maturation.}, journal = {Genes \& Development}, volume = {18}, year = {2004}, month = {2004 Dec 15}, pages = {3106-16}, abstract = {

BAF and PBAF are two related mammalian chromatin remodeling complexes essential for gene expression and development. PBAF, but not BAF, is able to potentiate transcriptional activation in vitro mediated by nuclear receptors, such as RXRalpha, VDR, and PPARgamma. Here we show that the ablation of PBAF-specific subunit BAF180 in mouse embryos results in severe hypoplastic ventricle development and trophoblast placental defects, similar to those found in mice lacking RXRalpha and PPARgamma. Embryonic aggregation analyses reveal that in contrast to PPARgamma-deficient mice, the heart defects are likely a direct result of BAF180 ablation, rather than an indirect consequence of trophoblast placental defects. We identified potential target genes for BAF180 in heart development, such as S100A13 as well as retinoic acid (RA)-induced targets RARbeta2 and CRABPII. Importantly, BAF180 is recruited to the promoter of these target genes and BAF180 deficiency affects the RA response for CRABPII and RARbeta2. These studies reveal unique functions of PBAF in cardiac chamber maturation.

}, keywords = {Animals, Cell Aggregation, Chromatin Assembly and Disassembly, Congenital, Developmental, DNA Primers, Gene Expression Regulation, Heart Defects, Immunoprecipitation, In Situ Hybridization, In Situ Nick-End Labeling, Knockout, Mice, Nuclear Proteins, Oligonucleotide Array Sequence Analysis, Placenta, Receptors, Retinoic Acid, Reverse Transcriptase Polymerase Chain Reaction, S100 Proteins, Transcription Factors}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Wang, Zhong and Zhai, Weiguo and Richardson, James A and Olson, Eric N and Meneses, Juanito J and Firpo, Meri T and Kang, Chulho and Skarnes, William C and Tjian, Robert} } @conference {45802, title = {Prospects in aphid genetics}, booktitle = {Aphids in a new millennium. Proceedings of the Sixth International Symposium on Aphids}, year = {2004}, month = {09/2004}, publisher = {Institut National de la Recherche Agronomique}, organization = {Institut National de la Recherche Agronomique}, address = {Rennes, France}, abstract = {

This paper identifies the prospects of using aphid species as ideal genetic model systems for the study of evolutionary developmental biology and genetic control of polyphenisms. The advantages and disadvantages of using aphids as genetic model organisms are discussed.

}, isbn = {2-7380-1113-6}, url = {http://www.cabdirect.org/abstracts/20043046841.html;jsessionid=4C6865DD4D971042FEB329F0DD6166E5}, author = {DL Stern and JC Simon and CA Dedryver and C Rispe and M Hull{\'e}} } @article {46632, title = {Rapid and chronic: two distinct forms of ethanol tolerance in Drosophila.}, journal = {Alcoholism, Clinical and Experimental Research}, volume = {28}, year = {2004}, month = {2004 Oct}, pages = {1469-80}, abstract = {

BACKGROUND: Ethanol tolerance, defined as a reduction in the intensity of the effects of ethanol upon continuous or repeated exposure, is a hallmark of alcoholism. Tolerance may develop at the cellular or neural systems levels. The molecular changes underlying ethanol tolerance are not well understood. We therefore explored the utility of Drosophila, with its accessibility to genetic, molecular, and behavioral analyses, as a model organism to study tolerance development in response to different ethanol-exposure regimens.

METHODS: We describe a new assay that quantifies recovery from ethanol intoxication in Drosophila. Using this recovery assay, we define ethanol pre-exposure paradigms that lead to the development of tolerance. We also use the inebriometer, an assay that measures the onset of intoxication, to study the effects of pharmacological and genetic manipulations on tolerance development.

RESULTS: We show that flies develop different forms of ethanol tolerance: rapid tolerance, induced by a single short exposure to a high concentration of ethanol, and chronic tolerance, elicited by prolonged exposure to a low concentration of the drug. Neither rapid nor chronic tolerance involves changes in ethanol pharmacokinetics, implying that they represent functional rather than dispositional tolerance. Chronic and rapid tolerance can be distinguished mechanistically: chronic tolerance is disrupted by treatment with the protein synthesis inhibitor cycloheximide, whereas rapid tolerance is resistant to this treatment. Furthermore, rapid and chronic tolerance rely on distinct genetic pathways: a mutant defective for octopamine biosynthesis shows reduced rapid tolerance but normal chronic tolerance.

CONCLUSIONS: Flies, like mammals, develop tolerance in response to different ethanol-exposure regimens, and this tolerance affects both the onset of and the recovery from acute intoxication. Two forms of tolerance, rapid and chronic, are mechanistically distinct, because they can be dissociated genetically and pharmacologically.

}, keywords = {Animals, Drosophila, Drug Tolerance, Ethanol, Male, Models, Animal, Time Factors}, issn = {0145-6008}, author = {Berger, Karen H and Heberlein, Ulrike and Moore, Monica S} } @article {1189, title = {Recombination of human mitochondrial DNA.}, journal = {Science}, volume = {304}, year = {2004}, month = {2004 May 14}, pages = {981}, keywords = {DNA, DNA Replication, Fathers, Female, Genetic, Humans, Male, Mitochondria, Mitochondrial, Mothers, Muscle, Polymerase Chain Reaction, Recombination}, issn = {1095-9203}, doi = {10.1126/science.1096342}, author = {Kraytsberg, Yevgenya and Schwartz, Marianne and Brown, Timothy A and Ebralidse, Konstantin and Kunz, Wolfram S and Clayton, David A and Vissing, John and Khrapko, Konstantin} } @article {2852, title = {Redundant mechanisms are used by Ssn6-Tup1 in repressing chromosomal gene transcription in Saccharomyces cerevisiae.}, journal = {The Journal of Biological Chemistry}, volume = {279}, year = {2004}, month = {2004 Sep 17}, pages = {39240-50}, abstract = {

The Ssn6-Tup1 corepressor complex regulates many genes in Saccharomyces cerevisiae. Three mechanisms have been proposed to explain its repression functions: 1) nucleosome positioning by binding histone tails; 2) recruitment of histone deacetylases; and 3) direct interference with the general transcription machinery or activators. It is unclear if Ssn6-Tup1 utilizes each of these mechanisms at a single gene in a redundant manner or each individually at different loci. A systematic analysis of the contribution of each mechanism at a native promoter has not been reported. Here we employed a genetic strategy to analyze the contributions of nucleosome positioning, histone deacetylation, and Mediator interference in the repression of chromosomal Tup1 target genes in vivo. We exploited the fact that Ssn6-Tup1 requires the ISW2 chromatin remodeling complex to establish nucleosome positioning in vivo to disrupt chromatin structure without affecting other Tup1 repression functions. Deleting ISW2, the histone deacetylase gene HDA1, or genes encoding Mediator subunits individually caused slight or no derepression of RNR3 and HUG1. However, when Mediator mutations were combined with Deltaisw2 or Deltahda1 mutations, enhanced transcription was observed, and the strongest level of derepression was observed in triple Deltaisw2/Deltahda1/Mediator mutants. The increased transcription in the mutants was not due to the loss of Tup1 at the promoter and correlated with increased TBP cross-linking to promoters. Thus, Tup1 utilizes multiple redundant mechanisms to repress transcription of native genes, which may be important for it to act as a global corepressor at a wide variety of promoters.

}, keywords = {Acetylation, Adenosine Triphosphatases, Chromatin, Chromosomes, DNA-Binding Proteins, Fungal, Fungal Proteins, Gene Expression Regulation, Genetic, Histone Deacetylases, Histones, Nuclear Proteins, Nucleosomes, Repressor Proteins, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription, Transcription Factors}, issn = {0021-9258}, doi = {10.1074/jbc.M407159200}, author = {Zhang, Zhengjian and Reese, Joseph C} } @article {2419, title = {Regulatory diversity among metazoan co-activator complexes.}, journal = {Nature Reviews. Molecular Cell Biology}, volume = {5}, year = {2004}, month = {2004 May}, pages = {403-10}, abstract = {

Transcription is a stepwise process that involves many specialized proteins and protein complexes, all of which must work together to express a given gene in a spatially and temporally regulated manner. An integral step in this regulatory process is carried out by large, multisubunit co-activator complexes, which have diverse roles in transcriptional control. Their diversity and large size allows for many potential regulatory inputs, but how is the versatility and specificity of these co-activator complexes determined?

}, keywords = {Animals, DNA-Binding Proteins, Evolution, Gene Expression Regulation, Genetic, Genetic Variation, Humans, Molecular, Promoter Regions, Repressor Proteins, Species Specificity, Transcription, Transcription Factors}, issn = {1471-0072}, doi = {10.1073/pnas.1100640108}, author = {Taatjes, Dylan J and Marr, Michael T and Tjian, Robert} } @article {1252, title = {Search for computational modules in the C. elegans brain.}, journal = {BMC Biology}, volume = {2}, year = {2004}, month = {2004 Dec 2}, pages = {25}, abstract = {

Does the C. elegans nervous system contain multi-neuron computational modules that perform stereotypical functions? We attempt to answer this question by searching for recurring multi-neuron inter-connectivity patterns in the C. elegans nervous system{\textquoteright}s wiring diagram.

}, keywords = {Animals, Brain, Caenorhabditis elegans, Nerve Net, Neural Networks (Computer), Neurons, Synapses, Systems Biology}, issn = {1741-7007}, doi = {10.1016/j.tins.2005.05.006}, author = {Reigl, Markus and Alon, Uri and Chklovskii, Dmitri B} } @article {1986, title = {Sensory neuron signaling to the brain: properties of transmitter release from olfactory nerve terminals.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {24}, year = {2004}, month = {2004 Mar 24}, pages = {3023-30}, abstract = {

Olfactory receptor neurons (ORNs) convey sensory information directly to the CNS via conventional glutamatergic synaptic contacts in olfactory bulb glomeruli. To better understand the process by which information contained in the odorant-evoked firing of ORNs is transmitted to the brain, we examined the properties of glutamate release from olfactory nerve (ON) terminals in slices of the rat olfactory bulb. We show that marked paired pulse depression is the same in simultaneously recorded periglomerular and tufted neurons, and that this form of short-term plasticity is attributable to a reduction of glutamate release from ON terminals. We used the progressive blockade of NMDA receptor (NMDAR) EPSCs by MK-801 [(5R,10S)-(+)-5-methyl-10,11-dihydro-5H-dibenzo[a,d]cyclohepten-5-10-imine hydrogen maleate] and stationary fluctuation analysis of AMPA receptor (AMPAR) EPSCs to determine the probability of release (P(r)) of ON terminals; both approaches indicated that P(r) is unusually high (\>/=0.8). The low-affinity glutamate receptor antagonists gamma-d-glutamylglycine and l-amino-5-phosphonovaleric acid blocked ON-evoked AMPAR- and NMDAR-mediated EPSCs, respectively, to the same extent under conditions of low and high P(r), suggesting that multivesicular release is not a feature of ON terminals. Although release from most synapses exhibits a highly nonlinear dependence on extracellular Ca(2+), we find that the relationship between glutamate release and extracellular Ca(2+) at ON terminals is nearly linear. Our results suggest that ON terminals have specialized features that may contribute to the reliable transmission of sensory information from nose to brain.

}, keywords = {Afferent, AMPA, Animals, Brain, Calcium, Electric Stimulation, Excitatory Amino Acid Antagonists, Excitatory Postsynaptic Potentials, Glutamate, Glutamic Acid, N-Methyl-D-Aspartate, Neuronal Plasticity, Neurons, Neurotransmitter Agents, Olfactory Bulb, Olfactory Nerve, Presynaptic Terminals, Rats, Receptors, Sprague-Dawley, Synaptic Transmission}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.5745-03.2004}, author = {Murphy, Gabe J and Glickfeld, Lindsey L and Balsen, Zev and Isaacson, Jeffry S} } @proceedings {4534, title = {A smorgasbord of features for statistical machine translation.}, year = {2004}, month = {2004 May}, abstract = {

We describe a methodology for rapid experimentation in statistical machine translation which we use to add a large number of features to a baseline system exploiting features from a wide range of levels of syntactic representation. Feature values were combined in a log-linear model to select the highest scoring candidate translation from an n-best list. Feature weights were optimized directly against the BLEU evaluation metric on held-out data. We present results for a small selection of features at each level of syntactic representation.

}, author = {Och, Franz J. and Gildea, Daniel and Khudanpur, Sanjeev and Sarkar, Anoop and Yamada, Kenji and Fraser, Alex and Kumar, Shankar and Shen, Libin and Smith, David and Eng, Katherine and Jain, Viren and Jin, Zhen and Radev, Dragomir} } @article {2853, title = {Ssn6-Tup1 requires the ISW2 complex to position nucleosomes in Saccharomyces cerevisiae.}, journal = {The EMBO Journal}, volume = {23}, year = {2004}, month = {2004 Jun 2}, pages = {2246-57}, abstract = {

The Imitation SWItch (ISWI) chromatin remodeling factors have been implicated in nucleosome positioning. In vitro, they can mobilize nucleosomes bi-directionally, making it difficult to envision how they can establish precise translational positioning of nucleosomes in vivo. It has been proposed that they require other cellular factors to do so, but none has been identified thus far. Here, we demonstrate that both ISW2 and TUP1 are required to position nucleosomes across the entire coding sequence of the DNA damage-inducible gene RNR3. The chromatin structure downstream of the URS is indistinguishable in Deltaisw2 and Deltatup1 mutants, and the crosslinking of Tup1 and Isw2 to RNR3 is independent of each other, indicating that both complexes are required to maintain repressive chromatin structure. Furthermore, Tup1 repressed RNR3 and blocked preinitiation complex formation in the Deltaisw2 mutant, even though nucleosome positioning was completely disrupted over the promoter and ORF. Our study has revealed a novel collaboration between two nucleosome-positioning activities in vivo, and suggests that disruption of nucleosome positioning is insufficient to cause a high level of transcription.

}, keywords = {Adenosine Triphosphatases, Cell Nucleus, Chromatin, Chromatin Immunoprecipitation, DNA-Binding Proteins, Genetic, Nuclear Proteins, Nucleosomes, Promoter Regions, Repressor Proteins, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription Factors}, issn = {0261-4189}, doi = {10.1038/sj.emboj.7600227}, author = {Zhang, Zhengjian and Reese, Joseph C} } @proceedings {46354, title = {Statistical clustering applied to adaptive matched field processing}, year = {2004}, author = {BH Tracey and NL Lee and SC Turaga} } @article {2418, title = {Structure and function of CRSP/Med2; a promoter-selective transcriptional coactivator complex.}, journal = {Molecular Cell}, volume = {14}, year = {2004}, month = {2004 Jun 4}, pages = {675-83}, abstract = {

The multi-subunit, human CRSP coactivator-also known as Mediator (Med)-regulates transcription by mediating signals between enhancer-bound factors (activators) and the core transcriptional machinery. Interestingly, different activators are known to bind distinct subunits within the CRSP/Med complex. We have isolated a stable, endogenous CRSP/Med complex (CRSP/Med2) that specifically lacks both the Med220 and the Med70 subunits. The three-dimensional structure of CRSP/Med2 was determined to 31 A resolution using electron microscopy and single-particle reconstruction techniques. Despite lacking both Med220 and Med70, CRSP/Med2 displays potent, activator-dependent transcriptional coactivator function in response to VP16, Sp1, and Sp1/SREBP-1a in vitro using chromatin templates. However, CRSP/Med2 is unable to potentiate activated transcription from a vitamin D receptor-responsive promoter, which requires interaction with Med220 for coactivator recruitment, whereas VDR-directed activation by CRSP/Med occurs normally. Thus, it appears that CRSP/Med may be regulated by a combinatorial assembly mechanism that allows promoter-selective function upon exchange of specific coactivator targets.

}, keywords = {CCAAT-Enhancer-Binding Proteins, DNA-Binding Proteins, Genes, Genetic, Hela Cells, Herpes Simplex Virus Protein Vmw65, Humans, Macromolecular Substances, Promoter Regions, Protein Structure, Protein Subunits, Regulator, Sp1 Transcription Factor, Sterol Regulatory Element Binding Protein 1, Tertiary, Trans-Activators, Transcription Factors, Transcriptional Activation, Vitamin D Response Element}, issn = {1097-2765}, doi = {10.1073/pnas.1100640108}, author = {Taatjes, Dylan J and Tjian, Robert} } @article {1590, title = {The structures of inhibitor complexes of Pyrococcus furiosus phosphoglucose isomerase provide insights into substrate binding and catalysis.}, journal = {Journal of Molecular Biology}, volume = {343}, year = {2004}, month = {2004 Oct 22}, pages = {649-57}, abstract = {

Pyrococcus furiosus phosphoglucose isomerase (PfPGI) is a metal-containing enzyme that catalyses the interconversion of glucose 6-phosphate (G6P) and fructose 6-phosphate (F6P). The recent structure of PfPGI has confirmed the hypothesis that the enzyme belongs to the cupin superfamily and identified the position of the active site. This fold is distinct from the alphabetaalpha sandwich fold commonly seen in phosphoglucose isomerases (PGIs) that are found in bacteria, eukaryotes and some archaea. Whilst the mechanism of the latter family is thought to proceed through a cis-enediol intermediate, analysis of the structure of PfPGI in the presence of inhibitors has led to the suggestion that the mechanism of this enzyme involves the metal-dependent direct transfer of a hydride between C1 and C2 atoms of the substrate. To gain further insight in the reaction mechanism of PfPGI, the structures of the free enzyme and the complexes with the inhibitor, 5-phospho-d-arabinonate (5PAA) in the presence and absence of metal have been determined. Comparison of these structures with those of equivalent complexes of the eukaryotic PGIs reveals similarities at the active site in the disposition of possible catalytic residues. These include the presence of a glutamic acid residue, Glu97 in PfPGI, which occupies the same position relative to the inhibitor as that of the glutamate that is thought to function as the catalytic base in the eukaryal-type PGIs. These similarities suggest that aspects of the catalytic mechanisms of these two structurally unrelated PGIs may be similar and based on an enediol intermediate.

}, keywords = {Archaeal Proteins, Binding Sites, Catalysis, Crystallography, Dimerization, Fructosephosphates, Glucose-6-Phosphate, Glucose-6-Phosphate Isomerase, Manganese, Models, Molecular, Molecular Structure, Pentosephosphates, Protein Binding, Protein Conformation, Pyrococcus furiosus, X-Ray}, issn = {0022-2836}, doi = {10.1016/j.jmb.2004.08.061}, author = {Berrisford, John M and Akerboom, Jasper and Brouns, Stan and Sedelnikova, Svetlana E and Turnbull, Andrew P and van der Oost, John and Salmon, Laurent and Hardr{\'e}, Renaud and Murray, Iain A and Blackburn, G Michael and Rice, David W and Baker, Patrick J} } @article {1739, title = {Sum frequency vibrational spectroscopy of leucine molecules adsorbed at air-water interface.}, journal = {The Journal of Chemical Physics}, volume = {120}, year = {2004}, month = {2004 Apr 15}, pages = {7107-12}, abstract = {

Sum frequency vibrational spectroscopy was used to study adsorption of leucine molecules at air-water interface from solutions with different concentrations and pH values. The surface density and the orientation of the isopropyl head group of the adsorbed leucine molecules could be deduced from the measurements. It was found that the orientation depends on the surface density, but only weakly on bulk pH value at the saturated surface density. The vibrational spectra of the interfacial water molecules appeared to be strongly affected by the charge state of the adsorbed leucine molecules. Enhancement and inversion of polar orientation of interfacial water molecules by surface charges or field controllable by the bulk pH value were observed.

}, keywords = {Adsorption, Air, Chemistry, Hydrogen-Ion Concentration, Leucine, Physical, Spectrophotometry, Spectrum Analysis, Surface Properties, Water}, issn = {0021-9606}, doi = {10.1063/1.1669375}, author = {Ji, Na and Shen, Yuen-Ron} } @article {1254, title = {Synaptic connectivity and neuronal morphology: two sides of the same coin.}, journal = {Neuron}, volume = {43}, year = {2004}, month = {2004 Sep 2}, pages = {609-17}, abstract = {

Neurons often possess elaborate axonal and dendritic arbors. Why do these arbors exist and what determines their form and dimensions? To answer these questions, I consider the wiring up of a large highly interconnected neuronal network, such as the cortical column. Implementation of such a network in the allotted volume requires all the salient features of neuronal morphology: the existence of branching dendrites and axons and the presence of dendritic spines. Therefore, the requirement of high interconnectivity is, in itself, sufficient to account for the existence of these features. Moreover, the actual lengths of axons and dendrites are close to the smallest possible length for a given interconnectivity, arguing that high interconnectivity is essential for cortical function.

}, keywords = {Animals, Cell Communication, Cell Differentiation, Cell Size, Cerebral Cortex, Dendrites, Humans, Models, Nerve Net, Neural Pathways, Neurological, Synapses}, issn = {0896-6273}, doi = {10.1016/j.tins.2005.05.006}, author = {Chklovskii, Dmitri B} } @article {47224, title = {Transformation of olfactory representations in the Drosophila antennal lobe.}, journal = {Science (New York, N.Y.)}, volume = {303}, year = {2004}, month = {2004 Jan 16}, pages = {366-70}, abstract = {

Molecular genetics has revealed a precise stereotypy in the projection of primary olfactory sensory neurons onto secondary neurons. A major challenge is to understand how this mapping translates into odor responses in these second-order neurons. We investigated this question in Drosophila using whole-cell recordings in vivo. We observe that monomolecular odors generally elicit responses in large ensembles of antennal lobe neurons. Comparison of odor-evoked activity from afferents and postsynaptic neurons in the same glomerulus revealed that second-order neurons display broader tuning and more complex responses than their primary afferents. This indicates a major transformation of odor representations, implicating lateral interactions within the antennal lobe.

}, keywords = {Action Potentials, Animals, Drosophila, Excitatory Postsynaptic Potentials, GABA Antagonists, GABA-A Receptor Antagonists, Nervous System Physiological Phenomena, Neural Inhibition, Neurons, Afferent, Odors, Olfactory Pathways, Olfactory Receptor Neurons, Patch-Clamp Techniques, Picrotoxin, Receptors, GABA-A, Sense Organs, Smell, Synapses}, issn = {1095-9203}, doi = {10.1126/science.1090782}, author = {Wilson, Rachel I and Turner, Glenn C and Laurent, Gilles} } @article {790, title = {Transmembrane/juxtamembrane domain-dependent Dscam distribution and function during mushroom body neuronal morphogenesis.}, journal = {Neuron}, volume = {43}, year = {2004}, month = {2004 Sep 2}, pages = {663-72}, abstract = {

Besides 19,008 possible ectodomains, Drosophila Dscam contains two alternative transmembrane/juxtamembrane segments, respectively, derived from exon 17.1 and exon 17.2. We wondered whether specific Dscam isoforms mediate formation and segregation of axonal branches in the Drosophila mushroom bodies (MBs). Removal of various subsets of the 12 exon 4s does not affect MB neuronal morphogenesis, while expression of a Dscam transgene only partially rescues Dscam mutant phenotypes. Interestingly, differential rescuing effects are observed between two Dscam transgenes that each possesses one of the two possible exon 17s. Axon bifurcation/segregation abnormalities are better rescued by the exon 17.2-containing transgene, but coexpression of both transgenes is required for rescuing mutant viability. Meanwhile, exon 17.1 targets ectopically expressed Dscam-GFP to dendrites while Dscam[exon 17.2]-GFP is enriched in axons; only Dscam[exon 17.2] affects MB axons. These results suggest that exon 17.1 is minimally involved in axonal morphogenesis and that morphogenesis of MB axons probably involves multiple distinct exon 17.2-containing Dscam isoforms.

}, keywords = {Alternative Splicing, Animals, Brain, Cell Adhesion Molecules, Cell Differentiation, Cell Membrane, Dendrites, Developmental, Drosophila melanogaster, Drosophila Proteins, Embryo, Exons, Gene Expression Regulation, Genetically Modified, Growth Cones, Larva, Morphogenesis, Mushroom Bodies, Mutation, Neurons, Nonmammalian, Protein Isoforms, Protein Structure, Proteins, Tertiary, Transgenes}, issn = {0896-6273}, doi = {10.1016/j.neuron.2004.06.033}, author = {Wang, Jian and Ma, Xiaojun and Yang, Jacob S and Zheng, Xiaoyan and Zugates, Christopher T and Lee, Ching-Hsien J and Lee, Tzumin} } @article {3938, title = {An unstructured initiation site is required for efficient proteasome-mediated degradation.}, journal = {Nature Structural \& Molecular Biology}, volume = {11}, year = {2004}, month = {2004 Sep}, pages = {830-7}, abstract = {

The proteasome is the main ATP-dependent protease in eukaryotic cells and controls the concentration of many regulatory proteins in the cytosol and nucleus. Proteins are targeted to the proteasome by the covalent attachment of polyubiquitin chains. The ubiquitin modification serves as the proteasome recognition element but by itself is not sufficient for efficient degradation of folded proteins. We report that proteolysis of tightly folded proteins is accelerated greatly when an unstructured region is attached to the substrate. The unstructured region serves as the initiation site for degradation and is hydrolyzed first, after which the rest of the protein is digested sequentially. These results identify the initiation site as a novel component of the targeting signal, which is required to engage the proteasome unfolding machinery efficiently. The proteasome degrades a substrate by first binding to its ubiquitin modification and then initiating unfolding at an unstructured region.

}, keywords = {Adenosine Triphosphate, Animals, Bacillus, Binding Sites, Biological, Catalysis, Cell Nucleus, Cysteine Endopeptidases, Cytosol, Electrophoresis, Endopeptidases, Escherichia coli, Genetic, Hydrolysis, Models, Multienzyme Complexes, Polyacrylamide Gel, Promoter Regions, Proteasome Endopeptidase Complex, Protein Binding, Protein Folding, Protein Structure, Rabbits, Temperature, Tertiary, Time Factors, Ubiquitin}, issn = {1545-9993}, doi = {10.1038/nsmb814}, author = {Prakash, Sumit and Tian, Lin and Ratliff, Kevin S and Lehotzky, Rebecca E and Matouschek, Andreas} } @article {1139, title = {X chromosome sites autonomously recruit the dosage compensation complex in Drosophila males.}, journal = {PLoS Biology}, volume = {2}, year = {2004}, month = {2004 Nov}, pages = {e341}, abstract = {

It has been proposed that dosage compensation in Drosophila males occurs by binding of two core proteins, MSL-1 and MSL-2, to a set of 35-40 X chromosome "entry sites" that serve to nucleate mature complexes, termed compensasomes, which then spread to neighboring sequences to double expression of most X-linked genes. Here we show that any piece of the X chromosome with which compensasomes are associated in wild-type displays a normal pattern of compensasome binding when inserted into an autosome, independently of the presence of an entry site. Furthermore, in chromosomal rearrangements in which a piece of X chromosome is inserted into an autosome, or a piece of autosome is translocated to the X chromosome, we do not observe spreading of compensasomes to regions of autosomes that have been juxtaposed to X chromosomal material. Taken together these results suggest that spreading is not involved in dosage compensation and that nothing distinguishes an entry site from the other X chromosome sites occupied by compensasomes beyond their relative affinities for compensasomes. We propose a new model in which the distribution of compensasomes along the X chromosome is achieved according to the hierarchical affinities of individual binding sites.

}, keywords = {Animals, Binding Sites, Chromosomes, Crosses, DNA-Binding Proteins, Dosage Compensation, Drosophila, Drosophila Proteins, Female, Fluorescence, Genetic, Genotype, In Situ Hybridization, Male, Microscopy, Nuclear Proteins, Protein Binding, Sex Factors, Transcription Factors, Translocation, X Chromosome}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0020341}, author = {Fagegaltier, Delphine and Baker, Bruce S} } @article {2682, title = {Axon pruning during Drosophila metamorphosis: evidence for local degeneration and requirement of the ubiquitin-proteasome system.}, journal = {Neuron}, volume = {38}, year = {2003}, month = {2003 Jun 19}, pages = {871-85}, abstract = {

Axon pruning is widely used for the refinement of neural circuits in both vertebrates and invertebrates, and may also contribute to the pathogenesis of neurodegenerative diseases. However, little is known about the cellular and molecular mechanisms of axon pruning. We use the stereotyped pruning of gamma neurons of the Drosophila mushroom bodies (MB) during metamorphosis to investigate these mechanisms. Detailed time course analyses indicate that MB axon pruning is mediated by local degeneration rather than retraction and that the disruption of the microtubule cytoskeleton precedes axon pruning. In addition, multiple lines of genetic evidence demonstrate an intrinsic role of the ubiquitin-proteasome system in axon pruning; for example, loss-of-function mutations of the ubiquitin activating enzyme (E1) or proteasome subunits in MB neurons block axon pruning. Our findings suggest that some forms of axon pruning during development may share similarities with degeneration of axons in response to injury.

}, keywords = {Animals, Axons, Biological, Cell Adhesion Molecules, Cysteine Endopeptidases, Cytoskeletal Proteins, Cytoskeleton, Cytosol, Drosophila, Endocytosis, Endopeptidases, Gene Expression, Ligases, Metamorphosis, Microtubules, Multienzyme Complexes, Mutation, Nerve Degeneration, Neurons, Proteasome Endopeptidase Complex, Saccharomyces cerevisiae, Synapses, Transfection, Ubiquitin, Ubiquitin-Activating Enzymes, Ubiquitin-Protein Ligases}, issn = {0896-6273}, author = {Watts, Ryan J and Hoopfer, Eric D and Luo, Liqun} } @article {2350, title = {A battery of tests for quantitative examination of idiothetic and allothetic place navigation modes in humans.}, journal = {Behavioural Brain Research}, volume = {147}, year = {2003}, month = {2003 Dec 17}, pages = {95-105}, abstract = {

Research into the neural mechanisms of place navigation in laboratory animals has led to the definition of allothetic and idiothetic navigation modes that can be examined by quantitative analysis of the generated tracks. In an attempt to use this approach in the study of human navigation behavior, 10 young subjects were examined in an enclosed arena (2.9 m in diameter, 3 m high) equipped with a computerized tracking system. Idiothetic navigation was studied in blindfolded subjects performing the following tasks-Simple Homing, Complex Homing and Idiothesis Supported by Floor-Related Signals. Allothetic navigation was examined in sighted subjects instructed to find in an empty arena the acoustically signaled unmarked goal region and later to retrieve its position using tasks (Natural Navigation, Cue-Controlled Navigation, Snapshot Memory, Map Reading) that evaluated different aspects of allothesis. The results indicate that allothetic navigation is more accurate than idiothetic, that the poor accuracy of idiothesis is due to angular rather than to distance errors, and that navigation performance is best when both allothetic and idiothetic modes contribute to the solution of the task. The proposed test battery may contribute to better understanding of the navigation disturbances accompanying various neurological disorders and to objective evaluation of the results of drug therapy and of rehabilitation procedures.

}, keywords = {Adult, Cues, Exploratory Behavior, Female, Humans, Locomotion, Male, Memory, Orientation, Space Perception, Spatial Behavior}, issn = {0166-4328}, doi = {10.1016/S0166-4328(03)00141-4}, author = {Stepankova, Katerina and Pastalkova, Eva and Kalova, Eva and Kalina, Miroslav and Bures, Jan} } @article {45765, title = {Body-size control: how an insect knows it has grown enough.}, journal = {Curr Biol}, volume = {13}, year = {2003}, month = {2003 Apr 1}, pages = {R267-9}, abstract = {

Insulin signaling controls organ growth and final body size in insects. Recent results have begun to clarify how insulin signaling drives organ growth to match nutrient levels, but have not yet elucidated how insulin signaling controls final body size.

}, keywords = {Animal Nutritional Physiological Phenomena, Animals, Body Constitution, Drosophila, Insect Hormones, Insulin, Models, Biological, Signal Transduction}, issn = {0960-9822}, author = {Stern, David} } @article {2425, title = {Bromodomains mediate an acetyl-histone encoded antisilencing function at heterochromatin boundaries.}, journal = {Molecular Cell}, volume = {11}, year = {2003}, month = {2003 Feb}, pages = {365-76}, abstract = {

Bromodomains bind acetylated histone H4 peptides in vitro. Since many chromatin remodeling complexes and the general transcription factor TFIID contain bromodomains, they may link histone acetylation to increased transcription. Here we show that yeast Bdf1 bromodomains recognize endogenous acetyl-histone H3/H4 as a mechanism for chromatin association in vivo. Surprisingly, deletion of BDF1 or a Bdf1 mutation that abolishes histone binding leads to transcriptional downregulation of genes located at heterochromatin-euchromatin boundaries. Wild-type Bdf1 protein imposes a physical barrier to the spreading of telomere- and mating-locus-proximal SIR proteins. Biochemical experiments indicate that Bdf1 competes with the Sir2 deacetylase for binding to acetylated histone H4. These data suggest an active role for Bdf1 in euchromatin maintenance and antisilencing through a histone tail-encoded boundary function.

}, keywords = {Acetylation, Biological, Down-Regulation, Fungal, Genes, Heterochromatin, Histones, Hydrogen Bonding, Models, Mutation, Protein Binding, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Silent Information Regulator Proteins, Transcription Factor TFIID, Transcription Factors}, issn = {1097-2765}, doi = {10.1073/pnas.1100640108}, author = {Ladurner, Andreas G and Inouye, Carla and Jain, Rajan and Tjian, Robert} } @article {46352, title = {Calculating free energies for diffusion in tight-fitting zeolite-guest systems: Local normal-mode Monte Carlo}, journal = {Journal of Chemical Physics}, volume = {118}, year = {2003}, month = {2003}, type = {Journal Article}, abstract = {

We present an efficient Monte Carlo algorithm for simulating diffusion in tight-fitting host{\textendash}guest systems, based on using zeolitenormal modes. Computational efficiency is gained by sampling framework distortions using normal-mode coordinates, and by exploiting the fact that zeolite distortion energies are well approximated by harmonic estimates. Additional savings are obtained by performing local normal-mode analysis, i.e., only including the motions of zeolite atoms close to the jumping molecule, hence focusing the calculation on zeolite distortions relevant to guest diffusion. We performed normal-mode analysis on various silicalite structures to demonstrate the accuracy of the harmonic approximation. We computed free energy surfaces for benzene in silicalite, finding excellent agreement with previous theoretical studies. Our method is found to be orders-of-magnitude faster than comparable Monte Carlo calculations that use conventional forcefields to quantify zeolite distortion energies. For tight-fitting guests, the efficiency of our new method allows flexible-lattice simulations to converge in less CPU time than that required for fixed-lattice simulations, because of the increased likelihood of jumping through a flexible lattice.

}, issn = {0021-9606}, doi = {10.1063/1.1558033}, author = {Srinivas C. Turaga and Scott M. Auerbach} } @article {1777, title = {Coding of sweet, bitter, and umami tastes: different receptor cells sharing similar signaling pathways.}, journal = {Cell}, volume = {112}, year = {2003}, month = {2003 Feb 7}, pages = {293-301}, abstract = {

Mammals can taste a wide repertoire of chemosensory stimuli. Two unrelated families of receptors (T1Rs and T2Rs) mediate responses to sweet, amino acids, and bitter compounds. Here, we demonstrate that knockouts of TRPM5, a taste TRP ion channel, or PLCbeta2, a phospholipase C selectively expressed in taste tissue, abolish sweet, amino acid, and bitter taste reception, but do not impact sour or salty tastes. Therefore, despite relying on different receptors, sweet, amino acid, and bitter transduction converge on common signaling molecules. Using PLCbeta2 taste-blind animals, we then examined a fundamental question in taste perception: how taste modalities are encoded at the cellular level. Mice engineered to rescue PLCbeta2 function exclusively in bitter-receptor expressing cells respond normally to bitter tastants but do not taste sweet or amino acid stimuli. Thus, bitter is encoded independently of sweet and amino acids, and taste receptor cells are not broadly tuned across these modalities.

}, keywords = {Action Potentials, Afferent, Animals, Cell Membrane, Cell Surface, Cells, Citric Acid, Cultured, Female, Glutamic Acid, GTP-Binding Proteins, Isoenzymes, Knockout, Male, Membrane Proteins, Mice, Neurons, Phospholipase C beta, Quinine, Receptors, Sensory Receptor Cells, Signal Transduction, Sucrose, Taste, Taste Buds, TRPM Cation Channels, Type C Phospholipases}, issn = {0092-8674}, author = {Zhang, Yifeng and Hoon, Mark A and Chandrashekar, Jayaram and Mueller, Ken L and Cook, Boaz and Wu, Dianqing and Zuker, Charles S and Ryba, Nicholas J P} } @article {45766, title = {A comparison of parthenogenetic and sexual embryogenesis of the pea aphid Acyrthosiphon pisum (Hemiptera: Aphidoidea).}, journal = {J Exp Zool B Mol Dev Evol}, volume = {295}, year = {2003}, month = {2003 Feb 15}, pages = {59-81}, abstract = {

Aphids exhibit divergent modes of embryogenesis during the sexual and asexual phases of the life cycle. To explore how a single genome can give rise to these alternative developmental modes, we have initiated embryological studies of the pea aphid, Acyrthosiphon pisum. Here we present a detailed description of parthenogenetic, viviparous embryonic development in the pea aphid. We compare and contrast development of the parthenogenetic embryo with that of the embryo resulting from sexual reproduction. The primary difference between the embryos is the scale on which development occurs: early parthenogenetic development occurs in a volume approximately three orders of magnitude smaller than the sexual egg, largely because of the apparent absence of yolk in the parthenogenetic egg. This results in a drastically different duration of syncytial energid cleavage and, presumably, patterning processes in the two embryos must act at scales that differ by orders of magnitude. The eggs also develop on time scales that differ approximately by an order of magnitude and the timing of the embryonic movements, collectively called blastokinesis, have temporally shifted relative to growth of the embryo. In addition, the endosymbiotic bacteria are transferred from mother to embryo in different ways in the two embryos. Finally, the function of the serosa has diverged greatly in the two embryos: in the sexual egg the serosa deposits a thick cuticle that protects the egg, whereas the serosa of the parthenogenetic embryo is greatly reduced and its function is unclear. The pea aphid is a useful model system for examining how a single genome has evolved to allow divergent modes of development.

}, keywords = {Animals, Aphids, Embryo, Nonmammalian, Female, Germ Cells, Male, Morphogenesis, Ovum, Parthenogenesis, Reproduction}, issn = {1552-5007}, doi = {10.1002/jez.b.3}, author = {Miura, Toru and Braendle, Christian and Shingleton, Alexander and Sisk, Geoffroy and Kambhampati, Srinivas and Stern, David L} } @article {2421, title = {Control of cell number by Drosophila FOXO: downstream and feedback regulation of the insulin receptor pathway.}, journal = {Genes \& Development}, volume = {17}, year = {2003}, month = {2003 Aug 15}, pages = {2006-20}, abstract = {

The Drosophila insulin receptor (dInR) regulates cell growth and proliferation through the dPI3K/dAkt pathway, which is conserved in metazoan organisms. Here we report the identification and functional characterization of the Drosophila forkhead-related transcription factor dFOXO, a key component of the insulin signaling cascade. dFOXO is phosphorylated by dAkt upon insulin treatment, leading to cytoplasmic retention and inhibition of its transcriptional activity. Mutant dFOXO lacking dAkt phosphorylation sites no longer responds to insulin inhibition, remains in the nucleus, and is constitutively active. dFOXO activation in S2 cells induces growth arrest and activates two key players of the dInR/dPI3K/dAkt pathway: the translational regulator d4EBP and the dInR itself. Induction of d4EBP likely leads to growth inhibition by dFOXO, whereas activation of dInR provides a novel transcriptionally induced feedback control mechanism. Targeted expression of dFOXO in fly tissues regulates organ size by specifying cell number with no effect on cell size. Our results establish dFOXO as a key transcriptional regulator of the insulin pathway that modulates growth and proliferation.

}, keywords = {Amino Acid, Amino Acid Sequence, Animals, Biological, Cell Count, Cell Division, Cell Nucleus, Chromones, Drosophila, Drosophila Proteins, Enzyme Inhibitors, Feedback, Forkhead Transcription Factors, Gene Expression Regulation, Insect Proteins, Insulin, Models, Molecular Sequence Data, Morpholines, Physiological, Post-Translational, Protein Processing, Protein-Serine-Threonine Kinases, Proto-Oncogene Proteins, Proto-Oncogene Proteins c-akt, Receptor, Recombinant Proteins, Sequence Homology, Signal Transduction, Trans-Activators, Transcription Factors}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Puig, Oscar and Marr, Michael T and Ruhf, M Laure and Tjian, Robert} } @article {1592, title = {Crystal structure of Pyrococcus furiosus phosphoglucose isomerase. Implications for substrate binding and catalysis.}, journal = {The Journal of Biological Chemistry}, volume = {278}, year = {2003}, month = {2003 Aug 29}, pages = {33290-7}, abstract = {

Phosphoglucose isomerase (PGI) catalyzes the reversible isomerization between d-fructose 6-phosphate and d-glucose 6-phosphate as part of the glycolytic pathway. PGI from the Archaea Pyrococcus furiosus (Pfu) was crystallized, and its structure was determined by x-ray diffraction to a 2-A resolution. Structural comparison of this archaeal PGI with the previously solved structures of bacterial and eukaryotic PGIs reveals a completely different structure. Each subunit of the homodimeric Pfu PGI consists of a cupin domain, for which the overall structure is similar to other cupin domain-containing proteins, and includes a conserved transition metal-binding site. Biochemical data on the recombinant enzyme suggests that Fe2+ is bound to Pfu PGI. However, as catalytic activity is not strongly influenced either by the replacement of Fe2+ by a range of transition metals or by the presence or absence of the bound metal ion, we suggest that the metal may not be directly involved in catalysis but rather may be implicated in substrate recognition.

}, keywords = {Amino Acid, Amino Acid Sequence, Binding Sites, Chemical, Crystallography, Dimerization, Fructosephosphates, Glucose-6-Phosphate, Glucose-6-Phosphate Isomerase, Ions, Iron, Metals, Models, Molecular, Molecular Sequence Data, Protein Binding, Protein Conformation, Protein Structure, Pyrococcus furiosus, Secondary, Selenomethionine, Sequence Homology, Substrate Specificity, Temperature, Tertiary, X-Ray, X-Ray Diffraction}, issn = {0021-9258}, doi = {10.1074/jbc.M305170200}, author = {Berrisford, John M and Akerboom, Jasper and Turnbull, Andrew P and de Geus, Daniel and Sedelnikova, Svetlana E and Staton, Ian and McLeod, Cameron W and Verhees, Corn{\'e} H and van der Oost, John and Rice, David W and Baker, Patrick J} } @article {46400, title = {Crystal structure of the nickel-responsive transcription factor NikR.}, journal = {Nature Structural Biology}, volume = {10}, year = {2003}, month = {2003 Oct}, pages = {794-9}, abstract = {

NikR is a metal-responsive transcription factor that controls nickel uptake in Escherichia coli by regulating expression of a nickel-specific ATP-binding cassette (ABC) transporter. We have determined the first two structures of NikR: the full-length apo repressor at a resolution of 2.3 A and the nickel-bound C-terminal regulatory domain at a resolution of 1.4 A. NikR is the only known metal-responsive member of the ribbon-helix-helix family of transcription factors, and its structure has a quaternary arrangement consisting of two dimeric DNA-binding domains separated by a tetrameric regulatory domain that binds nickel. The position of the C-terminal regulatory domain enforces a large spacing between the contacts that each NikR DNA-binding domain can make with the nik operator. The regulatory domain of NikR contains four nickel-binding sites at the tetramer interface, each exhibiting a novel square-planar coordination by three histidines and one cysteine side chain.

}, keywords = {Amino Acid Sequence, Crystallography, X-Ray, Escherichia coli, Escherichia coli Proteins, Molecular Sequence Data, Nickel, Protein Structure, Tertiary, Repressor Proteins}, issn = {1072-8368}, doi = {10.1038/nsb985}, author = {Schreiter, Eric R and Sintchak, Michael D and Guo, Yayi and Chivers, Peter T and Sauer, Robert T and Drennan, Catherine L} } @article {1110, title = {Design, synthesis, and development of novel caprolactam anticonvulsants.}, journal = {Bioorganic \& Medicinal Chemistry}, volume = {11}, year = {2003}, month = {2003 Sep 1}, pages = {4133-41}, abstract = {

Epilepsy afflicts 1-2\% of the world{\textquoteright}s population and often goes untreated; nearly 70\% of those with a form of epilepsy fail to receive proper treatment. Therefore, there is great demand for the design of novel, effective anticonvulsants to combat epilepsy in its numerous forms. Previously, alpha-hydroxy-alpha-phenylcaprolactam was found to have rather potent antiepileptic activity [anti-maximal electroshock (MES) ED(50)=63 mg/kg and anti-subcutaneous Metrazol (scMet) ED(50)=74 mg/kg] when administered intraperitoneally in mice. We focused our attention on the development of this compound through traditional medicinal chemistry techniques-including the Topliss approach, isosteric replacement, methylene insertion, and rigid analogue approach-in the hopes of determining the effect of caprolactam alpha-substitution and other structural modifications on anticonvulsant activity. A number of the desired targets were successfully synthesized and submitted to the Anticonvulsant Screening Program of the National Institute of Neurological Disorders and Stroke (NINDS). Phase I results were quite promising for at least three of the compounds: alpha-ethynyl-alpha-hydroxycaprolactam (10), alpha-benzyl-alpha-hydroxycaprolactam (11), and alpha-hydroxy-alpha-(phenylethynyl)caprolactam (13). Phase II results for 11 strongly suggested it as a new structural class for further development, as it exhibited an anti-MES T.I. in excess of 4.0. Further, the potent activity of 13 in all models also pointed to the substituted alkynylcaprolactams as a new anticonvulsant structural class.

}, keywords = {Administration, Animals, Anticonvulsants, Brain, Caprolactam, Drug Design, Epilepsy, Injections, Intraperitoneal, Mice, Oral, Rats, Structure-Activity Relationship}, issn = {0968-0896}, author = {Grimm, Jonathan B and Stables, James P and Brown, Milton L} } @article {45761, title = {Developmental origin and evolution of bacteriocytes in the aphid-Buchnera symbiosis.}, journal = {PLoS Biol}, volume = {1}, year = {2003}, month = {2003 Oct}, pages = {E21}, abstract = {

Symbiotic relationships between bacteria and insect hosts are common. Although the bacterial endosymbionts have been subjected to intense investigation, little is known of the host cells in which they reside, the bacteriocytes. We have studied the development and evolution of aphid bacteriocytes, the host cells that contain the endosymbiotic bacteria Buchnera aphidicola. We show that bacteriocytes of Acyrthosiphon pisum express several gene products (or their paralogues): Distal-less, Ultrabithorax/Abdominal-A, and Engrailed. Using these markers, we find that a subpopulation of the bacteriocytes is specified prior to the transmission of maternal bacteria to the embryo. In addition, we discovered that a second population of cells is recruited to the bacteriocyte fate later in development. We experimentally demonstrate that bacteriocyte induction and proliferation occur independently of B. aphidicola. Major features of bacteriocyte development, including the two-step recruitment of bacteriocytes, have been conserved in aphids for 80-150 million years. Furthermore, we have investigated two cases of evolutionary loss of bacterial symbionts: in one case, where novel extracellular, eukaryotic symbionts replaced the bacteria, the bacteriocyte is maintained; in another case, where symbionts are absent, the bacteriocytes are initiated but not maintained. The bacteriocyte represents an evolutionarily novel cell fate, which is developmentally determined independently of the bacteria. Three of five transcription factors we examined show novel expression patterns in bacteriocytes, suggesting that bacteriocytes may have evolved to express many additional transcription factors. The evolutionary transition to a symbiosis in which bacteria and an aphid cell form a functional unit, similar to the origin of plastids, has apparently involved extensive molecular adaptations on the part of the host cell.

}, keywords = {Animals, Aphids, Buchnera, Cell Lineage, Drosophila Proteins, Evolution, Molecular, Female, Gene Expression Regulation, Bacterial, Homeodomain Proteins, Male, Microscopy, Fluorescence, Models, Biological, Parthenogenesis, Species Specificity, Symbiosis, Time Factors, Transcription Factors}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0000021}, author = {Braendle, Christian and Miura, Toru and Bickel, Ryan and Shingleton, Alexander W and Kambhampati, Srinivas and Stern, David L} } @article {45763, title = {Diapause in the pea aphid (Acyrthosiphon pisum) is a slowing but not a cessation of development.}, journal = {BMC Dev Biol}, volume = {3}, year = {2003}, month = {2003 Aug 8}, pages = {7}, abstract = {

BACKGROUND: Many insects undergo a period of arrested development, called diapause, to avoid seasonally recurring adverse conditions. Whilst the phenology and endocrinology of insect diapause have been well studied, there has been comparatively little research into the developmental details of diapause. We investigated developmental aspects of diapause in sexually-produced embryos of the pea aphid, Acyrthosiphon pisum.

RESULTS: We found that early stages of embryogenesis progressed at a temperature-independent rate, characteristic of diapause, whereas later stages of embryogenesis progressed at a temperature-dependent rate. However, embryos maintained at very high temperatures during the temperature-independent stage showed severe developmental abnormalities. Under no temperature regime did embryos display a distinct resting stage. Rather, morphological development progressed slowly but continuously throughout embryogenesis.

CONCLUSION: Diapause in the pea aphid, and perhaps in many other insects, is a temperature-independent slowing but not a cessation of morphological development. This suggests that the mechanisms limiting developmental rate during diapause may be the same as those controlling developmental rate at other stages of growth.

}, keywords = {Animals, Aphids, Female, Life Cycle Stages, Male, Peas, Temperature}, issn = {1471-213X}, doi = {10.1186/1471-213X-3-7}, author = {Shingleton, Alexander W and Sisk, Geoffroy C and Stern, David L} } @article {2424, title = {Diversified transcription initiation complexes expand promoter selectivity and tissue-specific gene expression.}, journal = {Genes \& Development}, volume = {17}, year = {2003}, month = {2003 Jun 1}, pages = {1309-20}, keywords = {Animals, Developmental, Drosophila, Drosophila Proteins, Gene Expression Regulation, Genetic, Male, Messenger, Organ Specificity, Promoter Regions, RNA, RNA Polymerase III, Spermatogenesis, TATA Box Binding Protein-Like Proteins, Telomeric Repeat Binding Protein 2, Transcription}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Hochheimer, Andreas and Tjian, Robert} } @article {2322, title = {Dopamine D1 receptors mediate CREB phosphorylation via phosphorylation of the NMDA receptor at Ser897-NR1.}, journal = {Journal of Neurochemistry}, volume = {87}, year = {2003}, month = {2003 Nov}, pages = {922-34}, abstract = {

Addictive drugs such as amphetamine and cocaine stimulate the dopaminergic system, activate dopamine receptors and induce gene expression throughout the striatum. The signal transduction pathway leading from dopamine receptor stimulation at the synapse to gene expression in the nucleus has not been fully elucidated. Here, we present evidence that D1 receptor stimulation leads to phosphorylation of the transcription factor Ca2+ and cyclic AMP response element binding protein (CREB) in the nucleus by means of NMDA receptor-mediated Ca2+ signaling. Stimulation of D1 receptors induces the phosphorylation of Ser897 on the NR1 subunit by protein kinase A (PKA). This phosphorylation event is crucial for D1 receptor-mediated CREB phosphorylation. Dopamine cannot induce CRE-mediated gene expression in neurons transfected with a phosphorylation-deficient NR1 construct. Moreover, stimulation of D1 receptors or increase in cyclic AMP levels leads to an increase in cytosolic Ca2+ in the presence of glutamate, but not in the absence of glutamate, indicating the ability of dopamine and cyclic AMP to facilitate NMDA channel activity. The recruitment of the NMDA receptor signal transduction pathway by D1 receptors may provide a general mechanism for gene regulation that is fundamental for mechanisms of drug addiction and long-term memory.

}, keywords = {Animals, Calcium, Calcium-Calmodulin-Dependent Protein Kinases, Cells, Corpus Striatum, Cultured, Cyclic AMP Response Element-Binding Protein, Cyclic AMP-Dependent Protein Kinases, Dopamine D1, Glutamic Acid, Mutagenesis, N-Methyl-D-Aspartate, Neurons, Phosphorylation, Rats, Receptors, Signal Transduction, Site-Directed, Sprague-Dawley}, issn = {0022-3042}, doi = {10.3389/fnana.2010.00147}, author = {Dudman, Joshua T and Eaton, Molly E and Rajadhyaksha, Anjali and Mac{\'\i}as, Wendy and Taher, Muffadal and Barczak, Amy and Kameyama, Kimihiko and Huganir, Richard and Konradi, Christine} } @article {46636, title = {Drosophila melanogaster, a genetic model system for alcohol research.}, journal = {International Review of Neurobiology}, volume = {54}, year = {2003}, month = {2003}, pages = {199-228}, abstract = {

In its natural environment, which consists of fermenting plant materials, the fruit fly Drosophila melanogaster encounters high levels of ethanol. Flies are well equipped to deal with the toxic effects of ethanol; they use it as an energy source and for lipid biosynthesis. The primary ethanol-metabolizing pathway in flies involves the enzymes alcohol dehydrogenase (ADH) and acetaldehyde dehydrogenase (ALDH); their role in adaptation to ethanol-rich environments has been studied extensively. The similarity between Drosophila and mammals is not restricted to the manner in which they metabolize ethanol; behaviors elicited by ethanol exposure are also remarkably similar in these organisms. Flies show signs of acute intoxication, which range from locomotor stimulation at low doses to complete sedation at higher doses, they develop tolerance upon intermittent ethanol exposure, and they appear to like ethanol, showing preference for ethanol-containing media. Molecular genetic analysis of ethanol-induced behaviors in Drosophila, while still in its early stages, has already revealed some surprising parallels with mammals. The availability of powerful tools for genetic manipulation in Drosophila, together with the high degree of conservation at the genomic level, make Drosophila a promising model organism to study the mechanism by which ethanol regulates behavior and the mechanisms underlying the organism{\textquoteright}s adaptation to long-term ethanol exposure.

}, keywords = {Alcohol Dehydrogenase, Alcoholism, Aldehyde Oxidoreductases, Animals, Behavior, Animal, Cell Membrane, Conditioning (Psychology), Drosophila melanogaster, Drug Tolerance, Ethanol, Humans, Models, Animal, Mutation}, issn = {0074-7742}, author = {Guarnieri, Douglas J and Heberlein, Ulrike} } @article {2514, title = {E74 exhibits stage-specific hormonal regulation in the epidermis of the tobacco hornworm, manduca sexta.}, journal = {Developmental Biology}, volume = {258}, year = {2003}, month = {2003 Jun 1}, pages = {76-90}, abstract = {

The transcription factor E74 is one of the early genes induced by ecdysteroids during metamorphosis of Drosophila melanogaster. Here, we report the cloning and hormonal regulation of E74 from the tobacco hornworm, Manduca sexta (MsE74). MsE74 is 98\% identical to that of D. melanogaster within the DNA-binding ETS domain of the protein. The 5{\textquoteright}-isoform-specific regions of MsE74A and MsE74B share significantly lower sequence similarity (30-40\%). Developmental expression by Northern blot analysis reveals that, during the 5th larval instar, MsE74B expression correlates with pupal commitment on day 3 and is induced to maximal levels within 12h by low levels of 20-hydroxyecdysone (20E) and repressed by physiologically relevant levels of juvenile hormone I (JH I). Immunocytochemical analysis shows that MsE74B appears in the epidermis before the 20E-induced Broad transcription factor that is correlated with pupal commitment (Zhou and Riddiford, 2001). In contrast, MsE74A is expressed late in the larval and the pupal molts when the ecdysteroid titer has declined to low levels and in the adult molt just as the ecdysteroid titer begins to decline. This change in timing during the adult molt appears not to be due to the absence of JH as there was no change during the pupal molt of allatectomized animals. When either 4th or 5th instar larval epidermis was explanted and subjected to hormonal manipulations, MsE74A induction occurred only after exposure to 20E followed by its removal. Thus, MsE74B appears to have a similar role at the onset of metamorphosis in Manduca as it does in Drosophila, whereas MsE74A is regulated differently at pupation in Manduca than at pupariation in Drosophila.

}, keywords = {Amino Acid, Amino Acid Sequence, Animals, Base Sequence, Biological, Cells, Cultured, Developmental, Drosophila, Ecdysterone, Epidermis, Gene Expression Regulation, Genes, Insect, Insect Proteins, Juvenile Hormones, Larva, Manduca, Messenger, Metamorphosis, Molecular Sequence Data, Open Reading Frames, Protein Isoforms, Protein Structure, Pupa, RNA, Sequence Homology, Tertiary, Transcription Factors}, issn = {0012-1606}, author = {Stilwell, Geoffrey E and Nelson, Charles A and Weller, John and Cui, Haiyang and Hiruma, Kiyoshi and Truman, James W and Riddiford, Lynn M} } @article {6354, title = {Functional properties of a brain-specific NH2-terminally spliced modulator of Kv4 channels.}, journal = {American Journal of Physiology. Cell Physiology}, volume = {285}, year = {2003}, month = {2003 Jul}, pages = {C161-70}, abstract = {

Kv4/K channel-interacting protein (KChIP) potassium channels are a major class of rapidly inactivating K channels in brain and heart. Considering the importance of alternative splicing to the quantitative features of KChIP gating modulation, a previously uncharacterized splice form of KChIP1 was functionally characterized. The KChIP1b splice variant differs from the previously characterized KChIP1a splice form by the inclusion of a novel amino-terminal region that is encoded by an alternative exon that is conserved in mouse, rat, and human genes. The expression of KChIP1b mRNA was high in brain but undetectable in heart or liver by RT-PCR. In cerebellar tissue, KChIP1b and KChIP1a transcripts were expressed at nearly equal levels. Coexpression of KChIP1b or KChIP1a with Kv4.2 channels in oocytes slowed K current decay and destabilized open-inactivated channel gating. Like other KChIP subunits, KChIP1b increased Kv4.2 current amplitude and KChIP1b also shifted Kv4.2 conductance-voltage curves by -10 mV. The development of Kv4.2 channel inactivation accessed from closed gating states was faster with KChIP1b coexpression. Deletion of the novel amino-terminal region in KChIP1b selectively altered the subunit{\textquoteright}s modulation of Kv4.2 closed inactivation gating. The role of the KChIP1b NH2-terminal region was further confirmed by direct comparison of the properties of the NH2-terminal deletion mutant and the KChIP1a subunit, which is encoded by a transcript that lacks the novel exon. The features of KChIP1b modulation of Kv4 channels are likely to be conserved in mammals and demonstrate a role for the KChIP1 NH2-terminal region in the regulation of closed inactivation gating.

}, keywords = {Alternative Splicing, Amino Acid Sequence, Animals, Brain, Calcium-Binding Proteins, Exons, Ion Channel Gating, Kv Channel-Interacting Proteins, Mammals, Molecular Sequence Data, Mutagenesis, Oocytes, Potassium Channels, Protein Structure, Rats, Shal Potassium Channels, Tertiary, Voltage-Gated, Xenopus}, issn = {0363-6143}, doi = {10.1152/ajpcell.00416.2002}, author = {Boland, Linda M and Jiang, Min and Lee, So Yeong and Fahrenkrug, Scott C and Harnett, Mark T and O{\textquoteright}Grady, Scott M} } @article {2380, title = {Genetic specification of axonal arbors: atonal regulates robo3 to position terminal branches in the Drosophila nervous system.}, journal = {Neuron}, volume = {37}, year = {2003}, month = {2003 Jan 9}, pages = {41-51}, abstract = {

Drosophila sensory neurons form distinctive terminal branch patterns in the developing neuropile of the embryonic central nervous system. In this paper we make a genetic analysis of factors regulating arbor position. We show that mediolateral position is determined in a binary fashion by expression (chordotonal neurons) or nonexpression (multidendritic neurons) of the Robo3 receptor for the midline repellent Slit. Robo3 expression is one of a suite of chordotonal neuron properties that depend on expression of the proneural gene atonal. Different features of terminal branches are separately regulated: an arbor can be shifted mediolaterally without affecting its dorsoventral location, and the distinctive remodeling of one arbor continues as normal despite this arbor shifting to an abnormal position in the neuropile.

}, keywords = {Afferent, Animals, Axons, Basic Helix-Loop-Helix Transcription Factors, Cell Communication, Cell Differentiation, Developmental, DNA-Binding Proteins, Drosophila melanogaster, Drosophila Proteins, Embryo, Female, Functional Laterality, Gene Expression Regulation, Growth Cones, Immunologic, Larva, Male, Membrane Proteins, Mutation, Nerve Tissue Proteins, Nervous System, Nervous System Malformations, Neuronal Plasticity, Neurons, Nonmammalian, Presynaptic Terminals, Receptors}, issn = {0896-6273}, author = {Zlatic, Marta and Landgraf, Matthias and Bate, Michael} } @article {2139, title = {Haploinsufficiency at the Nkx3.1 locus. A paradigm for stochastic, dosage-sensitive gene regulation during tumor initiation.}, journal = {Cancer Cell}, volume = {3}, year = {2003}, month = {2003 Mar}, pages = {273-83}, abstract = {

Tumorigenesis requires sequential accumulation of multiple genetic lesions. In the prostate, tumor initiation is often linked to loss of heterozygosity at the Nkx3.1 locus. In mice, loss of even one Nkx3.1 allele causes prostatic epithelial hyperplasia and eventual prostatic intraepithelial neoplasia (PIN) formation. Here we demonstrate that Nkx3.1 allelic loss extends the proliferative stage of regenerating luminal cells, leading to epithelial hyperplasia. Microarray analysis identified Nkx3.1 target genes, many of which show exquisite dosage sensitivity. The number of Nkx3.1 alleles determines the relative probabilities of stochastic activation or inactivation of a given target gene. Thus, loss of a single Nkx3.1 allele likely results in hyperplasia and PIN by increasing the probability of completely inactivating select Nkx3.1-regulated pathways within a subset of affected cells.

}, keywords = {Alleles, Animals, Biological, Cell Division, Gene Deletion, Gene Dosage, Gene Expression Profiling, Gene Expression Regulation, Gene Targeting, Genes, Genetic Predisposition to Disease, Loss of Heterozygosity, Male, Mice, Models, Mutant Strains, Neoplastic, Orchiectomy, Prostatic Intraepithelial Neoplasia, Prostatic Neoplasms, Testosterone, Tumor Suppressor}, issn = {1535-6108}, doi = {10.1002/cbic.201000254}, author = {Magee, Jeffrey A and Abdulkadir, Sarki A and Milbrandt, Jeffrey} } @article {45764, title = {The Hox gene Ultrabithorax modulates the shape and size of the third leg of Drosophila by influencing diverse mechanisms.}, journal = {Dev Biol}, volume = {256}, year = {2003}, month = {2003 Apr 15}, pages = {355-66}, abstract = {

The developmental mechanisms that regulate the relative size and shape of organs have remained obscure despite almost a century of interest in the problem and the fact that changes in relative size represent the dominant mode of evolutionary change. Here, I investigate how the Hox gene Ultrabithorax (Ubx) instructs the legs on the third thoracic segment of Drosophila melanogaster to develop with a different size and shape from the legs on the second thoracic segment. Through loss-of-function and gain-of-function experiments, I demonstrate that different segments of the leg, the femur and the first tarsal segment, and even different regions of the femur, regulate their size in response to Ubx expression through qualitatively different mechanisms. In some regions, Ubx acts autonomously to specify shape and size, whereas in other regions, Ubx influences size through nonautonomous mechanisms. Loss of Ubx autonomously reduces cell size in the T3 femur, but this reduction seems to be partially compensated by an increase in cell numbers, so that it is unclear what effect cell size and number directly have on femur size. Loss of Ubx has both autonomous and nonautonomous effects on cell number in different regions of the basitarsus, but again there is not a strong correlation between cell size or number and organ size. Total organ size appears to be regulated through mechanisms that operate at the level of the entire leg segment (femur or basitarsus) relatively independently of the behavior of individual subpopulations of cells within the segment.

}, keywords = {Animals, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Extremities, Gene Expression Regulation, Developmental, Homeodomain Proteins, Pupa, Transcription Factors}, issn = {0012-1606}, author = {Stern, David L} } @article {2321, title = {The hyperpolarization-activated HCN1 channel is important for motor learning and neuronal integration by cerebellar Purkinje cells.}, journal = {Cell}, volume = {115}, year = {2003}, month = {2003 Nov 26}, pages = {551-64}, abstract = {

In contrast to our increasingly detailed understanding of how synaptic plasticity provides a cellular substrate for learning and memory, it is less clear how a neuron{\textquoteright}s voltage-gated ion channels interact with plastic changes in synaptic strength to influence behavior. We find, using generalized and regional knockout mice, that deletion of the HCN1 channel causes profound motor learning and memory deficits in swimming and rotarod tasks. In cerebellar Purkinje cells, which are a key component of the cerebellar circuit for learning of correctly timed movements, HCN1 mediates an inward current that stabilizes the integrative properties of Purkinje cells and ensures that their input-output function is independent of the previous history of their activity. We suggest that this nonsynaptic integrative function of HCN1 is required for accurate decoding of input patterns and thereby enables synaptic plasticity to appropriately influence the performance of motor activity.

}, keywords = {Action Potentials, Afferent Pathways, Animals, Cells, Conditioning (Psychology), Cultured, Cyclic Nucleotide-Gated Cation Channels, Ion Channels, Knockout, Learning, Maze Learning, Mice, Motor Skills, Movement, Nerve Tissue Proteins, Neuronal Plasticity, Potassium Channels, Purkinje Cells, Synapses, Synaptic Transmission}, issn = {0092-8674}, doi = {10.3389/fnana.2010.00147}, author = {Nolan, Matthew F and Malleret, Ga{\"e}l and Lee, Ka Hung and Gibbs, Emma and Dudman, Joshua T and Santoro, Bina and Yin, Deqi and Thompson, Richard F and Siegelbaum, Steven A and Kandel, Eric R and Morozov, Alexei} } @article {2137, title = {Impaired regulation of synaptic strength in hippocampal neurons from GluR1-deficient mice.}, journal = {The Journal of Physiology}, volume = {552}, year = {2003}, month = {2003 Oct 1}, pages = {35-45}, abstract = {

Neurons of the central nervous system (CNS) exhibit a variety of forms of synaptic plasticity, including associative long-term potentiation and depression (LTP/D), homeostatic activity-dependent scaling and distance-dependent scaling. Regulation of synaptic neurotransmitter receptors is currently thought to be a common mechanism amongst many of these forms of plasticity. In fact, glutamate receptor 1 (GluR1 or GluRA) subunits containing L-alpha-amino-3-hydroxy-5-methylisoxazole-4-propionate (AMPA) receptors have been shown to be required for several forms of hippocampal LTP and a particular hippocampal-dependent learning task. Because of this importance in associative plasticity, we sought to examine the role of these receptors in other forms of synaptic plasticity in the hippocampus. To do so, we recorded from the apical dendrites of hippocampal CA1 pyramidal neurons in mice lacking the GluR1 subunit (GluR1 -/-). Here we report data from outside-out patches that indicate GluR1-containing receptors are essential to the extrasynaptic population of AMPA receptors, as this pool was nearly empty in the GluR1 -/- mice. Additionally, these receptors appear to be a significant component of the synaptic glutamate receptor pool because the amplitude of spontaneous synaptic currents recorded at the site of input and synaptic AMPA receptor currents evoked by focal glutamate uncaging were both substantially reduced in these mice. Interestingly, the impact on synaptic weight was greatest at distant synapses such that the normal distance-dependent synaptic scaling used by these cells to counter dendritic attenuation was lacking in GluR1 -/- mice. Together the data suggest that the highly regulated movement of GluR1-containing AMPA receptors between extrasynaptic and synaptic receptor pools is critically involved in establishing two functionally diverse forms of synaptic plasticity: LTP and distance-dependent scaling.

}, keywords = {AMPA, Animals, Hippocampus, Inbred C57BL, Kinetics, Long-Term Potentiation, Mice, Mutant Strains, Neuronal Plasticity, Patch-Clamp Techniques, Pyramidal Cells, Receptors, Synapses}, issn = {0022-3751}, doi = {10.1002/cbic.201000254}, author = {Andrasfalvy, Bertalan K and Smith, Mark A and Borchardt, Thilo and Sprengel, Rolf and Magee, Jeffrey C} } @article {2014, title = {In vivo imaging of C. elegans mechanosensory neurons demonstrates a specific role for the MEC-4 channel in the process of gentle touch sensation.}, journal = {Neuron}, volume = {39}, year = {2003}, month = {2003 Sep 11}, pages = {1005-17}, abstract = {

In the nematode C. elegans, genes encoding components of a putative mechanotransducing channel complex have been identified in screens for light-touch-insensitive mutants. A long-standing question, however, is whether identified MEC proteins act directly in touch transduction or contribute indirectly by maintaining basic mechanoreceptor neuron physiology. In this study, we used the genetically encoded calcium indicator cameleon to record cellular responses of mechanosensory neurons to touch stimuli in intact, behaving nematodes. We defined a gentle touch sensory modality that adapts with a time course of approximately 500 ms and primarily senses motion rather than pressure. The DEG/ENaC channel subunit MEC-4 and channel-associated stomatin MEC-2 are specifically required for neural responses to gentle mechanical stimulation but do not affect the basic physiology of touch neurons or their in vivo responses to harsh mechanical stimulation. These results distinguish a specific role for the MEC channel proteins in the process of gentle touch mechanosensation.

}, keywords = {Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Calcium Channels, Cells, Cellular, Cultured, L-Type, Mechanoreceptors, Mechanotransduction, Membrane Potentials, Membrane Proteins, Neurons, Touch}, issn = {0896-6273}, author = {Suzuki, Hiroshi and Kerr, Rex and Bianchi, Laura and Fr{\o}kjaer-Jensen, Christian and Slone, Dan and Xue, Jian and Gerstbrein, Beate and Driscoll, Monica and Schafer, William R} } @article {2292, title = {Inducible nitric oxide synthase (NOS2) promoter CCTTT repeat polymorphism: relationship to in vivo nitric oxide production/NOS activity in an asymptomatic malaria-endemic population.}, journal = {The American Journal of Tropical Medicine and Hygiene}, volume = {69}, year = {2003}, month = {2003 Dec}, pages = {569-73}, abstract = {

Polymorphisms in the inducible nitric oxide synthase gene (NOS2) promoter have been associated with clinical outcome from malaria. These include a CCTTT repeat (CCTTTn) 2.5 kilobases upstream from the NOS2 transcription start site, and two single nucleotide substitutions: G{\textendash}\>C at position -954 (G-954C), and C{\textendash}\>T at position -1173 (C-1173T). Although hypothesized to influence NO production in vivo, the functional relevance of (CCTTT)n and G-954C is uncertain because disease association studies have yielded inconsistent results. This study found no association between CCTTT repeat number and levels of plasma NO metabolites or peripheral blood mononuclear cell NOS activity in a cohort of asymptomatic malaria-exposed coastal Papua New Guineans 1-60 years old. This suggests that (CCTTT)n does not independently influence NOS2 transcription in vivo. Neither the G-954C nor the C-1173T polymorphisms were identified in this population, indicating the variability and complexity of selection for NOS2 promoter polymorphisms in different malaria-endemic populations.

}, keywords = {Endemic Diseases, Female, Genetic, Genetic Predisposition to Disease, Humans, Malaria, Male, Nitric Oxide, Nitric Oxide Synthase, Nitric Oxide Synthase Type II, Nucleic Acid, Oceanic Ancestry Group, Papua New Guinea, Polymorphism, Promoter Regions, Repetitive Sequences}, issn = {0002-9637}, author = {Boutlis, Craig S and Hobbs, Maurine R and Marsh, Robyn L and Misukonis, Mary A and Tkachuk, Ariana N and Lagog, Moses and Booth, Jennifer and Granger, Donald L and Bockarie, Moses J and Mgone, Charles S and Levesque, Marc C and Weinberg, J Brice and Anstey, Nicholas M} } @article {45954, title = {Insertion of MP20 into lens fibre cell plasma membranes correlates with the formation of an extracellular diffusion barrier.}, journal = {Experimental Eye Research}, volume = {77}, year = {2003}, month = {2003 Nov}, pages = {567-74}, abstract = {

It is known that during lens differentiation a number of fibre cell specific membrane proteins change their expression profiles. In this study we have investigated how the profiles of the two most abundant fibre cell membrane proteins AQP0 (formerly known as Major Intrinsic Protein, MIP) and MP20 change as a function of fibre cell differentiation. While AQP0 was always found associated with fibre cell membranes, MP20 was initially found in the cytoplasm of peripheral fibre cells before becoming inserted into the membranes of deeper fibre cells. To determine at what stage in fibre cell differentiation MP20 becomes inserted into the membrane, sections were double-labelled with an antibody against MP20, and propidium iodide, a marker of cell nuclei. This showed that membrane insertion of MP20 occurs in a discrete transition zone that coincided with the degradation of cell nuclei. To test the significance of the membrane insertion of MP20 to overall lens function, whole lenses were incubated for varying times in a solution containing either Texas Red-dextran or Lucifer yellow as markers of extracellular space. Lenses were fixed and then processed for immunocytochemistry. Analysis of these sections showed that both tracer dyes were excluded from the extracellular space in an area that coincided with insertion of MP20 into the plasma membrane. Our results suggest that the insertion of MP20 into fibre cell membranes coincides with the creation of a barrier that restricts the diffusion of molecules into the lens core via the extracellular space.

}, keywords = {Animals, Aquaporins, Cell Differentiation, Cell Membrane, Cytoplasm, Extracellular Space, Eye Proteins, Lens, Crystalline, Membrane Glycoproteins, Rats, Sheep}, issn = {0014-4835}, author = {Grey, Angus C and Jacobs, Marc D and Gonen, Tamir and Kistler, Joerg and Donaldson, Paul J} } @article {1649, title = {Intensity versus identity coding in an olfactory system.}, journal = {Neuron}, volume = {39}, year = {2003}, month = {2003 Sep 11}, pages = {991-1004}, abstract = {

We examined the encoding and decoding of odor identity and intensity by neurons in the antennal lobe and the mushroom body, first and second relays, respectively, of the locust olfactory system. Increased odor concentration led to changes in the firing patterns of individual antennal lobe projection neurons (PNs), similar to those caused by changes in odor identity, thus potentially confounding representations for identity and concentration. However, when these time-varying responses were examined across many PNs, concentration-specific patterns clustered by identity, resolving the apparent confound. This is because PN ensemble representations changed relatively continuously over a range of concentrations of each odorant. The PNs{\textquoteright} targets in the mushroom body-Kenyon cells (KCs)-had sparse identity-specific responses with diverse degrees of concentration invariance. The tuning of KCs to identity and concentration and the patterning of their responses are consistent with piecewise decoding of their PN inputs over oscillation-cycle length epochs.

}, keywords = {Action Potentials, Animals, Female, Grasshoppers, Male, Mushroom Bodies, Neurons, Odors, Reaction Time, Smell}, issn = {0896-6273}, author = {Stopfer, Mark and Jayaraman, Vivek and Laurent, Gilles} } @article {45894, title = {Intracellular correlate of EPSP-spike potentiation in CA1 pyramidal neurons is controlled by GABAergic modulation.}, journal = {Hippocampus}, volume = {13}, year = {2003}, month = {2003}, pages = {801-5}, abstract = {

The hippocampus has been used extensively as a model to study plastic changes in the brain{\textquoteright}s neural circuitry. Immediately after high-frequency stimulation to hippocampal Schaffer collateral axons, a dramatic change occurs in the relationship between the presynaptic CA3 and the postsynaptic CA1 pyramidal neurons. For a fixed excitatory postsynaptic potential (EPSP), there arises an increased likelihood of action potential generation in the CA1 pyramidal neuron. This phenomenon is called EPSP-spike (E-S) potentiation. We explored E-S potentiation, using patch-clamp techniques in the hippocampal slice preparation. A specific protocol was developed to measure the action potential probability for a given synaptic strength, which allowed us to quantify the amount of E-S potentiation for a single neuron. E-S potentiation was greatest when gamma-aminobutyric acid (GABA)ergic inhibition was intact, suggesting that modulation of inhibition is a major aspect of E-S potentiation. Expression of E-S potentiation also correlated with a reduced action-potential threshold, which was greatest when GABAergic inhibition was intact. Conditioning stimuli produced a smaller threshold reduction when inhibition was blocked, but some reduction also occurred in the absence of a conditioning stimulus. Together, these results suggest that E-S potentiation is caused primarily through a reduction of GABAergic inhibition, leading to larger EPSPs and reduced action potential threshold. Our findings do not rule out, however, the possibility that modulation of voltage-gated conductances also contributes to E-S potentiation.

}, keywords = {Action Potentials, Animals, Dendrites, Excitatory Postsynaptic Potentials, GABA Antagonists, GABA-A Receptor Antagonists, GABA-B Receptor Antagonists, gamma-Aminobutyric Acid, Hippocampus, In Vitro Techniques, Intracellular Fluid, Neural Inhibition, Neuronal Plasticity, Patch-Clamp Techniques, Pyramidal Cells, Rats, Rats, Wistar, Receptors, GABA-A, Receptors, GABA-B, Synaptic Transmission}, issn = {1050-9631}, doi = {10.1002/hipo.10129}, author = {Staff, Nathan P and Spruston, Nelson} } @article {46639, title = {Invertebrate models of drug abuse.}, journal = {Journal of Neurobiology}, volume = {54}, year = {2003}, month = {2003 Jan}, pages = {161-78}, abstract = {

Susceptibility to drug addiction depends on genetic and environmental factors and their complex interactions. Studies with mammalian models have identified molecular targets, neurochemical systems, and brain regions that mediate some of the addictive properties of abused drugs. Yet, our understanding of how the primary effects of drugs lead to addiction remains incomplete. Recently, researchers have turned to the invertebrate model systems Drosophila melanogaster and Caenorhabditis elegans to dissect the mechanisms by which abused drugs modulate behavior. Due to their sophisticated genetics, relatively simple anatomy, and their remarkable molecular similarity to mammals, these invertebrate models should provide useful insights into the mechanisms of drug action. Here we review recent behavioral and genetic studies in flies and worms on the effects of ethanol, cocaine, and nicotine, three of the most widely abused drugs in the world.

}, keywords = {Alcoholic Intoxication, Animals, Behavior, Animal, Caenorhabditis elegans, Cocaine, Disease Models, Animal, Dopamine, Drosophila melanogaster, Drug Tolerance, Ethanol, Learning, Memory, Nicotine, Substance-Related Disorders}, issn = {0022-3034}, doi = {10.1002/neu.10166}, author = {Wolf, Fred W and Heberlein, Ulrike} } @article {2681, title = {Involvement of the ubiquitin-proteasome system in the early stages of wallerian degeneration.}, journal = {Neuron}, volume = {39}, year = {2003}, month = {2003 Jul 17}, pages = {217-25}, abstract = {

Local axon degeneration is a common pathological feature of many neurodegenerative diseases and peripheral neuropathies. While it is believed to operate with an apoptosis-independent molecular program, the underlying molecular mechanisms are largely unknown. In this study, we used the degeneration of transected axons, termed "Wallerian degeneration," as a model to examine the possible involvement of the ubiquitin proteasome system (UPS). Inhibiting UPS activity by both pharmacological and genetic means profoundly delays axon degeneration both in vitro and in vivo. In addition, we found that the fragmentation of microtubules is the earliest detectable change in axons undergoing Wallerian degeneration, which among other degenerative events, can be delayed by proteasome inhibitors. Interestingly, similar to transected axons, degeneration of axons from nerve growth factor (NGF)-deprived sympathetic neurons could also be suppressed by proteasome inhibitors. Our findings suggest a possibility that inhibiting UPS activity may serve to retard axon degeneration in pathological conditions.

}, keywords = {Amino Acids, Animal, Animals, Axons, Benzimidazoles, Blotting, Calpain, Cells, Chelating Agents, Cultured, Cysteine Endopeptidases, Cysteine Proteinase Inhibitors, Cytoskeleton, Disease Models, Drug Interactions, Egtazic Acid, Endopeptidases, Ganglia, Immunohistochemistry, Leupeptins, Microtubules, Multienzyme Complexes, Nerve Growth Factor, Newborn, Optic Nerve, Optic Nerve Injuries, Peptide Fragments, Proteasome Endopeptidase Complex, Rats, Sympathetic, Time Factors, Tubulin, Ubiquitin, Wallerian Degeneration, Western}, issn = {0896-6273}, author = {Zhai, Qiwei and Wang, Jing and Kim, Anna and Liu, Qing and Watts, Ryan and Hoopfer, Eric and Mitchison, Timothy and Luo, Liqun and He, Zhigang} } @article {46637, title = {Mechanism of hedgehog signaling during Drosophila eye development.}, journal = {Development}, volume = {130}, year = {2003}, month = {2003 Jul}, pages = {3053-62}, abstract = {

Although Hedgehog (Hh) signaling is essential for morphogenesis of the Drosophila eye, its exact link to the network of tissue-specific genes that regulate retinal determination has remained elusive. In this report, we demonstrate that the retinal determination gene eyes absent (eya) is the crucial link between the Hedgehog signaling pathway and photoreceptor differentiation. Specifically, we show that the mechanism by which Hh signaling controls initiation of photoreceptor differentiation is to alleviate repression of eya and decapentaplegic (dpp) expression by the zinc-finger transcription factor Cubitus interruptus (Ci(rep)). Furthermore, our results suggest that stabilized, full length Ci (Ci(act)) plays little or no role in Drosophila eye development. Moreover, while the effects of Hh are primarily concentration dependent in other tissues, hh signaling in the eye acts as a binary switch to initiate retinal morphogenesis by inducing expression of the tissue-specific factor Eya.

}, keywords = {Animals, Cell Differentiation, DNA-Binding Proteins, Drosophila melanogaster, Drosophila Proteins, Eye Proteins, Hedgehog Proteins, Models, Biological, Morphogenesis, Organisms, Genetically Modified, Photoreceptor Cells, Invertebrate, Signal Transduction, Transcription Factors, Wing}, issn = {0950-1991}, author = {Pappu, Kartik S and Chen, Rui and Middlebrooks, Brooke W and Woo, Catherine and Heberlein, Ulrike and Mardon, Graeme} } @article {2140, title = {Mechanism of the distance-dependent scaling of Schaffer collateral synapses in rat CA1 pyramidal neurons.}, journal = {The Journal of Physiology}, volume = {548}, year = {2003}, month = {2003 Apr 1}, pages = {245-58}, abstract = {

Schaffer collateral axons form excitatory synapses that are distributed across much of the dendritic arborization of hippocampal CA1 pyramidal neurons. Remarkably, AMPA-receptor-mediated miniature EPSP amplitudes at the soma are relatively independent of synapse location, despite widely different degrees of dendritic filtering. A progressive increase with distance in synaptic conductance is thought to produce this amplitude normalization. In this study we examined the mechanism(s) responsible for spatial scaling by making whole-cell recordings from the apical dendrites of CA1 pyramidal neurons. We found no evidence to suggest that there is any location dependence to the range of cleft glutamate concentrations found at Schaffer collateral synapses. Furthermore, we observed that release probability (Pr), paired-pulse facilitation and the size of the readily releasable vesicular pool are not dependent on synapse location. Thus, there do not appear to be any changes in the fundamental presynaptic properties of Schaffer collateral synapses that could account for distance-dependent scaling. On the other hand, two-photon uncaging of 4-methoxy-7-nitroindolinyl-caged L-glutamate onto isolated dendritic spines shows that the number of postsynaptic AMPA receptors per spine increases with distance from the soma. We conclude, therefore, that the main synaptic mechanism involved in the production of distance-dependent scaling of Schaffer collateral synapses is an elevated postsynaptic AMPA receptor density.

}, keywords = {Algorithms, alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid, AMPA, Animals, Computer Simulation, Dendrites, Electrophysiology, Excitatory Amino Acid Antagonists, Excitatory Postsynaptic Potentials, Glutamates, Glutamic Acid, Hippocampus, Indoles, Kinetics, Kynurenic Acid, N-Methyl-D-Aspartate, Neurotransmitter Agents, Patch-Clamp Techniques, Pyramidal Cells, Rats, Receptors, Sprague-Dawley, Synapses, Tetrodotoxin}, issn = {0022-3751}, doi = {10.1002/cbic.201000254}, author = {Smith, Mark A and Ellis-Davies, Graham C R and Magee, Jeffrey C} } @article {4481, title = {Microwave oven synthesis of esters promoted by imidazole.}, journal = {Tetrahedron Letters}, volume = {44}, year = {2003}, month = {2003 Feb 24}, pages = {1831-3}, abstract = {

Using imidazole as promotion agent, primary, secondary and phenolic alcohol compounds were esterified with aliphatic and aromatic carboxylic acid anhydrides. Heating a ternary mixture of alcohol, anhydride and imidazole in an unmodified microwave oven produced esters in low to high yields, depending on the steric bulk of the alcohol.

}, url = {http://www.sciencedirect.com/science/article/pii/S0040403903001047}, author = {Hirose, Takuji and Kopek, Benjamin G and Wang, Zhao-Hui and Yusa, Ritsuko and Baldwin, Bruce W.} } @article {45767, title = {Molecular phylogenetic evidence for multiple gains or losses of ant mutualism within the aphid genus Chaitophorus.}, journal = {Mol Phylogenet Evol}, volume = {26}, year = {2003}, month = {2003 Jan}, pages = {26-35}, abstract = {

Mutualism with ants is suspected to be a highly labile trait within homopteran evolution. We used molecular phylogenetic evidence to test whether the mutualism has multiple origins within a single aphid genus. We constructed a molecular phylogeny of 15 Chaitophorus Koch (Hemiptera: Aphidoidea) species, using mitochondrial cytochrome oxidase I and II sequences. Ant tending evolved, or was lost, at least five times during Chaitophorus evolution. Parametric bootstrapping rejected the hypothesis of a single origin of ant tending in this genus. Further, the Chaitophorus made at least two host genus switches from poplars (Populus) to willow (Salix), and four switches in feeding position, from leaf feeding to stem feeding or vice versa. This is the first phylogenetic confirmation that ant tending is an evolutionarily labile trait in aphids.

}, keywords = {Animals, Ants, Aphids, Behavior, Animal, Evolution, Molecular, Phylogeny, Symbiosis}, issn = {1055-7903}, author = {Shingleton, Alexander W and Stern, David L} } @article {2359, title = {Nitric oxide produced in rat liver mitochondria causes oxidative stress and impairment of respiration after transient hypoxia.}, journal = {The FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology}, volume = {17}, year = {2003}, month = {2003 Dec}, pages = {2194-201}, abstract = {

Nitric oxide (NO) is produced in mammals by different isoforms of NO synthase (NOS), including the constitutive mitochondrial enzyme (mtNOS). Here we demonstrate that the concentration of NO resulting from a mitochondrial NOS activity increases under hypoxic conditions in isolated rat liver mitochondria. We show that mitochondrially derived NO mediates the impairment of active (state 3) respiration as measured in the presence of the substrates glutamate and malate after reoxygenation. Simultaneously, NO induces oxidative stress in mitochondria, characterized by an increase in the amount of protein carbonyls and a decrease in glutathione (GSH). Both the accumulation of oxidative stress markers during and the impaired respiration after reoxygenation were prevented by blocking NO production with the NOS inhibitor L-NAME. These observations suggest that mitochondria are exposed to high amounts of NO generated by a mitochondrial NOS upon hypoxia/reoxygenation. Such increased NO levels, in turn, inhibit mitochondrial respiration and may cause oxidative stress that leads to irreversible impairment of mitochondria.

}, keywords = {Animals, Cell Hypoxia, Cell Respiration, Enzyme Inhibitors, Liver, Mitochondria, NG-Nitroarginine Methyl Ester, Nitric Oxide, Nitric Oxide Synthase, Oxidative Stress, Oxygen Consumption, Rats}, issn = {1530-6860}, doi = {10.1016/j.cub.2010.06.072}, author = {Schild, Lorenz and Reinheckel, Thomas and Reiser, Michael and Horn, Thomas F W and Wolf, Gerald and Augustin, Wolfgang} } @article {2138, title = {Normalization of Ca2+ signals by small oblique dendrites of CA1 pyramidal neurons.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {23}, year = {2003}, month = {2003 Apr 15}, pages = {3243-50}, abstract = {

Oblique dendrites of CA1 pyramidal neurons predominate in stratum radiatum and receive approximately 80\% of the synaptic input from Schaffer collaterals. Despite this fact, most of our understanding of dendritic signal processing in these neurons comes from studies of the main apical dendrite. Using a combination of Ca2+ imaging and whole-cell recording techniques in rat hippocampal slices, we found that the properties of the oblique dendrites differ markedly from those of the main dendrites. These different properties tend to equalize the Ca2+ rise from single action potentials as they backpropagate into the oblique dendrites from the main trunk. Evidence suggests that this normalization of Ca2+ signals results from a higher density of a transient, A-type K+ current [I(K(A))] in the oblique versus the main dendrites. The higher density of I(K(A)) may have important implications for our understanding of synaptic integration and plasticity in these structures.

}, keywords = {4-Aminopyridine, Action Potentials, Animals, Calcium, Calcium Channel Blockers, Calcium Signaling, Dendrites, Electric Stimulation, Fluorescent Dyes, Hippocampus, Patch-Clamp Techniques, Potassium Channel Blockers, Potassium Channels, Pyramidal Cells, Rats, Sodium Channels, Sprague-Dawley, Tetrodotoxin}, issn = {1529-2401}, doi = {10.1002/cbic.201000254}, author = {Frick, Andreas and Magee, Jeffrey and Koester, Helmut J and Migliore, Michele and Johnston, Daniel} } @article {3087, title = {Operant behavior can be triggered by the position of the rat relative to objects rotating on an inaccessible platform.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, year = {2003}, month = {2003 Feb 18}, pages = {2094-9}, abstract = {

The present study describes a task testing the ability of rats to trigger operant behavior by their relative spatial position to inaccessible rotating objects. Rats were placed in a Skinner box with a transparent front wall through which they could observe one or two adjacent objects fixed on a slowly rotating arena (d = 1 m) surrounded by an immobile black cylinder. The direction of arena rotation was alternated at a sequence of different time intervals. Rats were reinforced for the first bar-press that was emitted when a radius separating the two adjacent objects or dividing a single object into two halves (pointing radius) entered a 60 degrees sector of its circular trajectory defined with respect to the stationary Skinner box (reward sector). Well trained rats emitted 62.1 +/- 3.6\% of responses in a 60 degrees sector preceding the reward sector and in the first 30 degrees of the reward sector. Response rate increased only when the pointing radius was approaching the reward sector, regardless of the time elapsed from the last reward. In the extinction session, when no reward was delivered, rats responded during the whole passage of the pointing radius through the former reward sector and spontaneously decreased responding after the pointing radius left this area. This finding suggests that rats perceived the reward sector as a continuous single region. The same results were obtained when the Skinner box with the rat was orbiting around the immobile scene. It is concluded that rats can recognize and anticipate their position relative to movable objects.

}, keywords = {Animal, Animals, Behavior, Conditioning, Long-Evans, Male, Operant, Rats, Reward}, issn = {0027-8424}, doi = {10.1073/pnas.0438002100}, author = {Pastalkova, E and Kelemen, E and Bures, J} } @article {1257, title = {Power-law for axon diameters at branch point.}, journal = {BMC Neuroscience}, volume = {4}, year = {2003}, month = {2003 Aug 28}, pages = {18}, abstract = {

Axon calibers vary widely among different animals, neuron classes, and even within the same neuron. What determines the diameter of axon branches?

}, keywords = {Animals, Axons, Biological Evolution, Humans, Models, Neural Conduction, Neurological, Predictive Value of Tests, Reaction Time}, issn = {1471-2202}, doi = {10.1016/j.tins.2005.05.006}, author = {Chklovskii, Dmitri B and Stepanyants, Armen} } @article {1987, title = {Presynaptic cyclic nucleotide-gated ion channels modulate neurotransmission in the mammalian olfactory bulb.}, journal = {Neuron}, volume = {37}, year = {2003}, month = {2003 Feb 20}, pages = {639-47}, abstract = {

Cyclic nucleotide-gated channels (CNGCs) on the dendritic cilia of olfactory receptor neurons (ORNs) are critical for sensory transduction in the olfactory system. Do CNGCs also play a role in the axons and/or nerve terminals of ORNs? We find that the cyclic nucleotides cAMP and cGMP can both facilitate and depress synaptic transmission between olfactory nerve fibers and their targets in olfactory bulb glomeruli. Cyclic nucleotides increase intracellular Ca(2+) in ORN terminals and enhance spontaneous transmitter release; at higher concentrations, cyclic nucleotides depress evoked transmission by altering olfactory nerve excitability. Cyclic nucleotides have no effect on transmission or nerve excitability, however, in mice lacking olfactory CNGCs. Taken together, our results identify a novel role for presynaptic CNGCs in modulating neurotransmission.

}, keywords = {Animals, Calcium, Cyclic, Cyclic GMP, Electric Stimulation, Enzyme Inhibitors, Excitatory Postsynaptic Potentials, Forskolin, GABA Agonists, Inbred C57BL, Ion Channel Gating, Ion Channels, Mice, Nucleotides, Olfactory Bulb, Patch-Clamp Techniques, Presynaptic Terminals, Rats, Sprague-Dawley, Synaptic Transmission}, issn = {0896-6273}, author = {Murphy, Gabe J and Isaacson, Jeffry S} } @article {2141, title = {A prominent role for intrinsic neuronal properties in temporal coding.}, journal = {Trends in Neurosciences}, volume = {26}, year = {2003}, month = {2003 Jan}, pages = {14-6}, abstract = {

A recent report presents evidence that the exact timing of action potential output in rat hippocampal pyramidal neurons is similarly modulated during several diverse forms of behavior. These data suggest that it is, to a large degree, the intrinsic properties of the neurons themselves that produce this temporal coding of information. Thus, this report provides an outstanding example of the importance of single neuronal properties, even during complex behaviors.

}, keywords = {Animals, Automatic Data Processing, Hippocampus, Interneurons, Membrane Potentials, Neurons, Rats, Theta Rhythm, Time Factors}, issn = {0166-2236}, doi = {10.1002/cbic.201000254}, author = {Magee, Jeffrey C} } @article {1591, title = {Purification, crystallization and preliminary crystallographic analysis of phosphoglucose isomerase from the hyperthermophilic archaeon Pyrococcus furiosus.}, journal = {Acta Crystallographica. Section D, Biological Crystallography}, volume = {59}, year = {2003}, month = {2003 Oct 19}, pages = {1822-3}, abstract = {

The glycolytic enzyme phosphoglucose isomerase catalyses the reversible isomerization of glucose 6-phosphate to fructose 6-phosphate. The phosphoglucose isomerase from the hyperthermophilic archaeon Pyrococcus furiosus, which shows no sequence similarity to any known bacterial or eukaryotic phosphoglucose isomerase, has been cloned and overexpressed in Escherichia coli, purified and subsequently crystallized by the hanging-drop method of vapour diffusion using 1.6 M sodium citrate as the precipitant at pH 6.5. Multiple-wavelength anomalous dispersive X-ray data have been collected to a maximum resolution of 1.92 A on a single selenomethionine-incorporated crystal. This crystal belongs to space group C2, with approximate unit-cell parameters a = 84.7

}, keywords = {Crystallization, Crystallography, Escherichia coli, Glucose-6-Phosphate Isomerase, Protein Conformation, Pyrococcus furiosus, Recombinant Proteins, Selenomethionine, X-Ray}, issn = {0907-4449}, author = {Akerboom, Jasper and Turnbull, Andrew P and Hargreaves, David and Fisher, Martin and de Geus, Daniel and Sedelnikova, Svetlana E and Berrisford, John M and Baker, Patrick J and Verhees, Corn{\'e} H and van der Oost, John and Rice, David W} } @article {1776, title = {The receptors for mammalian sweet and umami taste.}, journal = {Cell}, volume = {115}, year = {2003}, month = {2003 Oct 31}, pages = {255-66}, abstract = {

Sweet and umami (the taste of monosodium glutamate) are the main attractive taste modalities in humans. T1Rs are candidate mammalian taste receptors that combine to assemble two heteromeric G-protein-coupled receptor complexes: T1R1+3, an umami sensor, and T1R2+3, a sweet receptor. We now report the behavioral and physiological characterization of T1R1, T1R2, and T1R3 knockout mice. We demonstrate that sweet and umami taste are strictly dependent on T1R-receptors, and show that selective elimination of T1R-subunits differentially abolishes detection and perception of these two taste modalities. To examine the basis of sweet tastant recognition and coding, we engineered animals expressing either the human T1R2-receptor (hT1R2), or a modified opioid-receptor (RASSL) in sweet cells. Expression of hT1R2 in mice generates animals with humanized sweet taste preferences, while expression of RASSL drives strong attraction to a synthetic opiate, demonstrating that sweet cells trigger dedicated behavioral outputs, but their tastant selectivity is determined by the nature of the receptors.

}, keywords = {Animals, Flavoring Agents, G-Protein-Coupled, Gene Deletion, Humans, In Situ Hybridization, kappa, Knockout, Mice, Opioid, Protein Isoforms, Protein Subunits, Receptors, Sodium Glutamate, Sucrose, Taste, Taste Buds}, issn = {0092-8674}, author = {Zhao, Grace Q and Zhang, Yifeng and Hoon, Mark A and Chandrashekar, Jayaram and Erlenbach, Isolde and Ryba, Nicholas J P and Zuker, Charles S} } @article {1559, title = {Redesigning an antibody fragment for faster association with its antigen.}, journal = {Biochemistry}, volume = {42}, year = {2003}, month = {2003 Jun 17}, pages = {7077-83}, abstract = {

Traditional approaches for increasing the affinity of protein-protein complexes focus on constructing highly complementary binding surfaces. Recent theoretical simulations and experimental results suggest that electrostatic steering forces can also be manipulated to increase association rates while leaving dissociation rates unchanged, thus increasing affinity. Here we demonstrate that electrostatic attraction can be enhanced between an antibody fragment and its cognate antigen through application of a few simple rules to identify potential on-rate amplification sites that lie at the periphery of the antigen-antibody interface.

}, keywords = {Amino Acid Substitution, Antibody Affinity, Antigen-Antibody Complex, Antigen-Antibody Reactions, Antigens, Computer Simulation, Drug Design, Endothelial Growth Factors, Fluorescence, Humans, Immunoglobulin Fragments, Intercellular Signaling Peptides and Proteins, Kinetics, Lymphokines, Models, Molecular, Osmolar Concentration, Protein Binding, Recombinant Proteins, Spectrometry, Static Electricity, Thermodynamics, Vascular Endothelial Growth Factor A, Vascular Endothelial Growth Factors}, issn = {0006-2960}, doi = {10.1021/bi026947q}, author = {Marvin, Jonathan S and Lowman, Henry B} } @article {2426, title = {Regulating the regulators: lysine modifications make their mark.}, journal = {Cell}, volume = {112}, year = {2003}, month = {2003 Jan 10}, pages = {11-7}, abstract = {

Decades of research have uncovered much of the molecular machinery responsible for establishing and maintaining proper gene transcription patterns in eukaryotes. Although the composition of this machinery is largely known, mechanisms regulating its activity by covalent modification are just coming into focus. Here, we review several cases of ubiquitination, sumoylation, and acetylation that link specific covalent modification of the transcriptional apparatus to their regulatory function. We propose that potential cascades of modifications serve as molecular rheostats that fine-tune the control of transcription in diverse organisms.

}, keywords = {Acetylation, Basic-Leucine Zipper Transcription Factors, Cell Nucleus, DNA-Binding Proteins, Gene Expression Regulation, Genetic, Humans, Lysine, Messenger, Models, Promoter Regions, RNA, RNA Polymerase II, Saccharomyces cerevisiae Proteins, Small Ubiquitin-Related Modifier Proteins, Trans-Activators, Transcription, Transcription Factors, Transcriptional Activation, Ubiquitins}, issn = {0092-8674}, doi = {10.1073/pnas.1100640108}, author = {Freiman, Richard N and Tjian, Robert} } @article {45762, title = {Regulatory evolution of shavenbaby/ovo underlies multiple cases of morphological parallelism.}, journal = {Nature}, volume = {424}, year = {2003}, month = {2003 Aug 21}, pages = {935-8}, abstract = {

Cases of convergent evolution that involve changes in the same developmental pathway, called parallelism, provide evidence that a limited number of developmental changes are available to evolve a particular phenotype. To our knowledge, in no case are the genetic changes underlying morphological convergence understood. However, morphological convergence is not generally assumed to imply developmental parallelism. Here we investigate a case of convergence of larval morphology in insects and show that the loss of particular trichomes, observed in one species of the Drosophila melanogaster species group, has independently evolved multiple times in the distantly related D. virilis species group. We present genetic and gene expression data showing that regulatory changes of the shavenbaby/ovo (svb/ovo) gene underlie all independent cases of this morphological convergence. Our results indicate that some developmental regulators might preferentially accumulate evolutionary changes and that morphological parallelism might therefore be more common than previously appreciated.

}, keywords = {Animals, Biological Evolution, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Gene Expression Regulation, Developmental, Genes, Insect, Larva, Molecular Sequence Data, Morphogenesis, Phylogeny, RNA, Messenger, Transcription Factors}, issn = {1476-4687}, doi = {10.1038/nature01768}, author = {Sucena, Elio and Delon, Isabelle and Jones, Isaac and Payre, Fran{\c c}ois and Stern, David L} } @article {2136, title = {Sleep deprivation causes behavioral, synaptic, and membrane excitability alterations in hippocampal neurons.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {23}, year = {2003}, month = {2003 Oct 22}, pages = {9687-95}, abstract = {

Although the function of sleep remains elusive, several lines of evidence suggest that sleep has an important role in learning and memory. In light of the available data and with the prevalence of sleep deprivation (SD), we sought to determine the effect of SD on neuronal functioning. We found that the exposure of rats to 72 hr of primarily rapid eye movement SD impaired their subsequent performance on a hippocampus-dependent spatial learning task but had no effect on an amygdala-dependent learning task. To determine the underlying cellular level mechanisms of this hippocampal deficit, we examined the impact of SD on several fundamental aspects of membrane excitability and synaptic physiology in hippocampal CA1 pyramidal neurons and dentate gyrus granule cells. We found that neuronal excitability was severely reduced in CA1 neurons but not in granule cells and that the production of long-term potentiation of synaptic strength was inhibited in both areas. Using multiple SD methods we further attempted to differentiate the effects of sleep deprivation from those associated with the nonspecific stress induced by the sleep deprivation methods. Together these data suggest that failure to acquire adequate sleep produces several molecular and cellular level alterations that profoundly inhibit hippocampal functioning.

}, keywords = {Amygdala, Animal, Animals, Behavior, Cell Membrane, Cues, Electroencephalography, Excitatory Postsynaptic Potentials, Hippocampus, Long-Term Potentiation, Long-Term Synaptic Depression, Male, Memory, Neuronal Plasticity, Neurons, Physiological, Pyramidal Cells, Rats, Sleep Deprivation, Sprague-Dawley, Stress, Synapses}, issn = {1529-2401}, doi = {10.1002/cbic.201000254}, author = {McDermott, Carmel M and LaHoste, Gerald J and Chen, Chu and Musto, Alberto and Bazan, Nicolas G and Magee, Jeffrey C} } @article {4152, title = {Spike sorting in the frequency domain with overlap detection.}, year = {2003}, abstract = {

This paper deals with the problem of extracting the activity of individual neurons from multi-electrode recordings. Important aspects of this work are: 1) the sorting is done in two stages - a statistical model of the spikes from different cells is built and only then are occurrences of these spikes in the data detected by scanning through the original data, 2) the spike sorting is done in the frequency domain, 3) strict statistical tests are applied to determine if and how a spike should be classiffed, 4) the statistical model for detecting overlaping spike events is proposed, 5) slow dynamics of spike shapes are tracked during long experiments. Results from the application of these techniques to data collected from the escape response system of the American cockroach, Periplaneta americana, are presented.

}, author = {Rinberg, D and Bialek, W and Davidowitz, H and Tishby, N} } @article {2323, title = {Striatal proenkephalin gene induction: coordinated regulation by cyclic AMP and calcium pathways.}, journal = {Brain Research. Molecular Brain Research}, volume = {115}, year = {2003}, month = {2003 Jul 23}, pages = {157-61}, abstract = {

Enkephalin modulates striatal function, thereby affecting motor performance and addictive behaviors. The proenkephalin gene is also used as a model to study cyclic AMP-mediated gene expression in striatal neurons. The second messenger pathway leading to proenkephalin expression demonstrates how cyclic AMP pathways are synchronized with depolarization. We show that cyclic AMP-mediated regulation of the proenkephalin gene is dependent on the activity of L-type Ca2+ channels. Inhibition of L-type Ca2+ channels blocks forskolin-mediated induction of proenkephalin. The Ca2+-activated kinase, Ca2+/calmodulin kinase, as well as the cyclic AMP-activated kinase, protein kinase A (PKA), are both necessary for the induction of the proenkephalin promoter. Similarly, both kinases are needed for the L-type Ca2+ channel-mediated induction of proenkephalin. This synchronization of second messenger pathways provides a coincidence mechanism that gates proenkephalin synthesis in striatal neurons, ensuring that levels are increased only in the presence of activated PKA and depolarization.

}, keywords = {1-(5-Isoquinolinesulfonyl)-2-Methylpiperazine, Animals, Antihypertensive Agents, Calcium, Calcium Channel Agonists, Calcium Channel Blockers, Carcinogens, Cells, Corpus Striatum, Cultured, Cyclic AMP, Developmental, Drug Interactions, Embryo, Enkephalins, Enzyme Inhibitors, Forskolin, Gene Expression Regulation, Humans, Isoquinolines, Mammalian, Neurons, Nifedipine, Protein Precursors, Pyrroles, Rats, Sprague-Dawley, Sulfonamides, Tetradecanoylphorbol Acetate, Transcriptional Activation, Transfection}, issn = {0169-328X}, doi = {10.3389/fnana.2010.00147}, author = {Konradi, Christine and Mac{\'\i}as, Wendy and Dudman, Joshua T and Carlson, Richard R} } @article {2730, title = {Sum-frequency vibrational spectroscopic study of surface glass transition of poly(vinyl alcohol).}, journal = {Macromolecules}, volume = {36}, year = {2003}, month = {2003 May}, pages = {3303}, abstract = {

Sum-frequency vibrational spectroscopy was employed to study surface glass transition of

poly(vinyl alcohol) by monitoring the relaxation of rubbing-induced alignment of surface chains with

increase of temperature. The observed chain relaxation is two-dimensional, parallel to the surface. The

surface transition temperature is 58 ( 2 {\textdegree}C, essentially the same as the bulk one.

}, doi = {10.1021/ma025681s}, author = {Ji, Na} } @article {1740, title = {Surface vibrational spectroscopy on shear-aligned poly(tetrafluoroethylene) films.}, journal = {Journal of the American Chemical Society}, volume = {125}, year = {2003}, month = {2003 Nov 26}, pages = {14218-9}, abstract = {

Sum-frequency vibrational spectroscopy was used to obtain the first surface vibrational spectra of shear-deposited highly oriented poly(tetrafluoroethylene) (PTFE, Teflon) thin films. The surface PTFE chains appeared to lie along the shearing direction. Vibrational modes observed at 1142 and 1204 cm-1 were found to have the E1 symmetry, in support of some earlier analysis in the long-lasting controversy over the assignment of these modes.

}, issn = {0002-7863}, doi = {10.1021/ja037964l}, author = {Ji, Na and Ostroverkhov, Victor and Lagugn{\'e}-Labarthet, Fran\c cois and Shen, Yuen-Ron} } @article {2423, title = {Targeting genes and transcription factors to segregated nuclear compartments.}, journal = {Current Opinion in Cell Biology}, volume = {15}, year = {2003}, month = {2003 Jun}, pages = {296-303}, abstract = {

With increasingly detailed images of nuclear structures revealed by advanced microscopy, a remarkably compartmentalized cell nucleus has come into focus. Although this complex nuclear organization remains largely unexplored, some progress has been made in deciphering the functional aspects of various subnuclear structures, revealing how this elaborate framework can influence gene activation. Several recent studies have helped illustrate how cells might utilize the nuclear architecture as an additional level of transcriptional control, perhaps by targeting genes and regulatory factors to specific sites within the nucleus that are designated for active RNA synthesis.

}, keywords = {Animals, Cell Nucleus Structures, Gene Expression, Humans, Protein Transport, Transcription Factors}, issn = {0955-0674}, doi = {10.1073/pnas.1100640108}, author = {Isogai, Yoh and Tjian, Robert} } @article {2360, title = {A test bed for insect-inspired robotic control.}, journal = {Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences}, volume = {361}, year = {2003}, month = {2003 Oct 15}, pages = {2267-85}, abstract = {

Flying insects are remarkable examples of sophisticated sensory-motor control systems. Insects have solved the fundamental challenge facing the field of mobile robots: robust sensory-motor mapping. Control models based on insects can contribute much to the design of robotic control systems. We present our work on a preliminary robotic control system inspired by current behavioural and physiological models of the fruit fly, Drosophila melanogaster. We designed a five-degrees-of-freedom robotic system that serves as a novel simulation/mobile robot hybrid. This design has allowed us to implement a fly-inspired control system that uses visual and mechanosensory feedback. Our results suggest that a simple control scheme can yield surprisingly robust fly-like robotic behaviour.

}, keywords = {Adaptation, Animal, Automated, Biological, Biomimetics, Computer Simulation, Equipment Design, Feedback, Flight, Models, Orientation, Pattern Recognition, Physiological, Pilot Projects, Robotics, Space Perception, Visual}, issn = {1364-503X}, doi = {10.1016/j.cub.2010.06.072}, author = {Reiser, Michael B and Dickinson, Michael H} } @article {788, title = {TGF-beta signaling activates steroid hormone receptor expression during neuronal remodeling in the Drosophila brain.}, journal = {Cell}, volume = {112}, year = {2003}, month = {2003 Feb 7}, pages = {303-15}, abstract = {

Metamorphosis of the Drosophila brain involves pruning of many larval-specific dendrites and axons followed by outgrowth of adult-specific processes. From a genetic mosaic screen, we recovered two independent mutations that block neuronal remodeling in the mushroom bodies (MBs). These phenotypically indistinguishable mutations affect Baboon function, a Drosophila TGF-beta/activin type I receptor, and dSmad2, its downstream transcriptional effector. We also show that Punt and Wit, two type II receptors, act redundantly in this process. In addition, knocking out dActivin around the mid-third instar stage interferes with remodeling. Binding of the insect steroid hormone ecdysone to distinct ecdysone receptor isoforms induces different metamorphic responses in various larval tissues. Interestingly, expression of the ecdysone receptor B1 isoform (EcR-B1) is reduced in activin pathway mutants, and restoring EcR-B1 expression significantly rescues remodeling defects. We conclude that the Drosophila Activin signaling pathway mediates neuronal remodeling in part by regulating EcR-B1 expression.

}, keywords = {Activin Receptors, Animals, Brain, Cell Differentiation, Cell Surface, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Female, Genes, Larva, Lethal, Male, Missense, Mushroom Bodies, Mutation, Neural Pathways, Neuronal Plasticity, Neurons, Protein Isoforms, Proteins, Receptors, Signal Transduction, Smad2 Protein, Steroid, Trans-Activators, Transforming Growth Factor beta, Type I, Type II}, issn = {0092-8674}, author = {Zheng, Xiaoyan and Wang, Jian and Haerry, Theodor E and Wu, Ann Y-H and Martin, Josephine and O{\textquoteright}Connor, Michael B and Lee, Ching-Hsien J and Lee, Tzumin} } @article {2422, title = {Transcription regulation and animal diversity.}, journal = {Nature}, volume = {424}, year = {2003}, month = {2003 Jul 10}, pages = {147-51}, abstract = {

Whole-genome sequence assemblies are now available for seven different animals, including nematode worms, mice and humans. Comparative genome analyses reveal a surprising constancy in genetic content: vertebrate genomes have only about twice the number of genes that invertebrate genomes have, and the increase is primarily due to the duplication of existing genes rather than the invention of new ones. How, then, has evolutionary diversity arisen? Emerging evidence suggests that organismal complexity arises from progressively more elaborate regulation of gene expression.

}, keywords = {Animals, Chromatin, DNA, Ecosystem, Gene Expression Regulation, Genetic, Humans, Nucleic Acid, Regulatory Sequences, Transcription, Transcription Factors}, issn = {1476-4687}, doi = {10.1073/pnas.1100640108}, author = {Levine, Michael and Tjian, Robert} } @article {46635, title = {Tre1, a G protein-coupled receptor, directs transepithelial migration of Drosophila germ cells.}, journal = {PLoS Biology}, volume = {1}, year = {2003}, month = {2003 Dec}, pages = {E80}, abstract = {

In most organisms, germ cells are formed distant from the somatic part of the gonad and thus have to migrate along and through a variety of tissues to reach the gonad. Transepithelial migration through the posterior midgut (PMG) is the first active step during Drosophila germ cell migration. Here we report the identification of a novel G protein-coupled receptor (GPCR), Tre1, that is essential for this migration step. Maternal tre1 RNA is localized to germ cells, and tre1 is required cell autonomously in germ cells. In tre1 mutant embryos, most germ cells do not exit the PMG. The few germ cells that do leave the midgut early migrate normally to the gonad, suggesting that this gene is specifically required for transepithelial migration and that mutant germ cells are still able to recognize other guidance cues. Additionally, inhibiting small Rho GTPases in germ cells affects transepithelial migration, suggesting that Tre1 signals through Rho1. We propose that Tre1 acts in a manner similar to chemokine receptors required during transepithelial migration of leukocytes, implying an evolutionarily conserved mechanism of transepithelial migration. Recently, the chemokine receptor CXCR4 was shown to direct migration in vertebrate germ cells. Thus, germ cells may more generally use GPCR signaling to navigate the embryo toward their target.

}, keywords = {Animals, Cell Movement, Cell Transplantation, Cloning, Molecular, Crosses, Genetic, Drosophila melanogaster, Drosophila Proteins, Embryo, Nonmammalian, Epithelium, Evolution, Molecular, Female, Gene Expression Regulation, Germ Cells, Humans, Immunohistochemistry, In Situ Hybridization, Inflammation, Leukocytes, Male, Models, Biological, Molecular Sequence Data, Mutation, Phenotype, Phylogeny, Receptors, Chemokine, Receptors, G-Protein-Coupled, rho GTP-Binding Proteins, RNA, Signal Transduction}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0000080}, author = {Kunwar, Prabhat S and Starz-Gaiano, Michelle and Bainton, Roland J and Heberlein, Ulrike and Lehmann, Ruth} } @article {48325, title = {Visualization of the domain structure of an L-type Ca2+ channel using electron cryo-microscopy.}, journal = {Journal of Molecular Biology}, volume = {332}, year = {2003}, month = {2003 Sep 05}, pages = {171-82}, abstract = {

The three-dimensional structure of the skeletal muscle voltage-gated L-type calcium channel (Ca(v)1.1; dihydropyridine receptor, DHPR) was determined using electron cryo-microscopy and single-particle averaging. The structure shows a single channel complex with an approximate total molecular mass of 550 kDa, corresponding to the five known subunits of the DHPR, and bound detergent and lipid. Features visible in our structure together with antibody labeling of the beta and alpha(2) subunits allowed us to assign locations for four of the five subunits within the structure. The most striking feature of the structure is the extra-cellular alpha(2) subunit that protrudes from the membrane domain in close proximity to the alpha(1) subunit. The cytosolic beta subunit is located close to the membrane and adjacent to subunits alpha(1), gamma and delta. Our structure correlates well with the functional and biochemical data available for this channel and suggests a three-dimensional model for the excitation-contraction coupling complex consisting of DHPR tetrads and the calcium release channel.

}, keywords = {Animals, Calcium Channels, L-Type, Cryoelectron Microscopy, Models, Molecular, Molecular Weight, Protein Structure, Quaternary, Protein Subunits, Rabbits, Ryanodine Receptor Calcium Release Channel}, issn = {0022-2836}, author = {Wolf, M and Eberhart, A and Glossmann, H and Striessnig, J and Grigorieff, N} } @article {45803, title = {What you didn{\textquoteright}t know about evo-devo}, journal = {Development}, volume = {130}, year = {2003}, month = {12/2003}, pages = {5560-5561}, abstract = {

As most of us are aware, today{\textquoteright}s primary school, high school and undergraduate biology programs are struggling to incorporate even a fraction of the {\textquoteright}molecular revolution{\textquoteright}of biological knowledge and technologies that surround us. In the first term alone, life science and biology classes of the new millennia routinely cover condensed versions of the year-long classes taught in the 60s, 70s and 80s. Teachers no longer have the luxury of spending half a year presenting Mendel and his peas.

}, doi = {10.1242/dev.00767}, author = {David L Stern} } @article {4149, title = {Wind spectra and the response of the cercal system in the cockroach.}, journal = {Journal of Comparative Physiology. A, Neuroethology, Sensory, Neural, and Behavioral Physiology}, volume = {189}, year = {2003}, month = {2003 Dec}, pages = {867-76}, abstract = {

Experiments on the cercal wind-sensing system of the American cockroach, Periplaneta americana, showed that the firing rate of the interneurons coding wind information depends on the bandwidth of random noise wind stimuli. The firing rate was shown to increase with decreases in the stimulus bandwidth, and be independent of changes in the total power of the stimulus with constant spectral composition. A detailed analysis of ethologically relevant stimulus parameters is presented. A phenomenological model of these relationships and their relevance to wind-mediated cockroach behavior is proposed.

}, keywords = {Action Potentials, Afferent, Afferent Pathways, Animal, Animals, Behavior, Central Nervous System, Cockroaches, Escape Reaction, Ganglia, Interneurons, Invertebrate, Male, Mechanoreceptors, Models, Neurological, Neurons, Physical Stimulation, Touch, Wind}, issn = {0340-7594}, doi = {10.1007/s00359-003-0460-9}, author = {Rinberg, D and Davidowitz, H} } @article {1778, title = {An amino-acid taste receptor.}, journal = {Nature}, volume = {416}, year = {2002}, month = {2002 Mar 14}, pages = {199-202}, abstract = {

The sense of taste provides animals with valuable information about the nature and quality of food. Mammals can recognize and respond to a diverse repertoire of chemical entities, including sugars, salts, acids and a wide range of toxic substances. Several amino acids taste sweet or delicious (umami) to humans, and are attractive to rodents and other animals. This is noteworthy because L-amino acids function as the building blocks of proteins, as biosynthetic precursors of many biologically relevant small molecules, and as metabolic fuel. Thus, having a taste pathway dedicated to their detection probably had significant evolutionary implications. Here we identify and characterize a mammalian amino-acid taste receptor. This receptor, T1R1+3, is a heteromer of the taste-specific T1R1 and T1R3 G-protein-coupled receptors. We demonstrate that T1R1 and T1R3 combine to function as a broadly tuned L-amino-acid sensor responding to most of the 20 standard amino acids, but not to their D-enantiomers or other compounds. We also show that sequence differences in T1R receptors within and between species (human and mouse) can significantly influence the selectivity and specificity of taste responses.

}, keywords = {Alleles, Amino Acids, Animals, Calcium Signaling, Cell Line, Cell Surface, Chorda Tympani Nerve, Dose-Response Relationship, Drug, G-Protein-Coupled, Genetic, Heterotrimeric GTP-Binding Proteins, Humans, Inosine Monophosphate, Mice, Mutation, Polymorphism, Protein Subunits, Receptors, Stereoisomerism, Structure-Activity Relationship, Substrate Specificity, Taste, Taste Buds, Transfection}, issn = {0028-0836}, doi = {10.1038/nature726}, author = {Nelson, Greg and Chandrashekar, Jayaram and Hoon, Mark A and Feng, Luxin and Zhao, Grace and Ryba, Nicholas J P and Zuker, Charles S} } @article {2683, title = {Basic transcription element binding protein is a thyroid hormone-regulated transcription factor expressed during metamorphosis in Xenopus laevis.}, journal = {Development, Growth \& Differentiation}, volume = {44}, year = {2002}, month = {2002 Oct}, pages = {365-81}, abstract = {

Basic transcription element binding protein (BTEB) is a member of the Kr{\"u}ppel family of zinc finger transcription factors. It has been shown that BTEB plays a role in promoting neuronal process formation during postembryonic development. In the present study, the biochemical properties, transactivation function, and the developmental and hormone-regulated expression of BTEB in Xenopus laevis (xBTEB) are described. xBTEB binds the GC-rich basic transcription element (BTE) with high affinity and functions as a transcriptional activator on promoters containing multiple or single GC boxes. xBTEB mRNA levels increase in the tadpole brain, intestine and tail during metamorphosis, and are correlated with tissue-specific morphological and biochemical transformations. xBTEB mRNA expression can be induced precociously in premetamorphic tadpole tissues by treatment with thyroid hormone. In situ hybridization histochemistry showed that thyroid hormone upregulates xBTEB mRNA throughout the brain of premetamorphic tadpoles, with the highest expression found in the subventricular zones of the telencephalon, diencephalon, optic tectum, cerebellum and spinal cord. xBTEB protein parallels changes in its mRNA, and it was found that xBTEB is not expressed in mitotic cells in the developing brain, but is expressed just distal to the proliferative zone, supporting the hypothesis that this protein plays a role in neural cell differentiation.

}, keywords = {Animals, Biological, Blotting, Brain, Cell Division, DNA-Binding Proteins, Genetic, Kruppel-Like Transcription Factors, Metamorphosis, Northern, Promoter Regions, Rats, Receptors, Thyroid Hormone, Transcription Factors, Triiodothyronine, Up-Regulation, Xenopus laevis, Xenopus Proteins}, issn = {0012-1592}, author = {Hoopfer, Eric D and Huang, Liyue and Denver, Robert J} } @article {2515, title = {Broad specifies pupal development and mediates the {\textquoteright}status quo{\textquoteright} action of juvenile hormone on the pupal-adult transformation in Drosophila and Manduca.}, journal = {Development }, volume = {129}, year = {2002}, month = {2002 May}, pages = {2259-69}, abstract = {

The understanding of the molecular basis of the endocrine control of insect metamorphosis has been hampered by the profound differences in responses of the Lepidoptera and the Diptera to juvenile hormone (JH). In both Manduca and Drosophila, the broad (br) gene is expressed in the epidermis during the formation of the pupa, but not during adult differentiation. Misexpression of BR-Z1 during either a larval or an adult molt of Drosophila suppressed stage-specific cuticle genes and activated pupal cuticle genes, showing that br is a major specifier of the pupal stage. Treatment with a JH mimic at the onset of the adult molt causes br re-expression and the formation of a second pupal cuticle in Manduca, but only in the abdomen of Drosophila. Expression of the BR isoforms during adult development of Drosophila suppressed bristle and hair formation when induced early or redirected cuticle production toward the pupal program when induced late. Expression of BR-Z1 at both of these times mimicked the effect of JH application but, unlike JH, it caused production of a new pupal cuticle on the head and thorax as well as on the abdomen. Consequently, the {\textquoteright}status quo{\textquoteright} action of JH on the pupal-adult transformation is mediated by the JH-induced re-expression of BR.

}, keywords = {Animals, Developmental, Drosophila, Gene Expression Regulation, Genes, Insect, Juvenile Hormones, Manduca, Messenger, Protein Isoforms, Pupa, RNA, Species Specificity}, issn = {0950-1991}, author = {Zhou, Xiaofeng and Riddiford, Lynn M} } @article {2143, title = {Conditional loss of Nkx3.1 in adult mice induces prostatic intraepithelial neoplasia.}, journal = {Molecular and Cellular Biology}, volume = {22}, year = {2002}, month = {2002 Mar}, pages = {1495-503}, abstract = {

The homeodomain-containing transcription factor NKX3.1 is a putative prostate tumor suppressor that is expressed in a largely prostate-specific and androgen-regulated manner. Loss of NKX3.1 protein expression is common in human prostate carcinomas and prostatic intraepithelial neoplasia (PIN) lesions and correlates with tumor progression. Disruption of the murine Nkx3.1 gene results in defects in prostate branching morphogenesis, secretions, and growth. To more closely mimic the pattern of NKX3.1 loss that occurs in human prostate tumors, we have used Cre- and loxP-mediated recombination to delete the Nkx3.1 gene in the prostates of adult transgenic mice. Conditional deletion of one or both alleles of Nkx3.1 leads to the development of preinvasive lesions that resemble PIN. The pattern of expression of several biomarkers (Ki-67, E-cadherin, and high-molecular-weight cytokeratins) in these PIN lesions resembled that observed in human cases of PIN. Furthermore, PIN foci in mice with conditional deletion of a single Nkx3.1 allele lose expression of the wild-type allele. Our results support the role of NKX3.1 as a prostate tumor suppressor and indicate a role for this gene in tumor initiation.

}, keywords = {Animals, Gene Deletion, Genes, Genetic Predisposition to Disease, Homeodomain Proteins, Homozygote, Hyperplasia, Integrases, Male, Mice, Prostate, Prostatic Intraepithelial Neoplasia, Prostatic Neoplasms, Transcription Factors, Transgenic, Tumor Suppressor, Viral Proteins}, issn = {0270-7306}, doi = {10.1002/cbic.201000254}, author = {Abdulkadir, Sarki A and Magee, Jeffrey A and Peters, Thomas J and Kaleem, Zahid and Naughton, Cathy K and Humphrey, Peter A and Milbrandt, Jeffrey} } @article {45915, title = {Dendritic spikes as a mechanism for cooperative long-term potentiation.}, journal = {Nature}, volume = {418}, year = {2002}, month = {2002 Jul 18}, pages = {326-31}, abstract = {

Strengthening of synaptic connections following coincident pre- and postsynaptic activity was proposed by Hebb as a cellular mechanism for learning. Contemporary models assume that multiple synapses must act cooperatively to induce the postsynaptic activity required for hebbian synaptic plasticity. One mechanism for the implementation of this cooperation is action potential firing, which begins in the axon, but which can influence synaptic potentiation following active backpropagation into dendrites. Backpropagation is limited, however, and action potentials often fail to invade the most distal dendrites. Here we show that long-term potentiation of synapses on the distal dendrites of hippocampal CA1 pyramidal neurons does require cooperative synaptic inputs, but does not require axonal action potential firing and backpropagation. Rather, locally generated and spatially restricted regenerative potentials (dendritic spikes) contribute to the postsynaptic depolarization and calcium entry necessary to trigger potentiation of distal synapses. We find that this mechanism can also function at proximal synapses, suggesting that dendritic spikes participate generally in a form of synaptic potentiation that does not require postsynaptic action potential firing in the axon.

}, keywords = {Action Potentials, Animals, Axons, Calcium, Calcium Signaling, Dendrites, Excitatory Postsynaptic Potentials, Long-Term Potentiation, Pyramidal Cells, Rats, Rats, Wistar, Synapses, Theta Rhythm}, issn = {0028-0836}, doi = {10.1038/nature00854}, author = {Golding, Nace L and Staff, Nathan P and Spruston, Nelson} } @article {2178, title = {Detection of large interaural delays and its implication for models of binaural interaction.}, journal = {Journal of the Association for Research in Otolaryngology: JARO}, volume = {3}, year = {2002}, month = {2002 Mar}, pages = {80-8}, abstract = {

The interaural time difference (ITD) is a major cue to sound localization along the horizontal plane. The maximum natural ITD occurs when a sound source is positioned opposite to one ear. We examined the ability of owls and humans to detect large ITDs in sounds presented through headphones. Stimuli consisted of either broad or narrow bands of Gaussian noise, 100 ms in duration. Using headphones allowed presentation of ITDs that are greater than the maximum natural ITD. Owls were able to discriminate a sound leading to the left ear from one leading to the right ear, for ITDs that are 5 times the maximum natural delay. Neural recordings from optic-tectum neurons, however, show that best ITDs are usually well within the natural range and are never as large as ITDs that are behaviorally discriminable. A model of binaural crosscorrelation with short delay lines is shown to explain behavioral detection of large ITDs. The model uses curved trajectories of a cross-correlation pattern as the basis for detection. These trajectories represent side peaks of neural ITD-tuning curves and successfully predict localization reversals by both owls and human subjects.

}, keywords = {Animals, Biological, Ear, Hearing, Humans, Models, Neurons, Noise, Strigiformes, Superior Colliculi, Time Factors}, issn = {1525-3961}, author = {Saberi, Kourosh and Takahashi, Yoshifumi and Egnor, Roian and Farahbod, Haleh and Mazer, James and Konishi, Masakazu} } @article {6365, title = {Developmental evolution: Hox proteins ring the changes.}, journal = {Current Biology}, volume = {12}, year = {2002}, month = {2002 Apr 16}, pages = {R291-3}, abstract = {

The evolution of body form is believed to involve changes in expression of developmental genes, largely through changes in cis-regulatory elements. Recent studies suggest that changes in the sequences of key developmental regulators, such as the Hox proteins, may also play an important role.

}, keywords = {Animals, Biological Evolution, Crustacea, Developmental, DNA-Binding Proteins, Drosophila Proteins, Gene Expression Regulation, Homeodomain Proteins, Insects, Transcription Factors}, issn = {0960-9822}, author = {Pavlopoulos, Anastasios and Averof, Michalis} } @article {1191, title = {Differences in nuclear gene expression between cells containing monomer and dimer mitochondrial genomes.}, journal = {Gene}, volume = {286}, year = {2002}, month = {2002 Mar 6}, pages = {91-104}, abstract = {

It is known that point mutations and rearrangements (deletions and duplications) of mammalian mitochondrial DNA (mtDNA) can result in mitochondrial dysfunction and human disease. Very little attention has been paid to mtDNA circular dimers (a complex form consisting of two genomes joined head-to-tail) despite their close association with human neoplasia. MtDNA dimers are frequently found in human leukemia, but the clinical relevance of their presence remains unknown. To begin to investigate the role of circular dimer mtDNA in the tumorigenic phenotype, we have created isogenic cell lines containing monomer and dimer mitochondrial genomes and compared the respective nuclear mRNA expression using Affymetrix gene array analysis. Surprisingly, a large number of nuclear gene changes were observed, with one of the largest category of genes being associated with remodeling of the cell surface and extracellular matrix. Since cell growth, migration, apoptosis, and many other cellular processes are influenced by signals initiating from the cell surface, the changes associated with the presence of mtDNA dimers could lead to significant alterations in tumorigenic potential and/or progression.

}, keywords = {Animals, Blotting, Cell Division, Cell Line, Cell Nucleus, Dimerization, DNA, Gene Expression Profiling, Gene Expression Regulation, Genotype, Mitochondrial, Oligonucleotide Array Sequence Analysis, Oxygen Consumption, Southern, Thymidine Kinase, Uridine}, issn = {0378-1119}, author = {Clark, Kim M and Brown, Timothy A and Davidson, Mercy M and Papadopoulou, Lefkothea C and Clayton, David A} } @article {2189, title = {Dissecting glucose signalling with diversity-oriented synthesis and small-molecule microarrays.}, journal = {Nature}, volume = {416}, year = {2002}, month = {2002 Apr 11}, pages = {653-7}, abstract = {

Small molecules that alter protein function provide a means to modulate biological networks with temporal resolution. Here we demonstrate a potentially general and scalable method of identifying such molecules by application to a particular protein, Ure2p, which represses the transcription factors Gln3p and Nil1p. By probing a high-density microarray of small molecules generated by diversity-oriented synthesis with fluorescently labelled Ure2p, we performed 3,780 protein-binding assays in parallel and identified several compounds that bind Ure2p. One compound, which we call uretupamine, specifically activates a glucose-sensitive transcriptional pathway downstream of Ure2p. Whole-genome transcription profiling and chemical epistasis demonstrate the remarkable Ure2p specificity of uretupamine and its ability to modulate the glucose-sensitive subset of genes downstream of Ure2p. These results demonstrate that diversity-oriented synthesis and small-molecule microarrays can be used to identify small molecules that bind to a protein of interest, and that these small molecules can regulate specific functions of the protein.

}, keywords = {Biological, Dioxanes, Dose-Response Relationship, Drug, Fungal, Gene Expression Profiling, Gene Expression Regulation, Genetic, Glucose, Glutathione Peroxidase, Ligands, Messenger, Models, Oligonucleotide Array Sequence Analysis, Oxazoles, Prions, Protein Binding, Repressor Proteins, RNA, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Signal Transduction, Structure-Activity Relationship, Substrate Specificity, Transcription}, issn = {0028-0836}, doi = {10.1038/416653a}, author = {Kuruvilla, Finny G and Shamji, Alykhan F and Sternson, Scott M and Hergenrother, Paul J and Schreiber, Stuart L} } @article {787, title = {Drosophila Dscam is required for divergent segregation of sister branches and suppresses ectopic bifurcation of axons.}, journal = {Neuron}, volume = {33}, year = {2002}, month = {2002 Feb 14}, pages = {559-71}, abstract = {

Axon bifurcation results in the formation of sister branches, and divergent segregation of the sister branches is essential for efficient innervation of multiple targets. From a genetic mosaic screen, we find that a lethal mutation in the Drosophila Down syndrome cell adhesion molecule (Dscam) specifically perturbs segregation of axonal branches in the mushroom bodies. Single axon analysis further reveals that Dscam mutant axons generate additional branches, which randomly segregate among the available targets. Moreover, when only one target remains, branching is suppressed in wild-type axons while Dscam mutant axons still form multiple branches at the original bifurcation point. Taken together, we conclude that Dscam controls axon branching and guidance such that a neuron can innervate multiple targets with minimal branching.

}, keywords = {Animals, Cell Adhesion Molecules, Cell Communication, Cell Differentiation, Central Nervous System, Choristoma, Clone Cells, Developmental, Drosophila melanogaster, Drosophila Proteins, Embryonic Induction, Female, Ganglia, Gene Expression Regulation, Genes, Growth Cones, Invertebrate, Male, Mutation, Phenotype, Proteins, Reporter}, issn = {0896-6273}, author = {Wang, Jian and Zugates, Christopher T and Liang, Inray H and Lee, Ching-Hsien J and Lee, Tzumin} } @article {46638, title = {Drugs, flies, and videotape: the effects of ethanol and cocaine on Drosophila locomotion.}, journal = {Current Opinion in Neurobiology}, volume = {12}, year = {2002}, month = {2002 Dec}, pages = {639-45}, abstract = {

Drosophila melanogaster has been introduced recently as a model organism in which to study the mechanisms by which drugs of abuse change behavior and by which the nervous system changes upon repeated drug exposure. Surprising similarities between flies and mammals have begun to emerge at the behavioral, neurochemical and molecular levels.

}, keywords = {Animals, Behavior, Animal, Circadian Rhythm, Cocaine, Cyclic AMP, Dopamine, Drosophila melanogaster, Drug Tolerance, Ethanol, Locomotion}, issn = {0959-4388}, author = {Rothenfluh, Adrian and Heberlein, Ulrike} } @article {1517, title = {Ectopic expression in the giant fiber system of Drosophila reveals distinct roles for roundabout (Robo), Robo2, and Robo3 in dendritic guidance and synaptic connectivity.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {22}, year = {2002}, month = {2002 Apr 15}, pages = {3117-29}, abstract = {

The Roundabout (Robo) receptors have been intensively studied for their role in regulating axon guidance in the embryonic nervous system, whereas a role in dendritic guidance has not been explored. In the adult giant fiber system of Drosophila, we have revealed that ectopic Robo expression can regulate the growth and guidance of specific motor neuron dendrites, whereas Robo2 and Robo3 have no effect. We also show that the effect of Robo on dendritic guidance can be suppressed by Commissureless coexpression. Although we confirmed a role for all three Robo receptors in giant fiber axon guidance, the strong axon guidance alterations caused by overexpression of Robo2 or Robo3 have no effect on synaptic connectivity. In contrast, Robo overexpression in the giant fiber seems to directly interfere with synaptic function. We conclude that axon guidance, dendritic guidance, and synaptogenesis are separable processes and that the different Robo family members affect them distinctly.

}, keywords = {Amino Acid Motifs, Animals, Axons, Dendrites, Drosophila, Drosophila Proteins, Electric Stimulation, Excitatory Postsynaptic Potentials, Gene Expression, Genetically Modified, Immunologic, Insect Proteins, Membrane Proteins, Motor Neurons, Nerve Fibers, Nerve Tissue Proteins, Phenotype, Pupa, Reaction Time, Receptors, Synapses}, issn = {1529-2401}, doi = {20026291}, author = {Godenschwege, Tanja A and Simpson, Julie H and Shan, Xiaoliang and Bashaw, Greg J and Goodman, Corey S and Murphey, Rodney K} } @article {956, title = {Evidence for large domains of similarly expressed genes in the Drosophila genome.}, journal = {Journal of Biology}, volume = {1}, year = {2002}, month = {2002 Jun 18}, pages = {5}, abstract = {

Transcriptional regulation in eukaryotes generally operates at the level of individual genes. Regulation of sets of adjacent genes by mechanisms operating at the level of chromosomal domains has been demonstrated in a number of cases, but the fraction of genes in the genome subject to regulation at this level is unknown.

}, keywords = {Animals, Chromosomes, Drosophila, Gene Expression Regulation, Genes, Genome, Insect, Multigene Family, Nucleic Acid, Sequence Homology}, issn = {1475-4924}, doi = {10.1186/gb-2007-8-7-r145}, author = {Spellman, Paul T and Rubin, Gerald M} } @article {5493, title = {Functional dissection of neuroanatomical loci regulating ethanol sensitivity in Drosophila.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {22}, year = {2002}, month = {2002 Nov 1}, pages = {9490-501}, abstract = {

Ethanol has complex but similar effects on behavior in mammals and the fruit fly Drosophila melanogaster. In addition, genetic and pharmacological approaches have implicated the cAMP pathway in the regulation of ethanol-induced behaviors in both flies and rodents. Here we examine the neuroanatomical loci that modulate ethanol sensitivity in Drosophila by targeting the expression of an inhibitor of cAMP-dependent protein kinase (PKA) to specific regions in the fly{\textquoteright}s brain. Expression of the inhibitor in most brain regions or in muscle has no effect on behavior. In contrast, inhibition of PKA in a relatively small number of cells, possibly neurosecretory cells, in the fly{\textquoteright}s brain is sufficient to decrease sensitivity to the incoordinating effects of ethanol. Additional brain areas are, however, also involved. The mushroom bodies, brain structures where cAMP signaling is required for olfactory classical conditioning, are dispensable for the regulation of ethanol sensitivity. Finally, different behavioral effects of ethanol, motor incoordination and sedation, appear to be regulated by PKA function in distinct brain regions. We conclude that the regulation of ethanol-induced behaviors by PKA involves complex interactions among groups of cells that mediate either increased or reduced sensitivity to the acute intoxicating effects of ethanol.

}, keywords = {Administration, Animal, Animals, Behavior, Catalytic Domain, Cyclic AMP-Dependent Protein Kinases, DNA-Binding Proteins, Drosophila melanogaster, Drug Resistance, Ethanol, Gene Expression, Genes, Genetically Modified, Hydroxyurea, Inhalation, Larva, Locomotion, Male, Motor Activity, Mushroom Bodies, Nervous System, Organ Specificity, Protein Subunits, Reporter, Saccharomyces cerevisiae Proteins, Transcription Factors, Transgenes}, issn = {1529-2401}, author = {Rodan, Aylin R and Kiger, John A and Heberlein, Ulrike} } @article {1143, title = {A genomic analysis of gene expresson during the Drosophila life cycle.}, journal = {Science}, year = {2002}, month = {2002}, pages = {2270-75}, author = {Baker, B.S. and Arbeitman, M. and Furlong, E. and Imam, F. and Johnson, E. and Null, B.} } @article {1259, title = {Geometry and structural plasticity of synaptic connectivity.}, journal = {Neuron}, volume = {34}, year = {2002}, month = {2002 Apr 11}, pages = {275-88}, abstract = {

Changes in synaptic connectivity patterns through the formation and elimination of dendritic spines may contribute to structural plasticity in the brain. We characterize this contribution quantitatively by estimating the number of different synaptic connectivity patterns attainable without major arbor remodeling. This number depends on the ratio of the synapses on a dendrite to the axons that pass within a spine length of that dendrite. We call this ratio the filling fraction and calculate it from geometrical analysis and anatomical data. The filling fraction is 0.26 in mouse neocortex, 0.22-0.34 in rat hippocampus. In the macaque visual cortex, the filling fraction increases by a factor of 1.6-1.8 from area V1 to areas V2, V4, and 7a. Since the filling fraction is much smaller than 1, spine remodeling can make a large contribution to structural plasticity.

}, keywords = {Animals, Macaca fascicularis, Male, Models, Neural Pathways, Neurological, Neuronal Plasticity, Synapses}, issn = {0896-6273}, doi = {10.1016/j.tins.2005.05.006}, author = {Stepanyants, Armen and Hof, Patrick R and Chklovskii, Dmitri B} } @article {2293, title = {Haemozoin as a marker of placental parasitization.}, journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene}, volume = {96}, year = {2002}, month = {2002 Nov-Dec}, pages = {644-6}, abstract = {

Both Plasmodium vivax and P. falciparum malaria can cause the delivery of low birthweight babies. In this report, we have quantitated haemozoin levels in placentas from women living on the Thai-Burmese border in a region of low transmission for both P. falciparum and P. vivax malaria from June 1995 to January 2000. P. falciparum malaria infections during pregnancy lead to the accumulation of haemozoin (malaria pigment) in the placenta, especially in infections near term and in primigravid pregnancies. Haemozoin concentration was not associated with adverse birth outcomes. Women with P. vivax infections during pregnancy do not have measurable levels of placental haemozoin suggesting that P. vivax-infected erythrocytes do not accumulate in the placenta as much as P. falciparum-infected ones.

}, keywords = {Analysis of Variance, Biological Markers, Falciparum, Female, Hemeproteins, Humans, Infant, Low Birth Weight, Malaria, Newborn, Parasitemia, Parasitic, Placenta, Placenta Diseases, Pregnancy, Pregnancy Complications, Regression Analysis, Vivax}, issn = {0035-9203}, author = {McGready, Rose and Brockman, Alan and Cho, Thein and Levesque, Martin A and Tkachuk, Ariana N and Meshnick, Steven R and Nosten, Fran\c cois} } @article {5492, title = {High-resolution analysis of ethanol-induced locomotor stimulation in Drosophila.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {22}, year = {2002}, month = {2002 Dec 15}, pages = {11035-44}, abstract = {

Understanding how ethanol influences behavior is key to deciphering the mechanisms of ethanol action and alcoholism. In mammals, low doses of ethanol stimulate locomotion, whereas high doses depress it. The acute stimulant effect of ethanol has been proposed to be a manifestation of its rewarding effects. In Drosophila, ethanol exposure transiently potentiates locomotor activity in a biphasic dose- and time-dependent manner. An initial short-lived peak of activity corresponds to an olfactory response to ethanol. A second, longer-lasting period of increased activity coincides with rising internal ethanol concentrations; these closely parallel concentrations that stimulate locomotion in mammals. High-resolution analysis of the walking pattern of individual flies revealed that locomotion consists of bouts of activity; bout structure can be quantified by bout frequency, bout length, and the time spent walking at high speeds. Ethanol exposure induces both dramatic and dynamic changes in bout structure. Mutants with increased ethanol sensitivity show distinct changes in ethanol-induced locomotor behavior, as well as genotype-specific changes in activity bout structure. Thus, the overall effect of ethanol on locomotor behavior in Drosophila is caused by changes in discrete quantifiable parameters of walking pattern. The effects of ethanol on locomotion are comparable in flies and mammals, suggesting that Drosophila is a suitable model system to study the underlying mechanisms.

}, keywords = {Afferent Pathways, Animal, Animals, Automation, Behavior, Cyclic AMP, Dose-Response Relationship, Drosophila, Drug, Ethanol, Kinetics, Locomotion, Male, Mutation, Sensitivity and Specificity}, issn = {1529-2401}, author = {Wolf, Fred W and Rodan, Aylin R and Tsai, Linus T-Y and Heberlein, Ulrike} } @article {2430, title = {Human CRSP interacts with RNA polymerase II CTD and adopts a specific CTD-bound conformation.}, journal = {Genes \& Development}, volume = {16}, year = {2002}, month = {2002 Jun 1}, pages = {1339-44}, abstract = {

Activation of gene transcription in mammalian cells requires several classes of coactivators that participate in different steps of the activation cascade. Using conventional and affinity chromatography, we have isolated a human coactivator complex that interacts directly with the C-terminal domain (CTD) of RNA polymerase II (Pol II). The CTD-binding complex is structurally and functionally indistinguishable from our previously isolated CRSP coactivator complex. The closely related, but transcriptionally inactive, ARC-L complex failed to interact with the CTD, indicating a significant biochemical difference between CRSP and ARC-L that may, in part, explain their functional divergence. Electron microscopy and three-dimensional single-particle reconstruction reveals a conformation for CTD-CRSP that is structurally distinct from unliganded CRSP or CRSP bound to SREBP-1a, but highly similar to CRSP bound to the VP16 activator. Together, our findings suggest that the human CRSP coactivator functions, at least in part, by mediating activator-dependent recruitment of RNA Pol II via the CTD.

}, keywords = {Binding Sites, Chromatin, Electron, Electrophoresis, Genetic, Glutathione Transferase, Hela Cells, Humans, Immunoblotting, Ligands, Microscopy, Models, Molecular, Polyacrylamide Gel, Protein Binding, Protein Conformation, Protein Structure, Recombinant Fusion Proteins, RNA Polymerase II, Tertiary, Trans-Activators, Transcription}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {N{\"a}{\"a}r, Anders M and Taatjes, Dylan J and Zhai, Weiguo and Nogales, Eva and Tjian, Robert} } @article {1340, title = {Memory of sequential experience in the hippocampus during slow wave sleep.}, journal = {Neuron}, volume = {36}, year = {2002}, month = {2002 Dec 19}, pages = {1183-94}, abstract = {

Rats repeatedly ran through a sequence of spatial receptive fields of hippocampal CA1 place cells in a fixed temporal order. A novel combinatorial decoding method reveals that these neurons repeatedly fired in precisely this order in long sequences involving four or more cells during slow wave sleep (SWS) immediately following, but not preceding, the experience. The SWS sequences occurred intermittently in brief ( approximately 100 ms) bursts, each compressing the behavioral sequence in time by approximately 20-fold. This rapid encoding of sequential experience is consistent with evidence that the hippocampus is crucial for spatial learning in rodents and the formation of long-term memories of events in time in humans.

}, keywords = {Action Potentials, Animals, Computer-Assisted, Hippocampus, Learning, Long-Evans, Male, Memory, Neural Pathways, Neuropsychological Tests, Pyramidal Cells, Rats, Signal Processing, Signal Transduction, Sleep, Synaptic Transmission}, issn = {0896-6273}, author = {Lee, Albert K and Wilson, Matthew A} } @article {1593, title = {Molecular and biochemical characterization of a distinct type of fructose-1,6-bisphosphatase from Pyrococcus furiosus.}, journal = {Journal of Bacteriology}, volume = {184}, year = {2002}, month = {2002 Jun}, pages = {3401-5}, abstract = {

The Pyrococcus furiosus fbpA gene was cloned and expressed in Escherichia coli, and the fructose-1,6-bisphosphatase produced was subsequently purified and characterized. The dimeric enzyme showed a preference for fructose-1,6-bisphosphate, with a K(m) of 0.32 mM and a V(max) of 12.2 U/mg. The P. furiosus fructose-1,6-bisphosphatase was strongly inhibited by Li(+) (50\% inhibitory concentration, 1 mM). Based on the presence of conserved sequence motifs and the substrate specificity of the P. furiosus fructose-1,6-bisphosphatase, we propose that this enzyme belongs to a new family, class IV fructose-1,6-bisphosphatase.

}, keywords = {Amino Acid Sequence, Archaeal Proteins, Cloning, DNA, Fructose-Bisphosphatase, Molecular, Molecular Sequence Data, Pyrococcus furiosus, Sequence Analysis, Substrate Specificity, Temperature}, issn = {0021-9193}, author = {Verhees, Corn{\'e} H and Akerboom, Jasper and Schiltz, Emile and de Vos, Willem M and van der Oost, John} } @article {2450, title = {Mutations in the Drosophila glycoprotein hormone receptor, rickets, eliminate neuropeptide-induced tanning and selectively block a stereotyped behavioral program.}, journal = {The Journal of Experimental Biology}, volume = {205}, year = {2002}, month = {2002 Sep}, pages = {2555-65}, abstract = {

Adult insects achieve their final form shortly after adult eclosion by the combined effects of specialized behaviors that generate increased blood pressure, which causes cuticular expansion, and hormones, which plasticize and then tan the cuticle. We examined the molecular mechanisms contributing to these processes in Drosophila by analyzing mutants for the rickets gene. These flies fail to initiate the behavioral and tanning processes that normally follow ecdysis. Sequencing of rickets mutants and STS mapping of deficiencies confirmed that rickets encodes the glycoprotein hormone receptor DLGR2. Although rickets mutants produce and release the insect-tanning hormone bursicon, they do not melanize when injected with extracts containing bursicon. In contrast, mutants do melanize in response to injection of an analog of cyclic AMP, the second messenger for bursicon. Hence, rickets appears to encode a component of the bursicon response pathway, probably the bursicon receptor itself. Mutants also have a behavioral deficit in that they fail to initiate the behavioral program for wing expansion. A set of decapitation experiments utilizing rickets mutants and flies that lack cells containing the neuropeptide eclosion hormone, reveals a multicomponent control to the activation of this behavioral program.

}, keywords = {Animals, Cell Surface, Drosophila, Drosophila Proteins, G-Protein-Coupled, Genes, Insect, Insect Hormones, Invertebrate Hormones, Molting, Mutation, Receptors, Sequence Tagged Sites, Stereotyped Behavior, Wing}, issn = {0022-0949}, author = {Baker, James D and Truman, James W} } @article {1265, title = {Network motifs: simple building blocks of complex networks.}, journal = {Science}, volume = {298}, year = {2002}, month = {2002 Oct 25}, pages = {824-7}, abstract = {

Complex networks are studied across many fields of science. To uncover their structural design principles, we defined {\textquotedblleft}network motifs,{\textquotedblright} patterns of interconnections occurring in complex networks at numbers that are significantly higher than those in randomized networks. We found such motifs in networks from biochemistry, neurobiology, ecology, and engineering. The motifs shared by ecological food webs were distinct from the motifs shared by the genetic networks of Escherichia coli and Saccharomyces cerevisiae or from those found in the World Wide Web. Similar motifs were found in networks that perform information processing, even though they describe elements as different as biomolecules within a cell and synaptic connections between neurons in Caenorhabditis elegans. Motifs may thus define universal classes of networks. This approach may uncover the basic building blocks of most networks.

}, issn = {1095-9203}, author = {Milo, R. and Shen-Orr, S. and Itzkovitz, S. and Kashtan, N. and Chklovskii, D.B. and Alon, U.} } @article {1779, title = {Neurobiology: a cool ion channel.}, journal = {Nature}, volume = {416}, year = {2002}, month = {2002 Mar 7}, pages = {27-8}, keywords = {Cold Temperature, Drug, Humans, Ion Channels, Menthol, Neoplasm Proteins, Neurons, Receptors, Thermoreceptors, TRPM Cation Channels}, issn = {0028-0836}, doi = {10.1038/416027a}, author = {Zuker, Charles S} } @article {2429, title = {Neurodegeneration. A glutamine-rich trail leads to transcription factors.}, journal = {Science }, volume = {296}, year = {2002}, month = {2002 Jun 21}, pages = {2149-50}, keywords = {Animals, Brain, CREB-Binding Protein, DNA-Binding Proteins, Dopamine D2, Gene Expression Regulation, Genetic, Humans, Huntington Disease, Mice, Models, Nerve Tissue Proteins, Neurodegenerative Diseases, Neurons, Nuclear Proteins, Peptides, Promoter Regions, Protein Binding, Protein Structure, Receptors, Sp1 Transcription Factor, TATA-Binding Protein Associated Factors, Tertiary, Trans-Activators, Transcription, Transcription Factor TFIID, Transcription Factors, Trinucleotide Repeat Expansion}, issn = {1095-9203}, doi = {10.1073/pnas.1100640108}, author = {Freiman, Richard N and Tjian, Robert} } @article {2295, title = {A new NOS2 promoter polymorphism associated with increased nitric oxide production and protection from severe malaria in Tanzanian and Kenyan children.}, journal = {Lancet}, volume = {360}, year = {2002}, month = {2002 Nov 9}, pages = {1468-75}, abstract = {

Nitric oxide (NO) is a mediator of immunity to malaria, and genetic polymorphisms in the promoter of the inducible NO synthase gene (NOS2) could modulate production of NO. We postulated that NOS2 promoter polymorphisms would affect resistance to severe malaria.

}, keywords = {Anemia, Cerebral, Child, DNA, Falciparum, Female, Genetic, Humans, Immunity, Infant, Innate, Kenya, Malaria, Male, Nitric Oxide, Nitric Oxide Synthase, Nitric Oxide Synthase Type II, Parasitemia, Polymorphism, Preschool, Sequence Analysis, Single-Stranded Conformational, Tanzania}, issn = {0140-6736}, doi = {10.1016/S0140-6736(02)11474-7}, author = {Hobbs, Maurine R and Udhayakumar, Venkatachalam and Levesque, Marc C and Booth, Jennifer and Roberts, Jacquelin M and Tkachuk, Ariana N and Pole, Ann and Coon, Hilary and Kariuki, Simon and Nahlen, Bernard L and Mwaikambo, Esther D and Lal, Altaf L and Granger, Donald L and Anstey, Nicholas M and Weinberg, J Brice} } @article {5823, title = {A novel invertebrate trophic factor related to invertebrate neurotrophins is involved in planarian body regional survival and asexual reproduction.}, journal = {Developmental biology}, volume = {252}, year = {2002}, month = {2002 Dec 15}, pages = {188-201}, abstract = {

Trophic factors are a heterogeneous group of molecules that promote cell growth and survival. In freshwater planarians, the small secreted protein TCEN49 is linked to the regional maintenance of the planarian central body region. To investigate its function in vivo, we performed loss-of-function and gain-of-function experiments by RNA interference and by the implantation of microbeads soaked in TCEN49, respectively. We show that TCEN49 behaves as a trophic factor involved in central body region neuron survival. In planarian tail regenerates, tcen49 expression inhibition by double-stranded RNA interference causes extensive apoptosis in various cell types, including nerve cells. This phenotype is rescued by the implantation of microbeads soaked in TCEN49 after RNA interference. On the other hand, in organisms committed to asexual reproduction, both tcen49 mRNA and its protein are detected not only in the central body region but also in the posterior region, expanding from cells close to the ventral nerve chords. In some cases, the implantation of microbeads soaked in TCEN49 in the posterior body region drives organisms to reproduce asexually, and the inhibition of tcen49 expression obstructs this process, suggesting a link between the central nervous system, TCEN49, regional induction, and asexual reproduction. Finally, the distribution of TCEN49 cysteine and tyrosine residues also points to a common evolutionary origin for TCEN49 and molluscan neurotrophins.

}, keywords = {Amino Acid, Amino Acid Sequence, Animals, Biological Factors, Immunohistochemistry, In Situ Hybridization, In Situ Nick-End Labeling, Molecular Sequence Data, Nerve Growth Factors, Planarians, Reproduction, Sequence Homology}, issn = {0012-1606}, author = {Bueno, David and Fern{\`a}ndez-Rodr{\'\i}guez, Juana and Cardona, Albert and Hern{\`a}ndez-Hern{\`a}ndez, Victor and Romero, Rafael} } @article {2472, title = {Nuclear degradation of p53 occurs during down-regulation of the p53 response after DNA damage.}, journal = {The FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology}, volume = {16}, year = {2002}, month = {2002 Mar}, pages = {420-2}, abstract = {

The principal regulator of p53 stability is HDM2, an E3 ligase that mediates p53 degradation via the ubiquitin-26S proteasome pathway. The current model holds that p53 degradation occurs exclusively on cytoplasmic proteasomes and hence has an absolute requirement for nuclear export of p53 via the CRM-1 pathway. However, proteasomes are abundant in both cytosol and nucleus, and no studies have been done to determine under what physiological circumstances p53 degradation might occur in the nucleus. We analyzed HDM2-mediated degradation of endogenous p53 in the presence of various nuclear export inhibitors of CRM-1, including leptomycin B (LMB), a noncompetitive, specific, and fast-acting inhibitor; and HTLV1-Rex protein, a potent competitive inhibitor. We found that significant HDM2-mediated p53 degradation took place in the presence of LMB or HTLV1-Rex, indicating that endogenous p53 degradation occurs locally in the nucleus, in parallel to cytoplasmic degradation. Moreover, p53 null cells that coexpressed export-defective mutants of p53 and HDM2 retained partial competence for p53 degradation. It is important that nuclear degradation of p53 occurred during the poststress recovery phase of a p53 response, after DNA damage ceased. We propose that the capability of local p53 degradation within the nucleus provides a tighter and faster control during the down-regulatory phase, when an active p53 program needs to be turned off quickly.

}, keywords = {Active Transport, Animals, Biological, Cell Line, Cell Nucleus, Cytoplasm, DNA Damage, Down-Regulation, Gene Products, Kinetics, Models, Mutation, Nuclear Localization Signals, Nuclear Proteins, Proto-Oncogene Proteins, Proto-Oncogene Proteins c-mdm2, rex, Transfection, Tumor Suppressor Protein p53}, issn = {1530-6860}, doi = {10.1096/fj.01-0617fje}, author = {Shirangi, Troy R and Zaika, Alex and Moll, Ute M} } @article {47225, title = {Oscillations and sparsening of odor representations in the mushroom body.}, journal = {Science (New York, N.Y.)}, volume = {297}, year = {2002}, month = {2002 Jul 19}, pages = {359-65}, abstract = {

In the insect olfactory system, oscillatory synchronization is functionally relevant and reflects the coherent activation of dynamic neural assemblies. We examined the role of such oscillatory synchronization in information transfer between networks in this system. The antennal lobe is the obligatory relay for olfactory afferent signals and generates oscillatory output. The mushroom body is responsible for formation and retrieval of olfactory and other memories. The format of odor representations differs significantly across these structures. Whereas representations are dense, dynamic, and seemingly redundant in the antennal lobe, they are sparse and carried by more selective neurons in the mushroom body. This transformation relies on a combination of oscillatory dynamics and intrinsic and circuit properties that act together to selectively filter and synthesize the output from the antennal lobe. These results provide direct support for the functional relevance of correlation codes and shed some light on the role of oscillatory synchronization in sensory networks.

}, keywords = {Action Potentials, Animals, Electric Stimulation, Electrodes, Evoked Potentials, Excitatory Postsynaptic Potentials, Female, gamma-Aminobutyric Acid, Grasshoppers, Interneurons, Male, Mushroom Bodies, Nerve Net, Neural Inhibition, Neurons, Odors, Patch-Clamp Techniques, Picrotoxin, Smell, Synaptic Transmission, Time Factors}, issn = {1095-9203}, doi = {10.1126/science.1070502}, author = {Perez-Orive, Javier and Mazor, Ofer and Turner, Glenn C and Cassenaer, Stijn and Wilson, Rachel I and Laurent, Gilles} } @article {2142, title = {Phosphorylation-dependent differences in the activation properties of distal and proximal dendritic Na+ channels in rat CA1 hippocampal neurons.}, journal = {The Journal of Physiology}, volume = {541}, year = {2002}, month = {2002 Jun 15}, pages = {665-72}, abstract = {

{At distal dendritic locations, the threshold for action potential generation is higher and the amplitude of back-propagating spikes is decreased. To study whether these characteristics depend upon Na+ channels, their voltage-dependent properties at proximal and distal dendritic locations were compared in CA1 hippocampal neurons. Distal Na+ channels activated at more hyperpolarized voltages than proximal (half-activation voltages were -20.4 +/- 2.4 mV vs. -12.0 +/- 1.7 mV for distal and proximal patches, respectively

}, keywords = {Algorithms, Animals, Axons, Dendrites, Electrophysiology, Enzyme Inhibitors, Hippocampus, Membrane Potentials, Neurons, Patch-Clamp Techniques, Phosphorylation, Protein Kinase Inhibitors, Rats, Sodium Channels, Sprague-Dawley, Staurosporine}, issn = {0022-3751}, doi = {10.1002/cbic.201000254}, author = {Gasparini, Sonia and Magee, Jeffrey C} } @article {2428, title = {Redundant role of tissue-selective TAF(II)105 in B lymphocytes.}, journal = {Molecular and Cellular Biology}, volume = {22}, year = {2002}, month = {2002 Sep}, pages = {6564-72}, abstract = {

Regulated gene expression is a complex process achieved through the function of multiple protein factors acting in concert at a given promoter. The transcription factor TFIID is a central component of the machinery regulating mRNA synthesis by RNA polymerase II. This large multiprotein complex is composed of the TATA box binding protein (TBP) and several TBP-associated factors (TAF(II)s). The recent discovery of multiple TBP-related factors and tissue-specific TAF(II)s suggests the existence of specialized TFIID complexes that likely play a critical role in regulating transcription in a gene- and tissue-specific manner. The tissue-selective factor TAF(II)105 was originally identified as a component of TFIID derived from a human B-cell line. In this report we demonstrate the specific induction of TAF(II)105 in cultured B cells in response to bacterial lipopolysaccharide (LPS). To examine the in vivo role of TAF(II)105, we have generated TAF(II)105-null mice by homologous recombination. Here we show that B-lymphocyte development is largely unaffected by the absence of TAF(II)105. TAF(II)105-null B cells can proliferate in response to LPS, produce relatively normal levels of resting antibodies, and can mount an immune response by producing antigen-specific antibodies in response to immunization. Taken together, we conclude that the function of TAF(II)105 in B cells is likely redundant with the function of other TAF(II)105-related cellular proteins.

}, keywords = {Animals, B-Lymphocytes, Blotting, Cell Division, Cell Separation, DNA-Binding Proteins, Dose-Response Relationship, Drug, Erythrocytes, Flow Cytometry, Genetic, Immunoglobulin A, Immunoglobulin G, Immunoglobulin M, Lipopolysaccharides, Messenger, Mice, Precipitin Tests, RNA, Spleen, TATA-Binding Protein Associated Factors, Time Factors, Transcription, Transcription Factor TFIID, Transcription Factors, Transcriptional Activation, Western}, issn = {0270-7306}, doi = {10.1073/pnas.1100640108}, author = {Freiman, Richard N and Albright, Shane R and Chu, Leslie E and Zheng, Shuang and Liang, Hong-Erh and Sha, William C and Tjian, Robert} } @article {1190, title = {Release of replication termination controls mitochondrial DNA copy number after depletion with 2{\textquoteright},3{\textquoteright}-dideoxycytidine.}, journal = {Nucleic Acids Research}, volume = {30}, year = {2002}, month = {2002 May 1}, pages = {2004-10}, abstract = {

Although cellular mitochondrial DNA (mtDNA) copy number varies widely among cell lines and tissues, little is known about the mechanism of mtDNA copy number control. Most nascent replication strands from the leading, heavy-strand origin (O(H)) are prematurely terminated, defining the 3{\textquoteright} boundary of the displacement loop (D-loop). We have depleted mouse LA9 cell mtDNA to approximately 20\% of normal levels by treating with 2{\textquoteright},3{\textquoteright}-dideoxycytidine (ddC) and subsequently allowed recovery to normal levels of mtDNA. A quantitative ligation-mediated PCR assay was used to determine the levels of both terminated and extended nascent O(H) strands during mtDNA depletion and repopulation. Depleting mtDNA leads to a release of replication termination until mtDNA copy number approaches a normal level. Detectable total nascent strands per mtDNA genome remain below normal. Therefore, it is likely that the level of replication termination plays a significant role in copy number regulation in this system. However, termination of D-loop strand synthesis is persistent, indicating formation of the D-loop structure has a purpose that is required under conditions of rapid recovery of depleted mtDNA.

}, keywords = {Animals, Antimetabolites, Cell Line, DNA, DNA Replication, Gene Dosage, Kinetics, Mice, Mitochondria, Mitochondrial, Nucleic Acid Conformation, Polymerase Chain Reaction, Zalcitabine}, issn = {1362-4962}, author = {Brown, Timothy A and Clayton, David A} } @article {46640, title = {Rough eye is a gain-of-function allele of amos that disrupts regulation of the proneural gene atonal during Drosophila retinal differentiation.}, journal = {Genetics}, volume = {160}, year = {2002}, month = {2002 Feb}, pages = {623-35}, abstract = {

The regular organization of the ommatidial lattice in the Drosophila eye originates in the precise regulation of the proneural gene atonal (ato), which is responsible for the specification of the ommatidial founder cells R8. Here we show that Rough eye (Roi), a dominant mutation manifested by severe roughening of the adult eye surface, causes defects in ommatidial assembly and ommatidial spacing. The ommatidial spacing defect can be ascribed to the irregular distribution of R8 cells caused by a disruption of the patterning of ato expression. Disruptions in the recruitment of other photoreceptors and excess Hedgehog production in differentiating cells may further contribute to the defects in ommatidial assembly. Our molecular characterization of the Roi locus demonstrates that it is a gain-of-function mutation of the bHLH gene amos that results from a chromosomal inversion. We show that Roi can rescue the retinal developmental defect of ato1 mutants and speculate that amos substitutes for some of ato{\textquoteright}s function in the eye or activates a residual function of the ato1 allele.

}, keywords = {Alleles, Animals, Basic Helix-Loop-Helix Transcription Factors, DNA-Binding Proteins, Drosophila melanogaster, Drosophila Proteins, Epistasis, Genetic, Gene Expression Regulation, Developmental, Nerve Growth Factors, Nerve Tissue Proteins, Retina, Signal Transduction, Transgenes}, issn = {0016-6731}, author = {Chanut, Fran{\c c}oise and Woo, Katherine and Pereira, Shalini and Donohoe, Terrence J and Chang, Shang-Yu and Laverty, Todd R and Jarman, Andrew P and Heberlein, Ulrike} } @article {2371, title = {A stimulus generating system for studying wind sensation in the American cockroach.}, journal = {Journal of Neuroscience Methods}, volume = {121}, year = {2002}, month = {2002 Nov 15}, pages = {1-11}, abstract = {

A novel system for the generation and measurement of a two dimensional wind stimulus is proposed and described. This system was used to investigate the wind sensation of the American cockroach. The new aspects of this system are (a) a pair of computer driven wind tunnels that are shown to produce non-turbulent flows and (b) a novel fiber optic wind detector that measures both amplitude and direction of the wind. Winds can be produced and measured in behaviorally relevant frequency and amplitude ranges without perturbing the airflow. The combination of both the wind generation system and wind detector makes the system very flexible and allows the generation of stimuli with any given spectrum. The two dimensional wind stimulus is shown to be very reproducible. The wind detector is independent of the wind generation system so it can be used for measuring natural winds as well. Experimental data obtained on the cockroach are presented.

}, keywords = {Air Movements, Algorithms, Animals, Calibration, Electrodes, Electrophysiology, Environmental Monitoring, Equipment Design, Fiber Optic Technology, Male, Optical Fibers, Periplaneta, Physical Stimulation, Reproducibility of Results, Sensation, Sense Organs, Time Factors, Wind}, issn = {0165-0270}, doi = {10.1523/JNEUROSCI.3613-08.2008}, author = {Rinberg, Dima and Davidowitz, Hanan} } @article {2431, title = {Structure, function, and activator-induced conformations of the CRSP coactivator.}, journal = {Science}, volume = {295}, year = {2002}, month = {2002 Feb 8}, pages = {1058-62}, abstract = {

The human cofactor complexes ARC (activator-recruited cofactor) and CRSP (cofactor required for Sp1 activation) mediate activator-dependent transcription in vitro. Although these complexes share several common subunits, their structural and functional relationships remain unknown. Here, we report that affinity-purified ARC consists of two distinct multisubunit complexes: a larger complex, denoted ARC-L, and a smaller coactivator, CRSP. Reconstituted in vitro transcription with biochemically separated ARC-L and CRSP reveals differential cofactor functions. The ARC-L complex is transcriptionally inactive, whereas the CRSP complex is highly active. Structural determination by electron microscopy (EM) and three-dimensional reconstruction indicate substantial differences in size and shape between ARC-L and CRSP. Moreover, EM analysis of independently derived CRSP complexes reveals distinct conformations induced by different activators. These results suggest that CRSP may potentiate transcription via specific activator-induced conformational changes.

}, keywords = {CCAAT-Enhancer-Binding Proteins, Chromatin, Computer-Assisted, DNA-Binding Proteins, Electron, Genetic, Hela Cells, Herpes Simplex Virus Protein Vmw65, Humans, Image Processing, Imaging, Macromolecular Substances, Microscopy, Models, Precipitin Tests, Protein Binding, Protein Structure, Protein Subunits, Quaternary, Recombinant Fusion Proteins, Recombinant Proteins, Sterol Regulatory Element Binding Protein 1, Tertiary, Three-Dimensional, Trans-Activators, Transcription, Transcription Factors, Transcriptional Activation}, issn = {1095-9203}, doi = {10.1073/pnas.1100640108}, author = {Taatjes, Dylan J and N{\"a}{\"a}r, Anders M and Andel, Frank and Nogales, Eva and Tjian, Robert} } @article {2731, title = {Sum-frequency spectroscopy of electronic resonances on a chiral surface monolayer of bi-naphthol.}, journal = {Physical Review B}, volume = {66}, year = {2002}, month = {2002 Oct 25}, pages = {165415}, abstract = {

We study chiral response in optical sum-frequency generation near electronic resonances from a 1,1\ '\ -bi-2\  -naphthol (BN) monolayer adsorbed on water. The polarization dependence of the spectra indicates that the molecules are well oriented at the surface with their symmetry axis along the surface normal. Orientational ordering effectively enhances the chiral response per BN molecule. The results can be quantitatively understood with a simple coupled-oscillator model for BN.

}, doi = {10.1103/PhysRevB.66.165415}, author = {Ji, Na} } @article {1266, title = {Theoretical neuroscience: state of the art.}, journal = {Neuron}, volume = {34}, year = {2002}, month = {2002 Jun 13}, pages = {863-4}, author = {Chklovskii, Dmitri B} } @article {2427, title = {TRF2 associates with DREF and directs promoter-selective gene expression in Drosophila.}, journal = {Nature}, volume = {420}, year = {2002}, month = {2002 Nov 28}, pages = {439-45}, abstract = {

Drosophila TATA-box-binding protein (TBP)-related factor 2 (TRF2) is a member of a family of TBP-related factors present in metazoan organisms. Recent evidence suggests that TRF2s are required for proper embryonic development and differentiation. However, true target promoters and the mechanisms by which TRF2 operates to control transcription remain elusive. Here we report the antibody affinity purification of a Drosophila TRF2-containing complex that contains components of the nucleosome remodelling factor (NURF) chromatin remodelling complex as well as the DNA replication-related element (DRE)-binding factor DREF. This latter finding led us to potential target genes containing TRF2-responsive promoters. We have used a combination of in vitro and in vivo assays to show that the DREF-containing TRF2 complex directs core promoter recognition of the proliferating cell nuclear antigen (PCNA) gene. We also identified additional TRF2-responsive target genes involved in DNA replication and cell proliferation. These data suggest that TRF2 functions as a core promoter-selectivity factor responsible for coordinating transcription of a subset of genes in Drosophila.

}, keywords = {Animals, Cell Line, Chromatin, Drosophila, Drosophila Proteins, Gene Expression Regulation, Genes, Genetic, Insect, Macromolecular Substances, Nuclease Protection Assays, Oligonucleotide Array Sequence Analysis, Precipitin Tests, Proliferating Cell Nuclear Antigen, Promoter Regions, Protein Binding, RNA Interference, Substrate Specificity, Telomeric Repeat Binding Protein 2, Transcription Factors, Transcription Initiation Site}, issn = {0028-0836}, doi = {10.1073/pnas.1100640108}, author = {Hochheimer, Andreas and Zhou, Sharleen and Zheng, Shuang and Holmes, Michael C and Tjian, Robert} } @article {1258, title = {Wiring optimization in cortical circuits.}, journal = {Neuron}, volume = {34}, year = {2002}, month = {2002 Apr 25}, pages = {341-7}, abstract = {

Wiring a brain presents a formidable problem because neural circuits require an enormous number of fast and durable connections. We propose that evolution was likely to have optimized neural circuits to minimize conduction delays in axons, passive cable attenuation in dendrites, and the length of "wire" used to construct circuits, and to have maximized the density of synapses. Here we ask the question: "What fraction of the volume should be taken up by axons and dendrites (i.e., wire) when these variables are at their optimal values?" The biophysical properties of axons and dendrites dictate that wire should occupy 3/5 of the volume in an optimally wired gray matter. We have measured the fraction of the volume occupied by each cellular component and find that the volume of wire is close to the predicted optimal value.

}, keywords = {Animals, Axons, Cerebral Cortex, Hippocampus, Mathematics, Mice, Nerve Net, Neurons}, issn = {0896-6273}, doi = {10.1016/j.tins.2005.05.006}, author = {Chklovskii, Dmitri B and Schikorski, Thomas and Stevens, Charles F} } @article {45927, title = {Action potential bursting in subicular pyramidal neurons is driven by a calcium tail current.}, journal = {J Neurosci}, volume = {21}, year = {2001}, month = {2001 May 15}, pages = {3312-21}, abstract = {

Subiculum is the primary output area of the hippocampus and serves as a key relay center in the process of memory formation and retrieval. A majority of subicular pyramidal neurons communicate via bursts of action potentials, a mode of signaling that may enhance the fidelity of information transfer and synaptic plasticity or contribute to epilepsy when unchecked. In the present study, we show that a Ca(2+) tail current drives bursting in subicular pyramidal neurons. An action potential activates voltage-activated Ca(2+) channels, which deactivate slowly enough during action potential repolarization to produce an afterdepolarization that triggers subsequent action potentials in the burst. The Ca(2+) channels underlying bursting are located primarily near the soma, and the amplitude of Ca(2+) tail currents correlates with the strength of bursting across cells. Multiple channel subtypes contribute to Ca(2+) tail current, but the need for an action potential to produce the slow depolarization suggests a central role for high-voltage-activated Ca(2+) channels in subicular neuron bursting.

}, keywords = {Action Potentials, Animals, Calcium, Calcium Channel Blockers, Calcium Channels, T-Type, Dendrites, Dose-Response Relationship, Drug, Electric Stimulation, Fluorescent Dyes, Fura-2, Hippocampus, In Vitro Techniques, Microelectrodes, Microinjections, Nickel, Patch-Clamp Techniques, Perfusion, Potassium Channels, Pyramidal Cells, Rats, Sodium Channels, Tetrodotoxin}, issn = {1529-2401}, author = {Jung, H Y and Staff, N P and Spruston, N} } @article {1142, title = {Are complex behaviors specified by dedicated regularoty genes? Reasoning from Drosophila.}, journal = {Cell}, volume = {105}, year = {2001}, month = {2001 Apr 6}, pages = {13-24}, issn = {0092-8674}, author = {Baker, B.S. and Taylor, B.T. and Hall, Jeffrey C} } @article {45768, title = {Body-size evolution: how to evolve a mammoth moth.}, journal = {Curr Biol}, volume = {11}, year = {2001}, month = {2001 Nov 13}, pages = {R917-9}, abstract = {

Separate recent studies have revealed the physiological changes underlying the evolution of body size in an insect and advanced our understanding of the genetics of insect growth. These studies highlight the gulf between physiological and genetic studies of growth control and the exciting opportunities for unification of these fields.

}, keywords = {Animals, Biological Evolution, Larva, Manduca}, issn = {0960-9822}, author = {Stern, D} } @article {1781, title = {A chemosensory gene family encoding candidate gustatory and olfactory receptors in Drosophila.}, journal = {Cell}, volume = {104}, year = {2001}, month = {2001 Mar 9}, pages = {661-73}, abstract = {

A novel family of candidate gustatory receptors (GRs) was recently identified in searches of the Drosophila genome. We have performed in situ hybridization and transgene experiments that reveal expression of these genes in both gustatory and olfactory neurons in adult flies and larvae. This gene family is likely to encode both odorant and taste receptors. We have visualized the projections of chemosensory neurons in the larval brain and observe that neurons expressing different GRs project to discrete loci in the antennal lobe and subesophageal ganglion. These data provide insight into the diversity of chemosensory recognition and an initial view of the representation of gustatory information in the fly brain.

}, keywords = {Amino Acid, Animal Structures, Animals, Brain, Cell Surface, Chemoreceptor Cells, Developmental, Drosophila, Drosophila Proteins, Gene Expression Regulation, Genetic Variation, Genetically Modified, Genome, Insect Proteins, Larva, Membrane Proteins, Molecular Sequence Data, Multigene Family, Odorant, Receptors, Sequence Homology, Smell, Taste, Transgenes}, issn = {0092-8674}, author = {Scott, K and Brady, R and Cravchik, A and Morozov, P and Rzhetsky, A and Zuker, C and Axel, R} } @article {4982, title = {The concepts of {\textquoteright}sameness{\textquoteright} and {\textquoteright}difference{\textquoteright} in an insect.}, journal = {Nature}, volume = {410}, year = {2001}, month = {2001 Apr 19}, pages = {930-3}, abstract = {

Insects process and learn information flexibly to adapt to their environment. The honeybee Apis mellifera constitutes a traditional model for studying learning and memory at behavioural, cellular and molecular levels. Earlier studies focused on elementary associative and non-associative forms of learning determined by either olfactory conditioning of the proboscis extension reflex or the learning of visual stimuli in an operant context. However, research has indicated that bees are capable of cognitive performances that were thought to occur only in some vertebrate species. For example, honeybees can interpolate visual information, exhibit associative recall, categorize visual information and learn contextual information. Here we show that honeybees can form {\textquoteright}sameness{\textquoteright} and {\textquoteright}difference{\textquoteright} concepts. They learn to solve {\textquoteright}delayed matching-to-sample{\textquoteright} tasks, in which they are required to respond to a matching stimulus, and {\textquoteright}delayed non-matching-to-sample{\textquoteright} tasks, in which they are required to respond to a different stimulus; they can also transfer the learned rules to new stimuli of the same or a different sensory modality. Thus, not only can bees learn specific objects and their physical parameters, but they can also master abstract inter-relationships, such as sameness and difference.

}, keywords = {Animals, Bees, Color, Discrimination Learning, Maze Learning, Odors}, issn = {0028-0836}, doi = {10.1038/35073582}, author = {Giurfa, M and Zhang, S and Jenett, A and Menzel, R and Srinivasan, M V} } @article {1561, title = {Conversion of a maltose receptor into a zinc biosensor by computational design.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, year = {2001}, month = {2001 Apr 24}, pages = {4955-60}, abstract = {

We have demonstrated that it is possible to radically change the specificity of maltose binding protein by converting it into a zinc sensor using a rational design approach. In this new molecular sensor, zinc binding is transduced into a readily detected fluorescence signal by use of an engineered conformational coupling mechanism linking ligand binding to reporter group response. An iterative progressive design strategy led to the construction of variants with increased zinc affinity by combining binding sites, optimizing the primary coordination sphere, and exploiting conformational equilibria. Intermediates in the design series show that the adaptive process involves both introduction and optimization of new functions and removal of adverse vestigial interactions. The latter demonstrates the importance of the rational design approach in uncovering cryptic phenomena in protein function, which cannot be revealed by the study of naturally evolved systems.

}, keywords = {Alanine, Allosteric Regulation, Bacterial Proteins, Binding Sites, Biosensing Techniques, Calorimetry, Carrier Proteins, Computer Simulation, Fluorescence, Kinetics, Ligands, Maltose, Maltose-Binding Proteins, Models, Molecular, Mutation, Protein Conformation, Protein Engineering, Signal Transduction, Software, Substrate Specificity, Temperature, Thermodynamics, Zinc}, issn = {0027-8424}, doi = {10.1073/pnas.091083898}, author = {Marvin, J S and Hellinga, H W} } @article {45890, title = {Dichotomy of action-potential backpropagation in CA1 pyramidal neuron dendrites.}, journal = {J Neurophysiol}, volume = {86}, year = {2001}, month = {2001 Dec}, pages = {2998-3010}, abstract = {

In hippocampal CA1 pyramidal neurons, action potentials are typically initiated in the axon and backpropagate into the dendrites, shaping the integration of synaptic activity and influencing the induction of synaptic plasticity. Despite previous reports describing action-potential propagation in the proximal apical dendrites, the extent to which action potentials invade the distal dendrites of CA1 pyramidal neurons remains controversial. Using paired somatic and dendritic whole cell recordings, we find that in the dendrites proximal to 280 microm from the soma, single backpropagating action potentials exhibit \<50\% attenuation from their amplitude in the soma. However, in dendritic recordings distal to 300 microm from the soma, action potentials in most cells backpropagated either strongly (26-42\% attenuation; n = 9/20) or weakly (71-87\% attenuation; n = 10/20) with only one cell exhibiting an intermediate value (45\% attenuation). In experiments combining dual somatic and dendritic whole cell recordings with calcium imaging, the amount of calcium influx triggered by backpropagating action potentials was correlated with the extent of action-potential invasion of the distal dendrites. Quantitative morphometric analyses revealed that the dichotomy in action-potential backpropagation occurred in the presence of only subtle differences in either the diameter of the primary apical dendrite or branching pattern. In addition, action-potential backpropagation was not dependent on a number of electrophysiological parameters (input resistance, resting potential, voltage sensitivity of dendritic spike amplitude). There was, however, a striking correlation of the shape of the action potential at the soma with its amplitude in the dendrite; larger, faster-rising, and narrower somatic action potentials exhibited more attenuation in the distal dendrites (300-410 microm from the soma). Simple compartmental models of CA1 pyramidal neurons revealed that a dichotomy in action-potential backpropagation could be generated in response to subtle manipulations of the distribution of either sodium or potassium channels in the dendrites. Backpropagation efficacy could also be influenced by local alterations in dendritic side branches, but these effects were highly sensitive to model parameters. Based on these findings, we hypothesize that the observed dichotomy in dendritic action-potential amplitude is conferred primarily by differences in the distribution, density, or modulatory state of voltage-gated channels along the somatodendritic axis.

}, keywords = {Action Potentials, Animals, Calcium, Dendrites, Diagnostic Imaging, Electrophysiology, Fluorescent Dyes, Fura-2, Hippocampus, In Vitro Techniques, Male, Models, Neurological, Patch-Clamp Techniques, Potassium Channels, Pyramidal Cells, Rats, Rats, Wistar, Sodium Channels}, issn = {0022-3077}, author = {Golding, N L and Kath, W L and Spruston, N} } @article {46641, title = {Drosophila fasciclinII is required for the formation of odor memories and for normal sensitivity to alcohol.}, journal = {Cell}, volume = {105}, year = {2001}, month = {2001 Jun 15}, pages = {757-68}, abstract = {

Drosophila fasciclinII (fasII) mutants perform poorly after olfactory conditioning due to a defect in encoding, stabilizing, or retrieving short-term memories. Performance was rescued by inducing the expression of a normal transgene just before training and immediate testing. Induction after training but before testing failed to rescue performance, showing that Fas II does not have an exclusive role in memory retrieval processes. The stability of odor memories in fasII mutants are indistinguishable from control animals when initial performance is normalized. Like several other mutants deficient in odor learning, fasII mutants exhibit a heightened sensitivity to ethanol vapors. A combination of behavioral and genetic strategies have therefore revealed a role for Fas II in the molecular operations of encoding short-term odor memories and conferring alcohol sensitivity. The preferential expression of Fas II in the axons of mushroom body neurons furthermore suggests that short-term odor memories are formed in these neurites.

}, keywords = {Animals, Animals, Genetically Modified, Axons, Brain Chemistry, Cell Adhesion Molecules, Neuronal, Conditioning, Classical, Drosophila melanogaster, Electroshock, Ethanol, Gene Expression Regulation, Male, Memory, Short-Term, Mutation, Neurons, Odors, Smell}, issn = {0092-8674}, author = {Cheng, Y and Endo, K and Wu, K and Rodan, A R and Heberlein, U and Davis, R L} } @article {4009, title = {Effects of binaural decorrelation on neural and behavioral processing of interaural level differences in the barn owl (Tyto alba).}, journal = {Journal of Comparative Physiology. A, Neuroethology, Sensory, Neural, and Behavioral Physiology}, volume = {187}, year = {2001}, month = {2001 Oct}, pages = {589-95}, abstract = {

The effect of binaural decorrelation on the processing of interaural level difference cues in the barn owl (Tyto alba) was examined behaviorally and electrophysiologically. The electrophysiology experiment measured the effect of variations in binaural correlation on the first stage of interaural level difference encoding in the central nervous system. The responses of single neurons in the posterior part of the ventral nucleus of the lateral lemniscus were recorded to stimulation with binaurally correlated and binaurally uncorrelated noise. No significant differences in interaural level difference sensitivity were found between conditions. Neurons in the posterior part of the ventral nucleus of the lateral lemniscus encode the interaural level difference of binaurally correlated and binaurally uncorrelated noise with equal accuracy and precision. This nucleus therefore supplies higher auditory centers with an undegraded interaural level difference signal for sound stimuli that lack a coherent interaural time difference. The behavioral experiment measured auditory saccades in response to interaural level differences presented in binaurally correlated and binaurally uncorrelated noise. The precision and accuracy of sound localization based on interaural level difference was reduced but not eliminated for binaurally uncorrelated signals. The observation that barn owls continue to vary auditory saccades with the interaural level difference of binaurally uncorrelated stimuli suggests that neurons that drive head saccades can be activated by incomplete auditory spatial information.

}, keywords = {Animal, Animals, Auditory Pathways, Behavior, Brain Stem, Electrophysiology, Inferior Colliculi, Sound Localization, Strigiformes}, issn = {0340-7594}, author = {Egnor, S E} } @article {1988, title = {Glutamate-mediated extrasynaptic inhibition: direct coupling of NMDA receptors to Ca(2+)-activated K+ channels.}, journal = {Neuron}, volume = {31}, year = {2001}, month = {2001 Sep 27}, pages = {1027-34}, abstract = {

NMDA receptors (NMDARs) typically contribute to excitatory synaptic transmission in the CNS. While Ca(2+) influx through NMDARs plays a critical role in synaptic plasticity, direct actions of NMDAR-mediated Ca(2+) influx on neuronal excitability have not been well established. Here we show that Ca(2+) influx through NMDARs is directly coupled to activation of BK-type Ca(2+)-activated K+ channels in outside-out membrane patches from rat olfactory bulb granule cells. Repetitive stimulation of glutamatergic synapses in olfactory bulb slices evokes a slow inhibitory postsynaptic current (IPSC) in granule cells that requires both NMDARs and BK channels. The slow IPSC is enhanced by glutamate uptake blockers, suggesting that extrasynaptic NMDARs underlie the response. These findings reveal a novel inhibitory action of extrasynaptic NMDARs in the brain.

}, keywords = {Animals, Calcium, Calcium Channel Blockers, Calcium Channels, Calcium-Activated, Evoked Potentials, Excitatory Postsynaptic Potentials, Glutamic Acid, Ion Channel Gating, Ion Transport, Large-Conductance Calcium-Activated Potassium Channels, Macromolecular Substances, Membrane Potentials, Models, N-Methyl-D-Aspartate, Nerve Tissue Proteins, Neurological, Neuronal Plasticity, Nicardipine, Olfactory Bulb, Olfactory Receptor Neurons, omega-Conotoxin GVIA, omega-Conotoxins, Patch-Clamp Techniques, Peptides, Potassium, Potassium Channels, Rats, Receptors, Smell, Sprague-Dawley}, issn = {0896-6273}, author = {Isaacson, J S and Murphy, G J} } @article {2516, title = {Hormonal regulation and patterning of the broad-complex in the epidermis and wing discs of the tobacco hornworm, Manduca sexta.}, journal = {Developmental Biology}, volume = {231}, year = {2001}, month = {2001 Mar 1}, pages = {125-37}, abstract = {

Expression of Manduca Broad-Complex (BR-C) mRNA in the larval epidermis is under the dual control of ecdysone and juvenile hormone (JH). Immunocytochemistry with antibodies that recognize the core, Z2, and Z4 domains of Manduca BR-C proteins showed that BR-C appearance not only temporally correlates with pupal commitment of the epidermis on day 3 of the fifth (final) larval instar, but also occurs in a strict spatial pattern within the abdominal segment similar to that seen for the loss of sensitivity to JH. Levels of Z2 and Z4 BR-C proteins shift with Z2 predominating at pupal commitment and Z4 dominant during early pupal cuticle synthesis. Both induction of BR-C mRNA in the epidermis by 20-hydroxyecdysone (20E) and its suppression by JH were shown to be independent of new protein synthesis. For suppression JH must be present during the initial exposure to 20E. When JH was given 6 h after 20E, suppression was only seen in those regions that had not yet expressed BR-C. In the wing discs BR-C was first detected earlier 1.5 days after ecdysis, coincident with the pupal commitment of the wing. Our findings suggest that BR-C expression is one of the first molecular events underlying pupal commitment of both epidermis and wing discs.

}, keywords = {Animals, Biological, Drosophila Proteins, Ecdysone, Epidermis, Juvenile Hormones, Manduca, Messenger, Metamorphosis, RNA, Transcription Factors, Wing, Zinc Fingers}, issn = {0012-1606}, doi = {10.1006/dbio.2000.0143}, author = {Zhou, B and Riddiford, L M} } @article {1782, title = {Independent anchoring and assembly mechanisms of INAD signaling complexes in Drosophila photoreceptors.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {21}, year = {2001}, month = {2001 Jan 1}, pages = {150-8}, abstract = {

In Drosophila photoreceptors the multivalent PDZ protein INAD organizes the phototransduction cascade into a macromolecular signaling complex containing the effector PLC, the light-activated TRP channels, and a regulatory PKC. Previously, we showed that the subcellular localization of INAD signaling complexes is critical for signaling. Now we have examined how INAD complexes are anchored and assembled in photoreceptor cells. We find that trp mutants, or transgenic flies expressing inaD alleles that disrupt the interaction between INAD and TRP, cause the mislocalization of the entire transduction complex. The INAD-TRP interaction is not required for targeting but rather for anchoring of complexes, because INAD and TRP can be targeted independently of each other. We also show that, in addition to its scaffold role, INAD functions to preassemble transduction complexes. Preassembly of signaling complexes helps to ensure that transduction complexes with the appropriate composition end up in the proper location. This may be a general mechanism used by cells to target different signaling machinery to the pertinent subcellular location.

}, keywords = {Animals, Calcium Channels, Cell Membrane, CHO Cells, Cricetinae, Drosophila, Drosophila Proteins, Eye Proteins, Invertebrate, Macromolecular Substances, Mutagenesis, Mutation, Ocular, Photoreceptor Cells, Precipitin Tests, Protein Kinase C, Protein Structure, Protein Transport, Site-Directed, Tertiary, TRPC Cation Channels, Type C Phospholipases, Vision}, issn = {1529-2401}, author = {Tsunoda, S and Sun, Y and Suzuki, E and Zuker, C} } @article {46432, title = {Ionic liquids based on FeCl(3) and FeCl(2). Raman scattering and ab initio calculations.}, journal = {Inorganic Chemistry}, volume = {40}, year = {2001}, month = {2001 May 7}, pages = {2298-304}, abstract = {

We have prepared ionic liquids by mixing either iron(II) chloride or iron(III) chloride with 1-butyl-3-methylimidazolium chloride (BMIC). Iron(II) chloride forms ionic liquids from a mole ratio of 1 FeCl(2)/3 BMIC to almost 1 FeCl(2)/1 BMIC. Both Raman scattering and ab initio calculations indicate that FeCl(4)(2-) is the predominant iron-containing species in these liquids. Iron(III) chloride forms ionic liquids from a mole ratio of 1 FeCl(3)/1.9 BMIC to 1.7 FeCl(3)/1 BMIC. When BMIC is in excess, Raman scattering indicates the presence of FeCl(4-). When FeCl(3) is in excess, Fe(2)Cl(7-) begins to appear and the amount of Fe(2)Cl(7-) increases with increasing amounts of FeCl(3). Ionic liquids were also prepared from a mixture of FeCl(2) and FeCl(3) and are discussed. Finally, we have used both Hartree-Fock and density functional theory methods to compute the optimized structures and vibrational spectra for these species. An analysis of the results using an all-electron basis set, 6-31G, as well as two different effective core potential basis sets, LANL2DZ and CEP-31G is presented.

}, issn = {0020-1669}, author = {Sitze, M S and Schreiter, E R and Patterson, E V and Freeman, R G} } @article {46417, title = {Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase. }, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, year = {2001}, month = {2001-10-09}, pages = {11973-8}, abstract = {

A crystal structure of the anaerobic Ni-Fe-S carbon monoxide dehydrogenase (CODH) from Rhodospirillum rubrum has been determined to 2.8-{\r A} resolution. The CODH family, for which the R. rubrum enzyme is the prototype, catalyzes the biological oxidation of CO at an unusual Ni-Fe-S cluster called the C-cluster. The Ni-Fe-S C-cluster contains a mononuclear site and a four-metal cubane. Surprisingly, anomalous dispersion data suggest that the mononuclear site contains Fe and not Ni, and the four-metal cubane has the form [NiFe3S4] and not [Fe4S4]. The mononuclear site and the four-metal cluster are bridged by means of Cys531 and one of the sulfides of the cube. CODH is organized as a dimer with a previously unidentified [Fe4S4] cluster bridging the two subunits. Each monomer is comprised of three domains: a helical domain at the N terminus, an α/β (Rossmann-like) domain in the middle, and an α/β (Rossmann-like) domain at the C terminus. The helical domain contributes ligands to the bridging [Fe4S4] cluster and another [Fe4S4] cluster, the B-cluster, which is involved in electron transfer. The two Rossmann domains contribute ligands to the active site C-cluster. This x-ray structure provides insight into the mechanism of biological CO oxidation and has broader significance for the roles of Ni and Fe in biological systems.

}, issn = {1091-6490}, doi = {10.1073/pnas.211429998}, author = {Drennan, Catherine L and Heo, Jongyun and Sintchak, Michael D and Schreiter, Eric R and Ludden, Paul W.} } @article {2296, title = {Malaria enhances expression of CC chemokine receptor 5 on placental macrophages.}, journal = {The Journal of Infectious Diseases}, volume = {183}, year = {2001}, month = {2001 Mar 15}, pages = {967-72}, abstract = {

Malaria and human immunodeficiency virus (HIV) coinfections are common in pregnant women in sub-Saharan Africa. The current study shows that placentas of malaria-infected women contain 3 times as much CC chemokine receptor 5 (CCR5) RNA as placentas of women without malaria. By immunohistochemistry, CCR5(+) maternal macrophages were seen in placentas from malaria-infected women but not in placentas from malaria-uninfected women. In addition, CCR5 also was found on fetal Hofbauer cells in placentas from both groups. Thus, malaria infections increase the potential reservoir for HIV in the placenta by increasing the number of HIV target cells.

}, keywords = {Antigens, CCR5, CD14, CD4, Chemokine, Direct, Female, Fetus, Fluorescent Antibody Technique, HIV Infections, Humans, Immunohistochemistry, Macrophages, Malaria, Messenger, Parasitic, Placenta, Pregnancy, Pregnancy Complications, Receptors, RNA, Transcriptional Activation}, issn = {0022-1899}, doi = {10.1086/319248}, author = {Tkachuk, A N and Moormann, A M and Poore, J A and Rochford, R A and Chensue, S W and Mwapasa, V and Meshnick, S R} } @article {1780, title = {Mammalian sweet taste receptors.}, journal = {Cell}, volume = {106}, year = {2001}, month = {2001 Aug 10}, pages = {381-90}, abstract = {

The sense of taste provides animals with valuable information about the quality and nutritional value of food. Previously, we identified a large family of mammalian taste receptors involved in bitter taste perception (the T2Rs). We now report the characterization of mammalian sweet taste receptors. First, transgenic rescue experiments prove that the Sac locus encodes T1R3, a member of the T1R family of candidate taste receptors. Second, using a heterologous expression system, we demonstrate that T1R2 and T1R3 combine to function as a sweet receptor, recognizing sweet-tasting molecules as diverse as sucrose, saccharin, dulcin, and acesulfame-K. Finally, we present a detailed analysis of the patterns of expression of T1Rs and T2Rs, thus providing a view of the representation of sweet and bitter taste at the periphery.

}, keywords = {Animals, Calcium Signaling, Cell Line, Cell Surface, Chromosomes, Cricetinae, Evolution, G-Protein-Coupled, Gene Expression Profiling, Genetic Complementation Test, Heterotrimeric GTP-Binding Proteins, Human, Humans, Messenger, Mice, Molecular, Molecular Sequence Data, Multigene Family, Pair 4, Phenylurea Compounds, Physical Chromosome Mapping, Receptors, RNA, Saccharin, Substrate Specificity, Sucrose, Sweetening Agents, Taste, Taste Buds, Thiazines, Transgenic}, issn = {0092-8674}, author = {Nelson, G and Hoon, M A and Chandrashekar, J and Zhang, Y and Ryba, N J and Zuker, C S} } @article {1560, title = {Manipulation of ligand binding affinity by exploitation of conformational coupling.}, journal = {Nature Structural Biology}, volume = {8}, year = {2001}, month = {2001 Sep 27}, pages = {795-8}, abstract = {

Traditional approaches for increasing the affinity of a protein for its ligand focus on constructing improved surface complementarity in the complex by altering the protein binding site to better fit the ligand. Here we present a novel strategy that leaves the binding site intact, while residues that allosterically affect binding are mutated. This method takes advantage of conformationally distinct states, each with different ligand-binding affinities, and manipulates the equilibria between these conformations. We demonstrate this approach in the Escherichia coli maltose binding protein by introducing mutations, located at some distance from the ligand binding pocket, that sterically affect the equilibrium between an open, apo-state and a closed, ligand-bound state. A family of 20 variants was generated with affinities ranging from an approximately 100-fold improvement (7.4 nM) to an approximately two-fold weakening (1.8 mM) relative to the wild type protein (800 nM).

}, keywords = {Allosteric Regulation, Allosteric Site, Apoproteins, ATP-Binding Cassette Transporters, Calorimetry, Carrier Proteins, Escherichia coli, Escherichia coli Proteins, Kinetics, Ligands, Maltose, Maltose-Binding Proteins, Models, Molecular, Monosaccharide Transport Proteins, Mutation, Protein Binding, Protein Conformation, Protein Engineering, Temperature, Thermodynamics}, issn = {1072-8368}, doi = {10.1038/nsb0901-795}, author = {Marvin, J S and Hellinga, H W} } @article {1744, title = {Miniature motorized microdrive and commutator system for chronic neural recording in small animals.}, journal = {Journal of Neuroscience Methods}, volume = {112}, year = {2001}, month = {2001 Dec 15}, pages = {83-94}, abstract = {

The use of chronically implanted electrodes for neural recordings in small, freely behaving animals poses several unique technical challenges. Because of the need for an extremely lightweight apparatus, chronic recording technology has been limited to manually operated microdrives, despite the advantage of motorized manipulators for positioning electrodes. Here we describe a motorized, miniature chronically implantable microdrive for independently positioning three electrodes in the brain. The electrodes are controlled remotely, avoiding the need to disturb the animal during electrode positioning. The microdrive is approximately 6 mm in diameter, 17 mm high and weighs only 1.5 g, including the headstage preamplifier. Use of the motorized microdrive has produced a ten-fold increase in our data yield compared to those experiments done using a manually operated drive. In addition, we are able to record from multiple single neurons in the behaving animal with signal quality comparable to that seen in a head-fixed anesthetized animal. We also describe a motorized commutator that actively tracks animal rotation based on a measurement of torque in the tether.

}, keywords = {Action Potentials, Animal, Animals, Behavior, Brain, Electrodes, Electronics, Electrophysiology, Feedback, Implanted, Male, Medical, Neurons, Neurophysiology, Songbirds, Torque}, issn = {0165-0270}, author = {Fee, M S and Leonardo, A} } @article {45953, title = {MP20, the second most abundant lens membrane protein and member of the tetraspanin superfamily, joins the list of ligands of galectin-3.}, journal = {BMC Cell Biology}, volume = {2}, year = {2001}, month = {2001 - Aug}, pages = {17}, abstract = {

BACKGROUND: Although MP20 is the second most highly expressed membrane protein in the lens its function remains an enigma. Putative functions for MP20 have recently been inferred from its assignment to the tetraspanin superfamily of integral membrane proteins. Members of this family have been shown to be involved in cellular proliferation, differentiation, migration, and adhesion. In this study, we show that MP20 associates with galectin-3, a known adhesion modulator.

RESULTS: MP20 and galectin-3 co-localized in selected areas of the lens fiber cell plasma membrane. Individually, these proteins purified with apparent molecular masses of 60 kDa and 22 kDa, respectively. A 104 kDa complex was formed in vitro upon mixing the purified proteins. A 102 kDa complex of MP20 and galectin-3 could also be isolated from detergent-solubilized native fiber cell membranes. Binding between MP20 and galectin-3 was disrupted by lactose suggesting the lectin site was involved in the interaction.

CONCLUSIONS: MP20 adds to a growing list of ligands of galectin-3 and appears to be the first representative of the tetraspanin superfamily identified to possess this specificity.

}, keywords = {Animals, Binding Sites, Cell Membrane, Eye Proteins, Galectin 3, Lectins, Lens, Crystalline, Ligands, Macromolecular Substances, Membrane Proteins, Rats}, issn = {1471-2121}, doi = {10.1186/1471-2121-2-17}, author = {Gonen, T and Grey, A C and Jacobs, M D and Donaldson, P J and Kistler, J} } @article {2452, title = {Neural network partitioning by NO and cGMP.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {21}, year = {2001}, month = {2001 Mar 1}, pages = {1610-8}, abstract = {

The stomatogastric ganglion (STG) of the crab Cancer productus contains approximately 30 neurons arrayed into two different networks (gastric mill and pyloric), each of which produces a distinct motor pattern in vitro. Here we show that the functional division of the STG into these two networks requires intact NO-cGMP signaling. Multiple nitric oxide synthase (NOS)-like proteins are expressed in the stomatogastric nervous system, and NO appears to be released as an orthograde transmitter from descending inputs to the STG. The receptor of NO, a soluble guanylate cyclase (sGC), is expressed in a subset of neurons in both motor networks. When NO diffusion or sGC activation are blocked within the ganglion, the two networks combine into a single conjoint circuit. The gastric mill motor rhythm breaks down, and several gastric neurons pattern switch and begin firing in pyloric time. The functional reorganization of the STG is both rapid and reversible, and the gastric mill motor rhythm is restored when the ganglion is returned to normal saline. Finally, pharmacological manipulations of the NO-cGMP pathway are ineffective when descending modulatory inputs to the STG are blocked. This suggests that the NO-cGMP pathway may interact with other biochemical cascades to partition rhythmic motor output from the ganglion.

}, keywords = {Animals, Arginine, Brachyura, Citrulline, Cyclic GMP, Digestive System, Enzyme Inhibitors, Fluorescent Dyes, Ganglia, Guanylate Cyclase, Immunohistochemistry, Invertebrate, Isoquinolines, Male, Nerve Net, Neurons, Neurotransmitter Agents, Nitric Oxide, Nitric Oxide Donors, Periodicity, Signal Transduction}, issn = {1529-2401}, author = {Scholz, N L and de Vente, J and Truman, J W and Graubard, K} } @article {1267, title = {Orientation preference maps in mammalian visual cortex: A wire length minimization approach.}, journal = {Neuron}, volume = {29}, year = {2001}, month = {2001 Feb}, pages = {519-27}, abstract = {

In the visual cortex of many mammals, orientation preference changes smoothly along the cortical surface, with the exception of singularities such as pinwheels and fractures. The reason for the existence of these singularities has remained elusive, suggesting that they are developmental artifacts. We show that singularities reduce the length of intracortical neuronal connections for some connection rules. Therefore, pinwheels and fractures could be evolutionary adaptations keeping cortical volume to a minimum. Wire length minimization approach suggests that interspecies differences in orientation preference maps reflect differences in intracortical neuronal circuits, thus leading to experimentally testable predictions. We discuss application of our model to direction preference maps.

}, issn = {0896-6273}, author = {Koulakov, Alexei A and Chklovskii, Dmitri B} } @article {1989, title = {Postnatal development of spike generation in rat medial vestibular nucleus neurons.}, journal = {Journal of Neurophysiology}, volume = {85}, year = {2001}, month = {2001 May}, pages = {1899-906}, abstract = {

Image stability during self motion depends on the combined actions of the vestibuloocular and optokinetic reflexes (VOR and OKR, respectively). Neurons in the medial vestibular nucleus (MVN) participate in the VOR and OKR by firing in response to both head and image motion. Their intrinsic spike-generating properties enable MVN neurons to modulate firing rates linearly over a broad range of input amplitudes and frequencies such as those that occur during natural head and image motion. This study examines the postnatal development of the intrinsic spike-generating properties of rat MVN neurons with respect to maturation of peripheral vestibular and visual function. Spike generation was studied in a brain stem slice preparation by recording firing responses to current injected intracellularly through whole cell patch electrodes. MVN neurons fired spontaneously and modulated their firing rate in response to injected current at all postnatal ages. However, the input-output properties of the spike generator changed dramatically during the first two postnatal weeks. Neurons younger than postnatal day 10 could not fire faster than 80 spikes/s, modulated their firing rates over a limited range of input amplitudes, and tended to exhibit a nonlinear relationship between input current and mean evoked firing rate. In response to sustained depolarization, firing rates declined significantly in young neurons. Response gains tended to be highest in the first few postnatal days but varied widely across neurons and were not correlated with age. By about the beginning of the third postnatal week, MVN neurons could fire faster than 100 spikes/s in response to a broad range of input amplitudes, exhibited predominantly linear current-firing rate relationships, and adapted little in response to sustained depolarization. Concomitant decreases in action potential width and the time course of the afterhyperpolarization suggest that changes in potassium currents contribute to the maturation of the MVN neuronal spike generator. The results demonstrate that developmental changes in intrinsic membrane properties enable MVN neurons to fire linearly in response to a broad range of stimuli in time for the onset of visual function at the beginning of the third postnatal week.

}, keywords = {Action Potentials, Age Factors, Animals, Electric Stimulation, Eye Movements, Head Movements, Ion Transport, Movement, Nerve Tissue Proteins, Nystagmus, Optokinetic, Potassium Channels, Rats, Reflex, Sodium Channels, Vestibular Nuclei, Vestibulo-Ocular, Visual Perception}, issn = {0022-3077}, author = {Murphy, G J and Du Lac, S} } @article {2015, title = {Rapid atomic density methods for molecular shape characterization.}, journal = {Journal of Molecular Graphics \& Modelling}, volume = {19}, year = {2001}, month = {2001 Jun}, pages = {325-30, 388-90}, abstract = {

Two methods for rapid characterization of molecular shape are presented. Both techniques are based on the density of atoms near the molecular surface. The Fast Atomic Density Evaluation (FADE) algorithm uses fast Fourier transforms to quickly estimate densities. The Pairwise Atomic Density Reverse Engineering (PADRE) method derives modified density measures from the relationship between atomic density and total potentials. While many shape-characterization techniques define shape relative to a surface, the descriptors returned by FADE and PADRE can measure local geometry from points within the three-dimensional space surrounding a molecule. The methods can be used to find crevices and protrusions near the surface of a molecule and to test shape complementarity at the interface between docking molecules.

}, keywords = {Algorithms, Binding Sites, Computer Simulation, Fourier Analysis, Models, Molecular, Protein Binding, Protein Conformation, Proteins}, issn = {1093-3263}, author = {Mitchell, J C and Kerr, R and Ten Eyck, L F} } @article {2707, title = {The sequence of the human genome.}, journal = {Science}, volume = {291}, year = {2001}, month = {2001 Feb 16}, pages = {1304-51}, abstract = {

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90\% of the genome is in scaffold assemblies of 100,000 bp or more, and 25\% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1\% of the genome is spanned by exons, whereas 24\% is in introns, with 75\% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1\% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

}, keywords = {Algorithms, Animals, Artificial, Bacterial, Chromosome Banding, Chromosome Mapping, Chromosomes, Computational Biology, Consensus Sequence, CpG Islands, Databases, DNA, Evolution, Exons, Factual, Female, Gene Duplication, Genes, Genetic Variation, Genome, Human, Human Genome Project, Humans, Intergenic, Introns, Male, Molecular, Nucleic Acid, Phenotype, Physical Chromosome Mapping, Polymorphism, Proteins, Pseudogenes, Repetitive Sequences, Retroelements, Sequence Analysis, Single Nucleotide, Species Specificity}, issn = {0036-8075}, doi = {10.1126/science.1058040}, author = {Venter, J C and Adams, M D and Myers, E W and Li, P W and Mural, R J and Sutton, G G and Smith, H O and Yandell, M and Evans, C A and Holt, R A and Gocayne, J D and Amanatides, P and Ballew, R M and Huson, D H and Wortman, J R and Zhang, Q and Kodira, C D and Zheng, X H and Chen, L and Skupski, M and Subramanian, G and Thomas, P D and Zhang, J and Gabor Miklos, G L and Nelson, C and Broder, S and Clark, A G and Nadeau, J and McKusick, V A and Zinder, N and Levine, A J and Roberts, R J and Simon, M and Slayman, C and Hunkapiller, M and Bolanos, R and Delcher, A and Dew, I and Fasulo, D and Flanigan, M and Florea, L and Halpern, A and Hannenhalli, S and Kravitz, S and Levy, S and Mobarry, C and Reinert, K and Remington, K and Abu-Threideh, J and Beasley, E and Biddick, K and Bonazzi, V and Brandon, R and Cargill, M and Chandramouliswaran, I and Charlab, R and Chaturvedi, K and Deng, Z and Di Francesco, V and Dunn, P and Eilbeck, K and Evangelista, C and Gabrielian, A E and Gan, W and Ge, W and Gong, F and Gu, Z and Guan, P and Heiman, T J and Higgins, M E and Ji, R R and Ke, Z and Ketchum, K A and Lai, Z and Lei, Y and Li, Z and Li, J and Liang, Y and Lin, X and Lu, F and Merkulov, G V and Milshina, N and Moore, H M and Naik, A K and Narayan, V A and Neelam, B and Nusskern, D and Rusch, D B and Salzberg, S and Shao, W and Shue, B and Sun, J and Wang, Z and Wang, A and Wang, X and Wang, J and Wei, M and Wides, R and Xiao, C and Yan, C and Yao, A and Ye, J and Zhan, M and Zhang, W and Zhang, H and Zhao, Q and Zheng, L and Zhong, F and Zhong, W and Zhu, S and Zhao, S and Gilbert, D and Baumhueter, S and Spier, G and Carter, C and Cravchik, A and Woodage, T and Ali, F and An, H and Awe, A and Baldwin, D and Baden, H and Barnstead, M and Barrow, I and Beeson, K and Busam, D and Carver, A and Center, A and Cheng, M L and Curry, L and Danaher, S and Davenport, L and Desilets, R and Dietz, S and Dodson, K and Doup, L and Ferriera, S and Garg, N and Gluecksmann, A and Hart, B and Haynes, J and Haynes, C and Heiner, C and Hladun, S and Hostin, D and Houck, J and Howland, T and Ibegwam, C and Johnson, J and Kalush, F and Kline, L and Koduru, S and Love, A and Mann, F and May, D and McCawley, S and McIntosh, T and McMullen, I and Moy, M and Moy, L and Murphy, B and Nelson, K and Pfannkoch, C and Pratts, E and Puri, V and Qureshi, H and Reardon, M and Rodriguez, R and Rogers, Y H and Romblad, D and Ruhfel, B and Scott, R and Sitter, C and Smallwood, M and Stewart, E and Strong, R and Suh, E and Thomas, R and Tint, N N and Tse, S and Vech, C and Wang, G and Wetter, J and Williams, S and Williams, M and Windsor, S and Winn-Deen, E and Wolfe, K and Zaveri, J and Zaveri, K and Abril, J F and Guig{\'o}, R and Campbell, M J and Sjolander, K V and Karlak, B and Kejariwal, A and Mi, H and Lazareva, B and Hatton, T and Narechania, A and Diemer, K and Muruganujan, A and Guo, N and Sato, S and Bafna, V and Istrail, S and Lippert, R and Schwartz, R and Walenz, B and Yooseph, S and Allen, D and Basu, A and Baxendale, J and Blick, L and Caminha, M and Carnes-Stine, J and Caulk, P and Chiang, Y H and Coyne, M and Dahlke, C and Mays, A and Dombroski, M and Donnelly, M and Ely, D and Esparham, S and Fosler, C and Gire, H and Glanowski, S and Glasser, K and Glodek, A and Gorokhov, M and Graham, K and Gropman, B and Harris, M and Heil, J and Henderson, S and Hoover, J and Jennings, D and Jordan, C and Jordan, J and Kasha, J and Kagan, L and Kraft, C and Levitsky, A and Lewis, M and Liu, X and Lopez, J and Ma, D and Majoros, W and McDaniel, J and Murphy, S and Newman, M and Nguyen, T and Nguyen, N and Nodell, M and Pan, S and Peck, J and Peterson, M and Rowe, W and Sanders, R and Scott, J and Simpson, M and Smith, T and Sprague, A and Stockwell, T and Turner, R and Venter, E and Wang, M and Wen, M and Wu, D and Wu, M and Xia, A and Zandieh, A and Zhu, X} } @article {45168, title = {Split--pool synthesis of 1,3-dioxanes leading to arrayed stock solutions of single compounds sufficient for multiple phenotypic and protein-binding assays.}, journal = {Journal of the American Chemical Society}, volume = {123}, year = {2001}, month = {2001 Feb 28}, pages = {1740-7}, abstract = {

Diversity-oriented organic synthesis offers the promise of advancing chemical genetics, where small molecules are used to explore biology. While the split--pool synthetic method is theoretically the most effective approach for the production of large collections of small molecules, it has not been widely adopted due to numerous technical and analytical hurdles. We have developed a split--pool synthesis leading to an array of stock solutions of single 1,3-dioxanes. The quantities of compounds are sufficient for hundreds of phenotypic and protein-binding assays. The average concentration of these stock solutions derived from a single synthesis bead was determined to be 5.4 mM in 5 microL of DMSO. A mass spectrometric strategy to identify the structure of molecules from a split--pool synthesis was shown to be highly accurate. Individual members of the 1,3-dioxane library have activity in a variety of phenotypic and protein-binding assays. The procedure developed in this study allows many assays to be performed with compounds derived from individual synthesis beads. The synthetic compounds identified in these assays should serve as useful probes of cellular and organismal processes.

}, keywords = {Animals, Cyclin B, Dioxanes, Female, Hela Cells, Humans, Mass Spectrometry, Oocytes, Phenotype, Protein Binding, Xenopus laevis, Zebrafish}, issn = {0002-7863}, author = {Sternson, S M and Louca, J B and Wong, J C and Schreiber, S L} } @article {1518, title = {Switching repulsion to attraction: changing responses to slit during transition in mesoderm migration.}, journal = {Science}, volume = {292}, year = {2001}, month = {2001 Apr 27}, pages = {737-40}, abstract = {

Slit is secreted by cells at the midline of the central nervous system, where it binds to Roundabout (Robo) receptors and functions as a potent repellent. We found that migrating mesodermal cells in vivo respond to Slit as both an attractant and a repellent and that Robo receptors are required for both functions. Mesoderm cells expressing Robo receptors initially migrate away from Slit at the midline. A few hours after migration, these same cells change their behavior and require Robo to extend toward Slit-expressing muscle attachment sites. Thus, Slit functions as a chemoattractant to provide specificity for muscle patterning.

}, keywords = {Animals, Body Patterning, Cell Fusion, Cell Movement, Confocal, Drosophila, Drosophila Proteins, Embryo, Epidermis, Immunologic, Mesoderm, Microscopy, Muscles, Mutation, Nerve Tissue Proteins, Nonmammalian, Receptors, Signal Transduction, Stem Cells}, issn = {0036-8075}, doi = {10.1126/science.1058766}, author = {Kramer, S G and Kidd, T and Simpson, J H and Goodman, C S} } @article {3312, title = {Synthesis of 7200 small molecules based on a substructural analysis of the histone deacetylase inhibitors trichostatin and trapoxin.}, journal = {Organic Letters}, volume = {3}, year = {2001}, month = {2001 Dec 27}, pages = {4239-42}, abstract = {

Seventy-two hundred potential inhibitors of the histone deacetylase (HDAC) enzyme family, based on a 1,3-dioxane diversity structure, were synthesized on polystyrene macrobeads. The compounds were arrayed for biological assays in a "one bead-one stock solution" format. Metal-chelating functional groups were used to direct the 1,3-dioxanes to HDAC enzymes, which are zinc hydrolases. Representative structures from this library were tested for inhibitory activity and the 1,3-dioxane structure was shown to be compatible with HDAC inhibition. [structure: see text]

}, keywords = {Amino Acid, Amino Acid Sequence, Anti-Bacterial Agents, Enzyme Inhibitors, Histone Deacetylase Inhibitors, Histone Deacetylases, Hydroxamic Acids, Peptides, Sequence Homology, Structure-Activity Relationship}, issn = {1523-7060}, author = {Sternson, S M and Wong, J C and Grozinger, C M and Schreiber, S L} } @article {2451, title = {Tiling of the body wall by multidendritic sensory neurons in Manduca sexta.}, journal = {The Journal of Comparative Neurology}, volume = {440}, year = {2001}, month = {2001 Nov 19}, pages = {271-83}, abstract = {

A plexus of multidendritic sensory neurons, the dendritic arborization (da) neurons, innervates the epidermis of soft-bodied insects. Previous studies have indicated that the plexus may comprise distinct subtypes of da neurons, which utilize diverse cyclic 3{\textquoteright},5{\textquoteright}-guanosine monophosphate signaling pathways and could serve several functions. Here, we identify three distinct classes of da neurons in Manduca, which we term the alpha, beta, and gamma classes. These three classes differ in their sensory responses, branch complexity, peripheral dendritic fields, and axonal projections. The two identified alpha neurons branch over defined regions of the body wall, which in some cases correspond to specific natural folds of the cuticle. These cells project to an intermediate region of the neuropil and appear to function as proprioceptors. Three beta neurons are characterized by long, sinuous dendritic branches and axons that terminate in the ventral neuropil. The function of this group of neurons is unknown. Four neurons belonging to the gamma class have the most complex peripheral dendrites. A representative gamma neuron responds to forceful touch of the cuticle. Although the dendrites of da neurons of different classes may overlap extensively, cells belonging to the same class show minimal dendritic overlap. As a result, the body wall is independently tiled by the beta and gamma da neurons and partially innervated by the alpha neurons. These properties of the da system likely allow insects to discriminate the quality and location of several types of stimuli acting on the cuticle.

}, keywords = {Afferent, Animals, Central Nervous System, Dendrites, Electrophysiology, Epidermis, Manduca, Neurons, Synaptic Transmission}, issn = {0021-9967}, doi = {10.1002/cne.1385}, author = {Grueber, W B and Graubard, K and Truman, J W} } @article {1269, title = {Binocular disparity can explain the orientation of ocular dominance stripes in primate primary visual area (V1).}, journal = {Vision Research}, volume = {40}, year = {2000}, month = {2000 Jun 16}, pages = {1765-73}, abstract = {

In the primate primary visual area (V1), the ocular dominance pattern consists of alternating monocular stripes. Stripe orientation follows systematic trends preserved across several species. I propose that these trends result from minimizing the length of intra-cortical wiring needed to recombine information from the two eyes in order to achieve the perception of depth. I argue that the stripe orientation at any point of V1 should follow the direction of binocular disparity in the corresponding point of the visual field. The optimal pattern of stripes determined from this argument agrees with the ocular dominance pattern of macaque and Cebus monkeys. This theory predicts that for any point in the visual field the limits of depth perception are greatest in the direction along the ocular dominance stripes at that point.

}, issn = {0042-6989}, author = {Chklovskii, Dmitri B} } @article {958, title = {Comparative genomics of the eukaryotes.}, journal = {Science}, volume = {287}, year = {2000}, month = {2000 Mar 24}, pages = {2204-15}, abstract = {

A comparative analysis of the genomes of Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae-and the proteins they are predicted to encode-was undertaken in the context of cellular, developmental, and evolutionary processes. The nonredundant protein sets of flies and worms are similar in size and are only twice that of yeast, but different gene families are expanded in each genome, and the multidomain proteins and signaling pathways of the fly and worm are far more complex than those of yeast. The fly has orthologs to 177 of the 289 human disease genes examined and provides the foundation for rapid analysis of some of the basic processes involved in human disease.

}, keywords = {Animals, Apoptosis, Biological Evolution, Caenorhabditis elegans, Cell Adhesion, Cell Cycle, Drosophila melanogaster, Duplicate, Fungal Proteins, Genes, Genetic Diseases, Genetics, Genome, Helminth Proteins, Humans, Immunity, Inborn, Insect Proteins, Medical, Multigene Family, Neoplasms, Protein Structure, Proteome, Saccharomyces cerevisiae, Signal Transduction, Tertiary}, issn = {0036-8075}, doi = {10.1186/gb-2007-8-7-r145}, author = {Rubin, G M and Yandell, M D and Wortman, J R and Gabor Miklos, G L and Nelson, C R and Hariharan, I K and Fortini, M E and Li, P W and Apweiler, R and Fleischmann, W and Cherry, J M and Henikoff, S and Skupski, M P and Misra, S and Ashburner, M and Birney, E and Boguski, M S and Brody, T and Brokstein, P and Celniker, S E and Chervitz, S A and Coates, D and Cravchik, A and Gabrielian, A and Galle, R F and Gelbart, W M and George, R A and Goldstein, L S and Gong, F and Guan, P and Harris, N L and Hay, B A and Hoskins, R A and Li, J and Li, Z and Hynes, R O and Jones, S J and Kuehl, P M and Lemaitre, B and Littleton, J T and Morrison, D K and Mungall, C and O{\textquoteright}Farrell, P H and Pickeral, O K and Shue, C and Vosshall, L B and Zhang, J and Zhao, Q and Zheng, X H and Lewis, S} } @article {45771, title = {Divergence of larval morphology between Drosophila sechellia and its sibling species caused by cis-regulatory evolution of ovo/shaven-baby.}, journal = {Proc Natl Acad Sci U S A}, volume = {97}, year = {2000}, month = {2000 Apr 25}, pages = {4530-4}, abstract = {

We report an extreme morphological difference between Drosophila sechellia and related species of the pattern of hairs on first-instar larvae. On the dorsum of most species, the posterior region of the anterior compartment of most segments is covered by a carpet of fine hairs. In D. sechellia, these hairs have been lost and replaced with naked cuticle. Genetic mapping experiments and interspecific complementation tests indicate that this difference is caused, in its entirety, by evolution at the ovo/shaven-baby locus. The pattern of expression of the ovo/shaven-baby transcript is correlated with this morphological change. The altered dorsal cuticle pattern is probably caused by evolution of the cis-regulatory region of ovo/shaven-baby in the D. sechellia lineage.

}, keywords = {Animals, Biological Evolution, Body Patterning, Crosses, Genetic, DNA-Binding Proteins, Drosophila, Drosophila melanogaster, Drosophila Proteins, Evolution, Molecular, Female, Genes, Insect, Genetic Complementation Test, Larva, Male, Phylogeny, Species Specificity, Transcription Factors, X Chromosome}, issn = {0027-8424}, author = {Sucena, E and Stern, D L} } @article {45914, title = {Diversity and dynamics of dendritic signaling.}, journal = {Science}, volume = {290}, year = {2000}, month = {2000 Oct 27}, pages = {739-44}, abstract = {

Communication between neurons in the brain occurs primarily through synapses made onto elaborate treelike structures called dendrites. New electrical and optical recording techniques have led to tremendous advances in our understanding of how dendrites contribute to neuronal computation in the mammalian brain. The varied morphology and electrical and chemical properties of dendrites enable a spectrum of local and long-range signaling, defining the input-output relationship of neurons and the rules for induction of synaptic plasticity. In this way, diversity in dendritic signaling allows individual neurons to carry out specialized functions within their respective networks.

}, keywords = {Action Potentials, Animals, Brain, Calcium Signaling, Dendrites, Electrophysiology, Humans, Ion Channel Gating, Ion Channels, Neuronal Plasticity, Neurons, Neurotransmitter Agents, Protein Biosynthesis, Signal Transduction, Synapses, Synaptic Transmission}, issn = {0036-8075}, author = {H{\"a}usser, M and Spruston, N and Stuart, G J} } @article {4151, title = {Do cockroaches {\textquoteright}know{\textquoteright} about fluid dynamics?}, journal = {Nature}, volume = {405}, year = {2000}, month = {2000 Jun 15}, pages = {756}, keywords = {Animals, Biomechanics, Interneurons, Periplaneta, Sense Organs, Wind}, issn = {0028-0836}, doi = {10.1038/35015677}, author = {Rinberg, D and Davidowitz, H} } @article {5495, title = {Dopamine modulates acute responses to cocaine, nicotine and ethanol in Drosophila.}, journal = {Current Biology}, volume = {10}, year = {2000}, month = {2000 Feb 24}, pages = {187-94}, abstract = {

Drugs of abuse have a common property in mammals, which is their ability to facilitate the release of the neurotransmitter and neuromodulator dopamine in specific brain regions involved in reward and motivation. This increase in synaptic dopamine levels is believed to act as a positive reinforcer and to mediate some of the acute responses to drugs. The mechanisms by which dopamine regulates acute drug responses and addiction remain unknown.

}, keywords = {Animal, Animals, Behavior, Cocaine, Dopamine, Drosophila, Ethanol, Male, Nicotine}, issn = {0960-9822}, author = {Bainton, R J and Tsai, L T and Singh, C M and Moore, M S and Neckameyer, W S and Heberlein, U} } @article {8264, title = {Drosophila genome takes flight.}, journal = {Nature Cell Biology}, volume = {2}, year = {2000}, month = {2000 Apr}, pages = {E53-4}, abstract = {

In the March 24 issue of Science, a flurry of papers report on the impending completion of the Drosophila melanogaster genome sequence. This historic achievement is the result of a unique collaboration between the Berkeley Drosophila Genome Project (BDGP), led by Gerry Rubin, and the genomics company Celera, headed by Craig Venter. With its genome almost completely sequenced ahead of schedule, Drosophila is another important model organism to enter the postgenomic age, and represents the largest genome sequenced to date.

}, keywords = {Animals, Chromosome Mapping, Drosophila melanogaster, Genome, Molecular Biology}, issn = {1465-7392}, doi = {10.1038/35008678}, author = {Boutros, M and Perrimon, N} } @article {46644, title = {Early retinal development in Drosophila.}, journal = {Results and Problems in Cell Differentiation}, volume = {31}, year = {2000}, month = {2000}, pages = {37-50}, keywords = {Animals, Cell Differentiation, Drosophila melanogaster, Retina}, issn = {0080-1844}, author = {Heberlein, U and Treisman, J E} } @article {2453, title = {Ecdysteroid coordinates optic lobe neurogenesis via a nitric oxide signaling pathway.}, journal = {Development}, volume = {127}, year = {2000}, month = {2000 Aug 15}, pages = {3543-51}, abstract = {

Proliferation of neural precursors in the optic lobe of Manduca sexta is controlled by circulating steroids and by local production of nitric oxide (NO). Diaphorase staining, anti-NO synthase (NOS) immunocytochemistry and the NO-indicator, DAF-2, show that cells throughout the optic anlage contain NOS and produce NO. Signaling via NO inhibits proliferation in the anlage. When exposed to low levels of ecdysteroid, NO production is stimulated and proliferation ceases. When steroid levels are increased, NO production begins to decrease within 15 minutes independent of RNA or protein synthesis and cells rapidly resume proliferation. Resumption of proliferation is not due simply to the removal of NO repression though, but also requires an ecdysteroid stimulatory pathway. The consequence of these opposing pathways is a sharpening of the responsiveness to the steroid, thereby facilitating a tight coordination between development of the different elements of the adult visual system.

}, keywords = {Animals, Cell Division, Ecdysterone, Enzyme Inhibitors, Manduca, Neurons, NG-Nitroarginine Methyl Ester, Nitric Oxide, Nitric Oxide Synthase, Nitric Oxide Synthase Type I, Nonmammalian, Optic Lobe, Signal Transduction, Stem Cells}, issn = {0950-1991}, author = {Champlin, D T and Truman, J W} } @article {45769, title = {Evolutionary biology. The problem of variation.}, journal = {Nature}, volume = {408}, year = {2000}, month = {2000 Nov 30}, pages = {529, 531}, keywords = {Animals, Biological Evolution, DNA, DNA-Binding Proteins, Drosophila melanogaster, Drosophila Proteins, Evolution, Molecular, Female, Gene Expression Regulation, Developmental, Genetic Variation, Male, Mutation, Pigmentation, Sex Characteristics, Sexual Behavior, Animal, Transcription Factors}, issn = {0028-0836}, doi = {10.1038/35046183}, author = {Stern, D L} } @article {45770, title = {Evolutionary developmental biology and the problem of variation.}, journal = {Evolution}, volume = {54}, year = {2000}, month = {2000 Aug}, pages = {1079-91}, abstract = {

One of the oldest problems in evolutionary biology remains largely unsolved. Which mutations generate evolutionarily relevant phenotypic variation? What kinds of molecular changes do they entail? What are the phenotypic magnitudes, frequencies of origin, and pleiotropic effects of such mutations? How is the genome constructed to allow the observed abundance of phenotypic diversity? Historically, the neo-Darwinian synthesizers stressed the predominance of micromutations in evolution, whereas others noted the similarities between some dramatic mutations and evolutionary transitions to argue for macromutationism. Arguments on both sides have been biased by misconceptions of the developmental effects of mutations. For example, the traditional view that mutations of important developmental genes always have large pleiotropic effects can now be seen to be a conclusion drawn from observations of a small class of mutations with dramatic effects. It is possible that some mutations, for example, those in cis-regulatory DNA, have few or no pleiotropic effects and may be the predominant source of morphological evolution. In contrast, mutations causing dramatic phenotypic effects, although superficially similar to hypothesized evolutionary transitions, are unlikely to fairly represent the true path of evolution. Recent developmental studies of gene function provide a new way of conceptualizing and studying variation that contrasts with the traditional genetic view that was incorporated into neo-Darwinian theory and population genetics. This new approach in developmental biology is as important for microevolutionary studies as the actual results from recent evolutionary developmental studies. In particular, this approach will assist in the task of identifying the specific mutations generating phenotypic variation and elucidating how they alter gene function. These data will provide the current missing link between molecular and phenotypic variation in natural populations.

}, keywords = {Animals, Biological Evolution, Evolution, Molecular, Genetic Variation, Genome, Mutation, Phenotype}, issn = {0014-3820}, author = {Stern, D L} } @article {5494, title = {Functional ethanol tolerance in Drosophila.}, journal = {Neuron}, volume = {28}, year = {2000}, month = {2000 Oct}, pages = {261-71}, abstract = {

In humans, repeated alcohol consumption leads to the development of tolerance, manifested as a reduced physiological and behavioral response to a particular dose of alcohol. Here we show that adult Drosophila develop tolerance to the sedating and motor-impairing effects of ethanol with kinetics of acquisition and dissipation that mimic those seen in mammals. Importantly, this tolerance is not caused by changes in ethanol absorption or metabolism. Rather, the development of tolerance requires the functional and structural integrity of specific central brain regions. Mutants unable to synthesize the catecholamine octopamine are also impaired in their ability to develop tolerance. Taken together, these data show that Drosophila is a suitable model system in which to study the molecular and neuroanatomical bases of ethanol tolerance.

}, keywords = {Animal, Animals, Behavior, Biological, Central Nervous System, Dose-Response Relationship, Drosophila, Drug, Drug Tolerance, Ethanol, Inhalation Exposure, Male, Models, Motor Activity, Mutation, Octopamine}, issn = {0896-6273}, author = {Scholz, H and Ramond, J and Singh, C M and Heberlein, U} } @article {45952, title = {Galectin-3 is associated with the plasma membrane of lens fiber cells.}, journal = {Investigative Ophthalmology \& Visual Science}, volume = {41}, year = {2000}, month = {2000 Jan}, pages = {199-203}, abstract = {

PURPOSE: To discover proteins that have the potential to contribute to the tight packing of fiber cells in the lens.

METHODS: Crude fiber cell membranes were isolated from ovine lens cortex. Proteins were separated by two-dimensional gel electrophoresis, and selected protein spots identified by micro-sequencing. The identification of galectin-3 was confirmed by immunoblotting with a specific antibody. The association of galectin-3 with the fiber cell plasma membrane was investigated using immunofluorescence microscopy, solubilization trials with selected reagents, and immunoprecipitation to identify candidate ligands.

RESULTS: A cluster of three protein spots with an apparent molecular weight of 31,000 and isoelectric points ranging between 7 and 8.5 were resolved and identified as galectin-3. This protein was associated peripherally with the fiber cell plasma membrane and interacted with MP20, an abundant intrinsic membrane protein that had been identified previously as a component of membrane junctions between fiber cells.

CONCLUSIONS: The detection of galectin-3 in the lens is a novel result and adds to the growing list of lens proteins with adhesive properties. Its location at the fiber cell membrane and its association with the junction-forming MP20 is consistent with a potential role in the development or maintenance of the tightly packed lens tissue architecture.

}, keywords = {Amino Acid Sequence, Animals, Antigens, Differentiation, Cell Membrane, Chromatography, High Pressure Liquid, Electrophoresis, Gel, Two-Dimensional, Eye Proteins, Galectin 3, Immunoblotting, Lens Cortex, Crystalline, Ligands, Membrane Glycoproteins, Microscopy, Fluorescence, Molecular Sequence Data, Rabbits, Sequence Homology, Amino Acid, Sheep}, issn = {0146-0404}, author = {Gonen, T and Donaldson, P and Kistler, J} } @article {46643, title = {Genetic control of acute ethanol-induced behaviors in Drosophila.}, journal = {Alcoholism, Clinical and Experimental Research}, volume = {24}, year = {2000}, month = {2000 Aug}, pages = {1127-36}, abstract = {

BACKGROUND: In most organisms in which acute ethanol exposure has been studied, it leads to similar changes in behavior. Generally, low ethanol doses activate the central nervous system, whereas high doses are sedative. Sensitivity to the acute intoxicating effects of ethanol is in part under genetic control in rodents and humans, and reduced sensitivity in humans predicts the development of alcoholism (Crabbe et al., 1994; Schuckit, 1994). We have established Drosophila melanogaster as a model organism to study the mechanisms that regulate acute sensitivity to ethanol.

METHODS: We measured the effects of ethanol vapor on Drosophila locomotor behaviors by using three different assays. Horizontal locomotion was quantified in a locomotor chamber, turning behavior was assayed in narrow tubes, and ethanol-induced loss of postural control was measured in an inebriometer. Mutants with altered sensitivity to the acute effects of ethanol were generated by treatment with ethyl methane sulfonate and isolated by selection in the inebriometer. We ascertained the effects of these mutations on ethanol pharmacokinetics by measuring ethanol levels in extracts of flies at various times during and after ethanol exposure.

RESULTS: Among nearly 30,000 potentially mutant flies tested, we isolated 19 mutant strains with reduced and 4 strains with increased sensitivity to the acute effects of ethanol as measured in the inebriometer. Of these mutants, four showed changes in ethanol absorption. Two mutants, named barfly and tipsy to reflect their reduced and increased ethanol sensitivity in the inebriometer, respectively, were analyzed for locomotor behaviors. Both mutants exhibited ethanol-induced hyperactivity that was indistinguishable from wild type. However, barfly and tipsy displayed reduced and increased sensitivity to the sedative effects of ethanol, respectively. Finally, both mutants showed an increased rate of ethanol-induced turning behavior.

CONCLUSIONS: The effects of acute ethanol exposure on Drosophila locomotor behaviors are remarkably similar to those described for mammals. The analysis of mutants with altered sensitivity to ethanol revealed that the genetic pathways which regulate these responses are complex and that single genes can affect hyperactivity, turning, and sedation independently.

}, keywords = {Absorption, Animals, Behavior, Animal, Drosophila melanogaster, Drug Resistance, Ethanol, Kinetics, Motor Activity, Mutation}, issn = {0145-6008}, author = {Singh, C M and Heberlein, U} } @article {957, title = {The genome sequence of Drosophila melanogaster.}, journal = {Science}, volume = {287}, year = {2000}, month = {2000 Mar 24}, pages = {2185-95}, abstract = {

The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.

}, keywords = {Animals, Biological Transport, Chromatin, Cloning, Computational Biology, Contig Mapping, Cytochrome P-450 Enzyme System, DNA, DNA Repair, DNA Replication, Drosophila melanogaster, Euchromatin, Gene Library, Genes, Genetic, Genome, Heterochromatin, Insect, Insect Proteins, Molecular, Nuclear Proteins, Protein Biosynthesis, Sequence Analysis, Transcription}, issn = {0036-8075}, doi = {10.1186/gb-2007-8-7-r145}, author = {Adams, M D and Celniker, S E and Holt, R A and Evans, C A and Gocayne, J D and Amanatides, P G and Scherer, S E and Li, P W and Hoskins, R A and Galle, R F and George, R A and Lewis, S E and Richards, S and Ashburner, M and Henderson, S N and Sutton, G G and Wortman, J R and Yandell, M D and Zhang, Q and Chen, L X and Brandon, R C and Rogers, Y H and Blazej, R G and Champe, M and Pfeiffer, B D and Wan, K H and Doyle, C and Baxter, E G and Helt, G and Nelson, C R and Gabor, G L and Abril, J F and Agbayani, A and An, H J and Andrews-Pfannkoch, C and Baldwin, D and Ballew, R M and Basu, A and Baxendale, J and Bayraktaroglu, L and Beasley, E M and Beeson, K Y and Benos, P V and Berman, B P and Bhandari, D and Bolshakov, S and Borkova, D and Botchan, M R and Bouck, J and Brokstein, P and Brottier, P and Burtis, K C and Busam, D A and Butler, H and Cadieu, E and Center, A and Chandra, I and Cherry, J M and Cawley, S and Dahlke, C and Davenport, L B and Davies, P and de Pablos, B and Delcher, A and Deng, Z and Mays, A D and Dew, I and Dietz, S M and Dodson, K and Doup, L E and Downes, M and Dugan-Rocha, S and Dunkov, B C and Dunn, P and Durbin, K J and Evangelista, C C and Ferraz, C and Ferriera, S and Fleischmann, W and Fosler, C and Gabrielian, A E and Garg, N S and Gelbart, W M and Glasser, K and Glodek, A and Gong, F and Gorrell, J H and Gu, Z and Guan, P and Harris, M and Harris, N L and Harvey, D and Heiman, T J and Hernandez, J R and Houck, J and Hostin, D and Houston, K A and Howland, T J and Wei, M H and Ibegwam, C and Jalali, M and Kalush, F and Karpen, G H and Ke, Z and Kennison, J A and Ketchum, K A and Kimmel, B E and Kodira, C D and Kraft, C and Kravitz, S and Kulp, D and Lai, Z and Lasko, P and Lei, Y and Levitsky, A A and Li, J and Li, Z and Liang, Y and Lin, X and Liu, X and Mattei, B and McIntosh, T C and McLeod, M P and McPherson, D and Merkulov, G and Milshina, N V and Mobarry, C and Morris, J and Moshrefi, A and Mount, S M and Moy, M and Murphy, B and Murphy, L and Muzny, D M and Nelson, D L and Nelson, D R and Nelson, K A and Nixon, K and Nusskern, D R and Pacleb, J M and Palazzolo, M and Pittman, G S and Pan, S and Pollard, J and Puri, V and Reese, M G and Reinert, K and Remington, K and Saunders, R D and Scheeler, F and Shen, H and Shue, B C and Sid{\'e}n-Kiamos, I and Simpson, M and Skupski, M P and Smith, T and Spier, E and Spradling, A C and Stapleton, M and Strong, R and Sun, E and Svirskas, R and Tector, C and Turner, R and Venter, E and Wang, A H and Wang, X and Wang, Z Y and Wassarman, D A and Weinstock, G M and Weissenbach, J and Williams, S M and Williams, S M and Worley, K C and Wu, D and Yang, S and Yao, Q A and Ye, J and Yeh, R F and Zaveri, J S and Zhan, M and Zhang, G and Zhao, Q and Zheng, L and Zheng, X H and Zhong, F N and Zhong, W and Zhou, X and Zhu, S and Zhu, X and Smith, H O and Gibbs, R A and Myers, E W and Rubin, G M and Venter, J C} } @article {2854, title = {Identification of a yeast transcription factor IID subunit, TSG2/TAF48.}, journal = {The Journal of Biological Chemistry}, volume = {275}, year = {2000}, month = {2000 Jun 9}, pages = {17391-8}, abstract = {

The RNA polymerase II general transcription factor TFIID is a complex containing the TATA-binding protein (TBP) and associated factors (TAFs). We have used a mutant allele of the gene encoding yeast TAF(II)68/61p to analyze its function in vivo. We provide biochemical and genetic evidence that the C-terminal alpha-helix of TAF(II)68/61p is required for its direct interaction with TBP, the stable incorporation of TBP into the TFIID complex, the integrity of the TFIID complex, and the transcription of most genes in vivo. This is the first evidence that a yeast TAF(II) other than TAF(II)145/130 interacts with TBP, and the implications of this on the interpretation of data obtained studying TAF(II) mutants in vivo are discussed. We have identified a high copy suppressor of the TAF68/61 mutation, TSG2, that has sequence similarity to a region of the SAGA subunit Ada1. We demonstrate that it directly interacts with TAF(II)68/61p in vitro, is a component of TFIID, is required for the stability of the complex in vivo, and is necessary for the transcription of many yeast genes. On the basis of these functions, we propose that Tsg2/TAF(II)48p is the histone 2A-like dimerization partner for the histone 2B-like TAF(II)68/61p in the yeast TFIID complex.

}, keywords = {Mutagenesis, Phenotype, Protein Structure, Recombinant Fusion Proteins, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Secondary, TATA-Binding Protein Associated Factors, Temperature, TFII, Transcription Factor TFIID, Transcription Factors}, issn = {0021-9258}, doi = {10.1074/jbc.M001635200}, author = {Reese, J C and Zhang, Z and Kurpad, H} } @article {1783, title = {A molecular pathway for light-dependent photoreceptor apoptosis in Drosophila.}, journal = {Neuron}, volume = {28}, year = {2000}, month = {2000 Oct 5}, pages = {139-52}, abstract = {

Light-induced photoreceptor apoptosis occurs in many forms of inherited retinal degeneration resulting in blindness in both vertebrates and invertebrates. Though mutations in several photoreceptor signaling proteins have been implicated in triggering this process, the molecular events relating light activation of rhodopsin to photoreceptor death are yet unclear. Here, we uncover a pathway by which activation of rhodopsin in Drosophila mediates apoptosis through a G protein-independent mechanism. This process involves the formation of membrane complexes of phosphorylated, activated rhodopsin and its inhibitory protein arrestin, and subsequent clathrin-dependent endocytosis of these complexes into a cytoplasmic compartment. Together, these data define the proapoptotic molecules in Drosophila photoreceptors and indicate a novel signaling pathway for light-activated rhodopsin molecules in control of photoreceptor viability.

}, keywords = {Animals, Apoptosis, Arrestins, Binding, Calcium-Binding Proteins, Clathrin, Competitive, Drosophila, Drosophila Proteins, Endocytosis, Gene Expression Regulation, Invertebrate, Light, Mutation, Phosphoprotein Phosphatases, Phosphoproteins, Phosphorylation, Photoreceptor Cells, Retinal Degeneration, Rhodopsin}, issn = {0896-6273}, author = {Kiselev, A and Socolich, M and Vin{\'o}s, J and Hardy, R W and Zuker, C S and Ranganathan, R} } @proceedings {45804, title = {Morphogenesis and gene expressions in the parthenogenetic embryogenesis of the pea aphid Acyrthosiphon pisum}, volume = {17}, year = {2000}, pages = {66}, publisher = {社団法人日本動物学会}, issn = {02890003}, url = {http://ci.nii.ac.jp/naid/110003371583/}, author = {T Miura and S Kambhampati and DL Stern} } @article {1785, title = {A novel family of mammalian taste receptors.}, journal = {Cell}, volume = {100}, year = {2000}, month = {2000 Mar 17}, pages = {693-702}, abstract = {

In mammals, taste perception is a major mode of sensory input. We have identified a novel family of 40-80 human and rodent G protein-coupled receptors expressed in subsets of taste receptor cells of the tongue and palate epithelia. These candidate taste receptors (T2Rs) are organized in the genome in clusters and are genetically linked to loci that influence bitter perception in mice and humans. Notably, a single taste receptor cell expresses a large repertoire of T2Rs, suggesting that each cell may be capable of recognizing multiple tastants. T2Rs are exclusively expressed in taste receptor cells that contain the G protein alpha subunit gustducin, implying that they function as gustducin-linked receptors. In the accompanying paper, we demonstrate that T2Rs couple to gustducin in vitro, and respond to bitter tastants in a functional expression assay.

}, keywords = {Amino Acid, Animals, Cell Surface, Chemoreceptor Cells, Cloning, Evolution, G-Protein-Coupled, Gene Expression, GTP-Binding Proteins, Humans, Mammals, Membrane Proteins, Messenger, Mice, Molecular, Molecular Sequence Data, Multigene Family, Rats, Receptors, RNA, Sequence Homology, Taste, Taste Buds, Transducin}, issn = {0092-8674}, author = {Adler, E and Hoon, M A and Mueller, K L and Chandrashekar, J and Ryba, N J and Zuker, C S} } @article {2016, title = {Optical imaging of calcium transients in neurons and pharyngeal muscle of C. elegans.}, journal = {Neuron}, volume = {26}, year = {2000}, month = {2000 Jun}, pages = {583-94}, abstract = {

Electrophysiology and optical indicators have been used in vertebrate systems to investigate excitable cell firing and calcium transients, but both techniques have been difficult to apply in organisms with powerful reverse genetics. To overcome this limitation, we expressed cameleon proteins, genetically encoded calcium indicators, in the pharyngeal muscle of the nematode worm Caenorhabditis elegans. In intact transgenic animals expressing cameleons, fluorescence ratio changes accompanied muscular contraction, verifying detection of calcium transients. By comparing the magnitude and duration of calcium influx in wild-type and mutant animals, we were able to determine the effects of calcium channel proteins on pharyngeal calcium transients. We also successfully used cameleons to detect electrically evoked calcium transients in individual C. elegans neurons. This technique therefore should have broad applications in analyzing the regulation of excitable cell activity in genetically tractable organisms.

}, keywords = {Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Calcium, Calcium Channels, Down-Regulation, Electrophysiology, Helminth Proteins, Muscle Proteins, Mutation, Neurons, Optics and Photonics, Pharyngeal Muscles, Protein Isoforms}, issn = {0896-6273}, author = {Kerr, R and Lev-Ram, V and Baird, G and Vincent, P and Tsien, R Y and Schafer, W R} } @article {1268, title = {Optimal sizes of dendritic and axonal arbors in a topographic projection.}, journal = {Journal of Neurophysiology}, volume = {83}, year = {2000}, month = {2000}, pages = {2113-19}, chapter = {2113}, abstract = {

I consider a topographic projection between two neuronal layers with different densities of neurons. Given the number of output neurons connected to each input neuron (divergence) and the number of input neurons synapsing on each output neuron (convergence), I determine the widths of axonal and dendritic arbors which minimize the total volume of axons and dendrites. Analytical results for one-dimensional and two-dimensional projections can be summarized qualitatively in the following rule: neurons of the sparser layer should have arbors wider than those of the denser layer. This agrees with the anatomic data for retinal, cerebellar, olfactory bulb, and neocortical neurons the morphology and connectivity of which are known. The rule may be used to infer connectivity of neurons from their morphology.

}, issn = {0022-3077}, author = {Chklovskii, Dmitri B} } @article {45925, title = {Resting and active properties of pyramidal neurons in subiculum and CA1 of rat hippocampus.}, journal = {J Neurophysiol}, volume = {84}, year = {2000}, month = {2000 Nov}, pages = {2398-408}, abstract = {

Action potentials are the end product of synaptic integration, a process influenced by resting and active neuronal membrane properties. Diversity in these properties contributes to specialized mechanisms of synaptic integration and action potential firing, which are likely to be of functional significance within neural circuits. In the hippocampus, the majority of subicular pyramidal neurons fire high-frequency bursts of action potentials, whereas CA1 pyramidal neurons exhibit regular spiking behavior when subjected to direct somatic current injection. Using patch-clamp recordings from morphologically identified neurons in hippocampal slices, we analyzed and compared the resting and active membrane properties of pyramidal neurons in the subiculum and CA1 regions of the hippocampus. In response to direct somatic current injection, three subicular firing types were identified (regular spiking, weak bursting, and strong bursting), while all CA1 neurons were regular spiking. Within subiculum strong bursting neurons were found preferentially further away from the CA1 subregion. Input resistance (R(N)), membrane time constant (tau(m)), and depolarizing "sag" in response to hyperpolarizing current pulses were similar in all subicular neurons, while R(N) and tau(m) were significantly larger in CA1 neurons. The first spike of all subicular neurons exhibited similar action potential properties; CA1 action potentials exhibited faster rising rates, greater amplitudes, and wider half-widths than subicular action potentials. Therefore both the resting and active properties of CA1 pyramidal neurons are distinct from those of subicular neurons, which form a related class of neurons, differing in their propensity to burst. We also found that both regular spiking subicular and CA1 neurons could be transformed into a burst firing mode by application of a low concentration of 4-aminopyridine, suggesting that in both hippocampal subfields, firing properties are regulated by a slowly inactivating, D-type potassium current. The ability of all subicular pyramidal neurons to burst strengthens the notion that they form a single neuronal class, sharing a burst generating mechanism that is stronger in some cells than others.

}, keywords = {Action Potentials, Animals, Cell Size, Electric Impedance, Electric Stimulation, Hippocampus, Patch-Clamp Techniques, Periodicity, Pyramidal Cells, Rats, Rats, Wistar, Synapses}, issn = {0022-3077}, author = {Staff, N P and Jung, H Y and Thiagarajan, T and Yao, M and Spruston, N} } @article {2454, title = {The RXR ortholog USP suppresses early metamorphic processes in Drosophila in the absence of ecdysteroids.}, journal = {Development}, volume = {127}, year = {2000}, month = {2000 Mar 15}, pages = {1151-9}, abstract = {

The steroid hormone 20-hydroxyecdysone (20E) initiates metamorphosis in insects by signaling through the ecdysone receptor complex, a heterodimer of the ecdysone receptor (EcR) and ultraspiracle (USP). Analysis of usp mutant clones in the wing disc of Drosophila shows that in the absence of USP, early hormone responsive genes such as EcR, DHR3 and E75B fail to up-regulate in response to 20E, but other genes that are normally expressed later, such as (\&bgr;)-Ftz-F1 and the Z1 isoform of the Broad-Complex (BRC-Z1), are expressed precociously. Sensory neuron formation and axonal outgrowth, two early metamorphic events, also occur prematurely. In vitro experiments with cultured wing discs showed that BRC-Z1 expression and early metamorphic development are rendered steroid-independent in the usp mutant clones. These results are consistent with a model in which these latter processes are induced by a signal arising during the middle of the last larval stage but suppressed by the unliganded EcR/USP complex. Our observations suggest that silencing by the unliganded EcR/USP receptor and the subsequent release of silencing by moderate steroid levels may play an important role in coordinating early phases of steroid driven development.

}, keywords = {Afferent, Animals, Biological, Developmental, DNA-Binding Proteins, Drosophila, Ecdysteroids, Ecdysterone, Female, Gene Expression Regulation, Gene Targeting, Genes, Insect, Male, Metamorphosis, Models, Neurons, Receptors, Signal Transduction, Steroid, Steroids, Transcription Factors, Up-Regulation, Wing}, issn = {0950-1991}, author = {Schubiger, M and Truman, J W} } @article {46642, title = {A screen for dominant modifiers of ro(Dom), a mutation that disrupts morphogenetic furrow progression in Drosophila, identifies groucho and hairless as regulators of atonal expression.}, journal = {Genetics}, volume = {156}, year = {2000}, month = {2000 Nov}, pages = {1203-17}, abstract = {

ro(Dom) is a dominant allele of rough (ro) that results in reduced eye size due to premature arrest in morphogenetic furrow (MF) progression. We found that the ro(Dom) stop-furrow phenotype was sensitive to the dosage of genes known to affect retinal differentiation, in particular members of the hedgehog (hh) signaling cascade. We demonstrate that ro(Dom) interferes with Hh{\textquoteright}s ability to induce the retina-specific proneural gene atonal (ato) in the MF and that normal eye size can be restored by providing excess Ato protein. We used ro(Dom) as a sensitive genetic background in which to identify mutations that affect hh signal transduction or regulation of ato expression. In addition to mutations in several unknown loci, we recovered multiple alleles of groucho (gro) and Hairless (H). Analysis of their phenotypes in somatic clones suggests that both normally act to restrict neuronal cell fate in the retina, although they control different aspects of ato{\textquoteright}s complex expression pattern.

}, keywords = {Animals, Basic Helix-Loop-Helix Transcription Factors, Crosses, Genetic, DNA-Binding Proteins, Drosophila melanogaster, Embryo, Nonmammalian, Ethyl Methanesulfonate, Female, Genes, Dominant, Genes, Insect, Helix-Loop-Helix Motifs, Male, Morphogenesis, Mutagenesis, Nerve Tissue Proteins, Phenotype, Signal Transduction}, issn = {0016-6731}, author = {Chanut, F and Luk, A and Heberlein, U} } @article {1519, title = {Short-range and long-range guidance by Slit and its Robo receptors: a combinatorial code of Robo receptors controls lateral position.}, journal = {Cell}, volume = {103}, year = {2000}, month = {2000 Dec 22}, pages = {1019-32}, abstract = {

Slit is secreted by midline glia in Drosophila and functions as a short-range repellent to control midline crossing. Although most Slit stays near the midline, some diffuses laterally, functioning as a long-range chemorepellent. Here we show that a combinatorial code of Robo receptors controls lateral position in the CNS by responding to this presumptive Slit gradient. Medial axons express only Robo, intermediate axons express Robo3 and Robo, while lateral axons express Robo2, Robo3, and Robo. Removal of robo2 or robo3 causes lateral axons to extend medially; ectopic expression of Robo2 or Robo3 on medial axons drives them laterally. Precise topography of longitudinal pathways appears to be controlled by a combination of long-range guidance (the Robo code determining region) and short-range guidance (discrete local cues determining specific location within a region).

}, keywords = {Animals, Cell Movement, Developmental, Drosophila, Drosophila Proteins, Gene Expression Regulation, Immunoelectron, Immunologic, Microscopy, Mutagenesis, Nerve Tissue Proteins, Nervous System, Neurons, Phenotype, Receptors}, issn = {0092-8674}, author = {Simpson, J H and Bland, K S and Fetter, R D and Goodman, C S} } @article {1520, title = {Short-range and long-range guidance by slit and its Robo receptors. Robo and Robo2 play distinct roles in midline guidance.}, journal = {Neuron}, volume = {28}, year = {2000}, month = {2000 Dec}, pages = {753-66}, abstract = {

Previous studies showed that Roundabout (Robo) in Drosophila is a repulsive axon guidance receptor that binds to Slit, a repellent secreted by midline glia. In robo mutants, growth cones cross and recross the midline, while, in slit mutants, growth cones enter the midline but fail to leave it. This difference suggests that Slit must have more than one receptor controlling midline guidance. In the absence of Robo, some other Slit receptor ensures that growth cones do not stay at the midline, even though they cross and recross it. Here we show that the Drosophila genome encodes three Robo receptors and that Robo and Robo2 have distinct functions, which together control repulsive axon guidance at the midline. The robo,robo2 double mutant is largely identical to slit.

}, keywords = {Animals, Axons, Cell Line, Cell Surface, Central Nervous System, Cloning, COS Cells, Dimerization, Down-Regulation, Drosophila, Drosophila Proteins, Gene Expression, Growth Cones, Humans, Immunologic, Insect Proteins, Insertional, Ligands, Membrane Proteins, Messenger, Molecular, Molecular Sequence Data, Mutagenesis, Nerve Tissue Proteins, Phenotype, Receptors, RNA}, issn = {0896-6273}, author = {Simpson, J H and Kidd, T and Bland, K S and Goodman, C S} } @article {1784, title = {T2Rs function as bitter taste receptors.}, journal = {Cell}, volume = {100}, year = {2000}, month = {2000 Mar 17}, pages = {703-11}, abstract = {

Bitter taste perception provides animals with critical protection against ingestion of poisonous compounds. In the accompanying paper, we report the characterization of a large family of putative mammalian taste receptors (T2Rs). Here we use a heterologous expression system to show that specific T2Rs function as bitter taste receptors. A mouse T2R (mT2R-5) responds to the bitter tastant cycloheximide, and a human and a mouse receptor (hT2R-4 and mT2R-8) responded to denatonium and 6-n-propyl-2-thiouracil. Mice strains deficient in their ability to detect cycloheximide have amino acid substitutions in the mT2R-5 gene; these changes render the receptor significantly less responsive to cycloheximide. We also expressed mT2R-5 in insect cells and demonstrate specific tastant-dependent activation of gustducin, a G protein implicated in bitter signaling. Since a single taste receptor cell expresses a large repertoire of T2Rs, these findings provide a plausible explanation for the uniform bitter taste that is evoked by many structurally unrelated toxic compounds.

}, keywords = {Afferent Pathways, Amino Acid Sequence, Animals, Calcium, Cell Line, Cell Surface, Chemoreceptor Cells, Cycloheximide, G-Protein-Coupled, Gene Expression, Humans, Inbred C57BL, Inbred DBA, Kidney, Mice, Molecular Sequence Data, Protein Synthesis Inhibitors, Quaternary Ammonium Compounds, Receptors, Recombinant Fusion Proteins, Signal Transduction, Taste, Taste Buds, Transducin, Transfection}, issn = {0092-8674}, author = {Chandrashekar, J and Mueller, K L and Hoon, M A and Adler, E and Feng, L and Guo, W and Zuker, C S and Ryba, N J} } @article {2705, title = {A whole-genome assembly of Drosophila.}, journal = {Science}, volume = {287}, year = {2000}, month = {2000 Mar 24}, pages = {2196-204}, abstract = {

We report on the quality of a whole-genome assembly of Drosophila melanogaster and the nature of the computer algorithms that accomplished it. Three independent external data sources essentially agree with and support the assembly{\textquoteright}s sequence and ordering of contigs across the euchromatic portion of the genome. In addition, there are isolated contigs that we believe represent nonrepetitive pockets within the heterochromatin of the centromeres. Comparison with a previously sequenced 2.9- megabase region indicates that sequencing accuracy within nonrepetitive segments is greater than 99. 99\% without manual curation. As such, this initial reconstruction of the Drosophila sequence should be of substantial value to the scientific community.

}, keywords = {Algorithms, Animals, Chromatin, Computational Biology, Contig Mapping, DNA, Drosophila melanogaster, Euchromatin, Genes, Genome, Heterochromatin, Insect, Molecular Sequence Data, Nucleic Acid, Physical Chromosome Mapping, Repetitive Sequences, Sequence Analysis, Sequence Tagged Sites}, issn = {0036-8075}, author = {Myers, E W and Sutton, G G and Delcher, A L and Dew, I M and Fasulo, D P and Flanigan, M J and Kravitz, S A and Mobarry, C M and Reinert, K H and Remington, K A and Anson, E L and Bolanos, R A and Chou, H H and Jordan, C M and Halpern, A L and Lonardi, S and Beasley, E M and Brandon, R C and Chen, L and Dunn, P J and Lai, Z and Liang, Y and Nusskern, D R and Zhan, M and Zhang, Q and Zheng, X and Rubin, G M and Adams, M D and Venter, J C} } @article {1270, title = {A wire length minimization approach to ocular dominance patterns in mammalian visual cortex.}, journal = {Physica A}, volume = {284}, year = {2000}, month = {2000}, pages = {318-34}, author = {Chklovskii, Dmitri B and Koulakov, Alexei A} } @article {959, title = {The Berkeley Drosophila genome project gene disruption project: single P-element insertions mutating 25\% of vital Drosophila genes.}, journal = {Genetics}, volume = {153}, year = {1999}, month = {1999 Sep}, pages = {135-77}, abstract = {

A fundamental goal of genetics and functional genomics is to identify and mutate every gene in model organisms such as Drosophila melanogaster. The Berkeley Drosophila Genome Project (BDGP) gene disruption project generates single P-element insertion strains that each mutate unique genomic open reading frames. Such strains strongly facilitate further genetic and molecular studies of the disrupted loci, but it has remained unclear if P elements can be used to mutate all Drosophila genes. We now report that the primary collection has grown to contain 1045 strains that disrupt more than 25\% of the estimated 3600 Drosophila genes that are essential for adult viability. Of these P insertions, 67\% have been verified by genetic tests to cause the associated recessive mutant phenotypes, and the validity of most of the remaining lines is predicted on statistical grounds. Sequences flanking \>920 insertions have been determined to exactly position them in the genome and to identify 376 potentially affected transcripts from collections of EST sequences. Strains in the BDGP collection are available from the Bloomington Stock Center and have already assisted the research community in characterizing \>250 Drosophila genes. The likely identity of 131 additional genes in the collection is reported here. Our results show that Drosophila genes have a wide range of sensitivity to inactivation by P elements, and provide a rationale for greatly expanding the BDGP primary collection based entirely on insertion site sequencing. We predict that this approach can bring \>85\% of all Drosophila open reading frames under experimental control.

}, keywords = {Alleles, Animals, California, Crosses, DNA, DNA Transposable Elements, Drosophila melanogaster, Essential, Expressed Sequence Tags, Female, Genes, Genetic, Genetic Linkage, Genome, Insect, Insertional, Male, Models, Mutagenesis, Mutation, Phenotype, Recessive, Reproducibility of Results, Sequence Analysis}, issn = {0016-6731}, doi = {10.1186/gb-2007-8-7-r145}, author = {Spradling, A C and Stern, D and Beaton, A and Rhem, E J and Laverty, T and Mozden, N and Misra, S and Rubin, G M} } @article {1745, title = {Decrystallization of adult birdsong by perturbation of auditory feedback.}, journal = {Nature}, volume = {399}, year = {1999}, month = {1999 Jun 3}, pages = {466-70}, abstract = {

Young birds learn to sing by using auditory feedback to compare their own vocalizations to a memorized or innate song pattern; if they are deafened as juveniles, they will not develop normal songs. The completion of song development is called crystallization. After this stage, song shows little variation in its temporal or spectral properties. However, the mechanisms underlying this stability are largely unknown. Here we present evidence that auditory feedback is actively used in adulthood to maintain the stability of song structure. We found that perturbing auditory feedback during singing in adult zebra finches caused their song to deteriorate slowly. This {\textquoteright}decrystallization{\textquoteright} consisted of a marked loss of the spectral and temporal stereotypy seen in crystallized song, including stuttering, creation, deletion and distortion of song syllables. After normal feedback was restored, these deviations gradually disappeared and the original song was recovered. Thus, adult birds that do not learn new songs nevertheless retain a significant amount of plasticity in the brain.

}, keywords = {Aging, Animals, Auditory Perception, Feedback, Learning, Male, Songbirds}, issn = {0028-0836}, doi = {10.1038/20933}, author = {Leonardo, A and Konishi, M} } @article {45919, title = {Dendritic calcium spike initiation and repolarization are controlled by distinct potassium channel subtypes in CA1 pyramidal neurons.}, journal = {J Neurosci}, volume = {19}, year = {1999}, month = {1999 Oct 15}, pages = {8789-98}, abstract = {

In CA1 pyramidal neurons of the hippocampus, calcium-dependent spikes occur in vivo during specific behavioral states and may be enhanced during epileptiform activity. However, the mechanisms that control calcium spike initiation and repolarization are poorly understood. Using dendritic and somatic patch-pipette recordings, we show that calcium spikes are initiated in the apical dendrites of CA1 pyramidal neurons and drive bursts of sodium-dependent action potentials at the soma. Initiation of calcium spikes at the soma was suppressed in part by potassium channels activated by sodium-dependent action potentials. Low-threshold, putative D-type potassium channels [blocked by 100 microM 4-aminopyridine (4-AP) and 0.5-1 microM alpha-dendrotoxin (alpha-DTX)] played a prominent role in setting a high threshold for somatic calcium spikes, thus restricting initiation to the dendrites. DTX- and 4-AP-sensitive channels were activated during sodium-dependent action potentials and mediated a large component of their afterhyperpolarization. Once initiated, repetitive firing of calcium spikes was limited by activation of putative BK-type calcium-activated potassium channels (blocked by 250 microM tetraethylammonium chloride, 70 nM charybdotoxin, or 100 nM iberiotoxin). Thus, the concerted action of calcium- and voltage-activated potassium channels serves to focus spatially and temporally the membrane depolarization and calcium influx generated by calcium spikes during strong, synchronous network excitation.

}, keywords = {4-Aminopyridine, Action Potentials, Animals, Calcium, Dendrites, Elapid Venoms, Electrophysiology, Hippocampus, Large-Conductance Calcium-Activated Potassium Channels, Male, Potassium Channel Blockers, Potassium Channels, Potassium Channels, Calcium-Activated, Protein Isoforms, Pyramidal Cells, Rats, Rats, Wistar, Sodium, Tetraethylammonium}, issn = {1529-2401}, author = {Golding, N L and Jung, H Y and Mickus, T and Spruston, N} } @article {786, title = {Development of the Drosophila mushroom bodies: sequential generation of three distinct types of neurons from a neuroblast.}, journal = {Development}, volume = {126}, year = {1999}, month = {1999 Sep}, pages = {4065-76}, abstract = {

The mushroom bodies (MBs) are prominent structures in the Drosophila brain that are essential for olfactory learning and memory. Characterization of the development and projection patterns of individual MB neurons will be important for elucidating their functions. Using mosaic analysis with a repressible cell marker (Lee, T. and Luo, L. (1999) Neuron 22, 451-461), we have positively marked the axons and dendrites of multicellular and single-cell mushroom body clones at specific developmental stages. Systematic clonal analysis demonstrates that a single mushroom body neuroblast sequentially generates at least three types of morphologically distinct neurons. Neurons projecting into the (gamma) lobe of the adult MB are born first, prior to the mid-3rd instar larval stage. Neurons projecting into the alpha{\textquoteright} and beta{\textquoteright} lobes are born between the mid-3rd instar larval stage and puparium formation. Finally, neurons projecting into the alpha and beta lobes are born after puparium formation. Visualization of individual MB neurons has also revealed how different neurons acquire their characteristic axon projections. During the larval stage, axons of all MB neurons bifurcate into both the dorsal and medial lobes. Shortly after puparium formation, larval MB neurons are selectively pruned according to birthdays. Degeneration of axon branches makes early-born gamma neurons retain only their main processes in the peduncle, which then project into the adult gamma lobe without bifurcation. In contrast, the basic axon projections of the later-born (alpha{\textquoteright}/beta{\textquoteright}) larval neurons are preserved during metamorphosis. This study illustrates the cellular organization of mushroom bodies and the development of different MB neurons at the single cell level. It allows for future studies on the molecular mechanisms of mushroom body development.

}, keywords = {Animals, Axons, Biological, Brain, Cell Differentiation, Clone Cells, Drosophila melanogaster, Genetic, Genetic Markers, Genetic Techniques, Genetically Modified, Larva, Metamorphosis, Mitosis, Neurons, Olfactory Pathways, Recombination}, issn = {0950-1991}, author = {Lee, T and Lee, A and Luo, L} } @article {45772, title = {The developmental basis for allometry in insects.}, journal = {Development}, volume = {126}, year = {1999}, month = {1999 Mar}, pages = {1091-101}, abstract = {

Within all species of animals, the size of each organ bears a specific relationship to overall body size. These patterns of organ size relative to total body size are called static allometry and have enchanted biologists for centuries, yet the mechanisms generating these patterns have attracted little experimental study. We review recent and older work on holometabolous insect development that sheds light on these mechanisms. In insects, static allometry can be divided into at least two processes: (1) the autonomous specification of organ identity, perhaps including the approximate size of the organ, and (2) the determination of the final size of organs based on total body size. We present three models to explain the second process: (1) all organs autonomously absorb nutrients and grow at organ-specific rates, (2) a centralized system measures a close correlate of total body size and distributes this information to all organs, and (3) autonomous organ growth is combined with feedback between growing organs to modulate final sizes. We provide evidence supporting models 2 and 3 and also suggest that hormones are the messengers of size information. Advances in our understanding of the mechanisms of allometry will come through the integrated study of whole tissues using techniques from development, genetics, endocrinology and population biology.

}, keywords = {Animals, Biological Evolution, Body Constitution, Insect Hormones, Insects, Metamorphosis, Biological, Organ Size, Vertebrates}, issn = {0950-1991}, author = {Stern, D L and Emlen, D J} } @article {3088, title = {Hippocampal damage induced by carbon monoxide poisoning and spreading depression is alleviated by chronic treatment with brain derived polypeptides.}, journal = {Brain Research}, volume = {816}, year = {1999}, month = {1999 Jan 23}, pages = {618-27}, abstract = {

A model of acute carbon monoxide poisoning combined with spreading depression (SD) induced metabolic stress was used to examine the protective effects of cerebrolysin (CL) on the development of electrophysiological, behavioral and morphological signs of hypoxic damage. Capillary electrodes were implanted into the neocortex and hippocampus of anesthetized rats which were then exposed for 90 min to breathing of 0.8\% to 0.5\% CO, while 3 to 4 waves of cortical and hippocampal SD were elicited by microinjections of 5\% KCl. Duration of SD-provoked depolarization of cerebral cortex and hippocampus was noted. Nine and 18 to 19 days later propagation of SD waves was recorded with the same electrodes and decrease of their amplitude was used as an index of brain damage which was significant in the hippocampus but not in the cortex. CL-treatment (2.5 ml/kg per day) started after CO administration and continued for 14 days significantly improved hippocampal recovery manifested by increased amplitude of SD waves. Behavioral tests performed 10 and 20 days after CO poisoning in the Morris water maze revealed better performance (escape latency 7 s) in the CL-treated than in untreated animals (14 s). Morphological analysis showed marked damage in the hippocampus consonant with electrophysiological and behavioral findings in the same animals. No apparent histological damage was found in rats exposed to CO inhalation alone without the additional SD-provoked depolarization. It is concluded that chronic CL-treatment enhances recovery of hippocampal tissue after hypoxic damage of intermediate severity.

}, keywords = {Acute Disease, Analysis of Variance, Animals, Brain, Carbon Monoxide Poisoning, Cortical Spreading Depression, Electrodes, Hippocampus, Hypoxia, Implanted, Long-Evans, Male, Maze Learning, Membrane Potentials, Neuropeptides, Rats, Reaction Time}, issn = {0006-8993}, author = {Koroleva, V I and Korolev, O S and Mares, V and Pastalkova, E and Bures, J} } @article {1210, title = {Modeling transcriptional regulation using microinjection into Xenopus oocytes.}, journal = {Methods}, volume = {17}, year = {1999}, month = {1999 Feb}, pages = {151-60}, abstract = {

Transcriptional regulation is a complex process that requires cooperation between specific DNA sequence elements, the DNA-binding proteins that bind to these sequences, the general transcriptional machinery, and chromatin. Oocyte microinjection offers a technique to study the integrated transcription process while still providing the opportunity to experimentally perturb this process. We describe here techniques for manipulating DNA templates and the protein complement of the oocyte to study multiple facets of transcriptional regulation. We present sample results showing that the GAL4-VP16 fusion activator is sensitive to distance in constructs containing only a minimal promoter, but can activate transcription at greater distances when proximal promoter elements are present.

}, keywords = {Animals, Biological, DNA, DNA Primers, DNA-Binding Proteins, Fungal Proteins, Gene Expression Regulation, Genetic, Herpes Simplex Virus Protein Vmw65, Microinjections, Models, Oocytes, Recombinant Fusion Proteins, Saccharomyces cerevisiae Proteins, Transcription, Transcription Factors, Transcriptional Activation, Xenopus}, issn = {1046-2023}, doi = {10.1006/meth.1998.0726}, author = {Robinett, C C and Dunaway, M} } @article {785, title = {Mosaic analysis with a repressible cell marker for studies of gene function in neuronal morphogenesis.}, journal = {Neuron}, volume = {22}, year = {1999}, month = {1999 Mar}, pages = {451-61}, abstract = {

We describe a genetic mosaic system in Drosophila, in which a dominant repressor of a cell marker is placed in trans to a mutant gene of interest. Mitotic recombination events between homologous chromosomes generate homozygous mutant cells, which are exclusively labeled due to loss of the repressor. Using this system, we are able to visualize axonal projections and dendritic elaboration in large neuroblast clones and single neuron clones with a membrane-targeted GFP marker. This new method allows for the study of gene functions in neuroblast proliferation, axon guidance, and dendritic elaboration in the complex central nervous system. As an example, we show that the short stop gene is required in mushroom body neurons for the extension and guidance of their axons.

}, keywords = {Animals, Axons, Central Nervous System, Chromosomes, Drosophila, Genetic Markers, Mitosis, Morphogenesis, Mosaicism, Mutation, Neurons, Repressor Proteins, Transgenes}, issn = {0896-6273}, author = {Lee, T and Luo, L} } @article {2455, title = {The origins of insect metamorphosis.}, journal = {Nature}, volume = {401}, year = {1999}, month = {1999 Sep 30}, pages = {447-52}, abstract = {

Insect metamorphosis is a fascinating and highly successful biological adaptation, but there is much uncertainty as to how it evolved. Ancestral insect species did not undergo metamorphosis and there are still some existing species that lack metamorphosis or undergo only partial metamorphosis. Based on endocrine studies and morphological comparisons of the development of insect species with and without metamorphosis, a novel hypothesis for the evolution of metamorphosis is proposed. Changes in the endocrinology of development are central to this hypothesis. The three stages of the ancestral insect species-pronymph, nymph and adult-are proposed to be equivalent to the larva, pupa and adult stages of insects with complete metamorphosis. This proposal has general implications for insect developmental biology.

}, keywords = {Animals, Biological, Biological Evolution, Insect Hormones, Insects, Juvenile Hormones, Metamorphosis, Nymph, Wing}, issn = {0028-0836}, doi = {10.1038/46737}, author = {Truman, J W and Riddiford, L M} } @article {45928, title = {Properties of slow, cumulative sodium channel inactivation in rat hippocampal CA1 pyramidal neurons.}, journal = {Biophys J}, volume = {76}, year = {1999}, month = {1999 Feb}, pages = {846-60}, abstract = {

Sodium channels in the somata and dendrites of hippocampal CA1 pyramidal neurons undergo a form of long-lasting, cumulative inactivation that is involved in regulating back-propagating action potential amplitude and can influence dendritic excitation. Using cell-attached patch-pipette recordings in the somata and apical dendrites of CA1 pyramidal neurons, we determined the properties of slow inactivation on response to trains of brief depolarizations. We find that the amount of slow inactivation gradually increases as a function of distance from the soma. Slow inactivation is also frequency and voltage dependent. Higher frequency depolarizations increase both the amount of slow inactivation and its rate of recovery. Hyperpolarized resting potentials and larger command potentials accelerate recovery from slow inactivation. We compare this form of slow inactivation to that reported in other cell types, using longer depolarizations, and construct a simplified biophysical model to examine the possible gating mechanisms underlying slow inactivation. Our results suggest that sodium channels can enter slow inactivation rapidly from the open state during brief depolarizations or slowly from a fast inactivation state during longer depolarizations. Because of these properties of slow inactivation, sodium channels will modulate neuronal excitability in a way that depends in a complicated manner on the resting potential and previous history of action potential firing.

}, keywords = {Animals, Electrophysiology, Hippocampus, Ion Channel Gating, Patch-Clamp Techniques, Pyramidal Cells, Rats, Rats, Wistar, Sodium Channels}, issn = {0006-3495}, author = {Mickus, T and Jung, H Y and Spruston, N} } @article {46434, title = {A room-temperature molten salt prepared from AuCl3 and 1-Ethyl-3-methylimidazolium chloride.}, journal = {Inorganic Chemistry}, volume = {38}, year = {1999}, month = {1999 Aug 23}, pages = {3935-7}, abstract = {

A room-temperature molten salt has been prepared from AuCl3 and 1-ethyl-3-methylimidazolium chloride (EMIC). At a ratio of 1 mol of AuCl3 to 2 mol of EMIC, the salt is a bright yellow-orange and shows Raman spectral features at 170, 328, and 352 cm-1, indicating the presence of AuCl4-. Ab initio calculations indicate that a dinuclear Au2Cl7- species containing a bridging chlorine should be stable, but no such species has been observed.

}, doi = {10.1021/ic990062u}, author = {Schreiter, Eric R and Stevens, Jonathan E. and Ortwerth, Michael F. and Freeman, R. Griffith} } @article {45934, title = {Slow sodium channel inactivation in CA1 pyramidal cells.}, journal = {Ann N Y Acad Sci}, volume = {868}, year = {1999}, month = {1999 Apr 30}, pages = {97-101}, keywords = {Animals, Electrophysiology, Ion Channel Gating, Microscopy, Phase-Contrast, Pyramidal Cells, Rats, Rats, Wistar, Sodium Channels}, issn = {0077-8923}, author = {Mickus, T and Jung, H Y and Spruston, N} } @article {1211, title = {Visualization of large-scale chromatin structure and dynamics using the lac operator/lac repressor reporter system.}, journal = {Methods in Cell Biology}, volume = {58}, year = {1999}, month = {1999}, pages = {203-22}, keywords = {Animals, Bacterial Proteins, Chromatin, Clone Cells, Dermatitis, Escherichia coli Proteins, Gene Amplification, Genes, Genetic, Green Fluorescent Proteins, Lac Operon, Lac Repressors, Luminescent Proteins, Nuclear Localization Signals, Operator Regions, Phototoxic, Reporter, Repressor Proteins, Staining and Labeling}, issn = {0091-679X}, author = {Belmont, A S and Li, G and Sudlow, G and Robinett, C} } @article {2190, title = {An acid- and base-stable o-nitrobenzyl photolabile linker for solid phase organic synthesis.}, journal = {Tetrahedron Letters}, volume = {39}, year = {1998}, month = {1998 Oct 8}, pages = {7451-54}, abstract = {

The synthesis of an o-nitrobenzyl photolabile linker (1) from o-nitrobenzaldehyde is described, and the efficiency of its light-mediated (365 nm) cleavage is found to be comparable to related, previously developed systems. In contrast, 1 is shown to be stable to acid, base, and Lewis acid/amine combinations while the previously developed linker 2 is shown to degrade under the latter two conditions.

}, issn = {0040-4039}, author = {Sternson, Scott M and Schreiber, Stuart L} } @article {45908, title = {Dendritic sodium spikes are variable triggers of axonal action potentials in hippocampal CA1 pyramidal neurons.}, journal = {Neuron}, volume = {21}, year = {1998}, month = {1998 Nov}, pages = {1189-200}, abstract = {

Several early studies suggested that spikes can be generated in the dendrites of CA1 pyramidal neurons, but their functional significance and the conditions under which they occur remain poorly understood. Here, we provide direct evidence from simultaneous dendritic and somatic patch-pipette recordings that excitatory synaptic inputs can elicit dendritic sodium spikes prior to axonal action potential initiation in hippocampal CA1 pyramidal neurons. Both the probability and amplitude of dendritic spikes depended on the previous synaptic and firing history of the cell. Moreover, some dendritic spikes occurred in the absence of somatic action potentials, indicating that their propagation to the soma and axon is unreliable. We show that dendritic spikes contribute a variable depolarization that summates with the synaptic potential and can act as a trigger for action potential initiation in the axon.

}, keywords = {Action Potentials, Animals, Axons, Dendrites, Electric Stimulation, Hippocampus, In Vitro Techniques, Male, Neurons, Patch-Clamp Techniques, Pyramidal Cells, Rats, Rats, Wistar, Sodium, Sodium Channels, Synapses}, issn = {0896-6273}, author = {Golding, N L and Spruston, N} } @article {45912, title = {Determinants of voltage attenuation in neocortical pyramidal neuron dendrites.}, journal = {J Neurosci}, volume = {18}, year = {1998}, month = {1998 May 15}, pages = {3501-10}, abstract = {

How effectively synaptic and regenerative potentials propagate within neurons depends critically on the membrane properties and intracellular resistivity of the dendritic tree. These properties therefore are important determinants of neuronal function. Here we use simultaneous whole-cell patch-pipette recordings from the soma and apical dendrite of neocortical layer 5 pyramidal neurons to directly measure voltage attenuation in cortical neurons. When combined with morphologically realistic compartmental models of the same cells, the data suggest that the intracellular resistivity of neocortical pyramidal neurons is relatively low ( approximately 70 to 100 Omegacm), but that voltage attenuation is substantial because of nonuniformly distributed resting conductances present at a higher density in the distal apical dendrites. These conductances, which were largely blocked by bath application of CsCl (5 mM), significantly increased steady-state voltage attenuation and decreased EPSP integral and peak in a manner that depended on the location of the synapse. Together these findings suggest that nonuniformly distributed Cs-sensitive and -insensitive resting conductances generate a "leaky" apical dendrite, which differentially influences the integration of spatially segregated synaptic inputs.

}, keywords = {Animals, Cesium, Chlorides, Computer Simulation, Dendrites, Electric Conductivity, Electric Impedance, Excitatory Postsynaptic Potentials, Membrane Potentials, Models, Neurological, Neocortex, Patch-Clamp Techniques, Pyramidal Cells, Rats, Rats, Wistar}, issn = {0270-6474}, author = {Stuart, G and Spruston, N} } @article {46647, title = {Dorsoventral patterning in the Drosophila retina by wingless.}, journal = {Development}, volume = {125}, year = {1998}, month = {1998 Feb}, pages = {567-77}, abstract = {

The eye imaginal disc displays dorsal-ventral (D-V) and anterior-posterior polarity prior to the onset of differentiation, which initiates at the intersection of the D-V midline with the posterior margin. As the wave of differentiation progresses anteriorly, additional asymmetry develops as ommatidial clusters rotate coordinately in opposite directions in the dorsal and ventral halves of the disc; this forms a line of mirror-image symmetry, the equator, which coincides with the D-V midline of the disc. How D-V pattern is established and how it relates to ommatidial rotation are unknown. Here we address this question by assaying the expression of various asymmetric markers under conditions that lead to ectopic differentiation, such as removal of patched or wingless function. We find that D-V patterning develops gradually and that wingless plays an important role in setting up this pattern. We show that wingless is necessary and sufficient to induce dorsal expression of the gene mirror prior to the start of differentiation and also to restrict the expression of the WR122 marker to differentiating photoreceptors near the equator. In addition, we find that manipulations in wingless expression shift the D-V axis of the disc as evidenced by changes in the expression domains of asymmetric markers, the position of the site of initiation and the equator, and the pattern of epithelial growth. Thus, Wg appears to coordinately regulate multiple events related to D-V patterning in the developing retina.

}, keywords = {Animals, Animals, Genetically Modified, Crosses, Genetic, Drosophila, Drosophila Proteins, Eye Proteins, Female, Gene Expression Regulation, Developmental, Genes, Insect, Genetic Markers, Homeodomain Proteins, Lac Operon, Larva, Male, Proto-Oncogene Proteins, Retina, Transcription Factors, Wnt1 Protein}, issn = {0950-1991}, author = {Heberlein, U and Borod, E R and Chanut, F A} } @article {2456, title = {Drosophila EcR-B ecdysone receptor isoforms are required for larval molting and for neuron remodeling during metamorphosis.}, journal = {Development}, volume = {125}, year = {1998}, month = {1998 Jun}, pages = {2053-62}, abstract = {

During the metamorphic reorganization of the insect central nervous system, the steroid hormone 20-hydroxyecdysone induces a wide spectrum of cellular responses including neuronal proliferation, maturation, cell death and the remodeling of larval neurons into their adult forms. In Drosophila, expression of specific ecdysone receptor (EcR) isoforms has been correlated with particular responses, suggesting that different EcR isoforms may govern distinct steroid-induced responses in these cells. We have used imprecise excision of a P element to create EcR deletion mutants that remove the EcR-B promoter and therefore should lack EcR-B1 and EcR-B2 expression but retain EcR-A expression. Most of these EcR-B mutant animals show defects in larval molting, arresting at the boundaries between the three larval stages, while a smaller percentage of EcR-B mutants survive into the early stages of metamorphosis. Remodeling of larval neurons at metamorphosis begins with the pruning back of larval-specific dendrites and occurs as these cells are expressing high levels of EcR-B1 and little EcR-A. This pruning response is blocked in the EcR-B mutants despite the fact that adult-specific neurons, which normally express only EcR-A, can progress in their development. These observations support the hypothesis that different EcR isoforms control cell-type-specific responses during remodeling of the nervous system at metamorphosis.

}, keywords = {Animals, Biological, Drosophila, Genes, Insect, Insertional, Larva, Lethal, Metamorphosis, Molting, Mutagenesis, Nervous System, Neurons, Receptors, Sequence Deletion, Steroid}, issn = {0950-1991}, author = {Schubiger, M and Wade, A A and Carney, G E and Truman, J W and Bender, M} } @article {8265, title = {The Drosophila genome project: a progress report.}, journal = {Trends in Genetics}, volume = {14}, year = {1998}, month = {1998 Sep}, pages = {340-3}, keywords = {Animals, Chromosome Mapping, Databases, Factual, Drosophila, Expressed Sequence Tags, Genome, Heterochromatin, Mutagenesis, Insertional}, issn = {0168-9525}, author = {Rubin, G M} } @article {2457, title = {Ecdysteroids govern two phases of eye development during metamorphosis of the moth, Manduca sexta.}, journal = {Development}, volume = {125}, year = {1998}, month = {1998 Jun}, pages = {2009-18}, abstract = {

The eye primordium of the moth, Manduca sexta, shows two different developmental responses to ecdysteroids depending on the concentration to which it is exposed. Tonic exposure to moderate levels of 20-hydroxyecdysone (20E) or its precursor, ecdysone, are required for progression of the morphogenetic furrow across the primordium. Proliferation, cell-type specification and organization of immature ommatidial clusters occur in conjunction with furrow progression. These events can be reversibly started or stopped in cultured primordia simply by adjusting levels of ecdysteroid to be above or below a critical threshold concentration. In contrast, high levels of 20E cause maturation of the photoreceptors and the support cells that comprise the ommatidia. Ommatidial maturation normally occurs after the furrow has crossed the primordium, but premature exposure to high levels of 20E at any time causes precocious maturation. In such cases, the furrow arrests irreversibly and cells behind the furrow produce a well-formed, but miniature, eye. Precocious and catastrophic metamorphosis occurs throughout such animals, suggesting that ecdysteroids control development of other tissues in a manner similar to the eye. The threshold concentrations of 20E required for furrow progression versus ommatidial maturation differ by about 17-fold. This capacity to regulate distinct phases of development by different concentrations of a single hormone is probably achieved by differential sensitivity of target gene promoters to induction by the hormone-bound receptor(s).

}, keywords = {Amphibians, Animals, Biological, Ecdysone, Ecdysteroids, Ecdysterone, Eye, Gene Expression Regulation, Genes, Insect, Invertebrate, Larva, Manduca, Metamorphosis, Photoreceptor Cells, Pupa, Species Specificity, Steroids, Time Factors}, issn = {0950-1991}, author = {Champlin, D T and Truman, J W} } @inbook {2557, title = {The effect of cross-linking on thermal inactivation of cellulases. In stability of stabilization of biocatalyst.}, booktitle = {Progress in Biotechnology}, year = {1998}, author = {Bilen, Julide and Bakir, U}, editor = {Ballesteros, A and Plou, FJ and Iborra, JL and Hallings, PJ} } @article {5496, title = {Ethanol intoxication in Drosophila: genetic and pharmacological evidence for regulation by the cAMP signaling pathway.}, journal = {Cell}, volume = {93}, year = {1998}, month = {1998 Jun 12}, pages = {997-1007}, abstract = {

Upon exposure to ethanol, Drosophila display behaviors that are similar to ethanol intoxication in rodents and humans. Using an inebriometer to measure ethanol-induced loss of postural control, we identified cheapdate, a mutant with enhanced sensitivity to ethanol. Genetic and molecular analyses revealed that cheapdate is an allele of the memory mutant amnesiac. amnesiac has been postulated to encode a neuropeptide that activates the cAMP pathway. Consistent with this, we find that enhanced ethanol sensitivity of cheapdate can be reversed by treatment with agents that increase cAMP levels or PKA activity. Conversely, genetic or pharmacological reduction in PKA activity results in increased sensitivity to ethanol. Taken together, our results provide functional evidence for the involvement of the cAMP signal transduction pathway in the behavioral response to intoxicating levels of ethanol.

}, keywords = {Adenylate Cyclase, Alleles, Amino Acid Sequence, Animal, Animals, Base Sequence, Behavior, Cloning, Cyclic AMP, Cyclic AMP-Dependent Protein Kinases, Drosophila melanogaster, Drosophila Proteins, Enzyme Activation, Enzyme Inhibitors, Ethanol, Forskolin, Genes, Genetic Complementation Test, Genetically Modified, Insect, Male, Messenger, Molecular, Molecular Sequence Data, Mutation, Neuropeptides, RNA, Signal Transduction}, issn = {0092-8674}, author = {Moore, M S and DeZazzo, J and Luk, A Y and Tully, T and Singh, C M and Heberlein, U} } @article {46648, title = {Eye development in Drosophila: formation of the eye field and control of differentiation.}, journal = {Current Topics in Developmental Biology}, volume = {39}, year = {1998}, month = {1998}, pages = {119-58}, keywords = {Animals, Cell Differentiation, Drosophila, Eye, Gene Expression Regulation, Developmental, Larva, Morphogenesis, Mutation, Visual Fields}, issn = {0070-2153}, author = {Treisman, J E and Heberlein, U} } @article {1167, title = {Initiation of mitochondrial DNA replication by transcription and R-loop processing.}, journal = {The Journal of Biological Chemistry}, volume = {273}, year = {1998}, month = {1998 Nov 13}, pages = {30614-21}, abstract = {

The mitochondrial genome of eukaryotic cells is maintained by a mechanism distinct from that employed in the nucleus. Mitochondrial DNA replication at the leading-strand origin is coupled to transcription through the formation of an RNA-DNA hybrid known as an R-loop. In vivo and in vitro evidence has implicated an RNA processing enzyme, RNase MRP, in primer maturation. In our investigation of mammalian RNase MRP, we have analyzed its specific endoribonuclease activity on model R-loops. We demonstrate here that human RNase MRP cleaves this distinctly configured substrate at virtually all of the major DNA replication sites previously mapped in vivo. We further show that the processed RNA products remain stably base-paired to the template DNA strand and are functional for initiating DNA synthesis on a closed circular plasmid. Thus, in vitro initiation of leading-strand mtDNA synthesis requires only the actions of RNA polymerase and RNase MRP for the generation of replication primers.

}, keywords = {Base Sequence, Catalytic Domain, Cell Line, Circular, DNA, DNA Replication, Endoribonucleases, Genetic, Humans, Mitochondrial, Molecular Sequence Data, Nucleic Acid Conformation, Ribonucleoproteins, RNA, Transcription}, issn = {0021-9258}, doi = {10.1101/gad.1352105}, author = {Lee, D Y and Clayton, D A} } @article {1567, title = {Introduction of fluorescent allosteric signal transduction elements into glucose-binding protein: construction of a novel glucose sensor.}, journal = {Journal of the American Chemical Society}, year = {1998}, month = {1998}, pages = {7-11}, author = {Marvin, Jonathan S and Hellinga, H W} } @article {1186, title = {Mitochondrial transcription factor A is necessary for mtDNA maintenance and embryogenesis in mice.}, journal = {Nature Genetics}, volume = {18}, year = {1998}, month = {1998 Mar}, pages = {231-6}, abstract = {

The regulation of mitochondrial DNA (mtDNA) expression is crucial for mitochondrial biogenesis during development and differentiation. We have disrupted the mouse gene for mitochondrial transcription factor A (Tfam; formerly known as m-mtTFA) by gene targetting of loxP-sites followed by cre-mediated excision in vivo. Heterozygous knockout mice exhibit reduced mtDNA copy number and respiratory chain deficiency in heart. Homozygous knockout embryos exhibit a severe mtDNA depletion with abolished oxidative phosphorylation. Mutant embryos proceed through implantation and gastrulation, but die prior to embryonic day (E)10.5. Thus, Tfam is the first mammalian protein demonstrated to regulate mtDNA copy number in vivo and is essential for mitochondrial biogenesis and embryonic development.

}, keywords = {Animals, Developmental, DNA, DNA-Binding Proteins, Embryo Implantation, Female, Fetal Death, Fetal Growth Retardation, Gene Dosage, Gene Expression Regulation, Heart, Heterozygote, High Mobility Group Proteins, Integrases, Knockout, Mice, Mitochondria, Mitochondrial, Mitochondrial Proteins, Mutation, Nuclear Proteins, Phosphorylation, Transcription Factors, Viral Proteins}, issn = {1061-4036}, doi = {10.1038/ng0398-231}, author = {Larsson, N G and Wang, J and Wilhelmsson, H and Oldfors, A and Rustin, P and Lewandoski, M and Barsh, G S and Clayton, D A} } @article {46646, title = {Mutual regulation of decapentaplegic and hedgehog during the initiation of differentiation in the Drosophila retina.}, journal = {Devopemental Biology}, volume = {197}, year = {1998}, month = {1998 May 15}, pages = {187-97}, abstract = {

Neuronal differentiation in the Drosophila retinal primordium, the eye imaginal disc, begins at the posterior tip of the disc and progresses anteriorly as a wave. The morphogenetic furrow (MF) marks the boundary between undifferentiated anterior cells and differentiating posterior cells. Anterior progression of differentiation is driven by Hedgehog, synthesized by cells located posterior to the MF. We report here that hedgehog (hh), which is expressed prior to the start of differentiation along the disc{\textquoteright}s posterior margin, also plays a crucial role in the initiation of differentiation. Using a temperature-sensitive allele we show that hh is normally required at the posterior margin to maintain the expression of decapentaplegic (dpp) and of the proneural gene atonal. In addition, we find that ectopic differentiation driven by ectopic dpp expression or loss of wingless function requires hh. Consistent with this is our observation that ectopic dpp induces the expression of hh along the anterior margin even in the absence of differentiation. Taken together, these data reveal a novel positive regulatory loop between dpp and hh that is essential for the initiation of differentiation in the eye disc.

}, keywords = {Animals, Animals, Genetically Modified, Basic Helix-Loop-Helix Transcription Factors, Cell Differentiation, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Female, Gene Expression Regulation, Developmental, Genes, Insect, Hedgehog Proteins, Immunohistochemistry, Insect Proteins, Larva, Male, Nerve Tissue Proteins, Neurons, Retina}, issn = {0012-1606}, doi = {10.1006/dbio.1998.8888}, author = {Borod, E R and Heberlein, U} } @article {45805, title = {Phylogeny of the Tribe Cerataphidini (Homoptera) and the Evolution of the Horned Soldier Aphids}, journal = {Evolution}, volume = {52}, year = {1998}, month = {02/1998}, pages = {155-165}, abstract = {

The horned soldier aphids of the Cerataphidini, unlike most social insects that reside in nests, live on the open surface of plants. The lack of a nest and other obvious ecological correlates makes it unclear why secondary-host soldiers might have evolved. Here I present a molecular phylogenetic analysis of 32 species of the Cerataphidini, including 10 species from the genera Ceratovacuna and Pseudoregma that produce horned soldiers. The phylogeny suggests that horned soldiers evolved once and were lost once or twice. Most horned soldiers are a morphologically specialized caste and two species that have unspecialized soldiers are independently derived from species with specialized castes. The genus Ceratovacuna appears to have undergone a relatively rapid radiation. Mapping secondary-host plants and geographic ranges onto the phylogeny suggests that bamboos were the ancestral secondary-host plants and that the Asian tropics and subtropics were the ancestral geographic regions for the genera Astegopteryx, Ceratoglyphina, Ceratovacuna Chaitoregma, and Pseudoregma and possibly for the entire tribe. There is evidence for vicariant events that separate the tropical and subtropical lineages in all of the major lineages of the tribe and for dispersal of some lineages. Based on these results, I present hypotheses for the causes and consequences of horned-soldier evolution.

}, url = {http://www.jstor.org/stable/2410930}, author = {David L Stern} } @article {1562, title = {Protein engineering and the development of generic biosensors.}, journal = {Trends in Biotechnology}, volume = {16}, year = {1998}, month = {1998 Apr}, pages = {183-9}, abstract = {

Biosensors exploit the remarkable specificity of biomolecular recognition to provide analytical tools that can measure the presence of a single molecular species in a complex mixture. A new strategy is emerging in the development of biosensor technologies: molecular-engineering techniques are being used to adapt the properties of proteins to simple, generic detector instrumentation, rather than adapting instruments to the unique requirements of a natural molecule.

}, keywords = {Binding Sites, Biosensing Techniques, Protein Binding, Protein Engineering, Proteins, Signal Transduction}, issn = {0167-7799}, author = {Hellinga, H W and Marvin, J S} } @article {45773, title = {A role of Ultrabithorax in morphological differences between Drosophila species.}, journal = {Nature}, volume = {396}, year = {1998}, month = {1998 Dec 3}, pages = {463-6}, abstract = {

The mechanisms underlying the evolution of morphology are poorly understood. Distantly related taxa sometimes exhibit correlations between morphological differences and patterns of gene expression, but such comparisons cannot establish how mechanisms evolve to generate diverse morphologies. Answers to these questions require resolution of the nature of developmental evolution within and between closely related species. Here I show how the detailed regulation of the Hox gene Ultrabithorax patterns trichomes on the posterior femur of the second leg in Drosophila melanogaster, and that evolution of Ultrabithorax has contributed to divergence of this feature among closely related species. The cis-regulatory regions of Ultrabithorax, and not the protein itself, appear to have evolved. This study provides experimental evidence that cis-regulatory evolution is one way in which conserved proteins have promoted morphological diversity.

}, keywords = {Alleles, Animals, Crosses, Genetic, DNA-Binding Proteins, Drosophila, Drosophila melanogaster, Drosophila Proteins, Evolution, Molecular, Extremities, Female, Gene Expression, Genes, Insect, Homeodomain Proteins, Insect Proteins, Male, Molecular Sequence Data, Species Specificity, Transcription Factors}, issn = {0028-0836}, doi = {10.1038/24863}, author = {Stern, D L} } @article {45896, title = {Specialized electrophysiological properties of anatomically identified neurons in the hilar region of the rat fascia dentata.}, journal = {J Neurophysiol}, volume = {79}, year = {1998}, month = {1998 Mar}, pages = {1518-34}, abstract = {

Because of their strategic position between the granule cell and pyramidal cell layers, neurons of the hilar region of the hippocampal formation are likely to play an important role in the information processing between the entorhinal cortex and the hippocampus proper. Here we present an electrophysiological characterization of anatomically identified neurons in the fascia dentata as studied using patch-pipette recordings and subsequent biocytin-staining of neurons in slices. The resting potential, input resistance (RN), membrane time constant (taum), "sag" in hyperpolarizing responses, maximum firing rate during a 1-s current pulse, spike width, and fast and slow afterhyperpolarizations (AHPs) were determined for several different types of hilar neurons. Basket cells had a dense axonal plexus almost exclusively within the granule cell layer and were distinguishable by their low RN, short taum, lack of sag, and rapid firing rates. Dentate granule cells also lacked sag and were identifiable by their higher RN, longer taum, and lower firing rates than basket cells. Mossy cells had extensive axon collaterals within the hilus and a few long-range collaterals to the inner molecular layer and CA3c and were characterized physiologically by small fast and slow AHPs. Spiny and aspiny hilar interneurons projected primarily either to the inner or outer segment of the molecular layer and had a dense intrahilar axonal plexus, terminating onto somata within the hilus and CA3c. Physiologically, spiny hilar interneurons generally had higher RN values than mossy cells and a smaller slow AHP than aspiny interneurons. The specialized physiological properties of different classes of hilar neurons are likely to be important determinants of their functional operation within the hippocampal circuitry.

}, keywords = {Animals, Axons, Dendrites, Dentate Gyrus, Electrophysiology, In Vitro Techniques, Interneurons, Membrane Potentials, Microscopy, Video, Neurons, Rats, Rats, Wistar, Regression Analysis}, issn = {0022-3077}, author = {L{\"u}bke, J and Frotscher, M and Spruston, N} } @article {46645, title = {Y do we drink?}, journal = {Cell}, volume = {95}, year = {1998}, month = {1998 Dec 11}, pages = {733-5}, keywords = {Alcohol Drinking, Alcoholic Intoxication, Animals, Ethanol, Feeding Behavior, Humans, Mice, Mice, Mutant Strains, Neuropeptide Y, Rats}, issn = {0092-8674}, author = {Tecott, L H and Heberlein, U} } @article {45923, title = {Action potential initiation and backpropagation in neurons of the mammalian CNS.}, journal = {Trends Neurosci}, volume = {20}, year = {1997}, month = {1997 Mar}, pages = {125-31}, abstract = {

Most neurons in the mammalian CNS encode and transmit information via action potentials. Knowledge of where these electrical events are initiated and how they propagate within neurons is therefore fundamental to an understanding of neuronal function. While work from the 1950s suggested that action potentials are initiated in the axon, many subsequent investigations have suggested that action potentials can also be initiated in the dendrites. Recently, experiments using simultaneous patch-pipette recordings from different locations on the same neuron have been used to address this issue directly. These studies show that the site of action potential initiation is in the axon, even when synaptic activation is powerful enough to elicit dendritic electrogenesis. Furthermore, these and other studies also show that following initiation, action potentials actively backpropagate into the dendrites of many neuronal types, providing a retrograde signal of neuronal output to the dendritic tree.

}, keywords = {Action Potentials, Animals, Central Nervous System, Neurons}, issn = {0166-2236}, author = {Stuart, G and Spruston, N and Sakmann, B and H{\"a}usser, M} } @article {45806, title = {Behavior and morphology of monomorphic soldiers from the aphid genus Pseudoregma (Cerataphidini, Hormaphididae): implications for the evolution of morphological castes in social aphids}, journal = {Insectes Sociaux}, volume = {44}, year = {1997}, month = {11/1997}, pages = {379-392}, abstract = {

Soldier-producing aphids have evolved at least nine separate times. The larvae of soldier-producing species can be organized into three general categories: monomorphic larvae, dimorphic larvae with a reproductive soldier caste, and dimorphic larvae with a sterile soldier caste. Here we report the discovery of a novel soldier type in an undescribed species of Pseudoregma that is morphologically similar to P. bambucicola. A colony of this species produced morphologically monomorphic first-instar larvae with a defensive behavioral dimorphism. These larvae attacked natural predators, and larval response to a simple assay, placing the tips of forceps in front of larvae, was correlated with this attacking behavior. Approximately one third of the first-instar larvae in the colony attacked and this proportion was uncorrelated with the time of day, the ambient temperature, or the diel migratory behavior of the aphids. Migrating larvae rarely attacked. Attacking behavior was correlated with another defensive behavior, hind-leg waving. Attackers were more likely to possess the next-instar skin, suggesting that they were older than non-attackers. This is the first example of a possible within-instar age polyethism in soldier-producing aphids. Canonical variates analysis of seven morphological measurements failed to discriminate between attacking and non-attacking larvae. The monomorphic larvae share some morphometric characteristics in common with the soldiers of P. bambucicola and other characteristics in common with normal larvae. We discuss these results with respect to the evolution and loss of soldier castes in the tribe Cerataphidini.

}, keywords = {castes, dimorphism, morphometrics, Soldier aphids}, issn = {0020-1812}, doi = {10.1007/s000400050059}, author = {DL Stern and JA Whitfield and WA Foster} } @article {45813, title = {Determining aphid taxonomic affinities and life cycles with molecular data: a case study of the tribe Cerataphidini (Hormaphididae: Aphidoidea: Hemiptera)}, journal = {Systematic Entomology}, volume = {22}, year = {1997}, month = {01/1997}, pages = {81-96}, abstract = {

Aphid taxonomy is often frustrated by the host alternation and extensive polyphenism displayed by many species. Here we examine the utility of using molecular data to assist in life cycle and taxonomic determination. We found that a relatively small amount of DNA sequence data can greatly assist in these tasks. Molecular data have identified the synonymy of five species: Tuberaphis plicator (Noordam) is a junior synonym of T.takenouchii (Takahashi), T.taiwana (Takahashi) is a junior synonym of T.coreana Takahashi, Hamiltonaphis styraci (Matsumura) is transferred to Tuberaphis Takahashi, Astegopteryx roepkei Hille Ris Lambers is transferred to Ceratoglyphina van der Goot, and A.vandermeermohri Hille Ris Lambers is transferred to Cerataphis Lichtenstein. We have elucidated the complete life cycles of five species: A.basalis (van der Goot) alternates between Styrax benzoin and bamboos, Ceratoglyphina bambusae van der Goot alternates between S.benzoin and bamboos, Pseudoregma sundanica (van der Goot) alternates between S.paralleloneura and Zingiberaceae, T.coreana alternates between S.formosana and Loranthaceae, and T.takenouchii alternates between S.japonica and Loranthaceae. In all cases the molecular data agreed with available morphological data. This analysis demonstrates the utility of DNA sequence comparisons for elucidating complex life cycles and the taxonomy of difficult insect groups.

}, doi = {10.1046/j.1365-3113.1997.d01-20.x}, author = {David Stern and Shigeyuki Aoki and Shigeyuki Kurosu} } @article {2458, title = {Disruption of a behavioral sequence by targeted death of peptidergic neurons in Drosophila.}, journal = {Neuron}, volume = {19}, year = {1997}, month = {1997 Oct}, pages = {813-23}, abstract = {

The neuropeptide eclosion hormone (EH) is a key regulator of insect ecdysis. We tested the role of the two EH-producing neurons in Drosophila by using an EH cell-specific enhancer to activate cell death genes reaper and head involution defective to ablate the EH cells. In the EH cell knockout flies, larval and adult ecdyses were disrupted, yet a third of the knockouts emerged as adults, demonstrating that EH has a significant but nonessential role in ecdysis. The EH cell knockouts had discrete behavioral deficits, including slow, uncoordinated eclosion and an insensitivity to ecdysis-triggering hormone. The knockouts lacked the lights-on eclosion response despite having a normal circadian eclosion rhythm. This study represents a novel approach to the dissection of neuropeptide regulation of a complex behavioral program.

}, keywords = {Animals, Cell Death, Circadian Rhythm, Crosses, Darkness, DNA Transposable Elements, Drosophila, Embryo, Genetic, Green Fluorescent Proteins, Insect Hormones, Invertebrate, Larva, Light, Luminescent Proteins, Mutagenesis, Neurons, Neuropeptides, Nonmammalian, Photoreceptor Cells, Recombinant Fusion Proteins}, issn = {0896-6273}, author = {McNabb, S L and Baker, J D and Agapite, J and Steller, H and Riddiford, L M and Truman, J W} } @article {45807, title = {The evolution of sociality in aphids: a clone{\textquoteright}s-eye view}, journal = {The evolution of social behavior in insects and arachnids.}, year = {1997}, month = {03/1997}, pages = {150-165}, abstract = {

A number of aphid species produce individuals, termed soldiers, that defend the colony by attacking predators. Soldiers have either reduced or zero direct reproductive fitness. Their behavior is therefore altruistic in the classical sense: an individual is behaving in a way that incurs reproductive costs on itself and confers reproductive benefits on another. However, comparison with the better{\textendash}known eusocial insects (Hymenoptera, Isoptera) indicates that there are important differences between clonal and sexual social animals.

Here we take a clone{\textquoteright}s{\textendash}eye view and conclude that many facets of aphid sociality are best thought of in terms of resource allocation: for example, the choice between investment in defense and reproduction. This view considerably simplifies some aspects of the problem and highlights the qualitatively different nature of genetic heterogeneity in colonies of aphids and of other social insects. In sexually reproducing social insects, each individual usually has a different genome, which leads to genetic conflicts of interest between individuals. In social aphids, all members of a clone have identical genomes, barring new mutations, and there should be no disagreement among clonemates about investment decisions. Genetic heterogeneity within colonies can arise, but principally through clonal mixing, and this means that investment decisions will vary between different clones rather than among all individuals.

}, isbn = {9780511721953}, doi = {10.1017/CBO9780511721953.008}, url = {http://ebooks.cambridge.org/chapter.jsf?bid=CBO9780511721953\&cid=CBO9780511721953A015}, author = {David L. Stern and William A. Foster} } @article {46649, title = {eyelid antagonizes wingless signaling during Drosophila development and has homology to the Bright family of DNA-binding proteins.}, journal = {Genes \& Development}, volume = {11}, year = {1997}, month = {1997 Aug 1}, pages = {1949-62}, abstract = {

In Drosophila, pattern formation at multiple stages of embryonic and imaginal development depends on the same intercellular signaling pathways. We have identified a novel gene, eyelid (eld), which is required for embryonic segmentation, development of the notum and wing margin, and photoreceptor differentiation. In these tissues, eld mutations have effects opposite to those caused by wingless (wg) mutations. eld encodes a widely expressed nuclear protein with a region homologous to a novel family of DNA-binding domains. Based on this homology and on the phenotypic analysis, we suggest that Eld could act as a transcription factor antagonistic to the Wg pathway.

}, keywords = {Amino Acid Sequence, Animals, Body Patterning, Cell Differentiation, Cloning, Molecular, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Gene Expression Regulation, Developmental, Genes, Insect, Molecular Sequence Data, Mutation, Phenotype, Photoreceptor Cells, Invertebrate, Proto-Oncogene Proteins, Recombinant Fusion Proteins, Restriction Mapping, Sequence Homology, Amino Acid, Signal Transduction, Trans-Activators, Transcription Factors, Wing, Wnt1 Protein}, issn = {0890-9369}, author = {Treisman, J E and Luk, A and Rubin, G M and Heberlein, U} } @article {2704, title = {Human whole-genome shotgun sequencing.}, journal = {Genome Research}, volume = {7}, year = {1997}, month = {1997 May}, pages = {401-9}, keywords = {Cloning, DNA, Forecasting, Genetic, Genome, Human, Human Genome Project, Humans, Molecular, Polymorphism, Sequence Analysis, Sequence Tagged Sites}, issn = {1088-9051}, author = {Weber, J L and Myers, E W} } @article {45903, title = {Interneurons in the stratum lucidum of the rat hippocampus: an anatomical and electrophysiological characterization.}, journal = {J Comp Neurol}, volume = {385}, year = {1997}, month = {1997 Sep 1}, pages = {427-40}, abstract = {

The anatomical and electrophysiological properties of neurons in the stratum lucidum of the CA3 subfield of the hippocampus were examined by using patch-pipette recordings combined with biocytin staining. This method facilitated the analysis of the morphological features and passive and active properties of a recently described class of spiny neurons in the stratum lucidum, as well as aspiny neurons in this region. Some, but not all, synaptic inputs of both types of neurons were found to arise from the mossy fiber system. The axons of spiny neurons in the stratum lucidum were heavily collateralized, terminating primarily in the stratum lucidum and stratum radiatum of CA3, and to a lesser extent in the stratum pyramidale and stratum oriens. Only a few axonal projections were found that extended beyond the CA3 region into CA1 and the hilus. Aspiny neurons fell into two classes: those projecting axons to the stratum lucidum and stratum radiatum of CA3 and those with axon terminations mainly in the stratum pyramidale and stratum oriens. The electrophysiological properties of spiny and aspiny neurons in the stratum lucidum were similar, but on average, the aspiny neurons had significantly higher maximal firing rates and narrower action potential half-widths. The results demonstrate that a diverse population of neurons exists in the region of mossy fiber termination in area CA3. These neurons may be involved in local-circuit feedback, or feed-forward systems controlling the flow of information through the hippocampus.

}, keywords = {Animals, Axons, Dendrites, Hippocampus, Interneurons, Neurons, Patch-Clamp Techniques, Rats, Rats, Wistar, Synapses, Synaptic Transmission}, issn = {0021-9967}, author = {Spruston, N and L{\"u}bke, J and Frotscher, M} } @article {2459, title = {Neuropeptide hierarchies and the activation of sequential motor behaviors in the hawkmoth, Manduca sexta.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {17}, year = {1997}, month = {1997 Jun 1}, pages = {4389-97}, abstract = {

In insects, the shedding of the old cuticle at the end of a molt involves a stereotyped sequence of distinct behaviors. Our studies on the isolated nervous system of Manduca sexta show that the peptides ecdysis-triggering hormone (ETH) and crustacean cardioactive peptide (CCAP) elicit the first two motor behaviors, the pre-ecdysis and ecdysis behaviors, respectively. Exposing isolated abdominal ganglia to ETH resulted in the generation of sustained pre-ecdysis bursts. By contrast, exposing the entire isolated CNS to ETH resulted in the sequential appearance of pre-ecdysis and ecdysis motor outputs. Previous research has shown that ETH activates neurons within the brain that then release eclosion hormone within the CNS. The latter elevates cGMP levels within and increases the excitability of a group of neurons containing CCAP. In our experiments, the ETH-induced onset of ecdysis bursts was always associated with a rise in intracellular cGMP within these CCAP neurons. We also found that CCAP immunoreactivity decreases centrally during normal ecdysis. Isolated, desheathed abdominal ganglia responded to CCAP by generating rhythmical ecdysis bursts. These ecdysis motor bursts persisted as long as CCAP was present and could be reinduced by successive application of the peptide. CCAP exposure also actively terminated pre-ecdysis bursts from the abdominal CNS, even in the continued presence of ETH. Thus, the sequential performance of the two behaviors arises from one modulator activating the first behavior and also initiating the release of the second modulator. The second modulator then turns off the first behavior while activating the second.

}, keywords = {Animal, Animals, Antibody Specificity, Behavior, Calcitonin, Cyclic GMP, Electrophysiology, Ganglia, Insect Hormones, Invertebrate, Larva, Manduca, Molting, Motor Activity, Nervous System, Nervous System Physiological Phenomena, Neuropeptides, Peptide Fragments, Peptides, Sensitivity and Specificity}, issn = {0270-6474}, author = {Gammie, S C and Truman, J W} } @article {45916, title = {Prolonged sodium channel inactivation contributes to dendritic action potential attenuation in hippocampal pyramidal neurons.}, journal = {J Neurosci}, volume = {17}, year = {1997}, month = {1997 Sep 1}, pages = {6639-46}, abstract = {

During low-frequency firing, action potentials actively invade the dendrites of CA1 pyramidal neurons. At higher firing rates, however, activity-dependent processes result in the attenuation of back-propagating action potentials, and propagation failures occur at some dendritic branch points. We tested two major hypotheses related to this activity-dependent attenuation of back-propagating action potentials: (1) that it is mediated by a prolonged form of sodium channel inactivation and (2) that it is mediated by a persistent dendritic shunt activated by back-propagating action potentials. We found no evidence for a persistent shunt, but we did find that cumulative, prolonged inactivation of sodium channels develops during repetitive action potential firing. This inactivation is significant after a single action potential and continues to develop during several action potentials thereafter, until a steady-state sodium current is established. Recovery from this form of inactivation is much slower than its induction, but recovery can be accelerated by hyperpolarization. The similarity of these properties to the time and voltage dependence of attenuation and recovery of dendritic action potentials suggests that dendritic sodium channel inactivation contributes to the activity dependence of action potential back-propagation in CA1 neurons. Hence, the biophysical properties of dendritic sodium channels will be important determinants of action potential-mediated effects on synaptic integration and plasticity in hippocampal neurons.

}, keywords = {Action Potentials, Animals, Dendrites, Electrophysiology, Hippocampus, In Vitro Techniques, Neurons, Pyramidal Cells, Rats, Rats, Wistar, Sodium Channels, Tetrodotoxin, Time Factors}, issn = {0270-6474}, author = {Jung, H Y and Mickus, T and Spruston, N} } @article {1563, title = {The rational design of allosteric interactions in a monomeric protein and its applications to the construction of biosensors.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {94}, year = {1997}, month = {1997 Apr 29}, pages = {4366-71}, abstract = {

Rational protein design is an emerging approach for testing general theories of structure and function. The ability to manipulate function rationally also offers the possibility of creating new proteins of biotechnological value. Here we use the design approach to test the current understanding of the structural principles of allosteric interactions in proteins and demonstrate how a simple allosteric system can form the basis for the construction of a generic biosensor molecular engineering system. We have identified regions in Escherichia coli maltose-binding protein that are predicted to be allosterically linked to its maltose-binding site. Environmentally sensitive fluorophores were covalently attached to unique thiols introduced by cysteine mutations at specific sites within these regions. The fluorescence of such conjugates changes cooperatively with respect to maltose binding, as predicted. Spatial separation of the binding site and reporter groups allows the intrinsic properties of each to be manipulated independently. Provided allosteric linkage is maintained, ligand binding can therefore be altered without affecting transduction of the binding event by fluorescence. To demonstrate applicability to biosensor technology, we have introduced a series of point mutations in the maltose-binding site that lower the affinity of the protein for its ligand. These mutant proteins have been combined in a composite biosensor capable of measuring substrate concentration within 5\% accuracy over a concentration range spanning five orders of magnitude.

}, keywords = {Allosteric Regulation, ATP-Binding Cassette Transporters, Binding Sites, Biosensing Techniques, Biotechnology, Carrier Proteins, Computer Simulation, Escherichia coli Proteins, Fluorescent Dyes, Maltose, Maltose-Binding Proteins, Models, Molecular, Monosaccharide Transport Proteins, Mutation, Protein Conformation}, issn = {0027-8424}, author = {Marvin, J S and Corcoran, E E and Hattangadi, N A and Zhang, J V and Gere, S A and Hellinga, H W} } @article {1141, title = {The regulation of the Drosophila msl-2 gene reveals a function for sex-lethal in translational control.}, journal = {Cell}, volume = {89}, year = {1997}, month = {1997 May 30}, pages = {789-98}, abstract = {

In Drosophila, dosage compensation occurs by increasing the transcription of the single male X chromosome. Four trans-acting factors encoded by the male-specific lethal genes are required for this process. Dosage compensation is restricted to males by the splicing regulator Sex-lethal, which functions to prevent the production of the MSL-2 protein in females by an unknown mechanism. In this report, we provide evidence that Sex-lethal acts synergistically through sequences in both the 5{\textquoteright} and 3{\textquoteright} untranslated regions of MSL-2 to mediate repression. We also provide evidence that the repression of MSL-2 is directly regulated by Sex-lethal at the level of translation.

}, issn = {0092-8674}, author = {Baker, B.S. and Bashaw, G.J.} } @article {1212, title = {The repeat organizer, a specialized insulator element within the intergenic spacer of the Xenopus rRNA genes.}, journal = {Molecular and Cellular Biology}, volume = {17}, year = {1997}, month = {1997 May}, pages = {2866-75}, abstract = {

We have identified a novel activity for the region of the intergenic spacer of the Xenopus laevis rRNA genes that contains the 35- and 100-bp repeats. We devised a new assay for this region by constructing DNA plasmids containing a tandem repeat of rRNA reporter genes that were separated by the 35- and 100-bp repeat region and a rRNA gene enhancer. When the 35- and 100-bp repeat region is present in its normal position and orientation at the 3{\textquoteright} end of the rRNA reporter genes, the enhancer activates the adjacent downstream promoter but not the upstream rRNA promoter on the same plasmid. Because this element can restrict the range of an enhancer{\textquoteright}s activity in the context of tandem genes, we have named it the repeat organizer (RO). The ability to restrict enhancer action is a feature of insulator elements, but unlike previously described insulator elements the RO does not block enhancer action in a simple enhancer-blocking assay. Instead, the activity of the RO requires that it be in its normal position and orientation with respect to the other sequence elements of the rRNA genes. The enhancer-binding transcription factor xUBF also binds to the repetitive sequences of the RO in vitro, but these sequences do not activate transcription in vivo. We propose that the RO is a specialized insulator element that organizes the tandem array of rRNA genes into single-gene expression units by promoting activation of a promoter by its proximal enhancers.

}, keywords = {Animals, Genes, Genetic, Models, Molecular, Nucleic Acid, Repetitive Sequences, Reporter, Ribosomal, RNA, Sequence Deletion, Transcription, Transcription Factors, Xenopus laevis, Xenopus Proteins}, issn = {0270-7306}, author = {Robinett, C C and O{\textquoteright}Connor, A and Dunaway, M} } @article {46650, title = {Retinal morphogenesis in Drosophila: hints from an eye-specific decapentaplegic allele.}, journal = {Developmental Genetics}, volume = {20}, year = {1997}, month = {1997}, pages = {197-207}, abstract = {

Decapentaplegic (dpp) regulates many aspects of imaginal disc growth and patterning in Drosophila. We have analyzed the phenotype of an eye-specific dpp allele, dppblk, which causes a reduction in the size of the retina due to a loss of ventral ommatidia. Prior to the onset of differentiation, dppblk eye discs are normal regarding size, shape, and ability to express dorsal and ventral markers. However, expression of a dpp-lacZ reporter is reduced at the ventral margin. Additional dorsoventral asymmetry appears during retinal differentiation: the morphogenetic furrow (MF) initiates normally at the posterior tip of the disc, but fails to propagate into the ventral epithelium. This defect can be rescued by increasing dpp expression along the ventral margin by local removal of patched function. We propose that the primary defect in dppblk is an inability to activate dpp expression properly at the ventral margin. This has two consequences: it prevents initiation from the ventral margin, and it renders the ventral epithelium unresponsive to differentiation signals emanating from the MF.

}, keywords = {Animals, Drosophila, Drosophila Proteins, Insect Proteins, Morphogenesis, Mutation, Phenotype, Photoreceptor Cells, Invertebrate, Retina}, issn = {0192-253X}, doi = {10.1002/(SICI)1520-6408(1997)20:3<197::AID-DVG3>3.0.CO;2-2}, author = {Chanut, F and Heberlein, U} } @article {1187, title = {RNase MRP correctly cleaves a novel R loop at the mitochondrial DNA leading-strand origin of replication.}, journal = {Genes \& Development}, volume = {11}, year = {1997}, month = {1997 Mar}, pages = {582-92}, abstract = {

The precursor primer RNA for mammalian mitochondrial DNA leading-strand replication remains as a persistent R loop formed during transcription through the mitochondrial DNA control region. We have examined model R loops, which exist in a novel and physiologically accurate preprimer conformation, as potential substrates for mammalian RNase mitochondrial RNA processing (MRP). Mouse RNase MRP accurately cleaves an R loop containing the mouse mitochondrial DNA origin. The multiple cleavage sites on the R-loop substrate match the priming sites observed in vivo, suggesting that RNase MRP alone is capable of generating virtually all of the leading-strand replication primers.

}, issn = {0890-9369}, author = {Clayton, D A and Lee, D Y} } @article {46651, title = {Role of decapentaplegic in initiation and progression of the morphogenetic furrow in the developing Drosophila retina.}, journal = {Development}, volume = {124}, year = {1997}, month = {1997 Jan}, pages = {559-67}, abstract = {

Morphogenesis in the Drosophila retina initiates at the posterior margin of the eye imaginal disc by an unknown mechanism. Upon initiation, a wave of differentiation, its forward edge marked by the morphogenetic furrow (MF), proceeds anteriorly across the disc. Progression of the MF is driven by hedgehog (hh), expressed by differentiating photoreceptor cells. The TGF-beta homolog encoded by decapentaplegic (dpp) is expressed at the disc{\textquoteright}s posterior margin prior to initiation and in the furrow, under the control of hh, during MF progression. While dpp has been implicated in eye disc growth and morphogenesis, its precise role in retinal differentiation has not been determined. To address the role of dpp in initiation and progression of retinal differentiation we analyzed the consequences of reduced and increased dpp function during eye development. We find that dpp is not only required for normal MF initiation, but is sufficient to induce ectopic initiation of differentiation. Inappropriate initiation is normally inhibited by wingless (wg). Loss of dpp function is accompanied by expansion of wg expression, while increased dpp function leads to loss of wg transcription. In addition, dpp is required to maintain, and sufficient to induce, its own expression along the disc{\textquoteright}s margins. We postulate that dpp autoregulation and dpp-mediated inhibition of wg expression are required for the coordinated regulation of furrow initiation and progression. Finally, we show that in the later stages of retinal differentiation, reduction of dpp function leads to an arrest in MF progression.

}, keywords = {Animals, Cell Differentiation, Chromosome Mapping, Drosophila, Drosophila Proteins, Embryo, Nonmammalian, Embryonic Induction, Gene Expression Regulation, Developmental, Genes, Insect, Hedgehog Proteins, Insect Proteins, Morphogenesis, Proto-Oncogene Proteins, Retina, Transcription, Genetic, Wnt1 Protein}, issn = {0950-1991}, author = {Chanut, F and Heberlein, U} } @article {45815, title = {Caste allometries in the soldier-producing aphidPseudoregma alexanderi (Hormaphididae: Aphidoidea)}, journal = {Insectes sociaux}, volume = {43}, year = {1996}, pages = {137-147}, abstract = {

Colonies of the aphidPseudoregma alexanderi produce morphologically-specialized first-instar larvae, termed soldiers, that defend the colony from predators. The environmental cues and physiological mechanisms governing soldier production are currently unknown. Here we present a morphometric study of soldiers and normal first-instar larvae ofP. alexanderi. Several morphological features (fore-leg length and width, hind-leg length, and horn length) plotted against body length display relationship that are similar to a sigmoidal curve. We found further support for an earlier finding that soldiers fall into two size categories, majors and minors, although both types of soldiers appear to follow the same allometry. The patterns of allometry in the soldier-producing aphids are very different from those found in other social insects and do not easily fit into the traditional categorization of allometries. We present two simple alternative models of soldier development as a framework for guiding future studies of the mechanisms of soldier production.

}, keywords = {castes, morphometrics, Soldier aphids}, issn = {1420-9098}, doi = {10.1007/BF01242566}, url = {http://link.springer.com/article/10.1007/BF01242566}, author = {D. L. Stern and A. Moon and C. Martinez del Rio} } @article {1163, title = {Control of male sexual behavior and sexual orientation in Drosophila by the fruitless gene.}, journal = {Cell}, volume = {87}, year = {1996}, month = {1996 Dec 13}, pages = {1079-89}, abstract = {

Sexual orientation and courtship behavior in Drosophila are regulated by fruitless (fru), the first gene in a branch of the sex-determination hierarchy functioning specifically in the central nervous system (CNS). The phenotypes of new fru mutants encompass nearly all aspects of male sexual behavior. Alternative splicing of fru transcripts produces sex-specific proteins belonging to the BTB-ZF family of transcriptional regulators. The sex-specific fru products are produced in only about 500 of the 10(5) neurons that comprise the CNS. The properties of neurons expressing these fru products suggest that fru specifies the fates or activities of neurons that carry out higher order control functions to elicit and coordinate the activities comprising male courtship behavior.

}, issn = {0092-8674}, author = {Baker, B.S. and Ryner, L.C. and Goodwin, S.F. and Castrillon, D.H. and Anand, A and Villella, A and Hall, J.C. and Taylor, B.J. and Wasserman, S.A.} } @article {46313, title = {The dosage compensation system of Drosophila is co-opted by newly evolved X chromosomes.}, journal = {Nature}, volume = {383}, year = {1996}, month = {1996 Sep 12}, pages = {160-3}, abstract = {

In species where males and females differ in number of sex chromosomes, the expression of sex-linked genes is equalized by a process known as dosage compensation. In Drosophila melanogaster, dosage compensation is mediated by the binding of the products of the male-specific lethal (msl) genes to the single male X chromosome. Here we report that the sex- and chromosome-specific binding of three of the msl proteins (MSLs) occurs in other drosophilid species, spanning four genera. Moreover, we show that MSL binding correlates with the evolution of the sex chromosomes: in species that have acquired a second X chromosome arm because of an X-autosome translocation, we observe binding of the MSLs to the {\textquoteright}new{\textquoteright} (previously autosomal) arm of the X chromosome, only when its homologue has degenerated. Moreover, in Drosophila miranda, a Y-autosome translocation has produced a new X chromosome (called neo-X), only some regions of which are dosage compensated. In this neo-X chromosome, the pattern of MSL binding correlates with the known pattern of dosage compensation.

}, keywords = {Animals, Biological Evolution, Dosage Compensation, Genetic, Drosophila, Drosophila melanogaster, Female, Genes, Insect, Male, Nuclear Proteins, Phylogeny, Protein Binding, Sex Chromosomes, Transcription Factors, X Chromosome}, issn = {0028-0836}, doi = {10.1038/383160a0}, author = {Marin, I and Franke, A and Bashaw, G J and Baker, B S} } @article {45774, title = {The evolution of soldiers in aphids.}, journal = {Biol Rev Camb Philos Soc}, volume = {71}, year = {1996}, month = {1996 Feb}, pages = {27-79}, abstract = {

1. Defensive individuals, termed soldiers, have recently been discovered in aphids, Soldiers are typically early instar larvae, and in many species the soldiers are reproductively sterile and morphologically and behaviourally specialized. 2. Since aphids reproduce parthenogenetically, we might expect soldier production to be more widespread in aphids than it is. We suggest that a more useful way to think about these problems is to attempt to understand how a clone (rather than an individual) should invest in defence and reproduction. 3. Known soldiers are currently restricted to two families of aphids, the Pemphigidae and Hormaphididae, although they are distributed widely among genera within these families. We discuss the use of a phylogenetic perspective to aid comparative studies of soldier production and we demonstrate this approach using current estimates of phylogenetic affinities among aphids. We show that the distribution of soldier production requires a minimum of six to nine evolutionary origins plus at least one loss. 4. At least four main types of soldiers exist and we present and discuss this diversity of soldiers. 5. Most soldier-producing species produce soldiers within plant galls and we discuss the importance of galls for the evolution of soldiers. 6. We summarize the evidence on the interactions between soldiers and predators and between soldier-producing aphids and ants. 7. We present an optimality model for soldier investment strategies to help guide investigations of the ecological factors selecting for soldiers. 8. The proximate mechanisms of soldier production are currently very poorly understood and we suggest several avenues for further research.

}, keywords = {Animals, Aphids, Biological Evolution, Infertility, Models, Biological, Reproduction}, issn = {1464-7931}, author = {Stern, D L and Foster, W A} } @article {1213, title = {GFP tagging of budding yeast chromosomes reveals that protein-protein interactions can mediate sister chromatid cohesion.}, journal = {Current Biology}, volume = {6}, year = {1996}, month = {1996 Dec 1}, pages = {1599-608}, abstract = {

Precise control of sister chromatid separation is essential for the accurate transmission of genetic information. Sister chromatids must remain linked to each other from the time of DNA replication until the onset of chromosome segregation, when the linkage must be promptly dissolved. Recent studies suggest that the machinery that is responsible for the destruction of mitotic cyclins also degrades proteins that play a role in maintaining sister chromatid linkage, and that this machinery is regulated by the spindle-assembly checkpoint. Studies on these problems in budding yeast are hampered by the inability to resolve its chromosomes by light or electron microscopy.

}, keywords = {Bacterial Proteins, Chromatids, Chromosomes, Escherichia coli Proteins, Fungal, Gene Expression, Green Fluorescent Proteins, Lac Repressors, Luminescent Proteins, Proteins, Recombinant Fusion Proteins, Repressor Proteins, Signal Transduction, Yeasts}, issn = {0960-9822}, author = {Straight, A F and Belmont, A S and Robinett, C C and Murray, A W} } @article {1214, title = {In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition.}, journal = {The Journal of Cell Biology}, volume = {135}, year = {1996}, month = {1996 Dec}, pages = {1685-700}, abstract = {

We report a new method for in situ localization of DNA sequences that allows excellent preservation of nuclear and chromosomal ultrastructure and direct, in vivo observations. 256 direct repeats of the lac operator were added to vector constructs used for transfection and served as a tag for labeling by lac repressor. This system was first characterized by visualization of chromosome homogeneously staining regions (HSRs) produced by gene amplification using a dihydrofolate reductase (DHFR) expression vector with methotrexate selection. Using electron microscopy, most HSRs showed approximately 100-nm fibers, as described previously for the bulk, large-scale chromatin organization in these cells, and by light microscopy, distinct, large-scale chromatin fibers could be traced in vivo up to 5 microns in length. Subsequent experiments demonstrated the potential for more general applications of this labeling technology. Single and multiple copies of the integrated vector could be detected in living CHO cells before gene amplification, and detection of a single 256 lac operator repeat and its stability during mitosis was demonstrated by its targeted insertion into budding yeast cells by homologous recombination. In both CHO cells and yeast, use of the green fluorescent protein-lac repressor protein allowed extended, in vivo observations of the operator-tagged chromosomal DNA. Future applications of this technology should facilitate structural, functional, and genetic analysis of chromatin organization, chromosome dynamics, and nuclear architecture.

}, keywords = {Anaphase, Animals, Base Sequence, CHO Cells, Chromatids, Chromatin, Chromosomes, Cricetinae, DNA, Electron, Gene Amplification, Gene Dosage, Green Fluorescent Proteins, In Situ Hybridization, Lac Operon, Luminescent Proteins, Microscopy, Mitosis, Molecular Sequence Data, Nucleic Acid, Recombinant Proteins, Repetitive Sequences, Staining and Labeling, Time Factors, Yeasts}, issn = {0021-9525}, author = {Robinett, C C and Straight, A and Li, G and Willhelm, C and Sudlow, G and Murray, A and Belmont, A S} } @article {2559, title = {Modal aproximation for the electromagnetic field of a near-field optical probe.}, journal = {Applied Optics}, volume = {35}, year = {1996}, month = {1996 Jul 1}, pages = {3488-95}, abstract = {

A formalism is given in which the optical field generated by a near-field optical aperture is described as an analytic expansion over a complete set of optical modes. This vectoral solution preserves the divergent behavior of the near field and the dipolar nature of the far field. Numerical calculation of the fields requires only evaluation of a well behaved, one-dimensional integral. The formalism is directly applicable to experiments in near-field scanning optical microscopy when relatively flat samples are evaluated.

}, issn = {0003-6935}, doi = {10.1364/AO.35.003488}, author = {Grober, R D and Rutherford, T and Harris, T D} } @article {2460, title = {Nitric oxide-sensitive guanylate cyclase activity is associated with the maturational phase of neuronal development in insects.}, journal = {Development}, volume = {122}, year = {1996}, month = {1996 Dec}, pages = {3949-58}, abstract = {

Many developing insect neurones pass through a phase when they respond to nitric oxide (NO) by producing cyclic GMP. Studies on identified grasshopper motoneurones show that this NO sensitivity appears after the growth cone has arrived at its target but before it has started to send out branches. NO sensitivity typically ends as synaptogenesis is nearing completion. Data from interneurones and sensory neurones are also consistent with the hypothesis that NO sensitivity appears as a developing neurone changes from axonal outgrowth to maturation and synaptogenesis. Cyclic GMP likely constitutes part of a retrograde signalling pathway between a neurone and its synaptic partner. NO sensitivity also appears in some mature neurones at times when they may be undergoing synaptic rearrangement. Comparative studies on other insects indicate that the association between an NO-sensitive guanylate cyclase and synaptogenesis is an ancient one, as evidenced by its presence in both ancient and more recently evolved insect groups.

}, keywords = {Afferent, Animals, Cyclic GMP, Dihydrolipoamide Dehydrogenase, Drosophila melanogaster, Grasshoppers, Guanylate Cyclase, Insects, Interneurons, Motor Neurons, Nervous System, Neurons, Nitric Oxide, Nitroprusside, Phylogeny}, issn = {0950-1991}, author = {Truman, J W and de Vente, J and Ball, E E} } @article {2374, title = {Parametric generation of second sound by first sound in superfluid helium.}, journal = {Physical Review Letters}, volume = {76}, year = {1996}, month = {1996 Mar 18}, pages = {2105-8}, abstract = {

We report the experimental studies of a parametric excitation of a second sound (SS) by a first sound (FS) in a superfluid helium in a resonance cavity. The results on several topics in this system are presented: (i) The linear properties of the instability, namely, the threshold, its temperature and geometrical dependencies, and the spectra of SS just above the onset were measured. They were found to be in a good quantitative agreement with the theory. (ii) It was shown that the mechanism of SS amplitude saturation is due to the nonlinear attenuation of SS via three wave interactions between the SS waves. Strong low frequency amplitude fluctuations of SS above the threshold were observed. The spectra of these fluctuations had a universal shape with exponentially decaying tails. Furthermore, the spectral width grew continuously with the FS amplitude. The role of three and four wave interactions are discussed with respect to the nonlinear SS behavior. The first evidence of Gaussian statistics of the wave amplitudes for the parametrically generated wave ensemble was obtained. (iii) The experiments on simultaneous pumping of the FS and independent SS waves revealed new effects. Below the instability threshold, the SS phase conjugation as a result of three-wave interactions between the FS and SS waves was observed. Above the threshold two new effects were found: a giant amplification of the SS wave intensity and strong resonance oscillations of the SS wave amplitude as a function of the FS amplitude. Qualitative explanations of these effects are suggested.

}, issn = {1079-7114}, doi = {10.1523/JNEUROSCI.3613-08.2008}, author = {Rinberg, D and Cherepanov, V and Steinberg, V} } @article {45814, title = {A phylogenetic reanalysis of allozyme variation among populations of Galapagos finches}, journal = {Zoological Journal of the Linnean Society}, volume = {118}, year = {1996}, pages = {119-134}, abstract = {

We reanalysed Yang \& Pattern{\textquoteright}s allozyme data, published in Auk in 1981, of Darwin{\textquoteright}s finches with a variety of distance and cladistic methods to estimate the phylogeny of the group. Different methods yielded different results, nevertheless there was widespread agreement among the distance methods on several groupings. First, the two species of Camarhynchus grouped near one another, but not always as a monophyletic group. Second, Cactospiza pallida and Platyspiza crassirostris formed a monophyletic group. Finally, all the methods (including parsimony) supported the monophyly of the ground finches. The three distance methods also found close relationships generally between each of two populations of Geospiza scandens, G. difficilis and G. conirostris. There is evidence for inconstancy of evolutionary rates among species. Results from distance methods allowing for rate variation among lineages suggest three conclusions which differ from Yang and Patton{\textquoteright}s findings. First, the monophyletic ground finches arose from the paraphyletic tree finches. Yang and Patton found that the ground finches and tree finches were sister monophyletic taxa. Second, Geospiza scandens appears to be a recently derived species, and not the most basal ground finch. Third, G. fuliginosa is not a recently derived species of ground finch, but was derived from an older split from the remaining ground finches. Most of these conclusions should be considered tentative both because the parsimony trees disagreed sharply with the distance trees and because no clades were strongly supported by the results of bootstrapping and statistical tests of alternative hypotheses. Absence of strong support for clades was probably due to insufficient data. Future phylogenetic studies, preferably using DNA sequence data from several unlinked loci, should sample several populations of each species, and should attempt to assess the importance of hybridization in species phylogeny.

}, doi = {10.1111/j.1096-3642.1996.tb00222.x}, author = {David L. Stern and Peter R. Grant} } @article {45913, title = {Activity-dependent action potential invasion and calcium influx into hippocampal CA1 dendrites.}, journal = {Science}, volume = {268}, year = {1995}, month = {1995 Apr 14}, pages = {297-300}, abstract = {

The temporal and spatial profile of activity-evoked changes in membrane potential and intracellular calcium concentration in the dendrites of hippocampal CA1 pyramidal neurons was examined with simultaneous somatic and dendritic patch-pipette recording and calcium imaging experiments. Action potentials are initiated close to the soma of these neurons and backpropagate into the dendrites in an activity-dependent manner; those occurring early in a train propagate actively, whereas those occurring later fail to actively invade the distal dendrites. Consistent with this finding, dendritic calcium transients evoked by single action potentials do not significantly attenuate with distance from the soma, whereas those evoked by trains attenuate substantially. Failure of action potential propagation into the distal dendrites often occurs at branch points. Consequently, neighboring regions of the dendritic tree can experience different voltage and calcium signals during repetitive action potential firing. The influence of backpropagating action potentials on synaptic integration and plasticity will therefore depend on both the extent of dendritic branching and the pattern of neuronal activity.

}, keywords = {Action Potentials, Animals, Calcium, Calcium Channels, Dendrites, Ion Channel Gating, Neuronal Plasticity, Patch-Clamp Techniques, Pyramidal Cells, Rats, Rats, Wistar, Sodium Channels, Synapses, Tetrodotoxin}, issn = {0036-8075}, author = {Spruston, N and Schiller, Y and Stuart, G and Sakmann, B} } @article {1169, title = {Addition of a 29 residue carboxyl-terminal tail converts a simple HMG box-containing protein into a transcriptional activator.}, journal = {Journal of Molecular Biology}, volume = {249}, year = {1995}, month = {1995 May 26}, pages = {11-28}, abstract = {

Human mitochondrial transcription factor A (h-mtTFA) is essential for initiation of transcription from the two promoters located in the displacement-loop region of human mitochondrial DNA. This 25 kDa protein contains two tandem, HMG box DNA-binding domains separated by a 27 amino acid residue linker region and followed by a 25 residue carboxyl-terminal tail; both the linker and tail are rich in basic amino acid residues. Mutational analysis of h-mtTFA revealed that the tail region is important for specific DNA recognition and essential for transcriptional activation. The critical role of the human tail in transcription was confirmed by constructing chimeric proteins that exchanged similar regions between h-mtTFA and its Saccharomyces cerevisiae homolog, sc-mtTFA. Wild-type sc-mtTFA is unable to activate transcription from the human mitochondrial light-strand promoter (LSP). Addition of the human tail region to sc-mtTFA conferred LSP-specific promoter activation. In all of the different h-mtTFA mutations tested, transcriptional activation was correlated with specific DNA-binding activity, suggesting that these two functions may be inseparable, a situation entirely consistent with previous mutational analyses of human mitochondrial promoters.

}, keywords = {Base Sequence, DNA, DNA-Binding Proteins, Genetic, High Mobility Group Proteins, Humans, Mitochondrial, Mitochondrial Proteins, Molecular Sequence Data, Mutagenesis, Nuclear Proteins, Promoter Regions, Saccharomyces cerevisiae, Site-Directed, Trans-Activators, Transcription Factors}, issn = {0022-2836}, doi = {10.1101/gad.1352105}, author = {Dairaghi, D J and Shadel, G S and Clayton, D A} } @article {45893, title = {Dendritic glutamate receptor channels in rat hippocampal CA3 and CA1 pyramidal neurons.}, journal = {J Physiol}, volume = {482 ( Pt 2)}, year = {1995}, month = {1995 Jan 15}, pages = {325-52}, abstract = {

1. Properties of dendritic glutamate receptor (GluR) channels were investigated using fast application of glutamate to outside-out membrane patches isolated from the apical dendrites of CA3 and CA1 pyramidal neurons in rat hippocampal slices. CA3 patches were formed (15-76 microns from the soma) in the region of mossy fibre (MF) synapses, and CA1 patches (25-174 microns from the soma) in the region of Schaffer collateral (SC) innervation. 2. Dual-component responses consisting of a rapidly rising and decaying component followed by a second, substantially slower, component were elicited by 1 ms pulses of 1 mM glutamate in the presence of 10 microM glycine and absence of external Mg2+. The fast component was selectively blocked by 2-5 microM 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX) and the slow component by 30 microM D-2-amino-5-phosphonopentanoic acid (D-AP5), suggesting that the fast and slow components were mediated by the GluR channels of the L-alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionate (AMPA) and NMDA type, respectively. The peak amplitude ratio of the NMDA to AMPA receptor-mediated components varied between 0.03 and 0.62 in patches from both CA3 and CA1 dendrites. Patches lacking either component were rarely observed. 3. The peak current-voltage (I-V) relationship of the fast component was almost linear, whereas the I-V relationship of the slow component showed a region of negative slope in the presence of 1 mM external Mg2+. The reversal potential for both components was close to 0 mV. 4. Kainate-preferring GluR channels did not contribute appreciably to the response to glutamate. The responses to 100 ms pulses of 1 mM glutamate were mimicked by application of 1 mM AMPA, whereas 1 mM kainate produced much smaller, weakly desensitizing currents. This suggests that the fast component is primarily mediated by the action of glutamate on AMPA-preferring receptors. 5. The mean elementary conductance of AMPA receptor channels was about 10 pS, as estimated by non-stationary fluctuation analysis. The permeability of these channels to Ca2+ was low (approximately 5\% of the permeability to Cs+). 6. The elementary conductance of NMDA receptor channels was larger, with a main conductance state of about 45 pS. These channels were 3.6 times more permeable to Ca2+ than to Cs+.(ABSTRACT TRUNCATED AT 400 WORDS)

}, keywords = {2-Amino-5-phosphonovalerate, 6-Cyano-7-nitroquinoxaline-2,3-dione, alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid, Animals, Calcium, Cell Membrane Permeability, Dendrites, Electric Conductivity, Hippocampus, Kainic Acid, Magnesium, Patch-Clamp Techniques, Pyramidal Cells, Rats, Rats, Wistar, Receptors, AMPA, Receptors, N-Methyl-D-Aspartate, Time Factors, Zinc}, issn = {0022-3751}, author = {Spruston, N and Jonas, P and Sakmann, B} } @article {961, title = {Drosophila homologs of baculovirus inhibitor of apoptosis proteins function to block cell death.}, journal = {Cell}, volume = {83}, year = {1995}, month = {1995 Dec 29}, pages = {1253-62}, abstract = {

Apoptotic cell death is a mechanism by which organisms eliminate superfluous or harmful cells. Expression of the cell death regulatory protein REAPER (RPR) in the developing Drosophila eye results in a small eye owing to excess cell death. We show that mutations in thread (th) are dominant enhancers of RPR-induced cell death and that th encodes a protein homologous to baculovirus inhibitors of apoptosis (IAPs), which we call Drosophila IAP1 (DIAP1). Overexpression of DIAP1 or a related protein, DIAP2, in the eye suppresses normally occurring cell death as well as death due to overexpression of rpr or head involution defective. IAP death-preventing activity localizes to the N-terminal baculovirus IAP repeats, a motif found in both viral and cellular proteins associated with death prevention.

}, keywords = {Amino Acid, Amino Acid Sequence, Animals, Apoptosis, Biological Evolution, Chromosome Deletion, Drosophila, Drosophila Proteins, Electron, Enhancer Elements, Eye, Genes, Genetic, Genetic Testing, Humans, Inhibitor of Apoptosis Proteins, Insect, Insect Proteins, Mammals, Microscopy, Molecular Sequence Data, Mutation, Neurons, Nucleic Acid, Peptides, Repetitive Sequences, Scanning, Sequence Homology, Viral Proteins}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Hay, B A and Wassarman, D A and Rubin, G M} } @article {46654, title = {Growth and differentiation in the Drosophila eye coordinated by hedgehog.}, journal = {Nature}, volume = {373}, year = {1995}, month = {1995 Feb 23}, pages = {709-11}, abstract = {

Differentiation of the Drosophila retina is asynchronous: it starts at the posterior margin of the eye imaginal disc and progresses anteriorly over two days. During this time the disc continues to grow, increasing in size by approximately eightfold. An indentation in the epithelium, the morphogenetic furrow, marks the front edge of the differentiation wave. Anterior progression of the furrow is thought to be driven by signals emanating from differentiating photoreceptor cells in the posterior eye disc. A good candidate for such a signal is the product of the hedgehog (hh) gene; it is expressed, and presumably secreted, by differentiating photoreceptors and its function is required for continued furrow movement. Here we show that ectopic expression of hedgehog sets in motion ectopic furrows in the anterior eye disc. In addition to changes in cell shape, these ectopic furrows are associated with a tightly orchestrated series of events, including proliferation, cell cycle synchronization and pattern formation, that parallel normal furrow progression. We propose that the morphogenetic furrow coincides with a transient boundary that coordinates growth and differentiation of the eye disc, and that hedgehog is necessary and sufficient to propagate this boundary across the epithelium.

}, keywords = {Animals, Basic Helix-Loop-Helix Transcription Factors, Cell Cycle, Cell Cycle Proteins, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Embryonic Induction, Eye, Hedgehog Proteins, Helix-Loop-Helix Motifs, Insect Hormones, Insect Proteins, Nerve Tissue Proteins, Phosphoprotein Phosphatases, Protein Tyrosine Phosphatases, Proteins, Repressor Proteins, Signal Transduction, Transcription Factors}, issn = {0028-0836}, doi = {10.1038/373709a0}, author = {Heberlein, U and Singh, C M and Luk, A Y and Donohoe, T J} } @article {45817, title = {The life cycle and natural history of the tropical aphid Cerataphis fransseni (Homoptera: Aphididae: Hormaphidinae), with reference to the evolution of host alternation in aphids}, journal = {Journal of natural history}, volume = {29}, year = {1995}, pages = {231-242}, abstract = {

We describe the life cycle and general biology of the tropical cerataphidine aphid Cerataphis fransseni. We demonstrate that this aphid migrates between trees of Styrax benzoin and various species of palms; palm-feeding populations have previously been known as C. variabilis and C. palmae, which now become synonyms of C. fransseni. On S. benzoin the fundatrix induces a relatively simple gall which can contain \>6000 aphids at maturity with a large number of reproductively sterile soldiers that protect the gall from predators. These galls are apparently produced throughout the year. Colonies on the secondary host plants, palms, are apparently obligately tended by ants whereas colonies within galls on Styrax are never tended by ants. We discuss the life cycle of this tropical aphid with respect to hypotheses for the evolution and maintenance of host alternation.

}, doi = {10.1080/00222939500770101}, url = {http://www.tandfonline.com/doi/abs/10.1080/00222939500770101$\#$.VKrUcHt79iZ}, author = {DL Stern and S Aoki and D U Kurosu} } @article {46653, title = {Mechanisms of Drosophila retinal morphogenesis: the virtues of being progressive.}, journal = {Cell}, volume = {81}, year = {1995}, month = {1995 Jun 30}, pages = {987-90}, keywords = {Animals, Cell Differentiation, Drosophila, Morphogenesis, Retina, Signal Transduction}, issn = {0092-8674}, author = {Heberlein, U and Moses, K} } @article {1159, title = {The msl-2 dosage compensation gene of Drosophila encodes a putative DNA-binding protein whose expression is sex-specifically regulated by Sex-lethal.}, journal = {Development}, volume = {121}, year = {1995}, month = {1995 Oct}, pages = {3245-58}, abstract = {

In Drosophila dosage compensation increases the rate of transcription of the male{\textquoteright}s X chromosome and depends on four autosomal male-specific lethal genes. We have cloned the msl-2 gene and shown that MSL-2 protein is co-localized with the other three MSL proteins at hundreds of sites along the male polytene X chromosome and that this binding requires the other three MSL proteins. msl-2 encodes a protein with a putative DNA-binding domain: the RING finger. MSL-2 protein is not produced in females and sequences in both the 5{\textquoteright} and 3{\textquoteright} UTRs are important for this sex-specific regulation. Furthermore, msl-2 pre-mRNA is alternatively spliced in a Sex-lethal-dependent fashion in its 5{\textquoteright} UTR.

}, issn = {0950-1991}, author = {Baker, B.S. and Bashaw, G.J.} } @article {1170, title = {A persistent RNA-DNA hybrid is formed during transcription at a phylogenetically conserved mitochondrial DNA sequence.}, journal = {Molecular and Cellular Biology}, volume = {15}, year = {1995}, month = {1995 Jan}, pages = {580-9}, abstract = {

Critical features of the mitochondrial leading-strand DNA replication origin are conserved from Saccharomyces cerevisiae to humans. These include a promoter and a downstream GC-rich sequence block (CSBII) that encodes rGs within the primer RNA. During in vitro transcription at yeast mitochondrial replication origins, there is stable and persistent RNA-DNA hybrid formation that begins at the 5{\textquoteright} end of the rG region. The short rG-dC sequence is the necessary and sufficient nucleic acid element for establishing stable hybrids, and the presence of rGs within the RNA strand of the RNA-DNA hybrid is required. The efficiency of hybrid formation depends on the length of RNA synthesized 5{\textquoteright} to CSBII and the type of RNA polymerase employed. Once made, the RNA strand of an RNA-DNA hybrid can serve as an effective primer for mitochondrial DNA polymerase. These results reveal a new mechanism for persistent RNA-DNA hybrid formation and suggest a step in priming mitochondrial DNA replication that requires both mitochondrial RNA polymerase and an rG-dC sequence-specific event to form an extensive RNA-DNA hybrid.

}, keywords = {Base Sequence, DNA, DNA Primers, DNA Replication, DNA-Directed DNA Polymerase, DNA-Directed RNA Polymerases, Genetic, Mitochondrial, Molecular Sequence Data, Nucleic Acid, Nucleic Acid Hybridization, Phylogeny, Regulatory Sequences, Ribonuclease H, RNA, Saccharomyces cerevisiae, Transcription}, issn = {0270-7306}, doi = {10.1101/gad.1352105}, author = {Xu, B and Clayton, D A} } @article {45816, title = {Phylogenetic evidence that aphids, rather than plants, determine gall morphology}, journal = {Proceedings of the Royal Society of London. Series B: Biological Sciences}, volume = {260}, year = {1995}, pages = {85-89}, abstract = {

Many diverse taxa have evolved independently the habit of living in plant galls. For all but some viral galls, it is unknown whether plants produce galls as a specialized plant reaction to certain types of herbivory, or whether herbivores direct gall development. Here I present a phylogenetic analysis of gallforming cerataphidine aphids which demonstrates that gall morphology is extremely conservative with respect to aphid phylogeny, but variable with respect to plant taxonomy. In addition, the phylogeny reveals at least three host plant switches where the aphids produce galls most similar to the galls of their closest relatives, rather than galls similar to the galls of aphids already present on the host plant. These results suggest that aphids determine the details of gall morphology essentially extending their phenotype to include plant material. Based on this and other evidence, I suggest that the aphids and other galling insects manipulate latent plant developmental programmes to produce modified atavistic plant morphologies rather than create new forms de novo.

}, doi = {10.1098/rspb.1995.0063}, url = {http://rspb.royalsocietypublishing.org/content/260/1357/85.short}, author = {David L Stern} } @article {45892, title = {Probing dendritic function with patch pipettes.}, journal = {Curr Opin Neurobiol}, volume = {5}, year = {1995}, month = {1995 Jun}, pages = {389-94}, abstract = {

Most neurons in the CNS have complex, branching dendritic trees, which receive the majority of all synaptic input. As it is difficult to make electrical recordings from dendrites because of their small size, most of what is known about their electrical properties has been inferred from recordings made at the soma. By taking advantage of the higher resolution offered by improved optics, it is now possible to make patch-pipette recordings from the dendrites of neurons in brain slices under visual control. This new technique promises to provide valuable new information concerning dendritic function.

}, keywords = {Animals, Dendritic Cells, Electrophysiology, Hippocampus, Patch-Clamp Techniques}, issn = {0959-4388}, author = {Stuart, G and Spruston, N} } @article {2092, title = {Proposed method for molecular optical imaging. (With commentary)}, journal = {Optics Letters}, volume = {20}, year = {1995}, month = {1995 Feb 1}, pages = {237-9}, abstract = {

We can resolve multiple discrete features within a focal region of m spatial dimensions by first isolating each on the basis of n \>/= 1 unique optical characteristics and then measuring their relative spatial coordinates. The minimum acceptable separation between features depends on the point-spread function in the (m + n)d-dimensional space formed by the spatial coordinates and the optical parameters, whereas the absolute spatial resolution is determined by the accuracy to which the coordinates can be measured. Estimates of each suggest that near-field fluorescence excitation microscopy/spectroscopy with molecular sensitivity and spatial resolution is possible.

Commentary: Inspired by my earlier work (see below) in single molecule imaging and the isolation of multiple exciton recombination sites within a single probe volume, here I proposed the principle which would eventually lead to PALM. Indeed, all methods of localization microscopy, including PALM, fPALM, PALMIRA, STORM, dSTORM, PAINT, GSDIM, etc. are specific embodiments of the general principle of single molecule isolation and localization I introduced here.

}, issn = {0146-9592}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19859146}, author = {Betzig, E} } @article {1192, title = {Regulation of nuclear genes encoding mitochondrial proteins in Saccharomyces cerevisiae.}, journal = {Journal of Bacteriology}, volume = {177}, year = {1995}, month = {1995 Dec}, pages = {6836-43}, abstract = {

Selection for mutants which release glucose repression of the CYB2 gene was used to identify genes which regulate repression of mitochondrial biogenesis. We have identified two of these as the previously described GRR1/CAT80 and ROX3 genes. Mutations in these genes not only release glucose repression of CYB2 but also generally release respiration of the mutants from glucose repression. In addition, both mutants are partially defective in CYB2 expression when grown on nonfermentable carbon sources, indicating a positive regulatory role as well. ROX3 was cloned by complementation of a glucose-inducible flocculating phenotype of an amber mutant and has been mapped as a new leftmost marker on chromosome 2. The ROX3 mutant has only a modest defect in glucose repression of GAL1 but is substantially compromised in galactose induction of GAL1 expression. This mutant also has increased SUC2 expression on nonrepressing carbon sources. We have also characterized the regulation of CYB2 in strains carrying null mutation in two other glucose repression genes, HXK2 and SSN6, and show that HXK2 is a negative regulator of CYB2, whereas SSN6 appears to be a positive effector of CYB2 expression.

}, keywords = {Base Sequence, Cell Compartmentation, Cell Nucleus, Chromosome Mapping, Chromosomes, Fermentation, Fungal, Fungal Proteins, Gene Expression Regulation, Genes, Genetic, Glucose, Mitochondria, Molecular Sequence Data, Mutagenesis, Oxygen Consumption, Saccharomyces cerevisiae, Selection, Telomere}, issn = {0021-9193}, author = {Brown, T A and Evangelista, C and Trumpower, B L} } @article {46652, title = {Role of the morphogenetic furrow in establishing polarity in the Drosophila eye.}, journal = {Development}, volume = {121}, year = {1995}, month = {1995 Dec}, pages = {4085-94}, abstract = {

The Drosophila retina is a crystalline array of 800 ommatidia whose organization and assembly suggest polarization of the retinal epithelium along anteroposterior and dorsoventral axes. The retina develops by a stepwise process following the posterior-to-anterior progression of the morphogenetic furrow across the eye disc. Ectopic expression of hedgehog or local removal of patched function generates ectopic furrows that can progress in any direction across the disc leaving in their wake differentiating fields of ectopic ommatidia. We have studied the effect of these ectopic furrows on the polarity of ommatidial assembly and rotation. We find that the anteroposterior asymmetry of ommatidial assembly parallels the progression of ectopic furrows, regardless of their direction. In addition, ommatidia developing behind ectopic furrows rotate coordinately, forming equators in various regions of the disc. Interestingly, the expression of a marker normally restricted to the equator is induced in ectopic ommatidial fields. Ectopic equators are stable as they persist to adulthood, where they can coexist with the normal equator. Our results suggest that ectopic furrows can impart polarity to the disc epithelium, regarding the direction of both assembly and rotation of ommatidia. We propose that these processes are polarized as a consequence of furrow propagation, while more global determinants of dorsoventral and anteroposterior polarity may act less directly by determining the site of furrow initiation.

}, keywords = {Animals, Drosophila, Drosophila Proteins, Eye, Gene Expression, Genes, Insect, Hedgehog Proteins, Immunohistochemistry, Insect Hormones, Membrane Proteins, Models, Biological, Morphogenesis, Proteins, Receptors, Cell Surface, Retina}, issn = {0950-1991}, author = {Chanut, F and Heberlein, U} } @article {1193, title = {Strain-dependent variation in carbon source regulation of nucleus-encoded mitochondrial proteins of Saccharomyces cerevisiae.}, journal = {Journal of Bacteriology}, volume = {177}, year = {1995}, month = {1995 Mar}, pages = {1380-2}, abstract = {

Nuclear genes encoding mitochondrial proteins are regulated by carbon source with significant heterogeneity among four Saccharomyces cerevisiae strains. This strain-dependent variation is seen both in respiratory capacity of the cells and in the expression of beta-galactosidase reporter fusions to the promoters of CYB2, CYC1, CYC3, MnSOD, and RPO41.

}, keywords = {Bacterial Proteins, Base Sequence, beta-Galactosidase, Carbon, Cell Nucleus, Cytochrome b Group, Cytochrome c Group, Ferritins, Fungal, Fungal Proteins, Gene Expression Regulation, Genes, Genetic, Genetic Variation, L-Lactate Dehydrogenase, L-Lactate Dehydrogenase (Cytochrome), Mitochondria, Molecular Sequence Data, Oxygen Consumption, Promoter Regions, Recombinant Fusion Proteins, Reporter, Saccharomyces cerevisiae, Species Specificity, Superoxide Dismutase}, issn = {0021-9193}, author = {Brown, T A and Trumpower, B L} } @article {2703, title = {Toward simplifying and accurately formulating fragment assembly.}, journal = {Journal of Computational Biology: A Journal of Computational Molecular Cell Biology}, volume = {2}, year = {1995}, month = {1995 Summer}, pages = {275-90}, abstract = {

The fragment assembly problem is that of reconstructing a DNA sequence from a collection of randomly sampled fragments. Traditionally, the objective of this problem has been to produce the shortest string that contains all the fragments as substrings, but in the case of repetitive target sequences this objective produces answers that are overcompressed. In this paper, the problem is reformulated as one of finding a maximum-likelihood reconstruction with respect to the two-sided Kolmogorov-Smirnov statistic, and it is argued that this is a better formulation of the problem. Next the fragment assembly problem is recast in graph-theoretic terms as one of finding a noncyclic subgraph with certain properties and the objectives of being shortest or maximally likely are also recast in this framework. Finally, a series of graph reduction transformations are given that dramatically reduce the size of the graph to be explored in practical instances of the problem. This reduction is very important as the underlying problems are NP-hard. In practice, the transformed problems are so small that simple branch-and-bound algorithms successfully solve them, thus permitting auxiliary experimental information to be taken into account in the form of overlap, orientation, and distance constraints.

}, keywords = {Base Sequence, DNA, Mathematics, Models, Oligodeoxyribonucleotides, Probability, Reproducibility of Results, Statistical}, issn = {1066-5277}, author = {Myers, E W} } @article {4010, title = {The uncertain response in the bottlenosed dolphin (Tursiops truncatus).}, journal = {Journal of Experimental Psychology}, volume = {124}, year = {1995}, month = {1995 Dec}, pages = {391-408}, abstract = {

Humans respond adaptively to uncertainty by escaping or seeking additional information. To foster a comparative study of uncertainty processes, we asked whether humans and a bottlenosed dolphin (Tursiops truncatus) would use similarly a psychophysical uncertain response. Human observers and the dolphin were given 2 primary discrimination responses and a way to escape chosen trials into easier ones. Humans escaped sparingly from the most difficult trials near threshold that left them demonstrably uncertain of the stimulus. The dolphin performed nearly identically. The behavior of both species is considered from the perspectives of signal detection theory and optimality theory, and its appropriate interpretation is discussed. Human and dolphin uncertain responses seem to be interesting cognitive analogs and may depend on cognitive or controlled decisional mechanisms. The capacity to monitor ongoing cognition, and use uncertainty appropriately, would be a valuable adaptation for animal minds. This recommends uncertainty processes as an important but neglected area for future comparative research.

}, keywords = {Animal, Animals, Auditory Threshold, Behavior, Biological, Cognition, Discrimination (Psychology), Humans, Kinetics, Models, Probability, Psychiatric Status Rating Scales, Reinforcement (Psychology), Task Performance and Analysis}, issn = {0096-3445}, author = {Smith, J D and Schull, J and Strote, J and McGee, K and Egnor, R and Erb, L} } @article {960, title = {Yan functions as a general inhibitor of differentiation and is negatively regulated by activation of the Ras1/MAPK pathway.}, journal = {Cell}, volume = {81}, year = {1995}, month = {1995 Jun 16}, pages = {857-66}, abstract = {

Drosophila yan has been postulated to act as an antagonist of the proneural signal mediated by the sevenless/Ras1/MAPK pathway. We have mutagenized the eight MAPK phosphorylation consensus sites of yan and examined the effects of overexpressing the mutant protein in transgenic flies and transfected S2 cultured cells. Our results suggest that phosphorylation by MAPK affects the stability and subcellular localization of yan, resulting in rapid down-regulation of yan activity. Furthermore, MAPK-mediated down-regulation of yan function appears to be critical for the proper differentiation of both neuronal and nonneuronal tissues throughout development, suggesting that yan is an essential component of a general timing mechanism controlling the competence of a cell to respond to inductive signals.

}, keywords = {Alleles, Animals, Binding Sites, Calcium-Calmodulin-Dependent Protein Kinases, Developmental, DNA-Binding Proteins, Down-Regulation, Drosophila, Drosophila Proteins, Eye, Eye Proteins, Gene Expression Regulation, GTP-Binding Proteins, Membrane Glycoproteins, Mutagenesis, Neurons, Phosphorylation, Receptor Protein-Tyrosine Kinases, Repressor Proteins, Signal Transduction, Site-Directed}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Rebay, I and Rubin, G M} } @article {963, title = {The activities of two Ets-related transcription factors required for Drosophila eye development are modulated by the Ras/MAPK pathway.}, journal = {Cell}, volume = {78}, year = {1994}, month = {1994 Jul 15}, pages = {137-47}, abstract = {

We show that the activities of two Ets-related transcription factors required for normal eye development in Drosophila, pointed and yan, are regulated by the Ras1/MAPK pathway. The pointed gene codes for two related proteins, and we show that one form is a constitutive activator of transcription, while the activity of the other form is stimulated by the Ras1/MAPK pathway. Mutation of the single consensus MAPK phosphorylation site in the second form abrogates this responsiveness. yan is a negative regulator of photoreceptor determination, and genetic data suggest that it acts as an antagonist of Ras1. We demonstrate that yan can repress transcription and that this repression activity is negatively regulated by the Ras1/MAPK signal, most likely through direct phosphorylation of yan by MAPK.

}, keywords = {Animals, Biological, Calcium-Calmodulin-Dependent Protein Kinases, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Extracellular Signal-Regulated MAP Kinases, Eye, Eye Proteins, Gene Expression Regulation, Genes, Genetic, Insect, Invertebrate, Models, Morphogenesis, Nerve Tissue Proteins, Phenotype, Photoreceptor Cells, Proto-Oncogene Proteins, Proto-Oncogene Proteins p21(ras), ras, Repressor Proteins, Signal Transduction, Transcription, Transcription Factors}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {O{\textquoteright}Neill, E M and Rebay, I and Tjian, R and Rubin, G M} } @article {1158, title = {Behavioral and neurobiological implications of sex-determining factors in Drosophila.}, journal = {Developmental. Genetics}, volume = {15}, year = {1994}, month = {1994}, pages = {275-96}, abstract = {

The function of the central nervous system as it controls sex-specific behaviors in Drosophila has been studied with renewed intensity, in the context of genetic factors that influence the development of sexually differentiated aspects of this insect. Three categories of genetic variations that cause anomalies in courtship and mating behaviors are discussed: (1) mutants isolated with regard to courtship defects, of which putatively courtship-specific variants such as the fruitless mutant are a subset; (2) general behavioral and neurological variants (including sensory and learning mutants), whose defects include subnormal reproductive performance; and (3) mutations of genes within the sex-determination regulatory hierarchy of Drosophila, the analysis of which has included studies of reproductive behavior. Recent studies of mutations in two of these categories have provided new insights into the control of neuronally based aspects of sex-specific behavior. The doublesex gene, the final factor acting in the sex-determination hierarchy, had been previously thought to regulate all aspects of sexual differentiation. Yet, it has been recently shown that doublesex does not control at least one neuronally-determined feature of sex-specific anatomy--a muscle in the male{\textquoteright}s abdomen, whose normal development is, however, dependent on the action of fruitless. These considerations prompted us to examine further (and in some cases re-examine) the influences exerted by sex-determination hierarchy genes on behavior. Our results--notably those obtained from assessments of doublesex mutations{\textquoteright} effects on general reproductive actions and on a particular component of the courtship sequence (male "singing" behavior)--lead to the suggestion that there is a previously unrecognized branch within the sex-determination hierarchy, which controls the differentiation of the male- and female- specific phenotypes of Drosophila. This new branch separates from the doublesex-related one immediately before the action of that gene (just after transformer and transformer-2) and appears to control as least some aspects of neuronally determined sexual differentiation of males.

}, issn = {0192-253X}, author = {Baker, B.S. and Taylor, B.J. and Villella. A. and Ryner, L.C. and Hall, J.C.} } @article {45897, title = {Dendritic attenuation of synaptic potentials and currents: the role of passive membrane properties.}, journal = {Trends Neurosci}, volume = {17}, year = {1994}, month = {1994 Apr}, pages = {161-6}, abstract = {

The dendritic trees of neurons are structurally and functionally complex integrative units receiving thousands of synaptic inputs that have excitatory and inhibitory, fast and slow, and electrical and biochemical effects. The pattern of activation of these synaptic inputs determines if the neuron will fire an action potential at any given point in time and how it will respond to similar inputs in the future. Two critical factors affect the integrative function of dendrites: the distribution of voltage-gated ion channels in the dendritic tree and the passive electrical properties, or {\textquoteright}electrotonic structure{\textquoteright}, upon which these active channels are superimposed. The authors review recent data from patch-clamp recordings that provide new estimates of the passive membrane properties of hippocampal neurons, and show, with examples, how these properties affect the shaping and attenuation of synaptic potentials as they propagate in the dendrites, as well as how they affect the measurement of current from synapses located in the dendrites. Voltage-gated channels might influence the measurement of {\textquoteright}passive{\textquoteright} membrane properties and, reciprocally, passive membrane properties might affect the activation of voltage-gated channels in dendrites.

}, keywords = {Animals, Cell Membrane, Dendrites, Hippocampus, Ion Channel Gating, Neurons, Rats, Synaptic Transmission}, issn = {0166-2236}, author = {Spruston, N and Jaffe, D B and Johnston, D} } @article {2561, title = {Dimensions of luminescent oxidized and porous silicon structures.}, journal = {Physical Review Letters}, volume = {72}, year = {1994}, month = {1994 Apr 18}, pages = {2648-51}, abstract = {

X-ray absorption measurements from H-passivated porous Si and from oxidized Si nanocrystals, combined with electron microscopy, ir absorption, α recoil, and luminescence emission data, provide a consistent structural picture of the species responsible for the visible luminescence observed in these samples. The mass-weighted average structures in por-Si are particles, not wires, with dimensions significantly smaller than previously reported or proposed.

}, issn = {1079-7114}, author = {Schuppler, S and Friedman, SL and Marcus, MA and Adler, DL and Xie, Y and Ross, FM and Harris, T D and Brown, WL and Chabal, YJ and Brus, LE and Citrin, PH} } @article {962, title = {The Drosophila peanut gene is required for cytokinesis and encodes a protein similar to yeast putative bud neck filament proteins.}, journal = {Cell}, volume = {77}, year = {1994}, month = {1994 May 6}, pages = {371-9}, abstract = {

We have identified a Drosophila gene, peanut (pnut), that is related in sequence to the CDC3, CDC10, CDC11, and CDC12 genes of S. cerevisiae. These genes are required for cytokinesis, and their products are present at the bud neck during cell division. We find that pnut is also required for cytokinesis: in pnut mutants, imaginal tissues fail to proliferate and instead develop clusters of large, multinucleate cells. Pnut protein is localized to the cleavage furrow of dividing cells during cytokinesis and to the intercellular bridge connecting postmitotic daughter cells. In addition to its role in cytokinesis, pnut displays genetic interactions with seven in absentia, a gene required for neuronal fate determination in the compound eye, suggesting that pnut may have pleiotropic functions. Our results suggest that this class of proteins is involved in aspects of cytokinesis that have been conserved between flies and yeast.

}, keywords = {Amino Acid, Amino Acid Sequence, Animals, Base Sequence, Cell Division, Cell Line, Cloning, Complementary, DNA, Drosophila, Drosophila Proteins, Enhancer Elements, Female, Fungal, Fungal Proteins, Gene Library, Genes, Genetic, Insect, Larva, Male, Mice, Microfilament Proteins, Molecular, Molecular Sequence Data, Proteins, Saccharomyces cerevisiae, Sequence Analysis, Sequence Homology}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Neufeld, T P and Rubin, G M} } @article {45929, title = {Mechanisms shaping glutamate-mediated excitatory postsynaptic currents in the CNS.}, journal = {Curr Opin Neurobiol}, volume = {4}, year = {1994}, month = {1994 Jun}, pages = {366-72}, abstract = {

Excitatory postsynaptic currents in neurones of the central nervous system have a dual-component time course that results from the co-activation of AMPA/kainate-type and NMDA-type glutamate receptors. New approaches in electrophysiology and molecular biology have provided a better understanding of the factors that determine the kinetics of excitatory postsynaptic currents. Recent studies suggest that the time course of neurotransmitter concentration in the synaptic cleft, the gating properties of the native channels, and the glutamate receptor subunit composition all appear to be important factors.

}, keywords = {Animals, Central Nervous System, Electrophysiology, Glutamic Acid, Humans, Ion Channels, Kinetics, Receptors, AMPA, Receptors, Glutamate, Receptors, Kainic Acid, Synapses}, issn = {0959-4388}, author = {Jonas, P and Spruston, N} } @article {2084, title = {Near-field spectroscopy of the quantum constituents of a luminescent system. (With commentary)}, journal = {Science}, volume = {264}, year = {1994}, month = {1994 Jun 17}, pages = {1740-5}, abstract = {

Luminescent centers with sharp (\<0.07 millielectron volt), spectrally distinct emission lines were imaged in a GaAs/AIGaAs quantum well by means of low-temperature near-field scanning optical microscopy. Temperature, magnetic field, and linewidth measurements establish that these centers arise from excitons laterally localized at interface fluctuations. For sufficiently narrow wells, virtually all emission originates from such centers. Near-field microscopy/spectroscopy provides a means to access energies and homogeneous line widths for the individual eigenstates of these centers, and thus opens a rich area of physics involving quantum resolved systems.

Commentary: Harald Hess and I joined forces, combining my near-field optical technology with his cryogenic scanned probe microscope to produce the first paper on high resolution spectroscopy beyond the diffraction limit. We discovered that the broad luminescence spectrum traditionally observed from quantum well heterostructures reflects a resolution-limited ensemble average of emission from numerous discrete sites of exciton recombination occurring at atomic-scale corrugations in the confining interfaces. With the combination of high spatial resolution from near-field excitation and high spectral resolution from cryogenic operation, we were able to isolate these emission sites in a multidimensional space of xy position and wavelength, even though their density was too great to isolate them on the basis of spatial resolution alone. This insight was very influential in the genesis of the concept (see above) that would eventually lead to far-field superresolution by PALM.

}, issn = {0036-8075}, doi = {10.1126/science.264.5166.1740}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17839907}, author = {Hess, H F and Betzig, E and Harris, T D and Pfeiffer, L N and West, K W} } @article {922, title = {Near-field spectroscopy of the quantum constituents of a luminescent system.}, journal = {Science}, volume = {264}, year = {1994}, month = {1994 Jun 17}, pages = {1740-5}, abstract = {

Luminescent centers with sharp (\<0.07 millielectron volt), spectrally distinct emission lines were imaged in a GaAs/AIGaAs quantum well by means of low-temperature near-field scanning optical microscopy. Temperature, magnetic field, and linewidth measurements establish that these centers arise from excitons laterally localized at interface fluctuations. For sufficiently narrow wells, virtually all emission originates from such centers. Near-field microscopy/spectroscopy provides a means to access energies and homogeneous line widths for the individual eigenstates of these centers, and thus opens a rich area of physics involving quantum resolved systems.

}, issn = {0036-8075}, doi = {10.1126/science.264.5166.1740}, author = {Hess, H F and Betzig, E and Harris, T D and Pfeiffer, L N and West, K W} } @article {2461, title = {Neuropeptide induction of cyclic GMP increases in the insect CNS: resolution at the level of single identifiable neurons.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {14}, year = {1994}, month = {1994 Dec}, pages = {7704-12}, abstract = {

In insects, the neuropeptide eclosion hormone (EH) acts on the CNS to evoke the stereotyped behaviors that cause ecdysis, the shedding of the cuticle at the end of each molt. Concomitantly, EH induces an increase in cyclic GMP (cGMP). Using antibodies against this second messenger, we show that this increase is confined to a network of 50 peptidergic neurons distributed throughout the CNS. Increases appeared 30 min after EH treatment, spread rapidly throughout these neurons, and were extremely long lived. We show that this response is synaptically driven, and does not involve the soluble, nitric oxide (NO)-activated, guanylate cyclase. Stereotyped variations in the duration of the cGMP response among neurons suggest a role in coordinating responses having different latencies and durations.

}, keywords = {Animals, Central Nervous System, Cyclic GMP, Enzyme Activation, Guanylate Cyclase, Immunohistochemistry, Insect Hormones, Manduca, Neurons, Synapses, Time Factors}, issn = {0270-6474}, author = {Ewer, J and de Vente, J and Truman, J W} } @article {45775, title = {A phylogenetic analysis of soldier evolution in the aphid family Hormaphididae.}, journal = {Proc Biol Sci}, volume = {256}, year = {1994}, month = {1994 May 23}, pages = {203-9}, abstract = {

Aphid soldiers, altruistic larvae that protect the colony from predators, are an example of highly social behaviour in an insect group with a natural history different from the eusocial Hymenoptera and Isoptera. Aphids therefore allow independent tests of theory developed to explain the evolution of eusociality. Although soldiers have been discovered in five tribes from two families, the number and pattern of origins and losses of soldiers is unknown due to a lack of phylogenetic data. Here I present a mtDNA based phylogeny for the Hormaphididae, and test the hypothesis that soldiers in the tribe Cerataphidini produced during two points in the life cycle represent independent origins. The results support this hypothesis. In addition, a minimum of five evolutionary events, either four origins and one loss or five origins, are required to explain the distribution of soldiers in the family. The positions of the origins and losses are well resolved, and this phylogeny provides an historical framework for studies on the causes of soldier aphid evolution.

}, keywords = {Animals, Aphids, Base Sequence, DNA Primers, DNA, Mitochondrial, Electron Transport Complex IV, Genes, Insect, Molecular Sequence Data, Phylogeny, Sequence Homology, Nucleic Acid}, issn = {0962-8452}, doi = {10.1098/rspb.1994.0071}, author = {Stern, D L} } @article {2725, title = {A sublinear algorithm for approximate keyword matching.}, journal = {Algorithmica}, volume = {12}, year = {1994}, month = {1994 Nov}, pages = {345-74}, abstract = {

Given a relatively short query stringW of lengthP, a long subject stringA of lengthN, and a thresholdD, theapproximate keyword search problem is to find all substrings ofA that align withW with not more than D insertions, deletions, and mismatches. In typical applications, such as searching a DNA sequence database, the size of the {\textquotedblleft}database{\textquotedblright}A is much larger than that of the queryW, e.g.,N is on the order of millions or billions andP is a hundred to a thousand. In this paper we present an algorithm that given a precomputedindex of the databaseA, finds rare matches in time that issublinear inN, i.e.,N c for somec\<1. The sequenceA must be overa. finite alphabet σ. More precisely, our algorithm requires 0(DN pow(ɛ)\  logN) expected-time where ɛ=D/P is the maximum number of differences as a percentage of query length, and pow(ɛ) is an increasing and concave function that is 0 when ɛ=0. Thus the algorithm is superior to current O(DN) algorithms when ɛ is small enough to guarantee that pow(ɛ) \< 1. As seen in the paper, this is true for a wide range of ɛ, e.g., ɛ. up to 33\% for DNA sequences ({\textbrokenbar}⌆{\textbrokenbar}=4) and 56\% for proteins sequences ({\textbrokenbar}⌆{\textbrokenbar}=20). In preliminary practical experiments, the approach gives a 50-to 500-fold improvement over previous algorithms for prolems of interest in molecular biology.

}, author = {Myers, Eugene} } @article {45818, title = {A test of geometric hypotheses for soldier investment patterns in the gall producing tropical aphidCerataphis fransseni (Homoptera, Hormaphididae)}, journal = {Insectes sociaux}, volume = {41}, year = {1994}, pages = {457-460}, abstract = {

The gall-forming aphidCerataphis fransseni produces soldiers that defend against predators. Soldiers are produced soon after colony foundation and the number of soldiers increases nonlinearly during colony growth. The number of soldiers scales to the square-root of the number of non-soldiers and linearly to the surface area of the gall. This suggests that soldiers are produced to defend an area, for example the perimeter of the colony or the surface of the gall, rather than individual aphids.

}, issn = {0020-1812}, doi = {10.1007/BF01240648}, url = {http://link.springer.com/article/10.1007/BF01240648}, author = {D. L. Stern and S. Aoki and U. Kurosu} } @article {965, title = {Analysis of genetic mosaics in developing and adult Drosophila tissues.}, journal = {Development}, volume = {117}, year = {1993}, month = {1993 Apr}, pages = {1223-37}, abstract = {

We have constructed a series of strains to facilitate the generation and analysis of clones of genetically distinct cells in developing and adult tissues of Drosophila. Each of these strains carries an FRT element, the target for the yeast FLP recombinase, near the base of a major chromosome arm, as well as a gratuitous cell-autonomous marker. Novel markers that carry epitope tags and that are localized to either the cell nucleus or cell membrane have been generated. As a demonstration of how these strains can be used to study a particular gene, we have analyzed the developmental role of the Drosophila EGF receptor homolog. Moreover, we have shown that these strains can be utilized to identify new mutations in mosaic animals in an efficient and unbiased way, thereby providing an unprecedented opportunity to perform systematic genetic screens for mutations affecting many biological processes.

}, keywords = {Animals, Drosophila, Embryo, Epidermal Growth Factor, Female, Genetic Markers, Genetic Testing, Immunohistochemistry, Male, Mosaicism, Mutation, Nonmammalian, Phenotype, Receptor}, issn = {0950-1991}, doi = {10.1186/gb-2007-8-7-r145}, author = {Xu, T and Rubin, G M} } @article {1171, title = {A human mitochondrial transcriptional activator can functionally replace a yeast mitochondrial HMG-box protein both in vivo and in vitro.}, journal = {Molecular and Cellular Biology}, volume = {13}, year = {1993}, month = {1993 Mar}, pages = {1951-61}, abstract = {

Human mitochondrial transcription factor A is a 25-kDa protein that binds immediately upstream of the two major mitochondrial promoters, thereby leading to correct and efficient initiation of transcription. Although the nature of yeast mitochondrial promoters is significantly different from that of human promoters, a potential functional homolog of the human transcriptional activator protein has been previously identified in yeast mitochondria. The importance of the yeast protein in yeast mitochondrial DNA function has been shown by inactivation of its nuclear gene (ABF2) in Saccharomyces cerevisiae cells resulting in loss of mitochondrial DNA. We report here that the nuclear gene for human mitochondrial transcription factor A can be stably expressed in yeast cells devoid of the yeast homolog protein. The human protein is imported efficiently into yeast mitochondria, is processed correctly, and rescues the loss-of-mitochondrial DNA phenotype in a yeast abf2 strain, thus functionally substituting for the yeast protein. Both human and yeast proteins affect yeast mitochondrial transcription initiation in vitro, suggesting that the two proteins may have a common role in this fundamental process.

}, keywords = {Amino Acid, Amino Acid Sequence, Base Sequence, Biological Transport, Cell Compartmentation, DNA-Binding Proteins, Genes, Genetic, Humans, Mitochondria, Mitochondrial Proteins, Molecular Sequence Data, Nuclear Proteins, Oxygen Consumption, Post-Translational, Protein Processing, Protein Sorting Signals, Saccharomyces cerevisiae, Sequence Alignment, Sequence Homology, Transcription, Transcription Factors, Transformation}, issn = {0270-7306}, doi = {10.1101/gad.1352105}, author = {Parisi, M A and Xu, B and Clayton, D A} } @article {2096, title = {Near-field fluorescence imaging of cytoskeletal actin. (With commentary)}, journal = {Bioimaging}, volume = {1}, year = {1993}, month = {1993 Sep}, pages = {129-35}, abstract = {

Near-field scanning optical microscopy (NSOM) has been used to generate high resolution flourescence images of cytoskeletal actin within fixed mouse fibroblast cells. Comparison with other microscopic methods indicates a transverse resolution well beyond that of confocal microscopy, and contrast far more revealing than in force microscopy. Effects unique to the near field are shown to be involved in the excitation of flourescence, yet the resulting images remain readily interpretable. As an initial demonstration of its utility, the technique is used to analyze the actin-based cytoskeletal structure between stress fibers and in cellular protrusions formed in the process of wound healing.

Commentary: The first superresolution fluorescence imaging of a biological system: the actin cytoskeleton in fixed, cultured fibroblast cells. This work strongly influenced me in two ways. First, calculations based on the signal-to-noise-ratio in images of single actin filaments in the paper suggested that single molecule imaging might be feasible. This was soon proven to be the case (see above). Second, the limitations of exogenous labeling for superresolution microscopy were revealed: samples which appeared correctly stained by conventional microscopy often exhibited sketchy, punctuate labeling of actin filaments as well as substantial non-specific background in the corresponding near field images. Indeed, it was the advent of GFP, with its promise of dense labeling and perfect specificity, that lured me back to superresolution microscopy when I first heard of it in 2003.

}, author = {Betzig, E and Chichester, R J and Lanni, F and Taylor, D L} } @article {45776, title = {Nonfloral sources of chemicals that attract male euglossine bees (Apidae: Euglossini).}, journal = {J Chem Ecol}, volume = {19}, year = {1993}, month = {1993 Dec}, pages = {3017-27}, abstract = {

We present chemical analysis of four rotten or fungus-infected logs that attracted fragrance-collecting male euglossine bees. Eight of the 10 volatile compounds detected have never been found in the fragrances of orchids pollinated by male euglossine bees. Nonfloral sources of chemicals such as rotting wood may constitute an important fragrance resource for male bees. Since rotten logs produce large quantities of chemicals over long periods of time, such nonfloral sources might be more important than flowers as a source of certain fragrances for some euglossine bee species. Fragrance collecting in euglossine bees might have evolved originally in relation with rotting wood rather than flowers.

}, issn = {0098-0331}, doi = {10.1007/BF00980599}, author = {Whitten, W M and Young, A M and Stern, D L} } @article {2562, title = {Raman studies of steric hindrance and surface relaxation of stepped H-terminated silicon surfaces.}, journal = {Physical Review Letters}, volume = {71}, year = {1993}, month = {1993 Oct 4}, pages = {2280-83}, abstract = {

Polarized angle-resolved Raman spectra of the Si-H stretching vibrations on stepped H-terminated Si(111) surfaces confirm the constrained orientation of the step dihydride derived from ab initio cluster calculations. They further show that the step normal modes involve little concerted motion of the step atoms, indicating that step relaxation reduces the steric interaction much further than predicted.

}, issn = {1079-7114}, author = {Hines, MA and Chabal, YJ and Harris, T D and Harris, AL} } @article {1157, title = {Sex-lethal, master and slave: the hierarchy of germline sex determination in Drosophila.}, journal = {Development}, volume = {119}, year = {1993}, month = {1993 Nov}, pages = {897-908}, abstract = {

Female sex determination in the germ line of Drosophila melanogaster is regulated by genes functioning in the soma as well as genes that function within the germ line. Genes known or suspected to be involved in germ-line sex determination in Drosophila melanogaster have been examined to determine if they are required upstream or downstream of Sex-lethal+, a known germ-line sex determination gene. Seven genes required for female-specific splicing of germ-line Sex-lethal+ pre-mRNA are identified. These results together with information about the tissues in which these genes function and whether they control sex determination and viability or just sex determination in the germ line have been used to deduce the genetic hierarchy regulating female germ-line sex determination. This hierarchy includes the somatic sex determination genes transformer+, transformer-2+ and doublesex+ (and by inference Sex-lethal+), which control a somatic signal required for female germ-line sex determination, and the germ-line ovarian tumor genes fused+, ovarian tumor+, ovo+, sans fille+, and Sex-lethal+, which are involved in either the reception or interpretation of this somatic sex determination signal. The fused+, ovarian tumor+, ovo+ and sans fille+ genes function upstream of Sex-lethal+ in the germ line.

}, issn = {0950-1991}, author = {Baker, B.S. and Oliver, B. and Kim, Yi Jin} } @article {2085, title = {Single molecules observed by near-field scanning optical microscopy. (With commentary)}, journal = {Science}, volume = {262}, year = {1993}, month = {1993 Nov 26}, pages = {1422-5}, abstract = {

Individual carbocyanine dye molecules in a sub-monolayer spread have been imaged with near-field scanning optical microscopy. Molecules can be repeatedly detected and spatially localized (to approximately lambda/50 where lambda is the wavelength of light) with a sensitivity of at least 0.005 molecules/(Hz)(1/2) and the orientation of each molecular dipole can be determined. This information is exploited to map the electric field distribution in the near-field aperture with molecular spatial resolution.

Commentary: A paper of many firsts: the first single molecule microscopy; the first extended observations of single molecules under ambient conditions; the first localization of single molecules to near-molecular precision (\ 15 nm), the first determination of the dipole axes of single fluorescent molecules; and the first near-molecular resolution optical microscopy, when a single fluorescent molecule was used to map the evanescent electric field components in the vicinity of a 100 nm diameter near-field aperture. Although eventually supplanted by simpler far-field methods, this paper ushered in the era of single molecule imaging and biophysics, and inspired the concept that would eventually lead to PALM. Even today, near-field single molecule detection lives on in the {\textquotedblleft}zero mode waveguide{\textquotedblright} sequencing approach promoted by Pacific Biosciences.

}, issn = {0036-8075}, doi = {10.1126/science.262.5138.1422}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17736823}, author = {Betzig, E and Chichester, R J} } @article {2724, title = {Suffix arrays: a new method for on-line string searches.}, journal = {SIAM Journal on Scientific Computing: A Publication of the Society for Industrial and Applied Mathematics}, volume = {22}, year = {1993}, month = {1993}, pages = {935-48}, abstract = {

A new and conceptually simple data structure, called a suffix array, for on-line string searches is introduced in this paper. Constructing and querying suffix arrays is reduced to a sort and search paradigm that employs novel algorithms. The main advantage of suffix arrays over suffix trees is that, in practice, they use three to five times less space. From a complexity standpoint, suffix arrays permit on-line string searches of the type, {\textquoteleft}{\textquoteleft}Is W a substring of A?{\textquoteright}{\textquoteright} to be answered in time O(P + log N), where P is the length of W and N is the length of A, which is competitive with (and in some cases slightly better than) suffix trees. The only drawback is that in those instances where the underlying alphabet is finite and small, suffix trees can be constructed in O(N) time in the worst case, versus O(N log N) time for suffix arrays.

However, we give an augmented algorithm that, regardless of the alphabet size, constructs suffix arrays in O(N) expected time, albeit with lesser space efficiency. We believe that suffix arrays will prove to be better in practice than suffix trees for many applications.

}, author = {Manber, U and Myers, Eugene} } @article {964, title = {The TGF beta homolog dpp and the segment polarity gene hedgehog are required for propagation of a morphogenetic wave in the Drosophila retina.}, journal = {Cell}, volume = {75}, year = {1993}, month = {1993 Dec 3}, pages = {913-26}, abstract = {

Development of the Drosophila retina occurs asynchronously; differentiation, its front marked by the morphogenetic furrow, progresses across the eye disc epithelium over a 2 day period. We have investigated the mechanism by which this front advances, and our results suggest that developing retinal cells drive the progression of morphogenesis utilizing the products of the hedgehog (hh) and decapentaplegic (dpp) genes. Analysis of hh and dpp genetic mosaics indicates that the products of these genes act as diffusible signals in this process. Expression of dpp in the morphogenetic furrow is closely correlated with the progression of the furrow under a variety of conditions. We show that hh, synthesized by differentiating cells, induces the expression of dpp, which appears to be a primary mediator of furrow movement.

}, keywords = {Animals, Cell Differentiation, Drosophila melanogaster, Drosophila Proteins, Eye, Gene Expression, Genes, Hedgehog Proteins, Insect, Insect Hormones, Invertebrate, Messenger, Morphogenesis, Mosaicism, Photoreceptor Cells, Proteins, Retina, RNA, Transforming Growth Factor beta}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Heberlein, U and Wolff, T and Rubin, G M} } @article {45933, title = {Voltage- and space-clamp errors associated with the measurement of electrotonically remote synaptic events.}, journal = {J Neurophysiol}, volume = {70}, year = {1993}, month = {1993 Aug}, pages = {781-802}, abstract = {

1. The voltage- and space-clamp errors associated with the use of a somatic electrode to measure current from dendritic synapses are evaluated using both equivalent-cylinder and morphologically realistic models of neuronal dendritic trees. 2. As a first step toward understanding the properties of synaptic current distortion under voltage-clamp conditions, the attenuation of step and sinusoidal voltage changes are evaluated in equivalent cylinder models. Demonstration of the frequency-dependent attenuation of voltage in the cable is then used as a framework for understanding the distortion of synaptic currents generated at sites remote from the somatic recording electrode and measured in the voltage-clamp recording configuration. 3. Increases in specific membrane resistivity (Rm) are shown to reduce steady-state voltage attenuation, while producing only minimal reduction in attenuation of transient voltage changes. Experimental manipulations that increase Rm therefore improve the accuracy of estimates of reversal potential for electrotonically remote synapses, but do not significantly reduce the attenuation of peak current. In addition, increases in Rm have the effect of slowing the kinetics of poorly clamped synaptic currents. 4. The effects of the magnitude of the synaptic conductance and its kinetics on the measured synaptic currents are also examined and discussed. The error in estimating parameters from measured synaptic currents is greatest for synapses with fast kinetics and large conductances. 5. A morphologically realistic model of a CA3 pyramidal neuron is used to demonstrate the generality of the conclusions derived from equivalent cylinder models. The realistic model is also used to fit synaptic currents generated by stimulation of mossy fiber (MF) and commissural/associational (C/A) inputs to CA3 neurons and to estimate the amount of distortion of these measured currents. 6. Anatomic data from the CA3 pyramidal neuron model are used to construct a simplified two-cylinder CA3 model. This model is used to estimate the electrotonic distances of MF synapses (which are located proximal to the soma) and perforant path (PP) synapses (which are located at the distal ends of the apical dendrites) and the distortion of synaptic current parameters measured for these synapses. 7. Results from the equivalent-cylinder models, the morphological CA3 model, and the simplified CA3 model all indicate that the amount of distortion of synaptic currents increases steeply as a function of distance from the soma. MF synapses close to the soma are likely to be subject only to small space-clamp errors, whereas MF synapses farther from the soma are likely to be substantially attenuated.(ABSTRACT TRUNCATED AT 400 WORDS)

}, keywords = {Animals, Dendrites, Guinea Pigs, Hippocampus, Membrane Potentials, Models, Neurological, Neural Conduction, Neurons, Synapses, Synaptic Transmission}, issn = {0022-3077}, author = {Spruston, N and Jaffe, D B and Williams, S H and Johnston, D} } @article {966, title = {The argos gene encodes a diffusible factor that regulates cell fate decisions in the Drosophila eye.}, journal = {Cell}, volume = {69}, year = {1992}, month = {1992 Jun 12}, pages = {963-75}, abstract = {

The argos gene encodes a protein that is required for viability and that regulates the determination of cells in the Drosophila eye. A developmental analysis of argos mutant eyes indicates that the mystery cells, which are usually nonneuronal, are transformed into extra photoreceptors, and that supernumerary cone cells and pigment cells are also recruited. Clonal analysis indicates that argos acts nonautonomously and can diffuse over the range of several cell diameters. Conceptual translation of the argos gene suggests that it encodes a secreted protein.

}, keywords = {Amino Acid Sequence, Animals, Base Sequence, Cell Communication, Clone Cells, Cloning, DNA, Drosophila melanogaster, Embryonic Induction, Eye, Gene Expression, Genes, Messenger, Molecular, Molecular Sequence Data, Phenotype, Restriction Mapping, RNA, Signal Transduction}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Freeman, M and Kl{\"a}mbt, C and Goodman, C S and Rubin, G M} } @article {2098, title = {Combined shear force and near-field scanning optical microscopy (With commentary)}, journal = {Applied Physics Letters}, volume = {60}, year = {1992}, month = {1002 Mar 9}, abstract = {

A distance regulation method has been developed to enhance the reliability, versatility, and ease of use of near-field scanning optical microscopy (NSOM). The method relies on the detection of shear forces between the end of a near-field probe and the sample of interest. The system can be used solely for distance regulation in NSOM, for simultaneous shear force and near-field imaging, or for shear force microscopy alone. In the latter case, uncoated optical fiber probes are found to yield images with consistently high resolution.

Commentary: To exploit the evanescent field that is the source of high resolution in near-field microscopy, the probe must be exceptionally close to the sample: \ 10 nm away for 30-50 nm resolution. Here we introduced a distance regulation mechanism based on transverse shear forces between the end of a dithered near-field probe and the sample, which permitted even samples of modest topography to be imaged. Simple, reliable, noninvasive, and applicable to a wide range of samples from whole fixed cells to semiconductor devices, shear force microscopy was a key enabling technology for near-field optics, and soon widely implemented.

}, author = {Betzig, E and Finn, P L and Weiner, J S} } @article {2097, title = {Near-field magneto-optics and high density data storage. (With commentary)}, journal = {Applied Physics Letters.}, volume = {61}, year = {1992}, month = {1992}, abstract = {

Near-field scanning optical microscopy (NSOM) has been used to image and record domains in thin-film magneto-optic (MO) materials. In the imaging mode, resolution of 30-50 nm has been consistently obtained, whereas in the recording mode, domains down to -60 nm have been written reproducibly. Data densities of -45 Gbits/in.{\textquoteright} have been achieved, well in excess\ of current magnetic or MO technologies. A brief analysis of speed and other issues indicates that the technique may represent a viable alternative to density data storage needs.

Commentary: The first demonstration of optical recording and playback beyond the diffraction limit, using magneto-optic multilayer films and polarization contrast near-field microscopy. Bits as small as 60 nm were recorded {\textendash} beyond estimates at the time of the superparamagnetic limit to bit stability. Bit densities of 45 Gbits/in2 were also achieved, well in excess of optical or magnetic recording technologies of the era. In the years following this work, massive resources were spent on the commercialization of near-field data storage, largely for naught.

}, author = {Betzig, E and Trautman, J K and Wolfe, R and Gyorgy, E M and Finn, P L and Kryder, M H and Chang, C H} } @article {2093, title = {Near-field optics: microscopy, spectroscopy, and surface modification beyond the diffraction limit. (With commentary)}, journal = {Science}, volume = {257}, year = {1992}, month = {1992 Jul 10}, pages = {189-95}, abstract = {

The near-field optical interaction between a sharp probe and a sample of interest can be exploited to image, spectroscopically probe, or modify surfaces at a resolution (down to approximately 12 nm) inaccessible by traditional far-field techniques. Many of the attractive features of conventional optics are retained, including noninvasiveness, reliability, and low cost. In addition, most optical contrast mechanisms can be extended to the near-field regime, resulting in a technique of considerable versatility. This versatility is demonstrated by several examples, such as the imaging of nanometric-scale features in mammalian tissue sections and the creation of ultrasmall, magneto-optic domains having implications for highdensity data storage. Although the technique may find uses in many diverse fields, two of the most exciting possibilities are localized optical spectroscopy of semiconductors and the fluorescence imaging of living cells.

Commentary: An overview of our work in near-field optics at the time, after our invention of the adiabatically tapered fiber probe and shear force feedback (see below) led to the first practical near-field scanning optical microscope. In this work, superresolution imaging via absorption, reflectivity, fluorescence, spectroscopy, polarization, and refractive index contrast were all demonstrated. Unlike all far-field superresolution fluorescence methods that were to appear a decade later, near-field microscopy remains the only superresolution technique capable of taking advantage of the full panoply of optical contrast mechanisms.

}, issn = {0036-8075}, doi = {10.1126/science.257.5067.189}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17794749}, author = {Betzig, E and Trautman, J K} } @article {45902, title = {Perforated patch-clamp analysis of the passive membrane properties of three classes of hippocampal neurons.}, journal = {J Neurophysiol}, volume = {67}, year = {1992}, month = {1992 Mar}, pages = {508-29}, abstract = {

1. Perforated patch-clamp recordings were made from the three major classes of hippocampal neurons in conventional in vitro slices prepared from adult guinea pigs. This technique provided experimental estimates of passive membrane properties (input resistance, RN, and membrane time constant, tau m) determined in the absence of the leak conductance associated with microelectrode impalement or the washout of cytoplasmic constituents associated with conventional whole-cell recordings. 2. To facilitate comparison of our data with previous results and to determine the passive membrane properties under conditions as physiological as possible, recordings were made at the resting potential, in physiological saline, and without any added blockers of voltage-dependent conductances. 3. Membrane-potential responses to current steps were analyzed, and four criteria were used to identify voltage responses that were the least affected by activation of voltage-dependent conductances. tau m was estimated from the slowest component (tau 0) of multiexponential fits of responses deemed passive by these criteria. RN was estimated from the slope of the linear region in the hyperpolarizing direction of the voltage-current relation. 4. It was not possible to measure purely passive membrane properties that were completely independent of membrane potential in any of the three classes of hippocampal neurons. Changing the membrane potential by constant current injection resulted in changes in RN and tau 0; subthreshold depolarization produced an increase, and hyperpolarization a decrease, in both RN and tau 0 for all three classes of hippocampal neurons. 5. Each of the three classes of hippocampal neurons also displayed a depolarizing "sag" during larger hyperpolarizing voltage transients. To evaluate the effect of the conductances underlying this sag on passive membrane properties, 2-5 mM Cs+ was added to the physiological saline. Extracellular Cs+ effectively blocked the sag in all three classes of hippocampal neurons, but the effect of Cs+ on RN, tau 0, and the voltage dependence of these parameters was unique for each class of neurons. 6. CA1 pyramidal neurons had an RN of 104 +/- 10 (SE) M omega and tau 0 of 28 +/- 2 ms at a resting potential of -64 +/- 2 mV (n = 12). RN and tau 0 were larger at more depolarized potentials in these neurons, but the addition of Cs+ to the physiological saline reversed this voltage dependence. 7. CA3 pyramidal neurons had an RN of 135 +/- 8 M omega and tau 0 of 66 +/- 4 ms at a resting potential of -64 +/- 1 mV (n = 14).(ABSTRACT TRUNCATED AT 400 WORDS)

}, keywords = {Animals, Cesium, Electrophysiology, Guinea Pigs, Hippocampus, In Vitro Techniques, Membrane Potentials, Membranes, Microelectrodes, Neurons, Pyramidal Tracts}, issn = {0022-3077}, author = {Spruston, N and Johnston, D} } @article {2563, title = {Polarization contrast in near-field scanning optical microscopy.}, journal = {Applied Optics}, volume = {31}, year = {1992}, month = {1992 Aug 1}, pages = {4563-8}, abstract = {

Recent advances in probe design have led to enhanced resolution (currently as significant as \  12 nm) in optical microscopes based on near-field imaging. We demonstrate that the polarization of emitted and detected light in such microscopes can be manipulated sensitively to generate contrast. We show that the contrast on certain patterns is consistent with a simple interpretation of the requisite boundary conditions, whereas in other cases a more complicated interaction between the probe and the sample is involved. Finally application of the technique to near-filed magneto-optic imaging is demonstrated.

}, issn = {0003-6935}, doi = {10.1364/AO.31.004563}, author = {Betzig, E and Trautman, J K and Weiner, J S and Harris, T D and Wolfe, R} } @article {45819, title = {Aphid soldiers discriminate between soldiers and non-soldiers, rather than between kin and non-kin, in Ceratoglyphina bambusae}, journal = {Animal behaviour}, volume = {42}, year = {1991}, pages = {865-866}, abstract = {

Examined kin discrimination and colony defense in soldier-producing aphids from the surface of 3 galls. Soldiers always attacked conspecific nonsoldiers, regardless of origin, and never attacked conspecific soldiers. Soldier attacks of nonsoldiers may exclude unrelated nonsoldier aphids from the gall where they would propagate and compete with resident aphids. (PsycINFO Database Record (c) 2012 APA, all rights reserved)

}, doi = {10.1016/S0003-3472(05)80135-6}, url = {http://psycnet.apa.org/psycinfo/1992-15421-001}, author = {Shigeyuki Aoki and Utako Kurosu and David L Stern} } @article {2095, title = {Breaking the diffraction barrier: optical microscopy on a nanometric scale. (With commentary)}, journal = {Science}, volume = {251}, year = {1991}, month = {1991 Mar 22}, pages = {1468-70}, abstract = {

In near-field scanning optical microscopy, a light source or detector with dimensions less than the wavelength (lambda) is placed in close proximity (lambda/50) to a sample to generate images with resolution better than the diffraction limit. A near-field probe has been developed that yields a resolution of approximately 12 nm ( approximately lambda/43) and signals approximately 10(4)- to 10(6)-fold larger than those reported previously. In addition, image contrast is demonstrated to be highly polarization dependent. With these probes, near-field microscopy appears poised to fulfill its promise by combining the power of optical characterization methods with nanometric spatial resolution.

Commentary: Introduced the adiabatically tapered single mode fiber probe to near-field scanning optical microscopy which, together with shear force feedback, made the technique a practical reality. Although earlier claims of superresolution via near-field microscopy existed for nearly a decade, this paper was the first to convincingly break Abbe{\textquoteright}s limit with visible light, as demonstrated by reproducibly resolving known, complex nanoscale patterns having features separated by much less than the wavelength. Whereas our fiber probe and shear force technologies were soon widely adopted and key to many novel applications (see above), the earlier methods proved to be technological dead ends, never achieving the results of their original claims. This experience taught me the most valuable lesson of my career: while it{\textquoteright}s bad to bullshit others, it{\textquoteright}s even worse to bullshit yourself. It{\textquoteright}s a lesson sadly unheeded by many current practitioners of superresolution microscopy.

}, issn = {0036-8075}, doi = {10.1126/science.251.5000.1468}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17779440}, author = {Betzig, E and Trautman, J K and Harris, T D and Weiner, J S and Kostelak, R L} } @article {2564, title = {Breaking the diffraction barrier: optical microscopy on a nanometric scale.}, journal = {Science}, volume = {251}, year = {1991}, month = {1991 Mar 22}, pages = {1468-70}, abstract = {

In near-field scanning optical microscopy, a light source or detector with dimensions less than the wavelength (lambda) is placed in close proximity (lambda/50) to a sample to generate images with resolution better than the diffraction limit. A near-field probe has been developed that yields a resolution of approximately 12 nm ( approximately lambda/43) and signals approximately 10(4)- to 10(6)-fold larger than those reported previously. In addition, image contrast is demonstrated to be highly polarization dependent. With these probes, near-field microscopy appears poised to fulfill its promise by combining the power of optical characterization methods with nanometric spatial resolution.

}, issn = {0036-8075}, doi = {10.1126/science.251.5000.1468}, author = {Betzig, E and Trautman, J K and Harris, T D and Weiner, J S and Kostelak, R L} } @article {1173, title = {Impairment of mitochondrial transcription termination by a point mutation associated with the MELAS subgroup of mitochondrial encephalomyopathies.}, journal = {Nature}, volume = {351}, year = {1991}, month = {1991 May 16}, pages = {236-9}, abstract = {

Defects in mitochondrial DNA (mtDNA) are associated with several different human diseases, including the mitochondrial encephalomyopathies. The mutations include deletions but also duplications and point mutations. Individuals with MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes) carry a common A-to-G substitution in a highly conserved portion of the gene for transfer RNA(Leu(UUR)). Although the MELAS mutation may be comparable to the defect in the tRNA(Lys) gene associated with MERRF (myoclonus epilepsy associated with ragged-red fibres), it is also embedded in the middle of a tridecamer sequence necessary for the formation of the 3{\textquoteright} ends of 16S ribosomal RNA in vitro. We found that the MELAS mutation results in severe impairment of 16S rRNA transcription termination, which correlates with a reduced affinity of the partially purified termination protein for the MELAS template. This suggests that the molecular defect in MELAS is the inability to produce the correct type and quantity of rRNA relative to other mitochondrial gene products.

}, keywords = {Base Sequence, Blotting, Brain Diseases, Chromosome Mapping, DNA, DNA Mutational Analysis, Genetic, Humans, Mitochondria, Mitochondrial, Molecular Sequence Data, Muscle, Mutation, Peptide Termination Factors, Ribosomal, RNA, Transcription, Transfer, Western}, issn = {0028-0836}, doi = {10.1101/gad.1352105}, author = {Hess, J F and Parisi, M A and Bennett, J L and Clayton, D A} } @article {45820, title = {Male territoriality and alternative male behaviors in the euglossine bee, Eulaema meriana (Hymenoptera: Apidae)}, journal = {Journal of the Kansas Entomological Society}, volume = {64}, year = {1991}, pages = {421-437}, abstract = {

During a four month study of male territoriality males of the euglossine bee Eulaema meriana exhibited the two alternative behavior patterns of territoriality and transiency. Territorial males patrolled an area adjacent to a tree upon which they perched. Territorial males utilized the same territory for up to 49 days, though often not on consecutive days, and appeared to non-violently relinquish territories to new males. Transients did not defend territories but flew from one territory to another and flew with the territorial male around the territory, rarely bumping, and never grappling. Transient males left the territory soon after the territorial male flew back and forth in front of the perch tree in a zig-zag flight. The alternative behaviors were correlated with wing wear such that males with little wing wear defended territories and males with considerable wing wear pursued a transient strategy. Behavior patterns were not correlated with head width. Comparison of territory trees with the territory trees of a closely related species indicate that each species utilized trees of a certain diameter class for perching. In addition, analysis of hemispherical canopy photographs indicates that males appeared to prefer territories that received a maximum of diffuse sunlight but a minimum of direct sunlight. Both territorial and transient males consistently returned to specific territories over their lifetime but appeared to travel long distances to forage for fragrances. Territorial and transient males visited fragrance baits with equal frequency suggesting that non-territorial, as well as territorial, males required fragrances.

}, url = {http://www.jstor.org/stable/25085309} } @article {1156, title = {The maleless protein associates with the X chromosome to regulate dosage compensation in Drosophila.}, journal = {Cell}, volume = {66}, year = {1991}, month = {1991 Sep 6}, pages = {935-48}, abstract = {

The maleless (mle) gene is one of four known regulatory loci required for increased transcription (dosage compensation) of X-linked genes in D. melanogaster males. A predicted mle protein (MLE) contains seven short segments that define a superfamily of known and putative RNA and DNA helicases. MLE, while present in the nuclei of both male and female cells, differs in its association with polytene X chromosomes in the two sexes. MLE is associated with hundreds of discrete sites along the length of the X chromosome in males and not in females. The predominant localization of MLE to the X chromosome in males makes it a strong candidate to be a direct regulator of dosage compensation.

}, issn = {0092-8674}, author = {Baker, B.S. and Kuroda, M.I. and Kreber, M.J. and Ganetzky, B.} } @article {968, title = {The optic lobe projection pattern of polarization-sensitive photoreceptor cells in Drosophila melanogaster.}, journal = {Cell and Tissue Research}, volume = {265}, year = {1991}, month = {1991 Jul}, pages = {185-91}, abstract = {

Histological staining of wild-type and sevenless transgenic Drosophila melanogaster bearing Rh3-lacZ fusion genes permits the selective visualization of polarization-sensitive R7 and R8 photoreceptor cells located along the dorsal anterior eye margin. Diffusion of beta-galactosidase throughout these cells reveals that they project long axons to the two most peripheral synaptic target rows of the dorsal posterior medulla, defining a specialized marginal zone of this optic lobe. Comparison of the staining patterns of marginal and nonmarginal Rh3-lacZ-expressing photoreceptor cells in the same histological preparations suggest that the marginal cells possess morphologically specialized axons and synaptic terminals. These findings are discussed with reference to the neuroanatomy of the corresponding dorsal marginal eye and optic lobe regions of the larger dipterans Musca and Calliphora, and in relation to the ability of Drosophila to orient to polarized light.

}, keywords = {Animals, beta-Galactosidase, Cloning, Drosophila melanogaster, Eye, Gene Expression, Histocytochemistry, Light, Molecular, Nonmammalian, Ocular, Ocular Physiological Phenomena, Optic Lobe, Photoreceptor Cells, Vision}, issn = {0302-766X}, doi = {10.1186/gb-2007-8-7-r145}, author = {Fortini, M E and Rubin, G M} } @article {967, title = {Ras1 and a putative guanine nucleotide exchange factor perform crucial steps in signaling by the sevenless protein tyrosine kinase.}, journal = {Cell}, volume = {67}, year = {1991}, month = {1991 Nov 15}, pages = {701-16}, abstract = {

We have conducted a genetic screen for mutations that decrease the effectiveness of signaling by a protein tyrosine kinase, the product of the Drosophila melanogaster sevenless gene. These mutations define seven genes whose wild-type products may be required for signaling by sevenless. Four of the seven genes also appear to be essential for signaling by a second protein tyrosine kinase, the product of the Ellipse gene. The putative products of two of these seven genes have been identified. One encodes a ras protein. The other locus encodes a protein that is homologous to the S. cerevisiae CDC25 protein, an activator of guanine nucleotide exchange by ras proteins. These results suggest that the stimulation of ras protein activity is a key element in the signaling by sevenless and Ellipse and that this stimulation may be achieved by activating the exchange of GTP for bound GDP by the ras protein.

}, keywords = {Amino Acid Sequence, DNA Mutational Analysis, Drosophila Proteins, Eye Proteins, Genes, GTP-Binding Proteins, Guanine Nucleotide Exchange Factors, Membrane Glycoproteins, Molecular Sequence Data, Photoreceptor Cells, Protein-Tyrosine Kinases, Proteins, Proto-Oncogene Proteins p21(ras), ras Guanine Nucleotide Exchange Factors, Receptor Protein-Tyrosine Kinases, Restriction Mapping, Saccharomyces cerevisiae, Schizosaccharomyces, Sequence Alignment, Signal Transduction, Structure-Activity Relationship}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Simon, M A and Bowtell, D D and Dodson, G S and Laverty, T R and Rubin, G M} } @article {2462, title = {The regulation of transmitter expression in postembryonic lineages in the moth Manduca sexta. II. Role of cell lineage and birth order.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {11}, year = {1991}, month = {1991 Jul}, pages = {1990-7}, abstract = {

The expression of GABA is restricted to the progeny of only six of the 24 identified postembryonic lineages in the thoracic ganglia of the tobacco hornworm, Manduca sexta (Witten and Truman, 1991). It is colocalized with a peptide similar to molluscan small cardioactive peptide B (SCPB) in some of the neurons in two of the six lineages. By combining chemical ablation of the neuroblasts at specific larval stages with birth dating of the progeny, we tested whether the expression of GABA and the SCPB-like peptide was determined strictly by cell lineage or involved cellular interactions among the members of individual clonal groups. Chemical ablation of the six specific neuroblasts that produced the GABA-positive neurons (E, K, M, N, T, and X) or of the two that produced the GABA + SCPB-like-immunoreactive neurons (K, M) prior to the generation of their lineages resulted in the loss of these immunoreactivities. These results suggest that regulation between lineages did not occur. Ablation of the K and M neuroblasts after they had produced a small portion of their lineages had no effect on the expression of GABA, but did affect the pattern of the SCPB-like immunoreactivity. Combining birth-dating techniques with transmitter immunocytochemistry revealed that it was the position in the birth order and not interactions among the clonally related neurons that influenced the peptidergic phenotype. These results suggest that cell lineage is involved in establishing the GABAergic phenotype and that both cell lineage and birth order influence the determination of the peptidergic phenotype.(ABSTRACT TRUNCATED AT 250 WORDS)

}, keywords = {Animals, Cell Communication, Cell Differentiation, gamma-Aminobutyric Acid, Ganglia, Immunohistochemistry, Invertebrate Hormones, Larva, Moths, Nervous System, Neurons, Neuropeptides, Neurotransmitter Agents, Phenotype, Pupa}, issn = {0270-6474}, author = {Witten, J L and Truman, J W} } @article {1172, title = {Similarity of human mitochondrial transcription factor 1 to high mobility group proteins.}, journal = {Science}, volume = {252}, year = {1991}, month = {1991 May 17}, pages = {965-9}, abstract = {

Human mitochondrial transcription factor 1 (mtTF1) has been sequenced and is a nucleus-encoded DNA binding protein of 204 amino acids (24,400 daltons). Expression of human mtTF1 in bacteria yields a protein with correct physical properties and the ability to activate mitochondrial DNA promoters. Analysis of the protein{\textquoteright}s sequence reveals no similarities to any other DNA binding proteins except for the existence of two domains that are characteristic of high mobility group (HMG) proteins. Human mtTF1 is most closely related to a DNA binding HMG-box region in hUBF, a human protein known to be important for transcription by RNA polymerase I.

}, keywords = {Amino Acid Sequence, Base Sequence, Blotting, DNA, DNA-Binding Proteins, Gene Library, Genetic, High Mobility Group Proteins, Humans, Messenger, Mitochondria, Mitochondrial, Mitochondrial Proteins, Molecular Sequence Data, Molecular Weight, Northern, Nuclear Proteins, Nucleic Acid, Nucleic Acid Hybridization, Oligonucleotide Probes, Open Reading Frames, Promoter Regions, RNA, Sequence Homology, Transcription Factors}, issn = {0036-8075}, doi = {10.1101/gad.1352105}, author = {Parisi, M A and Clayton, D A} } @article {45821, title = {Wing buzzing by male orchid bees, Eulaema meriana (Hymenoptera: Apidae)}, journal = {Journal of the Kansas Entomological Society}, volume = {64}, year = {1991}, pages = {88-94}, abstract = {

Male orchid bees of the species Eulaema meriana buzz their wings while stationary at territory perches. During buzzing, wings are first positioned laterally and then moved in a plane parallel to the ground, which probably generates a substantial airflow past the body. Within a perching episode, the ratio of buzz to pause duration decreases nonlinearly. The incidence of wing buzzing increases with ambient temperature and with duration of activity. Bees never defended territories when ambient temperatures exceeded 28.5{\textdegree}C. Wing buzzing may be a visual or acoustic display to conspecifics, although the brightly colored abdomen is never obscured by the wings during buzzing, and the sounds of wing buzzing are low in amplitude. The increase in buzzing frequency with increased ambient temperature and the nonlinear decrease in buzz to pause duration during perching suggest that wing buzzing may be a thermoregulatory mechanism.

}, url = {http://www.jstor.org/stable/25085249}, author = {David L Stern and Robert Dudley} } @article {45823, title = {Agonistic interactions between ants and gall-living soldier aphids}, journal = {Journal of Ethology}, volume = {8}, year = {1990}, pages = {139-141}, issn = {0289-0771}, doi = {10.1007/BF02350284}, author = {Utako Kurosu and David L Stern and Shigeyuki Aoki} } @article {970, title = {Analysis of cis-acting requirements of the Rh3 and Rh4 genes reveals a bipartite organization to rhodopsin promoters in Drosophila melanogaster.}, journal = {Genes \& Development}, volume = {4}, year = {1990}, month = {1990 Mar}, pages = {444-63}, abstract = {

The rhodopsin genes of Drosophila melanogaster are expressed in nonoverlapping subsets of photoreceptor cells within the insect visual system. Two of these genes, Rh3 and Rh4, are known to display complementary expression patterns in the UV-sensitive R7 photoreceptor cell population of the compound eye. In addition, we find that Rh3 is expressed in a small group of paired R7 and R8 photoreceptor cells at the dorsal eye margin that are apparently specialized for the detection of polarized light. In this paper we present a detailed characterization of the cis-acting requirements of both Rh3 and Rh4. Promoter deletion series demonstrate that small regulatory regions (less than 300 bp) of both R7 opsin genes contain DNA sequences sufficient to generate their respective expression patterns. Individual cis-acting elements were further identified by oligonucleotide-directed mutagenesis guided by interspecific sequence comparisons. Our results suggest that the Drosophila rhodopsin genes share a simple bipartite promoter structure, whereby the proximal region constitutes a functionally equivalent promoter "core" and the distal region determines cell-type specificity. The expression patterns of several hybrid rhodopsin promoters, in which all or part of the putative core regions have been replaced with the analogous regions of different rhodopsin promoters, provide additional evidence in support of this model.

}, keywords = {Animals, Base Sequence, DNA Mutational Analysis, Drosophila melanogaster, Eye Proteins, Gene Expression, Genes, Genetic, Histocytochemistry, Molecular Sequence Data, Mutation, Nucleic Acid, Promoter Regions, Retinal Pigments, Rhodopsin, Rod Opsins, Sequence Homology}, issn = {0890-9369}, doi = {10.1186/gb-2007-8-7-r145}, author = {Fortini, M E and Rubin, G M} } @article {2702, title = {Basic local alignment search tool.}, journal = {Journal of Molecular Biology}, volume = {215}, year = {1990}, month = {1990 Oct 5}, pages = {403-10}, abstract = {

A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.

}, keywords = {Algorithms, Amino Acid Sequence, Base Sequence, Databases, Factual, Mutation, Nucleic Acid, Sensitivity and Specificity, Sequence Homology, Software}, issn = {0022-2836}, doi = {10.1006/jmbi.1990.9999}, author = {Altschul, S F and Gish, W and Miller, W. and Myers, E W and Lipman, D J} } @article {2375, title = {Evidence for the influence of electron-electron interaction on the chemical potential of the two-dimensional electron gas.}, journal = {Physical Review. B, Condensed Matter}, volume = {42}, year = {1990}, month = {1990 Aug 15}, pages = {3741-44}, abstract = {

It is shown experimentally that the interaction between electrons strongly influences the chemical potential of the two-dimensional (2D) electron gas. At sufficiently low temperatures and in high magnetic fields, regions of filling factor appear where (i) the chemical potential μ diminishes with increasing carrier density, i.e., the thermodynamic density of states is negative; (ii) the derivative ∂μ/∂H (H is the magnetic field) is considerably higher than the maximum value for a noninteracting 2D electron gas. Using these results, we have estimated that the energy of the e-e interaction in Si inversion layers in a magnetic field is about 1 order of magnitude less than the classical Coulomb interaction calculated for Si metal-oxide-semiconductor field-effect transistors.

}, issn = {0163-1829}, doi = {10.1523/JNEUROSCI.3613-08.2008}, author = {Kravchenko, SV and Rinberg, DA and Semenchinsky, SG and Pudalov, VM} } @article {969, title = {The homeo domain protein rough is expressed in a subset of cells in the developing Drosophila eye where it can specify photoreceptor cell subtype.}, journal = {Genes \& Development}, volume = {4}, year = {1990}, month = {1990 May}, pages = {712-27}, abstract = {

The Drosophila homeo box gene rough is required in photoreceptor cells R2 and R5 for normal eye development. We show here that rough protein expression is limited to a subset of cells in the developing retina where it is transiently expressed for 30-60 hr. The rough protein is first expressed broadly in the morphogenetic furrow but is rapidly restricted to the R2, R3, R4, and R5 precursor cells. Ubiquitous expression of rough under the control of the hsp70 promoter in third-instar larvae suppresses the initial steps of ommatidial assembly. Structures derived from other imaginal discs are not affected. Ectopic expression of rough in the R7 precursor, through the use of the sevenless promoter, causes this cell to develop into an R1-6 photoreceptor subtype; however, this cell still requires sevenless function for its neural differentiation. Taken together with previous analyses of the rough mutant phenotype, these results suggest that the normal role of rough is to establish the unique cell identity of photoreceptors R2 and R5.

}, keywords = {Animals, Base Sequence, Cell Cycle Proteins, DNA-Binding Proteins, Drosophila melanogaster, Drosophila Proteins, Eye, Gene Expression, Genes, Genetic, Heat-Shock Proteins, Homeobox, Hot Temperature, Microtubule-Associated Proteins, Molecular Sequence Data, Morphogenesis, Phenotype, Photoreceptor Cells, Promoter Regions, Transcription Factors}, issn = {0890-9369}, doi = {10.1186/gb-2007-8-7-r145}, author = {Kimmel, B E and Heberlein, U and Rubin, G M} } @article {1195, title = {Isolation and characterization of QCR9, a nuclear gene encoding the 7.3-kDa subunit 9 of the Saccharomyces cerevisiae ubiquinol-cytochrome c oxidoreductase complex. An intron-containing gene with a conserved sequence occurring in the intron of COX4.}, journal = {The Journal of Biological Chemistry}, volume = {265}, year = {1990}, month = {1990 Dec 5}, pages = {20813-21}, abstract = {

A nuclear gene (QCR9) encoding the 7.3-kDa subunit 9 of the mitochondrial cytochrome bc1 complex from Saccharomyces cerevisiae has been isolated from a yeast genomic library by hybridization with a degenerate oligonucleotide corresponding to nine amino acids proximal to the N terminus of purified subunit 9. QCR9 includes a 195-base pair open reading frame capable of encoding a protein of 66 amino acids and having a predicted molecular weight of 7471. The N-terminal methionine of subunit 9 is removed posttranslationally because the N-terminal sequence of the purified protein begins with serine 2. The ATG triplet corresponding to the N-terminal methionine is separated from the open reading frame by an intron. The intron is 213 base pairs long and contains previously reported 5{\textquoteright} donor, 3{\textquoteright} acceptor, and TACTAAC sequences necessary for splicing. The splice junctions, as well as the 5{\textquoteright} end of the message, were confirmed by isolation and sequencing of a cDNA copy of QCR9. In addition, the intron contains a nucleotide sequence in which 15 out of 18 nucleotides are identical with a sequence in the intron of COX4, the nuclear gene encoding cytochrome c oxidase subunit 4. The deduced amino acid sequence of the yeast subunit 9 is 39\% identical with that of a protein of similar molecular weight from beef heart cytochrome bc1 complex. If conservative substitutions are allowed for, the two proteins are 56\% similar. The predicted secondary structure of the 7.3-kDa protein revealed a single possible transmembrane helix, in which the amino acids conserved between beef heart and yeast are asymmetrically arranged along one face of the helix, implying that this domain of the protein is involved in a conserved interaction with another hydrophobic protein of the cytochrome bc1 complex. Two yeast strains, JDP1 and JDP2, were constructed in which QCR9 was deleted. Both strains grew very poorly, or not at all, on nonfermentable carbon sources and exhibited, at most, only 5\% of wild-type ubiquinol-cytochrome c oxidoreductase activity. Optical spectra of mitochondrial membranes from the deletion strains revealed slightly reduced levels of cytochrome b. When JDP1 and JDP2 were complemented with a plasmid carrying QCR9, the resulting yeast grew normally on ethanol/glycerol and exhibited normal cytochrome c reductase activities and optical spectra. These results indicate that QCR9 encodes a 7.3-kDa subunit of the bc1 complex that is required for formation of a fully functional complex.(ABSTRACT TRUNCATED AT 400 WORDS)

}, keywords = {Amino Acid Sequence, Base Sequence, Cell Nucleus, Chromosome Deletion, Cloning, Electron Transport Complex III, Electron Transport Complex IV, Fungal, Genes, Genomic Library, Introns, Macromolecular Substances, Models, Molecular, Molecular Sequence Data, Protein Conformation, Restriction Mapping, Saccharomyces cerevisiae}, issn = {0021-9258}, author = {Phillips, J D and Schmitt, M E and Brown, T A and Beckmann, J D and Trumpower, B L} } @article {2182, title = {Merrill C. Sosman lecture. Drugs, behavior, and brain chemistry.}, journal = {American Journal of Roentgenology}, volume = {155}, year = {1990}, month = {1990 Nov}, pages = {925-31}, keywords = {Behavior, Brain Chemistry, Brain Diseases, Emission-Computed, Emotions, Humans, Reference Values, Single-Photon, Tomography}, issn = {0361-803X}, author = {Wagner, H N} } @article {2463, title = {Postmetamorphic cell death in the nervous and muscular systems of Drosophila melanogaster.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {10}, year = {1990}, month = {1990 Feb}, pages = {403-1}, abstract = {

Programmed cell death occurs in the nervous and muscular system of newly emerged adult Drosophila melanogaster. Many of the abdominal muscles that were used for eclosion and wing-spreading behavior degenerate by 12 hr after eclosion. Related neurons in the ventral ganglion also die within the first 24 hr. Ligation experiments showed that the muscle breakdown is triggered by a signal from the anterior region, presumably the head, that occurs about 1 hr before adult emergence. The timing of this signal suggests that eclosion hormone may be involved. Although muscle death is triggered prior to ecdysis, it can be delayed, at least temporarily, by forcing the emerging flies to show a prolonged ecdysis behavior. In contrast to the muscles, the death of the neurons is triggered after emergence. The signal for neuronal degeneration is closely correlated with the initiation of wing inflation behavior. Ligation and digging experiments and behavioral manipulations that either blocked or delayed wing expansion behavior had a parallel effect in suppressing or delaying neuronal death.

}, keywords = {Animal, Animals, Behavior, Biological, Cell Survival, Drosophila melanogaster, Female, Ligation, Male, Metamorphosis, Muscles, Nervous System, Neurons}, issn = {0270-6474}, author = {Kimura, K I and Truman, J W} } @article {1194, title = {A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae.}, journal = {Nucleic Acids Research}, volume = {18}, year = {1990}, month = {1990 May 25}, pages = {3091-2}, keywords = {Agar Gel, Electrophoresis, Fungal, Methods, RNA, Saccharomyces cerevisiae}, issn = {0305-1048}, author = {Schmitt, M E and Brown, T A and Trumpower, B L} } @article {971, title = {Spacing differentiation in the developing Drosophila eye: a fibrinogen-related lateral inhibitor encoded by scabrous.}, journal = {Science}, volume = {250}, year = {1990}, month = {1990 Dec 7}, pages = {1370-7}, abstract = {

In the development of multicellular organisms a diversity of cell types differentiate at specific positions. Spacing patterns, in which an array of two or more cell types forms from a uniform field of cells, are a common feature of development. Identical precursor cells may adopt different fates because of competition and inhibition between them. Such a pattern in the developing Drosophila eye is the evenly spaced array of R8 cells, around which other cell types are subsequently recruited. Genetic studies suggest that the scabrous mutation disrupts a signal produced by R8 cells that inhibits other cells from also becoming R8 cells. The scabrous locus was cloned, and it appears to encode a secreted protein partly related to the beta and gamma chains of fibrinogen. It is proposed that the sca locus encodes a lateral inhibitor of R8 differentiation. The roles of the Drosophila EGF-receptor homologue (DER) and Notch genes in this process were also investigated.

}, keywords = {Alleles, Amino Acid Sequence, Animals, Cell Differentiation, DNA Transposable Elements, Drosophila, Drosophila Proteins, Epidermal Growth Factor, Eye, Fibrinogen, Glycoproteins, Humans, Molecular Sequence Data, Mosaicism, Mutation, Nucleic Acid, Phenotype, Proteins, Receptor, Sequence Homology}, issn = {0036-8075}, doi = {10.1186/gb-2007-8-7-r145}, author = {Baker, N E and Mlodzik, M and Rubin, G M} } @article {6595, title = {Topographic EEG analysis in patients with benign focal epilepsy of childhood (BFEC).}, journal = {Acta Neurologica Belgica}, volume = {90}, year = {1990}, month = {1990}, pages = {183-9}, keywords = {Cerebral Palsy, Child, Electroencephalography, Epilepsy, Humans}, issn = {0300-9009}, author = {van Huffelen, A C and van der Meij, W} } @article {1155, title = {Drosophila doublesex gene controls somatic sexual differentiation by producing alternatively spliced mRNAs encoding related sex-specific polypeptides.}, journal = {Cell}, volume = {56}, year = {1989}, month = {1989 Mar 24}, pages = {997-1010}, abstract = {

The doublesex (dsx) gene regulates somatic sexual differentiation in both sexes in D. melanogaster. Two functional products are encoded by dsx: one product is expressed in females and represses male differentiation, and the other is expressed in males and represses female differentiation. We have determined that the dsx gene is transcribed to produce a common primary transcript that is alternatively spliced and polyadenylated to yield male- and female-specific mRNAs. These sex-specific mRNAs share a common 5{\textquoteright} end and three common exons, but possess alternative sex-specific 3{\textquoteright} exons, thus encoding polypeptides with a common amino-terminal sequence but sex-specific carboxyl termini. Genetic and molecular data suggest that sequences including and adjacent to the female-specific splice acceptor site play an important role in the regulation of dsx expression by the transformer and transformer-2 loci.

}, issn = {0092-8674}, author = {Baker, B.S. and Burtis, K C} } @article {1174, title = {Flexible recognition of rapidly evolving promoter sequences by mitochondrial transcription factor 1.}, journal = {Genes \& Development}, volume = {3}, year = {1989}, month = {1989 Dec}, pages = {2202-17}, abstract = {

Transcriptional promoters of mitochondrial DNA have diverged extensively in the course of mammalian evolution. Nevertheless, the transcriptional machinery and the overall mechanisms of transcriptional control and regulation seem to be conserved. We have compared the human and murine homologs of the major DNA-binding transcriptional activator, mitochondrial transcription factor 1 (mtTF1), with unexpected results. Both proteins have similar chromatographic and transcriptional properties and are the same size. Both recognize and bind sequences between -12 and -39 within their respective homologous promoters. However, the sequences that they recognize are markedly divergent; although the base pairs they contact are situated similarly or identically with respect to the transcriptional start site, sequence identity between the two species{\textquoteright} contact points is less than 50\%. Interestingly, the two proteins are functionally interchangeable; each can bind to the heterologous light-strand promoter and can activate transcription by the heterologous mitochondrial RNA polymerase. Thus, the RNA polymerase or some as yet undetected transcription factor, rather than mTF1, may determine the strict species specificity of mitochondrial transcription. Flexible DNA sequence recognition by mtTF1, on the other hand, may be a principal facilitating mechanism for rapid control sequence evolution.

}, keywords = {Animals, Base Sequence, Chromatography, DNA, Genetic, Humans, Ion Exchange, Methylation, Mice, Mitochondrial, Molecular Sequence Data, Nucleic Acid, Promoter Regions, Sequence Homology, Transcription, Transcription Factors}, issn = {0890-9369}, doi = {10.1101/gad.1352105}, author = {Fisher, R P and Parisi, M A and Clayton, D A} } @article {972, title = {The glass gene encodes a zinc-finger protein required by Drosophila photoreceptor cells.}, journal = {Nature}, volume = {340}, year = {1989}, month = {1989 Aug 17}, pages = {531-6}, abstract = {

Null mutations of glass specifically remove photoreceptor cells, leaving other cell types intact. We have isolated the glass gene and have shown that its transcript encodes a putative protein of 604 amino acids with five zinc-fingers. The glass product may be a transcription factor required for the development of a single neuronal cell type.

}, keywords = {Animals, Base Sequence, DNA, Drosophila, Gene Expression Regulation, Molecular Sequence Data, Mutation, Photoreceptor Cells}, issn = {0028-0836}, doi = {10.1186/gb-2007-8-7-r145}, author = {Moses, K and Ellis, M C and Rubin, G M} } @article {973, title = {Molecular characterization of the Drosophila trp locus: a putative integral membrane protein required for phototransduction.}, journal = {Neuron}, volume = {2}, year = {1989}, month = {1989 Apr}, pages = {1313-23}, abstract = {

Recent studies suggest that the fly uses the inositol lipid signaling system for visual excitation and that the Drosophila transient receptor potential (trp) mutation disrupts this process subsequent to the production of IP3. In this paper, we show that trp encodes a novel 1275 amino acid protein with eight putative transmembrane segments. Immunolocalization indicates that the trp protein is expressed predominantly in the rhabdomeric membranes of the photoreceptor cells.

}, keywords = {Amino Acid Sequence, Animals, Base Sequence, Calcium Channels, DNA, Drosophila melanogaster, Drosophila Proteins, Genes, Inositol Phosphates, Insect Hormones, Insect Proteins, Membrane Proteins, Molecular Sequence Data, Photoreceptor Cells, Protein Conformation, Signal Transduction, Transient Receptor Potential Channels}, issn = {0896-6273}, doi = {10.1186/gb-2007-8-7-r145}, author = {Montell, C and Rubin, G M} } @article {1175, title = {Mouse RNAase MRP RNA is encoded by a nuclear gene and contains a decamer sequence complementary to a conserved region of mitochondrial RNA substrate.}, journal = {Cell}, volume = {56}, year = {1989}, month = {1989 Jan 13}, pages = {131-9}, abstract = {

Using complementary oligonucleotide probes, we have isolated the nuclear gene for the RNA moiety of RNAase MRP; it is present as a single copy and encodes an uncapped primary transcript of 275 nucleotides. Direct sequence analysis revealed that the 136 nucleotide RNA that copurifies with RNAase MRP represents the 3{\textquoteright} half of the 275 nucleotide primary transcript. The 5{\textquoteright}-flanking region of the gene has putative transcriptional control elements homologous to the promoters of RNA polymerase II-transcribed U-series snRNA genes; however, the coding region possesses a box A sequence and terminates at four T residues, both features characteristic of polymerase III-transcribed genes. A decamer sequence, 5{\textquoteright}-CGA-CCCCUCC-3{\textquoteright}, complementary to a conserved sequence adjacent to the enzymatic cleavage site on the mitochondrial RNA substrate, is present in the RNAase MRP RNA. Isolation of a nuclear gene for the RNA component of a mitochondrial enzyme implies that nucleic acids can be transported across mitochondrial membranes.

}, keywords = {Animals, Blotting, DNA, Endoribonucleases, Genes, Genetic, Mice, Mitochondria, Mitochondrial, Nucleic Acid, Oligonucleotide Probes, Post-Transcriptional, Ribonucleases, RNA Processing, Sequence Homology, Southern, Transcription}, issn = {0092-8674}, doi = {10.1101/gad.1352105}, author = {Chang, D D and Clayton, D A} } @article {1149, title = {The sex determination locus transformer-2 of Drosophila encodes a polypeptide with similarity to RNA binding proteins.}, journal = {Cell}, volume = {56}, year = {1989}, month = {1989 Mar 24}, pages = {1011-18}, abstract = {

The D. melanogaster transformer-2 (tra-2) gene regulates somatic sexual differentiation in females and is necessary for spermatogenesis in males. Wild-type tra-2 function is required for the female-specific splicing of the pre-mRNA of the next known gene (doublesex) downstream of tra-2 in the sex determination regulatory hierarchy. The tra-2 gene was cloned, and P element-mediated transformation was used to demonstrate that a 3.9 kb genomic fragment contains all sequences necessary for tra-2 function. A 1.7 kb transcript was shown to be the product of the tra-2 locus based on its reduced level in flies containing a tra-2 mutant allele. The sequence of a cDNA corresponding to this transcript indicates that it encodes a polypeptide with strong similarity to a family of RNA binding proteins that includes proteins found associated with hnRNPs and snRNPs, suggesting that the tra-2 product may directly regulate the processing of the double-sex pre-mRNA in females.

}, issn = {0092-8674}, author = {Baker, B.S. and Goralski, T.J. and Edstrom, J.E.} } @article {924, title = {Evaporative cooling of spin-polarized atomic hydrogen.}, journal = {Physical Review Letters}, volume = {61}, year = {1988}, month = {1988 Aug 22}, pages = {935-8}, abstract = {

A gas of hydrogen atoms, confined in a static magnetic trap, has been evaporatively cooled to temperatures of a few millikelvin. The initial trap configuration held the gas at 38 mK for as long as 5 h. Evaporative cooling reduced the temperature to 3.0 mK while maintaining the central density at 7.6{\texttimes}10\ 12\ \  cm\ -3\ \  . These values were determined by measurement of the rate of electronic spin relaxation and are in agreement with model calculations. Further cooling to 1 mK (inferred from the model) has been achieved. Measurements were made of the efficiency of the evaporative cooling process.

}, issn = {1079-7114}, author = {Masuhara, N and Doyle, JM and Sandberg, JC and Kleppner, D and Greytak, TJ and Hess, H F and Kochanski, GP} } @article {974, title = {Localization of the sevenless protein, a putative receptor for positional information, in the eye imaginal disc of Drosophila.}, journal = {Cell}, volume = {51}, year = {1987}, month = {1987 Oct 9}, pages = {143-50}, abstract = {

The Drosophila gene sevenless encodes a putative trans-membrane receptor required for the formation of one particular cell, the R7 photoreceptor, in each ommatidium of the compound eye. Mutations in this gene result in the cell normally destined to form the R7 cell forming a non-neuronal cell type instead. These observations have led to the proposal that the sevenless protein receives at least part of the positional information required for the R7 developmental pathway. We have generated antibodies specific for sevenless and have examined expression of the protein by light and electron microscopy. sevenless protein is present transiently at high levels in at least 9 cells in each developing ommatidium and is detectable several hours before any overt differentiation of R7. The protein is mostly localized at the apices of the cells, in microvilli, but is also found deeper in the tissue where certain cells contact the R8 cell. This finding suggests that R8 expresses a ligand for the sevenless protein.

}, keywords = {Animals, Drosophila melanogaster, Electron, Epithelium, Eye, Eye Proteins, Histocytochemistry, Immunologic Techniques, Insect Hormones, Microscopy, Microvilli, Peptide Fragments, Photoreceptor Cells}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Tomlinson, A and Bowtell, D D and Hafen, E and Rubin, G M} } @article {1178, title = {A mammalian mitochondrial RNA processing activity contains nucleus-encoded RNA.}, journal = {Science}, volume = {235}, year = {1987}, month = {1987 Mar 6}, pages = {1178-84}, abstract = {

Ribonuclease mitochondrial RNA processing, a site-specific endoribonuclease involved in primer RNA metabolism in mammalian mitochondria, requires an RNA component for its activity. On the basis of copurification and selective inactivation with complementary oligonucleotides, a 135-nucleotide RNA species, not encoded in the mitochondrial genome, is identified as the RNA moiety of the endoribonuclease. This finding implies transport of a nucleus-encoded RNA, essential for organelle DNA replication, to the mitochondrial matrix.

}, keywords = {Animals, Base Sequence, Cell Nucleus, Chemical Phenomena, Chemistry, Drug Resistance, Endonucleases, Enzyme Activation, Genetic Code, Humans, Mammals, Micrococcal Nuclease, Mitochondria, Oligonucleotides, Organoids, Ribonucleases, RNA, Subcellular Fractions}, issn = {0036-8075}, doi = {10.1101/gad.1352105}, author = {Chang, D D and Clayton, D A} } @article {1148, title = {A molecular analysis of transformer, a gene in Drosophila that controls female sexual differentiation.}, journal = {Cell}, volume = {48}, year = {1987}, month = {1987 Feb}, pages = {489-99}, abstract = {

The transformer (tra) gene regulates all aspects of somatic sexual differentiation in Drosophila melanogaster females and has no function in males. We have isolated the tra gene as part of a 200 kb chromosomal walk. The 25 kb region around tra contains four genetically identified complementation groups and at least six transcriptional units. Germ-line transformation experiments indicate that a fragment of 2 kb is sufficient to supply tra+ function. Mapping of cDNAs from tra and from the adjacent genes indicates that the tra+ transcription unit is 1.2 kb or less. This transcription unit gives rise to a 1.0 kb RNA that is female-specific and a 1.2 kb RNA that is present in both sexes. tra+ and the gene at the 3{\textquoteright} side overlap slightly in the 3{\textquoteright} ends of their RNA coding sequences. These results suggest that tra+ function is regulated at the level of production of the female-specific tra RNA. The fact that a tra transcript is found in males raises interesting possibilities for how tra expression is controlled.

}, issn = {0092-8674}, author = {Baker, B.S. and McKeown, M. and Belote, J.M.} } @article {2464, title = {Postembryonic neurogenesis in the CNS of the tobacco hornworm, Manduca sexta. I. Neuroblast arrays and the fate of their progeny during metamorphosis.}, journal = {The Journal of Comparative Neurology}, volume = {255}, year = {1987}, month = {1987 Jan 22}, pages = {548-59}, abstract = {

The tobacco hornworm Manduca sexta exhibits dramatic changes in its body morphology and behavior as it is transformed from a larva into an adult during metamorphosis. Accompanying these changes is an extensive reorganization of this moth{\textquoteright}s central nervous system (CNS), which involves both the death and remodeling of subsets of larval neurons. We report here that the segmental ganglia of the larvae also contain a stereotyped array of identifiable neuronal stem cells (neuroblasts) that contribute over 2,000 cells to each thoracic ganglion and about 40-80 cells to each abdominal ganglion. The distribution of these neuroblasts varies in a segment specific manner. Dormant neuroblasts are found adjacent to the neuropil in late embryos and early first instar larvae. After the molt to the second instar, these cells enlarge and begin to divide. Through a series of asymmetrical divisions, each neuroblast generates a discrete nest of 10-90 progeny by the end of larval life. These progeny (the imaginal nest cells) are developmentally arrested at an early stage of differentiation and remain so until metamorphosis. At the onset of metamorphosis, a wave of cell death sweeps through the nests, the extent of the death being much greater within the abdominal nests than in the thoracic nests. The surviving imaginal nest cells then differentiate to become functional neurons that are incorporated into the adult CNS.

}, keywords = {Animals, Biological, Cell Division, Central Nervous System, Larva, Lepidoptera, Metamorphosis, Moths, Neurons}, issn = {0021-9967}, doi = {10.1002/cne.902550407}, author = {Booker, R and Truman, J W} } @article {1177, title = {Promoter selection in human mitochondria involves binding of a transcription factor to orientation-independent upstream regulatory elements.}, journal = {Cell}, volume = {50}, year = {1987}, month = {1987 Jul 17}, pages = {247-58}, abstract = {

Selective transcription of human mitochondrial DNA requires a transcription factor (mtTF) in addition to an essentially nonselective RNA polymerase. Partially purified mtTF is able to sequester promoter-containing DNA in preinitiation complexes in the absence of mitochondrial RNA polymerase, suggesting a DNA-binding mechanism for factor activity. Functional domains, required for positive transcriptional regulation by mtTF, are identified within both major promoters of human mtDNA through transcription of mutant promoter templates in a reconstituted in vitro system. These domains are essentially coextensive with DNA sequences protected from nuclease digestion by mtTF-binding. Comparison of the sequences of the two mtTF-responsive elements reveals significant homology only when one sequence is inverted; the binding sites are in opposite orientations with respect to the predominant direction of transcription. Thus mtTF may function bidirectionally, requiring additional protein-DNA interactions to dictate transcriptional polarity. The mtTF-responsive elements are arrayed as direct repeats, separated by approximately 80 bp within the displacement-loop region of human mitochondrial DNA; this arrangement may reflect duplication of an ancestral bidirectional promoter, giving rise to separate, unidirectional promoters for each strand.

}, keywords = {DNA, DNA-Directed RNA Polymerases, Genes, Genetic, Humans, KB Cells, Mitochondria, Mitochondrial, Promoter Regions, Regulator, Templates, Transcription, Transcription Factors}, issn = {0092-8674}, doi = {10.1101/gad.1352105}, author = {Fisher, R P and Topper, J N and Clayton, D A} } @article {975, title = {Sevenless, a cell-specific homeotic gene of Drosophila, encodes a putative transmembrane receptor with a tyrosine kinase domain.}, journal = {Science}, volume = {236}, year = {1987}, month = {1987 Apr 3}, pages = {55-63}, abstract = {

The determination of cell fates during the assembly of the ommatidia in the compound eye of Drosophila appears to be controlled by cell-cell interactions. In this process, the sevenless gene is essential for the development of a single type of photoreceptor cell. In the absence of proper sevenless function the cells that would normally become the R7 photoreceptors instead become nonneuronal cells. Previous morphological and genetic analysis has indicated that the product of the sevenless gene is involved in reading or interpreting the positional information that specifies this particular developmental pathway. The sevenless gene has now been isolated and characterized. The data indicate that sevenless encodes a transmembrane protein with a tyrosine kinase domain. This structural similarity between sevenless and certain hormone receptors suggests that similar mechanisms are involved in developmental decisions based on cell-cell interaction and physiological or developmental changes induced by diffusible factors.

}, keywords = {Amino Acid Sequence, Animals, Base Sequence, Cell Surface, Chromosome Mapping, Cloning, DNA Restriction Enzymes, Drosophila melanogaster, Eye, Gene Expression Regulation, Genes, Genetic, Growth Substances, Homeobox, Membrane Proteins, Molecular, Phenotype, Protein-Tyrosine Kinases, Receptors, Transcription}, issn = {0036-8075}, doi = {10.1186/gb-2007-8-7-r145}, author = {Hafen, E and Basler, K and Edstroem, J E and Rubin, G M} } @article {1176, title = {Yeast mitochondrial RNA polymerase is homologous to those encoded by bacteriophages T3 and T7.}, journal = {Cell}, volume = {51}, year = {1987}, month = {1987 Oct 9}, pages = {89-99}, abstract = {

Analysis of the nucleotide sequence of the genetic locus for yeast mitochondrial RNA polymerase (RPO41) reveals a continuous open reading frame with the coding potential for a polypeptide of 1351 amino acids, a size consistent with the electrophoretic mobility of this enzymatic activity. The transcription product from this gene spans the singular reading frame. In vivo transcript abundance reflects codon usage and growth under stringent conditions for mitochondrial biogenesis and function results in a several fold higher level of gene expression than growth under glucose repression. A comparison of the yeast mitochondrial RNA polymerase amino acid sequence to those of E. coli RNA polymerase subunits failed to demonstrate any regions of homology. Interestingly, the mitochondrial enzyme is highly homologous to the DNA-directed RNA polymerases of bacteriophages T3 and T7, especially in regions most highly conserved between the T3 and T7 enzymes themselves.

}, keywords = {Amino Acid Sequence, Base Sequence, DNA, DNA-Directed RNA Polymerases, Escherichia coli, Genetic, Mitochondria, Molecular Sequence Data, Nucleic Acid, Saccharomyces cerevisiae, Sequence Homology, T-Phages, Transcription}, issn = {0092-8674}, doi = {10.1101/gad.1352105}, author = {Masters, B S and Stohl, L L and Clayton, D A} } @article {1179, title = {DNA primase of human mitochondria is associated with structural RNA that is essential for enzymatic activity.}, journal = {Cell}, volume = {45}, year = {1986}, month = {1986 Jun 20}, pages = {817-25}, abstract = {

DNA primase isolated from human mitochondria sediments in glycerol density gradients at 30S and 70S. These unusually high sedimentation coefficients are a result of association of the primase activity with RNA. Treatment of primase with nuclease not only affects its sedimentation behavior, but also inactivates the primase activity. The major RNA species that cofractionates with primase activity is shown by direct sequence analysis to be cytosolic 5.8S ribosomal RNA (rRNA). Specific degradation of endogenous 5.8S rRNA using ribonuclease H and oligonucleotides complementary to 5.8S rRNA results in reduction of primase activity. Other small RNAs may play a structural role in the formation of an active DNA primase complex.

}, keywords = {Centrifugation, Density Gradient, DNA, DNA Primase, Endoribonucleases, Humans, Micrococcal Nuclease, Mitochondria, Mitochondrial, Ribonuclease H, Ribosomal, RNA, RNA Nucleotidyltransferases}, issn = {0092-8674}, doi = {10.1101/gad.1352105}, author = {Wong, T W and Clayton, D A} } @article {2465, title = {Endocrine regulation of the form and function of axonal arbors during insect metamorphosis.}, journal = {The Journal of Neuroscienc : The Official Journal of the Society for Neuroscience}, volume = {6}, year = {1986}, month = {1986 Jan}, pages = {293-9}, abstract = {

By discrete manipulation of the endocrine cues that control insect metamorphosis, it has been possible to examine the mechanisms governing the growth of neural processes during development. During the transition from larva to pupa in the hawkmoth, Manduca sexta, identified sensory neurons reorganize their central projections to evoke a new behavior{\textendash}the gintrap reflex. Topical application of a juvenile hormone analog to the peripheral cell bodies of these sensory neurons during a critical period of development caused them to retain their larval commitment rather than undergo pupal development with the rest of the animal. The sensory neurons retained the larval arborization pattern within the pupal CNS and were unable to evoke the gin-trap reflex. Thus, the hormonal environment of the cell body is critical for controlling growth and synapse formation by distant axonal processes.

}, keywords = {Animal, Animals, Axons, Behavior, Biological, Cobalt, Juvenile Hormones, Larva, Lepidoptera, Metamorphosis, Moths, Neurons}, issn = {0270-6474}, author = {Levine, R B and Truman, J W and Linn, D and Bate, C M} } @article {2723, title = {An O(ND) difference algorithm and its variations.}, journal = {Algorithmica}, volume = {1}, year = {1986}, month = {1986 Nov}, pages = {251-66}, abstract = {

The problems of finding a longest common subsequence of two sequences A and B and a shortest edit script for transforming A into B have long been known to be dual problems. In this paper, they are shown to be equivalent to finding a shortest/longest path in an edit graph. Using this perspective, a simple O(ND) time and space algorithm is developed where N is the sum of the lengths of A and B and D is the size of the minimum edit script for A and B. The algorithm performs well when differences are small (sequences are similar) and is consequently fast in typical applications. The algorithm is shown to have O(N +D expected-time performance under a basic stochastic model. A refinement of the algorithm requires only O(N) space, and the use of suffix trees leads to an O(NlgN +D ) time variation.

}, author = {Myers, Eugene} } @article {976, title = {Tissue specificity of Drosophila P element transposition is regulated at the level of mRNA splicing.}, journal = {Cell}, volume = {44}, year = {1986}, month = {1986 Jan 17}, pages = {7-19}, abstract = {

We show that the germline specificity of P element transposition is controlled at the level of mRNA splicing and not at the level of transcription. In the major P element RNA transcript, isolated from somatic cells, the first three open reading frames are joined by the removal of two introns. Using in vitro mutagenesis and genetic analysis we demonstrate the existence of a third intron whose removal is required for transposase production. We propose that this intron is only removed in the germline and that its removal is the sole basis for the germline restriction of P element transposition.

}, keywords = {Animals, Base Sequence, Cricetinae, DNA Transposable Elements, Drosophila melanogaster, Gene Expression Regulation, Genetic, Heat-Shock Proteins, Messenger, Nucleotidyltransferases, Organ Specificity, Promoter Regions, RNA, RNA Splicing, Transcription, Transposases}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Laski, F A and Rio, D C and Rubin, G M} } @article {1180, title = {In vitro replication of human mitochondrial DNA: accurate initiation at the origin of light-strand synthesis.}, journal = {Cell}, volume = {42}, year = {1985}, month = {1985 Oct}, pages = {951-8}, abstract = {

Synthesis of human light-strand mitochondrial DNA was accomplished in vitro using DNA primase, DNA polymerase, and other accessory proteins isolated from human mitochondria. Replication begins with the synthesis of primer RNA on a T-rich sequence in the origin stem-loop structure of the template DNA and absolutely requires ATP. A transition from RNA synthesis to DNA synthesis occurs near the base of the stem-loop structure and a potential recognition site for signaling that transition has been identified. The start sites of the in vitro products were mapped at the nucleotide level and were found to be in excellent agreement with those of in vivo nascent light-strand DNA. Isolated human mitochondrial enzymes recognize and utilize the bovine, but not the mouse, origin of light-strand replication.

}, keywords = {Animals, Base Sequence, Cattle, Cloning, DNA, DNA Replication, DNA Restriction Enzymes, Genetic, Humans, KB Cells, Macromolecular Substances, Mitochondrial, Molecular, Nucleic Acid Conformation, Templates}, issn = {0092-8674}, doi = {10.1101/gad.1352105}, author = {Wong, T W and Clayton, D A} } @article {977, title = {Isolation and structure of a rhodopsin gene from D. melanogaster.}, journal = {Cell}, volume = {40}, year = {1985}, month = {1985 Apr}, pages = {851-8}, abstract = {

Using a novel method for detecting cross-homologous nucleic acid sequences we have isolated the gene coding for the major rhodopsin of Drosophila melanogaster and mapped it to chromosomal region 92B8-11. Comparison of cDNA and genomic DNA sequences indicates that the gene is divided into five exons. The amino acid sequence deduced from the nucleotide sequence is 373 residues long, and the polypeptide chain contains seven hydrophobic segments that appear to correspond to the seven transmembrane segments characteristic of other rhodopsins. Three regions of Drosophila rhodopsin are highly conserved with the corresponding domains of bovine rhodopsin, suggesting an important role for these polypeptide regions.

}, keywords = {Amino Acid Sequence, Animals, Base Sequence, Cattle, Chromosome Mapping, DNA, Drosophila melanogaster, Genes, Messenger, Nucleic Acid Hybridization, Poly A, Retinal Pigments, Rhodopsin, RNA, Tissue Distribution}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Zuker, C S and Cowman, A F and Rubin, G M} } @article {1182, title = {Replication priming and transcription initiate from precisely the same site in mouse mitochondrial DNA.}, journal = {The EMBO Journal}, volume = {4}, year = {1985}, month = {1985 Jun}, pages = {1559-67}, abstract = {

Mammalian mitochondrial DNA maintains a novel displacement-loop region containing the major sites of transcriptional initiation and the origin of heavy strand DNA replication. Because the exact map positions of the 5{\textquoteright} termini of nascent mouse displacement-loop strands are known, it is possible to examine directly a potential relationship between replication priming and transcription. Analyses of in vivo nucleic acids complementary to the displacement-loop region reveal two species with identical 5{\textquoteright} ends at map position 16 183. One is entirely RNA and the other is RNA covalently linked to DNA. In the latter the transition from RNA to DNA is sharp, occurring near or within a series of previously identified conserved sequences 74-163 nucleotides downstream from the transcriptional initiation site. These data suggest that the initial events in replication priming and transcription are the same and that the decision to synthesize DNA or RNA is a downstream event under the control of short, conserved displacement-loop template sequences.

}, keywords = {Animals, Base Sequence, Chromosome Mapping, DNA, DNA Replication, Genetic, Mice, Mitochondrial, Operon, Ribonucleases, RNA, Transcription}, issn = {0261-4189}, doi = {10.1101/gad.1352105}, author = {Chang, D D and Hauswirth, W W and Clayton, D A} } @article {1147, title = {Sex-specific regulation of yolk protein gene expression in Drosophila.}, journal = {Cell}, volume = {40}, year = {1985}, month = {1985 Feb}, pages = {339-48}, abstract = {

Many of the genes in the regulatory hierarchy controlling sex determination in Drosophila melanogaster are known. Here we examine how this regulatory hierarchy controls the expression of the structural genes encoding the female-specific yolk polypeptides. Temperature shift experiments with a temperature-sensitive allele of the sex determination regulatory gene transformer-2 (tra-2) showed that tra-2+ function is required in the adult for both the sex-specific initiation and maintenance of YP synthesis. Control of the YP genes by this regulatory hierarchy is at the level of transcription, or transcript stability. The results of temperature shift experiments with abdomens isolated from tra-2ts homozygotes support the notion that the tra-2+ function acts in a cell-autonomous manner to control YP synthesis. These results provide a paradigm for the way this regulatory hierarchy controls the terminal differentiation functions for sexually dimorphic development.

}, issn = {0092-8674}, author = {Baker, B.S. and Belote, J.M. and Handler, A.M. and Wolfner, M.F. and Livak, K.J.} } @article {1181, title = {A transcription factor required for promoter recognition by human mitochondrial RNA polymerase. Accurate initiation at the heavy- and light-strand promoters dissected and reconstituted in vitro.}, journal = {The Journal of Biological Chemistry}, volume = {260}, year = {1985}, month = {1985 Sep 15}, pages = {11330-8}, abstract = {

Faithful transcription of human mitochondrial DNA has been reproduced in vitro, using a fraction of mitochondrial proteins capable of accurate initiation at both the heavy- and light-strand promoters. Here we report the initial dissection of this system into two nonfunctional components which, upon mixing, reconstitute promoter-specific transcriptional capacity in vitro. One of these components copurifies with the major nonspecific RNA polymerase activity, suggesting its identity. The other component lacks significant polymerase activity, but contains a protein or proteins required for accurate initiation at the two individual promoters by isolated mitochondrial RNA polymerase. This factor facilitates specific transcription, but has little or no effect on nonspecific transcription of a synthetic copolymer (poly(dA-dT)), indicating a positive role in proper promoter recognition. The transcription factor markedly stimulates light-strand transcription, but only moderately enhances transcription initiation at the heavy-strand promoter, suggesting different or additional factor requirements for heavy-strand transcription. These requirements may reflect the functional differences between heavy- and light-strand transcription in vivo and, in particular, the role of the light-strand promoter in priming of heavy-strand DNA replication.

}, keywords = {Carcinoma, Cell Line, DNA-Directed RNA Polymerases, Genetic, Humans, Kinetics, Messenger, Mitochondria, Mouth Neoplasms, Promoter Regions, RNA, Templates, Transcription, Transcription Factors}, issn = {0021-9258}, doi = {10.1101/gad.1352105}, author = {Fisher, R P and Clayton, D A} } @article {978, title = {Analysis of P transposable element functions in Drosophila.}, journal = {Cell}, volume = {38}, year = {1984}, month = {1984 Aug}, pages = {135-46}, abstract = {

We have made a P-element derivative called Pc[ry], which carries the selectable marker gene rosy, but which acts like a nondefective, intact P element. It transposes autonomously into the germline chromosomes of an M-strain Drosophila embryo and it mobilizes in trans the defective P elements of the singed-weak allele. Frameshift mutations introduced into any of the four major open reading frames of the P sequence were each sufficient to eliminate the transposase activity, but none affected signals required in cis for transposition of the element. Complementation tests between pairs of mutant elements suggest that a single polypeptide comprises the transposase. We have examined transcripts of P elements both from natural P strains and from lines containing only nondefective Pc[ry] elements, and have identified two RNA species that appear to be specific for autonomous elements.

}, keywords = {Alleles, Animals, Base Sequence, Crosses, DNA Restriction Enzymes, DNA Transposable Elements, Drosophila, Female, Genes, Genetic, Genetic Complementation Test, Male, Mutation, Nucleic Acid Hybridization}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Karess, R E and Rubin, G M} } @article {1183, title = {Precise identification of individual promoters for transcription of each strand of human mitochondrial DNA.}, journal = {Cell}, volume = {36}, year = {1984}, month = {1984 Mar}, pages = {635-43}, abstract = {

The major site of in vivo transcriptional initiation for both heavy and light strands of human mitochondrial DNA is the displacement-loop region. Transcripts synthesized in vitro by human mitochondrial RNA polymerase were mapped to the nucleotide level and have identical 5{\textquoteright} end map positions to those reported for in vivo primary transcripts. An ordered series of deletion clones, whose template sequences were truncated at either the 5{\textquoteright} or 3{\textquoteright} end, was used to identify the precise mitochondrial DNA sequence required for initiation of transcription. The data provide a definitive assignment of the promoter for heavy-strand transcription occurring within -16 to +7 of the transcriptional start site 16 nucleotides upstream of the 5{\textquoteright} end of the gene for tRNAPhe and of the promoter for light-strand transcription occurring within -28 to +16 of the transcriptional start site at the 5{\textquoteright} end of "7S RNA." Within each control sequence is a candidate promoter whose consensus sequence is 5{\textquoteright}-CANACC(G)CC(A)AAAGAPyA-3{\textquoteright} and in both cases transcriptional initiation occurs within six to eight nucleotides of the 3{\textquoteright} end of this sequence. The transcriptional start site is an integral part of each promoter and each promoter can function in the absence of the other.

}, keywords = {Chromosome Deletion, Chromosome Mapping, DNA, DNA-Directed RNA Polymerases, Genes, Genetic, Humans, Mitochondrial, Operon, Regulator, RNA, Transcription, Transfer}, issn = {0092-8674}, doi = {10.1101/gad.1352105}, author = {Chang, D D and Clayton, D A} } @article {979, title = {The effect of chromosomal position on the expression of the Drosophila xanthine dehydrogenase gene.}, journal = {Cell}, volume = {34}, year = {1983}, month = {1983 Aug}, pages = {47-57}, abstract = {

Thirty-six isogenic D. melanogaster strains that differed only in the chromosomal location of a 7.2 or an 8.1 kb DNA segment containing the (autosomal) rosy gene were constructed by P-element-mediated gene transfer. Since the flies were homozygous for a rosy- allele, rosy gene function in these indicated the influence of flanking sequences on gene expression. The tissue distribution of XDH activity in all the strains was normal. Each line exhibited a characteristic level of adult XDH-specific activity. The majority of these values were close to wild-type levels; however, the total variation in specific activity among the lines was nearly fivefold. Thus position effects influence expression of the rosy gene quantitatively but do not detectably alter tissue specificity. X-linked rosy insertions were expressed on average 1.6 times more activity in males than in females. Hence the gene acquires at least partial dosage compensation upon insertion into the X chromosome.

}, keywords = {Animals, Chromosomes, DNA Transposable Elements, Dosage Compensation, Drosophila melanogaster, Female, Gene Expression Regulation, Genetic, Ketone Oxidoreductases, Tissue Distribution, Transformation, X Chromosome, Xanthine Dehydrogenase}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Spradling, A C and Rubin, G M} } @article {1146, title = {Sex determination and dosage compensation in melanogaster.}, journal = {Annual Review of Genetics}, volume = {17}, year = {1983}, month = {1983 Dec}, pages = {345-93}, author = {Baker, B.S. and Belote, J.M.} } @article {980, title = {Genetic transformation of Drosophila with transposable element vectors.}, journal = {Science}, volume = {218}, year = {1982}, month = {1982 Oct 22}, pages = {348-53}, abstract = {

Exogenous DNA sequences were introduced into the Drosophila germ line. A rosy transposon (ry1), constructed by inserting a chromosomal DNA fragment containing the wild-type rosy gene into a P transposable element, transformed germ line cells in 20 to 50 percent of the injected rosy mutant embryos. Transformants contained one or two copies of chromosomally integrated, intact ry1 that were stably inherited in subsequent generations. These transformed flies had wild-type eye color indicating that the visible genetic defect in the host strain could be fully and permanently corrected by the transferred gene. To demonstrate the generality of this approach, a DNA segment that does not confer a recognizable phenotype on recipients was also transferred into germ line chromosomes.

}, keywords = {Animals, Chromosome Mapping, DNA Transposable Elements, Drosophila, Genes, Genetic, Genetic Engineering, Mutation, Nucleic Acid Hybridization, Plasmids, Transformation, Xanthine Dehydrogenase}, issn = {0036-8075}, doi = {10.1186/gb-2007-8-7-r145}, author = {Rubin, G M and Spradling, A C} } @article {981, title = {The molecular basis of P-M hybrid dysgenesis: the role of the P element, a P-strain-specific transposon family.}, journal = {Cell}, volume = {29}, year = {1982}, month = {1982 Jul}, pages = {995-1004}, abstract = {

We have shown previously that four of five white mutant alleles arising in P-M dysgenic hybrids result from the insertion of strongly homologous DNA sequence elements. We have named these P elements. We report that P elements are present in 30-50 copies per haploid genome in all P strains examined and apparently are missing entirely from all M strains examined, with one exception. Furthermore, members of the P family apparently transpose frequently in P-M dysgenic hybrids; chromosomes descendant from P-M dysgenic hybrids frequently show newly acquired P elements. Finally, the strain-specific breakpoint hotspots for the rearrangement of the pi 2 P X chromosome occurring in P-M dysgenic hybrids are apparently sites of residence of P elements. These observations strongly support the P factor hypothesis for the mechanistic basis of P-M hybrid dysgenesis.

}, keywords = {Base Sequence, Biological Evolution, DNA Transposable Elements, Drosophila, Female, Gene Expression Regulation, Genetic, Hybridization, Infertility, Male, Nucleic Acid, Recombination, Repetitive Sequences}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Bingham, P M and Kidwell, M G and Rubin, G M} } @article {1145, title = {Sex determination in Drosophila melanogaster: analysis of transformer-2 , a sex-transforming locus.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {79}, year = {1982}, month = {1982 Mar}, pages = {1568-72}, abstract = {

The transformer-2 (tra-2) locus is one of a set of regulatory loci that control sex determination in Drosophila melanogaster. Temperature-shift experiments with temperature-sensitive tra-2 mutants demonstrate that within single cell lineages tra-2+ function is required at several times, and probably continuously, during development for the occurrence of a series of determinative decisions necessary for female sexual differentiation. Analysis of the effects of tra-2 in the genital disc demonstrates that the tra-2+ function is necessary in females both to prevent male sexual differentiation and to permit female differentiation. These and other results support the model that the tra-2+ and tra+ loci act to control the expression of the bifunctional doublesex (dsx) locus.

}, issn = {0027-8424}, author = {Baker, B.S. and Belote, J.M.} } @article {982, title = {Cloning of DNA sequences from the white locus of D. melanogaster by a novel and general method.}, journal = {Cell}, volume = {25}, year = {1981}, month = {1981 Sep}, pages = {693-704}, abstract = {

We describe the isolation of a cloned DNA segment carrying unique sequences from the white locus of Drosophila melanogaster. Sequences within the cloned segment are shown to hybridize in situ to the white locus region on the polytene chromosomes of both wild-type strains and strains carrying chromosomal rearrangements whose breakpoints bracket the white locus. We further show that two small deficiency mutations, deleting white locus genetic elements but not those of complementation groups contiguous to white, delete the genomic sequences corresponding to a portion of the cloned segment. The strategy we have employed to isolate this cloned segment exploits the existence of an allele at the white locus containing a copy of a previously cloned transposable, reiterated DNA sequence element. We describe a simple, rapid method for retrieving cloned segments carrying a copy of the transposable element together with contiguous sequences corresponding to this allele. The strategy described is potentially general and we discuss its application to the cloning of the DNA sequences of other genes in Drosophila, including those identified only by genetic analysis and for which no RNA product is known.

}, keywords = {Animals, Bacteriophage lambda, Chromosome Mapping, Cloning, DNA Transposable Elements, Drosophila melanogaster, Genes, Genetic Linkage, Molecular, Nucleic Acid, Nucleic Acid Hybridization, Repetitive Sequences}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Bingham, P M and Levis, R and Rubin, G M} } @article {2518, title = {Pheromone binding and inactivation by moth antennae.}, journal = {Nature}, volume = {293}, year = {1981}, month = {1981 Sep 10-16}, pages = {161-3}, abstract = {

The antennae of male silk moths are extremely sensitive to the female sex pheromone such that a male moth can find a female up to 4.5 km away. This remarkable sensitivity is due to both the morphological and biochemical design of these antennae. Along the branches of the plumose antennae are the sensilla trichodea, each consisting of a hollow cuticular hair containing two unbranched dendrites bathed in a fluid, the receptor lymph ,3. The dendrites and receptor lymph are isolated from the haemolymph by a barrier of epidermal cells which secreted the cuticular hair. Pheromone molecules are thought to diffuse down 100 A-wide pore tubules through the cuticular wall and across the receptor lymph space to receptors located in the dendritic membrane. To prevent the accumulation of residual stimulant and hence sensory adaptation, the pheromone molecules are subsequently inactivated in an apparent two-step process of rapid {\textquoteright}early inactivation{\textquoteright} followed by much slower enzymatic degradation. The biochemistry involved in this sequence of events is largely unknown. We report here the identification of three proteins which interact with the pheromone of the wild silk moth Antheraea polyphemus: a pheromone-binding protein and a pheromone-degrading esterase, both uniquely located in the pheromone-sensitive sensilla; and a second esterase common to all cuticular tissues except the sensilla.

}, keywords = {Animal Structures, Animals, Bombyx, Esterases, Extremities, Female, Insect Proteins, Male, Protein Binding, Sex Attractants, Substrate Specificity, Tissue Extracts}, issn = {0028-0836}, author = {Vogt, R G and Riddiford, L M} } @article {1184, title = {Sequence and gene organization of mouse mitochondrial DNA.}, journal = {Cell}, volume = {26}, year = {1981}, month = {1981 Oct}, pages = {167-80}, abstract = {

The complete sequence of the 16,295 bp mouse L cell mitochondrial DNA genome has been determined. Genes for the 12S and 16S ribosomal RNAs; 22 tRNAs; cytochrome c oxidase subunits I, II and III; ATPase subunit 6; cytochrome b; and eight unidentified proteins have been located. The genome displays exceptional economy of organization, with tRNA genes interspersed between rRNA and protein-coding genes with zero or few noncoding nucleotides between coding sequences. Only two significant portions of the genome, the 879 nucleotide displacement-loop region containing the origin of heavy-strand replication and the 32 nucleotide origin of light-strand replication, do not encode a functional RNA species. All of the remaining nucleotide sequence serves as a defined coding function, with the exception of 32 nucleotides, of which 18 occur at the 5{\textquoteright} ends of open reading frames. Mouse mitochondrial DNA is unique in that the translational start codon is AUN, with any of the four nucleotides in the third position, whereas the only translational stop codon is the orthodox UAA. The mouse mitochondrial DNA genome is highly homologous in overall sequence and in gene organization to human mitochondrial DNA, with the descending order of conserved regions being tRNA genes; origin of light-strand replication; rRNA genes; known protein-coding genes; unidentified protein-coding genes; displacement-loop region.

}, keywords = {Animals, Base Sequence, Chromosome Mapping, Codon, Cytochromes, DNA, Genes, L Cells (Cell Line), Mice, Mitochondrial, NADH Dehydrogenase, Protein Biosynthesis, Ribosomal, RNA, Transfer}, issn = {0092-8674}, doi = {10.1101/gad.1352105}, author = {Bibb, M J and Van Etten, R A and Wright, C T and Walberg, M W and Clayton, D A} } @article {1144, title = {On the action of major loci affecting sex determination in Drosophila melanogaster.}, journal = {Genetics}, volume = {94}, year = {1980}, month = {1980 Feb}, pages = {383-423}, abstract = {

Sex determination in Drosophila melanogaster is under the control of the X chromosome:autosome ratio and at least four major regulatory genes: transformer (tra), transformer-2 (tra-2), doublesex (dsx) and intersex (ix). Attention is focused here on the roles of these four loci in sex determination. By examining the sexual phenotype of clones of homozygous mutant cells produced by mitotic recombination in flies heterozygous for a given recessive sex-determination mutant, we have shown that the tra, tra-2 and dsx loci determine sex in a cell-autonomous manner. The effect of removing the wild-type allele of each locus (by mitotic recombination) at a number of times during development has been used to determine when the wild-type alleles of the tra, tra-2 and dsx loci have been transcribed sufficiently to support normal sexual development. The wild-type alleles of all three loci are needed into the early pupal period for normal sex determination in the cells that produce the sexually dimorphic (in pigmentation) cuticle of the fifth and sixth dorsal abdominal segments. tra(+) and tra-2(+) cease being needed shortly before the termination of cell division in the abdomen, whereas dsx(+) is required at least until the end of division. By contrast, in the foreleg, the wild-type alleles of tra(+) and tra-2(+) have functioned sufficiently for normal sexual differentiation to occur by about 24 to 48 hours before pupariation, but dsx(+) is required in the foreleg at least until pupariation.--A comparison of the phenotypes produced in mutant/deficiency and homozygous mutant-bearing flies shows that dsx, tra-2 and tra mutants result in a loss of wild-type function and probably represent null alleles at these genes.-All possible homozygous doublemutant combinations of ix, tra-2 and dsx have been constructed and reveal a clear pattern of epistasis: dsx \> tra, tra-2 \> ix. We conclude that these genes function in a single pathway that determines sex. The data suggest that these mutants are major regulatory loci that control the batteries of genes necessary for the development of many, and perhaps all, secondary sexual characteristics.-The striking similarities between the properties of these loci and those of the homeotic loci that determine segmental and subsegmental specialization during development suggest that the basic mechanisms of regulation are the same in the two situations. The phenotypes and interactions of these sex-determination mutants provide the basis for the model of how the wild-type alleles of these loci act together to effect normal sex determination. Implications of these observations for the function of other homeotic loci are discussed.

}, issn = {0016-6731}, author = {Baker, B.S. and Ridge, K.} } @article {983, title = {Transposition of elements of the 412, copia and 297 dispersed repeated gene families in Drosophila.}, journal = {Cell}, volume = {17}, year = {1979}, month = {1979 Jun}, pages = {415-27}, abstract = {

The stability of elements of three different dispersed repeated gene families in the genome of Drosophila tissue culture cells has been examined. Different amounts of sequences homologous to elements of 412, copia and 297 dispersed repeated gene families are found in the genomes of D. melanogaster embryonic and tissue culture cells. In general the amount of these sequences is increased in the cell lines. The additional sequences homologous to 412, copia and 297 occur as intact elements and are dispersed to new sites in the cell culture genome. It appears that these elements can insert at many alternative sites. We also describe a DNA sequence arrangement found in the D. melanogaster embryo genome which appears to result from a transposition of an element of the copia dispersed repeated gene family into a new chromosomal site. The mechanism of insertion of this copia element is precise to within 90 bp and may involve a region of weak sequence homology between the site of insertion and the direct terminal repeats of the copia element.

}, keywords = {Animals, Base Sequence, Cells, Cultured, DNA, DNA Restriction Enzymes, Drosophila melanogaster, Genes, Genetic, Nucleic Acid Hybridization, Translocation}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Potter, S S and Brorein, W J and Dunsmuir, P and Rubin, G M} } @article {2466, title = {Dendritic reorganization of an identified motoneuron during metamorphosis of the tobacco hornworm moth.}, journal = {Science}, volume = {192}, year = {1976}, month = {1976 Apr 30}, pages = {477-9}, abstract = {

In the tobacco hornworm, many larval motoneurons become respecified and supply new muscles in the adult. Changes in the morphology of one such neuron were examined through metamorphosis. The dendritic pattern of the adult comes about both by outgrowth from the primary and secondary branches of the larval neuron and by the development of new branches that are unique to the adult.

}, keywords = {Age Factors, Animals, Biological, Cell Differentiation, Dendrites, Larva, Lepidoptera, Male, Metamorphosis, Moths, Motor Neurons, Pupa}, issn = {0036-8075}, author = {Truman, J W and Reiss, S E} } @article {2519, title = {Hormonal control of insect epidermal cell commitment in vitro.}, journal = {Nature}, volume = {259}, year = {1976}, month = {1976 Jan 15}, pages = {115-7}, keywords = {Age Factors, Animals, Cell Differentiation, Ecdysone, Insect Hormones, Invertebrate Hormones, Juvenile Hormones, Larva, Lepidoptera, Moths, Pupa, Skin}, issn = {0028-0836}, author = {Riddiford, L M} } @article {984, title = {The nucleotide sequence of Saccharomyces cerevisiae 5.8 S ribosomal ribonucleic acid.}, journal = {The Journal of Biological Chemistry}, volume = {248}, year = {1973}, month = {1973 Jun 10}, pages = {3860-75}, keywords = {Autoradiography, Base Sequence, Chemical Phenomena, Chemistry, Coliphages, Drug Stability, Electrophoresis, Models, Oligonucleotides, Pancreas, Phosphorus Isotopes, Polyacrylamide Gel, Ribonucleases, Ribonucleotides, Ribosomal, RNA, Saccharomyces cerevisiae, Species Specificity, Structural}, issn = {0021-9258}, doi = {10.1186/gb-2007-8-7-r145}, author = {Rubin, G M} } @article {2467, title = {Neuroendocrine control of ecdysis in silkmoths.}, journal = {Science}, volume = {167}, year = {1970}, month = {1970 Mar 20}, pages = {1624-6}, abstract = {

An adult moth sheds its pupal skin only during a specific period of the day. The brain is necessary for the synchronization of this behavior with the environmental photoperiod. This function is fully preserved when all the brain{\textquoteright}s nervous connections are severed or when a "loose" brain is transplanted into the tip of the abdomen. By appropriate experiments it was possible to show that the entire mechanism is brain-centered. The components include a photoreceptor mechanism, a clock, and a neuroendocrine output. The clock-controlled release of the hormone acts on the central nervous system to trigger a species-specific behavior pattern which culminates in ecdysis.

}, issn = {0036-8075}, doi = {10.1126/science.167.3925.1624}, author = {Truman, J W and Riddiford, L M} } @article {1185, title = {Circular dimer and catenate forms of mitochondrial DNA in human leukaemic leucocytes.}, journal = {Nature}, volume = {216}, year = {1967}, month = {1967 Nov 18}, pages = {652-7}, keywords = {Centrifugation, Chemical Phenomena, Chemistry, Chromatography, Cytogenetics, Density Gradient, DNA, Electron, Humans, Ion Exchange, Leukemia, Microscopy, Mitochondria, Molecular Weight, Neoplasm}, issn = {0028-0836}, doi = {10.1101/gad.1352105}, author = {Clayton, D A and Vinograd, J} } @article {68294, title = {Visual projection neuron convergence and compensation in developing sensorimotor circuits in the Drosophila optic glomeruli}, month = {2022 Aug 22}, abstract = {

Visual features detected by the early visual system must be combined into higher order representations to guide behavioral decision. Although key developmental mechanisms that enable the separation of visual feature channels in early visual circuits have been discovered, relatively little is known about the mechanisms that underlie their convergence in later stages of visual processing. Here we explore the development of a functionally well-characterized sensorimotor circuit in\ Drosophila melanogaster, the convergence of visual projection neurons (VPNs) onto the dendrites of a large descending neuron called the giant fiber (GF). We find two VPNs encoding different visual features that target the same giant fiber dendrite establish their territories on the dendrite, in part, through sequential axon arrival during development prior to synaptogenesis. Physical occupancy is important to maintain territories, as we find the ablation of one VPN results in expanded dendrite territory of the remaining VPN, and that this compensation enables the GF to remain responsive to ethologically relevant visual stimuli. Our data highlight temporal mechanisms for visual feature convergence and promote the GF circuit, and the\ Drosophila\ optic glomeruli where VPN to GF connectivity resides, as an ideal developmental model for investigating complex wiring programs and plasticity in visual feature convergence.

}, doi = {10.1101/2022.08.20.504653}, url = {https://doi.org/10.1101/2022.08.20.504653}, author = {Brennan W. McFarland and HyoJong Jang and Natalie Smolin and Tanja A. Godenschwege and Aljoscha Nern and Yerbol Z. Kurmangaliyev and Catherine R. von Reyn} }